1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 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 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019 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 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 Eric Brown <brown@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
22 ;;; This file is part of GNU Guix.
24 ;;; GNU Guix is free software; you can redistribute it and/or modify it
25 ;;; under the terms of the GNU General Public License as published by
26 ;;; the Free Software Foundation; either version 3 of the License, or (at
27 ;;; your option) any later version.
29 ;;; GNU Guix is distributed in the hope that it will be useful, but
30 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
31 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
32 ;;; GNU General Public License for more details.
34 ;;; You should have received a copy of the GNU General Public License
35 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
37 (define-module (gnu packages cran)
38 #:use-module ((guix licenses) #:prefix license:)
39 #:use-module (guix packages)
40 #:use-module (guix download)
41 #:use-module (guix git-download)
42 #:use-module (guix utils)
43 #:use-module (guix build-system r)
44 #:use-module (gnu packages algebra)
45 #:use-module (gnu packages base)
46 #:use-module (gnu packages bioinformatics)
47 #:use-module (gnu packages c)
48 #:use-module (gnu packages compression)
49 #:use-module (gnu packages curl)
50 #:use-module (gnu packages databases)
51 #:use-module (gnu packages fontutils)
52 #:use-module (gnu packages gcc)
53 #:use-module (gnu packages geo)
54 #:use-module (gnu packages ghostscript)
55 #:use-module (gnu packages gl)
56 #:use-module (gnu packages gnome)
57 #:use-module (gnu packages graph)
58 #:use-module (gnu packages gtk)
59 #:use-module (gnu packages haskell-xyz)
60 #:use-module (gnu packages icu4c)
61 #:use-module (gnu packages image)
62 #:use-module (gnu packages imagemagick)
63 #:use-module (gnu packages java)
64 #:use-module (gnu packages javascript)
65 #:use-module (gnu packages lisp)
66 #:use-module (gnu packages machine-learning)
67 #:use-module (gnu packages maths)
68 #:use-module (gnu packages mpi)
69 #:use-module (gnu packages multiprecision)
70 #:use-module (gnu packages networking)
71 #:use-module (gnu packages pcre)
72 #:use-module (gnu packages perl)
73 #:use-module (gnu packages pkg-config)
74 #:use-module (gnu packages python)
75 #:use-module (gnu packages python-xyz)
76 #:use-module (gnu packages statistics)
77 #:use-module (gnu packages tls)
78 #:use-module (gnu packages web)
79 #:use-module (gnu packages xorg))
81 (define-public r-clipr
88 (uri (cran-uri "clipr" version))
91 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
92 (build-system r-build-system)
93 (home-page "https://github.com/mdlincoln/clipr")
94 (synopsis "Read and write from the system clipboard")
96 "This package provides simple utility functions to read from and write to
97 the system clipboards.")
98 (license license:gpl3)))
100 (define-public r-scales
107 (uri (cran-uri "scales" version))
109 (base32 "00rdbfj5mwc3kr8pskidn3n2zkp4ms6cx36xazz54pxw3pysdr0y"))))
110 (build-system r-build-system)
112 `(("r-farver" ,r-farver)
113 ("r-labeling" ,r-labeling)
114 ("r-lifecycle" ,r-lifecycle)
115 ("r-munsell" ,r-munsell)
116 ("r-rcolorbrewer" ,r-rcolorbrewer)
118 ("r-viridislite" ,r-viridislite)))
119 (home-page "https://github.com/hadley/scales")
120 (synopsis "Scale functions for visualization")
122 "This package provides graphical scales that map data to aesthetics, and
123 provides methods for automatically determining breaks and labels for axes and
125 (license license:expat)))
127 (define-public r-pheatmap
134 (uri (cran-uri "pheatmap" version))
137 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
138 (build-system r-build-system)
140 `(("r-gtable" ,r-gtable)
141 ("r-rcolorbrewer" ,r-rcolorbrewer)
142 ("r-scales" ,r-scales)))
143 (home-page "https://cran.r-project.org/web/packages/pheatmap")
144 (synopsis "Pretty heatmaps")
146 "This package provides an implementation of heatmaps that offers more
147 control over dimensions and appearance.")
148 (license license:gpl2+)))
150 (define-public r-ellipsis
157 (uri (cran-uri "ellipsis" version))
160 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
161 (build-system r-build-system)
163 `(("r-rlang" ,r-rlang)))
164 (home-page "https://github.com/hadley/ellipsis")
165 (synopsis "Tools for working with additional arguments")
167 "In S3 generics, it's useful to take @code{...} so that methods can have
168 additional arguments. But this flexibility comes at a cost: misspelled
169 arguments will be silently ignored. The @code{ellipsis} package is an
170 experiment that allows a generic to warn if any arguments passed in @code{...}
172 (license license:gpl3)))
181 (uri (cran-uri "grr" version))
184 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
185 (build-system r-build-system)
186 (home-page "https://cran.r-project.org/web/packages/grr")
187 (synopsis "Alternative implementations of base R functions")
189 "This package provides alternative implementations of some base R
190 functions, including @code{sort}, @code{order}, and @code{match}. The
191 functions are simplified but can be faster or have other advantages.")
192 (license license:gpl3)))
194 (define-public r-matrix-utils
196 (name "r-matrix-utils")
201 (uri (cran-uri "Matrix.utils" version))
204 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
205 (properties `((upstream-name . "Matrix.utils")))
206 (build-system r-build-system)
209 ("r-matrix" ,r-matrix)))
210 (home-page "https://github.com/cvarrichio/Matrix.utils")
212 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
214 "This package implements data manipulation methods such as @code{cast},
215 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
217 (license license:gpl3)))
226 (uri (cran-uri "sys" version))
229 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
230 (build-system r-build-system)
231 (home-page "https://github.com/jeroen/sys")
232 (synopsis "Powerful and reliable tools for running system commands in R")
234 "This package provides drop-in replacements for the base @code{system2()}
235 function with fine control and consistent behavior across platforms. It
236 supports clean interruption, timeout, background tasks, and streaming STDIN /
237 STDOUT / STDERR over binary or text connections. The package also provides
238 functions for evaluating expressions inside a temporary fork. Such
239 evaluations have no side effects on the main R process, and support reliable
240 interrupts and timeouts. This provides the basis for a sandboxing
242 (license license:expat)))
244 (define-public r-askpass
251 (uri (cran-uri "askpass" version))
254 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
255 (build-system r-build-system)
256 (propagated-inputs `(("r-sys" ,r-sys)))
257 (home-page "https://github.com/jeroen/askpass")
258 (synopsis "Safe password entry for R")
260 "This package provides cross-platform utilities for prompting the user
261 for credentials or a passphrase, for example to authenticate with a server or
262 read a protected key.")
263 (license license:expat)))
265 (define-public r-vegan
272 (uri (cran-uri "vegan" version))
275 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
276 (build-system r-build-system)
278 `(("gfortran" ,gfortran)))
280 `(("r-cluster" ,r-cluster)
281 ("r-knitr" ,r-knitr) ; needed for vignettes
282 ("r-lattice" ,r-lattice)
285 ("r-permute" ,r-permute)))
286 (home-page "https://cran.r-project.org/web/packages/vegan")
287 (synopsis "Functions for community ecology")
289 "The vegan package provides tools for descriptive community ecology. It
290 has most basic functions of diversity analysis, community ordination and
291 dissimilarity analysis. Most of its multivariate tools can be used for other
292 data types as well.")
293 (license license:gpl2+)))
295 (define-public r-tidyverse
302 (uri (cran-uri "tidyverse" version))
305 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
306 (build-system r-build-system)
308 `(("r-broom" ,r-broom)
310 ("r-crayon" ,r-crayon)
311 ("r-dbplyr" ,r-dbplyr)
313 ("r-forcats" ,r-forcats)
314 ("r-ggplot2" ,r-ggplot2)
318 ("r-jsonlite" ,r-jsonlite)
319 ("r-lubridate" ,r-lubridate)
320 ("r-magrittr" ,r-magrittr)
321 ("r-modelr" ,r-modelr)
322 ("r-pillar" ,r-pillar)
325 ("r-readxl" ,r-readxl)
326 ("r-reprex" ,r-reprex)
328 ("r-rstudioapi" ,r-rstudioapi)
330 ("r-stringr" ,r-stringr)
331 ("r-tibble" ,r-tibble)
334 (home-page "https://tidyverse.tidyverse.org")
335 (synopsis "Install and load packages from the \"Tidyverse\"")
337 "The @code{tidyverse} is a set of packages that work in harmony because
338 they share common data representations and API design. This package is
339 designed to make it easy to install and load multiple tidyverse packages in a
341 (license license:gpl3)))
343 (define-public r-rvest
350 (uri (cran-uri "rvest" version))
352 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
353 (build-system r-build-system)
356 ("r-magrittr" ,r-magrittr)
357 ("r-selectr" ,r-selectr)
359 (home-page "https://github.com/hadley/rvest")
360 (synopsis "Simple web scraping for R")
362 "@code{r-rvest} helps you scrape information from web pages. It is
363 designed to work with @code{magrittr} to make it easy to express common web
364 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
365 (license license:gpl3)))
367 (define-public r-selectr
374 (uri (cran-uri "selectr" version))
376 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
377 (build-system r-build-system)
379 `(("r-stringr" ,r-stringr)
381 (home-page "https://sjp.co.nz/projects/selectr/")
382 (synopsis "Translate CSS selectors to XPath expressions")
384 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
385 expression. This allows you to use CSS selectors when working with the XML
386 package as it can only evaluate XPath expressions. Also provided are
387 convenience functions useful for using CSS selectors on XML nodes. This
388 package is a port of the Python package @code{cssselect}.")
389 (license license:bsd-3)))
391 (define-public r-reprex
398 (uri (cran-uri "reprex" version))
401 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
402 (build-system r-build-system)
404 `(("r-callr" ,r-callr)
408 ("r-rmarkdown" ,r-rmarkdown)
409 ("r-whisker" ,r-whisker)
410 ("r-withr" ,r-withr)))
411 (home-page "https://github.com/tidyverse/reprex")
412 (synopsis "Prepare reproducible R code examples for sharing")
414 "This package provides a convenience wrapper that uses the
415 @code{rmarkdown} package to render small snippets of code to target formats
416 that include both code and output. The goal is to encourage the sharing of
417 small, reproducible, and runnable examples on code-oriented websites or email.
418 @code{reprex} also extracts clean, runnable R code from various common formats,
419 such as copy/paste from an R session.")
420 (license license:expat)))
422 (define-public r-callr
429 (uri (cran-uri "callr" version))
432 "12dbqzjngbyaqdyw0yq1blyfx8pagcvx1vqj2jm451hs25nhdrnh"))))
433 (build-system r-build-system)
436 ("r-processx" ,r-processx)))
437 (home-page "https://github.com/r-lib/callr#readme")
438 (synopsis "Call R from R")
440 "It is sometimes useful to perform a computation in a separate R process,
441 without affecting the current R process at all. This package does exactly
443 (license license:expat)))
445 (define-public r-readxl
452 (uri (cran-uri "readxl" version))
455 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
456 (build-system r-build-system)
458 `(("r-cellranger" ,r-cellranger)
459 ("r-progress" ,r-progress)
461 ("r-tibble" ,r-tibble)))
462 (home-page "https://readxl.tidyverse.org")
463 (synopsis "Read Excel files")
465 "This package lets you import Excel files into R. It supports
466 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
467 the embedded @code{RapidXML} C++ library.")
468 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
469 ;; 'rapidxml' which is Boost.
470 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
472 (define-public r-modelr
479 (uri (cran-uri "modelr" version))
482 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
483 (build-system r-build-system)
485 `(("r-broom" ,r-broom)
487 ("r-magrittr" ,r-magrittr)
490 ("r-tibble" ,r-tibble)
491 ("r-tidyr" ,r-tidyr)))
492 (home-page "https://github.com/tidyverse/modelr")
493 (synopsis "Helper functions for modelling in pipelines")
495 "Functions for modelling that help you seamlessly integrate modelling
496 into a pipeline of data manipulation and visualisation.")
497 (license license:gpl3)))
499 (define-public r-httpuv
505 (uri (cran-uri "httpuv" version))
508 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
509 (build-system r-build-system)
513 ("r-promises" ,r-promises)
516 (home-page "https://github.com/rstudio/httpuv")
517 (synopsis "HTTP and WebSocket server library for R")
519 "The httpuv package provides low-level socket and protocol support for
520 handling HTTP and WebSocket requests directly from within R. It is primarily
521 intended as a building block for other packages, rather than making it
522 particularly easy to create complete web applications using httpuv alone.")
523 ;; This package includes third-party code that was originally released
524 ;; under various non-copyleft licenses. Full licensing information can be
525 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
526 (license license:gpl3+)))
528 (define-public r-jsonlite
534 (uri (cran-uri "jsonlite" version))
537 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
538 (build-system r-build-system)
539 (home-page "http://arxiv.org/abs/1403.2805")
540 (synopsis "Robust, high performance JSON parser and generator for R")
542 "The jsonlite package provides a fast JSON parser and generator optimized
543 for statistical data and the web. It offers flexible, robust, high
544 performance tools for working with JSON in R and is particularly powerful for
545 building pipelines and interacting with a web API. In addition to converting
546 JSON data from/to R objects, jsonlite contains functions to stream, validate,
547 and prettify JSON data. The unit tests included with the package verify that
548 all edge cases are encoded and decoded consistently for use with dynamic data
549 in systems and applications.")
550 (license license:expat)))
552 (define-public r-servr
558 (uri (cran-uri "servr" version))
561 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
562 (build-system r-build-system)
564 `(("r-httpuv" ,r-httpuv)
565 ("r-jsonlite" ,r-jsonlite)
568 (home-page "https://github.com/yihui/servr")
569 (synopsis "Simple HTTP server to serve static files or dynamic documents")
571 "Servr provides an HTTP server in R to serve static files, or dynamic
572 documents that can be converted to HTML files (e.g., R Markdown) under a given
574 (license license:expat)))
576 (define-public r-htmltools
582 (uri (cran-uri "htmltools" version))
585 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
586 (build-system r-build-system)
588 `(("r-digest" ,r-digest)
590 ("r-rlang" ,r-rlang)))
591 (home-page "https://cran.r-project.org/web/packages/htmltools")
592 (synopsis "R tools for HTML")
594 "This package provides tools for HTML generation and output in R.")
595 (license license:expat)))
597 (define-public r-htmlwidgets
599 (name "r-htmlwidgets")
603 (uri (cran-uri "htmlwidgets" version))
606 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
607 (build-system r-build-system)
609 `(("r-htmltools" ,r-htmltools)
610 ("r-jsonlite" ,r-jsonlite)
612 (home-page "https://github.com/ramnathv/htmlwidgets")
613 (synopsis "HTML Widgets for R")
615 "HTML widgets is a framework for creating HTML widgets that render in
616 various contexts including the R console, R Markdown documents, and Shiny web
618 (license license:expat)))
620 (define-public r-htmltable
627 (uri (cran-uri "htmlTable" version))
630 "0h6jslchlx1dzqqdb70c3n9xlapcym9ykycvr0hc4q3450y8qmvh"))))
631 (properties `((upstream-name . "htmlTable")))
632 (build-system r-build-system)
634 `(("r-checkmate" ,r-checkmate)
635 ("r-htmltools" ,r-htmltools)
636 ("r-htmlwidgets" ,r-htmlwidgets)
638 ("r-magrittr" ,r-magrittr)
639 ("r-rstudioapi" ,r-rstudioapi)
640 ("r-stringr" ,r-stringr)))
641 (home-page "http://gforge.se/packages/")
642 (synopsis "Advanced tables for Markdown/HTML")
644 "This package provides functions to build tables with advanced layout
645 elements such as row spanners, column spanners, table spanners, zebra
646 striping, and more. While allowing advanced layout, the underlying
647 CSS-structure is simple in order to maximize compatibility with word
648 processors such as LibreOffice. The package also contains a few text
649 formatting functions that help outputting text compatible with HTML or
651 (license license:gpl3+)))
653 (define-public r-curl
659 (uri (cran-uri "curl" version))
662 "0xh227gvb056wlipjxxbf555z1i1qcs7rr1igvs6k6645y9irrlp"))))
663 (build-system r-build-system)
666 (modify-phases %standard-phases
667 ;; The environment variable CURL_CA_BUNDLE is only respected when
668 ;; running Windows, so we disable the platform checks.
669 ;; This can be removed once the libcurl has been patched.
670 (add-after 'unpack 'allow-CURL_CA_BUNDLE
672 (substitute* "R/onload.R"
673 (("if \\(!grepl\\(\"mingw\".*")
675 (substitute* "src/handle.c"
676 (("#ifdef _WIN32") "#if 1"))
682 `(("pkg-config" ,pkg-config)))
683 (home-page "https://github.com/jeroenooms/curl")
684 (synopsis "HTTP client for R")
686 "The @code{curl()} and @code{curl_download()} functions provide highly
687 configurable drop-in replacements for base @code{url()} and
688 @code{download.file()} with better performance, support for encryption, gzip
689 compression, authentication, and other @code{libcurl} goodies. The core of
690 the package implements a framework for performing fully customized requests
691 where data can be processed either in memory, on disk, or streaming via the
692 callback or connection interfaces.")
693 (license license:expat)))
695 (define-public r-hwriter
702 (uri (cran-uri "hwriter" version))
705 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
706 (build-system r-build-system)
707 (home-page "https://cran.r-project.org/web/packages/hwriter")
708 (synopsis "Output R objects in HTML format")
710 "This package provides easy-to-use and versatile functions to output R
711 objects in HTML format.")
712 (license license:lgpl2.1+)))
714 (define-public r-rjson
721 (uri (cran-uri "rjson" version))
724 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
725 (build-system r-build-system)
726 (home-page "https://cran.r-project.org/web/packages/rjson")
727 (synopsis "JSON library for R")
729 "This package provides functions to convert R objects into JSON objects
731 (license license:gpl2+)))
733 (define-public r-shiny
741 (url "https://github.com/rstudio/shiny.git")
742 (commit (string-append "v" version))))
743 (file-name (git-file-name name version))
746 "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
747 (build-system r-build-system)
749 `(#:modules ((guix build r-build-system)
750 (guix build minify-build-system)
753 #:imported-modules (,@%r-build-system-modules
754 (guix build minify-build-system))
756 (modify-phases (@ (guix build r-build-system) %standard-phases)
757 (add-after 'unpack 'replace-bundled-minified-JavaScript
758 (lambda* (#:key inputs #:allow-other-keys)
759 (let ((replace-file (lambda (old new)
760 (format #t "replacing ~a with ~a\n" old new)
763 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
764 ;; contain just data. They are not minified code, so we don't
766 (with-directory-excursion "inst/www/shared"
767 (replace-file "bootstrap/shim/respond.min.js"
768 (string-append (assoc-ref inputs "js-respond")
769 "/share/javascript/respond.min.js"))
770 (replace-file "bootstrap/shim/html5shiv.min.js"
771 (string-append (assoc-ref inputs "js-html5shiv")
772 "/share/javascript/html5shiv.min.js"))
773 (replace-file "json2-min.js"
774 (string-append (assoc-ref inputs "js-json2")
775 "/share/javascript/json2.min.js"))
776 (replace-file "strftime/strftime-min.js"
777 (string-append (assoc-ref inputs "js-strftime")
778 "/share/javascript/strftime.min.js"))
779 (replace-file "highlight/highlight.pack.js"
780 (string-append (assoc-ref inputs "js-highlight")
781 "/share/javascript/highlight.min.js"))
782 (replace-file "datatables/js/jquery.dataTables.min.js"
783 (string-append (assoc-ref inputs "js-datatables")
784 "/share/javascript/jquery.dataTables.min.js"))
785 (replace-file "selectize/js/selectize.min.js"
786 (string-append (assoc-ref inputs "js-selectize")
787 "/share/javascript/selectize.min.js"))
788 (replace-file "selectize/js/es5-shim.min.js"
789 (string-append (assoc-ref inputs "js-es5-shim")
790 "/share/javascript/es5-shim.min.js"))
791 (for-each (match-lambda
794 (minify source #:target target)))
795 '(("jqueryui/jquery-ui.js" .
796 "jqueryui/jquery-ui.min.js")
797 ("datepicker/js/bootstrap-datepicker.js" .
798 "datepicker/js/bootstrap-datepicker.min.js")
799 ("ionrangeslider/js/ion.rangeSlider.js" .
800 "ionrangeslider/js/ion.rangeSlider.min.js")
801 ("bootstrap/js/bootstrap.js" .
802 "bootstrap/js/bootstrap.min.js")
809 `(("r-crayon" ,r-crayon)
810 ("r-httpuv" ,r-httpuv)
812 ("r-jsonlite" ,r-jsonlite)
813 ("r-xtable" ,r-xtable)
814 ("r-digest" ,r-digest)
815 ("r-htmltools" ,r-htmltools)
817 ("r-sourcetools" ,r-sourcetools)))
819 `(("js-datatables" ,js-datatables)
820 ("js-html5shiv" ,js-html5shiv)
821 ("js-json2" ,js-json2)
822 ("js-respond" ,js-respond)
823 ("js-selectize" ,js-selectize)
824 ("js-strftime" ,js-strftime)
825 ("js-highlight" ,js-highlight)
826 ("js-es5-shim" ,js-es5-shim)))
828 `(("uglify-js" ,uglify-js)))
829 (home-page "http://shiny.rstudio.com")
830 (synopsis "Easy interactive web applications with R")
832 "Makes it incredibly easy to build interactive web applications
833 with R. Automatic \"reactive\" binding between inputs and outputs and
834 extensive prebuilt widgets make it possible to build beautiful,
835 responsive, and powerful applications with minimal effort.")
836 (license license:artistic2.0)))
838 ;; This package includes minified JavaScript files. When upgrading please
839 ;; check that there are no new minified JavaScript files.
840 (define-public r-shinytree
847 (uri (cran-uri "shinyTree" version))
850 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
851 (modules '((guix build utils)))
854 ;; Delete minified JavaScript
855 (for-each delete-file
856 '("inst/www/jsTree-3.3.7/libs/require.js"
857 "inst/www/jsTree-3.3.7/libs/jquery.js"
858 "inst/www/jsTree-3.3.7/jstree.min.js"))
860 (properties `((upstream-name . "shinyTree")))
861 (build-system r-build-system)
863 `(#:modules ((guix build utils)
864 (guix build r-build-system)
868 (modify-phases %standard-phases
869 (add-after 'unpack 'replace-minified-javascript
870 (lambda* (#:key inputs #:allow-other-keys)
871 (with-directory-excursion "inst/www/jsTree-3.3.7/"
872 (symlink (string-append (assoc-ref inputs "js-requirejs")
873 "/share/javascript/require.min.js")
878 `((,(assoc-ref inputs "js-jquery")
882 (lambda (sources targets)
883 (for-each (lambda (source target)
884 (format #t "Processing ~a --> ~a~%"
886 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
887 (call-with-output-file target
889 (dump-port minified port)))))
893 `(("r-htmlwidgets" ,r-htmlwidgets)
894 ("r-jsonlite" ,r-jsonlite)
895 ("r-promises" ,r-promises)
897 ("r-stringr" ,r-stringr)))
899 `(("js-requirejs" ,js-requirejs)))
901 `(("uglify-js" ,uglify-js)
905 (uri "https://code.jquery.com/jquery-3.3.1.js")
908 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
909 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
910 (synopsis "jsTree bindings for Shiny")
912 "This package exposes R bindings to jsTree, a JavaScript library that
913 supports interactive trees, to enable rich, editable trees in Shiny.")
914 (license license:expat)))
916 (define-public r-shinydashboard
918 (name "r-shinydashboard")
922 (uri (cran-uri "shinydashboard" version))
925 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
926 (build-system r-build-system)
927 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
928 ;; Regenerate it from the included sources.
930 `(#:modules ((guix build utils)
931 (guix build r-build-system)
934 (modify-phases %standard-phases
935 (add-after 'unpack 'generate-minified-javascript
937 (with-directory-excursion "inst/AdminLTE"
938 (delete-file "app.min.js")
939 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
940 (call-with-output-file "app.min.js"
942 (dump-port minified port))))))))))
944 `(("r-htmltools" ,r-htmltools)
945 ("r-promises" ,r-promises)
946 ("r-shiny" ,r-shiny)))
948 `(("uglify-js" ,uglify-js)))
949 (home-page "http://rstudio.github.io/shinydashboard/")
950 (synopsis "Create dashboards with shiny")
951 (description "This package provides an extension to the Shiny web
952 application framework for R, making it easy to create attractive dashboards.")
953 ;; This package includes software that was released under the Expat
954 ;; license, but the whole package is released under GPL version 2 or
956 (license license:gpl2+)))
958 (define-public r-shinyfiles
960 (name "r-shinyfiles")
965 (uri (cran-uri "shinyFiles" version))
967 (base32 "1143m941hma9hc77c3xcw26c0ygfhn9ii2sbp9wrydxv4gc7mr8a"))))
968 (properties `((upstream-name . "shinyFiles")))
969 (build-system r-build-system)
972 ("r-htmltools" ,r-htmltools)
973 ("r-jsonlite" ,r-jsonlite)
975 ("r-tibble" ,r-tibble)))
976 (home-page "https://github.com/thomasp85/shinyFiles")
977 (synopsis "Server-side file system viewer for Shiny")
979 "This package provides functionality for client-side navigation of the
980 server side file system in shiny apps. In case the app is running locally
981 this gives the user direct access to the file system without the need to
982 \"download\" files to a temporary location. Both file and folder selection as
983 well as file saving is available.")
984 (license license:gpl2+)))
986 (define-public r-shinythemes
988 (name "r-shinythemes")
993 (uri (cran-uri "shinythemes" version))
996 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
997 (properties `((upstream-name . "shinythemes")))
998 (build-system r-build-system)
999 (propagated-inputs `(("r-shiny" ,r-shiny)))
1000 (home-page "http://rstudio.github.io/shinythemes/")
1001 (synopsis "Themes for Shiny")
1003 "This package provides themes for use with Shiny. It includes several
1004 Bootstrap themes, which are packaged for use with Shiny applications.")
1005 ;; The package is released under version 3 of the GPL, but it includes
1006 ;; source files that are covered by the Expat license. It also includes
1007 ;; fonts under SIL or the ASL.
1008 (license (list license:gpl3 license:expat
1009 license:silofl1.1 license:asl2.0))))
1011 ;; The package sources include minified variants of d3.js and non-minified
1012 ;; source code of d3-jetpack.
1013 (define-public r-d3r
1020 (uri (cran-uri "d3r" version))
1023 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
1024 (build-system r-build-system)
1026 `(#:modules ((guix build utils)
1027 (guix build r-build-system)
1031 (modify-phases %standard-phases
1032 (add-after 'unpack 'process-javascript
1033 (lambda* (#:key inputs #:allow-other-keys)
1034 (with-directory-excursion "inst/www/d3/"
1038 `((,(assoc-ref inputs "d3.v3.js")
1039 "v3/dist/d3.min.js")
1040 (,(assoc-ref inputs "d3.v4.js")
1041 "v4/dist/d3.min.js")
1042 (,(assoc-ref inputs "d3.v5.js")
1043 "v5/dist/d3.min.js"))))
1044 (lambda (sources targets)
1045 (for-each (lambda (source target)
1046 (format #t "Processing ~a --> ~a~%"
1048 (delete-file target)
1049 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1050 (call-with-output-file target
1052 (dump-port minified port)))))
1056 `(("r-dplyr" ,r-dplyr)
1057 ("r-htmltools" ,r-htmltools)
1058 ("r-tidyr" ,r-tidyr)))
1060 `(("uglify-js" ,uglify-js)
1064 (uri "https://d3js.org/d3.v3.js")
1067 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1071 (uri "https://d3js.org/d3.v4.js")
1074 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1078 (uri "https://d3js.org/d3.v5.js")
1081 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1082 (home-page "https://github.com/timelyportfolio/d3r")
1083 (synopsis "d3.js utilities for R")
1085 "This package provides a suite of functions to help ease the use of the
1086 d3.js visualization library in R. These helpers include
1087 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1088 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1089 R objects into the JSON format that the d3.js library expects.")
1090 (license license:bsd-3)))
1092 ;; We use the latest commit here because the last release was in 2016 while
1093 ;; the latest commit was in 2018.
1094 (define-public r-sankeyd3
1095 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1099 (version (git-version "0.3.2" revision commit))
1104 (url "https://github.com/fbreitwieser/sankeyD3.git")
1106 (file-name (git-file-name name version))
1109 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1110 (build-system r-build-system)
1113 ("r-htmlwidgets" ,r-htmlwidgets)
1114 ("r-shiny" ,r-shiny)
1115 ("r-magrittr" ,r-magrittr)))
1116 (home-page "https://github.com/fbreitwieser/sankeyD3")
1117 (synopsis "Sankey network graphs from R")
1119 "This package provides an R library to generate Sankey network graphs
1120 in R and Shiny via the D3 visualization library.")
1121 ;; The R code is licensed under GPLv3+. It includes the non-minified
1122 ;; JavaScript source code of d3-sankey, which is released under the
1123 ;; 3-clause BSD license.
1124 (license (list license:gpl3+ license:bsd-3)))))
1126 (define-public r-crosstalk
1128 (name "r-crosstalk")
1133 (uri (cran-uri "crosstalk" version))
1136 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1137 (build-system r-build-system)
1139 `(("r-ggplot2" ,r-ggplot2)
1140 ("r-htmltools" ,r-htmltools)
1141 ("r-jsonlite" ,r-jsonlite)
1142 ("r-lazyeval" ,r-lazyeval)
1144 ("r-shiny" ,r-shiny)))
1145 (home-page "https://rstudio.github.io/crosstalk/")
1146 (synopsis "Inter-widget interactivity for HTML widgets")
1148 "This package provides building blocks for allowing HTML widgets to
1149 communicate with each other, with Shiny or without (i.e. static @code{.html}
1150 files). It currently supports linked brushing and filtering.")
1151 (license license:expat)))
1153 (define-public r-rook
1160 (uri (cran-uri "Rook" version))
1163 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1164 (properties `((upstream-name . "Rook")))
1165 (build-system r-build-system)
1166 (propagated-inputs `(("r-brew" ,r-brew)))
1167 (home-page "https://cran.r-project.org/web/packages/Rook")
1168 (synopsis "Web server interface for R")
1170 "This package contains the Rook specification and convenience software
1171 for building and running Rook applications. A Rook application is an R
1172 reference class object that implements a @code{call} method or an R closure
1173 that takes exactly one argument, an environment, and returns a list with three
1174 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1175 (license license:gpl2)))
1177 (define-public r-miniui
1184 (uri (cran-uri "miniUI" version))
1187 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1188 (properties `((upstream-name . "miniUI")))
1189 (build-system r-build-system)
1191 `(("r-htmltools" ,r-htmltools)
1192 ("r-shiny" ,r-shiny)))
1193 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1194 (synopsis "Shiny UI widgets for small screens")
1196 "This package provides UI widget and layout functions for writing Shiny apps that
1197 work well on small screens.")
1198 (license license:gpl3)))
1200 (define-public r-feather
1207 (uri (cran-uri "feather" version))
1210 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1211 (build-system r-build-system)
1215 ("r-tibble" ,r-tibble)))
1216 (home-page "https://github.com/wesm/feather")
1217 (synopsis "R Bindings to the Feather API")
1218 (description "Read and write feather files, a lightweight binary columnar
1219 data store designed for maximum speed.")
1220 (license license:asl2.0)))
1222 (define-public r-maps
1229 (uri (cran-uri "maps" version))
1232 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1233 (build-system r-build-system)
1234 (home-page "https://cran.r-project.org/web/packages/maps")
1235 (synopsis "Draw geographical maps")
1236 (description "This package provides an R module for display of maps.
1237 Projection code and larger maps are in separate packages (@code{mapproj} and
1239 (license license:gpl2)))
1241 (define-public r-mapproj
1248 (uri (cran-uri "mapproj" version))
1251 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
1252 (build-system r-build-system)
1253 (propagated-inputs `(("r-maps" ,r-maps)))
1254 (home-page "https://cran.r-project.org/web/packages/mapproj")
1255 (synopsis "Map projection in R")
1256 (description "This package converts latitude/longitude into projected
1258 (license (list license:gpl2 ; The R interface
1259 (license:non-copyleft ; The C code
1260 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1261 "Lucent Public License Version 1.02")))))
1263 (define-public r-rgooglemaps
1265 (name "r-rgooglemaps")
1270 (uri (cran-uri "RgoogleMaps" version))
1273 "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
1274 (properties `((upstream-name . "RgoogleMaps")))
1275 (build-system r-build-system)
1276 (propagated-inputs `(("r-png" ,r-png)))
1277 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1278 (synopsis "Use Google Maps in R")
1279 (description "This package serves two purposes:
1281 @item Provide a comfortable R interface to query the Google server for static
1283 @item Use the map as a background image to overlay plots within R. This
1284 requires proper coordinate scaling.
1286 (license license:gpl2+)))
1288 (define-public r-geosphere
1290 (name "r-geosphere")
1295 (uri (cran-uri "geosphere" version))
1298 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1299 (build-system r-build-system)
1300 (propagated-inputs `(("r-sp" ,r-sp)))
1301 (home-page "https://cran.r-project.org/web/packages/geosphere")
1302 (synopsis "Spherical trigonometry")
1303 (description "This package computes spherical trigonometry for geographic
1304 applications. That is, compute distances and related measures for angular
1305 (longitude/latitude) locations.")
1306 (license license:gpl3+)))
1308 (define-public r-jpeg
1315 (uri (cran-uri "jpeg" version))
1318 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1319 (build-system r-build-system)
1320 (inputs `(("libjpeg" ,libjpeg)))
1321 (home-page "http://www.rforge.net/jpeg/")
1322 (synopsis "Read and write JPEG images with R")
1323 (description "This package provides a way to read, write and display
1324 bitmap images stored in the JPEG format with R. It can read and write both
1325 files and in-memory raw vectors.")
1326 (license license:gpl2+)))
1328 (define-public r-ggmap
1335 (uri (cran-uri "ggmap" version))
1338 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1339 (build-system r-build-system)
1341 `(("r-bitops" ,r-bitops)
1342 ("r-digest" ,r-digest)
1343 ("r-dplyr" ,r-dplyr)
1344 ("r-ggplot2" ,r-ggplot2)
1348 ("r-magrittr" ,r-magrittr)
1351 ("r-purrr" ,r-purrr)
1352 ("r-rgooglemaps" ,r-rgooglemaps)
1353 ("r-rjson" ,r-rjson)
1354 ("r-scales" ,r-scales)
1355 ("r-stringr" ,r-stringr)
1356 ("r-tibble" ,r-tibble)
1357 ("r-tidyr" ,r-tidyr)))
1358 (home-page "https://github.com/dkahle/ggmap")
1359 (synopsis "Spatial visualization with ggplot2")
1360 (description "This package provides a collection of functions to visualize
1361 spatial data and models on top of static maps from various online sources (e.g
1362 Google Maps and Stamen Maps). It includes tools common to those tasks,
1363 including functions for geolocation and routing.")
1364 (license license:gpl2)))
1366 (define-public r-haven
1373 (uri (cran-uri "haven" version))
1376 "0g9d6mxqmrw2zdms78jpx2sx73pczlyy771v1h5hmxqz9sqyk7hr"))))
1377 (build-system r-build-system)
1381 `(("r-forcats" ,r-forcats)
1384 ("r-rlang" ,r-rlang)
1385 ("r-readr" ,r-readr)
1386 ("r-tibble" ,r-tibble)
1387 ("r-tidyselect" ,r-tidyselect)))
1388 (home-page "https://haven.tidyverse.org")
1389 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1391 "This package lets you mport foreign statistical formats into R via the
1392 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1393 (license license:expat)))
1395 (define-public r-amap
1401 (uri (cran-uri "amap" version))
1404 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
1405 (build-system r-build-system)
1407 `(("gfortran" ,gfortran)))
1408 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1409 (synopsis "Another multidimensional analysis package")
1410 (description "This package provides tools for clustering and principal
1411 component analysis (with robust methods, and parallelized functions).")
1412 (license license:gpl2+)))
1414 (define-public r-ape
1421 (uri (cran-uri "ape" version))
1424 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1425 (build-system r-build-system)
1427 `(("r-lattice" ,r-lattice)
1429 ("r-rcpp" ,r-rcpp)))
1430 (home-page "http://ape-package.ird.fr/")
1431 (synopsis "Analyses of phylogenetics and evolution")
1433 "This package provides functions for reading, writing, plotting, and
1434 manipulating phylogenetic trees, analyses of comparative data in a
1435 phylogenetic framework, ancestral character analyses, analyses of
1436 diversification and macroevolution, computing distances from DNA sequences,
1437 and several other tools.")
1438 (license license:gpl2+)))
1440 (define-public r-abbyyr
1447 (uri (cran-uri "abbyyR" version))
1450 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1451 (properties `((upstream-name . "abbyyR")))
1452 (build-system r-build-system)
1454 `(("r-curl" ,r-curl)
1457 ("r-progress" ,r-progress)
1458 ("r-readr" ,r-readr)
1460 (home-page "https://github.com/soodoku/abbyyR")
1461 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1463 "This package provides tools to get text from images of text using Abbyy
1464 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1465 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1466 passports and get the results in a variety of formats including plain text and
1467 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1468 (license license:expat)))
1470 (define-public r-colorspace
1472 (name "r-colorspace")
1477 (uri (cran-uri "colorspace" version))
1479 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1480 (build-system r-build-system)
1481 (home-page "https://cran.r-project.org/web/packages/colorspace")
1482 (synopsis "Color space manipulation")
1484 "This package carries out a mapping between assorted color spaces
1485 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1486 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1487 colors are provided.")
1488 (license license:bsd-3)))
1490 (define-public r-glue
1497 (uri (cran-uri "glue" version))
1500 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1501 (build-system r-build-system)
1502 (home-page "https://github.com/tidyverse/glue")
1503 (synopsis "Interpreted string literals")
1505 "This package provides an implementation of interpreted string literals,
1506 inspired by Python's Literal String Interpolation (PEP-0498) and
1507 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1508 (license license:expat)))
1510 (define-public r-pastecs
1516 (uri (cran-uri "pastecs" version))
1519 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1520 (build-system r-build-system)
1522 `(("r-boot" ,r-boot)))
1523 (home-page "http://www.sciviews.org/pastecs")
1524 (synopsis "Analysis of space-time ecological series")
1526 "This package provides functions for regulation, decomposition and analysis
1527 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1528 initiative to bring PASSTEC 2000 functionalities to R.")
1529 (license license:gpl2+)))
1531 (define-public r-plogr
1538 (uri (cran-uri "plogr" version))
1541 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1542 (build-system r-build-system)
1543 (home-page "https://github.com/krlmlr/plogr")
1544 (synopsis "R bindings for the plog C++ logging library")
1546 "This package provides the header files for a stripped-down version of
1547 the plog header-only C++ logging library, and a method to log to R's standard
1549 (license license:expat)))
1551 (define-public r-pls
1558 (uri (cran-uri "pls" version))
1560 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1561 (build-system r-build-system)
1562 (home-page "http://mevik.net/work/software/pls.html")
1563 (synopsis "Partial Least Squares and Principal Component Regression")
1565 "The pls package implements multivariate regression methods: Partial Least
1566 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1567 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1570 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1571 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1572 @item multi-response models (or @dfn{PLS2})
1573 @item flexible cross-validation
1574 @item Jackknife variance estimates of regression coefficients
1575 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1576 (R)MSEP, R², and correlation loadings
1577 @item formula interface, modelled after @code{lm()}, with methods for predict,
1578 print, summary, plot, update, etc.
1579 @item extraction functions for coefficients, scores, and loadings
1580 @item MSEP, RMSEP, and R² estimates
1581 @item multiplicative scatter correction (@dfn{MSC})
1583 (license license:gpl2)))
1592 (uri (cran-uri "ps" version))
1594 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1595 (build-system r-build-system)
1596 (home-page "http://ps.r-lib.org")
1597 (synopsis "List, query, and manipulate system processes")
1599 "The ps package implements an API to list, query, and manipulate system
1600 processes. Most of its code is based on the @code{psutil} Python package.")
1601 (license license:bsd-3)))
1603 (define-public r-pkgbuild
1610 (uri (cran-uri "pkgbuild" version))
1612 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1613 (build-system r-build-system)
1615 `(("r-callr" ,r-callr)
1617 ("r-crayon" ,r-crayon)
1619 ("r-prettyunits" ,r-prettyunits)
1621 ("r-rprojroot" ,r-rprojroot)
1622 ("r-withr" ,r-withr)))
1623 (home-page "https://github.com/r-pkgs/pkgbuild")
1624 (synopsis "Find tools needed to build R packages")
1626 "This package provides functions used to build R packages. It locates
1627 compilers needed to build R packages on various platforms and ensures the PATH
1628 is configured appropriately so R can use them.")
1629 (license license:gpl3)))
1631 (define-public r-pkgload
1638 (uri (cran-uri "pkgload" version))
1641 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1642 (build-system r-build-system)
1644 `(("r-desc" ,r-desc)
1645 ("r-pkgbuild" ,r-pkgbuild)
1646 ("r-rlang" ,r-rlang)
1647 ("r-rprojroot" ,r-rprojroot)
1648 ("r-rstudioapi" ,r-rstudioapi)
1649 ("r-withr" ,r-withr)))
1650 (home-page "https://github.com/r-lib/pkgload")
1651 (synopsis "Simulate package installation and attach")
1653 "This package simulates the process of installing a package and then
1654 attaching it. This is a key part of the @code{devtools} package as it allows
1655 you to rapidly iterate while developing a package.")
1656 (license license:gpl3)))
1658 (define-public r-rcpp
1665 (uri (cran-uri "Rcpp" version))
1667 (base32 "03h3zyjq948y0hrrs95lfk4zgx6wfrg64hjlrfrzf5na7bfh0d9b"))))
1668 (build-system r-build-system)
1670 `(("r-knitr" ,r-knitr))) ; for vignettes
1671 (home-page "http://www.rcpp.org")
1672 (synopsis "Seamless R and C++ integration")
1674 "The Rcpp package provides R functions as well as C++ classes which offer
1675 a seamless integration of R and C++. Many R data types and objects can be
1676 mapped back and forth to C++ equivalents which facilitates both writing of new
1677 code as well as easier integration of third-party libraries. Documentation
1678 about Rcpp is provided by several vignettes included in this package, via the
1679 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1680 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1681 @code{citation(\"Rcpp\")} for details on these last two.")
1682 (license license:gpl2+)))
1684 (define-public r-bindr
1691 (uri (cran-uri "bindr" version))
1694 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1695 (build-system r-build-system)
1696 (home-page "https://github.com/krlmlr/bindr")
1697 (synopsis "Parametrized active bindings")
1699 "This package provides a simple interface for creating active bindings
1700 where the bound function accepts additional arguments.")
1701 (license license:expat)))
1703 (define-public r-bindrcpp
1710 (uri (cran-uri "bindrcpp" version))
1713 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1714 (build-system r-build-system)
1716 `(("r-bindr" ,r-bindr)
1717 ("r-plogr" ,r-plogr)
1718 ("r-rcpp" ,r-rcpp)))
1719 (home-page "https://github.com/krlmlr/bindrcpp")
1720 (synopsis "Rcpp interface to active bindings")
1722 "This package provides an easy way to fill an environment with active
1723 bindings that call a C++ function.")
1724 (license license:expat)))
1726 (define-public r-auc
1733 (uri (cran-uri "AUC" version))
1736 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1737 (properties `((upstream-name . "AUC")))
1738 (build-system r-build-system)
1739 (home-page "https://cran.r-project.org/web/packages/AUC")
1740 (synopsis "Compute the area under the curve of selected measures")
1742 "This package includes functions to compute the area under the curve of
1743 selected measures: the area under the sensitivity curve (AUSEC), the area
1744 under the specificity curve (AUSPC), the area under the accuracy
1745 curve (AUACC), and the area under the receiver operating characteristic
1746 curve (AUROC). The curves can also be visualized. Support for partial areas
1748 (license license:gpl2+)))
1750 (define-public r-calibrate
1752 (name "r-calibrate")
1757 (uri (cran-uri "calibrate" version))
1759 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1760 (build-system r-build-system)
1762 `(("r-mass" ,r-mass)))
1763 (home-page "https://cran.r-project.org/web/packages/calibrate")
1764 (synopsis "Calibration of scatterplot and biplot axes")
1766 "This is a package for drawing calibrated scales with tick marks
1767 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1768 (license license:gpl2)))
1770 (define-public r-shape
1777 (uri (cran-uri "shape" version))
1780 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1781 (build-system r-build-system)
1782 (home-page "https://cran.r-project.org/web/packages/shape")
1783 (synopsis "Functions for plotting graphical shapes")
1785 "This package provides functions for plotting graphical shapes such as
1786 ellipses, circles, cylinders, arrows, ...")
1787 (license license:gpl3+)))
1789 (define-public r-globaloptions
1791 (name "r-globaloptions")
1796 (uri (cran-uri "GlobalOptions" version))
1798 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1799 (properties `((upstream-name . "GlobalOptions")))
1800 (build-system r-build-system)
1801 (home-page "https://github.com/jokergoo/GlobalOptions")
1802 (synopsis "Generate functions to get or set global options")
1804 "This package provides more controls on the option values such as
1805 validation and filtering on the values, making options invisible or private.")
1806 (license license:gpl2+)))
1808 (define-public r-circlize
1815 (uri (cran-uri "circlize" version))
1818 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1819 (build-system r-build-system)
1821 `(("r-colorspace" ,r-colorspace)
1822 ("r-globaloptions" ,r-globaloptions)
1823 ("r-shape" ,r-shape)))
1824 (home-page "https://github.com/jokergoo/circlize")
1825 (synopsis "Circular visualization")
1827 "Circular layout is an efficient way to visualise huge amounts of
1828 information. This package provides an implementation of circular layout
1829 generation in R as well as an enhancement of available software. Its
1830 flexibility is based on the usage of low-level graphics functions such that
1831 self-defined high-level graphics can be easily implemented by users for
1832 specific purposes. Together with the seamless connection between the powerful
1833 computational and visual environment in R, it gives users more convenience and
1834 freedom to design figures for better understanding complex patterns behind
1835 multi-dimensional data.")
1836 (license license:gpl2+)))
1838 (define-public r-powerlaw
1845 (uri (cran-uri "poweRlaw" version))
1848 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1849 (properties `((upstream-name . "poweRlaw")))
1850 (build-system r-build-system)
1852 `(("r-vgam" ,r-vgam)))
1853 (home-page "https://github.com/csgillespie/poweRlaw")
1854 (synopsis "Tools for the analysis of heavy tailed distributions")
1856 "This package provides an implementation of maximum likelihood estimators
1857 for a variety of heavy tailed distributions, including both the discrete and
1858 continuous power law distributions. Additionally, a goodness-of-fit based
1859 approach is used to estimate the lower cut-off for the scaling region.")
1860 ;; Any of these GPL versions.
1861 (license (list license:gpl2 license:gpl3))))
1863 (define-public r-compare
1870 (uri (cran-uri "compare" version))
1873 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1874 (build-system r-build-system)
1875 (home-page "https://cran.r-project.org/web/packages/compare")
1876 (synopsis "Comparing objects for differences")
1878 "This package provides functions to compare a model object to a
1879 comparison object. If the objects are not identical, the functions can be
1880 instructed to explore various modifications of the objects (e.g., sorting
1881 rows, dropping names) to see if the modified versions are identical.")
1882 (license license:gpl2+)))
1884 (define-public r-dendextend
1886 (name "r-dendextend")
1891 (uri (cran-uri "dendextend" version))
1894 "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl"))))
1895 (build-system r-build-system)
1897 `(("r-ggplot2" ,r-ggplot2)
1898 ("r-magrittr" ,r-magrittr)
1899 ("r-viridis" ,r-viridis)))
1900 (home-page "https://cran.r-project.org/web/packages/dendextend")
1901 (synopsis "Extending 'dendrogram' functionality in R")
1903 "This package offers a set of functions for extending @code{dendrogram}
1904 objects in R, letting you visualize and compare trees of hierarchical
1905 clusterings. You can adjust a tree's graphical parameters (the color, size,
1906 type, etc of its branches, nodes and labels) and visually and statistically
1907 compare different dendrograms to one another.")
1908 ;; Any of these versions
1909 (license (list license:gpl2 license:gpl3))))
1911 (define-public r-getoptlong
1913 (name "r-getoptlong")
1918 (uri (cran-uri "GetoptLong" version))
1921 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1922 (properties `((upstream-name . "GetoptLong")))
1923 (build-system r-build-system)
1927 `(("r-globaloptions" ,r-globaloptions)
1928 ("r-rjson" ,r-rjson)))
1929 (home-page "https://github.com/jokergoo/GetoptLong")
1930 (synopsis "Parsing command-line arguments and variable interpolation")
1932 "This is yet another command-line argument parser which wraps the
1933 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1934 use in R. It also provides a simple way for variable interpolation in R.")
1935 (license license:gpl2+)))
1937 (define-public r-fastmatch
1939 (name "r-fastmatch")
1944 (uri (cran-uri "fastmatch" version))
1947 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1948 (build-system r-build-system)
1949 (home-page "http://www.rforge.net/fastmatch")
1950 (synopsis "Fast match function")
1952 "This package provides a fast @code{match} replacement for cases that
1953 require repeated look-ups. It is slightly faster that R's built-in
1954 @code{match} function on first match against a table, but extremely fast on
1955 any subsequent lookup as it keeps the hash table in memory.")
1956 (license license:gpl2)))
1965 (uri (cran-uri "ff" version))
1968 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1969 (build-system r-build-system)
1970 (propagated-inputs `(("r-bit" ,r-bit)))
1971 (home-page "http://ff.r-forge.r-project.org/")
1972 (synopsis "Memory-efficient storage of large data on disk and access functions")
1974 "This package provides data structures that are stored on disk but
1975 behave (almost) as if they were in RAM by transparently mapping only a section
1977 ;; error Architecture not supported.
1978 (supported-systems (delete "aarch64-linux" %supported-systems))
1979 (license license:gpl2)))
1981 (define-public r-ffbase
1988 (uri (cran-uri "ffbase" version))
1991 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
1992 (build-system r-build-system)
1995 ("r-fastmatch" ,r-fastmatch)
1997 (home-page "http://github.com/edwindj/ffbase")
1998 (synopsis "Basic statistical functions for package 'ff'")
2000 "This package extends the out of memory vectors of @code{ff} with
2001 statistical functions and other utilities to ease their usage.")
