1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
4 ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
5 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
6 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
7 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
8 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
9 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
10 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
11 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
12 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
13 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
14 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
15 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
16 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
17 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; This file is part of GNU Guix.
21 ;;; GNU Guix is free software; you can redistribute it and/or modify it
22 ;;; under the terms of the GNU General Public License as published by
23 ;;; the Free Software Foundation; either version 3 of the License, or (at
24 ;;; your option) any later version.
26 ;;; GNU Guix is distributed in the hope that it will be useful, but
27 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
28 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29 ;;; GNU General Public License for more details.
31 ;;; You should have received a copy of the GNU General Public License
32 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
34 (define-module (gnu packages cran)
35 #:use-module ((guix licenses) #:prefix license:)
36 #:use-module (guix packages)
37 #:use-module (guix download)
38 #:use-module (guix git-download)
39 #:use-module (guix utils)
40 #:use-module (guix build-system r)
41 #:use-module (gnu packages algebra)
42 #:use-module (gnu packages base)
43 #:use-module (gnu packages bioinformatics)
44 #:use-module (gnu packages c)
45 #:use-module (gnu packages compression)
46 #:use-module (gnu packages curl)
47 #:use-module (gnu packages databases)
48 #:use-module (gnu packages fontutils)
49 #:use-module (gnu packages gcc)
50 #:use-module (gnu packages geo)
51 #:use-module (gnu packages ghostscript)
52 #:use-module (gnu packages gl)
53 #:use-module (gnu packages gnome)
54 #:use-module (gnu packages graph)
55 #:use-module (gnu packages gtk)
56 #:use-module (gnu packages haskell)
57 #:use-module (gnu packages icu4c)
58 #:use-module (gnu packages image)
59 #:use-module (gnu packages imagemagick)
60 #:use-module (gnu packages java)
61 #:use-module (gnu packages javascript)
62 #:use-module (gnu packages lisp)
63 #:use-module (gnu packages machine-learning)
64 #:use-module (gnu packages maths)
65 #:use-module (gnu packages mpi)
66 #:use-module (gnu packages multiprecision)
67 #:use-module (gnu packages networking)
68 #:use-module (gnu packages pcre)
69 #:use-module (gnu packages perl)
70 #:use-module (gnu packages pkg-config)
71 #:use-module (gnu packages python)
72 #:use-module (gnu packages python-xyz)
73 #:use-module (gnu packages statistics)
74 #:use-module (gnu packages tls)
75 #:use-module (gnu packages web)
76 #:use-module (gnu packages xorg))
78 (define-public r-clipr
85 (uri (cran-uri "clipr" version))
88 "0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m"))))
89 (build-system r-build-system)
90 (home-page "https://github.com/mdlincoln/clipr")
91 (synopsis "Read and write from the system clipboard")
93 "This package provides simple utility functions to read from and write to
94 the system clipboards.")
95 (license license:gpl3)))
97 (define-public r-ellipsis
104 (uri (cran-uri "ellipsis" version))
107 "0pw94qpg81xmsdsagpqxddv7m2cmdszmyyq99dk3caqqj01z7wg6"))))
108 (build-system r-build-system)
109 (home-page "https://github.com/hadley/ellipsis")
110 (synopsis "Tools for working with additional arguments")
112 "In S3 generics, it's useful to take @code{...} so that methods can have
113 additional arguments. But this flexibility comes at a cost: misspelled
114 arguments will be silently ignored. The @code{ellipsis} package is an
115 experiment that allows a generic to warn if any arguments passed in @code{...}
117 (license license:gpl3)))
126 (uri (cran-uri "sys" version))
129 "1k5vk5q9wa5sin0n226i05nymg469s24f6lx64yyhb7yc624j698"))))
130 (build-system r-build-system)
131 (home-page "https://github.com/jeroen/sys")
132 (synopsis "Powerful and reliable tools for running system commands in R")
134 "This package provides drop-in replacements for the base @code{system2()}
135 function with fine control and consistent behavior across platforms. It
136 supports clean interruption, timeout, background tasks, and streaming STDIN /
137 STDOUT / STDERR over binary or text connections. The package also provides
138 functions for evaluating expressions inside a temporary fork. Such
139 evaluations have no side effects on the main R process, and support reliable
140 interrupts and timeouts. This provides the basis for a sandboxing
142 (license license:expat)))
144 (define-public r-askpass
151 (uri (cran-uri "askpass" version))
154 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
155 (build-system r-build-system)
156 (propagated-inputs `(("r-sys" ,r-sys)))
157 (home-page "https://github.com/jeroen/askpass")
158 (synopsis "Safe password entry for R")
160 "This package provides cross-platform utilities for prompting the user
161 for credentials or a passphrase, for example to authenticate with a server or
162 read a protected key.")
163 (license license:expat)))
165 (define-public r-vegan
172 (uri (cran-uri "vegan" version))
175 "0wb90ng02gi13854bjq0b8a2vrknyhb0s0l1v3z38c4zy9k54sw7"))))
176 (build-system r-build-system)
178 `(("gfortran" ,gfortran)))
180 `(("r-cluster" ,r-cluster)
181 ("r-knitr" ,r-knitr) ; needed for vignettes
182 ("r-lattice" ,r-lattice)
185 ("r-permute" ,r-permute)))
186 (home-page "https://cran.r-project.org/web/packages/vegan")
187 (synopsis "Functions for community ecology")
189 "The vegan package provides tools for descriptive community ecology. It
190 has most basic functions of diversity analysis, community ordination and
191 dissimilarity analysis. Most of its multivariate tools can be used for other
192 data types as well.")
193 (license license:gpl2+)))
195 (define-public r-tidyverse
202 (uri (cran-uri "tidyverse" version))
205 "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"))))
206 (build-system r-build-system)
208 `(("r-broom" ,r-broom)
210 ("r-crayon" ,r-crayon)
211 ("r-dbplyr" ,r-dbplyr)
213 ("r-forcats" ,r-forcats)
214 ("r-ggplot2" ,r-ggplot2)
218 ("r-jsonlite" ,r-jsonlite)
219 ("r-lubridate" ,r-lubridate)
220 ("r-magrittr" ,r-magrittr)
221 ("r-modelr" ,r-modelr)
224 ("r-readxl" ,r-readxl)
225 ("r-reprex" ,r-reprex)
227 ("r-rstudioapi" ,r-rstudioapi)
229 ("r-stringr" ,r-stringr)
230 ("r-tibble" ,r-tibble)
233 (home-page "https://tidyverse.tidyverse.org")
234 (synopsis "Install and load packages from the \"Tidyverse\"")
236 "The @code{tidyverse} is a set of packages that work in harmony because
237 they share common data representations and API design. This package is
238 designed to make it easy to install and load multiple tidyverse packages in a
240 (license license:gpl3)))
242 (define-public r-rvest
249 (uri (cran-uri "rvest" version))
252 "0ji5lk8g1gbv4d9c4jg1fg6rgsqrrwkm05j1id7drdw9kqdifgj1"))))
253 (build-system r-build-system)
256 ("r-magrittr" ,r-magrittr)
257 ("r-selectr" ,r-selectr)
259 (home-page "https://github.com/hadley/rvest")
260 (synopsis "Simple web scraping for R")
262 "@code{r-rvest} helps you scrape information from web pages. It is
263 designed to work with @code{magrittr} to make it easy to express common web
264 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
265 (license license:gpl3)))
267 (define-public r-selectr
274 (uri (cran-uri "selectr" version))
277 "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b"))))
278 (build-system r-build-system)
280 `(("r-stringr" ,r-stringr)
282 (home-page "https://sjp.co.nz/projects/selectr/")
283 (synopsis "Translate CSS selectors to XPath expressions")
285 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
286 expression. This allows you to use CSS selectors when working with the XML
287 package as it can only evaluate XPath expressions. Also provided are
288 convenience functions useful for using CSS selectors on XML nodes. This
289 package is a port of the Python package @code{cssselect}.")
290 (license license:bsd-3)))
292 (define-public r-reprex
299 (uri (cran-uri "reprex" version))
302 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
303 (build-system r-build-system)
305 `(("r-callr" ,r-callr)
309 ("r-rmarkdown" ,r-rmarkdown)
310 ("r-whisker" ,r-whisker)
311 ("r-withr" ,r-withr)))
312 (home-page "https://github.com/tidyverse/reprex")
313 (synopsis "Prepare reproducible R code examples for sharing")
315 "This package provides a convenience wrapper that uses the
316 @code{rmarkdown} package to render small snippets of code to target formats
317 that include both code and output. The goal is to encourage the sharing of
318 small, reproducible, and runnable examples on code-oriented websites or email.
319 @code{reprex} also extracts clean, runnable R code from various common formats,
320 such as copy/paste from an R session.")
321 (license license:expat)))
323 (define-public r-callr
330 (uri (cran-uri "callr" version))
333 "1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b"))))
334 (build-system r-build-system)
337 ("r-processx" ,r-processx)))
338 (home-page "https://github.com/r-lib/callr#readme")
339 (synopsis "Call R from R")
341 "It is sometimes useful to perform a computation in a separate R process,
342 without affecting the current R process at all. This package does exactly
344 (license license:expat)))
346 (define-public r-readxl
353 (uri (cran-uri "readxl" version))
356 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
357 (build-system r-build-system)
359 `(("r-cellranger" ,r-cellranger)
360 ("r-progress" ,r-progress)
362 ("r-tibble" ,r-tibble)))
363 (home-page "https://readxl.tidyverse.org")
364 (synopsis "Read Excel files")
366 "This package lets you import Excel files into R. It supports
367 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
368 the embedded @code{RapidXML} C++ library.")