2002 (license license:gpl3)))
2004 (define-public r-prettyunits
2006 (name "r-prettyunits")
2011 (uri (cran-uri "prettyunits" version))
2014 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
2015 (build-system r-build-system)
2017 `(("r-assertthat" ,r-assertthat)
2018 ("r-magrittr" ,r-magrittr)))
2019 (home-page "https://github.com/gaborcsardi/prettyunits")
2020 (synopsis "Pretty, human readable formatting of quantities")
2022 "This package provides tools for pretty, human readable formatting of
2024 (license license:expat)))
2026 (define-public r-reshape
2033 (uri (cran-uri "reshape" version))
2036 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2037 (build-system r-build-system)
2039 `(("r-plyr" ,r-plyr)
2040 ("r-rcpp" ,r-rcpp)))
2041 (home-page "http://had.co.nz/reshape")
2042 (synopsis "Flexibly reshape data")
2044 "Flexibly restructure and aggregate data using just two functions:
2045 @code{melt} and @code{cast}. This package provides them.")
2046 (license license:expat)))
2048 (define-public r-progress
2055 (uri (cran-uri "progress" version))
2058 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2059 (build-system r-build-system)
2061 `(("r-crayon" ,r-crayon)
2063 ("r-prettyunits" ,r-prettyunits)
2065 (home-page "https://github.com/gaborcsardi/progress")
2066 (synopsis "Terminal progress bars")
2068 "This package provides configurable progress bars. They may include
2069 percentage, elapsed time, and/or the estimated completion time. They work in
2070 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2071 package also provides a C++ API, that works with or without Rcpp.")
2072 (license license:expat)))
2074 (define-public r-ggally
2081 (uri (cran-uri "GGally" version))
2084 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2085 (properties `((upstream-name . "GGally")))
2086 (build-system r-build-system)
2088 `(("libressl" ,libressl)))
2090 `(("r-ggplot2" ,r-ggplot2)
2091 ("r-gtable" ,r-gtable)
2093 ("r-progress" ,r-progress)
2094 ("r-rcolorbrewer" ,r-rcolorbrewer)
2095 ("r-reshape" ,r-reshape)
2096 ("r-rlang" ,r-rlang)))
2097 (home-page "https://ggobi.github.io/ggally")
2098 (synopsis "Extension to ggplot2")
2100 "The R package ggplot2 is a plotting system based on the grammar of
2101 graphics. GGally extends ggplot2 by adding several functions to reduce the
2102 complexity of combining geometric objects with transformed data. Some of
2103 these functions include a pairwise plot matrix, a two group pairwise plot
2104 matrix, a parallel coordinates plot, a survival plot, and several functions to
2106 (license license:gpl2+)))
2108 (define-public r-proxy
2115 (uri (cran-uri "proxy" version))
2118 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2119 (build-system r-build-system)
2120 (home-page "https://cran.r-project.org/web/packages/proxy")
2121 (synopsis "Distance and similarity measures")
2123 "This package provides an extensible framework for the efficient
2124 calculation of auto- and cross-proximities, along with implementations of the
2125 most popular ones.")
2126 (license license:gpl2)))
2135 (uri (cran-uri "sp" version))
2137 (base32 "0kpjsqh3lzqp1m0avsvm54lazlgwfx3hyf0av3mvbyslsanj42ll"))))
2138 (build-system r-build-system)
2140 `(("r-lattice" ,r-lattice)))
2141 (home-page "https://cran.r-project.org/web/packages/sp")
2142 (synopsis "Classes and methods for spatial data")
2144 "This package provides classes and methods for spatial data; the classes
2145 document where the spatial location information resides, for 2D or 3D data.
2146 Utility functions are provided, e.g. for plotting data as maps, spatial
2147 selection, as well as methods for retrieving coordinates, for subsetting,
2148 print, summary, etc.")
2149 (license license:gpl2+)))
2151 (define-public r-rmtstat
2158 (uri (cran-uri "RMTstat" version))
2161 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2162 (properties `((upstream-name . "RMTstat")))
2163 (build-system r-build-system)
2164 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2165 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2167 "This package provides functions for working with the Tracy-Widom laws
2168 and other distributions related to the eigenvalues of large Wishart
2170 (license license:bsd-3)))
2172 (define-public r-rmpi
2178 (uri (cran-uri "Rmpi" version))
2181 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2182 (properties `((upstream-name . "Rmpi")))
2183 (build-system r-build-system)
2185 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2186 #:phases (modify-phases %standard-phases
2187 (add-before 'install 'mpi-setup
2190 `(("openmpi" ,openmpi)))
2192 `(("pkg-config" ,pkg-config)))
2193 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2194 (synopsis "R interface to message-passing interface (MPI)")
2196 "This package provides an interface (wrapper) to MPI APIs. It also
2197 provides an interactive R manager and worker environment.")
2198 (license license:gpl2+)))
2200 (define-public r-lmoments
2207 (uri (cran-uri "Lmoments" version))
2210 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2211 (properties `((upstream-name . "Lmoments")))
2212 (build-system r-build-system)
2214 `(("r-rcpp" ,r-rcpp)
2215 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2216 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2217 (synopsis "L-moments and quantile mixtures")
2219 "This package contains functions to estimate L-moments and trimmed
2220 L-moments from the data. It also contains functions to estimate the
2221 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2222 quantile mixture from L-moments and trimmed L-moments.")
2223 (license license:gpl2)))
2225 (define-public r-distillery
2227 (name "r-distillery")
2232 (uri (cran-uri "distillery" version))
2235 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2236 (build-system r-build-system)
2237 (home-page "http://www.ral.ucar.edu/staff/ericg")
2238 (synopsis "Functions for confidence intervals and object information")
2240 "This package provides some very simple method functions for confidence
2241 interval calculation and to distill pertinent information from a potentially
2242 complex object; primarily used in common with the packages extRemes and
2244 (license license:gpl2+)))
2246 (define-public r-extremes
2253 (uri (cran-uri "extRemes" version))
2256 "0hmgynxhzswqnhwb2sxrkczgam8c17s3vpxqc5bcz0bwczpxxyvm"))))
2257 (properties `((upstream-name . "extRemes")))
2258 (build-system r-build-system)
2260 `(("r-distillery" ,r-distillery)
2261 ("r-lmoments" ,r-lmoments)))
2262 (home-page "http://www.assessment.ucar.edu/toolkit/")
2263 (synopsis "Extreme value analysis")
2265 "ExtRemes is a suite of functions for carrying out analyses on the
2266 extreme values of a process of interest; be they block maxima over long blocks
2267 or excesses over a high threshold.")
2268 (license license:gpl2+)))
2270 (define-public r-lmtest
2277 (uri (cran-uri "lmtest" version))
2280 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2281 (build-system r-build-system)
2283 `(("r-zoo" ,r-zoo)))
2285 `(("gfortran" ,gfortran)))
2286 (home-page "https://cran.r-project.org/web/packages/lmtest")
2287 (synopsis "Testing linear regression models")
2289 "This package provides a collection of tests, data sets, and examples for
2290 diagnostic checking in linear regression models. Furthermore, some generic
2291 tools for inference in parametric models are provided.")
2292 ;; Either version is okay
2293 (license (list license:gpl2 license:gpl3))))
2295 (define-public r-idr
2301 (uri (cran-uri "idr" version))
2304 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2305 (build-system r-build-system)
2306 (home-page "https://cran.r-project.org/web/packages/idr/")
2307 (synopsis "Irreproducible discovery rate")
2309 "This is a package for estimating the copula mixture model and plotting
2310 correspondence curves in \"Measuring reproducibility of high-throughput
2311 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2312 by Li, Brown, Huang, and Bickel")
2313 (license license:gpl2+)))
2315 (define-public r-inline
2321 (uri (cran-uri "inline" version))
2324 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2325 (build-system r-build-system)
2326 (home-page "https://cran.r-project.org/web/packages/inline")
2327 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2329 "This package provides functionality to dynamically define R functions
2330 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2331 @code{.Call} calling conventions.")
2332 ;; Any version of the LGPL.
2333 (license license:lgpl3+)))
2335 (define-public r-bbmle
2342 (uri (cran-uri "bbmle" version))
2345 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2346 (build-system r-build-system)
2348 `(("r-lattice" ,r-lattice)
2350 ("r-numderiv" ,r-numderiv)))
2351 (home-page "https://cran.r-project.org/web/packages/bbmle")
2352 (synopsis "Tools for General Maximum Likelihood Estimation")
2354 "This package provides methods and functions for fitting maximum
2355 likelihood models in R. This package modifies and extends the @code{mle}
2356 classes in the @code{stats4} package.")
2357 ;; Any version of the GPL
2358 (license license:gpl2+)))
2360 (define-public r-emdbook
2367 (uri (cran-uri "emdbook" version))
2370 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2371 (build-system r-build-system)
2373 `(("r-bbmle" ,r-bbmle)
2375 ("r-lattice" ,r-lattice)
2378 ("r-rcpp" ,r-rcpp)))
2379 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2380 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2382 "This package provides auxiliary functions and data sets for \"Ecological
2383 Models and Data\", a book presenting maximum likelihood estimation and related
2384 topics for ecologists (ISBN 978-0-691-12522-0).")
2386 (license (list license:gpl2 license:gpl3))))
2388 (define-public r-lpsolve
2391 (version "5.6.13.3")
2395 (uri (cran-uri "lpSolve" version))
2398 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2399 (properties `((upstream-name . "lpSolve")))
2400 (build-system r-build-system)
2401 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2402 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2404 "Lp_solve is software for solving linear, integer and mixed integer
2405 programs. This implementation supplies a \"wrapper\" function in C and some R
2406 functions that solve general linear/integer problems, assignment problems, and
2407 transportation problems.")
2408 (license license:lgpl2.0)))
2410 (define-public r-limsolve
2417 (uri (cran-uri "limSolve" version))
2420 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2421 (properties `((upstream-name . "limSolve")))
2422 (build-system r-build-system)
2424 `(("r-lpsolve" ,r-lpsolve)
2426 ("r-quadprog" ,r-quadprog)))
2427 (native-inputs `(("gfortran" ,gfortran)))
2428 (home-page "https://cran.r-project.org/web/packages/limSolve")
2429 (synopsis "Solving linear inverse models")
2431 "This package provides functions that:
2434 @item find the minimum/maximum of a linear or quadratic function,
2435 @item sample an underdetermined or overdetermined system,
2436 @item solve a linear system Ax=B for the unknown x.
2439 It includes banded and tridiagonal linear systems. The package calls Fortran
2440 functions from LINPACK.")
2442 (license (list license:gpl2+ license:gpl3+))))
2444 (define-public r-fitdistrplus
2446 (name "r-fitdistrplus")
2451 (uri (cran-uri "fitdistrplus" version))
2454 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2455 (build-system r-build-system)
2457 `(("r-mass" ,r-mass)
2458 ("r-npsurv" ,r-npsurv)
2459 ("r-survival" ,r-survival)))
2460 (home-page "http://riskassessment.r-forge.r-project.org")
2461 (synopsis "Fitting a parametric distribution from data")
2463 "This package extends the @code{fitdistr} function of the MASS package
2464 with several functions to help the fit of a parametric distribution to
2465 non-censored or censored data. Censored data may contain left-censored,
2466 right-censored and interval-censored values, with several lower and upper
2467 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2468 provides moment matching (MME), quantile matching (QME) and maximum
2469 goodness-of-fit estimation (MGE) methods (available only for non-censored
2470 data). Weighted versions of MLE, MME and QME are available.")
2471 (license license:gpl2+)))
2473 (define-public r-energy
2480 (uri (cran-uri "energy" version))
2483 "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
2484 (build-system r-build-system)
2486 `(("r-boot" ,r-boot)
2487 ("r-rcpp" ,r-rcpp)))
2488 (home-page "https://cran.r-project.org/web/packages/energy")
2489 (synopsis "Multivariate inference via the energy of data")
2491 "This package provides e-statistics (energy) tests and statistics for
2492 multivariate and univariate inference, including distance correlation,
2493 one-sample, two-sample, and multi-sample tests for comparing multivariate
2494 distributions, are implemented. Measuring and testing multivariate
2495 independence based on distance correlation, partial distance correlation,
2496 multivariate goodness-of-fit tests, clustering based on energy distance,
2497 testing for multivariate normality, distance components (disco) for
2498 non-parametric analysis of structured data, and other energy
2499 statistics/methods are implemented.")
2500 (license license:gpl2+)))
2502 (define-public r-suppdists
2504 (name "r-suppdists")
2509 (uri (cran-uri "SuppDists" version))
2512 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2513 (properties `((upstream-name . "SuppDists")))
2514 (build-system r-build-system)
2515 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2516 (synopsis "Supplementary distributions")
2518 "This package provides ten distributions supplementing those built into
2519 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2520 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2521 coefficient, Johnson distributions, normal scores and generalized
2522 hypergeometric distributions. In addition two random number generators of
2523 George Marsaglia are included.")
2524 (license license:gpl2+)))
2526 (define-public r-ksamples
2533 (uri (cran-uri "kSamples" version))
2536 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2537 (properties `((upstream-name . "kSamples")))
2538 (build-system r-build-system)
2540 `(("r-suppdists" ,r-suppdists)))
2541 (home-page "https://cran.r-project.org/web/packages/kSamples")
2542 (synopsis "K-Sample rank tests and their combinations")
2544 "This package provides tools to compares k samples using the
2545 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2546 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2547 test. It computes asymptotic, simulated or (limited) exact P-values, all
2548 valid under randomization, with or without ties, or conditionally under random
2549 sampling from populations, given the observed tie pattern. Except for Steel's
2550 test and the JT test it also combines these tests across several blocks of
2552 (license license:gpl2+)))
2554 (define-public r-cvst
2561 (uri (cran-uri "CVST" version))
2564 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2565 (properties `((upstream-name . "CVST")))
2566 (build-system r-build-system)
2568 `(("r-kernlab" ,r-kernlab)
2569 ("r-matrix" ,r-matrix)))
2570 (home-page "https://cran.r-project.org/web/packages/CVST")
2571 (synopsis "Fast cross-validation via sequential testing")
2573 "This package implements the fast cross-validation via sequential
2574 testing (CVST) procedure. CVST is an improved cross-validation procedure
2575 which uses non-parametric testing coupled with sequential analysis to
2576 determine the best parameter set on linearly increasing subsets of the data.
2577 Additionally to the CVST the package contains an implementation of the
2578 ordinary k-fold cross-validation with a flexible and powerful set of helper
2579 objects and methods to handle the overall model selection process. The
2580 implementations of the Cochran's Q test with permutations and the sequential
2581 testing framework of Wald are generic and can therefore also be used in other
2583 (license license:gpl2+)))
2585 (define-public r-squarem
2588 (version "2017.10-1")
2592 (uri (cran-uri "SQUAREM" version))
2595 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2596 (properties `((upstream-name . "SQUAREM")))
2597 (build-system r-build-system)
2598 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2599 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2601 "This package provides algorithms for accelerating the convergence of
2602 slow, monotone sequences from smooth, contraction mapping such as the EM
2603 algorithm. It can be used to accelerate any smooth, linearly convergent
2604 acceleration scheme. A tutorial style introduction to this package is
2605 available in a vignette.")
2606 (license license:gpl2+)))
2608 (define-public r-lava
2615 (uri (cran-uri "lava" version))
2618 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2619 (build-system r-build-system)
2621 `(("r-numderiv" ,r-numderiv)
2622 ("r-squarem" ,r-squarem)
2623 ("r-survival" ,r-survival)))
2624 (home-page "https://github.com/kkholst/lava")
2625 (synopsis "Latent variable models")
2627 "This package provides tools for the estimation and simulation of latent
2629 (license license:gpl3)))
2631 (define-public r-drr
2638 (uri (cran-uri "DRR" version))
2641 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2642 (properties `((upstream-name . "DRR")))
2643 (build-system r-build-system)
2645 `(("r-cvst" ,r-cvst)
2646 ("r-kernlab" ,r-kernlab)
2647 ("r-matrix" ,r-matrix)))
2648 (home-page "https://cran.r-project.org/web/packages/DRR")
2649 (synopsis "Dimensionality reduction via regression")
2651 "This package provides an implementation of dimensionality reduction via
2652 regression using Kernel Ridge Regression.")
2653 (license license:gpl3)))
2655 (define-public r-prodlim
2658 (version "2019.11.13")
2662 (uri (cran-uri "prodlim" version))
2665 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
2666 (build-system r-build-system)
2668 `(("r-kernsmooth" ,r-kernsmooth)
2671 ("r-survival" ,r-survival)))
2672 (home-page "https://cran.r-project.org/web/packages/prodlim")
2673 (synopsis "Product-limit estimation for censored event history analysis")
2675 "This package provides a fast and user-friendly implementation of
2676 nonparametric estimators for censored event history (survival) analysis with
2677 the Kaplan-Meier and Aalen-Johansen methods.")
2678 (license license:gpl2+)))
2680 (define-public r-dimred
2687 (uri (cran-uri "dimRed" version))
2690 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2691 (properties `((upstream-name . "dimRed")))
2692 (build-system r-build-system)
2695 ("r-magrittr" ,r-magrittr)))
2696 (home-page "https://github.com/gdkrmr/dimRed")
2697 (synopsis "Framework for dimensionality reduction")
2699 "This package provides a collection of dimensionality reduction
2700 techniques from R packages and provides a common interface for calling the
2702 (license license:gpl3)))
2704 (define-public r-timedate
2707 (version "3043.102")
2711 (uri (cran-uri "timeDate" version))
2714 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2715 (properties `((upstream-name . "timeDate")))
2716 (build-system r-build-system)
2717 (home-page "https://www.rmetrics.org")
2718 (synopsis "Chronological and calendar objects")
2720 "This package provides an environment for teaching \"Financial
2721 Engineering and Computational Finance\" and for managing chronological and
2723 (license license:gpl2+)))
2725 (define-public r-magic
2732 (uri (cran-uri "magic" version))
2735 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2736 (build-system r-build-system)
2738 `(("r-abind" ,r-abind)))
2739 (home-page "https://github.com/RobinHankin/magic.git")
2740 (synopsis "Create and investigate magic squares")
2742 "This package provides a collection of efficient, vectorized algorithms
2743 for the creation and investigation of magic squares and hypercubes, including
2744 a variety of functions for the manipulation and analysis of arbitrarily
2745 dimensioned arrays.")
2746 (license license:gpl2)))
2748 (define-public r-rmysql
2755 (uri (cran-uri "RMySQL" version))
2758 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2759 (properties `((upstream-name . "RMySQL")))
2760 (build-system r-build-system)
2762 `(("mariadb" ,mariadb)
2765 `(("r-dbi" ,r-dbi)))
2766 (home-page "https://github.com/r-dbi/RMySQL")
2767 (synopsis "Database interface and MySQL driver for R")
2769 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2770 package contains an old implementation based on legacy code from S-PLUS which
2771 is being phased out. A modern MySQL client based on Rcpp is available from
2772 the RMariaDB package.")
2773 (license license:gpl2)))
2775 (define-public r-rpostgresql
2777 (name "r-rpostgresql")
2782 (uri (cran-uri "RPostgreSQL" version))
2785 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2786 (properties `((upstream-name . "RPostgreSQL")))
2787 (build-system r-build-system)
2789 `(("postgresql" ,postgresql)))
2791 `(("r-dbi" ,r-dbi)))
2792 (home-page "https://github.com/tomoakin/RPostgreSQL")
2793 (synopsis "R interface to the PostgreSQL database system")
2795 "This package provides a Database Interface (DBI) compliant driver for R
2796 to access PostgreSQL database systems.")
2797 ;; The whole package is released under GPL version 2. It includes code
2798 ;; under the PostgreSQL license.
2799 (license license:gpl2)))
2801 (define-public r-linprog
2808 (uri (cran-uri "linprog" version))
2811 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2812 (build-system r-build-system)
2813 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2814 (home-page "http://linprog.r-forge.r-project.org/")
2815 (synopsis "Linear programming and optimization")
2817 "This package can be used to solve Linear Programming / Linear
2818 Optimization problems by using the simplex algorithm.")
2819 (license license:gpl2+)))
2821 (define-public r-geometry
2828 (uri (cran-uri "geometry" version))
2831 "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8"))))
2832 (build-system r-build-system)
2834 `(("r-magic" ,r-magic)
2835 ("r-linprog" ,r-linprog)
2836 ("r-lpsolve" ,r-lpsolve)
2838 ("r-rcppprogress" ,r-rcppprogress)))
2839 (home-page "http://geometry.r-forge.r-project.org/")
2840 (synopsis "Mesh generation and surface tesselation")
2842 "This package makes the qhull library available in R, in a similar manner
2843 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2844 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2845 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2846 and higher dimensions. It implements the Quickhull algorithm for computing
2847 the convex hull. Qhull does not support constrained Delaunay triangulations,
2848 or mesh generation of non-convex objects, but the package does include some R
2849 functions that allow for this. Currently the package only gives access to
2850 Delaunay triangulation and convex hull computation.")
2851 ;; The Qhull sources are included and are distributed under a custom
2852 ;; non-copyleft license. The R sources are released under GPL version 2.
2853 (license (list license:gpl2
2854 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2856 (define-public r-ddalpha
2863 (uri (cran-uri "ddalpha" version))
2866 "1064g7y8d7kmvd5kjc2m48yvidmh2ci1y0xgil3pcx4ix6mf0ljz"))))
2867 (build-system r-build-system)
2870 ("r-class" ,r-class)
2871 ("r-geometry" ,r-geometry)
2874 ("r-robustbase" ,r-robustbase)
2875 ("r-sfsmisc" ,r-sfsmisc)))
2877 `(("gfortran" ,gfortran)))
2878 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2879 (synopsis "Depth-Based classification and calculation of data depth")
2881 "This package contains procedures for depth-based supervised learning,
2882 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2883 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2884 statistical depth function to a compact low-dimensional space, where the final
2885 classification is done. It also offers an extension to functional data and
2886 routines for calculating certain notions of statistical depth functions. 50
2887 multivariate and 5 functional classification problems are included.")
2888 (license license:gpl2)))
2890 (define-public r-gower
2897 (uri (cran-uri "gower" version))
2900 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2901 (build-system r-build-system)
2902 (home-page "https://github.com/markvanderloo/gower")
2903 (synopsis "Gower's distance")
2905 "This package provides tools to compute Gower's distance (or similarity)
2906 coefficient between records, and to compute the top-n matches between records.
2907 Core algorithms are executed in parallel on systems supporting OpenMP.")
2908 (license license:gpl3)))
2910 (define-public r-rcpproll
2917 (uri (cran-uri "RcppRoll" version))
2920 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2921 (properties `((upstream-name . "RcppRoll")))
2922 (build-system r-build-system)
2924 `(("r-rcpp" ,r-rcpp)))
2925 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2926 (synopsis "Efficient rolling and windowed operations")
2928 "This package provides fast and efficient routines for common rolling /
2929 windowed operations. Routines for the efficient computation of windowed mean,
2930 median, sum, product, minimum, maximum, standard deviation and variance are
2932 (license license:gpl2+)))
2934 (define-public r-ipred
2941 (uri (cran-uri "ipred" version))
2944 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2945 (build-system r-build-system)
2947 `(("r-class" ,r-class)
2950 ("r-prodlim" ,r-prodlim)
2951 ("r-rpart" ,r-rpart)
2952 ("r-survival" ,r-survival)))
2953 (home-page "https://cran.r-project.org/web/packages/ipred")
2954 (synopsis "Improved predictors")
2956 "This package provides improved predictive models by indirect
2957 classification and bagging for classification, regression and survival
2958 problems as well as resampling based estimators of prediction error.")
2959 (license license:gpl2+)))
2961 (define-public r-psych
2968 (uri (cran-uri "psych" version))
2971 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
2972 (build-system r-build-system)
2974 `(("r-foreign" ,r-foreign)
2975 ("r-lattice" ,r-lattice)
2976 ("r-mnormt" ,r-mnormt)
2977 ("r-nlme" ,r-nlme)))
2978 (home-page "https://cran.r-project.org/web/packages/psych/")
2979 (synopsis "Procedures for psychological, psychometric, and personality research")
2981 "This package provides a general purpose toolbox for personality,
2982 psychometric theory and experimental psychology. Functions are primarily for
2983 multivariate analysis and scale construction using factor analysis, principal
2984 component analysis, cluster analysis and reliability analysis, although others
2985 provide basic descriptive statistics. Item Response Theory is done using
2986 factor analysis of tetrachoric and polychoric correlations. Functions for
2987 analyzing data at multiple levels include within and between group statistics,
2988 including correlations and factor analysis. Functions for simulating and
2989 testing particular item and test structures are included. Several functions
2990 serve as a useful front end for structural equation modeling. Graphical
2991 displays of path diagrams, factor analysis and structural equation models are
2992 created using basic graphics.")
2993 (license license:gpl2+)))
2995 (define-public r-generics
3002 (uri (cran-uri "generics" version))
3005 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3006 (build-system r-build-system)
3007 (home-page "https://github.com/r-lib/generics")
3008 (synopsis "Common S3 generics not provided by base R methods")
3010 "In order to reduce potential package dependencies and conflicts,
3011 generics provides a number of commonly used S3 generics that are not provided
3012 by base R methods related to model fitting.")
3013 (license license:gpl2)))
3015 (define-public r-broom
3022 (uri (cran-uri "broom" version))
3025 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
3026 (build-system r-build-system)
3028 `(("r-backports" ,r-backports)
3029 ("r-dplyr" ,r-dplyr)
3030 ("r-generics" ,r-generics)
3032 ("r-purrr" ,r-purrr)
3033 ("r-reshape2" ,r-reshape2)
3034 ("r-stringr" ,r-stringr)
3035 ("r-tibble" ,r-tibble)
3036 ("r-tidyr" ,r-tidyr)))
3037 (home-page "https://github.com/tidyverse/broom")
3038 (synopsis "Convert statistical analysis objects into tidy data frames")
3040 "This package provides tools to convert statistical analysis objects from
3041 R into tidy data frames, so that they can more easily be combined, reshaped
3042 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3043 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3044 summarizes a model's statistical findings such as coefficients of a
3045 regression; @code{augment}, which adds columns to the original data such as
3046 predictions, residuals and cluster assignments; and @code{glance}, which
3047 provides a one-row summary of model-level statistics.")
3048 (license license:expat)))
3050 (define-public r-recipes
3057 (uri (cran-uri "recipes" version))
3060 "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
3061 (build-system r-build-system)
3063 `(("r-dplyr" ,r-dplyr)
3064 ("r-generics" ,r-generics)
3066 ("r-gower" ,r-gower)
3067 ("r-ipred" ,r-ipred)
3068 ("r-lubridate" ,r-lubridate)
3069 ("r-magrittr" ,r-magrittr)
3070 ("r-matrix" ,r-matrix)
3071 ("r-purrr" ,r-purrr)
3072 ("r-rlang" ,r-rlang)
3073 ("r-tibble" ,r-tibble)
3074 ("r-tidyr" ,r-tidyr)
3075 ("r-tidyselect" ,r-tidyselect)
3076 ("r-timedate" ,r-timedate)
3077 ("r-withr" ,r-withr)))
3078 (home-page "https://github.com/topepo/recipes")
3079 (synopsis "Preprocessing tools to create design matrices")
3081 "Recipes is an extensible framework to create and preprocess design
3082 matrices. Recipes consist of one or more data manipulation and analysis
3083 \"steps\". Statistical parameters for the steps can be estimated from an
3084 initial data set and then applied to other data sets. The resulting design
3085 matrices can then be used as inputs into statistical or machine learning
3087 (license license:gpl2)))
3089 (define-public r-pdist
3096 (uri (cran-uri "pdist" version))
3099 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3100 (build-system r-build-system)
3101 (home-page "https://github.com/jeffwong/pdist")
3102 (synopsis "Partitioned distance function")
3104 "Pdist computes the euclidean distance between rows of a matrix X and
3105 rows of another matrix Y. Previously, this could be done by binding the two
3106 matrices together and calling @code{dist}, but this creates unnecessary
3107 computation by computing the distances between a row of X and another row of
3108 X, and likewise for Y. Pdist strictly computes distances across the two
3109 matrices, not within the same matrix, making computations significantly faster
3110 for certain use cases.")
3111 (license license:gpl3+)))
3113 (define-public r-ggrepel
3120 (uri (cran-uri "ggrepel" version))
3123 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3124 (build-system r-build-system)
3126 `(("r-ggplot2" ,r-ggplot2)
3128 ("r-scales" ,r-scales)))
3129 (home-page "http://github.com/slowkow/ggrepel")
3130 (synopsis "Repulsive text and label geometries for ggplot2")
3132 "This package provides text and label geometries for ggplot2 that help to
3133 avoid overlapping text labels. Labels repel away from each other and away
3134 from the data points.")
3135 (license license:gpl3)))
3137 (define-public r-corrplot
3144 (uri (cran-uri "corrplot" version))
3147 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3148 (build-system r-build-system)
3149 (home-page "https://github.com/taiyun/corrplot")
3150 (synopsis "Visualization of a correlation matrix")
3152 "This package provides a graphical display of a correlation matrix or
3153 general matrix. It also contains some algorithms to do matrix reordering. In
3154 addition, corrplot is good at details, including choosing color, text labels,
3155 color labels, layout, etc.")
3156 ;; Any version of the GPL
3157 (license license:gpl2+)))
3159 (define-public r-stringdist
3161 (name "r-stringdist")
3166 (uri (cran-uri "stringdist" version))
3168 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3169 (build-system r-build-system)
3170 (home-page "https://github.com/markvanderloo/stringdist")
3171 (synopsis "Approximate string matching and string distance functions")
3173 "This package implements an approximate string matching version of R's
3174 native @code{match} function. It can calculate various string distances based
3175 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3176 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3177 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3178 can be computed between character vectors while taking proper care of encoding
3179 or between integer vectors representing generic sequences.")
3180 (license license:gpl3+)))
3182 (define-public r-ucminf
3189 (uri (cran-uri "ucminf" version))
3192 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3193 (build-system r-build-system)
3194 (native-inputs `(("gfortran" ,gfortran)))
3195 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3196 (synopsis "General-purpose unconstrained non-linear optimization")
3198 "This package provides an implementation of an algorithm for
3199 general-purpose unconstrained non-linear optimization. The algorithm is of
3200 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3201 search with a trust region type monitoring of the input to the line search
3202 algorithm. The interface of @code{ucminf} is designed for easy interchange
3203 with the package @code{optim}.")
3204 (license license:gpl2+)))
3206 (define-public r-ordinal
3209 (version "2019.4-25")
3213 (uri (cran-uri "ordinal" version))
3216 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
3217 (build-system r-build-system)
3219 `(("r-mass" ,r-mass)
3220 ("r-matrix" ,r-matrix)
3221 ("r-numderiv" ,r-numderiv)
3222 ("r-ucminf" ,r-ucminf)))
3223 (home-page "https://github.com/runehaubo/ordinal")
3224 (synopsis "Regression models for ordinal data")
3226 "This package provides an implementation of cumulative link (mixed)
3227 models also known as ordered regression models, proportional odds models,
3228 proportional hazards models for grouped survival times and ordered models.
3229 Estimation is via maximum likelihood and mixed models are fitted with the
3230 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3231 (license license:gpl2+)))
3233 (define-public r-jomo
3240 (uri (cran-uri "jomo" version))
3243 "1k9l4290g350zbw1pjs871q9bxj3j2h1dilxpp06v4wy4n7d8qs0"))))
3244 (build-system r-build-system)
3246 `(("r-lme4" ,r-lme4)
3248 ("r-ordinal" ,r-ordinal)
3249 ("r-survival" ,r-survival)))
3250 (home-page "https://cran.r-project.org/web/packages/jomo/")
3251 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3253 "Similarly to Schafer's package pan, jomo is a package for multilevel
3254 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3255 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3256 possibility of handling binary and categorical data through latent normal
3257 variables, the option to use cluster-specific covariance matrices and to
3258 impute compatibly with the substantive model.")
3259 (license license:gpl2)))
3261 (define-public r-pan
3268 (uri (cran-uri "pan" version))
3271 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3272 (build-system r-build-system)
3273 (native-inputs `(("gfortran" ,gfortran)))
3274 (home-page "https://cran.r-project.org/web/packages/pan/")
3275 (synopsis "Multiple imputation for multivariate panel or clustered data")
3277 "This package implements multiple imputation for multivariate panel or
3279 (license license:gpl3)))
3281 (define-public r-mitml
3288 (uri (cran-uri "mitml" version))
3291 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3292 (build-system r-build-system)
3294 `(("r-haven" ,r-haven)
3297 (home-page "https://cran.r-project.org/web/packages/mitml/")
3298 (synopsis "Tools for multiple imputation in multilevel modeling")
3300 "This package provides tools for multiple imputation of missing data in
3301 multilevel modeling. It includes a user-friendly interface to the packages
3302 pan and jomo, and several functions for visualization, data management and the
3303 analysis of multiply imputed data sets.")
3304 (license license:gpl2+)))
3306 (define-public r-mice
3313 (uri (cran-uri "mice" version))
3316 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
3317 (build-system r-build-system)
3319 `(("r-broom" ,r-broom)
3320 ("r-dplyr" ,r-dplyr)
3321 ("r-lattice" ,r-lattice)
3323 ("r-mitml" ,r-mitml)
3326 ("r-rlang" ,r-rlang)
3327 ("r-rpart" ,r-rpart)
3328 ("r-survival" ,r-survival)))
3329 (home-page "https://cran.r-project.org/web/packages/mice/")
3330 (synopsis "Multivariate imputation by chained equations")
3332 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3333 implemented by the MICE algorithm as described in @url{Van Buuren and
3334 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3335 variable has its own imputation model. Built-in imputation models are
3336 provided for continuous data (predictive mean matching, normal), binary
3337 data (logistic regression), unordered categorical data (polytomous logistic
3338 regression) and ordered categorical data (proportional odds). MICE can also
3339 impute continuous two-level data (normal model, pan, second-level variables).
3340 Passive imputation can be used to maintain consistency between variables.
3341 Various diagnostic plots are available to inspect the quality of the
3343 ;; Any of these two versions.
3344 (license (list license:gpl2 license:gpl3))))
3346 (define-public r-truncnorm
3348 (name "r-truncnorm")
3353 (uri (cran-uri "truncnorm" version))
3356 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3357 (build-system r-build-system)
3358 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3359 (synopsis "Truncated normal distribution")
3360 (description "This package provides functions for the truncated normal
3361 distribution with mean equal to @code{mean} and standard deviation equal to
3362 @code{sd}. It includes density, distribution, quantile, and expected value
3363 functions, as well as a random generation function.")
3364 (license license:gpl2)))
3366 (define-public r-rsolnp
3373 (uri (cran-uri "Rsolnp" version))
3376 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3377 (properties `((upstream-name . "Rsolnp")))
3378 (build-system r-build-system)
3380 `(("r-truncnorm" ,r-truncnorm)))
3381 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3382 (synopsis "General non-linear optimization")
3383 (description "The Rsolnp package implements a general non-linear augmented
3384 Lagrange multiplier method solver, a @dfn{sequential quadratic
3385 programming} (SQP) based solver).")
3386 ;; Any version of the GPL.
3387 (license license:gpl2+)))
3389 (define-public r-hardyweinberg
3391 (name "r-hardyweinberg")
3396 (uri (cran-uri "HardyWeinberg" version))
3399 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3400 (properties `((upstream-name . "HardyWeinberg")))
3401 (build-system r-build-system)
3403 `(("r-mice" ,r-mice)
3405 ("r-rsolnp" ,r-rsolnp)))
3406 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3407 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3409 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3410 diallelic genetic marker data. All classical tests (chi-square, exact,
3411 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3412 included in the package, as well as functions for power computation and for
3413 the simulation of marker data under equilibrium and disequilibrium. Routines
3414 for dealing with markers on the X-chromosome are included. Functions for
3415 testing equilibrium in the presence of missing data by using multiple
3416 imputation are also provided. Implements several graphics for exploring the
3417 equilibrium status of a large set of diallelic markers: ternary plots with
3418 acceptance regions, log-ratio plots and Q-Q plots.")
3419 (license license:gpl2+)))
3428 (uri (cran-uri "sm" version))
3431 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3432 (build-system r-build-system)
3433 (native-inputs `(("gfortran" ,gfortran)))
3434 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3435 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3437 "This is software accompanying the book 'Applied Smoothing Techniques for
3438 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3439 University Press. It provides smoothing methods for nonparametric regression
3440 and density estimation")
3441 (license license:gpl2+)))
3443 (define-public r-venndiagram
3445 (name "r-venndiagram")
3449 (uri (cran-uri "VennDiagram" version))
3452 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3453 (properties `((upstream-name . "VennDiagram")))
3454 (build-system r-build-system)
3456 `(("r-futile-logger" ,r-futile-logger)))
3457 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3458 (synopsis "Generate High-Resolution Venn and Euler Plots")
3460 "This package provides a set of functions to generate high-resolution
3461 Venn and Euler plots. It includes handling for several special cases,
3462 including two-case scaling, and extensive customization of plot shape and
3464 (license license:gpl2+)))
3466 (define-public r-vioplot
3473 (uri (cran-uri "vioplot" version))
3476 "1jjrsds7p1jnnr4970h43526b9cdv3azizjbalbfzjjylc53lrca"))))
3477 (build-system r-build-system)
3481 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3482 (synopsis "Violin plot")
3484 "This package provides a violin plot, which is a combination of a box
3485 plot and a kernel density plot.")
3486 (license license:bsd-3)))
3488 (define-public r-rsofia
3494 ;; This package has been removed from CRAN, so we can
3495 ;; only fetch it from the archives.
3496 (uri (string-append "https://cran.r-project.org/src/"
3497 "contrib/Archive/RSofia/RSofia_"
3501 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3502 (properties `((upstream-name . "RSofia")))
3503 (build-system r-build-system)
3505 `(("r-rcpp" ,r-rcpp)))
3506 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3507 (synopsis "Port of sofia-ml to R")
3508 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3509 suite of fast incremental algorithms for machine learning that can be used for
3510 training models for classification or ranking.")
3511 (license license:asl2.0)))
3513 (define-public r-xts
3520 (uri (cran-uri "xts" version))
3523 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3524 (build-system r-build-system)
3525 (propagated-inputs `(("r-zoo" ,r-zoo)))
3526 (home-page "https://github.com/joshuaulrich/xts")
3527 (synopsis "Extensible time series")
3529 "This package provides for uniform handling of R's different time-based
3530 data classes by extending @code{zoo}, maximizing native format information
3531 preservation and allowing for user-level customization and extension, while
3532 simplifying cross-class interoperability.")
3533 (license license:gpl2+)))
3535 (define-public r-performanceanalytics
3537 (name "r-performanceanalytics")
3542 (uri (cran-uri "PerformanceAnalytics" version))
3545 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3547 `((upstream-name . "PerformanceAnalytics")))
3548 (build-system r-build-system)
3550 `(("r-quadprog" ,r-quadprog)
3553 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3554 (synopsis "Econometric tools for performance and risk analysis")
3555 (description "This is a collection of econometric functions for
3556 performance and risk analysis. This package aims to aid practitioners and
3557 researchers in utilizing the latest research in analysis of non-normal return
3558 streams. In general, it is most tested on return (rather than price) data on
3559 a regular scale, but most functions will work with irregular return data as
3560 well, and increasing numbers of functions will work with P&L or price data
3562 ;; Either version may be picked.
3563 (license (list license:gpl2 license:gpl3))))
3565 (define-public r-laeken
3572 (uri (cran-uri "laeken" version))
3575 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3576 (build-system r-build-system)
3578 `(("r-boot" ,r-boot)
3579 ("r-mass" ,r-mass)))
3580 (home-page "https://cran.r-project.org/web/packages/laeken/")
3581 (synopsis "Estimation of indicators on social exclusion and poverty")
3582 (description "This package provides tools for the estimation of indicators
3583 on social exclusion and poverty, as well as an implementation of Pareto tail
3584 modeling for empirical income distributions.")
3585 (license license:gpl2+)))
3587 (define-public r-vcd
3594 (uri (cran-uri "vcd" version))
3597 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3598 (build-system r-build-system)
3600 `(("r-colorspace" ,r-colorspace)
3601 ("r-lmtest" ,r-lmtest)
3602 ("r-mass" ,r-mass)))
3603 (home-page "https://cran.r-project.org/web/packages/vcd/")
3604 (synopsis "Visualizing categorical data")
3605 (description "This package provides visualization techniques, data sets,
3606 summary and inference procedures aimed particularly at categorical data.
3607 Special emphasis is given to highly extensible grid graphics. The package was
3608 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3609 Friendly and is now the main support package for a new book, \"Discrete Data
3610 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3611 (license license:gpl2)))
3613 (define-public r-ica
3620 (uri (cran-uri "ica" version))
3623 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3624 (build-system r-build-system)
3625 (home-page "https://cran.r-project.org/web/packages/ica/")
3626 (synopsis "Independent component analysis")
3627 (description "This package provides tools for @dfn{Independent Component
3628 Analysis} (ICA) using various algorithms: FastICA,
3629 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3630 of Eigenmatrices} (JADE).")
3631 (license license:gpl2+)))
3633 (define-public r-dtw
3640 (uri (cran-uri "dtw" version))
3643 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3644 (build-system r-build-system)
3645 (propagated-inputs `(("r-proxy" ,r-proxy)))
3646 (home-page "http://dtw.r-forge.r-project.org/")
3647 (synopsis "Dynamic Time Warping Algorithms")
3648 (description "This package provides a comprehensive implementation of
3649 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3650 optimal (least cumulative distance) alignment between points of two time
3651 series. Common DTW variants covered include local (slope) and global (window)
3652 constraints, subsequence matches, arbitrary distance definitions,
3653 normalizations, minimum variance matching, and so on.")
3654 (license license:gpl2+)))
3656 (define-public r-sdmtools
3659 (version "1.1-221.1")
3663 (uri (cran-uri "SDMTools" version))
3666 "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q"))))
3667 (properties `((upstream-name . "SDMTools")))
3668 (build-system r-build-system)
3669 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3670 (home-page "http://www.rforge.net/SDMTools/")
3671 (synopsis "Species distribution modelling tools")
3672 (description "This package provides a set of tools for post processing
3673 the outcomes of species distribution modeling exercises. It includes novel
3674 methods for comparing models and tracking changes in distributions through
3675 time. It further includes methods for visualizing outcomes, selecting
3676 thresholds, calculating measures of accuracy and landscape fragmentation
3678 (license license:gpl3+)))
3680 (define-public r-scatterplot3d
3682 (name "r-scatterplot3d")
3687 (uri (cran-uri "scatterplot3d" version))
3690 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3691 (build-system r-build-system)
3692 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3693 (synopsis "3D scatter plot")
3694 (description "This package provides an implementation of scatter plots for
3695 plotting. a three dimensional point cloud.")
3696 (license license:gpl2)))
3698 (define-public r-ggridges
3705 (uri (cran-uri "ggridges" version))
3708 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3709 (build-system r-build-system)
3711 `(("r-ggplot2" ,r-ggplot2)
3713 ("r-scales" ,r-scales)
3714 ("r-withr" ,r-withr)))
3715 (home-page "https://github.com/clauswilke/ggridges")
3716 (synopsis "Ridgeline plots in ggplot2")
3718 "Ridgeline plots provide a convenient way of visualizing changes in
3719 distributions over time or space. This package enables the creation of such
3720 plots in @code{ggplot2}.")
3721 (license license:gpl2)))
3723 (define-public r-ggjoy
3730 (uri (cran-uri "ggjoy" version))
3733 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3734 (build-system r-build-system)
3736 `(("r-ggplot2" ,r-ggplot2)
3737 ("r-ggridges" ,r-ggridges)))
3738 (home-page "https://github.com/clauswilke/ggjoy")
3739 (synopsis "Joyplots in ggplot2")
3740 (description "Joyplots provide a convenient way of visualizing changes in
3741 distributions over time or space. This package enables the creation of such
3742 plots in @code{ggplot2}.")
3743 (license license:gpl2)))
3745 (define-public r-cli
3752 (uri (cran-uri "cli" version))
3755 "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g"))))
3756 (build-system r-build-system)
3758 `(("r-assertthat" ,r-assertthat)
3759 ("r-crayon" ,r-crayon)))
3760 (home-page "https://github.com/r-lib/cli#readme")
3761 (synopsis "Helpers for developing command line interfaces")
3762 (description "This package provides a suite of tools designed to build
3763 attractive command line interfaces (CLIs). It includes tools for drawing
3764 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3765 (license license:expat)))
3767 (define-public r-argparser
3769 (name "r-argparser")
3774 (uri (cran-uri "argparser" version))
3777 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3778 (build-system r-build-system)
3779 (home-page "https://bitbucket.org/djhshih/argparser")
3780 (synopsis "Command-line argument parser")
3782 "This package provides a cross-platform command-line argument parser
3783 written purely in R with no external dependencies. It is useful with the
3784 Rscript front-end and facilitates turning an R script into an executable
3786 (license license:gpl3+)))
3788 (define-public r-debugme
3795 (uri (cran-uri "debugme" version))
3798 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3799 (build-system r-build-system)
3800 (propagated-inputs `(("r-crayon" ,r-crayon)))
3801 (home-page "https://github.com/r-lib/debugme#readme")
3802 (synopsis "Debug R packages")
3804 "This package allows the user to specify debug messages as special string
3805 constants, and control debugging of packages via environment variables.")
3806 (license license:expat)))
3808 (define-public r-processx
3815 (uri (cran-uri "processx" version))
3818 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3819 (build-system r-build-system)
3823 (home-page "https://github.com/r-lib/processx3")
3824 (synopsis "Execute and control system processes")
3826 "This package provides portable tools to run system processes in the
3827 background. It can check if a background process is running; wait on a
3828 background process to finish; get the exit status of finished processes; kill
3829 background processes and their children; restart processes. It can read the
3830 standard output and error of the processes, using non-blocking connections.
3831 @code{processx} can poll a process for standard output or error, with a
3832 timeout. It can also poll several processes at once.")
3833 (license license:expat)))
3835 (define-public r-tsp
3842 (uri (cran-uri "TSP" version))
3845 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3846 (properties `((upstream-name . "TSP")))
3847 (build-system r-build-system)
3848 (propagated-inputs `(("r-foreach" ,r-foreach)))
3849 (home-page "https://cran.r-project.org/web/packages/TSP/")
3850 (synopsis "Traveling salesperson problem (TSP)")
3851 (description "This package provides basic infrastructure and some
3852 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3853 traveling salesman problem).")
3854 (license license:gpl3)))
3856 (define-public r-qap
3863 (uri (cran-uri "qap" version))
3866 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3867 (build-system r-build-system)
3868 (native-inputs `(("gfortran" ,gfortran)))
3869 (home-page "https://cran.r-project.org/web/packages/qap/")
3870 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3871 (description "This package implements heuristics for the @dfn{quadratic
3872 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3874 (license license:gpl3)))
3876 (define-public r-gclus
3883 (uri (cran-uri "gclus" version))
3886 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3887 (build-system r-build-system)
3888 (propagated-inputs `(("r-cluster" ,r-cluster)))
3889 (home-page "https://cran.r-project.org/web/packages/gclus/")
3890 (synopsis "Clustering graphics")
3891 (description "This package orders panels in scatterplot matrices and
3892 parallel coordinate displays by some merit index. It contains various indices
3893 of merit, ordering functions, and enhanced versions of @code{pairs} and
3894 @code{parcoord} which color panels according to their merit level.")
3895 (license license:gpl2+)))
3897 (define-public r-webshot
3904 (uri (cran-uri "webshot" version))
3907 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
3908 (build-system r-build-system)
3910 `(("r-callr" ,r-callr)
3911 ("r-jsonlite" ,r-jsonlite)
3912 ("r-magrittr" ,r-magrittr)))
3913 (home-page "https://github.com/wch/webshot/")
3914 (synopsis "Take screenshots of web pages")
3916 "Webshot makes it easy to take screenshots of web pages from within R.
3917 It can also run Shiny applications locally and take screenshots of the
3918 application; and it can render and screenshot static as well as interactive R
3919 Markdown documents.")
3920 (license license:gpl2)))
3922 (define-public r-seriation
3924 (name "r-seriation")
3929 (uri (cran-uri "seriation" version))
3932 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3933 (build-system r-build-system)
3935 `(("r-cluster" ,r-cluster)
3936 ("r-colorspace" ,r-colorspace)
3937 ("r-dendextend" ,r-dendextend)
3938 ("r-gclus" ,r-gclus)
3939 ("r-gplots" ,r-gplots)
3942 ("r-registry" ,r-registry)
3944 (native-inputs `(("gfortran" ,gfortran)))
3945 (home-page "http://s2.smu.edu/IDA/seriation/")
3946 (synopsis "Infrastructure for ordering objects using seriation")
3948 "This package provides infrastructure for seriation with an
3949 implementation of several seriation/sequencing techniques to reorder matrices,
3950 dissimilarity matrices, and dendrograms. It also provides (optimally)
3951 reordered heatmaps, color images and clustering visualizations like
3952 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3954 (license license:gpl3)))
3956 (define-public r-xfun
3963 (uri (cran-uri "xfun" version))
3965 (base32 "0dncw6bqkal7nyarrrrj9arxy0y3nkdzmrbibcjh84m1cxd4phiw"))))
3966 (build-system r-build-system)
3967 (home-page "https://github.com/yihui/xfun")
3968 (synopsis "Miscellaneous functions")
3970 "This package provides miscellaneous functions commonly used in other
3971 packages maintained by Yihui Xie.")
3972 (license license:expat)))
3974 (define-public r-utf8
3981 (uri (cran-uri "utf8" version))
3984 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
3985 (build-system r-build-system)
3986 (home-page "https://github.com/patperry/r-utf8")
3987 (synopsis "Unicode text processing")
3989 "This package provides tools to process and print UTF-8 encoded
3990 international text (Unicode). Input, validate, normalize, encode, format, and
3992 (license license:asl2.0)))
3994 (define-public r-zeallot
4001 (uri (cran-uri "zeallot" version))
4004 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4005 (build-system r-build-system)
4006 (home-page "https://github.com/nteetor/zeallot")
4007 (synopsis "Multiple, unpacking, and destructuring assignment")
4009 "This package provides a @code{%<-%} operator to perform multiple,
4010 unpacking, and destructuring assignment in R. The operator unpacks the
4011 right-hand side of an assignment into multiple values and assigns these values
4012 to variables on the left-hand side of the assignment.")