369 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
370 ;; 'rapidxml' which is Boost.
371 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
373 (define-public r-modelr
380 (uri (cran-uri "modelr" version))
383 "1ngxphbjkv7yl1rg30sj36mfwhc76g452drjrq9abgab4k0pgnml"))))
384 (build-system r-build-system)
386 `(("r-broom" ,r-broom)
388 ("r-lazyeval" ,r-lazyeval)
389 ("r-magrittr" ,r-magrittr)
391 ("r-tibble" ,r-tibble)
392 ("r-tidyr" ,r-tidyr)))
393 (home-page "https://github.com/tidyverse/modelr")
394 (synopsis "Helper functions for modelling in pipelines")
396 "Functions for modelling that help you seamlessly integrate modelling
397 into a pipeline of data manipulation and visualisation.")
398 (license license:gpl3)))
400 (define-public r-httpuv
406 (uri (cran-uri "httpuv" version))
409 "042piypg4c8sqrlcdl3dwajkafkbglsky3x7d0jpjv8s5wxnpfxm"))))
410 (build-system r-build-system)
414 ("r-promises" ,r-promises)
417 (home-page "https://github.com/rstudio/httpuv")
418 (synopsis "HTTP and WebSocket server library for R")
420 "The httpuv package provides low-level socket and protocol support for
421 handling HTTP and WebSocket requests directly from within R. It is primarily
422 intended as a building block for other packages, rather than making it
423 particularly easy to create complete web applications using httpuv alone.")
424 ;; This package includes third-party code that was originally released
425 ;; under various non-copyleft licenses. Full licensing information can be
426 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
427 (license license:gpl3+)))
429 (define-public r-jsonlite
435 (uri (cran-uri "jsonlite" version))
438 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
439 (build-system r-build-system)
440 (home-page "http://arxiv.org/abs/1403.2805")
441 (synopsis "Robust, high performance JSON parser and generator for R")
443 "The jsonlite package provides a fast JSON parser and generator optimized
444 for statistical data and the web. It offers flexible, robust, high
445 performance tools for working with JSON in R and is particularly powerful for
446 building pipelines and interacting with a web API. In addition to converting
447 JSON data from/to R objects, jsonlite contains functions to stream, validate,
448 and prettify JSON data. The unit tests included with the package verify that
449 all edge cases are encoded and decoded consistently for use with dynamic data
450 in systems and applications.")
451 (license license:expat)))
453 (define-public r-servr
459 (uri (cran-uri "servr" version))
462 "1n5haqkshrxcx557f1k7nrisvq3wak8v370s2r6yv691b8hvbscs"))))
463 (build-system r-build-system)
465 `(("r-httpuv" ,r-httpuv)
466 ("r-jsonlite" ,r-jsonlite)
469 (home-page "https://github.com/yihui/servr")
470 (synopsis "Simple HTTP server to serve static files or dynamic documents")
472 "Servr provides an HTTP server in R to serve static files, or dynamic
473 documents that can be converted to HTML files (e.g., R Markdown) under a given
475 (license license:expat)))
477 (define-public r-htmltools
483 (uri (cran-uri "htmltools" version))
486 "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4"))))
487 (build-system r-build-system)
490 (modify-phases %standard-phases
491 ;; See https://github.com/rstudio/htmltools/pull/68
492 ;; The resource files are in the store and have mode 444. After
493 ;; copying the files R fails to remove them again because it doesn't
494 ;; have write access to them.
495 (add-after 'unpack 'copy-files-without-mode
497 (substitute* "R/html_dependency.R"
498 (("file.copy\\(from, to, " prefix)
499 (string-append prefix
500 "copy.mode = FALSE, ")))
503 `(("r-digest" ,r-digest)
505 (home-page "https://cran.r-project.org/web/packages/htmltools")
506 (synopsis "R tools for HTML")
508 "This package provides tools for HTML generation and output in R.")
509 (license license:expat)))
511 (define-public r-htmlwidgets
513 (name "r-htmlwidgets")
517 (uri (cran-uri "htmlwidgets" version))
520 "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i"))))
521 (build-system r-build-system)
523 `(("r-htmltools" ,r-htmltools)
524 ("r-jsonlite" ,r-jsonlite)
526 (home-page "https://github.com/ramnathv/htmlwidgets")
527 (synopsis "HTML Widgets for R")
529 "HTML widgets is a framework for creating HTML widgets that render in
530 various contexts including the R console, R Markdown documents, and Shiny web
532 (license license:expat)))
534 (define-public r-htmltable
541 (uri (cran-uri "htmlTable" version))
544 "1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8"))))
545 (properties `((upstream-name . "htmlTable")))
546 (build-system r-build-system)
548 `(("r-checkmate" ,r-checkmate)
549 ("r-htmltools" ,r-htmltools)
550 ("r-htmlwidgets" ,r-htmlwidgets)
552 ("r-magrittr" ,r-magrittr)
553 ("r-rstudioapi" ,r-rstudioapi)
554 ("r-stringr" ,r-stringr)))
555 (home-page "http://gforge.se/packages/")
556 (synopsis "Advanced tables for Markdown/HTML")
558 "This package provides functions to build tables with advanced layout
559 elements such as row spanners, column spanners, table spanners, zebra
560 striping, and more. While allowing advanced layout, the underlying
561 CSS-structure is simple in order to maximize compatibility with word
562 processors such as LibreOffice. The package also contains a few text
563 formatting functions that help outputting text compatible with HTML or
565 (license license:gpl3+)))
567 (define-public r-curl
573 (uri (cran-uri "curl" version))
576 "1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c"))))
577 (build-system r-build-system)
580 (modify-phases %standard-phases
581 ;; The environment variable CURL_CA_BUNDLE is only respected when
582 ;; running Windows, so we disable the platform checks.
583 ;; This can be removed once the libcurl has been patched.
584 (add-after 'unpack 'allow-CURL_CA_BUNDLE
586 (substitute* "R/onload.R"
587 (("if \\(!grepl\\(\"mingw\".*")
589 (substitute* "src/handle.c"
590 (("#ifdef _WIN32") "#if 1"))
596 `(("pkg-config" ,pkg-config)))
597 (home-page "https://github.com/jeroenooms/curl")
598 (synopsis "HTTP client for R")
600 "The @code{curl()} and @code{curl_download()} functions provide highly
601 configurable drop-in replacements for base @code{url()} and
602 @code{download.file()} with better performance, support for encryption, gzip
603 compression, authentication, and other @code{libcurl} goodies. The core of
604 the package implements a framework for performing fully customized requests
605 where data can be processed either in memory, on disk, or streaming via the
606 callback or connection interfaces.")
607 (license license:expat)))
609 (define-public r-hwriter
616 (uri (cran-uri "hwriter" version))
619 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
620 (build-system r-build-system)
621 (home-page "https://cran.r-project.org/web/packages/hwriter")
622 (synopsis "Output R objects in HTML format")
624 "This package provides easy-to-use and versatile functions to output R
625 objects in HTML format.")
626 (license license:lgpl2.1+)))
628 (define-public r-rjson
635 (uri (cran-uri "rjson" version))
638 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
639 (build-system r-build-system)
640 (home-page "https://cran.r-project.org/web/packages/rjson")
641 (synopsis "JSON library for R")
643 "This package provides functions to convert R objects into JSON objects
645 (license license:gpl2+)))
647 (define-public r-shiny
655 (url "https://github.com/rstudio/shiny.git")
656 (commit (string-append "v" version))))
657 (file-name (git-file-name name version))
660 "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
661 (build-system r-build-system)
663 `(#:modules ((guix build r-build-system)
664 (guix build minify-build-system)
667 #:imported-modules (,@%r-build-system-modules
668 (guix build minify-build-system))
670 (modify-phases (@ (guix build r-build-system) %standard-phases)
671 (add-after 'unpack 'replace-bundled-minified-JavaScript
672 (lambda* (#:key inputs #:allow-other-keys)
673 (let ((replace-file (lambda (old new)
674 (format #t "replacing ~a with ~a\n" old new)
677 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
678 ;; contain just data. They are not minified code, so we don't
680 (with-directory-excursion "inst/www/shared"
681 (replace-file "bootstrap/shim/respond.min.js"
682 (string-append (assoc-ref inputs "js-respond")
683 "/share/javascript/respond.min.js"))
684 (replace-file "bootstrap/shim/html5shiv.min.js"
685 (string-append (assoc-ref inputs "js-html5shiv")
686 "/share/javascript/html5shiv.min.js"))
687 (replace-file "json2-min.js"
688 (string-append (assoc-ref inputs "js-json2")
689 "/share/javascript/json2.min.js"))
690 (replace-file "strftime/strftime-min.js"
691 (string-append (assoc-ref inputs "js-strftime")
692 "/share/javascript/strftime.min.js"))
693 (replace-file "highlight/highlight.pack.js"
694 (string-append (assoc-ref inputs "js-highlight")
695 "/share/javascript/highlight.min.js"))
696 (replace-file "datatables/js/jquery.dataTables.min.js"
697 (string-append (assoc-ref inputs "js-datatables")
698 "/share/javascript/jquery.dataTables.min.js"))
699 (replace-file "selectize/js/selectize.min.js"
700 (string-append (assoc-ref inputs "js-selectize")
701 "/share/javascript/selectize.min.js"))
702 (replace-file "selectize/js/es5-shim.min.js"
703 (string-append (assoc-ref inputs "js-es5-shim")
704 "/share/javascript/es5-shim.min.js"))
705 (for-each (match-lambda
708 (minify source #:target target)))
709 '(("jqueryui/jquery-ui.js" .
710 "jqueryui/jquery-ui.min.js")
711 ("datepicker/js/bootstrap-datepicker.js" .