4013 (license license:expat)))
4015 (define-public r-vctrs
4022 (uri (cran-uri "vctrs" version))
4025 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
4026 (build-system r-build-system)
4028 `(("r-backports" ,r-backports)
4029 ("r-digest" ,r-digest)
4030 ("r-ellipsis" ,r-ellipsis)
4032 ("r-rlang" ,r-rlang)
4033 ("r-zeallot" ,r-zeallot)))
4034 (home-page "https://github.com/r-lib/vctrs")
4035 (synopsis "Vector helpers")
4037 "There are three main goals to the @code{vctrs} package:
4040 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4041 @code{length()} and @code{class()}. These definitions are paired with a
4042 framework for type-coercion and size-recycling.
4043 @item To define type- and size-stability as desirable function properties, use
4044 them to analyse existing base function, and to propose better alternatives.
4045 This work has been particularly motivated by thinking about the ideal
4046 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4047 @item To provide a new @code{vctr} base class that makes it easy to create new
4048 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4049 a few new @code{vctrs} generics, making implementation considerably simpler
4052 (license license:gpl3)))
4054 (define-public r-pillar
4061 (uri (cran-uri "pillar" version))
4064 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
4065 (build-system r-build-system)
4068 ("r-crayon" ,r-crayon)
4069 ("r-fansi" ,r-fansi)
4070 ("r-rlang" ,r-rlang)
4072 ("r-vctrs" ,r-vctrs)))
4073 (home-page "https://github.com/r-lib/pillar")
4074 (synopsis "Coloured formatting for columns")
4076 "This package provides a @code{pillar} generic designed for formatting
4077 columns of data using the full range of colours provided by modern
4079 (license license:gpl3)))
4081 (define-public r-uuid
4088 (uri (cran-uri "uuid" version))
4091 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4092 (build-system r-build-system)
4093 (home-page "http://www.rforge.net/uuid")
4094 (synopsis "Tools for generating and handling of UUIDs")
4096 "This package provides tools for generating and handling of
4097 @dfn{Universally Unique Identifiers} (UUIDs).")
4098 (license license:expat)))
4100 (define-public r-tinytex
4107 (uri (cran-uri "tinytex" version))
4110 "0mgxrbj4gam2gvxfk26nq820vsfjggj81m2l7j9m8vp361k15r0w"))))
4111 (build-system r-build-system)
4113 `(("r-xfun" ,r-xfun)))
4114 (home-page "https://github.com/yihui/tinytex")
4115 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4117 "This package provides helper functions to install and maintain the LaTeX
4118 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4119 easy-to-maintain version of TeX Live. This package also contains helper
4120 functions to compile LaTeX documents, and install missing LaTeX packages
4122 (license license:expat)))
4124 (define-public r-metap
4131 (uri (cran-uri "metap" version))
4134 "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0"))))
4135 (build-system r-build-system)
4137 `(("r-lattice" ,r-lattice)
4138 ("r-rdpack" ,r-rdpack)))
4139 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4140 (synopsis "Meta-analysis of significance values")
4142 "The canonical way to perform meta-analysis involves using effect sizes.
4143 When they are not available this package provides a number of methods for
4144 meta-analysis of significance values including the methods of Edgington,
4145 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4146 published results; and a routine for graphical display.")
4147 (license license:gpl2)))
4149 (define-public r-network
4156 (uri (cran-uri "network" version))
4159 "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
4160 (build-system r-build-system)
4162 `(("r-magrittr" ,r-magrittr)
4163 ("r-tibble" ,r-tibble)))
4164 (home-page "https://statnet.org/")
4165 (synopsis "Classes for relational data")
4167 "This package provides tools to create and modify network objects. The
4168 @code{network} class can represent a range of relational data types, and
4169 supports arbitrary vertex/edge/graph attributes.")
4170 (license license:gpl2+)))
4172 (define-public r-statnet-common
4174 (name "r-statnet-common")
4179 (uri (cran-uri "statnet.common" version))
4182 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4184 `((upstream-name . "statnet.common")))
4185 (build-system r-build-system)
4187 `(("r-coda" ,r-coda)))
4188 (home-page "https://statnet.org")
4189 (synopsis "R scripts and utilities used by the Statnet software")
4190 (description "This package provides non-statistical utilities used by the
4191 software developed by the Statnet Project.")
4192 (license license:gpl3)))
4194 (define-public r-sna
4201 (uri (cran-uri "sna" version))
4204 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
4205 (build-system r-build-system)
4207 `(("r-network" ,r-network)
4208 ("r-statnet-common" ,r-statnet-common)))
4209 (home-page "https://statnet.org")
4210 (synopsis "Tools for social network analysis")
4212 "This package provides a range of tools for social network analysis,
4213 including node and graph-level indices, structural distance and covariance
4214 methods, structural equivalence detection, network regression, random graph
4215 generation, and 2D/3D network visualization.")
4216 (license license:gpl2+)))
4218 (define-public r-ttr
4225 (uri (cran-uri "TTR" version))
4228 "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
4229 (properties `((upstream-name . "TTR")))
4230 (build-system r-build-system)
4232 `(("r-curl" ,r-curl)
4235 (home-page "https://github.com/joshuaulrich/TTR")
4236 (synopsis "Technical trading rules")
4238 "This package provides functions and data to construct technical trading
4240 (license license:gpl2)))
4242 (define-public r-leaps
4249 (uri (cran-uri "leaps" version))
4252 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4253 (build-system r-build-system)
4254 (native-inputs `(("gfortran" ,gfortran)))
4255 (home-page "https://cran.r-project.org/web/packages/leaps/")
4256 (synopsis "Regression subset selection")
4258 "This package provides tools for regression subset selection, including
4259 exhaustive search.")
4260 (license license:gpl2+)))
4262 (define-public r-splus2r
4269 (uri (cran-uri "splus2R" version))
4272 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4273 (properties `((upstream-name . "splus2R")))
4274 (build-system r-build-system)
4275 (native-inputs `(("gfortran" ,gfortran)))
4276 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4277 (synopsis "Supplemental S-PLUS functionality in R")
4279 "Currently there are many functions in S-PLUS that are missing in R. To
4280 facilitate the conversion of S-PLUS packages to R packages, this package
4281 provides some missing S-PLUS functionality in R.")
4282 (license license:gpl2)))
4284 (define-public r-ifultools
4286 (name "r-ifultools")
4291 (uri (cran-uri "ifultools" version))
4294 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4295 (build-system r-build-system)
4297 `(("r-mass" ,r-mass)
4298 ("r-splus2r" ,r-splus2r)))
4299 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4300 (synopsis "Insightful research tools")
4301 (description "This package provides C code used by the wmtsa, fractal, and
4303 (license license:gpl2)))
4305 (define-public r-sapa
4312 (uri (cran-uri "sapa" version))
4315 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4316 (build-system r-build-system)
4318 `(("r-ifultools" ,r-ifultools)
4319 ("r-splus2r" ,r-splus2r)))
4320 (home-page "https://cran.r-project.org/web/packages/sapa/")
4321 (synopsis "Spectral analysis for physical applications")
4322 (description "This package provides software for the book Spectral
4323 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4324 Cambridge University Press, 1993.")
4325 (license license:gpl2)))
4327 (define-public r-aggregation
4329 (name "r-aggregation")
4334 (uri (cran-uri "aggregation" version))
4337 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4338 (build-system r-build-system)
4339 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4340 (synopsis "Methods for p-value aggregation")
4342 "This package contains functionality for performing the following methods
4343 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4344 Fisher's method), and Sidak correction.")
4345 (license license:gpl3)))
4347 (define-public r-quantmod
4354 (uri (cran-uri "quantmod" version))
4357 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4358 (build-system r-build-system)
4360 `(("r-curl" ,r-curl)
4364 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4365 (synopsis "Quantitative financial modelling framework")
4366 (description "This package provides a quantitative financial modelling
4367 framework to allow users to specify, build, trade, and analyse quantitative
4368 financial trading strategies.")
4369 (license license:gpl3)))
4371 (define-public r-tseries
4378 (uri (cran-uri "tseries" version))
4381 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4382 (build-system r-build-system)
4384 `(("r-quadprog" ,r-quadprog)
4385 ("r-quantmod" ,r-quantmod)
4388 `(("gfortran" ,gfortran)))
4389 (home-page "https://cran.r-project.org/web/packages/tseries/")
4390 (synopsis "Time series analysis and computational finance")
4392 "This package provides functions relating to time series analysis and
4393 computational finance.")
4394 (license license:gpl2)))
4396 (define-public r-wmtsa
4403 (uri (cran-uri "wmtsa" version))
4406 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4407 (build-system r-build-system)
4409 `(("r-ifultools" ,r-ifultools)
4411 ("r-splus2r" ,r-splus2r)))
4412 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4413 (synopsis "Wavelet methods for time series analysis")
4415 "This package provides software to accompany the book \"Wavelet Methods
4416 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4417 University Press, 2000.")
4418 (license license:gpl2)))
4420 (define-public r-tsa
4427 (uri (cran-uri "TSA" version))
4430 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4431 (properties `((upstream-name . "TSA")))
4432 (build-system r-build-system)
4434 `(("r-leaps" ,r-leaps)
4435 ("r-locfit" ,r-locfit)
4436 ("r-mgcv" ,r-mgcv)))
4437 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4438 (synopsis "Time series analysis")
4440 "This package contains R functions and datasets detailed in the book
4441 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4442 Cryer and Kung-Sik Chan.")
4443 (license license:gpl2+)))
4445 (define-public r-extradistr
4447 (name "r-extradistr")
4452 (uri (cran-uri "extraDistr" version))
4455 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4456 (properties `((upstream-name . "extraDistr")))
4457 (build-system r-build-system)
4459 `(("r-rcpp" ,r-rcpp)))
4460 (home-page "https://github.com/twolodzko/extraDistr")
4461 (synopsis "Additional univariate and multivariate distributions")
4463 "This package implements density, distribution functions, quantile
4464 functions and random generation functions for a large number of univariate and
4465 multivariate distributions.")
4466 (license license:gpl2)))
4468 (define-public r-fractal
4475 (uri (cran-uri "fractal" version))
4478 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4479 (build-system r-build-system)
4481 `(("r-ifultools" ,r-ifultools)
4484 ("r-scatterplot3d" ,r-scatterplot3d)
4485 ("r-splus2r" ,r-splus2r)
4486 ("r-wmtsa" ,r-wmtsa)))
4487 (home-page "https://cran.r-project.org/web/packages/fractal/")
4488 (synopsis "Fractal time series modeling and analysis")
4490 "This package provides tools for stochastic fractal and deterministic
4491 chaotic time series analysis.")
4492 (license license:gpl2)))
4494 (define-public r-urca
4501 (uri (cran-uri "urca" version))
4504 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4505 (build-system r-build-system)
4506 (propagated-inputs `(("r-nlme" ,r-nlme)))
4507 (native-inputs `(("gfortran" ,gfortran)))
4508 (home-page "https://cran.r-project.org/web/packages/urca/")
4509 (synopsis "Unit root and cointegration tests for time series data")
4511 "This package provides unit root and cointegration tests encountered in
4512 applied econometric analysis.")
4513 (license license:gpl2+)))
4515 (define-public r-cubature
4522 (uri (cran-uri "cubature" version))
4525 "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"))))
4526 (build-system r-build-system)
4528 `(("r-rcpp" ,r-rcpp)))
4529 (home-page "https://github.com/bnaras/cubature")
4530 (synopsis "Adaptive multivariate integration over hypercubes")
4532 "This package is an R wrapper around the cubature C library for adaptive
4533 multivariate integration over hypercubes. This version provides both
4534 @code{hcubature} and @code{pcubature} routines in addition to a vector
4536 ;; The included cubature C library is released under GPLv2+, but the
4537 ;; wrapper declares the license to be GPLv3+.
4538 (license (list license:gpl2+ license:gpl3+))))
4540 (define-public r-trend
4547 (uri (cran-uri "trend" version))
4550 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4551 (build-system r-build-system)
4553 `(("r-extradistr" ,r-extradistr)))
4555 `(("gfortran" ,gfortran)))
4556 (home-page "https://cran.r-project.org/web/packages/trend/")
4557 (synopsis "Non-parametric trend tests and change-point detection")
4559 "The analysis of environmental data often requires the detection of
4560 trends and change-points. This package includes tests for trend
4561 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4562 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4563 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4564 correlation trend test), change-point detection (Lanzante's test procedures,
4565 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4566 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4567 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4568 sample Robust Rank-Order Distributional Test.")
4569 (license license:gpl3)))
4571 (define-public r-expm
4578 (uri (cran-uri "expm" version))
4581 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4582 (build-system r-build-system)
4583 (propagated-inputs `(("r-matrix" ,r-matrix)))
4584 (native-inputs `(("gfortran" ,gfortran)))
4585 (home-page "https://r-forge.r-project.org/projects/expm/")
4586 (synopsis "Tools for matrix exponentials and related quantities")
4588 "This package provides tools for the computation of the matrix
4589 exponential, logarithm, square root, and related quantities.")
4590 (license license:gpl2+)))
4592 (define-public r-complexplus
4594 (name "r-complexplus")
4599 (uri (cran-uri "complexplus" version))
4602 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4603 (build-system r-build-system)
4605 `(("r-expm" ,r-expm)
4606 ("r-matrix" ,r-matrix)))
4607 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4608 (synopsis "Functions of complex or real variables")
4610 "This package extends several functions to the complex domain, including
4611 the matrix exponential and logarithm, and the determinant.")
4612 (license license:gpl2)))
4614 (define-public r-phontools
4616 (name "r-phontools")
4621 (uri (cran-uri "phonTools" version))
4624 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4625 (properties `((upstream-name . "phonTools")))
4626 (build-system r-build-system)
4627 (home-page "http://www.santiagobarreda.com/rscripts.html")
4628 (synopsis "Tools for phonetic and acoustic analyses")
4630 "This package contains tools for the organization, display, and analysis
4631 of the sorts of data frequently encountered in phonetics research and
4632 experimentation, including the easy creation of IPA vowel plots, and the
4633 creation and manipulation of WAVE audio files.")
4634 (license license:bsd-2)))
4643 (uri (cran-uri "np" version))
4646 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4647 (build-system r-build-system)
4649 `(("r-boot" ,r-boot)
4650 ("r-cubature" ,r-cubature)
4651 ("r-quadprog" ,r-quadprog)
4652 ("r-quantreg" ,r-quantreg)))
4653 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4654 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4655 (description "This package provides non-parametric (and semi-parametric)
4656 kernel methods that seamlessly handle a mix of continuous, unordered, and
4657 ordered factor data types.")
4658 ;; Any version of the GPL.
4659 (license license:gpl3+)))
4661 (define-public r-powerplus
4663 (name "r-powerplus")
4668 (uri (cran-uri "powerplus" version))
4671 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4672 (build-system r-build-system)
4674 `(("r-complexplus" ,r-complexplus)
4677 ("r-matrix" ,r-matrix)
4678 ("r-phontools" ,r-phontools)))
4679 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4680 (synopsis "Exponentiation operations")
4682 "This package provides tools for the computation of matrix and scalar
4684 (license license:gpl2)))
4686 (define-public r-heatmaply
4688 (name "r-heatmaply")
4693 (uri (cran-uri "heatmaply" version))
4696 "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1"))))
4697 (build-system r-build-system)
4699 `(("r-assertthat" ,r-assertthat)
4700 ("r-colorspace" ,r-colorspace)
4701 ("r-dendextend" ,r-dendextend)
4702 ("r-ggplot2" ,r-ggplot2)
4703 ("r-htmlwidgets" ,r-htmlwidgets)
4704 ("r-magrittr" ,r-magrittr)
4705 ("r-plotly" ,r-plotly)
4706 ("r-rcolorbrewer" ,r-rcolorbrewer)
4707 ("r-reshape2" ,r-reshape2)
4708 ("r-scales" ,r-scales)
4709 ("r-seriation" ,r-seriation)
4710 ("r-viridis" ,r-viridis)
4711 ("r-webshot" ,r-webshot)))
4712 (home-page "https://cran.r-project.org/package=heatmaply")
4713 (synopsis "Interactive cluster heat maps using plotly")
4715 "This package enables you to create interactive cluster heatmaps that can
4716 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4717 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4718 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4719 a popular graphical method for visualizing high-dimensional data, in which a
4720 table of numbers is encoded as a grid of colored cells. The rows and columns
4721 of the matrix are ordered to highlight patterns and are often accompanied by
4723 ;; Either version of the license.
4724 (license (list license:gpl2 license:gpl3))))
4733 (uri (cran-uri "h5" version))
4736 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4737 (build-system r-build-system)
4742 `(("which" ,which)))
4744 `(("r-rcpp" ,r-rcpp)))
4745 (home-page "https://github.com/mannau/h5")
4746 (synopsis "Interface to the HDF5 Library")
4748 "This package provides an S4 interface to the HDF5 library supporting
4749 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4750 binary files in a language independent format. The HDF5 format can therefore
4751 be used as an alternative to R's save/load mechanism. Since h5 is able to
4752 access only subsets of stored data it can also handle data sets which do not
4754 (license license:bsd-2)))
4756 (define-public r-cgdsr
4763 (uri (cran-uri "cgdsr" version))
4766 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4767 (build-system r-build-system)
4769 `(("r-httr" ,r-httr)
4770 ("r-r-methodss3" ,r-r-methodss3)
4771 ("r-r-oo" ,r-r-oo)))
4772 (home-page "https://github.com/cBioPortal/cgdsr")
4773 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4775 "This package provides a basic set of R functions for querying the Cancer
4776 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4777 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4778 (license license:lgpl3)))
4780 (define-public r-import
4787 (uri (cran-uri "import" version))
4790 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4791 (build-system r-build-system)
4792 (home-page "https://github.com/smbache/import")
4793 (synopsis "Import mechanism for R")
4795 "This is an alternative mechanism for importing objects from packages.
4796 The syntax allows for importing multiple objects from a package with a single
4797 command in an expressive way. The import package bridges some of the gap
4798 between using @code{library} (or @code{require}) and direct (single-object)
4799 imports. Furthermore the imported objects are not placed in the current
4800 environment. It is also possible to import objects from stand-alone @code{.R}
4802 (license license:expat)))
4804 (define-public r-shinyace
4811 (uri (cran-uri "shinyAce" version))
4814 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4815 (properties `((upstream-name . "shinyAce")))
4816 (build-system r-build-system)
4818 `(("r-shiny" ,r-shiny)
4819 ("r-jsonlite" ,r-jsonlite)))
4820 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4821 (synopsis "Ace editor bindings for Shiny")
4823 "This package provides Ace editor bindings to enable a rich text editing
4824 environment within Shiny.")
4825 (license license:expat)))
4827 (define-public r-base64url
4829 (name "r-base64url")
4834 (uri (cran-uri "base64url" version))
4837 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4838 (build-system r-build-system)
4840 `(("r-backports" ,r-backports)))
4841 (home-page "https://github.com/mllg/base64url")
4842 (synopsis "Fast and URL-safe base64 encoder and decoder")
4844 "This package provides a URL-safe base64 encoder and decoder. In
4845 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4846 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4847 encoder does not fill the string with trailing @code{=}. The resulting
4848 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4849 and thus are safe to use in URLs or for file names. The package also comes
4850 with a simple base32 encoder/decoder suited for case insensitive file
4852 (license license:gpl3)))
4854 (define-public r-radiant-data
4856 (name "r-radiant-data")
4861 (uri (cran-uri "radiant.data" version))
4864 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4865 (modules '((guix build utils)))
4868 ;; Delete files that are under CC-NC-SA.
4869 (delete-file-recursively "inst/app/tools/help")
4871 (properties `((upstream-name . "radiant.data")))
4872 (build-system r-build-system)
4874 `(("r-base64enc" ,r-base64enc)
4875 ("r-broom" ,r-broom)
4878 ("r-dplyr" ,r-dplyr)
4881 ("r-ggplot2" ,r-ggplot2)
4882 ("r-gridextra" ,r-gridextra)
4883 ("r-import" ,r-import)
4884 ("r-jsonlite" ,r-jsonlite)
4885 ("r-knitr" ,r-knitr)
4886 ("r-lubridate" ,r-lubridate)
4887 ("r-magrittr" ,r-magrittr)
4888 ("r-markdown" ,r-markdown)
4889 ("r-plotly" ,r-plotly)
4890 ("r-psych" ,r-psych)
4891 ("r-readr" ,r-readr)
4892 ("r-readxl" ,r-readxl)
4893 ("r-rlang" ,r-rlang)
4894 ("r-rmarkdown" ,r-rmarkdown)
4895 ("r-rstudioapi" ,r-rstudioapi)
4896 ("r-scales" ,r-scales)
4897 ("r-shiny" ,r-shiny)
4898 ("r-shinyfiles" ,r-shinyfiles)
4899 ("r-shinyace" ,r-shinyace)
4900 ("r-stringi" ,r-stringi)
4901 ("r-tibble" ,r-tibble)
4902 ("r-tidyr" ,r-tidyr)
4903 ("r-writexl" ,r-writexl)))
4904 (home-page "https://github.com/radiant-rstats/radiant.data")
4905 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4907 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4908 visualizing, summarizing, transforming, and combining data. It also contains
4909 functionality to generate reproducible reports of the analyses conducted in
4911 (license license:agpl3)))
4913 (define-public r-algdesign
4915 (name "r-algdesign")
4916 (version "1.1-7.3.1")
4920 (uri (cran-uri "AlgDesign" version))
4922 (base32 "1s69yx0wxi9kqj9kyib0yvd363d7g4zrz0cvz1hn97ladr8656bz"))))
4923 (properties `((upstream-name . "AlgDesign")))
4924 (build-system r-build-system)
4925 (home-page "https://github.com/jvbraun/AlgDesign")
4926 (synopsis "Algorithmic experimental design")
4928 "This package provides tools to calculate exact and approximate theory
4929 experimental designs for D, A, and I criteria. Very large designs may be
4930 created. Experimental designs may be blocked or blocked designs created from
4931 a candidate list, using several criteria. The blocking can be done when whole
4932 and within plot factors interact.")
4933 (license license:gpl2+)))
4935 (define-public r-signal
4942 (uri (cran-uri "signal" version))
4945 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
4946 (build-system r-build-system)
4947 (propagated-inputs `(("r-mass" ,r-mass)))
4948 (native-inputs `(("gfortran" ,gfortran)))
4949 (home-page "https://cran.r-project.org/web/packages/signal/")
4950 (synopsis "Signal processing")
4952 "This package provides a set of signal processing functions originally
4953 written for Matlab and GNU Octave. It includes filter generation utilities,
4954 filtering functions, resampling routines, and visualization of filter models.
4955 It also includes interpolation functions.")
4956 (license license:gpl2)))
4958 (define-public r-gsubfn
4965 (uri (cran-uri "gsubfn" version))
4968 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
4969 (build-system r-build-system)
4970 (propagated-inputs `(("r-proto" ,r-proto)))
4971 (home-page "http://gsubfn.googlecode.com")
4972 (synopsis "Utilities for strings and function arguments.")
4974 "This package provides @code{gsubfn} which is like @code{gsub} but can
4975 take a replacement function or certain other objects instead of the
4976 replacement string. Matches and back references are input to the replacement
4977 function and replaced by the function output. @code{gsubfn} can be used to
4978 split strings based on content rather than delimiters and for quasi-perl-style
4979 string interpolation. The package also has facilities for translating
4980 formulas to functions and allowing such formulas in function calls instead of
4982 (license license:gpl2+)))
4984 (define-public r-sqldf
4991 (uri (cran-uri "sqldf" version))
4994 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
4995 (build-system r-build-system)
4997 `(("r-chron" ,r-chron)
4999 ("r-gsubfn" ,r-gsubfn)
5000 ("r-proto" ,r-proto)
5001 ("r-rsqlite" ,r-rsqlite)))
5002 (home-page "https://github.com/ggrothendieck/sqldf")
5003 (synopsis "Manipulate R data frames using SQL")
5005 "The @code{sqldf} function is typically passed a single argument which is
5006 an SQL select statement where the table names are ordinary R data frame names.
5007 @code{sqldf} transparently sets up a database, imports the data frames into
5008 that database, performs the SQL statement and returns the result using a
5009 heuristic to determine which class to assign to each column of the returned
5010 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5011 used to read filtered files into R even if the original files are larger than
5012 R itself can handle.")
5013 (license license:gpl2)))
5015 (define-public r-abind
5022 (uri (cran-uri "abind" version))
5025 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5026 (build-system r-build-system)
5027 (home-page "https://cran.r-project.org/web/packages/abind/")
5028 (synopsis "Combine multidimensional arrays")
5030 "This package provides tools to combine multidimensional arrays into a
5031 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5032 works with vectors, matrices, and higher-dimensional arrays. It also provides
5033 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5034 extracting and replacing data in arrays.")
5035 (license license:lgpl2.0+)))
5037 (define-public r-prroc
5044 (uri (cran-uri "PRROC" version))
5047 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5048 (properties `((upstream-name . "PRROC")))
5049 (build-system r-build-system)
5050 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5051 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5053 "This package computes the areas under the @dfn{precision-recall} (PR)
5054 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5055 contrast to other implementations, the interpolation between points of the PR
5056 curve is done by a non-linear piecewise function. In addition to the areas
5057 under the curves, the curves themselves can also be computed and plotted by a
5058 specific S3-method.")
5059 (license license:gpl3)))
5061 (define-public r-vim
5068 (uri (cran-uri "VIM" version))
5071 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5072 (properties `((upstream-name . "VIM")))
5073 (build-system r-build-system)
5076 ("r-colorspace" ,r-colorspace)
5077 ("r-data-table" ,r-data-table)
5078 ("r-e1071" ,r-e1071)
5079 ("r-laeken" ,r-laeken)
5082 ("r-ranger" ,r-ranger)
5084 ("r-robustbase" ,r-robustbase)
5087 (home-page "https://github.com/alexkowa/VIM")
5088 (synopsis "Visualization and imputation of missing values")
5090 "This package provides tools for the visualization of missing and/or
5091 imputed values are introduced, which can be used for exploring the data and
5092 the structure of the missing and/or imputed values. Depending on this
5093 structure of the missing values, the corresponding methods may help to
5094 identify the mechanism generating the missing values and allows to explore the
5095 data including missing values. In addition, the quality of imputation can be
5096 visually explored using various univariate, bivariate, multiple and
5097 multivariate plot methods.")
5098 (license license:gpl2+)))
5100 (define-public r-fnn
5107 (uri (cran-uri "FNN" version))
5110 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5111 (properties `((upstream-name . "FNN")))
5112 (build-system r-build-system)
5113 (home-page "https://cran.r-project.org/web/packages/FNN")
5114 (synopsis "Fast nearest neighbor search algorithms and applications")
5116 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5117 search algorithms. Related applications including KNN classification,
5118 regression and information measures are implemented.")
5119 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5120 ;; later can be used.
5121 (license license:gpl2+)))
5123 (define-public r-smoother
5130 (uri (cran-uri "smoother" version))
5133 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5134 (build-system r-build-system)
5136 `(("r-ttr" ,r-ttr)))
5137 (home-page "http://cran.r-project.org/web/packages/smoother")
5138 (synopsis "Functions relating to the smoothing of numerical data")
5140 "This package provides a collection of methods for smoothing numerical
5141 data, commencing with a port of the Matlab gaussian window smoothing function.
5142 In addition, several functions typically used in smoothing of financial data
5144 (license license:gpl2)))
5146 (define-public r-riverplot
5148 (name "r-riverplot")
5153 (uri (cran-uri "riverplot" version))
5156 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5157 (build-system r-build-system)
5158 (home-page "https://logfc.wordpress.com")
5159 (synopsis "Sankey or ribbon plots")
5161 "Sankey plots are a type of diagram that is convenient to illustrate how
5162 flow of information, resources etc. separates and joins, much like observing
5163 how rivers split and merge. For example, they can be used to compare
5164 different clusterings. This package provides an implementation of Sankey
5166 (license license:gpl2+)))
5168 (define-public r-dyn
5175 (uri (cran-uri "dyn" version))
5178 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5179 (build-system r-build-system)
5181 `(("r-zoo" ,r-zoo)))
5182 (home-page "https://cran.r-project.org/web/packages/dyn")
5183 (synopsis "Time series regression")
5185 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5186 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5187 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5188 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5189 @code{randomForest::randomForest()} and other regression functions, allowing
5190 those functions to be used with time series including specifications that may
5191 contain lags, diffs and missing values.")
5193 (license license:gpl2+)))
5195 (define-public r-catdap
5202 (uri (cran-uri "catdap" version))
5205 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5206 (build-system r-build-system)
5208 `(("gfortran" ,gfortran)))
5209 (home-page "https://cran.r-project.org/web/packages/catdap/")
5210 (synopsis "Tools for categorical data analysis")
5212 "This package provides functions for analyzing multivariate data.
5213 Dependencies of the distribution of the specified variable (response
5214 variable) to other variables (explanatory variables) are derived and
5215 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5216 (license license:gpl2+)))
5218 (define-public r-arules
5225 (uri (cran-uri "arules" version))
5228 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5229 (build-system r-build-system)
5231 `(("r-matrix" ,r-matrix)))
5232 (home-page "https://github.com/mhahsler/arules")
5233 (synopsis "Mining association rules and frequent itemsets")
5235 "This package provides an infrastructure for representing, manipulating
5236 and analyzing transaction data and patterns (frequent itemsets and association rules).
5237 It also provides C implementations of the association mining algorithms Apriori
5239 (license license:gpl3)))
5241 (define-public r-parsedate
5243 (name "r-parsedate")
5248 (uri (cran-uri "parsedate" version))
5251 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5252 (build-system r-build-system)
5254 `(("r-rematch2" ,r-rematch2)))
5255 (home-page "https://github.com/gaborcsardi/parsedate")
5257 "Recognize and parse dates in various formats")
5259 "This package provides three functions for dealing with dates:
5260 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5261 time formats, @code{parse_date} parses dates in unspecified formats,
5262 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5263 (license license:gpl2)))
5265 (define-public r-abc-data
5272 (uri (cran-uri "abc.data" version))
5275 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5276 (properties `((upstream-name . "abc.data")))
5277 (build-system r-build-system)
5278 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5279 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5281 "This package contains data which are used by functions of the abc
5282 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5283 algorithms for performing parameter estimation, model selection, and
5285 (license license:gpl3+)))
5287 (define-public r-abc
5294 (uri (cran-uri "abc" version))
5297 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5298 (build-system r-build-system)
5300 `(("r-abc-data" ,r-abc-data)
5301 ("r-locfit" ,r-locfit)
5304 ("r-quantreg" ,r-quantreg)))
5305 (home-page "https://cran.r-project.org/web/packages/abc/")
5306 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5308 "This package implements several @dfn{Approximate Bayesian
5309 Computation} (ABC) algorithms for performing parameter estimation, model
5310 selection, and goodness-of-fit. Cross-validation tools are also available for
5311 measuring the accuracy of ABC estimates, and to calculate the
5312 misclassification probabilities of different models.")
5313 (license license:gpl3+)))
5315 (define-public r-zip
5322 (uri (cran-uri "zip" version))
5325 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5326 (build-system r-build-system)
5327 (home-page "https://github.com/gaborcsardi/zip")
5328 (synopsis "Cross-platform Zip compression")
5330 "This package provides a cross-platform Zip compression library for R.
5331 It is a replacement for the @code{zip} function, that does not require any
5332 additional external tools on any platform.")
5333 (license license:cc0)))
5335 (define-public r-openxlsx
5342 (uri (cran-uri "openxlsx" version))
5345 "087zivh9xdh1kk8zci67ys0m2xq0slzwgnf0jl05yy4gsgb6nmyx"))))
5346 (build-system r-build-system)
5348 `(("r-rcpp" ,r-rcpp)
5349 ("r-rlang" ,r-rlang)
5350 ("r-stringi" ,r-stringi)
5352 (home-page "https://github.com/awalker89/openxlsx")
5353 (synopsis "Read, write and edit XLSX files")
5355 "This package simplifies the creation of Excel @code{.xlsx} files by
5356 providing a high level interface to writing, styling and editing worksheets.
5357 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5358 and @code{XLConnect} packages with the added benefit of removing the
5359 dependency on Java.")
5360 (license license:gpl3)))
5362 (define-public r-rio
5369 (uri (cran-uri "rio" version))
5372 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5373 (build-system r-build-system)
5375 `(("r-curl" ,r-curl)
5376 ("r-data-table" ,r-data-table)
5377 ("r-foreign" ,r-foreign)
5378 ("r-haven" ,r-haven)
5379 ("r-openxlsx" ,r-openxlsx)
5380 ("r-readxl" ,r-readxl)
5381 ("r-tibble" ,r-tibble)))
5382 (home-page "https://github.com/leeper/rio")
5383 (synopsis "Swiss-army knife for data I/O")
5385 "This package provides streamlined data import and export infrastructure
5386 by making assumptions that the user is probably willing to make: @code{import}
5387 and @code{export} determine the data structure from the file extension,
5388 reasonable defaults are used for data import and export (e.g.,
5389 @code{stringsAsFactors=FALSE}), web-based import is natively
5390 supported (including from SSL/HTTPS), compressed files can be read directly
5391 without explicit decompression, and fast import packages are used where
5392 appropriate. An additional convenience function, @code{convert}, provides a
5393 simple method for converting between file types.")
5394 (license license:gpl2)))
5396 (define-public r-maptools
5403 (uri (cran-uri "maptools" version))
5406 "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x"))))
5407 (build-system r-build-system)
5409 `(("r-foreign" ,r-foreign)
5410 ("r-lattice" ,r-lattice)
5412 (home-page "http://r-forge.r-project.org/projects/maptools/")
5413 (synopsis "Tools for reading and handling spatial objects")
5415 "This package provides a set of tools for manipulating and reading
5416 geographic data, in particular ESRI Shapefiles. It includes binary access to
5417 GSHHG shoreline files. The package also provides interface wrappers for
5418 exchanging spatial objects with other R packages.")
5419 ;; The C source files from shapelib are released under the Expat license.
5420 ;; The R code is released under GPL version 2 or later.
5421 (license (list license:gpl2+
5424 (define-public r-later
5431 (uri (cran-uri "later" version))
5434 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5435 (build-system r-build-system)
5439 ("r-rlang" ,r-rlang)))
5440 (home-page "https://github.com/r-lib/later")
5441 (synopsis "Utilities for delaying function execution")
5443 "This package provides tools to execute arbitrary R or C functions some
5444 time after the current time, after the R execution stack has emptied.")
5445 (license license:gpl2+)))
5447 (define-public r-promises
5454 (uri (cran-uri "promises" version))
5457 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5458 (build-system r-build-system)
5460 `(("r-later" ,r-later)
5461 ("r-magrittr" ,r-magrittr)
5464 ("r-rlang" ,r-rlang)))
5465 (home-page "https://rstudio.github.io/promises")
5466 (synopsis "Abstractions for promise-based asynchronous programming")
5468 "This package provides fundamental abstractions for doing asynchronous
5469 programming in R using promises. Asynchronous programming is useful for
5470 allowing a single R process to orchestrate multiple tasks in the background
5471 while also attending to something else. Semantics are similar to JavaScript
5472 promises, but with a syntax that is idiomatic R.")
5473 (license license:expat)))
5475 (define-public r-dosnow
5482 (uri (cran-uri "doSNOW" version))
5485 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5486 (properties `((upstream-name . "doSNOW")))
5487 (build-system r-build-system)
5489 `(("r-foreach" ,r-foreach)
5490 ("r-iterators" ,r-iterators)
5491 ("r-snow" ,r-snow)))
5492 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5493 (synopsis "Foreach parallel adaptor for the snow package")
5495 "This package provides a parallel backend for the @code{%dopar%} function
5496 using the @code{snow} package.")
5497 (license license:gpl2)))
5499 (define-public r-snowfall
5502 (version "1.84-6.1")
5505 (uri (cran-uri "snowfall" version))
5507 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5508 (build-system r-build-system)
5510 `(("r-snow" ,r-snow)))
5511 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5512 (synopsis "Easier cluster computing")
5513 (description "This package is a usability wrapper around snow for easier
5514 development of parallel R programs. This package offers e.g. extended error
5515 checks, and additional functions. All functions work in sequential mode, too,
5516 if no cluster is present or wished. The package is also designed as connector
5517 to the cluster management tool @code{sfCluster}, but can also used without
5519 (license license:gpl2+)))
5521 (define-public r-rappdirs
5528 (uri (cran-uri "rappdirs" version))
5531 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5532 (build-system r-build-system)
5533 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5534 (synopsis "Determine where to save data, caches, and logs")
5536 "This package provides an easy way to determine which directories on the
5537 user's computer should be used to save data, caches and logs. It is a port of
5538 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5539 (license license:expat)))
5541 (define-public r-renv
5548 (uri (cran-uri "renv" version))
5551 "0034jlaq7z40q3hcpkjlaff37dpn46kvxvzw4scbwlw4x9q8sx9j"))))
5552 (properties `((upstream-name . "renv")))
5553 (build-system r-build-system)
5554 (home-page "https://rstudio.github.io/renv")
5555 (synopsis "Project environments")
5557 "This package provides a dependency management toolkit for R. Using
5558 renv, you can create and manage project-local R libraries, save the state of
5559 these libraries to a lockfile, and later restore your library as required.
5560 Together, these tools can help make your projects more isolated, portable, and
5562 (license license:expat)))
5564 (define-public r-learnr
5571 (uri (cran-uri "learnr" version))
5574 "0278q9nbkc4nb0rp930kjrwyidf0v7y38d1s187m4f4bs7ha82k6"))))
5575 (build-system r-build-system)
5577 `(("r-checkmate" ,r-checkmate)
5578 ("r-ellipsis" ,r-ellipsis)
5579 ("r-evaluate" ,r-evaluate)
5580 ("r-htmltools" ,r-htmltools)
5581 ("r-htmlwidgets" ,r-htmlwidgets)
5582 ("r-jsonlite" ,r-jsonlite)
5583 ("r-knitr" ,r-knitr)
5584 ("r-markdown" ,r-markdown)
5585 ("r-rappdirs" ,r-rappdirs)
5587 ("r-rmarkdown" ,r-rmarkdown)
5588 ("r-rprojroot" ,r-rprojroot)
5589 ("r-shiny" ,r-shiny)
5590 ("r-withr" ,r-withr)))
5591 (home-page "https://rstudio.github.io/learnr/")
5592 (synopsis "Interactive tutorials for R")
5594 "This package provides tools to create interactive tutorials using R
5595 Markdown. Use a combination of narrative, figures, videos, exercises, and
5596 quizzes to create self-paced tutorials for learning about R and R packages.")
5597 (license license:asl2.0)))
5599 (define-public r-analytics
5601 (name "r-analytics")
5606 (uri (cran-uri "analytics" version))
5609 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5610 (build-system r-build-system)
5613 ("r-cluster" ,r-cluster)
5614 ("r-fractal" ,r-fractal)
5615 ("r-lmtest" ,r-lmtest)
5618 ("r-powerplus" ,r-powerplus)
5619 ("r-robust" ,r-robust)
5620 ("r-trend" ,r-trend)
5624 (home-page "https://cran.r-project.org/web/packages/analytics/")
5625 (synopsis "Collection of data analysis tools")
5627 "This package is a collection of data analysis tools. It includes tools
5628 for regression outlier detection in a fitted linear model, stationary
5629 bootstrap using a truncated geometric distribution, a comprehensive test for
5630 weak stationarity, column means by group, weighted biplots, and a heuristic to
5631 obtain a better initial configuration in non-metric MDS.")
5632 (license license:gpl2)))
5634 (define-public r-reticulate
5636 (name "r-reticulate")
5641 (uri (cran-uri "reticulate" version))
5644 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
5645 (build-system r-build-system)
5646 (inputs `(("python" ,python)))
5648 `(("r-jsonlite" ,r-jsonlite)
5649 ("r-matrix" ,r-matrix)
5650 ("r-rcpp" ,r-rcpp)))
5651 (home-page "https://github.com/rstudio/reticulate")
5652 (synopsis "R interface to Python")
5654 "This package provides an interface from R to Python modules, classes,
5655 and functions. When calling into Python, R data types are automatically
5656 converted to their equivalent Python types. When values are returned from
5657 Python to R they are converted back to R types.")
5658 (license license:asl2.0)))
5660 (define-public r-bibtex
5667 (uri (cran-uri "bibtex" version))
5670 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5671 (build-system r-build-system)
5672 (propagated-inputs `(("r-stringr" ,r-stringr)))
5673 (home-page "https://github.com/romainfrancois/bibtex")
5674 (synopsis "Bibtex parser")
5675 (description "This package provides a utility for R to parse a bibtex
5677 (license license:gpl2+)))
5679 (define-public r-ggseqlogo
5681 (name "r-ggseqlogo")
5686 (uri (cran-uri "ggseqlogo" version))
5689 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5690 (build-system r-build-system)
5691 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5692 (home-page "https://github.com/omarwagih/ggseqlogo")
5693 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5695 "The range of functions provided by this package makes it possible to
5696 draw highly versatile genomic sequence logos. Features include, but are not
5697 limited to, modifying colour schemes and fonts used to draw the logo,
5698 generating multiple logo plots, and aiding the visualisation with annotations.
5699 Sequence logos can easily be combined with other ggplot2 plots.")
5700 ;; Unspecified version of the LGPL.
5701 (license license:lgpl3+)))
5703 (define-public r-ggsci
5710 (uri (cran-uri "ggsci" version))
5713 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5714 (build-system r-build-system)
5716 `(("r-ggplot2" ,r-ggplot2)
5717 ("r-scales" ,r-scales)))
5718 (home-page "https://nanx.me/ggsci/")
5719 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5721 "This package provides a collection of ggplot2 color palettes inspired by
5722 plots in scientific journals, data visualization libraries, science fiction
5723 movies, and TV shows.")
5724 (license license:gpl3)))
5726 (define-public r-ggsignif
5733 (uri (cran-uri "ggsignif" version))
5736 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5737 (build-system r-build-system)
5739 `(("r-ggplot2" ,r-ggplot2)))
5740 (home-page "https://github.com/const-ae/ggsignif")
5741 (synopsis "Significance brackets for ggplot2")
5743 "Enrich your ggplots with group-wise comparisons. This package provides
5744 an easy way to indicate if two groups are significantly different. Commonly
5745 this is shown by a bracket on top connecting the groups of interest which
5746 itself is annotated with the level of significance. The package provides a
5747 single layer that takes the groups for comparison and the test as arguments
5748 and adds the annotation to the plot.")
5749 (license license:gpl3)))
5751 (define-public r-ggpubr
5758 (uri (cran-uri "ggpubr" version))
5761 "0ln1gh3zlfx5s7zqcpvfdiksq74v1pma5kwkhc6r0riqnjjd19pf"))))
5762 (build-system r-build-system)
5764 `(("r-cowplot" ,r-cowplot)
5765 ("r-dplyr" ,r-dplyr)
5766 ("r-ggplot2" ,r-ggplot2)
5767 ("r-ggrepel" ,r-ggrepel)
5768 ("r-ggsci" ,r-ggsci)
5769 ("r-ggsignif" ,r-ggsignif)
5771 ("r-gridextra" ,r-gridextra)
5772 ("r-magrittr" ,r-magrittr)
5773 ("r-polynom" ,r-polynom)
5774 ("r-purrr" ,r-purrr)
5775 ("r-rlang" ,r-rlang)
5776 ("r-scales" ,r-scales)
5777 ("r-tidyr" ,r-tidyr)))
5778 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5779 (synopsis "ggplot2-based publication-ready plots")
5781 "The ggplot2 package is an excellent and flexible package for elegant
5782 data visualization in R. However the default generated plots require some
5783 formatting before we can send them for publication. The ggpubr package
5784 provides some easy-to-use functions for creating and customizing ggplot2-based
5785 publication-ready plots.")
5786 (license license:gpl2)))
5788 (define-public r-ellipse
5795 (uri (cran-uri "ellipse" version))
5798 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5799 (build-system r-build-system)
5800 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5801 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5803 "This package contains various routines for drawing ellipses and
5804 ellipse-like confidence regions, implementing the plots described in Murdoch
5805 and Chow (1996), A graphical display of large correlation matrices, The
5806 American Statistician 50, 178-180. There are also routines implementing the
5807 profile plots described in Bates and Watts (1988), Nonlinear Regression
5808 Analysis and its Applications.")
5809 (license license:gpl2+)))
5811 (define-public r-flashclust
5813 (name "r-flashclust")
5818 (uri (cran-uri "flashClust" version))
5821 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5822 (properties `((upstream-name . "flashClust")))
5823 (build-system r-build-system)
5824 (native-inputs `(("gfortran" ,gfortran)))
5825 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5826 (synopsis "Implementation of optimal hierarchical clustering")
5828 "This package provides a fast implementation of hierarchical
5830 (license license:gpl2+)))
5832 (define-public r-factominer
5834 (name "r-factominer")
5839 (uri (cran-uri "FactoMineR" version))
5842 "0qiw60ypf3bf5xsqz2b9l82i4jvprjm8lzpp12lhl8d9j5s8m0j8"))))
5843 (properties `((upstream-name . "FactoMineR")))
5844 (build-system r-build-system)
5847 ("r-cluster" ,r-cluster)
5848 ("r-ellipse" ,r-ellipse)
5849 ("r-flashclust" ,r-flashclust)
5850 ("r-ggplot2" ,r-ggplot2)
5851 ("r-ggrepel" ,r-ggrepel)
5852 ("r-lattice" ,r-lattice)
5853 ("r-leaps" ,r-leaps)
5855 ("r-scatterplot3d" ,r-scatterplot3d)))
5856 (home-page "http://factominer.free.fr")
5857 (synopsis "Multivariate exploratory data analysis and data mining")
5859 "This package provides exploratory data analysis methods to summarize,
5860 visualize and describe datasets. The main principal component methods are
5861 available, those with the largest potential in terms of applications:
5862 principal component analysis (PCA) when variables are quantitative,
5863 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5864 variables are categorical, Multiple Factor Analysis when variables are
5865 structured in groups, etc. and hierarchical cluster analysis.")
5866 (license license:gpl2+)))
5868 (define-public r-factoextra
5870 (name "r-factoextra")
5875 (uri (cran-uri "factoextra" version))
5878 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
5879 (build-system r-build-system)
5881 `(("r-abind" ,r-abind)
5882 ("r-cluster" ,r-cluster)
5883 ("r-dendextend" ,r-dendextend)
5884 ("r-factominer" ,r-factominer)
5885 ("r-ggplot2" ,r-ggplot2)
5886 ("r-ggpubr" ,r-ggpubr)
5887 ("r-ggrepel" ,r-ggrepel)
5888 ("r-reshape2" ,r-reshape2)
5889 ("r-tidyr" ,r-tidyr)))
5890 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5891 (synopsis "Extract and visualize the results of multivariate data analyses")
5893 "This package provides some easy-to-use functions to extract and
5894 visualize the output of multivariate data analyses, including
5895 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5896 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5897 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5898 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5899 packages. It contains also functions for simplifying some clustering analysis
5900 steps and provides ggplot2-based elegant data visualization.")
5901 (license license:gpl2)))
5903 (define-public r-fansi
5910 (uri (cran-uri "fansi" version))
5913 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
5914 (build-system r-build-system)
5916 `(("r-knitr" ,r-knitr))) ; for vignettes
5917 (home-page "https://github.com/brodieG/fansi")
5918 (synopsis "ANSI control sequence aware string functions")
5920 "This package provides counterparts to R string manipulation functions
5921 that account for the effects of ANSI text formatting control sequences.")
5922 (license license:gpl2+)))
5924 (define-public r-nbclust
5931 (uri (cran-uri "NbClust" version))
5934 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
5935 (properties `((upstream-name . "NbClust")))
5936 (build-system r-build-system)
5937 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
5938 (synopsis "Determine the best number of clusters in a data set")
5940 "NbClust provides 30 indexes for determining the optimal number of
5941 clusters in a data set and offers the best clustering scheme from different
5942 results to the user.")
5943 (license license:gpl2)))
5945 (define-public r-hdf5r
5952 (uri (cran-uri "hdf5r" version))
5955 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
5956 (build-system r-build-system)
5961 `(("r-bit64" ,r-bit64)
5963 (home-page "https://hhoeflin.github.io/hdf5r")
5964 (synopsis "Interface to the HDF5 binary data format")
5966 "HDF5 is a data model, library and file format for storing and managing
5967 large amounts of data. This package provides a nearly feature complete,
5968 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
5969 functionality is added so that HDF5 objects behave very similar to their
5970 corresponding R counterparts.")
5971 (license license:asl2.0)))
5973 (define-public r-itertools
5975 (name "r-itertools")
5980 (uri (cran-uri "itertools" version))
5983 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
5984 (build-system r-build-system)
5986 `(("r-iterators" ,r-iterators)))
5987 (home-page "https://cran.r-project.org/web/packages/itertools/")
5988 (synopsis "Iterator tools")
5990 "This package provides various tools for creating iterators, many
5991 patterned after functions in the Python @code{itertools} module, and others
5992 patterned after functions in the snow package.")
5993 (license license:gpl2)))
5995 (define-public r-polynom
6002 (uri (cran-uri "polynom" version))
6005 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6006 (build-system r-build-system)
6007 (home-page "https://cran.r-project.org/web/packages/polynom/")
6008 (synopsis "Functions for univariate polynomial manipulations")
6010 "This package provides a collection of functions to implement a class for
6011 univariate polynomial manipulations.")
6012 (license license:gpl2)))
6014 (define-public r-gbrd
6021 (uri (cran-uri "gbRd" version))
6024 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6025 (properties `((upstream-name . "gbRd")))
6026 (build-system r-build-system)
6027 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6028 (synopsis "Utilities for processing Rd objects and files")
6030 "This package provides utilities for processing Rd objects and files.
6031 Extract argument descriptions and other parts of the help pages of
6033 (license license:gpl2+)))
6035 (define-public r-rjags
6042 (uri (cran-uri "rjags" version))
6045 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6046 (build-system r-build-system)
6048 `(("r-coda" ,r-coda)))
6052 `(("pkg-config" ,pkg-config)))
6053 (home-page "http://mcmc-jags.sourceforge.net")
6054 (synopsis "Bayesian graphical models using MCMC")
6056 "This package provides an R interface to the JAGS MCMC library. JAGS is
6057 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6058 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6059 (license license:gpl2)))
6061 (define-public r-rdpack
6068 (uri (cran-uri "Rdpack" version))
6071 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
6072 (properties `((upstream-name . "Rdpack")))
6073 (build-system r-build-system)
6075 `(("r-bibtex" ,r-bibtex)
6076 ("r-gbrd" ,r-gbrd)))
6077 (home-page "https://github.com/GeoBosh/Rdpack")
6078 (synopsis "Update and manipulate Rd documentation objects")
6080 "This package provides functions for manipulation of R documentation
6081 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6082 updating Rd documentation for functions, methods and classes; it also includes
6083 Rd macros for citations and import of references from bibtex files for use in
6084 Rd files and roxygen2 comments, as well as many functions for manipulation of
6085 references and Rd files.")