712 "datepicker/js/bootstrap-datepicker.min.js")
713 ("ionrangeslider/js/ion.rangeSlider.js" .
714 "ionrangeslider/js/ion.rangeSlider.min.js")
715 ("bootstrap/js/bootstrap.js" .
716 "bootstrap/js/bootstrap.min.js")
723 `(("r-crayon" ,r-crayon)
724 ("r-httpuv" ,r-httpuv)
726 ("r-jsonlite" ,r-jsonlite)
727 ("r-xtable" ,r-xtable)
728 ("r-digest" ,r-digest)
729 ("r-htmltools" ,r-htmltools)
731 ("r-sourcetools" ,r-sourcetools)))
733 `(("js-datatables" ,js-datatables)
734 ("js-html5shiv" ,js-html5shiv)
735 ("js-json2" ,js-json2)
736 ("js-respond" ,js-respond)
737 ("js-selectize" ,js-selectize)
738 ("js-strftime" ,js-strftime)
739 ("js-highlight" ,js-highlight)
740 ("js-es5-shim" ,js-es5-shim)))
742 `(("uglify-js" ,uglify-js)))
743 (home-page "http://shiny.rstudio.com")
744 (synopsis "Easy interactive web applications with R")
746 "Makes it incredibly easy to build interactive web applications
747 with R. Automatic \"reactive\" binding between inputs and outputs and
748 extensive prebuilt widgets make it possible to build beautiful,
749 responsive, and powerful applications with minimal effort.")
750 (license license:artistic2.0)))
752 (define-public r-shinydashboard
754 (name "r-shinydashboard")
758 (uri (cran-uri "shinydashboard" version))
761 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
762 (build-system r-build-system)
763 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
764 ;; Regenerate it from the included sources.
766 `(#:modules ((guix build utils)
767 (guix build r-build-system)
770 (modify-phases %standard-phases
771 (add-after 'unpack 'generate-minified-javascript
773 (with-directory-excursion "inst/AdminLTE"
774 (delete-file "app.min.js")
775 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
776 (call-with-output-file "app.min.js"
778 (dump-port minified port))))))))))
780 `(("r-htmltools" ,r-htmltools)
781 ("r-promises" ,r-promises)
782 ("r-shiny" ,r-shiny)))
784 `(("uglify-js" ,uglify-js)))
785 (home-page "http://rstudio.github.io/shinydashboard/")
786 (synopsis "Create dashboards with shiny")
787 (description "This package provides an extension to the Shiny web
788 application framework for R, making it easy to create attractive dashboards.")
789 ;; This package includes software that was released under the Expat
790 ;; license, but the whole package is released under GPL version 2 or
792 (license license:gpl2+)))
794 (define-public r-shinyfiles
796 (name "r-shinyfiles")
801 (uri (cran-uri "shinyFiles" version))
804 "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i"))))
805 (properties `((upstream-name . "shinyFiles")))
806 (build-system r-build-system)
809 ("r-htmltools" ,r-htmltools)
810 ("r-jsonlite" ,r-jsonlite)
812 ("r-tibble" ,r-tibble)))
813 (home-page "https://github.com/thomasp85/shinyFiles")
814 (synopsis "Server-side file system viewer for Shiny")
816 "This package provides functionality for client-side navigation of the
817 server side file system in shiny apps. In case the app is running locally
818 this gives the user direct access to the file system without the need to
819 \"download\" files to a temporary location. Both file and folder selection as
820 well as file saving is available.")
821 (license license:gpl2+)))
823 (define-public r-crosstalk
830 (uri (cran-uri "crosstalk" version))
833 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
834 (build-system r-build-system)
836 `(("r-ggplot2" ,r-ggplot2)
837 ("r-htmltools" ,r-htmltools)
838 ("r-jsonlite" ,r-jsonlite)
839 ("r-lazyeval" ,r-lazyeval)
841 ("r-shiny" ,r-shiny)))
842 (home-page "https://rstudio.github.io/crosstalk/")
843 (synopsis "Inter-widget interactivity for HTML widgets")
845 "This package provides building blocks for allowing HTML widgets to
846 communicate with each other, with Shiny or without (i.e. static @code{.html}
847 files). It currently supports linked brushing and filtering.")
848 (license license:expat)))
850 (define-public r-rook
857 (uri (cran-uri "Rook" version))
860 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
861 (properties `((upstream-name . "Rook")))
862 (build-system r-build-system)
863 (propagated-inputs `(("r-brew" ,r-brew)))
864 (home-page "https://cran.r-project.org/web/packages/Rook")
865 (synopsis "Web server interface for R")
867 "This package contains the Rook specification and convenience software
868 for building and running Rook applications. A Rook application is an R
869 reference class object that implements a @code{call} method or an R closure
870 that takes exactly one argument, an environment, and returns a list with three
871 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
872 (license license:gpl2)))
874 (define-public r-miniui
881 (uri (cran-uri "miniUI" version))
884 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
885 (properties `((upstream-name . "miniUI")))
886 (build-system r-build-system)
888 `(("r-htmltools" ,r-htmltools)
889 ("r-shiny" ,r-shiny)))
890 (home-page "https://cran.r-project.org/web/packages/miniUI/")
891 (synopsis "Shiny UI widgets for small screens")
893 "This package provides UI widget and layout functions for writing Shiny apps that
894 work well on small screens.")
895 (license license:gpl3)))
897 (define-public r-feather
904 (uri (cran-uri "feather" version))
907 "0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa"))))
908 (build-system r-build-system)
912 ("r-tibble" ,r-tibble)))
913 (home-page "https://github.com/wesm/feather")
914 (synopsis "R Bindings to the Feather API")
915 (description "Read and write feather files, a lightweight binary columnar
916 data store designed for maximum speed.")
917 (license license:asl2.0)))
919 (define-public r-maps
926 (uri (cran-uri "maps" version))
929 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
930 (build-system r-build-system)
931 (home-page "https://cran.r-project.org/web/packages/maps")
932 (synopsis "Draw geographical maps")
933 (description "This package provides an R module for display of maps.
934 Projection code and larger maps are in separate packages (@code{mapproj} and
936 (license license:gpl2)))
938 (define-public r-mapproj
945 (uri (cran-uri "mapproj" version))
948 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
949 (build-system r-build-system)
950 (propagated-inputs `(("r-maps" ,r-maps)))
951 (home-page "https://cran.r-project.org/web/packages/mapproj")
952 (synopsis "Map projection in R")
953 (description "This package converts latitude/longitude into projected
955 (license (list license:gpl2 ; The R interface
956 (license:non-copyleft ; The C code
957 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
958 "Lucent Public License Version 1.02")))))
960 (define-public r-rgooglemaps
962 (name "r-rgooglemaps")
967 (uri (cran-uri "RgoogleMaps" version))
970 "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
971 (properties `((upstream-name . "RgoogleMaps")))
972 (build-system r-build-system)
973 (propagated-inputs `(("r-png" ,r-png)))
974 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
975 (synopsis "Use Google Maps in R")
976 (description "This package serves two purposes:
978 @item Provide a comfortable R interface to query the Google server for static
980 @item Use the map as a background image to overlay plots within R. This
981 requires proper coordinate scaling.
983 (license license:gpl2+)))
985 (define-public r-geosphere
992 (uri (cran-uri "geosphere" version))
995 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
996 (build-system r-build-system)
997 (propagated-inputs `(("r-sp" ,r-sp)))
998 (home-page "https://cran.r-project.org/web/packages/geosphere")
999 (synopsis "Spherical trigonometry")
1000 (description "This package computes spherical trigonometry for geographic
1001 applications. That is, compute distances and related measures for angular
1002 (longitude/latitude) locations.")
1003 (license license:gpl3+)))
1005 (define-public r-ggmap
1012 (uri (cran-uri "ggmap" version))
1015 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1016 (build-system r-build-system)
1018 `(("r-bitops" ,r-bitops)
1019 ("r-digest" ,r-digest)
1020 ("r-dplyr" ,r-dplyr)
1021 ("r-ggplot2" ,r-ggplot2)
1025 ("r-magrittr" ,r-magrittr)
1028 ("r-purrr" ,r-purrr)
1029 ("r-rgooglemaps" ,r-rgooglemaps)
1030 ("r-rjson" ,r-rjson)
1031 ("r-scales" ,r-scales)
1032 ("r-stringr" ,r-stringr)
1033 ("r-tibble" ,r-tibble)
1034 ("r-tidyr" ,r-tidyr)))
1035 (home-page "https://github.com/dkahle/ggmap")
1036 (synopsis "Spatial visualization with ggplot2")
1037 (description "This package provides a collection of functions to visualize
1038 spatial data and models on top of static maps from various online sources (e.g
1039 Google Maps and Stamen Maps). It includes tools common to those tasks,
1040 including functions for geolocation and routing.")
1041 (license license:gpl2)))
1043 (define-public r-haven
1050 (uri (cran-uri "haven" version))
1053 "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0"))))
1054 (build-system r-build-system)
1058 `(("r-forcats" ,r-forcats)
1061 ("r-readr" ,r-readr)
1062 ("r-tibble" ,r-tibble)))
1063 (home-page "https://haven.tidyverse.org")
1064 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1066 "This package lets you mport foreign statistical formats into R via the
1067 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1068 (license license:expat)))
1070 (define-public r-amap
1076 (uri (cran-uri "amap" version))
1079 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
1080 (build-system r-build-system)
1082 `(("gfortran" ,gfortran)))
1083 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1084 (synopsis "Another multidimensional analysis package")
1085 (description "This package provides tools for clustering and principal
1086 component analysis (with robust methods, and parallelized functions).")