6086 (license license:gpl2+)))
6088 (define-public r-officer
6095 (uri (cran-uri "officer" version))
6098 "1i6jmnbkx7gd0qyf6akhizmxp7y1dh3h7a886mcbmrzka9d60zh4"))))
6099 (build-system r-build-system)
6101 `(("r-base64enc" ,r-base64enc)
6102 ("r-digest" ,r-digest)
6103 ("r-htmltools" ,r-htmltools)
6104 ("r-magrittr" ,r-magrittr)
6107 ("r-rlang" ,r-rlang)
6111 (home-page "https://davidgohel.github.io/officer")
6112 (synopsis "Manipulation of Word and PowerPoint documents")
6114 "This package provides tools to access and manipulate Word and PowerPoint
6115 documents from R. The package focuses on tabular and graphical reporting from
6116 R; it also provides two functions that let users get document content into
6117 data objects. A set of functions lets add and remove images, tables and
6118 paragraphs of text in new or existing documents. When working with PowerPoint
6119 presentations, slides can be added or removed; shapes inside slides can also
6120 be added or removed. When working with Word documents, a cursor can be used
6121 to help insert or delete content at a specific location in the document.")
6122 (license license:gpl3)))
6124 (define-public r-abn
6131 (uri (cran-uri "abn" version))
6134 "19w6bdjyp4zwqs6p0flry4qxqynf9rh8ykdrfrp61wrdf7kysw0d"))))
6135 (build-system r-build-system)
6139 `(("r-lme4" ,r-lme4)
6143 ("r-rcpparmadillo" ,r-rcpparmadillo)
6144 ("r-rjags" ,r-rjags)))
6145 (home-page "http://www.r-bayesian-networks.org")
6146 (synopsis "Modelling multivariate data with additive bayesian networks")
6148 "Bayesian network analysis is a form of probabilistic graphical models
6149 which derives from empirical data a directed acyclic graph, DAG, describing
6150 the dependency structure between random variables. An additive Bayesian
6151 network model consists of a form of a DAG where each node comprises a
6152 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6153 equivalent to Bayesian multivariate regression using graphical modelling, they
6154 generalises the usual multivariable regression, GLM, to multiple dependent
6155 variables. This package provides routines to help determine optimal Bayesian
6156 network models for a given data set, where these models are used to identify
6157 statistical dependencies in messy, complex data.")
6158 (license license:gpl2+)))
6160 (define-public r-acd
6167 (uri (cran-uri "ACD" version))
6170 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6171 (properties `((upstream-name . "ACD")))
6172 (build-system r-build-system)
6173 (home-page "https://cran.r-project.org/web/packages/ACD/")
6174 (synopsis "Categorical data analysis with complete or missing responses")
6176 "This package provides tools for categorical data analysis with complete
6177 or missing responses.")
6178 (license license:gpl2+)))
6180 (define-public r-acdm
6187 (uri (cran-uri "ACDm" version))
6190 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6191 (properties `((upstream-name . "ACDm")))
6192 (build-system r-build-system)
6194 `(("r-dplyr" ,r-dplyr)
6195 ("r-ggplot2" ,r-ggplot2)
6197 ("r-rsolnp" ,r-rsolnp)
6199 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6200 (synopsis "Tools for Autoregressive Conditional Duration Models")
6202 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6203 and Russell, 1998) models. It creates trade, price or volume durations from
6204 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6206 (license license:gpl2+)))
6208 (define-public r-overlap
6215 (uri (cran-uri "overlap" version))
6218 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6219 (build-system r-build-system)
6220 (home-page "https://cran.r-project.org/web/packages/overlap/")
6221 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6223 "This package provides functions to fit kernel density functions to data
6224 on temporal activity patterns of animals; estimate coefficients of overlapping
6225 of densities for two species; and calculate bootstrap estimates of confidence
6227 (license license:gpl3+)))
6229 (define-public r-snakecase
6231 (name "r-snakecase")
6236 (uri (cran-uri "snakecase" version))
6239 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6240 (build-system r-build-system)
6242 `(("r-stringi" ,r-stringi)
6243 ("r-stringr" ,r-stringr)))
6244 (home-page "https://github.com/Tazinho/snakecase")
6245 (synopsis "Convert strings into any case")
6247 "This package provides a consistent, flexible and easy to use tool to
6248 parse and convert strings into cases like snake or camel among others.")
6249 (license license:gpl3)))
6251 (define-public r-prediction
6253 (name "r-prediction")
6258 (uri (cran-uri "prediction" version))
6261 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6262 (build-system r-build-system)
6264 `(("r-data-table" ,r-data-table)))
6265 (home-page "https://github.com/leeper/prediction")
6266 (synopsis "Tidy, type-safe prediction methods")
6268 "This package provides the @code{prediction()} function, a type-safe
6269 alternative to @code{predict()} that always returns a data frame. The package
6270 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6271 from the @code{stats} package, as well as numerous other model classes from
6272 other add-on packages.")
6273 (license license:expat)))
6275 (define-public r-insight
6282 (uri (cran-uri "insight" version))
6285 "1alxc483r3d1ydp983m2872mxd4nj3j25qv47zzgj10nbi4y32sq"))))
6286 (build-system r-build-system)
6287 (home-page "https://easystats.github.io/insight/")
6288 (synopsis "Easy access to model information for various model objects")
6290 "This package provides a tool to provide an easy, intuitive and
6291 consistent access to information contained in various R models, like model
6292 formulas, model terms, information about random effects, data that was used to
6293 fit the model or data from response variables. The package mainly revolves
6294 around two types of functions: Functions that find (the names of) information,
6295 starting with @code{find_}, and functions that get the underlying data,
6296 starting with @code{get_}. The package has a consistent syntax and works with
6297 many different model objects, where otherwise functions to access these
6298 information are missing.")
6299 (license license:gpl3)))
6301 (define-public r-sjlabelled
6303 (name "r-sjlabelled")
6308 (uri (cran-uri "sjlabelled" version))
6311 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6312 (build-system r-build-system)
6314 `(("r-haven" ,r-haven)
6315 ("r-insight" ,r-insight)
6316 ("r-magrittr" ,r-magrittr)
6317 ("r-purrr" ,r-purrr)
6318 ("r-rlang" ,r-rlang)
6319 ("r-tidyselect" ,r-tidyselect)))
6320 (home-page "https://github.com/strengejacke/sjlabelled")
6321 (synopsis "Labelled data utility functions")
6323 "This package provides a collection of functions dealing with labelled
6324 data, like reading and writing data between R and other statistical software
6325 packages. This includes easy ways to get, set or change value and variable
6326 label attributes, to convert labelled vectors into factors or numeric (and
6327 vice versa), or to deal with multiple declared missing values.")
6328 (license license:gpl3)))
6330 (define-public r-sjmisc
6337 (uri (cran-uri "sjmisc" version))
6340 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6341 (build-system r-build-system)
6343 `(("r-dplyr" ,r-dplyr)
6344 ("r-insight" ,r-insight)
6345 ("r-magrittr" ,r-magrittr)
6346 ("r-purrr" ,r-purrr)
6347 ("r-rlang" ,r-rlang)
6348 ("r-sjlabelled" ,r-sjlabelled)
6349 ("r-tidyselect" ,r-tidyselect)))
6350 (home-page "https://github.com/strengejacke/sjmisc")
6351 (synopsis "Data and variable transformation functions")
6353 "This package is a collection of miscellaneous utility functions,
6354 supporting data transformation tasks like recoding, dichotomizing or grouping
6355 variables, setting and replacing missing values. The data transformation
6356 functions also support labelled data, and all integrate seamlessly into a
6357 tidyverse workflow.")
6358 (license license:gpl3)))
6360 (define-public r-nortest
6367 (uri (cran-uri "nortest" version))
6370 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6371 (build-system r-build-system)
6372 (home-page "https://cran.r-project.org/web/packages/nortest/")
6373 (synopsis "Tests for normality")
6375 "This package provides five omnibus tests for testing the composite
6376 hypothesis of normality.")
6377 (license license:gpl2+)))
6379 (define-public r-moonbook
6386 (uri (cran-uri "moonBook" version))
6389 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6390 (properties `((upstream-name . "moonBook")))
6391 (build-system r-build-system)
6393 `(("r-magrittr" ,r-magrittr)
6394 ("r-nortest" ,r-nortest)
6395 ("r-purrr" ,r-purrr)
6396 ("r-sjmisc" ,r-sjmisc)
6397 ("r-stringr" ,r-stringr)
6398 ("r-survival" ,r-survival)))
6399 (home-page "https://github.com/cardiomoon/moonBook")
6400 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6402 "This package provides several analysis-related functions for the book
6403 entitled \"R statistics and graph for medical articles\" (written in Korean),
6404 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6406 (license license:gpl2)))
6408 (define-public r-flextable
6410 (name "r-flextable")
6415 (uri (cran-uri "flextable" version))
6418 "1f869f2dfqkzhf6yix7xcbs8rn1nwq3sg623h74zg6h1pl6px66w"))))
6419 (build-system r-build-system)
6421 `(("r-base64enc" ,r-base64enc)
6422 ("r-data-table" ,r-data-table)
6423 ("r-gdtools" ,r-gdtools)
6424 ("r-htmltools" ,r-htmltools)
6425 ("r-knitr" ,r-knitr)
6426 ("r-officer" ,r-officer)
6427 ("r-rlang" ,r-rlang)
6428 ("r-rmarkdown" ,r-rmarkdown)
6429 ("r-xml2" ,r-xml2)))
6430 (home-page "https://davidgohel.github.io/flextable")
6431 (synopsis "Functions for tabular reporting")
6433 "This package provides tools to create pretty tables for HTML documents
6434 and other formats. Functions are provided to let users create tables, modify
6435 and format their content. It extends the @code{officer} package and can be
6436 used within R markdown documents when rendering to HTML and to Word
6438 (license license:gpl3)))
6440 (define-public r-writexl
6447 (uri (cran-uri "writexl" version))
6450 "09fhdip6igcg97fjx4c7727cx2lb49l4d74l4i8rg2bag2s5lrj3"))))
6451 (build-system r-build-system)
6452 (inputs `(("zlib" ,zlib)))
6453 (home-page "https://github.com/ropensci/writexl")
6454 (synopsis "Export data frames to xlsx format")
6456 "This package provides a data frame to xlsx exporter based on
6458 (license license:bsd-2)))
6460 (define-public r-biasedurn
6462 (name "r-biasedurn")
6467 (uri (cran-uri "BiasedUrn" version))
6470 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6471 (properties `((upstream-name . "BiasedUrn")))
6472 (build-system r-build-system)
6473 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6474 (synopsis "Biased Urn model distributions")
6476 "This package provides statistical models of biased sampling in the form
6477 of univariate and multivariate noncentral hypergeometric distributions,
6478 including Wallenius' noncentral hypergeometric distribution and Fisher's
6479 noncentral hypergeometric distribution (also called extended hypergeometric
6481 (license license:gpl3)))
6483 (define-public r-goplot
6490 (uri (cran-uri "GOplot" version))
6493 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6494 (properties `((upstream-name . "GOplot")))
6495 (build-system r-build-system)
6497 `(("r-ggdendro" ,r-ggdendro)
6498 ("r-ggplot2" ,r-ggplot2)
6499 ("r-gridextra" ,r-gridextra)
6500 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6501 (home-page "https://github.com/wencke/wencke.github.io")
6502 (synopsis "Visualization of functional analysis data")
6504 "This package provides an implementation of multilayered visualizations
6505 for enhanced graphical representation of functional analysis data. It
6506 combines and integrates omics data derived from expression and functional
6507 annotation enrichment analyses. Its plotting functions have been developed
6508 with an hierarchical structure in mind: starting from a general overview to
6509 identify the most enriched categories (modified bar plot, bubble plot) to a
6510 more detailed one displaying different types of relevant information for the
6511 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6512 Venn diagram, heatmap).")
6513 (license license:gpl2)))
6515 (define-public r-getopt
6522 (uri (cran-uri "getopt" version))
6525 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6526 (build-system r-build-system)
6527 (home-page "https://github.com/trevorld/getopt")
6528 (synopsis "Command-line option processor for R")
6530 "This package is designed to be used with Rscript to write shebang
6531 scripts that accept short and long options. Many users will prefer to
6532 use the packages @code{optparse} or @code{argparse} which add extra
6533 features like automatically generated help options and usage texts,
6534 support for default values, positional argument support, etc.")
6535 (license license:gpl2+)))
6537 (define-public r-findpython
6539 (name "r-findpython")
6544 (uri (cran-uri "findpython" version))
6547 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6548 (build-system r-build-system)
6549 (home-page "https://github.com/trevorld/findpython")
6550 (synopsis "Functions to find an acceptable Python binary")
6552 "This package was designed to find an acceptable Python binary that
6553 matches version and feature constraints.")
6554 (license license:expat)))
6556 ;; This in not the same as "r-argparser"
6557 (define-public r-argparse
6564 (uri (cran-uri "argparse" version))
6567 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6568 (build-system r-build-system)
6569 (inputs `(("python" ,python)))
6571 `(("r-findpython" ,r-findpython)
6572 ("r-jsonlite" ,r-jsonlite)
6574 (home-page "https://github.com/trevorld/argparse")
6575 (synopsis "Command line optional and positional argument parser")
6577 "This package provides a command line parser to be used with Rscript to
6578 write shebang scripts that gracefully accept positional and optional arguments
6579 and automatically generate usage notices.")
6580 (license license:gpl2+)))
6582 (define-public r-hash
6589 (uri (cran-uri "hash" version))
6592 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6593 (build-system r-build-system)
6594 (home-page "https://cran.r-project.org/web/packages/hash/")
6595 (synopsis "Implementation of hash/associated arrays/dictionaries")
6597 "This package implements a data structure similar to hashes in Perl and
6598 dictionaries in Python but with a purposefully R flavor. For objects of
6599 appreciable size, access using hashes outperforms native named lists and
6601 (license license:gpl2+)))
6603 (define-public r-orddom
6610 (uri (cran-uri "orddom" version))
6613 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6614 (build-system r-build-system)
6615 (propagated-inputs `(("r-psych" ,r-psych)))
6616 (home-page "https://cran.r-project.org/web/packages/orddom/")
6617 (synopsis "Ordinal dominance statistics")
6619 "This package provides tools to compute ordinal, statistics and effect
6620 sizes as an alternative to mean comparison: Cliff's delta or success rate
6621 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6622 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6623 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6624 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6625 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6626 Group (Non-)Overlap considerations.")
6627 (license license:gpl2)))
6629 (define-public r-deriv
6636 (uri (cran-uri "Deriv" version))
6639 "0hlqm216bg3l79gq6m0am0xz6vd3l2hgjnjm6lym3mkmgkka4kxw"))))
6640 (properties `((upstream-name . "Deriv")))
6641 (build-system r-build-system)
6642 (home-page "https://cran.r-project.org/web/packages/Deriv")
6643 (synopsis "Symbolic differentiation")
6645 "This package provides an R-based solution for symbolic differentiation.
6646 It admits user-defined functions as well as function substitution in arguments
6647 of functions to be differentiated. Some symbolic simplification is part of
6649 (license license:gpl3+)))
6651 (define-public r-doby
6658 (uri (cran-uri "doBy" version))
6661 "1d0d6pwai1g4i5jls0jm9va29ci5hy92n5957608f3fzi1jwy635"))))
6662 (properties `((upstream-name . "doBy")))
6663 (build-system r-build-system)
6665 `(("r-broom" ,r-broom)
6666 ("r-deriv" ,r-deriv)
6667 ("r-dplyr" ,r-dplyr)
6668 ("r-magrittr" ,r-magrittr)
6670 ("r-matrix" ,r-matrix)
6672 ("r-pbkrtest" ,r-pbkrtest)
6673 ("r-tibble" ,r-tibble)))
6674 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6675 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6677 "This package contains:
6680 @item facilities for working with grouped data: @code{do}
6681 something to data stratified @code{by} some variables.
6682 @item implementations of least-squares means, general linear contrasts, and
6683 @item miscellaneous other utilities.
6685 (license license:gpl2+)))
6687 (define-public r-refgenome
6689 (name "r-refgenome")
6694 (uri (cran-uri "refGenome" version))
6697 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6698 (properties `((upstream-name . "refGenome")))
6699 (build-system r-build-system)
6703 ("r-rsqlite" ,r-rsqlite)))
6704 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6706 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6708 "This package contains functionality for importing and managing of
6709 downloaded genome annotation data from the Ensembl genome browser (European
6710 Bioinformatics Institute) and from the UCSC genome browser (University of
6711 California, Santa Cruz) and annotation routines for genomic positions and
6712 splice site positions.")
6713 (license license:gpl2)))
6715 (define-public r-basix
6722 (uri (cran-uri "BASIX" version))
6725 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6726 (properties `((upstream-name . "BASIX")))
6727 (build-system r-build-system)
6728 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6729 (synopsis "Efficient C/C++ toolset for R")
6731 "BASIX provides some efficient C/C++ implementations of native R
6732 procedures to speed up calculations in R.")
6733 (license license:gpl2)))
6735 (define-public r-blockfest
6737 (name "r-blockfest")
6742 (uri (cran-uri "BlockFeST" version))
6745 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6746 (properties `((upstream-name . "BlockFeST")))
6747 (build-system r-build-system)
6748 (propagated-inputs `(("r-basix" ,r-basix)))
6749 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6750 (synopsis "Bayesian calculation of region-specific fixation index")
6752 "This package provides an R implementation of an extension of the
6753 BayeScan software for codominant markers, adding the option to group
6754 individual SNPs into pre-defined blocks. A typical application of this new
6755 approach is the identification of genomic regions, genes, or gene sets
6756 containing one or more SNPs that evolved under directional selection.")
6757 (license license:gpl2)))
6759 (define-public r-proc
6766 (uri (cran-uri "pROC" version))
6769 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6770 (properties `((upstream-name . "pROC")))
6771 (build-system r-build-system)
6773 `(("r-plyr" ,r-plyr)
6774 ("r-rcpp" ,r-rcpp)))
6775 (home-page "http://expasy.org/tools/pROC/")
6776 (synopsis "Display and analyze ROC curves")
6778 "This package provides tools for visualizing, smoothing and comparing
6779 receiver operating characteristic (ROC curves). The area under the
6780 curve (AUC) can be compared with statistical tests based on U-statistics or
6781 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6782 (license license:gpl3+)))
6784 (define-public r-rootsolve
6786 (name "r-rootsolve")
6791 (uri (cran-uri "rootSolve" version))
6794 "0skrspq7sd7gaq73w91km14v8znc8chncgy64hvjgcng2xw15phx"))))
6795 (properties `((upstream-name . "rootSolve")))
6796 (build-system r-build-system)
6797 (native-inputs `(("gfortran" ,gfortran)))
6798 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6799 (synopsis "Tools for the analysis of ordinary differential equations")
6801 "This package provides routines to find the root of nonlinear functions,
6802 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6803 differential equations} (ODE). It includes routines that:
6806 @item generate gradient and jacobian matrices (full and banded),
6807 @item find roots of non-linear equations by the Newton-Raphson method,
6808 @item estimate steady-state conditions of a system of (differential) equations
6809 in full, banded or sparse form, using the Newton-Raphson method, or by
6810 dynamically running,
6811 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6812 and 3-D partial differential equations, that have been converted to ordinary
6813 differential equations by numerical differencing (using the method-of-lines
6816 (license license:gpl2+)))
6818 (define-public r-abcanalysis
6820 (name "r-abcanalysis")
6825 (uri (cran-uri "ABCanalysis" version))
6827 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6828 (properties `((upstream-name . "ABCanalysis")))
6829 (build-system r-build-system)
6830 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6831 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6832 (synopsis "Computed ABC Analysis")
6834 "Multivariate data sets often differ in several factors or derived statistical
6835 parameters, which have to be selected for a valid interpretation. Basing this
6836 selection on traditional statistical limits leads occasionally to the perception
6837 of losing information from a data set. This package provides tools to calculate
6838 these limits on the basis of the mathematical properties of the distribution of
6839 the analyzed items.")
6840 (license license:gpl3)))
6842 (define-public r-slam
6849 (uri (cran-uri "slam" version))
6851 (base32 "1ihhbx76miwys35gsbhijriadvrw4f51lc3v45pnn6cvcfd9hr0b"))))
6852 (build-system r-build-system)
6853 (home-page "https://cran.r-project.org/web/packages/slam/")
6854 (synopsis "Sparse lightweight arrays and matrices")
6856 "This package contains data structures and algorithms for sparse arrays and matrices,
6857 based on index arrays and simple triplet representations, respectively.")
6858 (license license:gpl2)))
6860 (define-public r-manipulatewidget
6862 (name "r-manipulatewidget")
6867 (uri (cran-uri "manipulateWidget" version))
6869 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6871 `((upstream-name . "manipulateWidget")))
6872 (build-system r-build-system)
6874 `(("r-base64enc" ,r-base64enc)
6875 ("r-codetools" ,r-codetools)
6876 ("r-htmltools" ,r-htmltools)
6877 ("r-htmlwidgets" ,r-htmlwidgets)
6878 ("r-knitr" ,r-knitr)
6879 ("r-miniui" ,r-miniui)
6880 ("r-shiny" ,r-shiny)
6881 ("r-webshot" ,r-webshot)))
6882 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6883 (synopsis "Add even more interactivity to interactive charts")
6885 "This package lets you create in just a few lines of R code a nice user interface to
6886 modify the data or the graphical parameters of one or multiple interactive
6887 charts. It is useful to quickly explore visually some data or for package
6888 developers to generate user interfaces easy to maintain.")
6889 (license license:gpl2+)))
6898 (uri (cran-uri "A3" version))
6900 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6901 (properties `((upstream-name . "A3")))
6902 (build-system r-build-system)
6904 `(("r-pbapply" ,r-pbapply)
6905 ("r-xtable" ,r-xtable)))
6906 (home-page "https://cran.r-project.org/web/packages/A3/")
6907 (synopsis "Error metrics for predictive models")
6909 "This package supplies tools for tabulating and analyzing the results of predictive
6910 models. The methods employed are applicable to virtually any predictive model
6911 and make comparisons between different methodologies straightforward.")
6912 (license license:gpl2+)))
6914 (define-public r-infotheo
6921 (uri (cran-uri "infotheo" version))
6924 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
6925 (build-system r-build-system)
6926 (home-page "http://homepage.meyerp.com/software")
6927 (synopsis "Information-theoretic measures")
6929 "This package implements various measures of information theory based on
6930 several entropy estimators.")
6931 (license license:gpl3+)))
6933 (define-public r-abcoptim
6940 (uri (cran-uri "ABCoptim" version))
6942 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
6943 (properties `((upstream-name . "ABCoptim")))
6944 (build-system r-build-system)
6945 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
6946 (home-page "https://github.com/gvegayon/ABCoptim/")
6947 (synopsis "Optimization of Artificial Bee Colony algorithm")
6949 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
6950 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
6951 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
6952 algorithms, and uses only common control parameters such as colony size and
6953 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
6954 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
6955 This version is a work-in-progress and is written in R code.")
6956 (license license:expat)))
6958 (define-public r-abcp2
6965 (uri (cran-uri "ABCp2" version))
6967 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
6968 (properties `((upstream-name . "ABCp2")))
6969 (build-system r-build-system)
6970 (propagated-inputs `(("r-mass" ,r-mass)))
6971 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
6972 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
6974 "This package tests the goodness of fit of a distribution of offspring to the Normal,
6975 Poisson, and Gamma distribution and estimates the proportional paternity of the
6976 second male (P2) based on the best fit distribution.")
6977 (license license:gpl2)))
6979 (define-public r-abcrf
6986 (uri (cran-uri "abcrf" version))
6988 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
6989 (build-system r-build-system)
6991 `(("r-doparallel" ,r-doparallel)
6992 ("r-foreach" ,r-foreach)
6994 ("r-matrixstats" ,r-matrixstats)
6995 ("r-ranger" ,r-ranger)
6997 ("r-rcpparmadillo" ,r-rcpparmadillo)
6998 ("r-readr" ,r-readr)
6999 ("r-stringr" ,r-stringr)))
7000 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7001 (synopsis "Approximate bayesian computation via random forests")
7003 "This package performs approximate bayesian computation (ABC) model choice and
7004 parameter inference via random forests. This machine learning tool named random
7005 forests (RF) can conduct selection among the highly complex models covered by
7007 (license license:gpl2+)))
7009 (define-public r-abctools
7016 (uri (cran-uri "abctools" version))
7018 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7019 (build-system r-build-system)
7022 ("r-abind" ,r-abind)
7023 ("r-hmisc" ,r-hmisc)
7024 ("r-plyr" ,r-plyr)))
7025 (home-page "https://github.com/dennisprangle/abctools/")
7026 (synopsis "Tools for ABC analyses")
7028 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7029 including summary statistic selection and assessing coverage. This includes
7030 recent dimension reduction algorithms to tune the choice of summary statistics,
7031 and coverage methods to tune the choice of threshold.")
7032 (license license:gpl2+)))
7034 (define-public r-ggstance
7041 (uri (cran-uri "ggstance" version))
7043 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
7044 (build-system r-build-system)
7046 `(("r-ggplot2" ,r-ggplot2)
7048 ("r-rlang" ,r-rlang)
7049 ("r-withr" ,r-withr)))
7050 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7051 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7053 "This package is a @code{r-ggplot2} extension that provides flipped components:
7055 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7056 @item vertical versions of @code{r-ggplot2} positions.
7058 (license license:gpl3)))
7060 (define-public r-mosaiccore
7062 (name "r-mosaiccore")
7067 (uri (cran-uri "mosaicCore" version))
7069 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7070 (properties `((upstream-name . "mosaicCore")))
7071 (build-system r-build-system)
7073 `(("r-dplyr" ,r-dplyr)
7074 ("r-lazyeval" ,r-lazyeval)
7076 ("r-rlang" ,r-rlang)
7077 ("r-tidyr" ,r-tidyr)))
7078 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7079 (synopsis "Common utilities for mosaic family packages")
7081 "Common utilities used in other Mosaic family packages are collected here.")
7082 (license license:gpl2+)))
7084 (define-public r-ggformula
7086 (name "r-ggformula")
7091 (uri (cran-uri "ggformula" version))
7093 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
7094 (build-system r-build-system)
7096 `(("r-ggplot2" ,r-ggplot2)
7097 ("r-ggstance" ,r-ggstance)
7098 ("r-magrittr" ,r-magrittr)
7099 ("r-mosaiccore" ,r-mosaiccore)
7100 ("r-rlang" ,r-rlang)
7101 ("r-stringr" ,r-stringr)
7102 ("r-tibble" ,r-tibble)
7103 ("r-tidyr" ,r-tidyr)))
7104 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7105 (synopsis "Formula interface for the @code{r-ggplot2}")
7107 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7108 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7109 and extends the excellent simplicity of the lattice-graphics formula interface,
7110 while providing the intuitive capabilities of @code{r-ggplot2}.")
7111 (license license:expat)))
7113 (define-public r-mosaicdata
7115 (name "r-mosaicdata")
7120 (uri (cran-uri "mosaicData" version))
7122 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
7123 (properties `((upstream-name . "mosaicData")))
7124 (build-system r-build-system)
7125 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7126 (synopsis "Data sets for project Mosaic")
7128 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7129 used to teach mathematics, statistics, computation and modeling.")
7130 (license license:gpl2+)))
7132 (define-public r-raster
7139 (uri (cran-uri "raster" version))
7142 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7143 (build-system r-build-system)
7145 `(("r-rcpp" ,r-rcpp)
7147 (home-page "https://www.rspatial.org/")
7148 (synopsis "Geographic data analysis and modeling")
7150 "The package implements basic and high-level functions for reading,
7151 writing, manipulating, analyzing and modeling of gridded spatial data.
7152 Processing of very large files is supported.")
7153 (license license:gpl3+)))
7155 (define-public r-mosaic
7162 (uri (cran-uri "mosaic" version))
7164 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7165 (build-system r-build-system)
7167 `(("r-broom" ,r-broom)
7168 ("r-dplyr" ,r-dplyr)
7169 ("r-ggdendro" ,r-ggdendro)
7170 ("r-ggformula" ,r-ggformula)
7171 ("r-ggplot2" ,r-ggplot2)
7172 ("r-ggrepel" ,r-ggrepel)
7174 ("r-gridextra" ,r-gridextra)
7175 ("r-lattice" ,r-lattice)
7176 ("r-latticeextra" ,r-latticeextra)
7177 ("r-lazyeval" ,r-lazyeval)
7179 ("r-matrix" ,r-matrix)
7180 ("r-mosaiccore" ,r-mosaiccore)
7181 ("r-mosaicdata" ,r-mosaicdata)
7182 ("r-readr" ,r-readr)
7183 ("r-tidyr" ,r-tidyr)))
7184 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7185 (synopsis "Mathematics, statistics, and computation teaching utilities")
7187 "This package contain data sets and utilities from
7188 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7189 statistics, computation and modeling. Project MOSAIC is a community of
7190 educators working to tie together aspects of quantitative work that students
7191 in science, technology, engineering and mathematics will need in their
7192 professional lives, but which are usually taught in isolation, if at all.")
7193 (license license:gpl2+)))
7195 (define-public r-abd
7202 (uri (cran-uri "abd" version))
7204 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7205 (build-system r-build-system)
7207 `(("r-lattice" ,r-lattice)
7208 ("r-mosaic" ,r-mosaic)
7209 ("r-nlme" ,r-nlme)))
7210 (home-page "https://cran.r-project.org/web/packages/abd/")
7211 (synopsis "Analysis of biological data")
7213 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7214 biological data by Michael Whitlock and Dolph Schluter.")
7215 (license license:gpl2)))
7217 (define-public r-svgui
7224 (uri (cran-uri "svGUI" version))
7226 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7227 (properties `((upstream-name . "svGUI")))
7228 (build-system r-build-system)
7229 (home-page "https://github.com/SciViews/svGUI/")
7230 (synopsis "Functions for managing GUI clients in R")
7232 "The SciViews @code{svGUI} package eases the management of Graphical User
7233 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7234 centralizes info about GUI elements currently used, and it dispatches GUI
7235 calls to the particular toolkits in use in function of the context.")
7236 (license license:gpl2)))
7238 (define-public r-svdialogs
7240 (name "r-svdialogs")
7245 (uri (cran-uri "svDialogs" version))
7247 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7248 (properties `((upstream-name . "svDialogs")))
7249 (build-system r-build-system)
7252 ("zenity" ,zenity)))
7254 `(("r-rstudioapi" ,r-rstudioapi)
7255 ("r-svgui" ,r-svgui)))
7256 (home-page "https://github.com/SciViews/svDialogs/")
7257 (synopsis "Portable dialog boxes")
7259 "This package helps to construct standard dialog boxes for your GUI, including
7260 message boxes, input boxes, list, file or directory selection, and others. In
7261 case R cannot display GUI dialog boxes, a simpler command line version of these
7262 interactive elements is also provided as a fallback solution.")
7263 (license license:gpl2)))
7265 (define-public r-abe
7272 (uri (cran-uri "abe" version))
7275 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7276 (build-system r-build-system)
7277 (home-page "https://cran.r-project.org/web/packages/abe/")
7278 (synopsis "Augmented backward elimination")
7280 "This package performs augmented backward elimination and checks the
7281 stability of the obtained model. Augmented backward elimination combines
7282 significance or information based criteria with the change in estimate to
7283 either select the optimal model for prediction purposes or to serve as a tool
7284 to obtain a practically sound, highly interpretable model.")
7285 (license license:gpl2+)))
7287 (define-public r-abf2
7294 (uri (cran-uri "abf2" version))
7296 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7297 (build-system r-build-system)
7298 (home-page "https://cran.r-project.org/web/packages/abf2/")
7299 (synopsis "Load gap-free axon @code{r-abf2} files")
7301 "This package loads electrophysiology data from ABF2 files, as created by
7302 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7303 mode are currently supported.")
7304 (license license:artistic2.0)))
7306 (define-public r-abhgenotyper
7308 (name "r-abhgenotyper")
7313 (uri (cran-uri "ABHgenotypeR" version))
7315 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7316 (properties `((upstream-name . "ABHgenotypeR")))
7317 (build-system r-build-system)
7319 `(("r-ggplot2" ,r-ggplot2)
7320 ("r-reshape2" ,r-reshape2)))
7321 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7322 (synopsis "Visualize and manipulate ABH genotypes")
7324 "The @code{r-abhgenotyper} package provides simple imputation,
7325 error-correction and plotting capacities for genotype data. The package is
7326 supposed to serve as an intermediate but independent analysis tool between the
7327 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7328 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7329 genotypes as \"graphical genotypes\".")
7330 (license license:gpl3)))
7332 (define-public r-furrr
7339 (uri (cran-uri "furrr" version))
7342 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7343 (build-system r-build-system)
7345 `(("r-future" ,r-future)
7346 ("r-globals" ,r-globals)
7347 ("r-purrr" ,r-purrr)
7348 ("r-rlang" ,r-rlang)))
7349 (home-page "https://github.com/DavisVaughan/furrr")
7350 (synopsis "Apply mapping functions in parallel using futures")
7352 "This package provides implementations of the family of @code{map()}
7353 functions from the @code{purrr} package that can be resolved using any
7354 @code{future}-supported backend, e.g. parallel on the local machine or
7355 distributed on a compute cluster.")
7356 (license license:lgpl2.1+)))
7358 (define-public r-abjutils
7365 (uri (cran-uri "abjutils" version))
7367 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7368 (build-system r-build-system)
7370 `(("r-devtools" ,r-devtools)
7371 ("r-dplyr" ,r-dplyr)
7372 ("r-furrr" ,r-furrr)
7373 ("r-future" ,r-future)
7376 ("r-magrittr" ,r-magrittr)
7377 ("r-progress" ,r-progress)
7378 ("r-purrr" ,r-purrr)
7379 ("r-readr" ,r-readr)
7380 ("r-rlang" ,r-rlang)
7381 ("r-rstudioapi" ,r-rstudioapi)
7382 ("r-scales" ,r-scales)
7383 ("r-stringi" ,r-stringi)
7384 ("r-stringr" ,r-stringr)
7385 ("r-tibble" ,r-tibble)
7386 ("r-tidyr" ,r-tidyr)))
7387 (home-page "https://github.com/abjur/abjutils/")
7388 (synopsis "Collection of tools for jurimetrical analysis")
7390 "This package implements general purpose tools, such as functions for
7391 sampling and basic manipulation of Brazilian lawsuits identification number.
7392 It also implements functions for text cleaning, such as accentuation
7394 (license license:expat)))
7396 (define-public r-abnormality
7398 (name "r-abnormality")
7403 (uri (cran-uri "abnormality" version))
7405 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7406 (build-system r-build-system)
7408 `(("r-mass" ,r-mass)
7409 ("r-matrix" ,r-matrix)))
7410 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7411 (synopsis "Measure a subject's abnormality with respect to a reference population")
7413 "This package contains functions to implement the methodology and
7414 considerations laid out by Marks et al. in the article \"Measuring abnormality
7415 in high dimensional spaces: applications in biomechanical gait analysis\".
7416 Using high-dimensional datasets to measure a subject's overall level of
7417 abnormality as compared to a reference population is often needed in outcomes
7419 (license license:expat)))
7421 (define-public r-abodoutlier
7423 (name "r-abodoutlier")
7428 (uri (cran-uri "abodOutlier" version))
7430 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7431 (properties `((upstream-name . "abodOutlier")))
7432 (build-system r-build-system)
7434 `(("r-cluster" ,r-cluster)))
7435 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7436 (synopsis "Angle-based outlier detection")
7438 "This package performs angle-based outlier detection on a given data
7439 frame. It offers three methods to process data:
7441 @item full but slow implementation using all the data that has cubic
7443 @item a fully randomized method;
7444 @item a method using k-nearest neighbours.
7446 These algorithms are well suited for high dimensional data outlier
7448 (license license:expat)))
7450 (define-public r-abps
7457 (uri (cran-uri "ABPS" version))
7459 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7460 (properties `((upstream-name . "ABPS")))
7461 (build-system r-build-system)
7462 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7463 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7464 (synopsis "Abnormal blood profile score to detect blood doping")
7466 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7467 The ABPS is a part of the Athlete biological passport program of the World
7468 anti-doping agency, which combines several blood parameters into a single
7469 score in order to detect blood doping. The package also contains functions to
7470 calculate other scores used in anti-doping programs, such as the ratio of
7471 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7472 (license license:gpl2+)))
7474 (define-public r-parmigene
7476 (name "r-parmigene")
7481 (uri (cran-uri "parmigene" version))
7484 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7485 (build-system r-build-system)
7486 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7487 (synopsis "Mutual information estimation for gene network reconstruction")
7489 "This package provides a parallel estimation of the mutual information
7490 based on entropy estimates from k-nearest neighbors distances and algorithms
7491 for the reconstruction of gene regulatory networks.")
7492 (license license:agpl3+)))
7494 (define-public r-pscl
7501 (uri (cran-uri "pscl" version))
7503 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7504 (build-system r-build-system)
7506 `(("r-mass" ,r-mass)))
7507 (home-page "https://github.com/atahk/pscl/")
7508 (synopsis "Political science computational laboratory")
7510 "The @code{pscl} is an R package providing classes and methods for:
7512 @item Bayesian analysis of roll call data (item-response models);
7513 @item elementary Bayesian statistics;
7514 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7516 @item utility functions.
7518 (license license:gpl2)))
7520 (define-public r-accelmissing
7522 (name "r-accelmissing")
7527 (uri (cran-uri "accelmissing" version))
7529 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7530 (build-system r-build-system)
7532 `(("r-mice" ,r-mice)
7533 ("r-pscl" ,r-pscl)))
7534 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7535 (synopsis "Missing value imputation for accelerometer data")
7537 "This package provides a statistical method to impute the missing values in
7538 accelerometer data. The methodology includes both parametric and
7539 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7540 model. It also provides multiple functions to preprocess the accelerometer data
7541 previous to the missing data imputation. These include detecting the wearing
7542 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7543 (license license:gpl2+)))
7545 (define-public r-mhsmm
7552 (uri (cran-uri "mhsmm" version))
7554 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7555 (build-system r-build-system)
7556 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7557 (home-page "https://github.com/jaredo/mhsmm/")
7558 (synopsis "Inference for hidden Markov and semi-Markov models")
7560 "The @code{r-mhsmm} package implements estimation and prediction methods for
7561 hidden Markov and semi-Markov models for multiple observation sequences. Such
7562 techniques are of interest when observed data is thought to be dependent on some
7563 unobserved (or hidden) state. Also, this package is suitable for equidistant
7564 time series data, with multivariate and/or missing data. Allows user defined
7565 emission distributions.")
7566 (license license:gpl2+)))
7568 (define-public r-nleqslv
7575 (uri (cran-uri "nleqslv" version))
7577 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7578 (build-system r-build-system)
7579 (native-inputs `(("gfortran" ,gfortran)))
7580 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7581 (synopsis "Solve systems of nonlinear equations")
7583 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7584 Broyden or a Newton method with a choice of global strategies such as line
7585 search and trust region. There are options for using a numerical or user
7586 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7587 singular or ill-conditioned Jacobian.")
7588 (license license:gpl2+)))
7590 (define-public r-physicalactivity
7592 (name "r-physicalactivity")
7597 (uri (cran-uri "PhysicalActivity" version))
7599 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7601 `((upstream-name . "PhysicalActivity")))
7602 (build-system r-build-system)
7603 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7604 (synopsis "Procesing accelerometer data for physical activity measurement")
7606 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7607 for classification of monitor wear and nonwear time intervals in accelerometer
7608 data collected to assess physical activity. The package also contains functions
7609 for making plots of accelerometer data and obtaining the summary of various
7610 information including daily monitor wear time and the mean monitor wear time
7611 during valid days. The revised package version 0.2-1 improved the functions
7612 regarding speed, robustness and add better support for time zones and daylight
7613 saving. In addition, several functions were added:
7615 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7616 @item the @code{markPAI} can categorize physical activity intensity level based
7617 on user-defined cut-points of accelerometer counts.
7619 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7620 @code{queryActigraph} functions.")
7621 (license license:gpl3+)))
7623 (define-public r-acc
7630 (uri (cran-uri "acc" version))
7632 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7633 (build-system r-build-system)
7635 `(("r-circlize" ,r-circlize)
7637 ("r-ggplot2" ,r-ggplot2)
7638 ("r-iterators" ,r-iterators)
7639 ("r-mhsmm" ,r-mhsmm)
7640 ("r-nleqslv" ,r-nleqslv)
7641 ("r-physicalactivity" ,r-physicalactivity)
7643 ("r-r-utils" ,r-r-utils)
7645 ("r-rcpparmadillo" ,r-rcpparmadillo)
7646 ("r-rsqlite" ,r-rsqlite)
7648 (home-page "https://cran.r-project.org/web/packages/acc/")
7649 (synopsis "Exploring accelerometer data")
7651 "This package processes accelerometer data from uni-axial and tri-axial devices
7652 and generates data summaries. Also, includes functions to plot, analyze, and
7653 simulate accelerometer data.")
7654 (license license:gpl2+)))
7656 (define-public r-rbenchmark
7658 (name "r-rbenchmark")
7663 (uri (cran-uri "rbenchmark" version))
7665 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7666 (build-system r-build-system)
7667 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7668 (synopsis "Benchmarking routine for R")
7670 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7671 and is intended to facilitate benchmarking of arbitrary R code. The library
7672 consists of just one function, benchmark, which is a simple wrapper around
7673 system.time. Given a specification of the benchmarking process (counts of
7674 replications, evaluation environment) and an arbitrary number of expressions,
7675 benchmark evaluates each of the expressions in the specified environment,
7676 replicating the evaluation as many times as specified, and returning the results
7677 conveniently wrapped into a data frame.")
7678 (license license:gpl2+)))
7680 (define-public r-mitools
7687 (uri (cran-uri "mitools" version))
7690 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7691 (build-system r-build-system)
7692 (propagated-inputs `(("r-dbi" ,r-dbi)))
7693 (home-page "https://cran.r-project.org/web/packages/mitools/")
7694 (synopsis "Tools for multiple imputation of missing data")
7696 "This package provides tools to perform analyses and combine results from
7697 multiple-imputation datasets.")
7698 (license license:gpl2)))
7700 (define-public r-magick
7707 (uri (cran-uri "magick" version))
7710 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7711 (build-system r-build-system)
7713 `(("imagemagick" ,imagemagick)
7716 `(("r-curl" ,r-curl)
7717 ("r-magrittr" ,r-magrittr)
7718 ("r-rcpp" ,r-rcpp)))
7720 `(("pkg-config" ,pkg-config)))
7721 (home-page "https://github.com/ropensci/magick")
7722 (synopsis "Advanced graphics and image-processing in R")
7724 "This package provides bindings to ImageMagick, a comprehensive image
7725 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7726 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7727 operations are vectorized via the Magick++ STL meaning they operate either on
7728 a single frame or a series of frames for working with layers, collages, or
7729 animation. In RStudio, images are automatically previewed when printed to the
7730 console, resulting in an interactive editing environment.")
7731 (license license:expat)))
7733 (define-public r-survey
7740 (uri (cran-uri "survey" version))
7743 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7744 (build-system r-build-system)
7746 `(("r-lattice" ,r-lattice)
7747 ("r-matrix" ,r-matrix)
7748 ("r-minqa" ,r-minqa)
7749 ("r-mitools" ,r-mitools)
7750 ("r-numderiv" ,r-numderiv)
7751 ("r-survival" ,r-survival)))
7752 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7753 (synopsis "Analysis of complex survey samples")
7755 "This package provides tools for the analysis of complex survey samples.
7756 The provided features include: summary statistics, two-sample tests, rank
7757 tests, generalised linear models, cumulative link models, Cox models,
7758 loglinear models, and general maximum pseudolikelihood estimation for
7759 multistage stratified, cluster-sampled, unequally weighted survey samples;
7760 variances by Taylor series linearisation or replicate weights;
7761 post-stratification, calibration, and raking; two-phase subsampling designs;
7762 graphics; PPS sampling without replacement; principal components, and factor
7764 ;; Either version of the GPL.
7765 (license (list license:gpl2 license:gpl3))))
7767 (define-public r-dvmisc
7774 (uri (cran-uri "dvmisc" version))
7776 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7777 (build-system r-build-system)
7779 `(("r-cubature" ,r-cubature)
7780 ("r-data-table" ,r-data-table)
7781 ("r-dplyr" ,r-dplyr)
7782 ("r-ggplot2" ,r-ggplot2)
7784 ("r-mvtnorm" ,r-mvtnorm)
7785 ("r-pracma" ,r-pracma)
7786 ("r-purrr" ,r-purrr)
7787 ("r-rbenchmark" ,r-rbenchmark)
7789 ("r-survey" ,r-survey)))
7790 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7791 (synopsis "Faster computation of common statistics and miscellaneous functions")
7793 "This package implements faster versions of base R functions (e.g. mean, standard
7794 deviation, covariance, weighted mean), mostly written in C++, along with
7795 miscellaneous functions for various purposes (e.g. create the histogram with
7796 fitted probability density function or probability mass function curve, create
7797 the body mass index groups, assess the linearity assumption in logistic
7799 (license license:gpl2)))
7801 (define-public r-accelerometry
7803 (name "r-accelerometry")
7808 (uri (cran-uri "accelerometry" version))
7810 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7811 (build-system r-build-system)
7813 `(("r-dvmisc" ,r-dvmisc)
7814 ("r-rcpp" ,r-rcpp)))
7815 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7816 (synopsis "Functions for processing accelerometer data")
7818 "This package provides a collection of functions that perform operations on
7819 time-series accelerometer data, such as identify the non-wear time, flag minutes
7820 that are part of an activity bout, and find the maximum 10-minute average count
7821 value. The functions are generally very flexible, allowing for a variety of
7822 algorithms to be implemented.")
7823 (license license:gpl3)))
7825 (define-public r-absim
7832 (uri (cran-uri "AbSim" version))
7834 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7835 (properties `((upstream-name . "AbSim")))
7836 (build-system r-build-system)
7839 ("r-powerlaw" ,r-powerlaw)))
7840 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7841 (synopsis "Time resolved simulations of antibody repertoires")
7843 "This package provides simulation methods for the evolution of antibody repertoires.
7844 The heavy and light chain variable region of both human and C57BL/6 mice can
7845 be simulated in a time-dependent fashion. Both single lineages using one set of
7846 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7847 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7848 Upon completion, the main loop of the algorithm begins, with each iteration
7849 representing one simulated time step. Various mutation events are possible at
7850 each time step, contributing to a diverse final repertoire.")
7851 (license license:gpl2)))
7853 (define-public r-quic
7860 (uri (cran-uri "QUIC" version))
7862 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7863 (properties `((upstream-name . "QUIC")))
7864 (build-system r-build-system)
7865 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7866 (synopsis "Regularized sparse inverse covariance matrix estimation")
7868 "This package implements the regularized Gaussian maximum likelihood
7869 estimation of the inverse of a covariance matrix. It uses Newton's method and
7870 coordinate descent to solve the regularized inverse covariance matrix
7871 estimation problem.")
7872 ;; The project home page states that the release is under GPLv3 or later.
7873 ;; The CRAN page only says GPL-3.
7874 (license license:gpl3+)))
7876 (define-public r-abundant
7883 (uri (cran-uri "abundant" version))
7885 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7886 (build-system r-build-system)
7888 `(("r-quic" ,r-quic)))
7889 (home-page "https://cran.r-project.org/web/packages/abundant/")
7890 (synopsis "Abundant regression and high-dimensional principal fitted components")
7892 "This package provides tools to fit and predict with the high-dimensional
7893 principal fitted components model. This model is described by Cook, Forzani,
7894 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7895 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7896 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7897 (license license:gpl2+)))
7899 (define-public r-ac3net
7906 (uri (cran-uri "Ac3net" version))
7908 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7909 (properties `((upstream-name . "Ac3net")))
7910 (build-system r-build-system)
7912 `(("r-data-table" ,r-data-table)))
7913 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
7914 (synopsis "Inferring directional conservative causal core gene networks")
7915 (description "This package infers directional Conservative causal core
7916 (gene) networks (C3NET). This is a version of the algorithm C3NET with
7917 directional network.")
7918 (license license:gpl3+)))
7920 (define-public r-aca
7927 (uri (cran-uri "ACA" version))
7929 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
7930 (properties `((upstream-name . "ACA")))
7931 (build-system r-build-system)
7932 (home-page "https://cran.r-project.org/web/packages/ACA/")
7933 (synopsis "Abrupt change-point or aberration detection in point series")
7935 "This package offers an interactive function for the detection of breakpoints in
7937 ;; Any version of the GPL
7938 (license (list license:gpl2+ license:gpl3+))))
7940 (define-public r-acceptancesampling
7942 (name "r-acceptancesampling")
7947 (uri (cran-uri "AcceptanceSampling" version))
7949 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
7951 `((upstream-name . "AcceptanceSampling")))
7952 (build-system r-build-system)
7953 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
7954 (synopsis "Creation and evaluation of acceptance sampling plans")
7956 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
7957 acceptance sampling plans. Acceptance sampling is a methodology commonly used
7958 in quality control and improvement. International standards of acceptance
7959 sampling provide sampling plans for specific circumstances. The aim of this
7960 package is to provide an easy-to-use interface to visualize single, double or
7961 multiple sampling plans. In addition, methods have been provided to enable the
7962 user to assess sampling plans against pre-specified levels of performance, as
7963 measured by the probability of acceptance for a given level of quality in the
7965 (license license:gpl3+)))
7967 (define-public r-acclma
7974 (uri (cran-uri "ACCLMA" version))
7976 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
7977 (properties `((upstream-name . "ACCLMA")))
7978 (build-system r-build-system)
7979 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
7980 (synopsis "ACC & LMA graph plotting")
7982 "This package contains a function that imports data from a @acronym{CSV,
7983 Comma-Separated Values} file, or uses manually entered data from the format (x,
7984 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
7985 Curve} vs @acronym{LOI, Line of Independence} graph and
7986 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
7987 function is @code{plotLMA} (source file, header) that takes a data set and plots the
7988 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
7989 string) was passed, a manual data entry window is opened. The header parameter
7990 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
7991 a header row or not. The dataset should contain only one independent variable
7992 (x) and one dependent variable (y) and can contain a weight for each
7994 (license license:gpl2)))
7996 (define-public r-aspi
8003 (uri (cran-uri "aspi" version))
8005 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8006 (build-system r-build-system)
8008 "https://cran.r-project.org/web/packages/aspi/")
8010 "Analysis of symmetry of parasitic infections")
8012 "This package provides tools for the analysis and visualization of bilateral
8013 asymmetry in parasitic infections.")