1087 (license license:gpl2+)))
1089 (define-public r-ape
1096 (uri (cran-uri "ape" version))
1099 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1100 (build-system r-build-system)
1102 `(("r-lattice" ,r-lattice)
1104 ("r-rcpp" ,r-rcpp)))
1105 (home-page "http://ape-package.ird.fr/")
1106 (synopsis "Analyses of phylogenetics and evolution")
1108 "This package provides functions for reading, writing, plotting, and
1109 manipulating phylogenetic trees, analyses of comparative data in a
1110 phylogenetic framework, ancestral character analyses, analyses of
1111 diversification and macroevolution, computing distances from DNA sequences,
1112 and several other tools.")
1113 (license license:gpl2+)))
1115 (define-public r-abbyyr
1122 (uri (cran-uri "abbyyR" version))
1125 "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx"))))
1126 (properties `((upstream-name . "abbyyR")))
1127 (build-system r-build-system)
1129 `(("r-curl" ,r-curl)
1132 ("r-progress" ,r-progress)
1133 ("r-readr" ,r-readr)
1135 (home-page "https://github.com/soodoku/abbyyR")
1136 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1138 "This package provides tools to get text from images of text using Abbyy
1139 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1140 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1141 passports and get the results in a variety of formats including plain text and
1142 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1143 (license license:expat)))
1145 (define-public r-colorspace
1147 (name "r-colorspace")
1152 (uri (cran-uri "colorspace" version))
1154 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1155 (build-system r-build-system)
1156 (home-page "https://cran.r-project.org/web/packages/colorspace")
1157 (synopsis "Color space manipulation")
1159 "This package carries out a mapping between assorted color spaces
1160 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1161 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1162 colors are provided.")
1163 (license license:bsd-3)))
1165 (define-public r-glue
1172 (uri (cran-uri "glue" version))
1175 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1176 (build-system r-build-system)
1177 (home-page "https://github.com/tidyverse/glue")
1178 (synopsis "Interpreted string literals")
1180 "This package provides an implementation of interpreted string literals,
1181 inspired by Python's Literal String Interpolation (PEP-0498) and
1182 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1183 (license license:expat)))
1185 (define-public r-pastecs
1191 (uri (cran-uri "pastecs" version))
1194 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1195 (build-system r-build-system)
1197 `(("r-boot" ,r-boot)))
1198 (home-page "http://www.sciviews.org/pastecs")
1199 (synopsis "Analysis of space-time ecological series")
1201 "This package provides functions for regulation, decomposition and analysis
1202 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1203 initiative to bring PASSTEC 2000 functionalities to R.")
1204 (license license:gpl2+)))
1206 (define-public r-plogr
1213 (uri (cran-uri "plogr" version))
1216 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1217 (build-system r-build-system)
1218 (home-page "https://github.com/krlmlr/plogr")
1219 (synopsis "R bindings for the plog C++ logging library")
1221 "This package provides the header files for a stripped-down version of
1222 the plog header-only C++ logging library, and a method to log to R's standard
1224 (license license:expat)))
1226 (define-public r-pls
1233 (uri (cran-uri "pls" version))
1236 "0jw3zl5z06023zxr74phnvwax8m3i4a4i6lsqiq6j15aq9zq3zgq"))))
1237 (build-system r-build-system)
1238 (home-page "http://mevik.net/work/software/pls.html")
1239 (synopsis "Partial Least Squares and Principal Component Regression")
1241 "The pls package implements multivariate regression methods: Partial Least
1242 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1243 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1246 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1247 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1248 @item multi-response models (or @dfn{PLS2})
1249 @item flexible cross-validation
1250 @item Jackknife variance estimates of regression coefficients
1251 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1252 (R)MSEP, R², and correlation loadings
1253 @item formula interface, modelled after @code{lm()}, with methods for predict,
1254 print, summary, plot, update, etc.
1255 @item extraction functions for coefficients, scores, and loadings
1256 @item MSEP, RMSEP, and R² estimates
1257 @item multiplicative scatter correction (@dfn{MSC})
1259 (license license:gpl2)))
1268 (uri (cran-uri "ps" version))
1270 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1271 (build-system r-build-system)
1272 (home-page "http://ps.r-lib.org")
1273 (synopsis "List, query, and manipulate system processes")
1275 "The ps package implements an API to list, query, and manipulate system
1276 processes. Most of its code is based on the @code{psutil} Python package.")
1277 (license license:bsd-3)))
1279 (define-public r-pkgbuild
1286 (uri (cran-uri "pkgbuild" version))
1289 "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9"))))
1290 (build-system r-build-system)
1292 `(("r-callr" ,r-callr)
1294 ("r-crayon" ,r-crayon)
1296 ("r-prettyunits" ,r-prettyunits)
1298 ("r-rprojroot" ,r-rprojroot)
1299 ("r-withr" ,r-withr)))
1300 (home-page "https://github.com/r-pkgs/pkgbuild")
1301 (synopsis "Find tools needed to build R packages")
1303 "This package provides functions used to build R packages. It locates
1304 compilers needed to build R packages on various platforms and ensures the PATH
1305 is configured appropriately so R can use them.")
1306 (license license:gpl3)))
1308 (define-public r-pkgload
1315 (uri (cran-uri "pkgload" version))
1318 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1319 (build-system r-build-system)
1321 `(("r-desc" ,r-desc)
1322 ("r-pkgbuild" ,r-pkgbuild)
1323 ("r-rlang" ,r-rlang)
1324 ("r-rprojroot" ,r-rprojroot)
1325 ("r-rstudioapi" ,r-rstudioapi)
1326 ("r-withr" ,r-withr)))
1327 (home-page "https://github.com/r-lib/pkgload")
1328 (synopsis "Simulate package installation and attach")
1330 "This package simulates the process of installing a package and then
1331 attaching it. This is a key part of the @code{devtools} package as it allows
1332 you to rapidly iterate while developing a package.")
1333 (license license:gpl3)))
1335 (define-public r-rcpp
1342 (uri (cran-uri "Rcpp" version))
1344 (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7"))))
1345 (build-system r-build-system)
1347 `(("r-knitr" ,r-knitr))) ; for vignettes
1348 (home-page "http://www.rcpp.org")
1349 (synopsis "Seamless R and C++ integration")
1351 "The Rcpp package provides R functions as well as C++ classes which offer
1352 a seamless integration of R and C++. Many R data types and objects can be
1353 mapped back and forth to C++ equivalents which facilitates both writing of new
1354 code as well as easier integration of third-party libraries. Documentation
1355 about Rcpp is provided by several vignettes included in this package, via the
1356 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1357 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1358 @code{citation(\"Rcpp\")} for details on these last two.")
1359 (license license:gpl2+)))
1361 (define-public r-bindr
1368 (uri (cran-uri "bindr" version))
1371 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1372 (build-system r-build-system)
1373 (home-page "https://github.com/krlmlr/bindr")
1374 (synopsis "Parametrized active bindings")
1376 "This package provides a simple interface for creating active bindings
1377 where the bound function accepts additional arguments.")
1378 (license license:expat)))
1380 (define-public r-bindrcpp
1387 (uri (cran-uri "bindrcpp" version))
1390 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1391 (build-system r-build-system)
1393 `(("r-bindr" ,r-bindr)
1394 ("r-plogr" ,r-plogr)
1395 ("r-rcpp" ,r-rcpp)))
1396 (home-page "https://github.com/krlmlr/bindrcpp")
1397 (synopsis "Rcpp interface to active bindings")
1399 "This package provides an easy way to fill an environment with active
1400 bindings that call a C++ function.")
1401 (license license:expat)))
1403 (define-public r-auc
1410 (uri (cran-uri "AUC" version))
1413 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1414 (properties `((upstream-name . "AUC")))
1415 (build-system r-build-system)
1416 (home-page "https://cran.r-project.org/web/packages/AUC")
1417 (synopsis "Compute the area under the curve of selected measures")
1419 "This package includes functions to compute the area under the curve of
1420 selected measures: the area under the sensitivity curve (AUSEC), the area
1421 under the specificity curve (AUSPC), the area under the accuracy
1422 curve (AUACC), and the area under the receiver operating characteristic
1423 curve (AUROC). The curves can also be visualized. Support for partial areas
1425 (license license:gpl2+)))
1427 (define-public r-calibrate
1429 (name "r-calibrate")
1434 (uri (cran-uri "calibrate" version))
1437 "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
1438 (build-system r-build-system)
1440 `(("r-mass" ,r-mass)))
1441 (home-page "https://cran.r-project.org/web/packages/calibrate")
1442 (synopsis "Calibration of scatterplot and biplot axes")
1444 "This is a package for drawing calibrated scales with tick marks
1445 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1446 (license license:gpl2)))
1448 (define-public r-shape
1455 (uri (cran-uri "shape" version))
1458 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1459 (build-system r-build-system)
1460 (home-page "https://cran.r-project.org/web/packages/shape")
1461 (synopsis "Functions for plotting graphical shapes")
1463 "This package provides functions for plotting graphical shapes such as
1464 ellipses, circles, cylinders, arrows, ...")
1465 (license license:gpl3+)))
1467 (define-public r-globaloptions
1469 (name "r-globaloptions")
1474 (uri (cran-uri "GlobalOptions" version))
1477 "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn"))))
1478 (properties `((upstream-name . "GlobalOptions")))
1479 (build-system r-build-system)
1480 (home-page "https://github.com/jokergoo/GlobalOptions")
1481 (synopsis "Generate functions to get or set global options")
1483 "This package provides more controls on the option values such as
1484 validation and filtering on the values, making options invisible or private.")