8014 (license license:gpl3+)))
8016 (define-public r-sandwich
8023 (uri (cran-uri "sandwich" version))
8026 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8027 (build-system r-build-system)
8029 `(("r-zoo" ,r-zoo)))
8030 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8031 (synopsis "Robust Covariance Matrix Estimators")
8033 "This package provides model-robust standard error estimators for
8034 cross-sectional, time series, clustered, panel, and longitudinal data.")
8035 ;; Either version of the license.
8036 (license (list license:gpl2 license:gpl3))))
8038 (define-public r-th-data
8045 (uri (cran-uri "TH.data" version))
8048 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8049 (properties `((upstream-name . "TH.data")))
8050 (build-system r-build-system)
8052 `(("r-mass" ,r-mass)
8053 ("r-survival" ,r-survival)))
8054 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8055 (synopsis "Shared data sets")
8057 "This package contains supporting data sets that are used in other
8058 packages maintained by Torsten Hothorn.")
8059 (license license:gpl3)))
8061 (define-public r-multcomp
8068 (uri (cran-uri "multcomp" version))
8071 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
8072 (build-system r-build-system)
8074 `(("r-codetools" ,r-codetools)
8075 ("r-mvtnorm" ,r-mvtnorm)
8076 ("r-sandwich" ,r-sandwich)
8077 ("r-survival" ,r-survival)
8078 ("r-th-data" ,r-th-data)))
8079 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8080 (synopsis "Simultaneous inference in general parametric models")
8082 "Simultaneous tests and confidence intervals for general linear
8083 hypotheses in parametric models, including linear, generalized linear, linear
8084 mixed effects, and survival models. The package includes demos reproducing
8085 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8086 Hothorn, Westfall, 2010, CRC Press).")
8087 (license license:gpl2)))
8089 (define-public r-emmeans
8092 (version "1.4.3.01")
8096 (uri (cran-uri "emmeans" version))
8099 "16v5j31516nbqnj2zhgqvyp5yxd4zcs5zi0aspa5plr2qikvrkmg"))))
8100 (build-system r-build-system)
8102 `(("r-estimability" ,r-estimability)
8103 ("r-mvtnorm" ,r-mvtnorm)
8104 ("r-numderiv" ,r-numderiv)
8106 ("r-xtable" ,r-xtable)))
8107 (home-page "https://github.com/rvlenth/emmeans")
8108 (synopsis "Estimated marginal means, aka least-squares means")
8110 "This package provides tools to obtain @dfn{estimated marginal
8111 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8112 be used to compute contrasts or linear functions of EMMs, trends, and
8113 comparisons of slopes.")
8114 ;; Either version of the license.
8115 (license (list license:gpl2 license:gpl3))))
8117 (define-public r-pwr
8124 (uri (cran-uri "pwr" version))
8127 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8128 (build-system r-build-system)
8130 `(("r-knitr" ,r-knitr)))
8131 (home-page "https://github.com/heliosdrm/pwr")
8132 (synopsis "Basic functions for power analysis")
8134 "This package provides power analysis functions along the lines of
8136 (license license:gpl3+)))
8138 (define-public r-libcoin
8145 (uri (cran-uri "libcoin" version))
8148 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8149 (build-system r-build-system)
8150 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8151 (home-page "https://cran.r-project.org/web/packages/libcoin")
8152 (synopsis "Linear test statistics for permutation inference")
8154 "This package provides basic infrastructure for linear test statistics
8155 and permutation inference in the framework of Strasser and Weber (1999).")
8156 (license license:gpl2)))
8158 (define-public r-coin
8165 (uri (cran-uri "coin" version))
8168 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8169 (build-system r-build-system)
8171 `(("r-libcoin" ,r-libcoin)
8172 ("r-matrixstats" ,r-matrixstats)
8173 ("r-modeltools" ,r-modeltools)
8174 ("r-multcomp" ,r-multcomp)
8175 ("r-mvtnorm" ,r-mvtnorm)
8176 ("r-survival" ,r-survival)))
8177 (home-page "http://coin.r-forge.r-project.org")
8178 (synopsis "Conditional inference procedures in a permutation test framework")
8180 "This package provides conditional inference procedures for the general
8181 independence problem including two-sample, K-sample (non-parametric ANOVA),
8182 correlation, censored, ordered and multivariate problems.")
8183 (license license:gpl2)))
8185 (define-public r-bayesplot
8187 (name "r-bayesplot")
8192 (uri (cran-uri "bayesplot" version))
8195 "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
8196 (build-system r-build-system)
8198 `(("pandoc" ,ghc-pandoc)
8199 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8201 `(("r-dplyr" ,r-dplyr)
8202 ("r-ggplot2" ,r-ggplot2)
8203 ("r-ggridges" ,r-ggridges)
8205 ("r-reshape2" ,r-reshape2)
8206 ("r-rlang" ,r-rlang)
8207 ("r-tibble" ,r-tibble)
8208 ("r-tidyselect" ,r-tidyselect)))
8209 (home-page "http://mc-stan.org/bayesplot")
8210 (synopsis "Plotting for Bayesian models")
8212 "This package provides plotting functions for posterior analysis, model
8213 checking, and MCMC diagnostics. The package is designed not only to provide
8214 convenient functionality for users, but also a common set of functions that
8215 can be easily used by developers working on a variety of R packages for
8216 Bayesian modeling.")
8217 (license license:gpl3+)))
8219 (define-public r-tmb
8226 (uri (cran-uri "TMB" version))
8229 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8230 (properties `((upstream-name . "TMB")))
8231 (build-system r-build-system)
8233 `(("r-matrix" ,r-matrix)
8234 ("r-rcppeigen" ,r-rcppeigen)))
8235 (home-page "http://tmb-project.org")
8236 (synopsis "Template model builder: a general random effect tool")
8238 "With this tool, a user should be able to quickly implement complex
8239 random effect models through simple C++ templates. The package combines
8240 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8241 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8242 from R) to obtain an efficient implementation of the applied Laplace
8243 approximation with exact derivatives. Key features are: Automatic sparseness
8244 detection, parallelism through BLAS and parallel user templates.")
8245 (license license:gpl2)))
8247 (define-public r-sjstats
8254 (uri (cran-uri "sjstats" version))
8256 (base32 "029rl05p88bp01favz300m980r1khcx2a2kn88yqbnbgkjjgqqc6"))))
8257 (build-system r-build-system)
8259 `(("r-bayestestr" ,r-bayestestr)
8260 ("r-broom" ,r-broom)
8261 ("r-dplyr" ,r-dplyr)
8262 ("r-emmeans" ,r-emmeans)
8263 ("r-insight" ,r-insight)
8265 ("r-magrittr" ,r-magrittr)
8267 ("r-modelr" ,r-modelr)
8268 ("r-parameters" ,r-parameters)
8269 ("r-performance" ,r-performance)
8270 ("r-purrr" ,r-purrr)
8271 ("r-rlang" ,r-rlang)
8272 ("r-sjlabelled" ,r-sjlabelled)
8273 ("r-sjmisc" ,r-sjmisc)
8274 ("r-tidyr" ,r-tidyr)))
8275 (home-page "https://github.com/strengejacke/sjstats")
8276 (synopsis "Functions for common statistical computations")
8278 "This package provides a collection of convenient functions for common
8279 statistical computations, which are not directly provided by R's @code{base}
8280 or @code{stats} packages. This package aims at providing, first, shortcuts
8281 for statistical measures, which otherwise could only be calculated with
8282 additional effort. Second, these shortcut functions are generic, and can be
8283 applied not only to vectors, but also to other objects as well. The focus of
8284 most functions lies on summary statistics or fit measures for regression
8285 models, including generalized linear models, mixed effects models and Bayesian
8287 (license license:gpl3)))
8289 (define-public r-glmmtmb
8296 (uri (cran-uri "glmmTMB" version))
8299 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8300 (properties `((upstream-name . "glmmTMB")))
8301 (build-system r-build-system)
8303 `(("r-lme4" ,r-lme4)
8304 ("r-matrix" ,r-matrix)
8306 ("r-rcppeigen" ,r-rcppeigen)
8309 `(("r-knitr" ,r-knitr))) ; for vignettes
8310 (home-page "https://github.com/glmmTMB")
8311 (synopsis "Generalized linear mixed models")
8313 "Fit linear and generalized linear mixed models with various extensions,
8314 including zero-inflation. The models are fitted using maximum likelihood
8315 estimation via the Template Model Builder. Random effects are assumed to be
8316 Gaussian on the scale of the linear predictor and are integrated out using the
8317 Laplace approximation. Gradients are calculated using automatic
8319 (license license:agpl3+)))
8321 (define-public r-bayestestr
8323 (name "r-bayestestr")
8328 (uri (cran-uri "bayestestR" version))
8331 "1d3f50rzjzgzclwd6j887dssyhv7hdq7pik9nnlr3w775v3f69zc"))))
8332 (properties `((upstream-name . "bayestestR")))
8333 (build-system r-build-system)
8335 `(("r-insight" ,r-insight)))
8336 (home-page "https://github.com/easystats/bayestestR")
8337 (synopsis "Describe Bayesian models and posterior distributions")
8339 "This package provides utilities to understand and describe posterior
8340 distributions and Bayesian models. It includes point-estimates such as
8341 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8342 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8343 ROPE percentage and pd).")
8344 (license license:gpl3)))
8346 (define-public r-performance
8348 (name "r-performance")
8353 (uri (cran-uri "performance" version))
8356 "0lxpmp9smn5r3xvfik36nr608wcpmmximjh0v2sckyvjf7hnb4s0"))))
8357 (build-system r-build-system)
8359 `(("r-bayestestr" ,r-bayestestr)
8360 ("r-insight" ,r-insight)))
8361 (home-page "https://easystats.github.io/performance/")
8362 (synopsis "Assessment of regression models performance")
8364 "This package provides utilities for computing measures to assess model
8365 quality, which are not directly provided by R's @code{base} or @code{stats}
8366 packages. These include e.g. measures like r-squared, intraclass correlation
8367 coefficient, root mean squared error or functions to check models for
8368 overdispersion, singularity or zero-inflation and more. Functions apply to a
8369 large variety of regression models, including generalized linear models, mixed
8370 effects models and Bayesian models.")
8371 (license license:gpl3)))
8373 (define-public r-ggeffects
8375 (name "r-ggeffects")
8380 (uri (cran-uri "ggeffects" version))
8383 "0ryfbaav0k874kbwmhbiv7fan93dmkpaimm1iw5kryjhhs3917lb"))))
8384 (build-system r-build-system)
8386 `(("r-dplyr" ,r-dplyr)
8387 ("r-insight" ,r-insight)
8388 ("r-magrittr" ,r-magrittr)
8390 ("r-purrr" ,r-purrr)
8391 ("r-rlang" ,r-rlang)
8392 ("r-sjlabelled" ,r-sjlabelled)
8393 ("r-sjmisc" ,r-sjmisc)))
8394 (home-page "https://github.com/strengejacke/ggeffects")
8395 (synopsis "Create tidy data frames of marginal effects for ggplot")
8397 "This package provides tools to compute marginal effects from statistical
8398 models and return the result as tidy data frames. These data frames are ready
8399 to use with the @code{ggplot2} package. Marginal effects can be calculated
8400 for many different models. Interaction terms, splines and polynomial terms
8401 are also supported. The two main functions are @code{ggpredict()} and
8402 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8403 results using @code{ggplot2}.")
8404 (license license:gpl3)))
8406 (define-public r-effectsize
8408 (name "r-effectsize")
8413 (uri (cran-uri "effectsize" version))
8416 "07vgmxdl75798hgdh90zysafjh97rmmj2wjjyr6xff4fbhi8rlkb"))))
8417 (properties `((upstream-name . "effectsize")))
8418 (build-system r-build-system)
8420 `(("r-bayestestr" ,r-bayestestr)
8421 ("r-insight" ,r-insight)
8422 ("r-parameters" ,r-parameters)))
8423 (home-page "https://github.com/easystats/effectsize")
8424 (synopsis "Indices of effect size and standardized parameters")
8426 "This package provides utilities to work with indices of effect size and
8427 standardized parameters for a wide variety of models, allowing computation and
8428 conversion of indices such as Cohen's d, r, odds, etc.")
8429 (license license:gpl3)))
8431 (define-public r-sjplot
8438 (uri (cran-uri "sjPlot" version))
8440 (base32 "0ahz6v6bhvq1537inwakmrafs44hs2m9w0ra8q17fz626nn9rb9b"))))
8441 (properties `((upstream-name . "sjPlot")))
8442 (build-system r-build-system)
8444 `(("r-bayestestr" ,r-bayestestr)
8445 ("r-dplyr" ,r-dplyr)
8446 ("r-effectsize" ,r-effectsize)
8447 ("r-forcats" ,r-forcats)
8448 ("r-ggeffects" ,r-ggeffects)
8449 ("r-ggplot2" ,r-ggplot2)
8450 ("r-ggrepel" ,r-ggrepel)
8451 ("r-glmmtmb" ,r-glmmtmb)
8452 ("r-insight" ,r-insight)
8453 ("r-knitr" ,r-knitr)
8455 ("r-magrittr" ,r-magrittr)
8457 ("r-modelr" ,r-modelr)
8458 ("r-parameters" ,r-parameters)
8459 ("r-performance" ,r-performance)
8460 ("r-psych" ,r-psych)
8461 ("r-purrr" ,r-purrr)
8462 ("r-rlang" ,r-rlang)
8463 ("r-scales" ,r-scales)
8464 ("r-sjlabelled" ,r-sjlabelled)
8465 ("r-sjmisc" ,r-sjmisc)
8466 ("r-sjstats" ,r-sjstats)
8467 ("r-tidyr" ,r-tidyr)))
8468 (home-page "https://strengejacke.github.io/sjPlot/")
8469 (synopsis "Data visualization for statistics in social science")
8471 "This package represents a collection of plotting and table output
8472 functions for data visualization. Results of various statistical
8473 analyses (that are commonly used in social sciences) can be visualized using
8474 this package, including simple and cross tabulated frequencies, histograms,
8475 box plots, (generalized) linear models, mixed effects models, principal
8476 component analysis and correlation matrices, cluster analyses, scatter plots,
8477 stacked scales, effects plots of regression models (including interaction
8478 terms) and much more. This package supports labelled data.")
8479 (license license:gpl3)))
8481 (define-public r-ini
8488 (uri (cran-uri "ini" version))
8491 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8492 (build-system r-build-system)
8493 (home-page "https://github.com/dvdscripter/ini")
8494 (synopsis "Read and write configuration files")
8496 "This package provides tools to parse simple @code{.ini} configuration
8497 files to an structured list. Users can manipulate this resulting list with
8498 @code{lapply()} functions. This same structured list can be used to write
8499 back to file after modifications.")
8500 (license license:gpl3)))
8509 (uri (cran-uri "gh" version))
8512 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8513 (build-system r-build-system)
8515 `(("r-httr" ,r-httr)
8517 ("r-jsonlite" ,r-jsonlite)))
8518 (home-page "https://github.com/r-lib/gh#readme")
8519 (synopsis "Access the GitHub API via R")
8521 "This package provides a minimal R client to access the GitHub API.")
8522 (license license:expat)))
8531 (uri (cran-uri "fs" version))
8534 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8535 (build-system r-build-system)
8537 `(("r-rcpp" ,r-rcpp)))
8539 `(("pkg-config" ,pkg-config)))
8540 (home-page "http://fs.r-lib.org")
8541 (synopsis "Cross-platform file system operations based on libuv")
8543 "This package provides a cross-platform interface to file system
8544 operations, built on top of the libuv C library.")
8545 (license license:gpl3)))
8547 (define-public r-clisymbols
8549 (name "r-clisymbols")
8554 (uri (cran-uri "clisymbols" version))
8557 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8558 (build-system r-build-system)
8559 (home-page "https://github.com/gaborcsardi/clisymbols")
8560 (synopsis "Unicode symbols at the R prompt")
8562 "This package provides a small subset of Unicode symbols, that are useful
8563 when building command line applications. They fall back to alternatives on
8564 terminals that do not support Unicode.")
8565 (license license:expat)))
8567 (define-public r-usethis
8574 (uri (cran-uri "usethis" version))
8577 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8578 (build-system r-build-system)
8580 `(("r-clipr" ,r-clipr)
8581 ("r-clisymbols" ,r-clisymbols)
8582 ("r-crayon" ,r-crayon)
8587 ("r-git2r" ,r-git2r)
8589 ("r-purrr" ,r-purrr)
8590 ("r-rlang" ,r-rlang)
8591 ("r-rprojroot" ,r-rprojroot)
8592 ("r-rstudioapi" ,r-rstudioapi)
8593 ("r-whisker" ,r-whisker)
8594 ("r-withr" ,r-withr)
8595 ("r-yaml" ,r-yaml)))
8596 (home-page "https://github.com/r-lib/usethis")
8597 (synopsis "Automate R package and project setup")
8599 "This package helps you to automate R package and project setup tasks
8600 that are otherwise performed manually. This includes setting up unit testing,
8601 test coverage, continuous integration, Git, GitHub integration, licenses,
8602 Rcpp, RStudio projects, and more.")
8603 (license license:gpl3)))
8605 (define-public r-sessioninfo
8607 (name "r-sessioninfo")
8612 (uri (cran-uri "sessioninfo" version))
8615 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8616 (build-system r-build-system)
8619 ("r-withr" ,r-withr)))
8620 (home-page "https://github.com/r-lib/sessioninfo#readme")
8621 (synopsis "R session information")
8623 "This package provides tools to query and print information about the
8624 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8625 more information about packages, and where they were installed from.")
8626 (license license:gpl2)))
8628 (define-public r-remotes
8635 (uri (cran-uri "remotes" version))
8638 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8639 (build-system r-build-system)
8640 (home-page "https://github.com/r-lib/remotes#readme")
8641 (synopsis "R package installation from remote repositories")
8643 "Download and install R packages stored in GitHub, BitBucket, or plain
8644 subversion or git repositories. This package is a lightweight replacement of
8645 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8646 the code was copied over from @code{devtools}.")
8647 (license license:gpl2+)))
8649 (define-public r-xopen
8656 (uri (cran-uri "xopen" version))
8659 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8660 (build-system r-build-system)
8662 `(("r-processx" ,r-processx)))
8663 (home-page "https://github.com/r-lib/xopen#readme")
8664 (synopsis "Open system files, URLs, anything")
8666 "This package provides a cross-platform solution to open files,
8667 directories or URLs with their associated programs.")
8668 (license license:expat)))
8670 (define-public r-rcmdcheck
8672 (name "r-rcmdcheck")
8677 (uri (cran-uri "rcmdcheck" version))
8680 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8681 (build-system r-build-system)
8683 `(("r-callr" ,r-callr)
8685 ("r-crayon" ,r-crayon)
8687 ("r-digest" ,r-digest)
8688 ("r-pkgbuild" ,r-pkgbuild)
8689 ("r-prettyunits" ,r-prettyunits)
8691 ("r-rprojroot" ,r-rprojroot)
8692 ("r-sessioninfo" ,r-sessioninfo)
8693 ("r-withr" ,r-withr)
8694 ("r-xopen" ,r-xopen)))
8695 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8696 (synopsis "Run R CMD check from R and capture results")
8698 "Run @code{R CMD check} from R programmatically, and capture the results
8699 of the individual checks.")
8700 (license license:expat)))
8702 (define-public r-rapportools
8704 (name "r-rapportools")
8709 (uri (cran-uri "rapportools" version))
8712 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8713 (build-system r-build-system)
8715 `(("r-pander" ,r-pander)
8717 ("r-reshape" ,r-reshape)))
8718 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8719 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8721 "This package provides helper functions that act as wrappers to more
8722 advanced statistical methods with the advantage of having sane defaults for
8724 (license license:agpl3+)))
8726 (define-public r-pander
8733 (uri (cran-uri "pander" version))
8736 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8737 (build-system r-build-system)
8739 `(("r-digest" ,r-digest)
8740 ("r-rcpp" ,r-rcpp)))
8741 (home-page "https://rapporter.github.io/pander")
8742 (synopsis "Render R objects into Pandoc's markdown")
8744 "The main aim of the pander R package is to provide a minimal and easy
8745 tool for rendering R objects into Pandoc's markdown. The package is also
8746 capable of exporting/converting complex Pandoc documents (reports) in various
8748 ;; This package is licensed under either the AGPLv3+ or the very rarely
8750 (license license:agpl3+)))
8752 (define-public r-summarytools
8754 (name "r-summarytools")
8759 (uri (cran-uri "summarytools" version))
8762 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8763 (build-system r-build-system)
8765 `(("r-checkmate" ,r-checkmate)
8766 ("r-dplyr" ,r-dplyr)
8767 ("r-htmltools" ,r-htmltools)
8768 ("r-lubridate" ,r-lubridate)
8769 ("r-magick" ,r-magick)
8770 ("r-matrixstats" ,r-matrixstats)
8771 ("r-pander" ,r-pander)
8773 ("r-rapportools" ,r-rapportools)
8774 ("r-rcurl" ,r-rcurl)
8775 ("r-tibble" ,r-tibble)
8776 ("r-tidyr" ,r-tidyr)))
8777 (home-page "https://github.com/dcomtois/summarytools")
8778 (synopsis "Tools to quickly and neatly summarize data")
8780 "This package provides tools for data frame summaries, cross-tabulations,
8781 weight-enabled frequency tables and common univariate statistics in concise
8782 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8783 good point-of-entry for exploring data, both for experienced and new R
8785 (license license:gpl2)))
8787 (define-public r-lsei
8794 (uri (cran-uri "lsei" version))
8797 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8798 (build-system r-build-system)
8800 `(("gfortran" ,gfortran)))
8801 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8802 (synopsis "Solve regression problems under equality/inequality constraints")
8804 "It contains functions that solve least squares linear regression
8805 problems under linear equality/inequality constraints. Functions for solving
8806 quadratic programming problems are also available, which transform such
8807 problems into least squares ones first.")
8808 (license license:gpl2+)))
8810 (define-public r-npsurv
8817 (uri (cran-uri "npsurv" version))
8820 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8821 (build-system r-build-system)
8823 `(("r-lsei" ,r-lsei)))
8824 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8825 (synopsis "Nonparametric survival analysis")
8827 "This package contains functions for non-parametric survival analysis of
8828 exact and interval-censored observations.")
8829 (license license:gpl2+)))
8831 (define-public r-clusteval
8833 (name "r-clusteval")
8838 (uri (cran-uri "clusteval" version))
8841 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8842 (build-system r-build-system)
8844 `(("r-mvtnorm" ,r-mvtnorm)
8845 ("r-rcpp" ,r-rcpp)))
8846 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8847 (synopsis "Evaluation of clustering algorithms")
8849 "This R package provides a suite of tools to evaluate clustering
8850 algorithms, clusterings, and individual clusters.")
8851 (license license:expat)))
8853 (define-public r-tweedie
8860 (uri (cran-uri "tweedie" version))
8863 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8864 (build-system r-build-system)
8865 (native-inputs `(("gfortran" ,gfortran)))
8866 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8867 (synopsis "Evaluation of Tweedie exponential family models")
8869 "Maximum likelihood computations for Tweedie families, including the
8870 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8871 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8872 and related methods.")
8873 (license license:gpl2+)))
8875 (define-public r-rcppgsl
8882 (uri (cran-uri "RcppGSL" version))
8884 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
8885 (properties `((upstream-name . "RcppGSL")))
8886 (build-system r-build-system)
8888 `(("r-rcpp" ,r-rcpp)
8891 `(("r-knitr" ,r-knitr))) ; for vignettes
8892 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8893 (synopsis "Rcpp integration for GSL vectors and matrices")
8895 "The GNU Scientific Library (or GSL) is a collection of numerical
8896 routines for scientific computing. It is particularly useful for C and C++
8897 programs as it provides a standard C interface to a wide range of mathematical
8898 routines. There are over 1000 functions in total with an extensive test
8899 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8900 structures and R using concepts from Rcpp which is itself a package that eases
8901 the interfaces between R and C++.")
8902 (license license:gpl2+)))
8904 (define-public r-mvabund
8911 (uri (cran-uri "mvabund" version))
8914 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
8915 (build-system r-build-system)
8917 `(("r-mass" ,r-mass)
8919 ("r-rcppgsl" ,r-rcppgsl)
8920 ("r-statmod" ,r-statmod)
8921 ("r-tweedie" ,r-tweedie)))
8922 (home-page "https://cran.r-project.org/web/packages/mvabund/")
8923 (synopsis "Statistical methods for analysing multivariate abundance data")
8925 "This package provides a set of tools for displaying, modeling and
8926 analysing multivariate abundance data in community ecology.")
8927 (license license:lgpl2.1+)))
8929 (define-public r-afex
8936 (uri (cran-uri "afex" version))
8939 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
8940 (build-system r-build-system)
8944 ("r-lmertest" ,r-lmertest)
8945 ("r-pbkrtest" ,r-pbkrtest)
8946 ("r-reshape2" ,r-reshape2)))
8947 (home-page "https://afex.singmann.science/")
8948 (synopsis "Analysis of factorial experiments")
8950 "This package provides convenience functions for analyzing factorial
8951 experiments using ANOVA or mixed models.")
8952 (license license:gpl2+)))
8954 (define-public r-lmertest
8961 (uri (cran-uri "lmerTest" version))
8964 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
8965 (properties `((upstream-name . "lmerTest")))
8966 (build-system r-build-system)
8968 `(("r-ggplot2" ,r-ggplot2)
8971 ("r-numderiv" ,r-numderiv)))
8972 (home-page "https://github.com/runehaubo/lmerTestR")
8973 (synopsis "Tests in linear mixed effects models")
8975 "This package provides p-values in type I, II or III anova and summary
8976 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
8977 method. A Kenward-Roger method is also available via the @code{pbkrtest}
8978 package. Model selection methods include step, drop1 and anova-like tables
8979 for random effects (ranova). Methods for Least-Square means (LS-means) and
8980 tests of linear contrasts of fixed effects are also available.")
8981 (license license:gpl2+)))
8983 (define-public r-r2glmm
8990 (uri (cran-uri "r2glmm" version))
8993 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
8994 (build-system r-build-system)
8996 `(("r-afex" ,r-afex)
8997 ("r-data-table" ,r-data-table)
8998 ("r-dplyr" ,r-dplyr)
8999 ("r-ggplot2" ,r-ggplot2)
9000 ("r-gridextra" ,r-gridextra)
9001 ("r-lmertest" ,r-lmertest)
9003 ("r-matrix" ,r-matrix)
9005 ("r-pbkrtest" ,r-pbkrtest)))
9006 (home-page "https://github.com/bcjaeger/r2glmm")
9007 (synopsis "Compute R squared for mixed (multilevel) models")
9009 "This package computes model and semi partial R squared with confidence
9010 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9011 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9012 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9014 (license license:gpl2)))
9016 (define-public r-weights
9023 (uri (cran-uri "weights" version))
9026 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
9027 (build-system r-build-system)
9029 `(("r-gdata" ,r-gdata)
9030 ("r-hmisc" ,r-hmisc)
9031 ("r-mice" ,r-mice)))
9033 "https://cran.r-project.org/web/packages/weights/")
9034 (synopsis "Weighting and weighted statistics")
9035 (description "This package Provides a variety of functions for producing
9036 simple weighted statistics, such as weighted Pearson's correlations, partial
9037 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9038 includes some software for quickly recoding survey data and plotting point
9039 estimates from interaction terms in regressions (and multiply imputed
9040 regressions). NOTE: Weighted partial correlation calculations pulled to
9042 (license license:gpl2+)))
9044 (define-public r-rcppannoy
9046 (name "r-rcppannoy")
9051 (uri (cran-uri "RcppAnnoy" version))
9054 "1wiigx5g5788j6lyc3f6bs1rsvc4alyc3052g35hxl1giinxmhn4"))))
9055 (properties `((upstream-name . "RcppAnnoy")))
9056 (build-system r-build-system)
9058 `(("r-rcpp" ,r-rcpp)))
9060 `(("r-knitr" ,r-knitr))) ; for vignettes
9061 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9062 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9064 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9065 for efficient memory usage as well an ability to load from and save to disk.
9066 This package provides an R interface.")
9067 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9069 (license (list license:gpl2+ license:asl2.0))))
9071 (define-public r-rcpphnsw
9078 (uri (cran-uri "RcppHNSW" version))
9081 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9082 (properties `((upstream-name . "RcppHNSW")))
9083 (build-system r-build-system)
9084 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9085 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9086 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9088 "Hnswlib is a C++ library for approximate nearest neighbors. This
9089 package provides a minimal R interface by relying on the Rcpp package.")
9090 ;; hnswlib is released under Version 2.0 of the Apache License.
9091 (license (list license:gpl3 license:asl2.0))))
9093 (define-public r-rcppparallel
9095 (name "r-rcppparallel")
9100 (uri (cran-uri "RcppParallel" version))
9103 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
9104 (properties `((upstream-name . "RcppParallel")))
9105 (build-system r-build-system)
9106 (home-page "http://rcppcore.github.io/RcppParallel")
9107 (synopsis "Parallel programming tools for Rcpp")
9109 "This package provides high level functions for parallel programming with
9110 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9111 the work of a standard serial @code{for} loop into a parallel one and the
9112 @code{parallelReduce()} function can be used for accumulating aggregates or
9114 (license license:gpl2)))
9116 (define-public r-ncdf4
9123 (uri (cran-uri "ncdf4" version))
9126 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9127 (build-system r-build-system)
9129 `(("netcdf" ,netcdf)
9131 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9132 (synopsis "R interface to Unidata netCDF format data files")
9134 "This package provides a high-level R interface to data files written
9135 using Unidata's netCDF library (version 4 or earlier), which are binary data
9136 files that are portable across platforms and include metadata information in
9137 addition to the data sets. Using this package, netCDF files can be opened and
9138 data sets read in easily. It is also easy to create new netCDF dimensions,
9139 variables, and files, in either version 3 or 4 format, and manipulate existing
9141 (license license:gpl3+)))
9143 (define-public r-biocmanager
9145 (name "r-biocmanager")
9150 (uri (cran-uri "BiocManager" version))
9152 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9153 (properties `((upstream-name . "BiocManager")))
9154 (build-system r-build-system)
9155 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9156 (synopsis "Access the Bioconductor project package repository")
9158 "This package provides a convenient tool to install and update
9159 Bioconductor packages.")
9160 (license license:artistic2.0)))
9162 (define-public r-rgl
9165 (version "0.100.30")
9169 (uri (cran-uri "rgl" version))
9172 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9173 (build-system r-build-system)
9175 `(("pkg-config" ,pkg-config)))
9177 `(("freetype" ,freetype)
9181 ("ghc-pandoc" ,ghc-pandoc)
9184 `(("r-crosstalk" ,r-crosstalk)
9185 ("r-htmltools" ,r-htmltools)
9186 ("r-htmlwidgets" ,r-htmlwidgets)
9187 ("r-jsonlite" ,r-jsonlite)
9188 ("r-knitr" ,r-knitr)
9189 ("r-magrittr" ,r-magrittr)
9190 ("r-manipulatewidget" ,r-manipulatewidget)
9191 ("r-shiny" ,r-shiny)))
9192 (home-page "https://r-forge.r-project.org/projects/rgl/")
9193 (synopsis "3D visualization using OpenGL")
9195 "This package provides medium to high level functions for 3D interactive graphics,
9196 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9197 as functions for constructing representations of geometric
9198 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9199 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9200 image formats, including PNG, Postscript, SVG, PGF.")
9201 ;; Any version of the GPL.
9202 (license (list license:gpl2+ license:gpl3+))))
9204 (define-public r-multicool
9206 (name "r-multicool")
9211 (uri (cran-uri "multicool" version))
9214 "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
9215 (build-system r-build-system)
9216 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9217 (home-page "https://cran.r-project.org/web/packages/multicool/")
9218 (synopsis "Permutations of multisets in cool-lex order")
9220 "This package provides a set of tools to permute multisets without loops
9221 or hash tables and to generate integer partitions. Cool-lex order is similar
9222 to colexicographical order.")
9223 (license license:gpl2)))
9225 (define-public r-misc3d
9232 (uri (cran-uri "misc3d" version))
9235 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9236 (build-system r-build-system)
9237 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9238 (synopsis "Miscellaneous 3D Plots")
9240 "This package provides a collection of miscellaneous 3d plots, including
9242 ;; Any version of the GPL.
9243 (license (list license:gpl2+ license:gpl3+))))
9252 (uri (cran-uri "ks" version))
9254 (base32 "0hcccjfqnzdxkmnfzq8c5a7yhc138azwyl7rp29d1vl1jawwrwfq"))))
9255 (build-system r-build-system)
9258 ("r-kernlab" ,r-kernlab)
9259 ("r-kernsmooth" ,r-kernsmooth)
9260 ("r-matrix" ,r-matrix)
9261 ("r-mclust" ,r-mclust)
9263 ("r-multicool" ,r-multicool)
9264 ("r-mvtnorm" ,r-mvtnorm)))
9265 (home-page "http://www.mvstat.net/tduong/")
9266 (synopsis "Kernel smoothing")
9268 "This package provides kernel smoothers for univariate and multivariate
9269 data, including density functions, density derivatives, cumulative
9270 distributions, modal clustering, discriminant analysis, and two-sample
9271 hypothesis testing.")
9272 ;; Either version of the GPL.
9273 (license (list license:gpl2 license:gpl3))))
9275 (define-public r-feature
9282 (uri (cran-uri "feature" version))
9285 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9286 (build-system r-build-system)
9289 ("r-misc3d" ,r-misc3d)
9291 (home-page "http://www.mvstat.net/tduong/")
9292 (synopsis "Inferential feature significance for kernel density estimation")
9294 "The feature package contains functions to display and compute kernel
9295 density estimates, significant gradient and significant curvature regions.
9296 Significant gradient and/or curvature regions often correspond to significant
9297 features (e.g. local modes).")
9298 ;; Either version of the GPL.
9299 (license (list license:gpl2 license:gpl3))))
9301 (define-public r-arm
9308 (uri (cran-uri "arm" version))
9311 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9312 (build-system r-build-system)
9314 `(("r-abind" ,r-abind)
9318 ("r-matrix" ,r-matrix)
9319 ("r-nlme" ,r-nlme)))
9320 (home-page "https://cran.r-project.org/web/packages/arm/")
9321 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9323 "This package provides functions to accompany A. Gelman and J. Hill,
9324 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9325 University Press, 2007.")
9326 (license license:gpl3+)))
9328 (define-public r-circular
9335 (uri (cran-uri "circular" version))
9338 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9339 (build-system r-build-system)
9341 `(("r-boot" ,r-boot)
9342 ("r-mvtnorm" ,r-mvtnorm)))
9344 `(("gfortran" ,gfortran)))
9345 (home-page "https://cran.r-project.org/web/packages/circular/")
9346 (synopsis "Circular statistics")
9348 "This package provides tools for circular statistics, from \"Topics in
9349 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9351 (license license:gpl2+)))
9353 (define-public r-activity
9360 (uri (cran-uri "activity" version))
9363 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9364 (build-system r-build-system)
9366 `(("r-circular" ,r-circular)
9367 ("r-insol" ,r-insol)
9368 ("r-pbapply" ,r-pbapply)))
9369 (home-page "https://cran.r-project.org/web/packages/activity/")
9370 (synopsis "Animal activity statistics")
9372 "This package provides functions to fit kernel density functions to
9373 animal activity time data; plot activity distributions; quantify overall
9374 levels of activity; statistically compare activity metrics through
9375 bootstrapping; and evaluate variation in linear variables with time (or other
9376 circular variables).")
9377 (license license:gpl3)))
9379 (define-public r-ouch
9386 (uri (cran-uri "ouch" version))
9389 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9390 (build-system r-build-system)
9391 (propagated-inputs `(("r-subplex" ,r-subplex)))
9392 (home-page "http://kingaa.github.io/ouch/")
9393 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9395 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9396 for evolution along a phylogenetic tree.")
9397 (license license:gpl2+)))
9399 (define-public r-fmsb
9406 (uri (cran-uri "fmsb" version))
9409 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
9410 (build-system r-build-system)
9411 (home-page "http://minato.sip21c.org/msb/")
9412 (synopsis "Functions for medical statistics book with demographic data")
9414 "This package provides several utility functions for the book entitled
9415 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9416 Japan, 2007) with Japanese demographic data and some demographic analysis
9417 related functions.")
9418 (license license:gpl2+)))
9420 (define-public r-stabledist
9422 (name "r-stabledist")
9427 (uri (cran-uri "stabledist" version))
9430 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9431 (build-system r-build-system)
9432 (home-page "http://www.rmetrics.org")
9433 (synopsis "Stable distribution functions")
9435 "This package provides density, probability and quantile functions, and
9436 random number generation for (skew) stable distributions, using the
9437 parametrizations of Nolan.")
9438 (license license:gpl2+)))
9440 (define-public r-gsl
9447 (uri (cran-uri "gsl" version))
9450 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9451 (build-system r-build-system)
9454 (home-page "https://cran.r-project.org/web/packages/gsl")
9455 (synopsis "Wrapper for the GNU Scientific Library")
9457 "This package provides an R wrapper for the special functions and quasi
9458 random number generators of the GNU Scientific Library.")
9459 (license license:gpl2+)))
9461 (define-public r-adgoftest
9463 (name "r-adgoftest")
9468 (uri (cran-uri "ADGofTest" version))
9471 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9472 (properties `((upstream-name . "ADGofTest")))
9473 (build-system r-build-system)
9474 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9475 (synopsis "Anderson-Darling GoF test")
9477 "This package provides an implementation of the Anderson-Darling GoF test
9478 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9479 Anderson-Darling Distribution\".")
9480 ;; Any version of the GPL.
9481 (license license:gpl3+)))
9483 (define-public r-softimpute
9485 (name "r-softimpute")
9490 (uri (cran-uri "softImpute" version))
9493 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9494 (properties `((upstream-name . "softImpute")))
9495 (build-system r-build-system)
9497 `(("r-matrix" ,r-matrix)))
9499 `(("gfortran" ,gfortran)))
9500 (home-page "https://cran.r-project.org/web/packages/softImpute")
9501 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9503 "This package provides iterative methods for matrix completion that use
9504 nuclear-norm regularization. The package includes procedures for centering
9505 and scaling rows, columns or both, and for computing low-rank @dfn{single
9506 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9508 (license license:gpl2)))
9510 (define-public r-fftwtools
9512 (name "r-fftwtools")
9517 (uri (cran-uri "fftwtools" version))
9520 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9521 (build-system r-build-system)
9522 (inputs `(("fftw" ,fftw)))
9523 (home-page "https://github.com/krahim/fftwtools")
9524 (synopsis "Wrapper for FFTW3")
9526 "This package provides a wrapper for several FFTW functions. It provides
9527 access to the two-dimensional FFT, the multivariate FFT, and the
9528 one-dimensional real to complex FFT using the FFTW3 library. The package
9529 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9530 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9531 The FFT functions have a parameter that allows them to not return the
9532 redundant complex conjugate when the input is real data.")
9533 (license license:gpl2+)))
9535 (define-public r-tiff
9542 (uri (cran-uri "tiff" version))
9545 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9546 (build-system r-build-system)
9548 `(("libtiff" ,libtiff)
9549 ("libjpeg" ,libjpeg)
9551 (home-page "http://www.rforge.net/tiff/")
9552 (synopsis "Read and write TIFF images")
9554 "This package provides an easy and simple way to read, write and display
9555 bitmap images stored in the TIFF format. It can read and write both files and
9556 in-memory raw vectors.")
9557 ;; Either of these two license versions.
9558 (license (list license:gpl2 license:gpl3))))
9560 (define-public r-nlp
9567 (uri (cran-uri "NLP" version))
9570 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9571 (properties `((upstream-name . "NLP")))
9572 (build-system r-build-system)
9573 (home-page "https://cran.r-project.org/web/packages/NLP/")
9574 (synopsis "Natural language processing infrastructure")
9576 "This package provides basic classes and methods for Natural Language
9578 (license license:gpl3)))
9587 (uri (cran-uri "tm" version))
9590 "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
9591 (properties `((upstream-name . "tm")))
9592 (build-system r-build-system)
9598 ("r-xml2" ,r-xml2)))
9599 (home-page "http://tm.r-forge.r-project.org/")
9600 (synopsis "Text mining package")
9602 "This package provides a framework for text mining applications within R.")
9603 (license license:gpl3)))
9605 (define-public r-waveslim
9612 (uri (cran-uri "waveslim" version))
9615 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9616 (build-system r-build-system)
9618 `(("gfortran" ,gfortran)))
9619 (home-page "http://waveslim.blogspot.com")
9620 (synopsis "Basic wavelet routines for signal processing")
9622 "This package provides basic wavelet routines for time series (1D),
9623 image (2D) and array (3D) analysis. The code provided here is based on
9624 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9625 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9626 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9627 pairs (Selesnick 2001, 2002).")
9628 (license license:bsd-3)))
9630 (define-public r-wordcloud
9632 (name "r-wordcloud")
9637 (uri (cran-uri "wordcloud" version))
9640 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9641 (build-system r-build-system)
9643 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9645 ;; The "tm" package is only "suggested" according to CRAN, but the
9646 ;; wordcloud package cannot be loaded without it.
9648 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9649 (synopsis "Word clouds")
9651 "This package provides functionality to create pretty word clouds,
9652 visualize differences and similarity between documents, and avoid
9653 over-plotting in scatter plots with text.")
9654 (license license:lgpl2.1)))
9656 (define-public r-colorramps
9658 (name "r-colorramps")
9663 (uri (cran-uri "colorRamps" version))
9666 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9667 (properties `((upstream-name . "colorRamps")))
9668 (build-system r-build-system)
9669 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9670 (synopsis "Build color tables")
9671 (description "This package provides features to build gradient color
9673 ;; Any version of the GPL
9674 (license license:gpl3+)))
9676 (define-public r-tidytree
9683 (uri (cran-uri "tidytree" version))
9685 (base32 "1sbfwcxf9v1lhpa0392b49b6qfjrq7nlqz2djqzk5aknj9j64zvy"))))
9686 (build-system r-build-system)
9689 ("r-dplyr" ,r-dplyr)
9690 ("r-lazyeval" ,r-lazyeval)
9691 ("r-magrittr" ,r-magrittr)
9692 ("r-rlang" ,r-rlang)
9693 ("r-tibble" ,r-tibble)))
9694 (home-page "https://github.com/GuangchuangYu/tidytree")
9695 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9697 "Phylogenetic trees generally contain multiple components including nodes,
9698 edges, branches and associated data. This package provides an approach to
9699 convert tree objects to tidy data frames. It also provides tidy interfaces to
9700 manipulate tree data.")
9701 (license license:artistic2.0)))
9703 (define-public r-rvcheck
9710 (uri (cran-uri "rvcheck" version))
9712 (base32 "11n3qxapxcqsa0771s9q8n95kxmfyflya1d6wz4mm0lz0i6q55ia"))))
9713 (build-system r-build-system)
9715 `(("r-biocmanager" ,r-biocmanager)
9716 ("r-rlang" ,r-rlang)))
9717 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9718 (synopsis "R package version check")
9720 "This package provides tools to check the latest release version of R and
9721 R packages (on CRAN, Bioconductor or Github).")
9722 (license license:artistic2.0)))
9724 (define-public r-docopt
9731 (uri (cran-uri "docopt" version))
9734 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9735 (build-system r-build-system)
9736 (home-page "https://github.com/docopt/docopt.R")
9737 (synopsis "Command-line interface specification language")
9739 "This package enables you to define a command-line interface by just
9740 giving it a description in the specific format.")
9741 (license license:expat)))
9743 (define-public r-sparsesvd
9745 (name "r-sparsesvd")
9750 (uri (cran-uri "sparsesvd" version))
9753 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9754 (build-system r-build-system)
9755 (propagated-inputs `(("r-matrix" ,r-matrix)))
9756 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9757 (synopsis "Sparse truncated singular value decomposition")
9759 "This package provides a Wrapper around the SVDLIBC library
9760 for (truncated) singular value decomposition of a sparse matrix. Currently,
9761 only sparse real matrices in Matrix package format are supported.")
9762 ;; SVDLIBC is released under BSD-2. The R interface is released under
9764 (license (list license:bsd-3 license:bsd-2))))
9766 (define-public r-speedglm
9773 (uri (cran-uri "speedglm" version))
9776 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9777 (build-system r-build-system)
9779 `(("r-mass" ,r-mass)
9780 ("r-matrix" ,r-matrix)))
9781 (home-page "https://cran.r-project.org/web/packages/speedglm")
9782 (synopsis "Fit linear and generalized linear models to large data sets")
9784 "This package provides tools for fitting linear models and generalized
9785 linear models to large data sets by updating algorithms.")
9786 ;; Any version of the GPL
9787 (license license:gpl2+)))
9789 (define-public r-densityclust
9791 (name "r-densityclust")
9796 (uri (cran-uri "densityClust" version))
9799 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9800 (properties `((upstream-name . "densityClust")))
9801 (build-system r-build-system)
9804 ("r-ggplot2" ,r-ggplot2)
9805 ("r-ggrepel" ,r-ggrepel)
9806 ("r-gridextra" ,r-gridextra)
9807 ("r-rcolorbrewer" ,r-rcolorbrewer)
9809 ("r-rtsne" ,r-rtsne)))
9810 (home-page "https://cran.r-project.org/web/packages/densityClust")
9811 (synopsis "Clustering by fast search and find of density peaks")
9813 "This package provides an improved implementation (based on k-nearest
9814 neighbors) of the density peak clustering algorithm, originally described by
9815 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9816 large datasets (> 100,000 samples) very efficiently.")
9817 (license license:gpl2+)))
9819 (define-public r-combinat
9826 (uri (cran-uri "combinat" version))
9829 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9830 (build-system r-build-system)
9831 (home-page "https://cran.r-project.org/web/packages/combinat")
9832 (synopsis "Combinatorics utilities")
9833 (description "This package provides assorted routines for combinatorics.")
9834 (license license:gpl2)))
9836 (define-public r-qlcmatrix
9838 (name "r-qlcmatrix")
9843 (uri (cran-uri "qlcMatrix" version))
9846 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9847 (properties `((upstream-name . "qlcMatrix")))
9848 (build-system r-build-system)
9850 `(("r-docopt" ,r-docopt)
9851 ("r-matrix" ,r-matrix)
9853 ("r-sparsesvd" ,r-sparsesvd)))
9854 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9855 (synopsis "Sparse matrix functions for quantitative language comparison")
9857 "This package provides an extension of the functionality of the Matrix
9858 package for using sparse matrices. Some of the functions are very general,
9859 while other are highly specific for the special data format used for
9860 @dfn{quantitative language comparison} (QLC).")
9861 (license license:gpl3)))
9863 (define-public r-ddrtree
9870 (uri (cran-uri "DDRTree" version))
9873 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9874 (properties `((upstream-name . "DDRTree")))
9875 (build-system r-build-system)
9878 ("r-irlba" ,r-irlba)
9880 ("r-rcppeigen" ,r-rcppeigen)))
9881 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9882 (synopsis "Learning principal graphs with DDRTree")
9884 "This package provides an implementation of the framework of
9885 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9886 dimensional space while constructs a principal tree which passes through the
9887 middle of the data simultaneously. DDRTree shows superiority to
9888 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9889 intrinsic structure of single cell genomics data. In general, it could be
9890 used to reconstruct the temporal progression as well as the bifurcation
9891 structure of any data type.")
9892 (license license:asl2.0)))
9894 (define-public r-corpcor
9901 (uri (cran-uri "corpcor" version))
9904 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9905 (build-system r-build-system)
9906 (home-page "http://strimmerlab.org/software/corpcor/")
9907 (synopsis "Efficient estimation of covariance and (partial) correlation")
9909 "This package implements a James-Stein-type shrinkage estimator for the
9910 covariance matrix, with separate shrinkage for variances and correlations.
9911 Furthermore, functions are available for fast singular value decomposition,
9912 for computing the pseudoinverse, and for checking the rank and positive
9913 definiteness of a matrix.")
9914 (license license:gpl3+)))
9916 (define-public r-rspectra
9923 (uri (cran-uri "RSpectra" version))
9926 "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s"))))
9927 (properties `((upstream-name . "RSpectra")))
9928 (build-system r-build-system)
9930 `(("r-matrix" ,r-matrix)
9932 ("r-rcppeigen" ,r-rcppeigen)))
9933 (home-page "https://github.com/yixuan/RSpectra")
9934 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
9936 "This package provides an R interface to the Spectra library for
9937 large-scale eigenvalue and SVD problems. It is typically used to compute a
9938 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
9939 which is usually more efficient than @code{eigen()} if k << n.")
9941 (license license:mpl2.0)))
9943 (define-public r-vbsr
9950 (uri (cran-uri "vbsr" version))
9953 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
9954 (build-system r-build-system)
9955 (home-page "https://cran.r-project.org/web/packages/vbsr")
9956 (synopsis "Variational Bayes spike regression regularized linear models")
9958 "This package provides an efficient algorithm for solving ultra-sparse
9959 regularized regression models using a variational Bayes algorithm with a spike
9960 prior. The algorithm is solved on a path, with coordinate updates, and is
9961 capable of generating very sparse models. Very general model
9962 diagnostics for controlling type-1 errors are also provided.")
9963 (license license:gpl2)))
9965 (define-public r-flare
9972 (uri (cran-uri "flare" version))
9975 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
9976 (build-system r-build-system)
9978 `(("r-igraph" ,r-igraph)
9979 ("r-lattice" ,r-lattice)
9981 ("r-matrix" ,r-matrix)))
9982 (home-page "https://cran.r-project.org/web/packages/flare")
9983 (synopsis "Family of Lasso regression implementations")
9985 "This package provides implementations of a family of Lasso variants
9986 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
9987 high dimensional sparse linear models.")
9988 (license license:gpl2)))
9990 (define-public r-lassopv
9997 (uri (cran-uri "lassopv" version))
10000 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10001 (build-system r-build-system)
10002 (propagated-inputs `(("r-lars" ,r-lars)))
10003 (home-page "https://github.com/lingfeiwang/lassopv")
10004 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10006 "This package enables you to estimate the p-values for predictors x
10007 against target variable y in Lasso regression, using the regularization
10008 strength when each predictor enters the active set of regularization path for
10009 the first time as the statistic.")
10010 (license license:gpl3)))
10012 (define-public r-splitstackshape
10014 (name "r-splitstackshape")
10019 (uri (cran-uri "splitstackshape" version))
10022 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10023 (build-system r-build-system)
10025 `(("r-data-table" ,r-data-table)))
10026 (home-page "https://github.com/mrdwab/splitstackshape")
10027 (synopsis "Stack and reshape datasets after splitting concatenated values")
10029 "Online data collection tools like Google Forms often export
10030 multiple-response questions with data concatenated in cells. The
10031 @code{concat.split} (cSplit) family of functions provided by this package
10032 splits such data into separate cells. This package also includes functions to
10033 stack groups of columns and to reshape wide data, even when the data are
10034 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10035 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10037 (license license:gpl3)))
10039 (define-public r-tfmpvalue
10041 (name "r-tfmpvalue")
10046 (uri (cran-uri "TFMPvalue" version))
10049 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10050 (properties `((upstream-name . "TFMPvalue")))
10051 (build-system r-build-system)
10052 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10053 (home-page "https://github.com/ge11232002/TFMPvalue")
10054 (synopsis "P-value computation for position weight matrices")
10056 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10057 identification from sequence/alignments, we are interested in the significance
10058 of certain match scores. TFMPvalue provides the accurate calculation of a
10059 p-value with a score threshold for position weight matrices, or the score with
10060 a given p-value. It is an interface to code originally made available by
10061 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10062 Touzet and Varre (2007).")
10063 (license license:gpl2)))
10065 (define-public r-rnifti
10072 (uri (cran-uri "RNifti" version))
10075 "0hfid40pgfi1ykqka8y3v0m7h0iyd6fbvycvqlad3ibmbg621f0w"))))
10076 (properties `((upstream-name . "RNifti")))
10077 (build-system r-build-system)
10078 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10079 (home-page "https://github.com/jonclayden/RNifti")
10080 (synopsis "Fast R and C++ access to NIfTI images")
10082 "This package provides very fast read and write access to images stored
10083 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10084 compiled C and interpreted R code. It also provides a C/C++ API that can be
10085 used by other packages.")
10086 (license license:gpl2)))
10088 (define-public r-shades
10095 (uri (cran-uri "shades" version))
10098 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10099 (build-system r-build-system)
10100 (home-page "https://github.com/jonclayden/shades")
10101 (synopsis "Simple color manipulation")
10103 "This package provides functions for easily manipulating colors,
10104 creating color scales and calculating color distances.")
10105 (license license:bsd-3)))
10107 (define-public r-ore
10114 (uri (cran-uri "ore" version))
10116 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10117 (build-system r-build-system)
10118 (home-page "https://github.com/jonclayden/ore")
10119 (synopsis "R interface to the Onigmo regular expression library")
10121 "This package provides an alternative to R's built-in functionality for
10122 handling regular expressions, based on the Onigmo library. It offers
10123 first-class compiled regex objects, partial matching and function-based
10124 substitutions, amongst other features.")
10125 (license license:bsd-3)))
10127 (define-public r-reportr
10134 (uri (cran-uri "reportr" version))
10137 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10138 (build-system r-build-system)
10139 (propagated-inputs `(("r-ore" ,r-ore)))
10140 (home-page "https://github.com/jonclayden/reportr")
10141 (synopsis "General message and error reporting system")
10143 "This package provides a system for reporting messages, which offers
10144 certain useful features over the standard R system, such as the incorporation
10145 of output consolidation, message filtering, assertions, expression
10146 substitution, automatic generation of stack traces for debugging, and
10147 conditional reporting based on the current \"output level\".")
10148 (license license:gpl2)))
10150 (define-public r-tractor-base
10152 (name "r-tractor-base")
10157 (uri (cran-uri "tractor.base" version))
10160 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10161 (properties `((upstream-name . "tractor.base")))
10162 (build-system r-build-system)
10165 ("r-reportr" ,r-reportr)
10166 ("r-rnifti" ,r-rnifti)
10167 ("r-shades" ,r-shades)))
10168 (home-page "http://www.tractor-mri.org.uk")
10169 (synopsis "Read, manipulate and visualize magnetic resonance images")
10171 "This package provides functions for working with magnetic resonance
10172 images. It supports reading and writing of popular file formats (DICOM,
10173 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10174 visualization; flexible image manipulation; metadata and sparse image
10176 (license license:gpl2)))
10178 (define-public r-grimport
10180 (name "r-grimport")
10185 (uri (cran-uri "grImport" version))
10188 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10189 (properties `((upstream-name . "grImport")))
10190 (build-system r-build-system)
10192 `(("ghostscript" ,ghostscript)))
10194 `(("r-xml" ,r-xml)))
10195 (home-page "https://cran.r-project.org/web/packages/grImport")
10196 (synopsis "Convert, import, and draw PostScript pictures")
10198 "This package provides functions for converting, importing, and drawing
10199 PostScript pictures in R plots.")
10200 (license license:gpl2+)))
10202 (define-public r-grimport2
10204 (name "r-grimport2")
10209 (uri (cran-uri "grImport2" version))
10212 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10213 (properties `((upstream-name . "grImport2")))
10214 (build-system r-build-system)
10216 `(("r-base64enc" ,r-base64enc)
10220 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10221 (synopsis "Import SVG graphics")
10223 "This package provides functions for importing external vector images and
10224 drawing them as part of R plots. This package is different from the
10225 @code{grImport} package because, where that package imports PostScript format
10226 images, this package imports SVG format images. Furthermore, this package
10227 imports a specific subset of SVG, so external images must be preprocessed
10228 using a package like @code{rsvg} to produce SVG that this package can import.
10229 SVG features that are not supported by R graphics, such as gradient fills, can
10230 be imported and then exported via the @code{gridSVG} package.")
10231 (license license:gpl2+)))
10233 (define-public r-kohonen
10240 (uri (cran-uri "kohonen" version))
10243 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10244 (build-system r-build-system)
10246 `(("r-rcpp" ,r-rcpp)))
10247 (home-page "https://cran.r-project.org/web/packages/kohonen")
10248 (synopsis "Supervised and unsupervised self-organising maps")
10250 "This package provides functions to train @dfn{self-organising
10251 maps} (SOMs). Also interrogation of the maps and prediction using trained
10252 maps are supported. The name of the package refers to Teuvo Kohonen, the
10253 inventor of the SOM.")
10254 (license license:gpl2+)))
10256 (define-public r-nnls
10263 (uri (cran-uri "nnls" version))
10266 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10267 (build-system r-build-system)
10268 (native-inputs `(("gfortran" ,gfortran)))
10269 (home-page "https://cran.r-project.org/web/packages/nnls")
10270 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10272 "This package provides an R interface to the Lawson-Hanson implementation
10273 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10274 the combination of non-negative and non-positive constraints.")
10275 (license license:gpl2+)))
10277 (define-public r-iso
10284 (uri (cran-uri "Iso" version))
10287 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10288 (properties `((upstream-name . "Iso")))
10289 (build-system r-build-system)
10290 (native-inputs `(("gfortran" ,gfortran)))
10291 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10292 (synopsis "Functions to perform isotonic regression")
10294 "This package provides support for linear order and unimodal
10295 order (univariate) isotonic regression and bivariate isotonic regression with
10296 linear order on both variables.")
10297 (license license:gpl2+)))
10299 (define-public r-chemometricswithr
10301 (name "r-chemometricswithr")
10306 (uri (cran-uri "ChemometricsWithR" version))
10309 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10311 `((upstream-name . "ChemometricsWithR")))
10312 (build-system r-build-system)
10314 `(("r-devtools" ,r-devtools)
10315 ("r-kohonen" ,r-kohonen)
10318 (home-page "https://github.com/rwehrens/CWR")
10319 (synopsis "Chemometrics with R")
10321 "This package provides functions and scripts used in the book
10322 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10323 Life Sciences\" by Ron Wehrens, Springer (2011).")
10324 (license license:gpl2+)))
10326 (define-public r-als
10333 (uri (cran-uri "ALS" version))
10336 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10337 (properties `((upstream-name . "ALS")))
10338 (build-system r-build-system)
10341 ("r-nnls" ,r-nnls)))
10342 (home-page "https://cran.r-project.org/web/packages/ALS")
10343 (synopsis "Multivariate curve resolution alternating least squares")
10345 "Alternating least squares is often used to resolve components
10346 contributing to data with a bilinear structure; the basic technique may be
10347 extended to alternating constrained least squares. This package provides an
10348 implementation of @dfn{multivariate curve resolution alternating least
10349 squares} (MCR-ALS).
10351 Commonly applied constraints include unimodality, non-negativity, and
10352 normalization of components. Several data matrices may be decomposed
10353 simultaneously by assuming that one of the two matrices in the bilinear
10354 decomposition is shared between datasets.")
10355 (license license:gpl2+)))
10357 (define-public r-strucchange
10359 (name "r-strucchange")
10364 (uri (cran-uri "strucchange" version))
10367 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10368 (build-system r-build-system)
10370 `(("r-sandwich" ,r-sandwich)
10372 (home-page "https://cran.r-project.org/web/packages/strucchange")
10373 (synopsis "Testing, monitoring, and dating structural changes")
10375 "This package provides tools for testing, monitoring and dating
10376 structural changes in (linear) regression models. It features tests/methods
10377 from the generalized fluctuation test framework as well as from the F
10378 test (Chow test) framework. This includes methods to fit, plot and test
10379 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10380 statistics, respectively. It is possible to monitor incoming data online
10381 using fluctuation processes. Finally, the breakpoints in regression models
10382 with structural changes can be estimated together with confidence intervals.
10383 Emphasis is always given to methods for visualizing the data.")
10384 ;; Either of these two GPL versions
10385 (license (list license:gpl2 license:gpl3))))
10387 (define-public r-pixmap
10394 (uri (cran-uri "pixmap" version))
10397 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10398 (build-system r-build-system)
10399 (home-page "https://cran.r-project.org/web/packages/pixmap")
10400 (synopsis "Tools for bitmap images")
10402 "This package provides functions for importing, exporting, plotting and
10403 other manipulations of bitmapped images.")
10404 (license license:gpl2)))
10406 (define-public r-rapidjsonr
10408 (name "r-rapidjsonr")
10413 (uri (cran-uri "rapidjsonr" version))
10416 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10417 (build-system r-build-system)
10418 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10419 (synopsis "JSON parser")
10421 "This package provides JSON parsing capability through the Rapidjson
10423 (license license:expat)))
10425 (define-public r-ontologyindex
10427 (name "r-ontologyindex")
10432 (uri (cran-uri "ontologyIndex" version))
10435 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10436 (properties `((upstream-name . "ontologyIndex")))
10437 (build-system r-build-system)
10438 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10439 (synopsis "Functions for processing ontologies in R")
10441 "This package provides functions for reading ontologies into R as lists
10442 and manipulating sets of ontological terms.")
10443 (license license:gpl2+)))
10445 (define-public r-gargle
10452 (uri (cran-uri "gargle" version))
10455 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10456 (build-system r-build-system)
10461 ("r-jsonlite" ,r-jsonlite)
10462 ("r-rlang" ,r-rlang)
10463 ("r-withr" ,r-withr)))
10464 (home-page "https://gargle.r-lib.org")
10465 (synopsis "Utilities for working with Google APIs")
10467 "This package provides utilities for working with Google APIs. This
10468 includes functions and classes for handling common credential types and for
10469 preparing, executing, and processing HTTP requests.")
10470 (license license:expat)))
10472 (define-public r-bigrquery
10474 (name "r-bigrquery")
10479 (uri (cran-uri "bigrquery" version))
10482 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10483 (build-system r-build-system)
10485 `(("r-assertthat" ,r-assertthat)
10486 ("r-bit64" ,r-bit64)
10489 ("r-gargle" ,r-gargle)
10492 ("r-jsonlite" ,r-jsonlite)
10493 ("r-prettyunits" ,r-prettyunits)
10494 ("r-progress" ,r-progress)
10495 ("r-rapidjsonr" ,r-rapidjsonr)
10497 ("r-rlang" ,r-rlang)
10498 ("r-tibble" ,r-tibble)))
10499 (home-page "https://github.com/rstats-db/bigrquery")
10500 (synopsis "R interface to Google's BigQuery API")
10502 "This package provides an R interface to Google's BigQuery database.")
10503 (license license:gpl3)))
10505 (define-public r-gmp
10508 (version "0.5-13.5")
10512 (uri (cran-uri "gmp" version))
10515 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10516 (build-system r-build-system)
10519 (modify-phases %standard-phases
10520 (add-after 'unpack 'set-CC
10521 (lambda _ (setenv "CC" "gcc") #t)))))
10522 (inputs `(("gmp" ,gmp)))
10523 (home-page "https://cran.r-project.org/web/packages/gmp")
10524 (synopsis "Multiple precision arithmetic")
10526 "This package supports multiple precision arithmetic (big integers and
10527 rationals, prime number tests, matrix computation), \"arithmetic without
10528 limitations\" using the GNU Multiple Precision library.")
10529 ;; Any version of the GPL.
10530 (license license:gpl3+)))
10532 (define-public r-rmpfr
10539 (uri (cran-uri "Rmpfr" version))
10542 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10543 (properties `((upstream-name . "Rmpfr")))
10544 (build-system r-build-system)
10548 `(("r-gmp" ,r-gmp)))
10549 (home-page "http://rmpfr.r-forge.r-project.org/")
10550 (synopsis "R bindings to the MPFR library")
10552 "This package supports arithmetic (via S4 classes and methods) for
10553 arbitrary precision floating point numbers, including transcendental
10554 functions. To this end, the package interfaces with the @dfn{Multiple
10555 Precision Floating-Point Reliable} (MPFR) library.")
10556 (license license:gpl2+)))
10558 (define-public r-assertive-base
10560 (name "r-assertive-base")
10565 (uri (cran-uri "assertive.base" version))
10568 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10570 `((upstream-name . "assertive.base")))
10571 (build-system r-build-system)
10572 (home-page "https://bitbucket.org/richierocks/assertive.base")
10573 (synopsis "Core of the assertive package")
10575 "This package provides a minimal set of predicates and assertions used by
10576 the assertive package. This is mainly for use by other package developers who
10577 want to include run-time testing features in their own packages.")
10578 (license license:gpl3+)))
10580 (define-public r-assertive-properties
10582 (name "r-assertive-properties")
10587 (uri (cran-uri "assertive.properties" version))
10590 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10592 `((upstream-name . "assertive.properties")))
10593 (build-system r-build-system)
10595 `(("r-assertive-base" ,r-assertive-base)))
10596 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10597 (synopsis "Assertions to check properties of variables")
10599 "This package provides a set of predicates and assertions for checking
10600 the properties of variables, such as length, names and attributes. This is
10601 mainly for use by other package developers who want to include run-time
10602 testing features in their own packages.")
10603 (license license:gpl3+)))
10605 (define-public r-assertive-numbers
10607 (name "r-assertive-numbers")
10612 (uri (cran-uri "assertive.numbers" version))
10615 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10617 `((upstream-name . "assertive.numbers")))
10618 (build-system r-build-system)
10620 `(("r-assertive-base" ,r-assertive-base)))
10621 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10622 (synopsis "Assertions to check properties of numbers")
10624 "This package provides a set of predicates and assertions for checking
10625 the properties of numbers. This is mainly for use by other package developers
10626 who want to include run-time testing features in their own packages.")
10627 (license license:gpl3+)))
10629 (define-public r-assertive-sets
10631 (name "r-assertive-sets")
10636 (uri (cran-uri "assertive.sets" version))
10639 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10641 `((upstream-name . "assertive.sets")))
10642 (build-system r-build-system)
10644 `(("r-assertive-base" ,r-assertive-base)))
10645 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10646 (synopsis "Assertions to check properties of sets")
10648 "This package provides a set of predicates and assertions for checking
10649 the properties of sets. This is mainly for use by other package developers
10650 who want to include run-time testing features in their own packages.")
10651 (license license:gpl3+)))
10653 (define-public r-assertive-matrices
10655 (name "r-assertive-matrices")
10660 (uri (cran-uri "assertive.matrices" version))
10663 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10665 `((upstream-name . "assertive.matrices")))
10666 (build-system r-build-system)
10668 `(("r-assertive-base" ,r-assertive-base)))
10669 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10670 (synopsis "Assertions to check properties of matrices")
10672 "This package provides a set of predicates and assertions for checking
10673 the properties of matrices. This is mainly for use by other package
10674 developers who want to include run-time testing features in their own
10676 (license license:gpl3+)))
10678 (define-public r-assertive-models
10680 (name "r-assertive-models")
10685 (uri (cran-uri "assertive.models" version))
10688 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10690 `((upstream-name . "assertive.models")))
10691 (build-system r-build-system)
10693 `(("r-assertive-base" ,r-assertive-base)))
10694 (home-page "https://bitbucket.org/richierocks/assertive.models")
10695 (synopsis "Assertions to check properties of models")
10697 "This package provides a set of predicates and assertions for checking
10698 the properties of models. This is mainly for use by other package developers
10699 who want to include run-time testing features in their own packages.")
10700 (license license:gpl3+)))
10702 (define-public r-assertive-reflection
10704 (name "r-assertive-reflection")
10709 (uri (cran-uri "assertive.reflection" version))
10712 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10714 `((upstream-name . "assertive.reflection")))
10715 (build-system r-build-system)
10717 `(("r-assertive-base" ,r-assertive-base)))
10718 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10719 (synopsis "Assertions for checking the state of R")
10721 "This package provides a set of predicates and assertions for checking
10722 the state and capabilities of R, the operating system it is running on, and
10723 the IDE being used. This is mainly for use by other package developers who
10724 want to include run-time testing features in their own packages.")
10725 (license license:gpl3+)))
10727 (define-public r-assertive-types
10729 (name "r-assertive-types")
10734 (uri (cran-uri "assertive.types" version))
10737 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10739 `((upstream-name . "assertive.types")))
10740 (build-system r-build-system)
10742 `(("r-assertive-base" ,r-assertive-base)
10743 ("r-assertive-properties" ,r-assertive-properties)
10744 ("r-codetools" ,r-codetools)))
10745 (home-page "https://bitbucket.org/richierocks/assertive.types")
10746 (synopsis "Assertions to check types of variables")
10748 "This package provides a set of predicates and assertions for checking
10749 the types of variables. This is mainly for use by other package developers
10750 who want to include run-time testing features in their own packages.")
10751 (license license:gpl3+)))
10753 (define-public r-assertive-files
10755 (name "r-assertive-files")
10760 (uri (cran-uri "assertive.files" version))
10763 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10765 `((upstream-name . "assertive.files")))
10766 (build-system r-build-system)
10768 `(("r-assertive-base" ,r-assertive-base)
10769 ("r-assertive-numbers" ,r-assertive-numbers)))
10770 (home-page "https://bitbucket.org/richierocks/assertive.files")
10771 (synopsis "Assertions to check properties of files")
10773 "This package provides a set of predicates and assertions for checking
10774 the properties of files and connections. This is mainly for use by other
10775 package developers who want to include run-time testing features in their own
10777 (license license:gpl3+)))
10779 (define-public r-assertive-code
10781 (name "r-assertive-code")
10786 (uri (cran-uri "assertive.code" version))
10789 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10791 `((upstream-name . "assertive.code")))
10792 (build-system r-build-system)
10794 `(("r-assertive-base" ,r-assertive-base)
10795 ("r-assertive-properties" ,r-assertive-properties)
10796 ("r-assertive-types" ,r-assertive-types)))
10797 (home-page "https://bitbucket.org/richierocks/assertive.code")
10798 (synopsis "Assertions to check properties of code")
10800 "This package provides a set of predicates and assertions for checking
10801 the properties of code. This is mainly for use by other package developers
10802 who want to include run-time testing features in their own packages.")
10803 (license license:gpl3+)))
10805 (define-public r-assertive-datetimes
10807 (name "r-assertive-datetimes")
10812 (uri (cran-uri "assertive.datetimes" version))
10815 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10817 `((upstream-name . "assertive.datetimes")))
10818 (build-system r-build-system)
10820 `(("r-assertive-base" ,r-assertive-base)
10821 ("r-assertive-types" ,r-assertive-types)))
10822 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10823 (synopsis "Assertions to check properties of dates and times")
10825 "This package provides a set of predicates and assertions for checking
10826 the properties of dates and times. This is mainly for use by other package
10827 developers who want to include run-time testing features in their own
10829 (license license:gpl3+)))
10831 (define-public r-assertive-strings
10833 (name "r-assertive-strings")
10838 (uri (cran-uri "assertive.strings" version))
10841 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10843 `((upstream-name . "assertive.strings")))
10844 (build-system r-build-system)
10846 `(("r-assertive-base" ,r-assertive-base)
10847 ("r-assertive-types" ,r-assertive-types)
10848 ("r-stringi" ,r-stringi)))
10849 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10850 (synopsis "Assertions to check properties of strings")
10852 "This package provides a set of predicates and assertions for checking
10853 the properties of strings. This is mainly for use by other package developers
10854 who want to include run-time testing features in their own packages.")
10855 (license license:gpl3+)))
10857 (define-public r-assertive-data-us
10859 (name "r-assertive-data-us")
10864 (uri (cran-uri "assertive.data.us" version))
10867 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10869 `((upstream-name . "assertive.data.us")))
10870 (build-system r-build-system)
10872 `(("r-assertive-base" ,r-assertive-base)
10873 ("r-assertive-strings" ,r-assertive-strings)))
10874 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10875 (synopsis "Assertions to check properties of strings")
10877 "This package provides a set of predicates and assertions for checking
10878 the properties of US-specific complex data types. This is mainly for use by
10879 other package developers who want to include run-time testing features in
10880 their own packages.")
10881 (license license:gpl3+)))
10883 (define-public r-assertive-data-uk
10885 (name "r-assertive-data-uk")
10890 (uri (cran-uri "assertive.data.uk" version))
10893 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10895 `((upstream-name . "assertive.data.uk")))
10896 (build-system r-build-system)
10898 `(("r-assertive-base" ,r-assertive-base)
10899 ("r-assertive-strings" ,r-assertive-strings)))
10900 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10901 (synopsis "Assertions to check properties of strings")
10903 "This package provides a set of predicates and assertions for checking
10904 the properties of UK-specific complex data types. This is mainly for use by
10905 other package developers who want to include run-time testing features in
10906 their own packages.")
10907 (license license:gpl3+)))
10909 (define-public r-assertive-data
10911 (name "r-assertive-data")
10916 (uri (cran-uri "assertive.data" version))
10919 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
10921 `((upstream-name . "assertive.data")))
10922 (build-system r-build-system)
10924 `(("r-assertive-base" ,r-assertive-base)
10925 ("r-assertive-strings" ,r-assertive-strings)))
10926 (home-page "https://bitbucket.org/richierocks/assertive.data")
10927 (synopsis "Assertions to check properties of data")
10929 "This package provides a set of predicates and assertions for checking
10930 the properties of (country independent) complex data types. This is mainly
10931 for use by other package developers who want to include run-time testing
10932 features in their own packages.")
10933 (license license:gpl3+)))
10935 (define-public r-assertive
10937 (name "r-assertive")
10942 (uri (cran-uri "assertive" version))
10945 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
10946 (build-system r-build-system)
10948 `(("r-assertive-base" ,r-assertive-base)
10949 ("r-assertive-code" ,r-assertive-code)
10950 ("r-assertive-data" ,r-assertive-data)
10951 ("r-assertive-data-uk" ,r-assertive-data-uk)
10952 ("r-assertive-data-us" ,r-assertive-data-us)
10953 ("r-assertive-datetimes" ,r-assertive-datetimes)
10954 ("r-assertive-files" ,r-assertive-files)
10955 ("r-assertive-matrices" ,r-assertive-matrices)
10956 ("r-assertive-models" ,r-assertive-models)
10957 ("r-assertive-numbers" ,r-assertive-numbers)
10958 ("r-assertive-properties" ,r-assertive-properties)
10959 ("r-assertive-reflection" ,r-assertive-reflection)
10960 ("r-assertive-sets" ,r-assertive-sets)
10961 ("r-assertive-strings" ,r-assertive-strings)
10962 ("r-assertive-types" ,r-assertive-types)
10963 ("r-knitr" ,r-knitr)))
10964 (home-page "https://bitbucket.org/richierocks/assertive")
10965 (synopsis "Readable check functions to ensure code integrity")
10967 "This package provides lots of predicates (@code{is_*} functions) to
10968 check the state of your variables, and assertions (@code{assert_*} functions)
10969 to throw errors if they aren't in the right form.")
10970 (license license:gpl3+)))
10972 (define-public r-dotcall64
10974 (name "r-dotcall64")
10979 (uri (cran-uri "dotCall64" version))
10982 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
10983 (properties `((upstream-name . "dotCall64")))
10984 (build-system r-build-system)
10985 (native-inputs `(("gfortran" ,gfortran)))
10986 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
10987 (synopsis "Enhanced foreign function interface supporting long vectors")
10989 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
10990 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
10991 supports long vectors, arguments of type 64-bit integer, and provides a
10992 mechanism to avoid unnecessary copies of read-only and write-only arguments.
10993 This makes it a convenient and fast interface to C/C++ and Fortran code.")
10994 (license license:gpl2+)))
10996 (define-public r-spam
11003 (uri (cran-uri "spam" version))
11005 (base32 "0xb7a0x1i93kzijr518m9plzmg8s3mxh5anwfx9xrkg5ipldvz10"))))
11006 (build-system r-build-system)
11008 `(("r-dotcall64" ,r-dotcall64)))
11009 (native-inputs `(("gfortran" ,gfortran)))
11010 (home-page "https://www.math.uzh.ch/pages/spam/")
11011 (synopsis "Sparse matrix algebra")
11013 "This package provides a set of functions for sparse matrix algebra.
11014 Differences with other sparse matrix packages are:
11017 @item it only supports (essentially) one sparse matrix format;
11018 @item it is based on transparent and simple structure(s);
11019 @item it is tailored for MCMC calculations within G(M)RF;
11020 @item and it is fast and scalable (with the extension package @code{spam64}).
11022 ;; Either of these licenses
11023 (license (list license:bsd-3 license:lgpl2.0))))
11025 (define-public r-fields
11032 (uri (cran-uri "fields" version))
11034 (base32 "173zm5vr236ydiq0v27qy0l3x7h9fc7jly38iakg77j26i0a01il"))))
11035 (build-system r-build-system)
11037 `(("r-maps" ,r-maps)
11038 ("r-spam" ,r-spam)))
11040 `(("gfortran" ,gfortran)))
11041 (home-page "https://www.image.ucar.edu/fields")
11042 (synopsis "Tools for spatial data")
11044 "This is a package for curve, surface and function fitting with an
11045 emphasis on splines, spatial data and spatial statistics. The major methods
11046 include cubic, and thin plate splines, Kriging, and compactly supported
11047 covariance functions for large data sets.")
11048 (license license:gpl2+)))
11050 (define-public r-spatialextremes
11052 (name "r-spatialextremes")
11053 (version "2.0-7.2")
11057 (uri (cran-uri "SpatialExtremes" version))
11060 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
11062 `((upstream-name . "SpatialExtremes")))
11063 (build-system r-build-system)
11065 `(("r-fields" ,r-fields)
11066 ("r-maps" ,r-maps)))
11067 (home-page "http://spatialextremes.r-forge.r-project.org/")
11068 (synopsis "Modelling spatial extremes")
11070 "This package provides tools for the statistical modelling of spatial
11071 extremes using max-stable processes, copula or Bayesian hierarchical models.
11072 More precisely, this package allows (conditional) simulations from various
11073 parametric max-stable models, analysis of the extremal spatial dependence, the
11074 fitting of such processes using composite likelihoods or least square (simple
11075 max-stable processes only), model checking and selection and prediction.")
11076 (license license:gpl2+)))
11078 (define-public r-drc
11085 (uri (cran-uri "drc" version))
11088 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11089 (build-system r-build-system)
11092 ("r-gtools" ,r-gtools)
11094 ("r-multcomp" ,r-multcomp)
11095 ("r-plotrix" ,r-plotrix)
11096 ("r-scales" ,r-scales)))
11097 (home-page "https://cran.r-project.org/web/packages/drc")
11098 (synopsis "Analysis of dose-response curves")
11100 "This package provides a suite of flexible and versatile model fitting
11101 and after-fitting functions for the analysis of dose-response data.")
11102 (license license:gpl2+)))
11104 (define-public r-rmeta
11111 (uri (cran-uri "rmeta" version))
11114 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11115 (build-system r-build-system)
11116 (home-page "https://cran.r-project.org/web/packages/rmeta")
11117 (synopsis "Tools for meta-analysis")
11119 "This package provides functions for simple fixed and random effects
11120 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11121 draws standard summary plots, funnel plots, and computes summaries and tests
11122 for association and heterogeneity.")
11123 (license license:gpl2)))
11125 (define-public r-bootstrap
11127 (name "r-bootstrap")
11132 (uri (cran-uri "bootstrap" version))
11135 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11136 (build-system r-build-system)
11137 (native-inputs `(("gfortran" ,gfortran)))
11138 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11139 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11141 "This package provides software and data for the book \"An Introduction
11142 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11143 This package is primarily provided for projects already based on it, and for
11144 support of the book. New projects should preferentially use the recommended
11145 package \"boot\".")
11146 (license license:bsd-3)))
11148 (define-public r-survivalroc
11150 (name "r-survivalroc")
11155 (uri (cran-uri "survivalROC" version))
11158 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11159 (properties `((upstream-name . "survivalROC")))
11160 (build-system r-build-system)
11161 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11162 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11164 "Compute time-dependent ROC curve from censored survival data using
11165 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11166 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11167 (license license:gpl2+)))
11169 (define-public r-longitudinal
11171 (name "r-longitudinal")
11176 (uri (cran-uri "longitudinal" version))
11179 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11180 (build-system r-build-system)
11181 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11182 (home-page "http://strimmerlab.org/software/longitudinal/")
11183 (synopsis "Analysis of multiple time course data")
11185 "This package contains general data structures and functions for
11186 longitudinal data with multiple variables, repeated measurements, and
11187 irregularly spaced time points. It also implements a shrinkage estimator of
11188 dynamical correlation and dynamical covariance.")
11189 (license license:gpl3+)))
11191 (define-public r-genenet
11198 (uri (cran-uri "GeneNet" version))
11201 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11202 (properties `((upstream-name . "GeneNet")))
11203 (build-system r-build-system)
11205 `(("r-corpcor" ,r-corpcor)
11206 ("r-fdrtool" ,r-fdrtool)
11207 ("r-longitudinal" ,r-longitudinal)))
11208 (home-page "http://strimmerlab.org/software/genenet/")
11209 (synopsis "Modeling and inferring gene networks")
11211 "This package analyzes gene expression (time series) data with focus on
11212 the inference of gene networks. In particular, GeneNet implements the methods
11213 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11214 for learning large-scale gene association networks (including assignment of
11215 putative directions).")
11216 (license license:gpl3+)))
11218 (define-public r-rbamtools
11220 (name "r-rbamtools")
11221 (version "2.16.17")
11225 (uri (cran-uri "rbamtools" version))
11228 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11229 (build-system r-build-system)
11230 (inputs `(("zlib" ,zlib)))
11232 `(("r-refgenome" ,r-refgenome)))
11233 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11234 (synopsis "Read and write BAM (binary alignment) files")
11236 "This package provides an R interface to functions of the SAMtools
11238 (license license:artistic2.0)))
11240 (define-public r-protviz
11247 (uri (cran-uri "protViz" version))
11250 "0cznzm1ijlq33yd5wsa61prav77y2vi698w0n2fx1xcv504c4bjv"))))
11251 (properties `((upstream-name . "protViz")))
11252 (build-system r-build-system)
11253 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11254 (home-page "https://github.com/protViz/protViz/")
11255 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11257 "This package helps with quality checks, visualizations and analysis of
11258 mass spectrometry data, coming from proteomics experiments. The package is
11259 developed, tested and used at the Functional Genomics Center Zurich, where it
11260 is used mainly for prototyping, teaching, and having fun with proteomics data.
11261 But it can also be used to do data analysis for small scale data sets.")
11262 (license license:gpl3)))
11264 (define-public r-cmprsk
11271 (uri (cran-uri "cmprsk" version))
11273 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11274 (build-system r-build-system)
11276 `(("r-survival" ,r-survival)))
11278 `(("gfortran" ,gfortran)))
11279 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11280 (synopsis "Subdistribution analysis of competing risks")
11282 "This package provides tool for estimation, testing and regression
11283 modeling of subdistribution functions in competing risks, as described in
11284 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11285 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11286 A proportional hazards model for the subdistribution of a competing risk,
11287 JASA, 94:496-509.")
11288 (license license:gpl2+)))
11290 (define-public r-etm
11297 (uri (cran-uri "etm" version))
11300 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11301 (build-system r-build-system)
11303 `(("r-data-table" ,r-data-table)
11304 ("r-lattice" ,r-lattice)
11306 ("r-rcpparmadillo" ,r-rcpparmadillo)
11307 ("r-survival" ,r-survival)))
11308 (home-page "https://cran.r-project.org/web/packages/etm")
11309 (synopsis "Empirical transition matrix")
11311 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11312 the matrix of transition probabilities for any time-inhomogeneous multistate
11313 model with finite state space using the Aalen-Johansen estimator.")
11314 (license license:expat)))
11316 (define-public r-epi
11323 (uri (cran-uri "Epi" version))
11326 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
11327 (properties `((upstream-name . "Epi")))
11328 (build-system r-build-system)
11330 `(("r-cmprsk" ,r-cmprsk)
11331 ("r-data-table" ,r-data-table)
11334 ("r-matrix" ,r-matrix)
11336 ("r-numderiv" ,r-numderiv)
11338 ("r-survival" ,r-survival)
11340 (home-page "http://BendixCarstensen.com/Epi/")
11341 (synopsis "Statistical analysis in epidemiology")
11343 "This package provides functions for demographic and epidemiological
11344 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11345 particular representation, manipulation and simulation of multistate data -
11346 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11347 @code{etm} and @code{cmprsk} packages. It also contains functions for
11348 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11349 data and some useful functions for tabulation and plotting, as well as a
11350 number of epidemiological data sets.")
11351 (license license:gpl2)))
11353 (define-public r-ppls
11356 (version "1.6-1.1")
11360 (uri (cran-uri "ppls" version))
11363 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11364 (build-system r-build-system)
11365 (propagated-inputs `(("r-mass" ,r-mass)))
11366 (home-page "https://cran.r-project.org/web/packages/ppls")
11367 (synopsis "Penalized partial least squares")
11369 "This package contains linear and nonlinear regression methods based on
11370 partial least squares and penalization techniques. Model parameters are
11371 selected via cross-validation, and confidence intervals ans tests for the
11372 regression coefficients can be conducted via jackknifing.")
11373 (license license:gpl2+)))
11375 (define-public r-huge
11382 (uri (cran-uri "huge" version))
11384 (base32 "07n3j1va2z4v30rj22cww72khgzbz2xsp0yc0qswlrwyxi4my5i3"))))
11385 (build-system r-build-system)
11387 `(("r-igraph" ,r-igraph)
11389 ("r-matrix" ,r-matrix)
11391 ("r-rcppeigen" ,r-rcppeigen)))
11392 (home-page "https://cran.r-project.org/web/packages/huge")
11393 (synopsis "High-dimensional undirected graph estimation")
11395 "This package provides a general framework for high-dimensional
11396 undirected graph estimation. It integrates data preprocessing, neighborhood
11397 screening, graph estimation, and model selection techniques into a pipeline.")
11398 (license license:gpl2)))
11400 (define-public r-parcor
11407 (uri (cran-uri "parcor" version))
11410 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11411 (build-system r-build-system)
11414 ("r-genenet" ,r-genenet)
11415 ("r-glmnet" ,r-glmnet)
11417 ("r-ppls" ,r-ppls)))
11418 (home-page "https://cran.r-project.org/web/packages/parcor")
11419 (synopsis "Regularized estimation of partial correlation matrices")
11421 "This package estimates the matrix of partial correlations based on
11422 different regularized regression methods: lasso, adaptive lasso, PLS, and
11423 Ridge Regression. In addition, the package provides model selection for
11424 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11425 (license license:gpl2+)))
11427 (define-public r-mcmc
11434 (uri (cran-uri "mcmc" version))
11437 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11438 (build-system r-build-system)
11439 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11440 (synopsis "Markov chain Monte Carlo")
11442 "This package simulates continuous distributions of random vectors using
11443 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11444 function that evaluates the log unnormalized density. Algorithms are random
11445 walk Metropolis algorithm (function @code{metrop}), simulated
11446 tempering (function @code{temper}), and morphometric random walk
11447 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11448 by change of variable.")
11449 (license license:expat)))
11451 (define-public r-listenv
11458 (uri (cran-uri "listenv" version))
11461 "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1"))))
11462 (build-system r-build-system)
11464 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11465 (home-page "https://github.com/HenrikBengtsson/listenv")
11466 (synopsis "Environments behaving (almost) as lists")
11468 "This package implements list environments. List environments are
11469 environments that have list-like properties. For instance, the elements of a
11470 list environment are ordered and can be accessed and iterated over using index
11472 (license license:lgpl2.1+)))
11474 (define-public r-globals
11481 (uri (cran-uri "globals" version))
11484 "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br"))))
11485 (build-system r-build-system)
11487 `(("r-codetools" ,r-codetools)))
11488 (home-page "https://github.com/HenrikBengtsson/globals")
11489 (synopsis "Identify global objects in R expressions")
11491 "This package provides tools to identify global (\"unknown\" or \"free\")
11492 objects in R expressions by code inspection using various strategies, e.g.
11493 conservative or liberal. The objective of this package is to make it as
11494 simple as possible to identify global objects for the purpose of exporting
11495 them in distributed compute environments.")
11496 (license license:lgpl2.1+)))
11498 (define-public r-future
11505 (uri (cran-uri "future" version))
11508 "101hi8warqa0py9l6c5p98f7i9xjhx01w655z6a35jx1dhspykzd"))))
11509 (build-system r-build-system)
11511 `(("r-digest" ,r-digest)
11512 ("r-globals" ,r-globals)
11513 ("r-listenv" ,r-listenv)))
11515 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11516 (home-page "https://github.com/HenrikBengtsson/future")
11517 (synopsis "Unified parallel and distributed processing in R")
11519 "The purpose of this package is to provide a lightweight and unified
11520 Future API for sequential and parallel processing of R expression via futures.
11521 This package implements sequential, multicore, multisession, and cluster
11522 futures. With these, R expressions can be evaluated on the local machine, in
11523 parallel a set of local machines, or distributed on a mix of local and remote
11524 machines. Extensions to this package implement additional backends for
11525 processing futures via compute cluster schedulers etc. Because of its unified
11526 API, there is no need to modify any code in order to switch from sequential on
11527 the local machine to, say, distributed processing on a remote compute cluster.")
11528 (license license:lgpl2.1+)))
11530 (define-public r-future-apply
11532 (name "r-future-apply")
11537 (uri (cran-uri "future.apply" version))
11540 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11541 (properties `((upstream-name . "future.apply")))
11542 (build-system r-build-system)
11544 `(("r-future" ,r-future)
11545 ("r-globals" ,r-globals)))
11547 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11548 (home-page "https://github.com/HenrikBengtsson/future.apply")
11549 (synopsis "Apply function to elements in parallel using futures")
11551 "This package provides implementations of @code{apply()},
11552 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11553 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11554 can be resolved using any future-supported backend, e.g. parallel on the local
11555 machine or distributed on a compute cluster.")
11556 (license license:gpl2+)))
11558 (define-public r-rsvd
11565 (uri (cran-uri "rsvd" version))
11568 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11569 (build-system r-build-system)
11571 `(("r-matrix" ,r-matrix)))
11572 (home-page "https://github.com/erichson/rSVD")
11573 (synopsis "Randomized singular value decomposition")
11575 "Low-rank matrix decompositions are fundamental tools and widely used for
11576 data analysis, dimension reduction, and data compression. Classically, highly
11577 accurate deterministic matrix algorithms are used for this task. However, the
11578 emergence of large-scale data has severely challenged our computational
11579 ability to analyze big data. The concept of randomness has been demonstrated
11580 as an effective strategy to quickly produce approximate answers to familiar
11581 problems such as the @dfn{singular value decomposition} (SVD). This package
11582 provides several randomized matrix algorithms such as the randomized singular
11583 value decomposition (@code{rsvd}), randomized principal component
11584 analysis (@code{rpca}), randomized robust principal component
11585 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11586 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11587 functions are provided.")
11588 (license license:gpl3+)))
11590 (define-public r-sloop
11597 (uri (cran-uri "sloop" version))
11600 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11601 (build-system r-build-system)
11603 `(("r-codetools" ,r-codetools)
11604 ("r-crayon" ,r-crayon)
11605 ("r-purrr" ,r-purrr)
11606 ("r-rlang" ,r-rlang)
11607 ("r-tibble" ,r-tibble)))
11608 (home-page "https://github.com/r-lib/sloop")
11609 (synopsis "Helpers for object-oriented programming in R")
11611 "This package provides a collection of helper functions designed to
11612 help you to better understand object oriented programming in R, particularly
11614 (license license:gpl3)))
11616 (define-public r-capushe
11623 (uri (cran-uri "capushe" version))
11626 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11627 (build-system r-build-system)
11628 (propagated-inputs `(("r-mass" ,r-mass)))
11629 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11630 (synopsis "Calibrating penalties using slope heuristics")
11632 "This package provides tools for the calibration of penalized criteria
11633 for model selection. The calibration methods available are based on the slope
11635 (license license:gpl2+)))
11637 (define-public r-dorng
11644 (uri (cran-uri "doRNG" version))
11647 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11648 (properties `((upstream-name . "doRNG")))
11649 (build-system r-build-system)
11651 `(("r-foreach" ,r-foreach)
11652 ("r-iterators" ,r-iterators)
11653 ("r-pkgmaker" ,r-pkgmaker)
11654 ("r-rngtools" ,r-rngtools)))
11655 (home-page "https://renozao.github.io/doRNG/")
11656 (synopsis "Generic reproducible parallel backend for foreach loops")
11658 "This package provides functions to perform reproducible parallel
11659 @code{foreach} loops, using independent random streams as generated by
11660 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11661 convert standard @code{%dopar%} loops into fully reproducible loops,
11662 independently of the number of workers, the task scheduling strategy, or the
11663 chosen parallel environment and associated foreach backend.")
11664 (license license:gpl2+)))
11666 (define-public r-blockmodeling
11668 (name "r-blockmodeling")
11673 (uri (cran-uri "blockmodeling" version))
11676 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11677 (build-system r-build-system)
11679 `(("r-doparallel" ,r-doparallel)
11680 ("r-dorng" ,r-dorng)
11681 ("r-foreach" ,r-foreach)
11682 ("r-matrix" ,r-matrix)))
11683 (native-inputs `(("gfortran" ,gfortran)))
11684 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11685 (synopsis "Generalized and classical blockmodeling of valued networks")
11687 "This package is primarily meant as an implementation of generalized
11688 blockmodeling for valued networks. In addition, measures of similarity or
11689 dissimilarity based on structural equivalence and regular equivalence (REGE
11690 algorithms) can be computed and partitioned matrices can be plotted.")
11691 (license license:gpl2+)))
11693 (define-public r-upsetr
11700 (uri (cran-uri "UpSetR" version))
11703 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11704 (properties `((upstream-name . "UpSetR")))
11705 (build-system r-build-system)
11707 `(("r-ggplot2" ,r-ggplot2)
11708 ("r-gridextra" ,r-gridextra)
11710 ("r-scales" ,r-scales)))
11711 (home-page "https://github.com/hms-dbmi/UpSetR")
11712 (synopsis "Visualize intersecting sets")
11714 "This package provides a more scalable alternative to Venn and Euler
11715 diagrams for visualizing intersecting sets. Create visualizations of
11716 intersecting sets using a novel matrix design, along with visualizations of
11717 several common set, element and attribute related tasks.")
11718 (license license:expat)))
11720 ;; This package includes a JavaScript file, which is not minified. When
11721 ;; upgrading please check that there are no new minified JavaScript files.
11722 (define-public r-shinybs
11729 (uri (cran-uri "shinyBS" version))
11732 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11733 (properties `((upstream-name . "shinyBS")))
11734 (build-system r-build-system)
11735 ;; The tests spawn Shiny browser apps. They cannot be run
11736 ;; non-interactively.
11737 (arguments '(#:tests? #f))
11739 `(("r-htmltools" ,r-htmltools)
11740 ("r-shiny" ,r-shiny)))
11741 (home-page "https://ebailey78.github.io/shinyBS/")
11742 (synopsis "Twitter Bootstrap components for Shiny")
11744 "This package adds additional Twitter Bootstrap components to Shiny.")
11745 (license license:gpl3)))
11747 (define-public r-outliers
11749 (name "r-outliers")
11754 (uri (cran-uri "outliers" version))
11757 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11758 (build-system r-build-system)
11759 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11760 (synopsis "Tests for outliers")
11762 "This package provides a collection of some tests commonly used for
11763 identifying outliers.")
11764 (license license:gpl2+)))
11766 (define-public r-bayesm
11773 (uri (cran-uri "bayesm" version))
11775 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11776 (build-system r-build-system)
11778 `(("r-rcpp" ,r-rcpp)
11779 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11780 (home-page "http://www.perossi.org/home/bsm-1")
11781 (synopsis "Bayesian inference for marketing/micro-econometrics")
11783 "This package covers many important models used in marketing and
11784 micro-econometrics applications, including Bayes Regression (univariate or
11785 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11786 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11787 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11788 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11789 Estimation with normal base, Hierarchical Linear Models with normal prior and
11790 covariates, Hierarchical Linear Models with a mixture of normals prior and
11791 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11792 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11793 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11794 analysis of choice-based conjoint data, Bayesian treatment of linear
11795 instrumental variables models, Analysis of Multivariate Ordinal survey data
11796 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11797 Coefficient Logit Models.")
11798 (license license:gpl2+)))
11800 (define-public r-tensora
11807 (uri (cran-uri "tensorA" version))
11810 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11811 (properties `((upstream-name . "tensorA")))
11812 (build-system r-build-system)
11813 (home-page "http://www.stat.boogaart.de/tensorA")
11814 (synopsis "Advanced tensor arithmetic with named indices")
11816 "This package provides convenience functions for advanced linear algebra
11817 with tensors and computation with datasets of tensors on a higher level
11818 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11819 co- and contravariate indices, and parallel computations on sequences of
11821 (license license:gpl2+)))
11823 (define-public r-rarpack
11830 (uri (cran-uri "rARPACK" version))
11833 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11834 (properties `((upstream-name . "rARPACK")))
11835 (build-system r-build-system)
11836 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11837 (home-page "https://github.com/yixuan/rARPACK")
11838 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11840 "This package was previously an R wrapper of the ARPACK library, and now
11841 a shell of the R package RSpectra, an R interface to the Spectra library for
11842 solving large scale eigenvalue/vector problems. The current version of
11843 rARPACK simply imports and exports the functions provided by RSpectra. New
11844 users of rARPACK are advised to switch to the RSpectra package.")
11845 (license license:bsd-3)))
11847 (define-public r-compositions
11849 (name "r-compositions")
11854 (uri (cran-uri "compositions" version))
11857 "103hbmibrf1n333pn4xpll1gqqsv4szms0n5gdq7zak31aar0bg4"))))
11858 (build-system r-build-system)
11860 `(("r-bayesm" ,r-bayesm)
11861 ("r-robustbase" ,r-robustbase)
11862 ("r-tensora" ,r-tensora)))
11863 (home-page "http://www.stat.boogaart.de/compositions")
11864 (synopsis "Compositional data analysis")
11866 "This package provides functions for the consistent analysis of
11867 compositional data (e.g. portions of substances) and positive
11868 numbers (e.g. concentrations).")
11869 (license license:gpl2+)))
11871 (define-public r-cobs
11878 (uri (cran-uri "cobs" version))
11881 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11882 (build-system r-build-system)
11884 `(("r-quantreg" ,r-quantreg)
11885 ("r-sparsem" ,r-sparsem)))
11886 (home-page "https://cran.r-project.org/web/packages/cobs")
11887 (synopsis "Constrained B-Splines (sparse matrix based)")
11889 "This package provides qualitatively constrained (regression) smoothing
11890 splines via linear programming and sparse matrices.")
11891 (license license:gpl2+)))
11893 (define-public r-drimpute
11895 (name "r-drimpute")
11900 (uri (cran-uri "DrImpute" version))
11903 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11904 (properties `((upstream-name . "DrImpute")))
11905 (build-system r-build-system)
11907 `(("r-rcpp" ,r-rcpp)
11908 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11909 (home-page "https://github.com/ikwak2/DrImpute")
11910 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11912 "This is an R package for imputing dropout events. Many statistical
11913 methods in cell type identification, visualization and lineage reconstruction
11914 do not account for dropout events. DrImpute can improve the performance of
11915 such software by imputing dropout events.")
11916 (license license:gpl3)))
11918 (define-public r-gamlss-dist
11920 (name "r-gamlss-dist")
11925 (uri (cran-uri "gamlss.dist" version))
11927 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
11928 (properties `((upstream-name . "gamlss.dist")))
11929 (build-system r-build-system)
11930 (propagated-inputs `(("r-mass" ,r-mass)))
11931 (home-page "http://www.gamlss.org/")
11932 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
11934 "This package provides a set of distributions which can be used for
11935 modelling the response variables in Generalized Additive Models for Location
11936 Scale and Shape. The distributions can be continuous, discrete or mixed
11937 distributions. Extra distributions can be created, by transforming, any
11938 continuous distribution defined on the real line, to a distribution defined on
11939 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
11940 transformation, respectively.")
11941 ;; Either version of the GPL.
11942 (license (list license:gpl2 license:gpl3))))
11944 ;; This package includes JavaScript files, which are not minified. When
11945 ;; upgrading please check that there are no new minified JavaScript files.
11946 (define-public r-shinyjs
11953 (uri (cran-uri "shinyjs" version))
11956 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
11957 (build-system r-build-system)
11959 `(("r-digest" ,r-digest)
11960 ("r-htmltools" ,r-htmltools)
11961 ("r-jsonlite" ,r-jsonlite)
11962 ("r-shiny" ,r-shiny)))
11963 (home-page "https://deanattali.com/shinyjs")
11964 (synopsis "Improve the user experience of your Shiny apps")
11966 "Perform common useful JavaScript operations in Shiny apps that will
11967 greatly improve your apps without having to know any JavaScript. Examples
11968 include: hiding an element, disabling an input, resetting an input back to its
11969 original value, delaying code execution by a few seconds, and many more useful
11970 functions for both the end user and the developer. Shinyjs can also be used
11971 to easily call your own custom JavaScript functions from R.")
11972 (license license:agpl3+)))
11974 ;; This package includes minified JavaScript files. When upgrading please
11975 ;; check that there are no new minified JavaScript files.