1485 (license license:gpl2+)))
1487 (define-public r-circlize
1494 (uri (cran-uri "circlize" version))
1497 "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f"))))
1498 (build-system r-build-system)
1500 `(("r-colorspace" ,r-colorspace)
1501 ("r-globaloptions" ,r-globaloptions)
1502 ("r-shape" ,r-shape)))
1503 (home-page "https://github.com/jokergoo/circlize")
1504 (synopsis "Circular visualization")
1506 "Circular layout is an efficient way to visualise huge amounts of
1507 information. This package provides an implementation of circular layout
1508 generation in R as well as an enhancement of available software. Its
1509 flexibility is based on the usage of low-level graphics functions such that
1510 self-defined high-level graphics can be easily implemented by users for
1511 specific purposes. Together with the seamless connection between the powerful
1512 computational and visual environment in R, it gives users more convenience and
1513 freedom to design figures for better understanding complex patterns behind
1514 multi-dimensional data.")
1515 (license license:gpl2+)))
1517 (define-public r-powerlaw
1524 (uri (cran-uri "poweRlaw" version))
1527 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1528 (properties `((upstream-name . "poweRlaw")))
1529 (build-system r-build-system)
1531 `(("r-vgam" ,r-vgam)))
1532 (home-page "https://github.com/csgillespie/poweRlaw")
1533 (synopsis "Tools for the analysis of heavy tailed distributions")
1535 "This package provides an implementation of maximum likelihood estimators
1536 for a variety of heavy tailed distributions, including both the discrete and
1537 continuous power law distributions. Additionally, a goodness-of-fit based
1538 approach is used to estimate the lower cut-off for the scaling region.")
1539 ;; Any of these GPL versions.
1540 (license (list license:gpl2 license:gpl3))))
1542 (define-public r-compare
1549 (uri (cran-uri "compare" version))
1552 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1553 (build-system r-build-system)
1554 (home-page "https://cran.r-project.org/web/packages/compare")
1555 (synopsis "Comparing objects for differences")
1557 "This package provides functions to compare a model object to a
1558 comparison object. If the objects are not identical, the functions can be
1559 instructed to explore various modifications of the objects (e.g., sorting
1560 rows, dropping names) to see if the modified versions are identical.")
1561 (license license:gpl2+)))
1563 (define-public r-dendextend
1565 (name "r-dendextend")
1570 (uri (cran-uri "dendextend" version))
1573 "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl"))))
1574 (build-system r-build-system)
1576 `(("r-ggplot2" ,r-ggplot2)
1577 ("r-magrittr" ,r-magrittr)
1578 ("r-viridis" ,r-viridis)))
1579 (home-page "https://cran.r-project.org/web/packages/dendextend")
1580 (synopsis "Extending 'dendrogram' functionality in R")
1582 "This package offers a set of functions for extending @code{dendrogram}
1583 objects in R, letting you visualize and compare trees of hierarchical
1584 clusterings. You can adjust a tree's graphical parameters (the color, size,
1585 type, etc of its branches, nodes and labels) and visually and statistically
1586 compare different dendrograms to one another.")
1587 ;; Any of these versions
1588 (license (list license:gpl2 license:gpl3))))
1590 (define-public r-getoptlong
1592 (name "r-getoptlong")
1597 (uri (cran-uri "GetoptLong" version))
1600 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1601 (properties `((upstream-name . "GetoptLong")))
1602 (build-system r-build-system)
1606 `(("r-globaloptions" ,r-globaloptions)
1607 ("r-rjson" ,r-rjson)))
1608 (home-page "https://github.com/jokergoo/GetoptLong")
1609 (synopsis "Parsing command-line arguments and variable interpolation")
1611 "This is yet another command-line argument parser which wraps the
1612 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1613 use in R. It also provides a simple way for variable interpolation in R.")
1614 (license license:gpl2+)))
1616 (define-public r-fastmatch
1618 (name "r-fastmatch")
1623 (uri (cran-uri "fastmatch" version))
1626 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1627 (build-system r-build-system)
1628 (home-page "http://www.rforge.net/fastmatch")
1629 (synopsis "Fast match function")
1631 "This package provides a fast @code{match} replacement for cases that
1632 require repeated look-ups. It is slightly faster that R's built-in
1633 @code{match} function on first match against a table, but extremely fast on
1634 any subsequent lookup as it keeps the hash table in memory.")
1635 (license license:gpl2)))
1644 (uri (cran-uri "ff" version))
1647 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1648 (build-system r-build-system)
1649 (propagated-inputs `(("r-bit" ,r-bit)))
1650 (home-page "http://ff.r-forge.r-project.org/")
1651 (synopsis "Memory-efficient storage of large data on disk and access functions")
1653 "This package provides data structures that are stored on disk but
1654 behave (almost) as if they were in RAM by transparently mapping only a section
1656 ;; error Architecture not supported.
1657 (supported-systems (delete "aarch64-linux" %supported-systems))
1658 (license license:gpl2)))
1660 (define-public r-ffbase
1667 (uri (cran-uri "ffbase" version))
1670 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
1671 (build-system r-build-system)
1674 ("r-fastmatch" ,r-fastmatch)
1676 (home-page "http://github.com/edwindj/ffbase")
1677 (synopsis "Basic statistical functions for package 'ff'")
1679 "This package extends the out of memory vectors of @code{ff} with
1680 statistical functions and other utilities to ease their usage.")
1681 (license license:gpl3)))
1683 (define-public r-prettyunits
1685 (name "r-prettyunits")
1690 (uri (cran-uri "prettyunits" version))
1693 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
1694 (build-system r-build-system)
1696 `(("r-assertthat" ,r-assertthat)
1697 ("r-magrittr" ,r-magrittr)))
1698 (home-page "https://github.com/gaborcsardi/prettyunits")
1699 (synopsis "Pretty, human readable formatting of quantities")
1701 "This package provides tools for pretty, human readable formatting of
1703 (license license:expat)))
1705 (define-public r-reshape
1712 (uri (cran-uri "reshape" version))
1715 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
1716 (build-system r-build-system)
1718 `(("r-plyr" ,r-plyr)
1719 ("r-rcpp" ,r-rcpp)))
1720 (home-page "http://had.co.nz/reshape")
1721 (synopsis "Flexibly reshape data")
1723 "Flexibly restructure and aggregate data using just two functions:
1724 @code{melt} and @code{cast}. This package provides them.")
1725 (license license:expat)))
1727 (define-public r-progress
1734 (uri (cran-uri "progress" version))
1737 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
1738 (build-system r-build-system)
1740 `(("r-crayon" ,r-crayon)
1742 ("r-prettyunits" ,r-prettyunits)
1744 (home-page "https://github.com/gaborcsardi/progress")
1745 (synopsis "Terminal progress bars")
1747 "This package provides configurable progress bars. They may include
1748 percentage, elapsed time, and/or the estimated completion time. They work in
1749 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
1750 package also provides a C++ API, that works with or without Rcpp.")
1751 (license license:expat)))
1753 (define-public r-ggally
1760 (uri (cran-uri "GGally" version))
1763 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
1764 (properties `((upstream-name . "GGally")))
1765 (build-system r-build-system)
1767 `(("libressl" ,libressl)))
1769 `(("r-ggplot2" ,r-ggplot2)
1770 ("r-gtable" ,r-gtable)
1772 ("r-progress" ,r-progress)
1773 ("r-rcolorbrewer" ,r-rcolorbrewer)
1774 ("r-reshape" ,r-reshape)
1775 ("r-rlang" ,r-rlang)))
1776 (home-page "https://ggobi.github.io/ggally")
1777 (synopsis "Extension to ggplot2")
1779 "The R package ggplot2 is a plotting system based on the grammar of
1780 graphics. GGally extends ggplot2 by adding several functions to reduce the
1781 complexity of combining geometric objects with transformed data. Some of
1782 these functions include a pairwise plot matrix, a two group pairwise plot
1783 matrix, a parallel coordinates plot, a survival plot, and several functions to
1785 (license license:gpl2+)))
1787 (define-public r-proxy
1794 (uri (cran-uri "proxy" version))
1797 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
1798 (build-system r-build-system)
1799 (home-page "https://cran.r-project.org/web/packages/proxy")
1800 (synopsis "Distance and similarity measures")
1802 "This package provides an extensible framework for the efficient
1803 calculation of auto- and cross-proximities, along with implementations of the
1804 most popular ones.")
1805 (license license:gpl2)))
1814 (uri (cran-uri "sp" version))
1817 "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p"))))
1818 (build-system r-build-system)
1820 `(("r-lattice" ,r-lattice)))
1821 (home-page "https://cran.r-project.org/web/packages/sp")
1822 (synopsis "Classes and methods for spatial data")
1824 "This package provides classes and methods for spatial data; the classes
1825 document where the spatial location information resides, for 2D or 3D data.
1826 Utility functions are provided, e.g. for plotting data as maps, spatial
1827 selection, as well as methods for retrieving coordinates, for subsetting,
1828 print, summary, etc.")
1829 (license license:gpl2+)))
1831 (define-public r-rmtstat
1838 (uri (cran-uri "RMTstat" version))
1841 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
1842 (properties `((upstream-name . "RMTstat")))
1843 (build-system r-build-system)
1844 (home-page "https://cran.r-project.org/web/packages/RMTstat")
1845 (synopsis "Distributions, statistics and tests derived from random matrix theory")
1847 "This package provides functions for working with the Tracy-Widom laws
1848 and other distributions related to the eigenvalues of large Wishart
1850 (license license:bsd-3)))
1852 (define-public r-rmpi
1858 (uri (cran-uri "Rmpi" version))
1861 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
1862 (properties `((upstream-name . "Rmpi")))
1863 (build-system r-build-system)
1865 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
1866 #:phases (modify-phases %standard-phases
1867 (add-before 'install 'mpi-setup
1870 `(("openmpi" ,openmpi)))
1872 `(("pkg-config" ,pkg-config)))
1873 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
1874 (synopsis "R interface to message-passing interface (MPI)")
1876 "This package provides an interface (wrapper) to MPI APIs. It also
1877 provides an interactive R manager and worker environment.")
1878 (license license:gpl2+)))
1880 (define-public r-lmoments
1887 (uri (cran-uri "Lmoments" version))
1890 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
1891 (properties `((upstream-name . "Lmoments")))
1892 (build-system r-build-system)
1894 `(("r-rcpp" ,r-rcpp)
1895 ("r-rcpparmadillo" ,r-rcpparmadillo)))
1896 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
1897 (synopsis "L-moments and quantile mixtures")
1899 "This package contains functions to estimate L-moments and trimmed
1900 L-moments from the data. It also contains functions to estimate the
1901 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
1902 quantile mixture from L-moments and trimmed L-moments.")
1903 (license license:gpl2)))
1905 (define-public r-distillery
1907 (name "r-distillery")
1912 (uri (cran-uri "distillery" version))
1915 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
1916 (build-system r-build-system)
1917 (home-page "http://www.ral.ucar.edu/staff/ericg")
1918 (synopsis "Functions for confidence intervals and object information")
1920 "This package provides some very simple method functions for confidence
1921 interval calculation and to distill pertinent information from a potentially
1922 complex object; primarily used in common with the packages extRemes and
1924 (license license:gpl2+)))
1926 (define-public r-extremes
1933 (uri (cran-uri "extRemes" version))
1936 "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic"))))
1937 (properties `((upstream-name . "extRemes")))
1938 (build-system r-build-system)
1940 `(("r-distillery" ,r-distillery)
1941 ("r-lmoments" ,r-lmoments)))
1942 (home-page "http://www.assessment.ucar.edu/toolkit/")
1943 (synopsis "Extreme value analysis")
1945 "ExtRemes is a suite of functions for carrying out analyses on the
1946 extreme values of a process of interest; be they block maxima over long blocks
1947 or excesses over a high threshold.")
1948 (license license:gpl2+)))
1950 (define-public r-lmtest
1957 (uri (cran-uri "lmtest" version))
1960 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
1961 (build-system r-build-system)
1963 `(("r-zoo" ,r-zoo)))
1965 `(("gfortran" ,gfortran)))
1966 (home-page "https://cran.r-project.org/web/packages/lmtest")
1967 (synopsis "Testing linear regression models")
1969 "This package provides a collection of tests, data sets, and examples for
1970 diagnostic checking in linear regression models. Furthermore, some generic
1971 tools for inference in parametric models are provided.")
1972 ;; Either version is okay
1973 (license (list license:gpl2 license:gpl3))))
1975 (define-public r-idr
1981 (uri (cran-uri "idr" version))
1984 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
1985 (build-system r-build-system)
1986 (home-page "https://cran.r-project.org/web/packages/idr/")
1987 (synopsis "Irreproducible discovery rate")
1989 "This is a package for estimating the copula mixture model and plotting
1990 correspondence curves in \"Measuring reproducibility of high-throughput
1991 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
1992 by Li, Brown, Huang, and Bickel")
1993 (license license:gpl2+)))
1995 (define-public r-inline
2001 (uri (cran-uri "inline" version))
2004 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2005 (build-system r-build-system)
2006 (home-page "https://cran.r-project.org/web/packages/inline")
2007 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2009 "This package provides functionality to dynamically define R functions
2010 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2011 @code{.Call} calling conventions.")
2012 ;; Any version of the LGPL.
2013 (license license:lgpl3+)))
2015 (define-public r-bbmle
2022 (uri (cran-uri "bbmle" version))
2025 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2026 (build-system r-build-system)
2028 `(("r-lattice" ,r-lattice)
2030 ("r-numderiv" ,r-numderiv)))
2031 (home-page "https://cran.r-project.org/web/packages/bbmle")
2032 (synopsis "Tools for General Maximum Likelihood Estimation")
2034 "This package provides methods and functions for fitting maximum
2035 likelihood models in R. This package modifies and extends the @code{mle}
2036 classes in the @code{stats4} package.")
2037 ;; Any version of the GPL
2038 (license license:gpl2+)))
2040 (define-public r-emdbook
2047 (uri (cran-uri "emdbook" version))
2050 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2051 (build-system r-build-system)
2053 `(("r-bbmle" ,r-bbmle)
2055 ("r-lattice" ,r-lattice)
2058 ("r-rcpp" ,r-rcpp)))
2059 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2060 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2062 "This package provides auxiliary functions and data sets for \"Ecological
2063 Models and Data\", a book presenting maximum likelihood estimation and related
2064 topics for ecologists (ISBN 978-0-691-12522-0).")
2066 (license (list license:gpl2 license:gpl3))))
2068 (define-public r-lpsolve
2071 (version "5.6.13.1")
2075 (uri (cran-uri "lpSolve" version))
2078 "1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a"))))
2079 (properties `((upstream-name . "lpSolve")))
2080 (build-system r-build-system)
2081 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2082 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2084 "Lp_solve is software for solving linear, integer and mixed integer
2085 programs. This implementation supplies a \"wrapper\" function in C and some R
2086 functions that solve general linear/integer problems, assignment problems, and
2087 transportation problems.")
2088 (license license:lgpl2.0)))
2090 (define-public r-limsolve
2097 (uri (cran-uri "limSolve" version))
2100 "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
2101 (properties `((upstream-name . "limSolve")))
2102 (build-system r-build-system)
2104 `(("r-lpsolve" ,r-lpsolve)
2106 ("r-quadprog" ,r-quadprog)))
2107 (native-inputs `(("gfortran" ,gfortran)))
2108 (home-page "https://cran.r-project.org/web/packages/limSolve")
2109 (synopsis "Solving linear inverse models")
2111 "This package provides functions that:
2114 @item find the minimum/maximum of a linear or quadratic function,
2115 @item sample an underdetermined or overdetermined system,
2116 @item solve a linear system Ax=B for the unknown x.
2119 It includes banded and tridiagonal linear systems. The package calls Fortran
2120 functions from LINPACK.")
2122 (license (list license:gpl2+ license:gpl3+))))
2124 (define-public r-fitdistrplus
2126 (name "r-fitdistrplus")
2131 (uri (cran-uri "fitdistrplus" version))
2134 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2135 (build-system r-build-system)
2137 `(("r-mass" ,r-mass)
2138 ("r-npsurv" ,r-npsurv)
2139 ("r-survival" ,r-survival)))
2140 (home-page "http://riskassessment.r-forge.r-project.org")
2141 (synopsis "Fitting a parametric distribution from data")
2143 "This package extends the @code{fitdistr} function of the MASS package
2144 with several functions to help the fit of a parametric distribution to
2145 non-censored or censored data. Censored data may contain left-censored,
2146 right-censored and interval-censored values, with several lower and upper
2147 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2148 provides moment matching (MME), quantile matching (QME) and maximum
2149 goodness-of-fit estimation (MGE) methods (available only for non-censored
2150 data). Weighted versions of MLE, MME and QME are available.")
2151 (license license:gpl2+)))
2153 (define-public r-energy
2160 (uri (cran-uri "energy" version))
2163 "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4"))))
2164 (build-system r-build-system)
2166 `(("r-boot" ,r-boot)
2167 ("r-rcpp" ,r-rcpp)))
2168 (home-page "https://cran.r-project.org/web/packages/energy")
2169 (synopsis "Multivariate inference via the energy of data")
2171 "This package provides e-statistics (energy) tests and statistics for
2172 multivariate and univariate inference, including distance correlation,
2173 one-sample, two-sample, and multi-sample tests for comparing multivariate
2174 distributions, are implemented. Measuring and testing multivariate
2175 independence based on distance correlation, partial distance correlation,
2176 multivariate goodness-of-fit tests, clustering based on energy distance,
2177 testing for multivariate normality, distance components (disco) for
2178 non-parametric analysis of structured data, and other energy
2179 statistics/methods are implemented.")
2180 (license license:gpl2+)))
2182 (define-public r-suppdists
2184 (name "r-suppdists")
2189 (uri (cran-uri "SuppDists" version))
2192 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2193 (properties `((upstream-name . "SuppDists")))
2194 (build-system r-build-system)
2195 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2196 (synopsis "Supplementary distributions")
2198 "This package provides ten distributions supplementing those built into
2199 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2200 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2201 coefficient, Johnson distributions, normal scores and generalized
2202 hypergeometric distributions. In addition two random number generators of
2203 George Marsaglia are included.")
2204 (license license:gpl2+)))
2206 (define-public r-ksamples
2213 (uri (cran-uri "kSamples" version))
2216 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2217 (properties `((upstream-name . "kSamples")))
2218 (build-system r-build-system)
2220 `(("r-suppdists" ,r-suppdists)))
2221 (home-page "https://cran.r-project.org/web/packages/kSamples")
2222 (synopsis "K-Sample rank tests and their combinations")
2224 "This package provides tools to compares k samples using the
2225 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2226 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2227 test. It computes asymptotic, simulated or (limited) exact P-values, all
2228 valid under randomization, with or without ties, or conditionally under random
2229 sampling from populations, given the observed tie pattern. Except for Steel's
2230 test and the JT test it also combines these tests across several blocks of
2232 (license license:gpl2+)))
2234 (define-public r-cvst
2241 (uri (cran-uri "CVST" version))
2244 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2245 (properties `((upstream-name . "CVST")))
2246 (build-system r-build-system)
2248 `(("r-kernlab" ,r-kernlab)
2249 ("r-matrix" ,r-matrix)))
2250 (home-page "https://cran.r-project.org/web/packages/CVST")
2251 (synopsis "Fast cross-validation via sequential testing")
2253 "This package implements the fast cross-validation via sequential
2254 testing (CVST) procedure. CVST is an improved cross-validation procedure
2255 which uses non-parametric testing coupled with sequential analysis to
2256 determine the best parameter set on linearly increasing subsets of the data.