11976 (define-public r-colourpicker
11978 (name "r-colourpicker")
11983 (uri (cran-uri "colourpicker" version))
11986 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
11987 (build-system r-build-system)
11989 `(#:modules ((guix build utils)
11990 (guix build r-build-system)
11994 (modify-phases %standard-phases
11995 (add-after 'unpack 'process-javascript
11996 (lambda* (#:key inputs #:allow-other-keys)
11997 (with-directory-excursion "inst"
12001 `((,(assoc-ref inputs "js-salvattore")
12002 "examples/colourInput/www/salvattore.min.js")
12003 (,(assoc-ref inputs "js-jquery")
12004 "htmlwidgets/lib/jquery/jquery.min.js")
12005 ("www/shared/colourpicker/js/colourpicker.js"
12006 "www/shared/colourpicker/js/colourpicker.min.js"))))
12007 (lambda (sources targets)
12008 (for-each (lambda (source target)
12009 (format #t "Processing ~a --> ~a~%"
12011 (delete-file target)
12012 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12013 (call-with-output-file target
12015 (dump-port minified port)))))
12016 sources targets))))
12019 `(("r-ggplot2" ,r-ggplot2)
12020 ("r-htmltools" ,r-htmltools)
12021 ("r-htmlwidgets" ,r-htmlwidgets)
12022 ("r-jsonlite" ,r-jsonlite)
12023 ("r-miniui" ,r-miniui)
12024 ("r-shiny" ,r-shiny)
12025 ("r-shinyjs" ,r-shinyjs)))
12027 `(("uglify-js" ,uglify-js)
12031 (uri "https://code.jquery.com/jquery-3.3.1.js")
12034 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12038 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12041 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12042 (home-page "https://github.com/daattali/colourpicker")
12043 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12045 "This package provides a color picker that can be used as an input in
12046 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12047 custom color palettes, and many more options. A plot color helper tool is
12048 available as an RStudio Addin, which helps you pick colors to use in your
12049 plots. A more generic color picker RStudio Addin is also provided to let you
12050 select colors to use in your R code.")
12051 (license license:expat)))
12053 (define-public r-ggextra
12060 (uri (cran-uri "ggExtra" version))
12063 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12064 (properties `((upstream-name . "ggExtra")))
12065 (build-system r-build-system)
12067 `(("r-colourpicker" ,r-colourpicker)
12068 ("r-ggplot2" ,r-ggplot2)
12069 ("r-gtable" ,r-gtable)
12070 ("r-miniui" ,r-miniui)
12072 ("r-scales" ,r-scales)
12073 ("r-shiny" ,r-shiny)
12074 ("r-shinyjs" ,r-shinyjs)))
12075 (home-page "https://github.com/daattali/ggExtra")
12076 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12078 "This package is a collection of functions and layers to enhance ggplot2.
12079 The flagship function is @code{ggMarginal()}, which can be used to add
12080 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12081 (license license:expat)))
12083 (define-public r-minpack-lm
12085 (name "r-minpack-lm")
12090 (uri (cran-uri "minpack.lm" version))
12093 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12094 (properties `((upstream-name . "minpack.lm")))
12095 (build-system r-build-system)
12096 (native-inputs `(("gfortran" ,gfortran)))
12097 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12098 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12100 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12101 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12102 problems by a modification of the Levenberg-Marquardt algorithm, with support
12103 for lower and upper parameter bounds. The implementation can be used via
12104 @code{nls}-like calls using the @code{nlsLM} function.")
12105 (license license:gpl3)))
12107 (define-public r-moments
12114 (uri (cran-uri "moments" version))
12117 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12118 (build-system r-build-system)
12119 (home-page "https://cran.r-project.org/web/packages/moments")
12120 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12122 "This package provides functions to calculate: moments, Pearson's
12123 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12124 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12125 (license license:gpl2+)))
12127 (define-public r-msir
12134 (uri (cran-uri "msir" version))
12137 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12138 (build-system r-build-system)
12140 `(("r-mclust" ,r-mclust)))
12141 (home-page "https://cran.r-project.org/web/packages/msir")
12142 (synopsis "Model-based sliced inverse regression")
12144 "This is an R package for dimension reduction based on finite Gaussian
12145 mixture modeling of inverse regression.")
12146 (license license:gpl2+)))
12148 (define-public r-pbivnorm
12150 (name "r-pbivnorm")
12155 (uri (cran-uri "pbivnorm" version))
12158 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12159 (build-system r-build-system)
12160 (native-inputs `(("gfortran" ,gfortran)))
12161 (home-page "https://github.com/brentonk/pbivnorm")
12162 (synopsis "Vectorized bivariate normal CDF")
12164 "This package provides a vectorized R function for calculating
12165 probabilities from a standard bivariate normal CDF.")
12166 (license license:gpl2+)))
12168 (define-public r-lavaan
12175 (uri (cran-uri "lavaan" version))
12178 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12179 (build-system r-build-system)
12181 `(("r-mass" ,r-mass)
12182 ("r-mnormt" ,r-mnormt)
12183 ("r-numderiv" ,r-numderiv)
12184 ("r-pbivnorm" ,r-pbivnorm)))
12185 (home-page "http://lavaan.ugent.be")
12186 (synopsis "Latent variable analysis")
12188 "This package provides tools to fit a variety of latent variable models,
12189 including confirmatory factor analysis, structural equation modeling and
12190 latent growth curve models.")
12191 (license license:gpl2+)))
12193 (define-public r-nonnest2
12195 (name "r-nonnest2")
12200 (uri (cran-uri "nonnest2" version))
12203 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12204 (build-system r-build-system)
12206 `(("r-compquadform" ,r-compquadform)
12207 ("r-lavaan" ,r-lavaan)
12208 ("r-mvtnorm" ,r-mvtnorm)
12209 ("r-sandwich" ,r-sandwich)))
12210 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12211 (synopsis "Tests of non-nested models")
12213 "This package allows for testing of non-nested models. It includes tests
12214 of model distinguishability and of model fit that can be applied to both
12215 nested and non-nested models. The package also includes functionality to
12216 obtain confidence intervals associated with AIC and BIC.")
12217 ;; Either version of the GPL.
12218 (license (list license:gpl2 license:gpl3))))
12220 (define-public r-penalized
12222 (name "r-penalized")
12227 (uri (cran-uri "penalized" version))
12230 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12231 (build-system r-build-system)
12233 `(("r-rcpp" ,r-rcpp)
12234 ("r-rcpparmadillo" ,r-rcpparmadillo)
12235 ("r-survival" ,r-survival)))
12236 (home-page "https://cran.r-project.org/web/packages/penalized/")
12237 (synopsis "Penalized estimation in GLMs and in the Cox model")
12239 "This package provides tools for fitting possibly high dimensional
12240 penalized regression models. The penalty structure can be any combination of
12241 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12242 constraint on the regression coefficients. The supported regression models
12243 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12244 model. Cross-validation routines allow optimization of the tuning
12246 (license license:gpl2+)))
12248 (define-public r-zim
12255 (uri (cran-uri "ZIM" version))
12258 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12259 (properties `((upstream-name . "ZIM")))
12260 (build-system r-build-system)
12261 (propagated-inputs `(("r-mass" ,r-mass)))
12262 (home-page "https://github.com/biostatstudio/ZIM")
12263 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12265 "Analyze count time series with excess zeros. Two types of statistical
12266 models are supported: Markov regression and state-space models. They are also
12267 known as observation-driven and parameter-driven models respectively in the
12268 time series literature. The functions used for Markov regression or
12269 observation-driven models can also be used to fit ordinary regression models
12270 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12271 negative binomial (ZINB) assumption. The package also contains miscellaneous
12272 functions to compute density, distribution, quantile, and generate random
12273 numbers from ZIP and ZINB distributions.")
12274 (license license:gpl3)))
12276 (define-public r-nor1mix
12283 (uri (cran-uri "nor1mix" version))
12286 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12287 (build-system r-build-system)
12288 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12289 (synopsis "Normal (1-d) mixture models")
12291 "This package provides S3 classes and methods for one-dimensional normal
12292 mixture models, for, e.g., density estimation or clustering algorithms
12293 research and teaching; it provides the widely used Marron-Wand densities. It
12294 also provides tools for efficient random number generation and graphics.")
12295 (license license:gpl2+)))
12297 (define-public r-beanplot
12299 (name "r-beanplot")
12304 (uri (cran-uri "beanplot" version))
12307 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12308 (build-system r-build-system)
12309 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12310 (synopsis "Visualization via beanplots")
12312 "This package provides beanplots, an alternative to
12313 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12315 (license license:gpl2)))
12317 (define-public r-pbdzmq
12324 (uri (cran-uri "pbdZMQ" version))
12327 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12328 (properties `((upstream-name . "pbdZMQ")))
12329 (build-system r-build-system)
12331 `(("zeromq" ,zeromq)
12334 `(("pkg-config" ,pkg-config)))
12335 (home-page "https://pbdr.org/")
12336 (synopsis "R interface to ZeroMQ")
12338 "ZeroMQ is a well-known library for high-performance asynchronous
12339 messaging in scalable, distributed applications. This package provides high
12340 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12341 interactive client/server programming frameworks. A few wrapper functions
12342 compatible with @code{rzmq} are also provided.")
12343 (license license:gpl3)))
12345 (define-public r-repr
12352 (uri (cran-uri "repr" version))
12355 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
12356 (build-system r-build-system)
12358 `(("r-base64enc" ,r-base64enc)
12359 ("r-htmltools" ,r-htmltools)
12360 ("r-jsonlite" ,r-jsonlite)
12361 ("r-pillar" ,r-pillar)))
12362 (home-page "https://cran.r-project.org/web/packages/repr/")
12363 (synopsis "Serializable representations")
12365 "This package provides string and binary representations of objects for
12366 several formats and MIME types.")
12367 (license license:gpl3)))
12369 (define-public r-irdisplay
12371 (name "r-irdisplay")
12376 (uri (cran-uri "IRdisplay" version))
12379 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12380 (properties `((upstream-name . "IRdisplay")))
12381 (build-system r-build-system)
12383 `(("r-repr" ,r-repr)))
12384 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12385 (synopsis "Jupyter display machinery")
12387 "This package provides an interface to the rich display capabilities of
12388 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12389 running IRkernel session.")
12390 (license license:expat)))
12392 (define-public r-irkernel
12394 (name "r-irkernel")
12399 (uri (cran-uri "IRkernel" version))
12402 "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
12403 (properties `((upstream-name . "IRkernel")))
12404 (build-system r-build-system)
12407 (modify-phases %standard-phases
12408 (add-after 'install 'install-kernelspec
12409 (lambda* (#:key outputs #:allow-other-keys)
12410 (let ((out (assoc-ref outputs "out")))
12411 (setenv "HOME" "/tmp")
12412 (invoke "jupyter" "kernelspec" "install"
12415 (string-append out "/site-library/IRkernel/kernelspec"))
12418 `(("jupyter" ,jupyter)))
12420 `(("r-crayon" ,r-crayon)
12421 ("r-digest" ,r-digest)
12422 ("r-evaluate" ,r-evaluate)
12423 ("r-irdisplay" ,r-irdisplay)
12424 ("r-jsonlite" ,r-jsonlite)
12425 ("r-pbdzmq" ,r-pbdzmq)
12427 ("r-uuid" ,r-uuid)))
12428 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12429 (synopsis "Native R kernel for Jupyter")
12431 "The R kernel for the Jupyter environment executes R code which the
12432 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12434 (license license:expat)))
12436 (define-public r-gmodels
12443 (uri (cran-uri "gmodels" version))
12446 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12447 (build-system r-build-system)
12449 `(("r-gdata" ,r-gdata)
12450 ("r-mass" ,r-mass)))
12451 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12452 (synopsis "Various R programming tools for model fitting")
12454 "This package provides various R programming tools for model fitting.")
12455 (license license:gpl2)))
12457 (define-public r-apcluster
12459 (name "r-apcluster")
12464 (uri (cran-uri "apcluster" version))
12467 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12468 (build-system r-build-system)
12470 `(("r-matrix" ,r-matrix)
12471 ("r-rcpp" ,r-rcpp)))
12472 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12473 (synopsis "Affinity propagation clustering")
12475 "This package implements affinity propagation clustering introduced by
12476 Frey and Dueck (2007). The package further provides leveraged affinity
12477 propagation and an algorithm for exemplar-based agglomerative clustering that
12478 can also be used to join clusters obtained from affinity propagation. Various
12479 plotting functions are available for analyzing clustering results.")
12480 (license license:gpl2+)))
12482 (define-public r-valr
12489 (uri (cran-uri "valr" version))
12492 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12493 (build-system r-build-system)
12495 `(("r-broom" ,r-broom)
12496 ("r-dplyr" ,r-dplyr)
12497 ("r-ggplot2" ,r-ggplot2)
12499 ("r-readr" ,r-readr)
12500 ("r-rlang" ,r-rlang)
12501 ("r-stringr" ,r-stringr)
12502 ("r-tibble" ,r-tibble)))
12503 (home-page "http://github.com/rnabioco/valr")
12504 (synopsis "Genome interval arithmetic in R")
12506 "This package enables you to read and manipulate genome intervals and
12507 signals. It provides functionality similar to command-line tool suites within
12508 R, enabling interactive analysis and visualization of genome-scale data.")
12509 (license license:expat)))
12511 (define-public r-rematch2
12513 (name "r-rematch2")
12518 (uri (cran-uri "rematch2" version))
12521 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12522 (build-system r-build-system)
12524 `(("r-tibble" ,r-tibble)))
12525 (home-page "https://github.com/r-lib/rematch2")
12526 (synopsis "Tidy output from regular expression matching")
12528 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12529 return the match results in tidy data frames.")
12530 (license license:expat)))
12532 (define-public r-picante
12539 (uri (cran-uri "picante" version))
12542 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12543 (build-system r-build-system)
12547 ("r-vegan" ,r-vegan)))
12548 (home-page "https://cran.r-project.org/web/packages/picante/")
12549 (synopsis "Integrating phylogenies and ecology")
12551 "This package provides functions for phylocom integration, community
12552 analyses, null-models, traits and evolution. It implements numerous
12553 ecophylogenetic approaches including measures of community phylogenetic and
12554 trait diversity, phylogenetic signal, estimation of trait values for
12555 unobserved taxa, null models for community and phylogeny randomizations, and
12556 utility functions for data input/output and phylogeny plotting. A full
12557 description of package functionality and methods are provided by Kembel et
12559 (license license:gpl2)))
12561 (define-public r-reinforcelearn
12563 (name "r-reinforcelearn")
12568 (uri (cran-uri "reinforcelearn" version))
12571 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12572 (build-system r-build-system)
12574 `(("r-checkmate" ,r-checkmate)
12576 ("r-purrr" ,r-purrr)
12578 (home-page "https://markusdumke.github.io/reinforcelearn")
12579 (synopsis "Reinforcement learning")
12581 "This package implements reinforcement learning environments and
12582 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12583 can be used with function approximation, eligibility traces (Singh & Sutton,
12584 1996) and experience replay (Mnih et al., 2013).")
12585 (license license:expat)))
12587 (define-public r-lemon
12594 (uri (cran-uri "lemon" version))
12597 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12598 (build-system r-build-system)
12600 `(("r-ggplot2" ,r-ggplot2)
12601 ("r-gridextra" ,r-gridextra)
12602 ("r-gtable" ,r-gtable)
12603 ("r-knitr" ,r-knitr)
12604 ("r-lattice" ,r-lattice)
12606 ("r-scales" ,r-scales)))
12607 (home-page "https://github.com/stefanedwards/lemon")
12608 (synopsis "Freshen up your ggplot2 plots")
12610 "This package provides functions for working with legends and axis lines
12611 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12613 (license license:gpl3)))
12615 (define-public r-wgaim
12622 (uri (cran-uri "wgaim" version))
12624 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12625 (build-system r-build-system)
12627 `(("r-ggplot2" ,r-ggplot2)
12629 (home-page "https://cran.r-project.org/web/packages/wgaim")
12630 (synopsis "Whole genome average interval mapping for QTL detection")
12632 "This package integrates sophisticated mixed modelling methods with a
12633 whole genome approach to detecting significant QTL in linkage maps.")
12634 (license license:gpl2+)))
12636 (define-public r-bedr
12643 (uri (cran-uri "bedr" version))
12646 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12647 (build-system r-build-system)
12649 `(("r-data-table" ,r-data-table)
12650 ("r-r-utils" ,r-r-utils)
12651 ("r-testthat" ,r-testthat)
12652 ("r-venndiagram" ,r-venndiagram)
12655 ("bedtools" ,bedtools)
12656 ("htslib" ,htslib))) ; for tabix
12658 `(("r-knitr" ,r-knitr))) ; for vignettes
12659 (home-page "https://cran.r-project.org/web/packages/bedr")
12660 (synopsis "Genomic region processing")
12662 "This package is for genomic regions processing using command line tools
12663 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12664 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12665 The bedr package's API enhances access to these tools as well as offers
12666 additional utilities for genomic regions processing.")
12667 (license license:gpl2)))
12669 (define-public r-sets
12676 (uri (cran-uri "sets" version))
12679 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
12680 (properties `((upstream-name . "sets")))
12681 (build-system r-build-system)
12682 (home-page "https://cran.r-project.org/web/packages/sets")
12683 (synopsis "Sets, generalized sets, customizable sets and intervals")
12685 "This package provides data structures and basic operations for ordinary
12686 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
12687 customizable sets, and intervals.")
12688 (license license:gpl2)))
12690 (define-public r-partitions
12692 (name "r-partitions")
12697 (uri (cran-uri "partitions" version))
12700 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
12701 (build-system r-build-system)
12704 ("r-polynom" ,r-polynom)
12705 ("r-sets" ,r-sets)))
12706 (home-page "https://cran.r-project.org/web/packages/partitions")
12707 (synopsis "Additive partitions of integers")
12709 "This package provides tools to enumerates the partitions, unequal
12710 partitions, and restricted partitions of an integer; the three corresponding
12711 partition functions are also given.")
12712 ;; Any version of the GPL
12713 (license license:gpl2+)))
12715 (define-public r-brobdingnag
12717 (name "r-brobdingnag")
12722 (uri (cran-uri "Brobdingnag" version))
12725 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12726 (properties `((upstream-name . "Brobdingnag")))
12727 (build-system r-build-system)
12728 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12729 (synopsis "Very large numbers in R")
12731 "This package handles very large numbers in R. Real numbers are held
12732 using their natural logarithms, plus a logical flag indicating sign. The
12733 package includes a vignette that gives a step-by-step introduction to using S4
12735 ;; Any version of the GPL
12736 (license license:gpl2+)))
12738 (define-public r-untb
12745 (uri (cran-uri "untb" version))
12748 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12749 (build-system r-build-system)
12751 `(("r-brobdingnag" ,r-brobdingnag)
12752 ("r-partitions" ,r-partitions)
12753 ("r-polynom" ,r-polynom)))
12754 (home-page "https://github.com/RobinHankin/untb.git")
12755 (synopsis "Ecological drift under the UNTB")
12757 "This package provides numerical simulations, and visualizations, of
12758 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12759 (license license:gpl2+)))
12761 (define-public r-stepwise
12763 (name "r-stepwise")
12768 (uri (cran-uri "stepwise" version))
12771 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12772 (build-system r-build-system)
12773 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12774 (synopsis "Stepwise detection of recombination breakpoints")
12776 "This package provides a stepwise approach to identifying recombination
12777 breakpoints in a genomic sequence alignment.")
12778 (license license:gpl2+)))
12780 (define-public r-snpmaxsel
12782 (name "r-snpmaxsel")
12787 (uri (cran-uri "SNPmaxsel" version))
12790 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12791 (properties `((upstream-name . "SNPmaxsel")))
12792 (build-system r-build-system)
12794 `(("r-combinat" ,r-combinat)
12795 ("r-mvtnorm" ,r-mvtnorm)))
12796 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12797 (synopsis "Maximally selected statistics for SNP data")
12799 "This package implements asymptotic methods related to maximally selected
12800 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12802 (license license:gpl2+)))
12804 (define-public r-acsnminer
12806 (name "r-acsnminer")
12807 (version "0.16.8.25")
12810 (uri (cran-uri "ACSNMineR" version))
12813 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12814 (properties `((upstream-name . "ACSNMineR")))
12815 (build-system r-build-system)
12817 `(("r-ggplot2" ,r-ggplot2)
12818 ("r-gridextra" ,r-gridextra)))
12819 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12820 (synopsis "Gene enrichment analysis")
12822 "This package provides tools to compute and represent gene set enrichment
12823 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12824 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12825 enrichment can be run with hypergeometric test or Fisher exact test, and can
12826 use multiple corrections. Visualization of data can be done either by
12827 barplots or heatmaps.")
12828 (license license:gpl2+)))
12830 (define-public r-seqinr
12837 (uri (cran-uri "seqinr" version))
12840 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12841 (build-system r-build-system)
12843 `(("r-ade4" ,r-ade4)
12844 ("r-segmented" ,r-segmented)))
12847 (home-page "http://seqinr.r-forge.r-project.org/")
12848 (synopsis "Biological sequences retrieval and analysis")
12850 "This package provides tools for exploratory data analysis and data
12851 visualization of biological sequence (DNA and protein) data. It also includes
12852 utilities for sequence data management under the ACNUC system.")
12853 (license license:gpl2+)))
12855 (define-public r-units
12862 (uri (cran-uri "units" version))
12865 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
12866 (build-system r-build-system)
12868 `(("udunits" ,udunits)))
12870 `(("r-rcpp" ,r-rcpp)))
12871 (home-page "https://github.com/r-quantities/units/")
12872 (synopsis "Measurement Units for R Vectors")
12874 "This package provides support for measurement units in R vectors,
12875 matrices and arrays: automatic propagation, conversion, derivation and
12876 simplification of units; raising errors in case of unit incompatibility. It
12877 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12879 (license license:gpl2)))
12881 (define-public r-classint
12883 (name "r-classint")
12888 (uri (cran-uri "classInt" version))
12891 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
12892 (properties `((upstream-name . "classInt")))
12893 (build-system r-build-system)
12895 `(("r-class" ,r-class)
12896 ("r-e1071" ,r-e1071)
12897 ("r-kernsmooth" ,r-kernsmooth)))
12898 (native-inputs `(("gfortran" ,gfortran)))
12899 (home-page "https://github.com/r-spatial/classInt/")
12900 (synopsis "Choose univariate class intervals")
12902 "This package provides selected commonly used methods for choosing
12903 univariate class intervals for mapping or other graphics purposes.")
12904 (license license:gpl2+)))
12906 (define-public r-spdata
12913 (uri (cran-uri "spData" version))
12916 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
12917 (properties `((upstream-name . "spData")))
12918 (build-system r-build-system)
12919 (home-page "https://github.com/Nowosad/spData")
12920 (synopsis "Datasets for spatial analysis")
12922 "This a package containing diverse spatial datasets for demonstrating,
12923 benchmarking and teaching spatial data analysis. It includes R data of class
12924 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
12925 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
12926 of the datasets are designed to illustrate specific analysis techniques.
12927 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
12928 illustrate point pattern analysis techniques.")
12929 (license license:cc0)))
12931 (define-public r-learnbayes
12933 (name "r-learnbayes")
12938 (uri (cran-uri "LearnBayes" version))
12941 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
12942 (properties `((upstream-name . "LearnBayes")))
12943 (build-system r-build-system)
12944 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
12945 (synopsis "Functions for learning Bayesian inference")
12947 "This package provides a collection of functions helpful in learning the
12948 basic tenets of Bayesian statistical inference. It contains functions for
12949 summarizing basic one and two parameter posterior distributions and predictive
12950 distributions. It contains MCMC algorithms for summarizing posterior
12951 distributions defined by the user. It also contains functions for regression
12952 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
12954 (license license:gpl2+)))
12956 (define-public r-deldir
12963 (uri (cran-uri "deldir" version))
12966 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
12967 (build-system r-build-system)
12968 (native-inputs `(("gfortran" ,gfortran)))
12969 (home-page "https://cran.r-project.org/web/packages/deldir")
12970 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
12972 "This package provides tools for calculating the Delaunay triangulation
12973 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
12974 of a planar point set. It plots triangulations and tessellations in various
12975 ways, clips tessellations to sub-windows, calculates perimeters of
12976 tessellations, and summarizes information about the tiles of the
12978 (license license:gpl2+)))
12980 (define-public r-sf
12987 (uri (cran-uri "sf" version))
12990 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
12991 (build-system r-build-system)
12998 `(("r-classint" ,r-classint)
13000 ("r-magrittr" ,r-magrittr)
13002 ("r-units" ,r-units)))
13003 (native-inputs `(("pkg-config" ,pkg-config)))
13004 (home-page "https://github.com/r-spatial/sf/")
13005 (synopsis "Simple features for R")
13007 "This package provides support for simple features, a standardized way to
13008 encode spatial vector data. It binds to GDAL for reading and writing data, to
13009 GEOS for geometrical operations, and to PROJ for projection conversions and
13010 datum transformations.")
13011 ;; Either of these licenses
13012 (license (list license:gpl2 license:expat))))
13014 (define-public r-spdep
13021 (uri (cran-uri "spdep" version))
13024 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13025 (build-system r-build-system)
13027 `(("r-boot" ,r-boot)
13029 ("r-deldir" ,r-deldir)
13031 ("r-gmodels" ,r-gmodels)
13032 ("r-learnbayes" ,r-learnbayes)
13034 ("r-matrix" ,r-matrix)
13038 ("r-spdata" ,r-spdata)))
13039 (home-page "https://github.com/r-spatial/spdep/")
13040 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13042 "This package provides a collection of functions to create spatial
13043 weights matrix objects from polygon contiguities, from point patterns by
13044 distance and tessellations, for summarizing these objects, and for permitting
13045 their use in spatial data analysis, including regional aggregation by minimum
13047 (license license:gpl2+)))
13049 (define-public r-adegenet
13051 (name "r-adegenet")
13056 (uri (cran-uri "adegenet" version))
13059 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
13060 (build-system r-build-system)
13062 `(("r-ade4" ,r-ade4)
13065 ("r-dplyr" ,r-dplyr)
13066 ("r-ggplot2" ,r-ggplot2)
13067 ("r-igraph" ,r-igraph)
13069 ("r-reshape2" ,r-reshape2)
13070 ("r-seqinr" ,r-seqinr)
13071 ("r-shiny" ,r-shiny)
13072 ("r-spdep" ,r-spdep)
13073 ("r-vegan" ,r-vegan)))
13074 (home-page "https://github.com/thibautjombart/adegenet")
13075 (synopsis "Exploratory analysis of genetic and genomic data")
13077 "This package provides a toolset for the exploration of genetic and
13078 genomic data. Adegenet provides formal (S4) classes for storing and handling
13079 various genetic data, including genetic markers with varying ploidy and
13080 hierarchical population structure (@code{genind} class), alleles counts by
13081 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13082 also implements original multivariate methods (DAPC, sPCA), graphics,
13083 statistical tests, simulation tools, distance and similarity measures, and
13084 several spatial methods. A range of both empirical and simulated datasets is
13085 also provided to illustrate various methods.")
13086 (license license:gpl2+)))
13088 (define-public r-pegas
13095 (uri (cran-uri "pegas" version))
13097 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
13098 (build-system r-build-system)
13100 `(("r-adegenet" ,r-adegenet)
13102 (home-page "http://ape-package.ird.fr/pegas.html")
13103 (synopsis "Population and evolutionary genetics analysis system")
13105 "This package provides functions for reading, writing, plotting,
13106 analysing, and manipulating allelic and haplotypic data, including from VCF
13107 files, and for the analysis of population nucleotide sequences and
13108 micro-satellites including coalescent analyses, linkage disequilibrium,
13109 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13110 minimum spanning tree and network, and median-joining networks.")
13111 (license license:gpl2+)))
13113 (define-public r-rmetasim
13115 (name "r-rmetasim")
13120 (uri (cran-uri "rmetasim" version))
13123 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
13124 (build-system r-build-system)
13126 `(("r-ade4" ,r-ade4)
13127 ("r-adegenet" ,r-adegenet)
13128 ("r-gtools" ,r-gtools)
13129 ("r-pegas" ,r-pegas)))
13130 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13131 (synopsis "Individual-based population genetic simulation environment")
13133 "This package provides an interface between R and the metasim simulation
13134 engine. The simulation environment is documented in: Strand, A.(2002),
13135 Metasim 1.0: an individual-based environment for simulating population
13136 genetics of complex population dynamics.")
13138 (license license:gpl2+)))
13140 (define-public r-genetics
13142 (name "r-genetics")
13143 (version "1.3.8.1.2")
13147 (uri (cran-uri "genetics" version))
13150 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13151 (build-system r-build-system)
13153 `(("r-combinat" ,r-combinat)
13154 ("r-gdata" ,r-gdata)
13155 ("r-gtools" ,r-gtools)
13157 ("r-mvtnorm" ,r-mvtnorm)))
13158 (home-page "https://cran.r-project.org/web/packages/genetics/")
13159 (synopsis "Population genetics")
13161 "This package provides classes and methods for handling genetic data.
13162 It includes classes to represent genotypes and haplotypes at single markers up
13163 to multiple markers on multiple chromosomes. Function include allele
13164 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13165 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13166 and testing for linkage disequilibrium, ...")
13167 ;; Any GPL version.
13168 (license license:gpl2+)))
13170 (define-public r-snp-plotter
13172 (name "r-snp-plotter")
13177 (uri (cran-uri "snp.plotter" version))
13180 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13181 (properties `((upstream-name . "snp.plotter")))
13182 (build-system r-build-system)
13183 (propagated-inputs `(("r-genetics" ,r-genetics)))
13184 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13185 (synopsis "Plot p-values using single SNP and/or haplotype data")
13187 "This package helps you create plots of p-values using single SNP and/or
13188 haplotype data. Main features of the package include options to display a
13189 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13190 datasets simultaneously. Plots can be created using global and/or individual
13191 haplotype p-values along with single SNP p-values. Images are created as
13192 either PDF/EPS files.")
13193 (license license:gpl2+)))
13195 (define-public r-polspline
13197 (name "r-polspline")
13202 (uri (cran-uri "polspline" version))
13204 (base32 "0c7fnxpqpy3hibiim4yib6l6bq363s97wwvllxp4lp8h06fjcyyn"))))
13205 (build-system r-build-system)
13206 (native-inputs `(("gfortran" ,gfortran)))
13207 (home-page "https://cran.r-project.org/web/packages/polspline/")
13208 (synopsis "Polynomial spline routines")
13210 "This package provides routines for the polynomial spline fitting
13211 routines hazard regression, hazard estimation with flexible tails, logspline,
13212 lspec, polyclass, and polymars.")
13213 (license license:gpl2+)))
13215 (define-public r-rms
13222 (uri (cran-uri "rms" version))
13224 (base32 "19knh1sw0icw6jh9wfb2hq5jf49i2qfvp9myvqm5paa495689x9q"))))
13225 (build-system r-build-system)
13227 `(("r-ggplot2" ,r-ggplot2)
13228 ("r-hmisc" ,r-hmisc)
13229 ("r-htmltable" ,r-htmltable)
13230 ("r-htmltools" ,r-htmltools)
13231 ("r-lattice" ,r-lattice)
13232 ("r-multcomp" ,r-multcomp)
13234 ("r-polspline" ,r-polspline)
13235 ("r-quantreg" ,r-quantreg)
13236 ("r-rpart" ,r-rpart)
13237 ("r-sparsem" ,r-sparsem)
13238 ("r-survival" ,r-survival)))
13239 (native-inputs `(("gfortran" ,gfortran)))
13240 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13241 (synopsis "Regression modeling strategies")
13243 "This is a package for regression modeling, testing, estimation,
13244 validation, graphics, prediction, and typesetting by storing enhanced model
13245 design attributes in the fit. The rms package is a collection of functions
13246 that assist with and streamline modeling. It also contains functions for
13247 binary and ordinal logistic regression models, ordinal models for continuous Y
13248 with a variety of distribution families, and the Buckley-James multiple
13249 regression model for right-censored responses, and implements penalized
13250 maximum likelihood estimation for logistic and ordinary linear models. The
13251 package works with almost any regression model, but it was especially written
13252 to work with binary or ordinal regression models, Cox regression, accelerated
13253 failure time models, ordinary linear models, the Buckley-James model,
13254 generalized least squares for serially or spatially correlated observations,
13255 generalized linear models, and quantile regression.")
13256 (license license:gpl2+)))
13258 (define-public r-haplo-stats
13260 (name "r-haplo-stats")
13265 (uri (cran-uri "haplo.stats" version))
13268 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13269 (properties `((upstream-name . "haplo.stats")))
13270 (build-system r-build-system)
13272 `(("r-rms" ,r-rms)))
13274 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13275 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13276 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13278 "This package provides routines for the analysis of indirectly measured
13279 haplotypes. The statistical methods assume that all subjects are unrelated
13280 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13281 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13282 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13283 examples in the vignette.")
13284 (license license:gpl2+)))
13286 (define-public r-bqtl
13293 (uri (cran-uri "bqtl" version))
13296 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13297 (build-system r-build-system)
13298 (native-inputs `(("gfortran" ,gfortran)))
13299 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13300 (synopsis "Bayesian QTL mapping toolkit")
13302 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13303 lines. It includes maximum likelihood and Bayesian tools.")
13304 (license license:gpl2+)))
13306 (define-public r-ibdreg
13313 (uri (cran-uri "ibdreg" version))
13316 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13317 (build-system r-build-system)
13318 (home-page "https://www.mayo.edu/research/labs/\
13319 statistical-genetics-genetic-epidemiology/software")
13320 (synopsis "Regression methods for IBD linkage with covariates")
13322 "This package provides a method to test genetic linkage with covariates
13323 by regression methods with response IBD sharing for relative pairs. Account
13324 for correlations of IBD statistics and covariates for relative pairs within
13325 the same pedigree.")
13326 (license license:gpl2+)))
13328 (define-public r-dlmap
13335 (uri (cran-uri "dlmap" version))
13338 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13339 (build-system r-build-system)
13341 `(("r-ibdreg" ,r-ibdreg)
13345 ("r-wgaim" ,r-wgaim)))
13346 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13347 (synopsis "Detection localization mapping for QTL")
13349 "This is package for QTL mapping in a mixed model framework with separate
13350 detection and localization stages. The first stage detects the number of QTL
13351 on each chromosome based on the genetic variation due to grouped markers on
13352 the chromosome; the second stage uses this information to determine the most
13353 likely QTL positions. The mixed model can accommodate general fixed and
13354 random effects, including spatial effects in field trials and pedigree
13355 effects. It is applicable to backcrosses, doubled haploids, recombinant
13356 inbred lines, F2 intercrosses, and association mapping populations.")
13357 (license license:gpl2)))
13359 (define-public r-ldheatmap
13361 (name "r-ldheatmap")
13366 (uri (cran-uri "LDheatmap" version))
13369 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13370 (properties `((upstream-name . "LDheatmap")))
13371 (build-system r-build-system)
13373 `(("r-genetics" ,r-genetics)
13375 ("r-snpstats" ,r-snpstats)))
13376 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13377 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13379 "This package provides tools to produce a graphical display, as a heat
13380 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13381 optionally include the physical locations or genetic map distances of each SNP
13383 (license license:gpl3)))
13385 (define-public r-hwde
13392 (uri (cran-uri "hwde" version))
13395 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13396 (build-system r-build-system)
13397 (home-page "https://cran.r-project.org/web/packages/hwde/")
13398 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13400 "This package fits models for genotypic disequilibria, as described in
13401 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13402 terms are available that account for first order interactions between loci.
13403 It also implements, for a single locus in a single population, a conditional
13404 exact test for Hardy-Weinberg equilibrium.")
13405 (license license:gpl2+)))
13407 (define-public r-tdthap
13414 (uri (cran-uri "tdthap" version))
13417 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13418 (build-system r-build-system)
13419 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13420 (synopsis "TDT tests for extended haplotypes")
13422 "Functions and examples are provided for transmission/disequilibrium
13423 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13424 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13425 (license license:artistic2.0)))
13427 (define-public r-sparql
13433 (uri (cran-uri "SPARQL" version))
13436 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13437 (properties `((upstream-name . "SPARQL")))
13438 (build-system r-build-system)
13440 `(("r-rcurl" ,r-rcurl)
13442 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13443 (synopsis "SPARQL client for R")
13444 (description "This package provides an interface to use SPARQL to pose
13445 SELECT or UPDATE queries to an end-point.")
13446 ;; The only license indication is found in the DESCRIPTION file,
13447 ;; which states GPL-3. So we cannot assume GPLv3+.
13448 (license license:gpl3)))
13450 (define-public r-bookdown
13452 (name "r-bookdown")
13456 (uri (cran-uri "bookdown" version))
13459 "1gwgvx1yg6q3wccnhidr3gshdvlgr42i4pvlg4h29kpsa7smjiv1"))))
13460 (build-system r-build-system)
13462 `(("r-htmltools" ,r-htmltools)
13463 ("r-knitr" ,r-knitr)
13464 ("r-rmarkdown" ,r-rmarkdown)
13465 ("r-tinytex" ,r-tinytex)
13467 ("pandoc" ,ghc-pandoc)))
13468 (home-page "https://github.com/rstudio/bookdown")
13469 (synopsis "Authoring books and technical documents with R markdown")
13470 (description "This package provides output formats and utilities for
13471 authoring books and technical documents with R Markdown.")
13472 (license license:gpl3)))
13474 (define-public r-optparse
13476 (name "r-optparse")
13481 (uri (cran-uri "optparse" version))
13484 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13485 (build-system r-build-system)
13487 `(("r-getopt" ,r-getopt)))
13488 (home-page "https://github.com/trevorld/optparse")
13489 (synopsis "Command line option parser")
13491 "This package provides a command line parser inspired by Python's
13492 @code{optparse} library to be used with Rscript to write shebang scripts
13493 that accept short and long options.")
13494 (license license:gpl2+)))
13496 (define-public r-wgcna
13503 (uri (cran-uri "WGCNA" version))
13506 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13507 (properties `((upstream-name . "WGCNA")))
13508 (build-system r-build-system)
13510 `(("r-annotationdbi" ,r-annotationdbi)
13511 ("r-doparallel" ,r-doparallel)
13512 ("r-dynamictreecut" ,r-dynamictreecut)
13513 ("r-fastcluster" ,r-fastcluster)
13514 ("r-foreach" ,r-foreach)
13515 ("r-go-db" ,r-go-db)
13516 ("r-hmisc" ,r-hmisc)
13517 ("r-impute" ,r-impute)
13519 ("r-robust" ,r-robust)
13520 ("r-survival" ,r-survival)
13521 ("r-matrixstats" ,r-matrixstats)
13522 ("r-preprocesscore" ,r-preprocesscore)))
13524 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13525 (synopsis "Weighted correlation network analysis")
13527 "This package provides functions necessary to perform Weighted
13528 Correlation Network Analysis on high-dimensional data. It includes functions
13529 for rudimentary data cleaning, construction and summarization of correlation
13530 networks, module identification and functions for relating both variables and
13531 modules to sample traits. It also includes a number of utility functions for
13532 data manipulation and visualization.")
13533 (license license:gpl2+)))
13535 (define-public r-kernlab
13542 (uri (cran-uri "kernlab" version))
13544 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
13545 (build-system r-build-system)
13546 (home-page "https://cran.r-project.org/web/packages/kernlab")
13547 (synopsis "Kernel-based machine learning tools")
13549 "This package provides kernel-based machine learning methods for
13550 classification, regression, clustering, novelty detection, quantile regression
13551 and dimensionality reduction. Among other methods @code{kernlab} includes
13552 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13554 (license license:gpl2)))
13556 (define-public r-hierfstat
13558 (name "r-hierfstat")
13559 (version "0.04-22")
13563 (uri (cran-uri "hierfstat" version))
13566 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13567 (build-system r-build-system)
13569 `(("r-ade4" ,r-ade4)
13570 ("r-adegenet" ,r-adegenet)
13571 ("r-gtools" ,r-gtools)))
13572 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13573 (synopsis "Estimation and tests of hierarchical F-statistics")
13575 "This package allows the estimation of hierarchical F-statistics from
13576 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13577 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13578 are also given to test via randomisations the significance of each F and
13579 variance components, using the likelihood-ratio statistics G.")
13580 (license license:gpl2+)))
13582 (define-public r-hapassoc
13584 (name "r-hapassoc")
13589 (uri (cran-uri "hapassoc" version))
13592 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13593 (build-system r-build-system)
13594 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13595 (synopsis "Inference of trait associations with SNP haplotypes")
13597 "Hapassoc performs likelihood inference of trait associations with
13598 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13599 functions are developed primarily for data collected in cohort or
13600 cross-sectional studies. They can accommodate uncertain haplotype phase and
13601 handle missing genotypes at some SNPs.")
13602 (license license:gpl2)))
13604 (define-public r-sampling
13606 (name "r-sampling")
13611 (uri (cran-uri "sampling" version))
13614 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13615 (build-system r-build-system)
13617 `(("r-lpsolve" ,r-lpsolve)
13618 ("r-mass" ,r-mass)))
13619 (home-page "https://cran.r-project.org/web/packages/sampling/")
13620 (synopsis "Survey sampling")
13622 "This package provides functions for drawing and calibrating samples.")
13623 (license license:gpl2+)))
13625 (define-public r-r2html
13632 (uri (cran-uri "R2HTML" version))
13635 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13636 (properties `((upstream-name . "R2HTML")))
13637 (build-system r-build-system)
13638 (home-page "https://github.com/nalimilan/R2HTML")
13639 (synopsis "HTML export for R objects")
13641 "This package includes HTML functions and methods to write in an HTML
13642 file. Thus, making HTML reports is easy. It includes a function that allows
13643 redirection on the fly, which appears to be very useful for teaching purposes,
13644 as the student can keep a copy of the produced output to keep all that they
13645 did during the course. The package comes with a vignette describing how to
13646 write HTML reports for statistical analysis. Finally, a driver for Sweave
13647 allows to parse HTML flat files containing R code and to automatically write
13648 the corresponding outputs (tables and graphs).")
13649 (license license:gpl2+)))
13651 (define-public r-rjava
13658 (uri (cran-uri "rJava" version))
13661 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13662 (properties `((upstream-name . "rJava")))
13663 (build-system r-build-system)
13665 `(#:modules ((guix build utils)
13666 (guix build r-build-system)
13669 (modify-phases %standard-phases
13670 (add-after 'unpack 'set-JAVA_HOME
13671 (lambda* (#:key inputs #:allow-other-keys)
13672 (let ((jdk (assoc-ref inputs "jdk")))
13673 (setenv "JAVA_HOME" jdk)
13674 (setenv "JAVA" (which "java"))
13675 (setenv "JAR" (which "jar"))
13676 (setenv "JAVAC" (which "javac"))
13677 (setenv "JAVAH" (which "javah"))
13678 (setenv "JAVA_CPPFLAGS"
13679 (string-append "-I" jdk "/include "
13680 "-I" jdk "/include/linux"))
13681 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13682 ((lib) (setenv "JAVA_LIBS" lib))
13683 (_ (error "Could not find libjvm.so"))))
13687 ("jdk" ,icedtea-8 "jdk")
13690 (home-page "http://www.rforge.net/rJava/")
13691 (synopsis "Low-Level R to Java interface")
13693 "This package provides a low-level interface to the Java VM very much
13694 like .C/.Call and friends. It allows the creation of objects, calling methods
13695 and accessing fields.")
13696 (license license:gpl2)))
13698 (define-public r-svmisc
13705 (uri (cran-uri "svMisc" version))
13708 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13709 (properties `((upstream-name . "svMisc")))
13710 (build-system r-build-system)
13711 (home-page "https://github.com/SciViews/svMisc")
13712 (synopsis "Miscellaneous functions for SciViews")
13714 "This package provides miscellaneous functions for SciViews or general
13715 use, including tools to manage a temporary environment attached to the search
13716 path for temporary variables you do not want to @code{save()} or
13717 @code{load()}; test the current platform; showing progress bars, etc.")
13718 (license license:gpl2)))
13720 (define-public r-xyz
13727 (uri (cran-uri "xyz" version))
13730 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13731 (build-system r-build-system)
13733 `(("r-rcpp" ,r-rcpp)))
13734 (home-page "https://cran.r-project.org/web/packages/xyz/")
13735 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13737 "High dimensional interaction search by brute force requires a quadratic
13738 computational cost in the number of variables. The xyz algorithm provably
13739 finds strong interactions in almost linear time. For details of the algorithm
13740 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13741 interaction search in high-dimensional data.")
13742 ;; Any version of the GPL.
13743 (license license:gpl2+)))
13745 (define-public r-rttf2pt1
13747 (name "r-rttf2pt1")
13752 (uri (cran-uri "Rttf2pt1" version))
13755 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13756 (properties `((upstream-name . "Rttf2pt1")))
13757 (build-system r-build-system)
13758 (home-page "https://github.com/wch/Rttf2pt1")
13759 (synopsis "Font conversion utility")
13761 "This package contains the program @code{ttf2pt1}, for use with the
13762 @code{extrafont} package.")
13763 ;; Most of the files are covered under the Expat license. Some files are
13764 ;; covered under BSD-3. Deviations for individual files are recorded in
13765 ;; the LICENSE file.
13766 (license (list license:bsd-3 license:expat
13767 (license:non-copyleft "file://LICENSE")))))
13769 (define-public r-extrafontdb
13771 (name "r-extrafontdb")
13776 (uri (cran-uri "extrafontdb" version))
13779 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13780 (build-system r-build-system)
13781 (home-page "https://github.com/wch/extrafontdb")
13782 (synopsis "Database for the extrafont package")
13784 "This package holds the database for the @code{extrafont} package.")
13785 (license license:gpl2)))
13787 (define-public r-extrafont
13789 (name "r-extrafont")
13794 (uri (cran-uri "extrafont" version))
13797 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13798 (build-system r-build-system)
13800 `(("r-extrafontdb" ,r-extrafontdb)
13801 ("r-rttf2pt1" ,r-rttf2pt1)))
13802 (home-page "https://github.com/wch/extrafont")
13803 (synopsis "Tools for using fonts in R")
13805 "The extrafont package makes it easier to use fonts other than the basic
13806 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13807 used with PDF or PostScript output files. There are two hurdles for using
13808 fonts in PDF (or Postscript) output files:
13811 @item Making R aware of the font and the dimensions of the characters.
13812 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13813 properly on a device that doesn't have the font. This is usually needed if
13814 you want to print the PDF file or share it with others.
13817 The extrafont package makes both of these things easier.")
13818 (license license:gpl2)))
13820 (define-public r-xkcd
13827 (uri (cran-uri "xkcd" version))
13830 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13831 (build-system r-build-system)
13833 `(("r-extrafont" ,r-extrafont)
13834 ("r-ggplot2" ,r-ggplot2)
13835 ("r-hmisc" ,r-hmisc)))
13836 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13837 (synopsis "Plot ggplot2 graphics in the XKCD style")
13839 "This package provides the means to plot ggplot2 graphs in the style of
13840 the XKCD web comic.")
13841 (license license:gpl3)))
13843 (define-public r-msigdbr
13850 (uri (cran-uri "msigdbr" version))
13853 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
13854 (build-system r-build-system)
13856 `(("r-dplyr" ,r-dplyr)
13857 ("r-magrittr" ,r-magrittr)
13858 ("r-rlang" ,r-rlang)
13859 ("r-tibble" ,r-tibble)))
13860 (home-page "https://github.com/igordot/msigdbr")
13861 (synopsis "MSigDB gene sets for multiple organisms")
13863 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13864 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13865 software in a standard R data frame with key-value pairs. Included are the
13866 original human gene symbols and Entrez IDs as well as the equivalents for
13867 various frequently studied model organisms such as mouse, rat, pig, fly, and
13869 ;; The package is covered under the Expat license, but the upstream MSigDB
13870 ;; files are made available under the Creative Commons Attribution 4.0
13871 ;; International license.
13872 (license (list license:expat license:cc-by4.0))))
13874 (define-public r-gridgraphics
13876 (name "r-gridgraphics")
13881 (uri (cran-uri "gridGraphics" version))
13884 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13885 (properties `((upstream-name . "gridGraphics")))
13886 (build-system r-build-system)
13887 (home-page "https://github.com/pmur002/gridgraphics")
13888 (synopsis "Redraw base graphics using @code{grid} graphics")
13890 "This package provides functions to convert a page of plots drawn with
13891 the @code{graphics} package into identical output drawn with the @code{grid}
13892 package. The result looks like the original @code{graphics}-based plot, but
13893 consists of @code{grid} grobs and viewports that can then be manipulated with
13894 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13895 (license license:gpl2+)))
13897 (define-public r-farver
13904 (uri (cran-uri "farver" version))
13907 "0aq1hk561pz3s3lpay1adwsihha6mxp7zbj4n1m6307g34awlhhn"))))
13908 (build-system r-build-system)
13909 (home-page "https://github.com/thomasp85/farver")
13910 (synopsis "Vectorized color conversion and comparison")
13912 "The encoding of color can be handled in many different ways, using
13913 different color spaces. As different color spaces have different uses,
13914 efficient conversion between these representations are important. This
13915 package provides a set of functions that gives access to very fast color space
13916 conversion and comparisons implemented in C++, and offers 100-fold speed
13917 improvements over the @code{convertColor} function in the @code{grDevices}
13919 (license license:expat)))
13921 (define-public r-ggplotify
13923 (name "r-ggplotify")
13928 (uri (cran-uri "ggplotify" version))
13931 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
13932 (build-system r-build-system)
13934 `(("r-ggplot2" ,r-ggplot2)
13935 ("r-gridgraphics" ,r-gridgraphics)
13936 ("r-rvcheck" ,r-rvcheck)))
13937 (home-page "https://github.com/GuangchuangYu/ggplotify")
13938 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
13940 "This package provides tools to convert plot function calls (using
13941 expression or formula) to @code{grob} or @code{ggplot} objects that are
13942 compatible with the @code{grid} and @code{ggplot2} environment. With this
13943 package, we are able to e.g. use @code{cowplot} to align plots produced by
13944 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
13945 converting them to @code{ggplot} objects.")
13946 (license license:artistic2.0)))
13948 (define-public r-triebeard
13950 (name "r-triebeard")
13955 (uri (cran-uri "triebeard" version))
13958 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
13959 (build-system r-build-system)
13960 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13961 (home-page "https://github.com/Ironholds/triebeard/")
13962 (synopsis "Radix trees in Rcpp")
13964 "Radix trees, or tries, are key-value data structures optimized for
13965 efficient lookups, similar in purpose to hash tables. This package provides
13966 an implementation of radix trees for use in R programming and in developing
13967 packages with Rcpp.")