2257 Additionally to the CVST the package contains an implementation of the
2258 ordinary k-fold cross-validation with a flexible and powerful set of helper
2259 objects and methods to handle the overall model selection process. The
2260 implementations of the Cochran's Q test with permutations and the sequential
2261 testing framework of Wald are generic and can therefore also be used in other
2263 (license license:gpl2+)))
2265 (define-public r-squarem
2268 (version "2017.10-1")
2272 (uri (cran-uri "SQUAREM" version))
2275 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2276 (properties `((upstream-name . "SQUAREM")))
2277 (build-system r-build-system)
2278 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2279 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2281 "This package provides algorithms for accelerating the convergence of
2282 slow, monotone sequences from smooth, contraction mapping such as the EM
2283 algorithm. It can be used to accelerate any smooth, linearly convergent
2284 acceleration scheme. A tutorial style introduction to this package is
2285 available in a vignette.")
2286 (license license:gpl2+)))
2288 (define-public r-lava
2295 (uri (cran-uri "lava" version))
2298 "13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f"))))
2299 (build-system r-build-system)
2301 `(("r-numderiv" ,r-numderiv)
2302 ("r-squarem" ,r-squarem)
2303 ("r-survival" ,r-survival)))
2304 (home-page "https://github.com/kkholst/lava")
2305 (synopsis "Latent variable models")
2307 "This package provides tools for the estimation and simulation of latent
2309 (license license:gpl3)))
2311 (define-public r-drr
2318 (uri (cran-uri "DRR" version))
2321 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2322 (properties `((upstream-name . "DRR")))
2323 (build-system r-build-system)
2325 `(("r-cvst" ,r-cvst)
2326 ("r-kernlab" ,r-kernlab)
2327 ("r-matrix" ,r-matrix)))
2328 (home-page "https://cran.r-project.org/web/packages/DRR")
2329 (synopsis "Dimensionality reduction via regression")
2331 "This package provides an implementation of dimensionality reduction via
2332 regression using Kernel Ridge Regression.")
2333 (license license:gpl3)))
2335 (define-public r-prodlim
2338 (version "2018.04.18")
2342 (uri (cran-uri "prodlim" version))
2345 "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb"))))
2346 (build-system r-build-system)
2348 `(("r-kernsmooth" ,r-kernsmooth)
2351 ("r-survival" ,r-survival)))
2352 (home-page "https://cran.r-project.org/web/packages/prodlim")
2353 (synopsis "Product-limit estimation for censored event history analysis")
2355 "This package provides a fast and user-friendly implementation of
2356 nonparametric estimators for censored event history (survival) analysis with
2357 the Kaplan-Meier and Aalen-Johansen methods.")
2358 (license license:gpl2+)))
2360 (define-public r-dimred
2367 (uri (cran-uri "dimRed" version))
2370 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2371 (properties `((upstream-name . "dimRed")))
2372 (build-system r-build-system)
2375 ("r-magrittr" ,r-magrittr)))
2376 (home-page "https://github.com/gdkrmr/dimRed")
2377 (synopsis "Framework for dimensionality reduction")
2379 "This package provides a collection of dimensionality reduction
2380 techniques from R packages and provides a common interface for calling the
2382 (license license:gpl3)))
2384 (define-public r-timedate
2387 (version "3043.102")
2391 (uri (cran-uri "timeDate" version))
2394 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2395 (properties `((upstream-name . "timeDate")))
2396 (build-system r-build-system)
2397 (home-page "https://www.rmetrics.org")
2398 (synopsis "Chronological and calendar objects")
2400 "This package provides an environment for teaching \"Financial
2401 Engineering and Computational Finance\" and for managing chronological and
2403 (license license:gpl2+)))
2405 (define-public r-magic
2412 (uri (cran-uri "magic" version))
2415 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2416 (build-system r-build-system)
2418 `(("r-abind" ,r-abind)))
2419 (home-page "https://github.com/RobinHankin/magic.git")
2420 (synopsis "Create and investigate magic squares")
2422 "This package provides a collection of efficient, vectorized algorithms
2423 for the creation and investigation of magic squares and hypercubes, including
2424 a variety of functions for the manipulation and analysis of arbitrarily
2425 dimensioned arrays.")
2426 (license license:gpl2)))
2428 (define-public r-rmysql
2435 (uri (cran-uri "RMySQL" version))
2438 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2439 (properties `((upstream-name . "RMySQL")))
2440 (build-system r-build-system)
2442 `(("mariadb" ,mariadb)
2445 `(("r-dbi" ,r-dbi)))
2446 (home-page "https://github.com/r-dbi/RMySQL")
2447 (synopsis "Database interface and MySQL driver for R")
2449 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2450 package contains an old implementation based on legacy code from S-PLUS which
2451 is being phased out. A modern MySQL client based on Rcpp is available from
2452 the RMariaDB package.")
2453 (license license:gpl2)))
2455 (define-public r-rpostgresql
2457 (name "r-rpostgresql")
2462 (uri (cran-uri "RPostgreSQL" version))
2465 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2466 (properties `((upstream-name . "RPostgreSQL")))
2467 (build-system r-build-system)
2469 `(("postgresql" ,postgresql)))
2471 `(("r-dbi" ,r-dbi)))
2472 (home-page "https://github.com/tomoakin/RPostgreSQL")
2473 (synopsis "R interface to the PostgreSQL database system")
2475 "This package provides a Database Interface (DBI) compliant driver for R
2476 to access PostgreSQL database systems.")
2477 ;; The whole package is released under GPL version 2. It includes code
2478 ;; under the PostgreSQL license.
2479 (license license:gpl2)))
2481 (define-public r-geometry
2488 (uri (cran-uri "geometry" version))
2491 "0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm"))))
2492 (build-system r-build-system)
2494 `(("r-magic" ,r-magic)
2495 ("r-lpsolve" ,r-lpsolve)
2497 ("r-rcppprogress" ,r-rcppprogress)))
2498 (home-page "http://geometry.r-forge.r-project.org/")
2499 (synopsis "Mesh generation and surface tesselation")
2501 "This package makes the qhull library available in R, in a similar manner
2502 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2503 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2504 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2505 and higher dimensions. It implements the Quickhull algorithm for computing
2506 the convex hull. Qhull does not support constrained Delaunay triangulations,
2507 or mesh generation of non-convex objects, but the package does include some R
2508 functions that allow for this. Currently the package only gives access to
2509 Delaunay triangulation and convex hull computation.")
2510 ;; The Qhull sources are included and are distributed under a custom
2511 ;; non-copyleft license. The R sources are released under GPL version 2.
2512 (license (list license:gpl2
2513 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2515 (define-public r-ddalpha
2522 (uri (cran-uri "ddalpha" version))
2525 "1vzs0cvl6xw3h9i00rg3hs02xwgxcnh8326y10kxmhs3qq4m7nb2"))))
2526 (build-system r-build-system)
2529 ("r-class" ,r-class)
2530 ("r-geometry" ,r-geometry)
2533 ("r-robustbase" ,r-robustbase)
2534 ("r-sfsmisc" ,r-sfsmisc)))
2536 `(("gfortran" ,gfortran)))
2537 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2538 (synopsis "Depth-Based classification and calculation of data depth")
2540 "This package contains procedures for depth-based supervised learning,
2541 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2542 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2543 statistical depth function to a compact low-dimensional space, where the final
2544 classification is done. It also offers an extension to functional data and
2545 routines for calculating certain notions of statistical depth functions. 50
2546 multivariate and 5 functional classification problems are included.")
2547 (license license:gpl2)))
2549 (define-public r-gower
2556 (uri (cran-uri "gower" version))
2559 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2560 (build-system r-build-system)
2561 (home-page "https://github.com/markvanderloo/gower")
2562 (synopsis "Gower's distance")
2564 "This package provides tools to compute Gower's distance (or similarity)
2565 coefficient between records, and to compute the top-n matches between records.
2566 Core algorithms are executed in parallel on systems supporting OpenMP.")
2567 (license license:gpl3)))
2569 (define-public r-rcpproll
2576 (uri (cran-uri "RcppRoll" version))
2579 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2580 (properties `((upstream-name . "RcppRoll")))
2581 (build-system r-build-system)
2583 `(("r-rcpp" ,r-rcpp)))
2584 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2585 (synopsis "Efficient rolling and windowed operations")
2587 "This package provides fast and efficient routines for common rolling /
2588 windowed operations. Routines for the efficient computation of windowed mean,
2589 median, sum, product, minimum, maximum, standard deviation and variance are
2591 (license license:gpl2+)))
2593 (define-public r-ipred
2600 (uri (cran-uri "ipred" version))
2603 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2604 (build-system r-build-system)
2606 `(("r-class" ,r-class)
2609 ("r-prodlim" ,r-prodlim)
2610 ("r-rpart" ,r-rpart)
2611 ("r-survival" ,r-survival)))
2612 (home-page "https://cran.r-project.org/web/packages/ipred")
2613 (synopsis "Improved predictors")
2615 "This package provides improved predictive models by indirect
2616 classification and bagging for classification, regression and survival
2617 problems as well as resampling based estimators of prediction error.")