13968 (license license:expat)))
13970 (define-public r-tweenr
13977 (uri (cran-uri "tweenr" version))
13980 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
13981 (build-system r-build-system)
13983 `(("r-farver" ,r-farver)
13984 ("r-magrittr" ,r-magrittr)
13986 ("r-rlang" ,r-rlang)))
13987 (home-page "https://github.com/thomasp85/tweenr")
13988 (synopsis "Interpolate data for smooth animations")
13990 "In order to create smooth animation between states of data, tweening is
13991 necessary. This package provides a range of functions for creating tweened
13992 data that can be used as basis for animation. Furthermore it adds a number of
13993 vectorized interpolaters for common R data types such as numeric, date and
13995 (license license:expat)))
13997 (define-public r-polyclip
13999 (name "r-polyclip")
14004 (uri (cran-uri "polyclip" version))
14007 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14008 (build-system r-build-system)
14009 (native-inputs `(("pkg-config" ,pkg-config)))
14010 (home-page "http://www.angusj.com/delphi/clipper.php")
14011 (synopsis "Polygon clipping")
14013 "This package provides an R port of the library Clipper. It performs
14014 polygon clipping operations (intersection, union, set minus, set difference)
14015 for polygonal regions of arbitrary complexity, including holes. It computes
14016 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14017 dilations) for polygonal regions and polygonal lines. It computes the
14018 Minkowski Sum of general polygons. There is a function for removing
14019 self-intersections from polygon data.")
14020 (license license:boost1.0)))
14022 (define-public r-urltools
14024 (name "r-urltools")
14029 (uri (cran-uri "urltools" version))
14032 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14033 (build-system r-build-system)
14035 `(("r-rcpp" ,r-rcpp)
14036 ("r-triebeard" ,r-triebeard)))
14037 (home-page "https://github.com/Ironholds/urltools/")
14038 (synopsis "Vectorized tools for URL handling and parsing")
14040 "This package provides a toolkit for all URL-handling needs, including
14041 encoding and decoding, parsing, parameter extraction and modification. All
14042 functions are designed to be both fast and entirely vectorized. It is
14043 intended to be useful for people dealing with web-related datasets, such as
14044 server-side logs, although may be useful for other situations involving large
14046 (license license:expat)))
14048 (define-public r-ggforce
14055 (uri (cran-uri "ggforce" version))
14058 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14059 (build-system r-build-system)
14061 `(("r-ggplot2" ,r-ggplot2)
14062 ("r-gtable" ,r-gtable)
14064 ("r-polyclip" ,r-polyclip)
14066 ("r-rcppeigen" ,r-rcppeigen)
14067 ("r-rlang" ,r-rlang)
14068 ("r-scales" ,r-scales)
14069 ("r-tidyselect" ,r-tidyselect)
14070 ("r-tweenr" ,r-tweenr)
14071 ("r-withr" ,r-withr)))
14072 (home-page "https://ggforce.data-imaginist.com")
14073 (synopsis "Accelerating ggplot2")
14075 "The aim of the ggplot2 package is to aid in visual data investigations.
14076 This focus has led to a lack of facilities for composing specialized plots.
14077 Thi package aims to be a collection of mainly new statistics and geometries
14078 that fills this gap.")
14079 (license license:expat)))
14081 (define-public r-europepmc
14083 (name "r-europepmc")
14088 (uri (cran-uri "europepmc" version))
14091 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
14092 (build-system r-build-system)
14094 `(("r-dplyr" ,r-dplyr)
14096 ("r-jsonlite" ,r-jsonlite)
14098 ("r-progress" ,r-progress)
14099 ("r-purrr" ,r-purrr)
14100 ("r-urltools" ,r-urltools)
14101 ("r-xml2" ,r-xml2)))
14102 (home-page "https://github.com/ropensci/europepmc/")
14103 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14105 "This package provides an R Client for the
14106 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14107 Service}. It gives access to both metadata on life science literature and
14108 open access full texts. Europe PMC indexes all PubMed content and other
14109 literature sources including Agricola, a bibliographic database of citations
14110 to the agricultural literature, or Biological Patents. In addition to
14111 bibliographic metadata, the client allows users to fetch citations and
14112 reference lists. Links between life-science literature and other EBI
14113 databases, including ENA, PDB or ChEMBL are also accessible.")
14114 (license license:gpl3)))
14116 (define-public r-ggraph
14123 (uri (cran-uri "ggraph" version))
14126 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
14127 (build-system r-build-system)
14129 `(("r-digest" ,r-digest)
14130 ("r-dplyr" ,r-dplyr)
14131 ("r-ggforce" ,r-ggforce)
14132 ("r-ggplot2" ,r-ggplot2)
14133 ("r-ggrepel" ,r-ggrepel)
14134 ("r-graphlayouts" ,r-graphlayouts)
14135 ("r-gtable" ,r-gtable)
14136 ("r-igraph" ,r-igraph)
14139 ("r-rlang" ,r-rlang)
14140 ("r-scales" ,r-scales)
14141 ("r-tidygraph" ,r-tidygraph)
14142 ("r-viridis" ,r-viridis)))
14143 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14144 (synopsis "Implementation of grammar of graphics for graphs and networks")
14146 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14147 graph and network visualizations due to its reliance on tabular data input.
14148 The ggraph package is an extension of the ggplot2 API tailored to graph
14149 visualizations and provides the same flexible approach to building up plots
14151 (license license:gpl3)))
14153 (define-public r-varselrf
14155 (name "r-varselrf")
14160 (uri (cran-uri "varSelRF" version))
14163 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14164 (properties `((upstream-name . "varSelRF")))
14165 (build-system r-build-system)
14167 `(("r-randomforest" ,r-randomforest)))
14168 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14169 (synopsis "Variable selection using random forests")
14171 "This package provides tools for the variable selection from random
14172 forests using both backwards variable elimination (for the selection of small
14173 sets of non-redundant variables) and selection based on the importance
14174 spectrum (somewhat similar to scree plots; for the selection of large,
14175 potentially highly-correlated variables). The main applications are in
14176 high-dimensional data (e.g., microarray data, and other genomics and
14177 proteomics applications).")
14178 (license license:gpl2+)))
14180 (define-public r-pamr
14187 (uri (cran-uri "pamr" version))
14190 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14191 (build-system r-build-system)
14193 `(("r-cluster" ,r-cluster)
14194 ("r-survival" ,r-survival)))
14195 (native-inputs `(("gfortran" ,gfortran)))
14196 (home-page "https://cran.r-project.org/web/packages/pamr/")
14197 (synopsis "Prediction Analysis for Microarrays")
14199 "This package provides some functions for sample classification in
14201 (license license:gpl2)))
14203 (define-public r-rda
14206 (version "1.0.2-2.1")
14210 (uri (cran-uri "rda" version))
14213 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14214 (build-system r-build-system)
14215 (home-page "https://cran.r-project.org/web/packages/rda/")
14216 (synopsis "Shrunken centroids regularized discriminant analysis")
14218 "This package provides tools for shrunken centroids regularized
14219 discriminant analysis for the purpose of classifying high dimensional data.")
14220 (license license:gpl2+)))
14222 (define-public r-ggvis
14229 (uri (cran-uri "ggvis" version))
14232 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14233 (build-system r-build-system)
14235 `(("r-assertthat" ,r-assertthat)
14236 ("r-dplyr" ,r-dplyr)
14237 ("r-htmltools" ,r-htmltools)
14238 ("r-jsonlite" ,r-jsonlite)
14239 ("r-lazyeval" ,r-lazyeval)
14240 ("r-magrittr" ,r-magrittr)
14241 ("r-shiny" ,r-shiny)))
14242 (home-page "https://ggvis.rstudio.com/")
14243 (synopsis "Interactive grammar of graphics")
14245 "This package is a data visualization package for R providing an
14246 implementation of an interactive grammar of graphics, taking the best parts of
14247 ggplot2, combining them with the reactive framework of Shiny and drawing web
14248 graphics using Vega.")
14249 (license license:gpl2)))
14251 (define-public r-gbm
14258 (uri (cran-uri "gbm" version))
14261 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14262 (build-system r-build-system)
14264 `(("r-gridextra" ,r-gridextra)
14265 ("r-lattice" ,r-lattice)
14266 ("r-survival" ,r-survival)))
14267 (home-page "https://github.com/gbm-developers/gbm")
14268 (synopsis "Generalized boosted regression models")
14270 "This package is an implementation of extensions to Freund and Schapire's
14271 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14272 regression methods for least squares, absolute loss, t-distribution loss,
14273 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14274 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14275 and Learning to Rank measures (LambdaMart).")
14276 (license license:gpl2+)))
14278 (define-public r-threejs
14285 (uri (cran-uri "threejs" version))
14288 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14289 (build-system r-build-system)
14291 `(#:modules ((guix build utils)
14292 (guix build r-build-system)
14296 (modify-phases %standard-phases
14297 (add-after 'unpack 'process-javascript
14298 (lambda* (#:key inputs #:allow-other-keys)
14299 (with-directory-excursion "inst"
14303 `((,(assoc-ref inputs "js-jquery")
14304 "htmlwidgets/lib/jquery/jquery.min.js")
14305 (,(assoc-ref inputs "js-threejs-85")
14306 "htmlwidgets/lib/threejs-85/three.min.js"))))
14307 (lambda (sources targets)
14308 (for-each (lambda (source target)
14309 (format #t "Processing ~a --> ~a~%"
14311 (delete-file target)
14312 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14313 (call-with-output-file target
14315 (dump-port minified port)))))
14316 sources targets))))
14319 `(("r-base64enc" ,r-base64enc)
14320 ("r-crosstalk" ,r-crosstalk)
14321 ("r-htmlwidgets" ,r-htmlwidgets)
14322 ("r-igraph" ,r-igraph)))
14324 `(("uglify-js" ,uglify-js)
14328 (uri "https://code.jquery.com/jquery-3.3.1.js")
14331 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14335 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14338 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14339 (home-page "https://bwlewis.github.io/rthreejs")
14340 (synopsis "Interactive 3D scatter plots, networks and globes")
14342 "Create interactive 3D scatter plots, network plots, and globes in R
14343 using the three.js visualization library.")
14344 (license license:expat)))
14346 (define-public r-mlbench
14353 (uri (cran-uri "mlbench" version))
14356 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14357 (build-system r-build-system)
14358 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14359 (synopsis "Machine learning benchmark problems")
14361 "This package provides a collection of artificial and real-world machine
14362 learning benchmark problems, including, e.g., several data sets from the UCI
14364 (license license:gpl2)))
14366 (define-public r-mpm
14373 (uri (cran-uri "mpm" version))
14376 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14377 (build-system r-build-system)
14379 `(("r-kernsmooth" ,r-kernsmooth)
14380 ("r-mass" ,r-mass)))
14381 (home-page "http://mpm.r-forge.r-project.org")
14382 (synopsis "Multivariate projection methods")
14384 "This is a package for exploratory graphical analysis of multivariate
14385 data, specifically gene expression data with different projection methods:
14386 principal component analysis, correspondence analysis, spectral map
14388 (license license:gpl2+)))
14390 (define-public r-png
14396 (uri (cran-uri "png" version))
14399 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14400 (build-system r-build-system)
14402 `(("libpng" ,libpng)
14404 (home-page "http://www.rforge.net/png/")
14405 (synopsis "Read and write PNG images")
14407 "This package provides an easy and simple way to read, write and display
14408 bitmap images stored in the PNG format. It can read and write both files and
14409 in-memory raw vectors.")
14410 ;; Any of these GPL versions.
14411 (license (list license:gpl2 license:gpl3))))
14413 (define-public r-ggcorrplot
14415 (name "r-ggcorrplot")
14420 (uri (cran-uri "ggcorrplot" version))
14423 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14424 (build-system r-build-system)
14426 `(("r-ggplot2" ,r-ggplot2)
14427 ("r-reshape2" ,r-reshape2)))
14428 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14429 (synopsis "Visualization of a correlation matrix using ggplot2")
14431 "The ggcorrplot package can be used to visualize easily a correlation
14432 matrix using ggplot2. It provides a solution for reordering the correlation
14433 matrix and displays the significance level on the plot. It also includes a
14434 function for computing a matrix of correlation p-values.")
14435 (license license:gpl2)))
14437 (define-public r-flexdashboard
14439 (name "r-flexdashboard")
14440 (version "0.5.1.1")
14444 (uri (cran-uri "flexdashboard" version))
14447 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14448 (build-system r-build-system)
14450 `(#:modules ((guix build utils)
14451 (guix build r-build-system)
14455 (ice-9 textual-ports))
14457 (modify-phases %standard-phases
14458 (add-after 'unpack 'process-javascript
14459 (lambda* (#:key inputs #:allow-other-keys)
14460 (with-directory-excursion "inst"
14461 ;; Concatenate all components of prism.js
14462 (let ((contents (string-join
14463 (map (lambda (name)
14464 (call-with-input-file
14465 (assoc-ref inputs name)
14469 "js-prism-line-numbers"))
14471 (call-with-output-file "prism-src.js"
14472 (cut display contents <>)))
14476 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14477 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14479 "www/sly/sly.min.js")
14481 "www/prism/prism.js")
14482 (,(assoc-ref inputs "js-raphael")
14483 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14484 (,(assoc-ref inputs "js-featherlight")
14485 "www/featherlight/featherlight.min.js"))))
14486 (lambda (sources targets)
14487 (for-each (lambda (source target)
14488 (format #t "Processing ~a --> ~a~%"
14490 (delete-file target)
14491 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14492 (call-with-output-file target
14494 (dump-port minified port)))))
14495 sources targets))))
14498 `(("r-htmltools" ,r-htmltools)
14499 ("r-htmlwidgets" ,r-htmlwidgets)
14500 ("r-jsonlite" ,r-jsonlite)
14501 ("r-knitr" ,r-knitr)
14502 ("r-rmarkdown" ,r-rmarkdown)
14503 ("r-shiny" ,r-shiny)))
14505 `(("uglify-js" ,uglify-js)
14509 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14512 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14516 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14519 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14523 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14526 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14527 ("js-prism-line-numbers"
14530 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14533 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14537 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14540 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14541 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14542 (synopsis "R Markdown format for flexible dashboards")
14544 "This package provides an R Markdown format for converting an R Markdown
14545 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14546 of its components to the containing web page.")
14547 (license license:expat)))
14549 (define-public r-preseqr
14556 (uri (cran-uri "preseqR" version))
14559 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14560 (properties `((upstream-name . "preseqR")))
14561 (build-system r-build-system)
14563 `(("r-polynom" ,r-polynom)))
14564 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14565 (synopsis "Predicting species accumulation curves")
14567 "This package can be used to predict the r-species accumulation
14568 curve (r-SAC), which is the number of species represented at least r times as
14569 a function of the sampling effort. When r = 1, the curve is known as the
14570 species accumulation curve, or the library complexity curve in high-throughput
14571 genomic sequencing. The package includes both parametric and nonparametric
14572 methods, as described by Deng C, et al. (2018).")
14573 (license license:gpl3)))
14575 (define-public r-mapplots
14577 (name "r-mapplots")
14582 (uri (cran-uri "mapplots" version))
14585 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14586 (build-system r-build-system)
14587 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14588 (synopsis "Data visualization on maps")
14590 "This package helps you create simple maps; add sub-plots like pie plots
14591 to a map or any other plot; format, plot and export gridded data. The package
14592 was developed for displaying fisheries data but most functions can be used for
14593 more generic data visualisation.")
14594 (license license:gpl2+)))
14596 (define-public r-pmcmr
14603 (uri (cran-uri "PMCMR" version))
14606 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14607 (properties `((upstream-name . "PMCMR")))
14608 (build-system r-build-system)
14609 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14610 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14612 "This is a deprecated package for calculating pairwise multiple
14613 comparisons of mean rank sums. This package is superseded by the novel
14614 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14615 compatibility of dependent packages for some time.")
14616 (license license:gpl3+)))
14618 (define-public r-downloader
14620 (name "r-downloader")
14625 (uri (cran-uri "downloader" version))
14628 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14629 (build-system r-build-system)
14631 `(("r-digest" ,r-digest)))
14632 (home-page "https://github.com/wch/downloader")
14633 (synopsis "Download files over HTTP and HTTPS")
14635 "This package provides a wrapper for the @code{download.file} function,
14636 making it possible to download files over HTTPS across platforms. The
14637 @code{RCurl} package provides this functionality (and much more) but has
14638 external dependencies. This package has is implemented purely in R.")
14639 (license license:gpl2)))
14641 (define-public r-rex
14648 (uri (cran-uri "rex" version))
14651 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14652 (build-system r-build-system)
14654 `(("r-lazyeval" ,r-lazyeval)
14655 ("r-magrittr" ,r-magrittr)))
14656 (home-page "https://github.com/kevinushey/rex")
14657 (synopsis "Friendly regular expressions")
14659 "This package provides a friendly interface for the construction of
14660 regular expressions. Regular expressions are a very powerful feature, however
14661 they are often difficult to interpret. Rex allows you to build complex
14662 regular expressions from human readable expressions")
14663 (license license:expat)))
14665 (define-public r-sctransform
14667 (name "r-sctransform")
14672 (uri (cran-uri "sctransform" version))
14675 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14676 (build-system r-build-system)
14678 `(("r-future" ,r-future)
14679 ("r-future-apply" ,r-future-apply)
14680 ("r-ggplot2" ,r-ggplot2)
14681 ("r-gridextra" ,r-gridextra)
14683 ("r-matrix" ,r-matrix)
14685 ("r-rcppeigen" ,r-rcppeigen)
14686 ("r-reshape2" ,r-reshape2)))
14687 (home-page "https://github.com/ChristophH/sctransform")
14688 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14690 "This package provides a normalization method for single-cell UMI count
14691 data using a variance stabilizing transformation. The transformation is based
14692 on a negative binomial regression model with regularized parameters. As part
14693 of the same regression framework, this package also provides functions for
14694 batch correction, and data correction.")
14695 (license license:gpl3)))
14697 (define-public r-styler
14704 (uri (cran-uri "styler" version))
14707 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14708 (build-system r-build-system)
14710 `(("r-backports" ,r-backports)
14712 ("r-magrittr" ,r-magrittr)
14713 ("r-purrr" ,r-purrr)
14714 ("r-rematch2" ,r-rematch2)
14715 ("r-rlang" ,r-rlang)
14716 ("r-rprojroot" ,r-rprojroot)
14717 ("r-tibble" ,r-tibble)
14718 ("r-withr" ,r-withr)
14719 ("r-xfun" ,r-xfun)))
14720 (home-page "https://github.com/r-lib/styler")
14721 (synopsis "Non-invasive pretty printing of R code")
14723 "This is a package for pretty-printing R code without changing the user's
14724 formatting intent.")
14725 (license license:gpl3)))
14727 (define-public r-scrime
14734 (uri (cran-uri "scrime" version))
14737 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14738 (build-system r-build-system)
14739 (home-page "https://cran.r-project.org/web/packages/scrime/")
14740 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14742 "This package provides tools for the analysis of high-dimensional data
14743 developed/implemented at the group \"Statistical Complexity Reduction In
14744 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14745 the functions can also be applied to other types of categorical data.")
14746 (license license:gpl2)))
14748 (define-public r-pbmcapply
14750 (name "r-pbmcapply")
14755 (uri (cran-uri "pbmcapply" version))
14758 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14759 (build-system r-build-system)
14760 (home-page "https://github.com/kvnkuang/pbmcapply")
14761 (synopsis "Track the progress of apply procedures with a progress bar")
14763 "This light-weight package helps you track and visualize the progress of
14764 parallel versions of vectorized R functions of the @code{mc*apply} family.")
14765 (license license:expat)))
14767 (define-public r-blme
14774 (uri (cran-uri "blme" version))
14777 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14778 (build-system r-build-system)
14779 (propagated-inputs `(("r-lme4" ,r-lme4)))
14780 (home-page "https://github.com/vdorie/blme")
14781 (synopsis "Bayesian linear mixed-effects models")
14783 "This package provides tools for maximum a posteriori estimation for
14784 linear and generalized linear mixed-effects models in a Bayesian setting. It
14785 extends the lme4 package.")
14786 (license license:gpl2+)))
14788 (define-public r-batchtools
14790 (name "r-batchtools")
14795 (uri (cran-uri "batchtools" version))
14798 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14799 (build-system r-build-system)
14801 `(("r-backports" ,r-backports)
14802 ("r-base64url" ,r-base64url)
14804 ("r-checkmate" ,r-checkmate)
14805 ("r-data-table" ,r-data-table)
14806 ("r-digest" ,r-digest)
14808 ("r-progress" ,r-progress)
14810 ("r-rappdirs" ,r-rappdirs)
14811 ("r-stringi" ,r-stringi)
14812 ("r-withr" ,r-withr)))
14813 (home-page "https://github.com/mllg/batchtools")
14814 (synopsis "Tools for computation on batch systems")
14816 "As a successor of the packages BatchJobs and BatchExperiments, this
14817 package provides a parallel implementation of the Map function for high
14818 performance computing systems managed by various schedulers. A multicore and
14819 socket mode allow the parallelization on a local machines, and multiple
14820 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14821 the package provides an abstraction mechanism to define large-scale computer
14822 experiments in a well-organized and reproducible way.")
14823 (license license:lgpl3)))
14825 (define-public r-clue
14832 (uri (cran-uri "clue" version))
14835 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
14836 (build-system r-build-system)
14837 (propagated-inputs `(("r-cluster" ,r-cluster)))
14838 (home-page "https://cran.r-project.org/web/packages/clue/")
14839 (synopsis "Tools for analyzing cluster ensembles")
14840 (description "Cluster ensembles are collections of individual solutions to
14841 a given clustering problem which are useful or necessary to consider in a wide
14842 range of applications. This R package provides an extensible computational
14843 environment for creating and analyzing cluster ensembles, with basic data
14844 structures for representing partitions and hierarchies, and facilities for
14845 computing on them, including methods for measuring proximity and obtaining
14846 consensus and secondary clusterings.")
14847 (license license:gpl2)))
14849 (define-public r-sitmo
14856 (uri (cran-uri "sitmo" version))
14859 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
14860 (build-system r-build-system)
14861 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14862 (home-page "https://github.com/coatless/sitmo/")
14863 (synopsis "Parallel pseudo random number generator header files")
14865 "This package provides two high quality and fast PPRNGs that may be used
14866 in an OpenMP parallel environment. In addition, there is a generator for one
14867 dimensional low-discrepancy sequence.")
14868 (license license:expat)))
14870 (define-public r-dqrng
14877 (uri (cran-uri "dqrng" version))
14880 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
14881 (build-system r-build-system)
14885 ("r-sitmo" ,r-sitmo)))
14886 (home-page "https://www.daqana.org/dqrng")
14887 (synopsis "Fast pseudo random number generators")
14889 "Several fast random number generators are provided as C++ header-only
14890 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
14891 Additionally, fast functions for generating random numbers according to a
14892 uniform, normal and exponential distribution are included. The latter two use
14893 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
14894 functions are exported to R and as a C++ interface and are enabled for use
14895 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
14896 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
14897 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
14898 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
14899 ;; whole is distributed under the terms of the AGPL 3.
14900 (license license:agpl3)))
14902 (define-public r-dalex
14909 (uri (cran-uri "DALEX" version))
14912 "1zviaf7530v8w996lbma0vplabrapgwldi7h70pr0439sxaqd421"))))
14913 (properties `((upstream-name . "DALEX")))
14914 (build-system r-build-system)
14915 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
14916 (home-page "https://pbiecek.github.io/DALEX/")
14917 (synopsis "Descriptive machine learning explanations")
14919 "Machine Learning models are widely used and have various applications in
14920 classification or regression. Models created with boosting, bagging, stacking
14921 or similar techniques are often used due to their high performance, but such
14922 black-box models usually lack interpretability. The DALEX package contains
14923 various explainers that help to understand the link between input variables
14924 and model output.")
14925 ;; Any version of the GPL
14926 (license license:gpl3+)))
14928 (define-public r-enrichr
14935 (uri (cran-uri "enrichR" version))
14938 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
14939 (properties `((upstream-name . "enrichR")))
14940 (build-system r-build-system)
14942 `(("r-httr" ,r-httr)
14943 ("r-rjson" ,r-rjson)))
14944 (home-page "https://cran.r-project.org/web/packages/enrichR/")
14945 (synopsis "R Interface to Enrichr database for analyzing gene sets")
14947 "This package provides an R interface to all Enrichr databases, a
14948 web-based tool for analyzing gene sets and returns any enrichment of common
14949 annotated biological functions.")
14950 (license license:gpl2+)))
14952 (define-public r-plot3d
14959 (uri (cran-uri "plot3D" version))
14962 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
14963 (properties `((upstream-name . "plot3D")))
14964 (build-system r-build-system)
14965 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
14966 (home-page "https://cran.r-project.org/web/packages/plot3D")
14967 (synopsis "Plot multi-dimensional data")
14969 "This package provides functions for viewing 2D and 3D data, including
14970 perspective plots, slice plots, surface plots, scatter plots, etc. It
14971 includes data sets from oceanography.")
14972 (license license:gpl3+)))
14974 (define-public r-ggfortify
14976 (name "r-ggfortify")
14981 (uri (cran-uri "ggfortify" version))
14984 "191q2z7w0l4v7swjlxs2hjgbjngw2838688s7ygnj0kigsm310f3"))))
14985 (build-system r-build-system)
14987 `(("r-dplyr" ,r-dplyr)
14988 ("r-ggplot2" ,r-ggplot2)
14989 ("r-gridextra" ,r-gridextra)
14990 ("r-scales" ,r-scales)
14991 ("r-stringr" ,r-stringr)
14992 ("r-tibble" ,r-tibble)
14993 ("r-tidyr" ,r-tidyr)))
14994 (home-page "https://github.com/sinhrks/ggfortify")
14995 (synopsis "Data visualization tools for statistical analysis results")
14997 "This package provides unified plotting tools for statistics commonly
14998 used, such as GLM, time series, PCA families, clustering and survival
14999 analysis. The package offers a single plotting interface for these analysis
15000 results and plots in a unified style using the @code{ggplot2} package.")
15001 (license license:gpl2)))
15003 (define-public r-refmanager
15005 (name "r-refmanager")
15010 (uri (cran-uri "RefManageR" version))
15013 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15014 (properties `((upstream-name . "RefManageR")))
15015 (build-system r-build-system)
15017 `(("r-bibtex" ,r-bibtex)
15019 ("r-jsonlite" ,r-jsonlite)
15020 ("r-lubridate" ,r-lubridate)
15022 ("r-stringr" ,r-stringr)
15023 ("r-xml2" ,r-xml2)))
15024 (home-page "https://github.com/ropensci/RefManageR/")
15025 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15027 "This package provides tools for importing and working with bibliographic
15028 references. It greatly enhances the @code{bibentry} class by providing a
15029 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15030 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15031 by various formats for name lists (author by last names, translator by full
15032 names, etc.). Entries can be updated, combined, sorted, printed in a number
15033 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15034 into R and converted to @code{BibEntry} objects.")
15035 ;; Any of these licenses may be picked.
15036 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15038 (define-public r-citr
15045 (uri (cran-uri "citr" version))
15048 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15049 (build-system r-build-system)
15051 `(("r-assertthat" ,r-assertthat)
15054 ("r-miniui" ,r-miniui)
15055 ("r-refmanager" ,r-refmanager)
15056 ("r-rstudioapi" ,r-rstudioapi)
15057 ("r-shiny" ,r-shiny)
15058 ("r-shinyjs" ,r-shinyjs)
15059 ("r-yaml" ,r-yaml)))
15060 (home-page "https://github.com/crsh/citr")
15061 (synopsis "RStudio add-in to insert Markdown citations")
15063 "This package provides functions and an RStudio add-in that search a
15064 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15065 the current document.")
15066 (license license:expat)))
15068 (define-public r-xgboost
15071 (version "0.90.0.2")
15075 (uri (cran-uri "xgboost" version))
15078 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
15079 (build-system r-build-system)
15081 `(("r-data-table" ,r-data-table)
15082 ("r-magrittr" ,r-magrittr)
15083 ("r-matrix" ,r-matrix)
15084 ("r-stringi" ,r-stringi)))
15085 (home-page "https://github.com/dmlc/xgboost")
15086 (synopsis "Extreme gradient boosting")
15088 "This package provides an R interface to Extreme Gradient Boosting, which
15089 is an efficient implementation of the gradient boosting framework from Chen
15090 and Guestrin (2016). The package includes efficient linear model solver and
15091 tree learning algorithms. The package can automatically do parallel
15092 computation on a single machine. It supports various objective functions,
15093 including regression, classification and ranking. The package is made to be
15094 extensible, so that users are also allowed to define their own objectives
15096 (license license:asl2.0)))
15098 (define-public r-umap
15101 (version "0.2.3.1")
15105 (uri (cran-uri "umap" version))
15108 "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d"))))
15109 (build-system r-build-system)
15111 `(("r-openssl" ,r-openssl)
15113 ("r-reticulate" ,r-reticulate)
15114 ("r-rspectra" ,r-rspectra)))
15115 (home-page "https://github.com/tkonopka/umap")
15116 (synopsis "Uniform manifold approximation and projection")
15118 "Uniform manifold approximation and projection is a technique for
15119 dimension reduction. This package provides an interface to the UMAP algorithm
15120 in R, including a translation of the original algorithm into R.")
15121 (license license:expat)))
15123 (define-public r-uwot
15130 (uri (cran-uri "uwot" version))
15133 "1y9wpzs92d1fl2x5figfywd48lkyhwx37j542z0rf6ckrl46n89n"))))
15134 (build-system r-build-system)
15136 `(("r-dqrng" ,r-dqrng)
15138 ("r-irlba" ,r-irlba)
15139 ("r-matrix" ,r-matrix)
15141 ("r-rcppannoy" ,r-rcppannoy)
15142 ("r-rcppparallel" ,r-rcppparallel)
15143 ("r-rcppprogress" ,r-rcppprogress)
15144 ("r-rspectra" ,r-rspectra)))
15145 (home-page "https://github.com/jlmelville/uwot")
15146 (synopsis "Uniform manifold approximation and projection")
15148 "This package provides an implementation of the Uniform Manifold
15149 Approximation and Projection dimensionality reduction by McInnes et
15150 al. (2018). It also provides means to transform new data and to carry out
15151 supervised dimensionality reduction. An implementation of the related
15152 LargeVis method of Tang et al. (2016) is also provided.")
15153 (license license:gpl3)))
15155 (define-public r-kableextra
15157 (name "r-kableextra")
15162 (uri (cran-uri "kableExtra" version))
15165 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15166 (properties `((upstream-name . "kableExtra")))
15167 (build-system r-build-system)
15169 `(("r-digest" ,r-digest)
15171 ("r-htmltools" ,r-htmltools)
15172 ("r-knitr" ,r-knitr)
15173 ("r-magrittr" ,r-magrittr)
15174 ("r-readr" ,r-readr)
15175 ("r-rmarkdown" ,r-rmarkdown)
15176 ("r-rstudioapi" ,r-rstudioapi)
15177 ("r-rvest" ,r-rvest)
15178 ("r-scales" ,r-scales)
15179 ("r-stringr" ,r-stringr)
15180 ("r-viridislite" ,r-viridislite)
15181 ("r-webshot" ,r-webshot)
15182 ("r-xml2" ,r-xml2)))
15183 (home-page "https://haozhu233.github.io/kableExtra/")
15184 (synopsis "Construct complex tables with pipe syntax")
15186 "Build complex HTML or LaTeX tables using @code{kable()} from
15187 @code{knitr} and the piping syntax from @code{magrittr}. The function
15188 @code{kable()} is a light weight table generator coming from @code{knitr}.
15189 This package simplifies the way to manipulate the HTML or LaTeX codes
15190 generated by @code{kable()} and allows users to construct complex tables and
15191 customize styles using a readable syntax.")
15192 (license license:expat)))
15194 (define-public r-glasso
15201 (uri (cran-uri "glasso" version))
15203 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15204 (build-system r-build-system)
15205 (native-inputs `(("gfortran" ,gfortran)))
15206 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15207 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15209 "This is a package for estimation of a sparse inverse covariance matrix
15210 using a lasso (L1) penalty. Facilities are provided for estimates along a
15211 path of values for the regularization parameter.")
15212 (license license:gpl2)))
15214 (define-public r-rhpcblasctl
15216 (name "r-rhpcblasctl")
15217 (version "0.18-205")
15221 (uri (cran-uri "RhpcBLASctl" version))
15224 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15225 (properties `((upstream-name . "RhpcBLASctl")))
15226 (build-system r-build-system)
15227 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15228 (synopsis "Control the number of threads on BLAS")
15230 "This package allows you to control the number of threads the BLAS
15231 library uses. It is also possible to control the number of threads in
15233 (license license:agpl3+)))
15235 (define-public r-lda
15242 (uri (cran-uri "lda" version))
15245 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15246 (build-system r-build-system)
15247 (home-page "https://cran.r-project.org/web/packages/lda/")
15248 (synopsis "Collapsed Gibbs sampling methods for topic models")
15250 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15251 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15252 mixed-membership stochastic blockmodel. Inference for all of these models is
15253 implemented via a fast collapsed Gibbs sampler written in C. Utility
15254 functions for reading/writing data typically used in topic models, as well as
15255 tools for examining posterior distributions are also included.")
15256 ;; Any version of the LGPL
15257 (license license:lgpl3+)))
15259 (define-public r-rann-l1
15266 (uri (cran-uri "RANN.L1" version))
15269 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15270 (properties `((upstream-name . "RANN.L1")))
15271 (build-system r-build-system)
15272 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15273 (synopsis "Fast nearest neighbour search using L1 metric")
15275 "This package provides tools to find the k nearest neighbours for every
15276 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15277 library. There is support for approximate as well as exact searches, fixed
15278 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15279 computed using the L1 (Manhattan, taxicab) metric.")
15280 (license license:gpl3+)))
15282 (define-public r-leiden
15289 (uri (cran-uri "leiden" version))
15292 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15293 (properties `((upstream-name . "leiden")))
15294 (build-system r-build-system)
15296 `(("r-igraph" ,r-igraph)
15297 ("r-matrix" ,r-matrix)
15298 ("r-reticulate" ,r-reticulate)))
15299 (home-page "https://github.com/TomKellyGenetics/leiden")
15300 (synopsis "R implementation of Leiden clustering algorithm")
15302 "This package implements the Python @code{leidenalg} module to be called
15303 in R. It enables clustering using the Leiden algorithm for partitioning a
15304 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15305 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15306 (license license:gpl3)))
15308 (define-public r-patchwork
15309 ;; There has been no public release yet.
15310 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15313 (name "r-patchwork")
15314 (version (git-version "0.0.1" revision commit))
15318 (uri (git-reference
15319 (url "https://github.com/thomasp85/patchwork.git")
15321 (file-name (git-file-name name version))
15324 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15325 (build-system r-build-system)
15327 `(("r-ggplot2" ,r-ggplot2)
15328 ("r-gtable" ,r-gtable)))
15329 (home-page "https://github.com/thomasp85/patchwork")
15330 (synopsis "Compose ggplot2 plots")
15332 "The @code{ggplot2} package provides a strong API for sequentially
15333 building up a plot, but does not concern itself with composition of multiple
15334 plots. Patchwork is a package that expands the API to allow for arbitrarily
15335 complex composition of plots by providing mathmatical operators for combining
15337 (license license:expat))))
15339 (define-public r-liger
15346 (uri (git-reference
15347 (url "https://github.com/MacoskoLab/liger.git")
15348 (commit (string-append "v" version))))
15349 (file-name (git-file-name name version))
15352 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15353 (modules '((guix build utils)))
15356 (delete-file "inst/java/ModularityOptimizer.jar")
15358 (build-system r-build-system)
15361 (modify-phases %standard-phases
15362 (add-after 'unpack 'build-java-part
15363 (lambda* (#:key inputs #:allow-other-keys)
15364 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15365 (for-each (lambda (file) (invoke "javac" file))
15366 (find-files "." "\\.java$"))
15367 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15368 (find-files "." "\\.class$"))
15371 `(("r-cowplot" ,r-cowplot)
15372 ("r-dosnow" ,r-dosnow)
15373 ("r-dplyr" ,r-dplyr)
15375 ("r-foreach" ,r-foreach)
15376 ("r-ggplot2" ,r-ggplot2)
15377 ("r-ggrepel" ,r-ggrepel)
15378 ("r-hmisc" ,r-hmisc)
15380 ("r-irlba" ,r-irlba)
15381 ("r-matrix" ,r-matrix)
15382 ("r-mclust" ,r-mclust)
15383 ("r-patchwork" ,r-patchwork)
15385 ("r-rann-l1" ,r-rann-l1)
15387 ("r-rcpparmadillo" ,r-rcpparmadillo)
15388 ("r-riverplot" ,r-riverplot)
15389 ("r-rtsne" ,r-rtsne)
15390 ("r-snow" ,r-snow)))
15392 `(("jdk" ,icedtea "jdk")
15393 ;; See https://github.com/MacoskoLab/liger/issues/96
15394 ;; The optimizer is released under the Expat license.
15398 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15401 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15403 ("r-knitr" ,r-knitr))) ; for vignettes
15404 (home-page "https://github.com/MacoskoLab/liger")
15405 (synopsis "Integrate and analyze multiple single-cell datasets")
15407 "LIGER is a package for integrating and analyzing multiple single-cell
15408 datasets, developed and maintained by the Macosko lab. It relies on
15409 integrative non-negative matrix factorization to identify shared and
15410 dataset-specific factors.")
15411 (license license:gpl3)))
15413 (define-public r-harmony
15414 ;; There are no tagged commits
15415 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15419 (version (git-version "1.0" revision commit))
15423 (uri (git-reference
15424 (url "https://github.com/immunogenomics/harmony")
15426 (file-name (git-file-name name version))
15429 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15430 (build-system r-build-system)
15432 `(("r-cowplot" ,r-cowplot)
15433 ("r-dplyr" ,r-dplyr)
15434 ("r-ggplot2" ,r-ggplot2)
15435 ("r-irlba" ,r-irlba)
15436 ("r-matrix" ,r-matrix)
15438 ("r-rcpparmadillo" ,r-rcpparmadillo)
15439 ("r-rcppprogress" ,r-rcppprogress)
15440 ("r-rlang" ,r-rlang)
15441 ("r-tibble" ,r-tibble)
15442 ("r-tidyr" ,r-tidyr)))
15443 (home-page "https://github.com/immunogenomics/harmony")
15444 (synopsis "Integration of single cell sequencing data")
15446 "This package provides an implementation of the Harmony algorithm for
15447 single cell integration, described in Korsunsky et al
15448 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15449 function and interfaces to external frameworks.")
15450 (license license:gpl3))))
15452 (define-public r-covr
15459 (uri (cran-uri "covr" version))
15461 (base32 "0p44kr6yz5sqza5zvq6divqglzkpv0if9pjpjmzhmdaaddjrqzg5"))))
15462 (properties `((upstream-name . "covr")))
15463 (build-system r-build-system)
15465 `(("r-crayon" ,r-crayon)
15466 ("r-digest" ,r-digest)
15468 ("r-jsonlite" ,r-jsonlite)
15470 ("r-withr" ,r-withr)
15471 ("r-yaml" ,r-yaml)))
15472 (home-page "https://github.com/r-lib/covr")
15473 (synopsis "Test coverage for R packages")
15475 "Thisp package enables you to track and report code coverage for your
15476 package and (optionally) upload the results to a coverage service. Code
15477 coverage is a measure of the amount of code being exercised by a set of tests.
15478 It is an indirect measure of test quality and completeness. This package is
15479 compatible with any testing methodology or framework and tracks coverage of
15480 both R code and compiled C/C++/FORTRAN code.")
15481 (license license:gpl3)))
15483 (define-public r-systemfonts
15485 (name "r-systemfonts")
15490 (uri (cran-uri "systemfonts" version))
15493 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15494 (properties `((upstream-name . "systemfonts")))
15495 (build-system r-build-system)
15497 `(("fontconfig" ,fontconfig)
15498 ("freetype" ,freetype)
15501 `(("pkg-config" ,pkg-config)))
15502 (home-page "https://github.com/r-lib/systemfonts")
15503 (synopsis "System native font finding")
15505 "This package provides system native access to the font catalogue. As
15506 font handling varies between systems it is difficult to correctly locate
15507 installed fonts across different operating systems. The 'systemfonts' package
15508 provides bindings to the native libraries for finding font files that can then
15509 be used further by e.g. graphic devices.")
15510 (license license:expat)))
15512 (define-public r-graphlayouts
15514 (name "r-graphlayouts")
15519 (uri (cran-uri "graphlayouts" version))
15522 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15523 (properties `((upstream-name . "graphlayouts")))
15524 (build-system r-build-system)
15526 `(("r-igraph" ,r-igraph)
15528 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15529 (home-page "https://github.com/schochastics/graphlayouts")
15530 (synopsis "Additional layout algorithms for network visualizations")
15532 "This package provides several layout algorithms to visualize networks
15533 which are not part of the igraph library. Most are based on the concept of
15534 stress majorization by Gansner et al. (2004)
15535 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15536 emphasize hidden group structures in networks or focus on specific nodes.")
15537 (license license:expat)))
15539 (define-public r-tidygraph
15541 (name "r-tidygraph")
15546 (uri (cran-uri "tidygraph" version))
15549 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15550 (properties `((upstream-name . "tidygraph")))
15551 (build-system r-build-system)
15553 `(("r-dplyr" ,r-dplyr)
15554 ("r-igraph" ,r-igraph)
15555 ("r-magrittr" ,r-magrittr)
15556 ("r-pillar" ,r-pillar)
15559 ("r-rlang" ,r-rlang)
15560 ("r-tibble" ,r-tibble)
15561 ("r-tidyr" ,r-tidyr)))
15562 (home-page "https://github.com/thomasp85/tidygraph")
15563 (synopsis "Tidy API for graph manipulation")
15565 "This package provides a graph implementation that can be thought of as
15566 two tidy data frames describing node and edge data respectively. It provides
15567 an approach to manipulate these two virtual data frames using the API defined
15568 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15569 common graph algorithms.")
15570 (license license:expat)))
15572 (define-public r-soupx
15573 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15577 (version (git-version "0.3.1" revision commit))
15581 (uri (git-reference
15582 (url "https://github.com/constantAmateur/SoupX")
15584 (file-name (git-file-name name version))
15587 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15588 (properties `((upstream-name . "SoupX")))
15589 (build-system r-build-system)
15591 `(("r-ggplot2" ,r-ggplot2)
15592 ("r-matrix" ,r-matrix)
15593 ("r-seurat" ,r-seurat)))
15594 (home-page "https://github.com/constantAmateur/SoupX")
15595 (synopsis "Single cell mRNA Soup eXterminator")
15597 "This package provides a package for quantifying, profiling and
15598 removing cell free mRNA contamination (the \"soup\") from droplet based single
15599 cell RNA-seq experiments.")
15600 (license license:gpl2))))
15602 (define-public r-assertr
15609 (uri (cran-uri "assertr" version))
15612 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15613 (build-system r-build-system)
15615 `(("r-dplyr" ,r-dplyr)
15617 ("r-rlang" ,r-rlang)))
15619 `(("r-knitr" ,r-knitr))) ; needed for vignette
15620 (home-page "https://github.com/ropensci/assertr")
15621 (synopsis "Assertive programming for R analysis pipelines")
15623 "This package provides functionality to assert conditions that have to be
15624 met so that errors in data used in analysis pipelines can fail quickly. It is
15625 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15627 (license license:expat)))
15629 (define-public r-parameters
15631 (name "r-parameters")
15636 (uri (cran-uri "parameters" version))
15639 "0ifb9g1h8sn661q7jf9d8glk58gxdcym5ywbmx7phwn0y3is5wdv"))))
15640 (properties `((upstream-name . "parameters")))
15641 (build-system r-build-system)
15643 `(("r-bayestestr" ,r-bayestestr)
15644 ("r-insight" ,r-insight)))
15645 (home-page "https://cran.r-project.org/web/packages/parameters")
15646 (synopsis "Processing of model parameters")
15648 "This package provides utilities for processing the parameters of various
15649 statistical models. Beyond computing p values, CIs, and other indices for a
15650 wide variety of models, this package implements features like standardization
15651 or bootstrapping of parameters and models, feature reduction (feature
15652 extraction and variable selection) as well as conversion between indices of
15654 (license license:gpl3)))
15656 (define-public r-rgdal
15663 (uri (cran-uri "rgdal" version))
15665 (base32 "1jd691amf3ghznq5im15gvhl6v6k25klpl75m4ngrqf9xlxaa3as"))))
15666 (properties `((upstream-name . "rgdal")))
15667 (build-system r-build-system)
15675 `(("pkg-config" ,pkg-config)))
15676 (home-page "http://rgdal.r-forge.r-project.org")
15677 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15679 "This package provides bindings to the Geospatial Data Abstraction
15680 Library (GDAL) and access to projection/transformation operations from the
15682 (license license:gpl2+)))
15684 (define-public r-insol
15691 (uri (cran-uri "insol" version))
15694 "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
15695 (properties `((upstream-name . "insol")))
15696 (build-system r-build-system)
15698 `(("r-raster" ,r-raster)
15699 ("r-rgdal" ,r-rgdal)))
15701 `(("gfortran" ,gfortran)))
15702 (home-page "https://meteoexploration.com/R/insol/index.html")
15703 (synopsis "Tools for calculating solar radiation")
15705 "This package provides functions to compute insolation on tilted
15706 surfaces, computes atmospheric transmittance and related parameters such as:
15707 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15708 time, vector in the direction of the sun, vector normal to surface, and some
15709 atmospheric physics.")
15710 (license license:gpl2+)))
15712 (define-public r-lifecycle
15714 (name "r-lifecycle")
15719 (uri (cran-uri "lifecycle" version))
15722 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15723 (properties `((upstream-name . "lifecycle")))
15724 (build-system r-build-system)
15726 `(("r-glue" ,r-glue)
15727 ("r-rlang" ,r-rlang)))
15728 (home-page "https://github.com/r-lib/lifecycle")
15729 (synopsis "Manage the life cycle of your package functions")
15731 "Manage the life cycle of your exported functions with shared
15732 conventions, documentation badges, and non-invasive deprecation warnings. The
15733 lifecycle package defines four development stages (experimental, maturing,
15734 stable, and questioning) and three deprecation stages (soft-deprecated,
15735 deprecated, and defunct). It makes it easy to insert badges corresponding to
15736 these stages in your documentation. Usage of deprecated functions are
15737 signalled with increasing levels of non-invasive verbosity.")
15738 (license license:gpl3)))
15740 (define-public r-assertable
15742 (name "r-assertable")
15747 (uri (cran-uri "assertable" version))
15750 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15751 (build-system r-build-system)
15753 `(("r-data-table" ,r-data-table)))
15754 (home-page "https://cran.r-project.org/web/packages/assertable/")
15755 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15756 (description "This package provides simple, flexible assertions on
15757 data.frame or data.table objects with verbose output for vetting. While other
15758 assertion packages apply towards more general use-cases, @code{assertable} is
15759 tailored towards tabular data. It includes functions to check variable names
15760 and values, whether the dataset contains all combinations of a given set of
15761 unique identifiers, and whether it is a certain length. In addition,
15762 @code{assertable} includes utility functions to check the existence of target
15763 files and to efficiently import multiple tabular data files into one
15765 (license license:gpl3)))
15767 (define-public r-quadprog
15769 (name "r-quadprog")
15774 (uri (cran-uri "quadprog" version))
15776 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
15777 (build-system r-build-system)
15779 `(("gfortran" ,gfortran)))
15780 (home-page "https://cran.r-project.org/web/packages/quadprog")
15781 (synopsis "Functions to solve quadratic programming problems")
15783 "This package contains routines and documentation for solving quadratic
15784 programming problems.")
15785 (license license:gpl3+)))
15787 (define-public r-desolve
15794 (uri (cran-uri "deSolve" version))
15796 (base32 "0735y3p5glhqx69rzrc8qgmvs7p7w0p98qxmvylb6bgqp6kp0cbp"))))
15797 (properties `((upstream-name . "deSolve")))
15798 (build-system r-build-system)
15800 `(("gfortran" ,gfortran)))
15801 (home-page "https://desolve.r-forge.r-project.org/")
15802 (synopsis "Solvers for initial value problems of differential equations")
15803 (description "This package provides functions that solve initial
15804 value problems of a system of first-order ordinary differential equations (ODE),
15805 of partial differential equations (PDE), of differential algebraic equations
15806 (DAE), and of delay differential equations. The functions provide an interface
15807 to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection,
15808 to the FORTRAN functions dvode and daspk and a C-implementation of solvers of
15809 the Runge-Kutta family with fixed or variable time steps. The package contains
15810 routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial
15811 differential equations (PDE) that have been converted to ODEs by numerical
15813 (license license:gpl2+)))
15815 (define-public r-pracma
15821 (uri (cran-uri "pracma" version))
15823 (base32 "0isd3s0i4mzmva8lkh0j76hwjy1w50q7d1n9lhxsnnkgalx3xs1g"))))
15824 (build-system r-build-system)
15825 (home-page "https://cran.r-project.org/web/packages/pracma/")
15826 (synopsis "Practical numerical math functions")
15827 (description "This package provides functions for numerical analysis and
15828 linear algebra, numerical optimization, differential equations, plus some
15829 special functions. It uses Matlab function names where appropriate to simplify
15831 (license license:gpl3+)))
15833 (define-public r-subplex
15840 (uri (cran-uri "subplex" version))
15843 "10cbgbx1bgsax5z7gz6716g360xpq4mvq19cf4qqrxv02mmwz57z"))))
15844 (build-system r-build-system)
15846 `(("gfortran" ,gfortran)))
15847 (home-page "https://cran.r-project.org/web/packages/subplex")
15848 (synopsis "Unconstrained optimization using the subplex algorithm")
15850 "This package implements the Subplex optimization algorithm.
15851 It solves unconstrained optimization problems using a simplex method on
15852 subspaces. The method is well suited for optimizing objective functions that
15853 are noisy or are discontinuous at the solution.")
15854 (license license:gpl3+)))
15856 (define-public r-txtplot
15863 (uri (cran-uri "txtplot" version))
15866 "1949ab1bzvysdb79g8x1gaknj0ih3d6g63pv9512h5m5l3a6c31h"))))
15867 (build-system r-build-system)
15868 (home-page "https://cran.r-project.org/web/packages/txtplot/")
15869 (synopsis "Text-based plotting")
15870 (description "This package provides functions to produce rudimentary ASCII
15871 graphics directly in the terminal window. This package provides a basic
15872 plotting function (and equivalents of curve, density, acf and barplot) as well
15873 as a boxplot function.")
15874 (license license:lgpl3+)))