2618 (license license:gpl2+)))
2620 (define-public r-psych
2627 (uri (cran-uri "psych" version))
2630 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
2631 (build-system r-build-system)
2633 `(("r-foreign" ,r-foreign)
2634 ("r-lattice" ,r-lattice)
2635 ("r-mnormt" ,r-mnormt)
2636 ("r-nlme" ,r-nlme)))
2637 (home-page "https://cran.r-project.org/web/packages/psych/")
2638 (synopsis "Procedures for psychological, psychometric, and personality research")
2640 "This package provides a general purpose toolbox for personality,
2641 psychometric theory and experimental psychology. Functions are primarily for
2642 multivariate analysis and scale construction using factor analysis, principal
2643 component analysis, cluster analysis and reliability analysis, although others
2644 provide basic descriptive statistics. Item Response Theory is done using
2645 factor analysis of tetrachoric and polychoric correlations. Functions for
2646 analyzing data at multiple levels include within and between group statistics,
2647 including correlations and factor analysis. Functions for simulating and
2648 testing particular item and test structures are included. Several functions
2649 serve as a useful front end for structural equation modeling. Graphical
2650 displays of path diagrams, factor analysis and structural equation models are
2651 created using basic graphics.")
2652 (license license:gpl2+)))
2654 (define-public r-generics
2661 (uri (cran-uri "generics" version))
2664 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
2665 (build-system r-build-system)
2666 (home-page "https://github.com/r-lib/generics")
2667 (synopsis "Common S3 generics not provided by base R methods")
2669 "In order to reduce potential package dependencies and conflicts,
2670 generics provides a number of commonly used S3 generics that are not provided
2671 by base R methods related to model fitting.")
2672 (license license:gpl2)))
2674 (define-public r-broom
2681 (uri (cran-uri "broom" version))
2684 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
2685 (build-system r-build-system)
2687 `(("r-backports" ,r-backports)
2688 ("r-dplyr" ,r-dplyr)
2689 ("r-generics" ,r-generics)
2691 ("r-purrr" ,r-purrr)
2692 ("r-reshape2" ,r-reshape2)
2693 ("r-stringr" ,r-stringr)
2694 ("r-tibble" ,r-tibble)
2695 ("r-tidyr" ,r-tidyr)))
2696 (home-page "https://github.com/tidyverse/broom")
2697 (synopsis "Convert statistical analysis objects into tidy data frames")
2699 "This package provides tools to convert statistical analysis objects from
2700 R into tidy data frames, so that they can more easily be combined, reshaped
2701 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
2702 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
2703 summarizes a model's statistical findings such as coefficients of a
2704 regression; @code{augment}, which adds columns to the original data such as
2705 predictions, residuals and cluster assignments; and @code{glance}, which
2706 provides a one-row summary of model-level statistics.")
2707 (license license:expat)))
2709 (define-public r-recipes
2716 (uri (cran-uri "recipes" version))
2719 "056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg"))))
2720 (build-system r-build-system)
2722 `(("r-dplyr" ,r-dplyr)
2723 ("r-generics" ,r-generics)
2725 ("r-gower" ,r-gower)
2726 ("r-ipred" ,r-ipred)
2727 ("r-lubridate" ,r-lubridate)
2728 ("r-magrittr" ,r-magrittr)
2729 ("r-matrix" ,r-matrix)
2730 ("r-purrr" ,r-purrr)
2731 ("r-rcpproll" ,r-rcpproll)
2732 ("r-rlang" ,r-rlang)
2733 ("r-tibble" ,r-tibble)
2734 ("r-tidyr" ,r-tidyr)
2735 ("r-tidyselect" ,r-tidyselect)
2736 ("r-timedate" ,r-timedate)
2737 ("r-withr" ,r-withr)))
2738 (home-page "https://github.com/topepo/recipes")
2739 (synopsis "Preprocessing tools to create design matrices")
2741 "Recipes is an extensible framework to create and preprocess design
2742 matrices. Recipes consist of one or more data manipulation and analysis
2743 \"steps\". Statistical parameters for the steps can be estimated from an
2744 initial data set and then applied to other data sets. The resulting design
2745 matrices can then be used as inputs into statistical or machine learning
2747 (license license:gpl2)))
2749 (define-public r-pdist
2756 (uri (cran-uri "pdist" version))
2759 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
2760 (build-system r-build-system)
2761 (home-page "https://github.com/jeffwong/pdist")
2762 (synopsis "Partitioned distance function")
2764 "Pdist computes the euclidean distance between rows of a matrix X and
2765 rows of another matrix Y. Previously, this could be done by binding the two
2766 matrices together and calling @code{dist}, but this creates unnecessary
2767 computation by computing the distances between a row of X and another row of
2768 X, and likewise for Y. Pdist strictly computes distances across the two
2769 matrices, not within the same matrix, making computations significantly faster
2770 for certain use cases.")
2771 (license license:gpl3+)))
2773 (define-public r-ggrepel
2780 (uri (cran-uri "ggrepel" version))
2783 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
2784 (build-system r-build-system)
2786 `(("r-ggplot2" ,r-ggplot2)
2788 ("r-scales" ,r-scales)))
2789 (home-page "http://github.com/slowkow/ggrepel")
2790 (synopsis "Repulsive text and label geometries for ggplot2")
2792 "This package provides text and label geometries for ggplot2 that help to
2793 avoid overlapping text labels. Labels repel away from each other and away
2794 from the data points.")
2795 (license license:gpl3)))
2797 (define-public r-corrplot
2804 (uri (cran-uri "corrplot" version))
2807 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
2808 (build-system r-build-system)
2809 (home-page "https://github.com/taiyun/corrplot")
2810 (synopsis "Visualization of a correlation matrix")
2812 "This package provides a graphical display of a correlation matrix or
2813 general matrix. It also contains some algorithms to do matrix reordering. In
2814 addition, corrplot is good at details, including choosing color, text labels,
2815 color labels, layout, etc.")
2816 ;; Any version of the GPL
2817 (license license:gpl2+)))
2819 (define-public r-stringdist
2821 (name "r-stringdist")
2826 (uri (cran-uri "stringdist" version))
2829 "0nw8c317qkfq63pr0prl0hx522ddfq4cbgixb5r4pq3fxk9z303l"))))
2830 (build-system r-build-system)
2831 (home-page "https://github.com/markvanderloo/stringdist")
2832 (synopsis "Approximate string matching and string distance functions")
2834 "This package implements an approximate string matching version of R's
2835 native @code{match} function. It can calculate various string distances based
2836 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
2837 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
2838 Jaro-Winkler). An implementation of soundex is provided as well. Distances
2839 can be computed between character vectors while taking proper care of encoding
2840 or between integer vectors representing generic sequences.")
2841 (license license:gpl3+)))
2843 (define-public r-ucminf
2850 (uri (cran-uri "ucminf" version))
2853 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
2854 (build-system r-build-system)
2855 (native-inputs `(("gfortran" ,gfortran)))
2856 (home-page "https://cran.r-project.org/web/packages/ucminf/")
2857 (synopsis "General-purpose unconstrained non-linear optimization")
2859 "This package provides an implementation of an algorithm for
2860 general-purpose unconstrained non-linear optimization. The algorithm is of
2861 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
2862 search with a trust region type monitoring of the input to the line search
2863 algorithm. The interface of @code{ucminf} is designed for easy interchange
2864 with the package @code{optim}.")
2865 (license license:gpl2+)))
2867 (define-public r-ordinal
2870 (version "2019.4-25")
2874 (uri (cran-uri "ordinal" version))
2877 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
2878 (build-system r-build-system)
2880 `(("r-mass" ,r-mass)
2881 ("r-matrix" ,r-matrix)
2882 ("r-numderiv" ,r-numderiv)
2883 ("r-ucminf" ,r-ucminf)))
2884 (home-page "https://github.com/runehaubo/ordinal")
2885 (synopsis "Regression models for ordinal data")
2887 "This package provides an implementation of cumulative link (mixed)
2888 models also known as ordered regression models, proportional odds models,
2889 proportional hazards models for grouped survival times and ordered models.
2890 Estimation is via maximum likelihood and mixed models are fitted with the
2891 Laplace approximation and adaptive Gauss-Hermite quadrature.")
2892 (license license:gpl2+)))
2894 (define-public r-jomo
2901 (uri (cran-uri "jomo" version))
2904 "097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb"))))
2905 (build-system r-build-system)
2907 `(("r-lme4" ,r-lme4)
2909 ("r-ordinal" ,r-ordinal)
2910 ("r-survival" ,r-survival)))
2911 (home-page "https://cran.r-project.org/web/packages/jomo/")
2912 (synopsis "Multilevel Joint Modelling Multiple Imputation")
2914 "Similarly to Schafer's package pan, jomo is a package for multilevel
2915 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
2916 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
2917 possibility of handling binary and categorical data through latent normal
2918 variables, the option to use cluster-specific covariance matrices and to
2919 impute compatibly with the substantive model.")
2920 (license license:gpl2)))
2922 (define-public r-pan
2929 (uri (cran-uri "pan" version))
2932 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
2933 (build-system r-build-system)
2934 (native-inputs `(("gfortran" ,gfortran)))
2935 (home-page "https://cran.r-project.org/web/packages/pan/")
2936 (synopsis "Multiple imputation for multivariate panel or clustered data")
2938 "This package implements multiple imputation for multivariate panel or
2940 (license license:gpl3)))
2942 (define-public r-mitml
2949 (uri (cran-uri "mitml" version))
2952 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
2953 (build-system r-build-system)
2955 `(("r-haven" ,r-haven)
2958 (home-page "https://cran.r-project.org/web/packages/mitml/")
2959 (synopsis "Tools for multiple imputation in multilevel modeling")
2961 "This package provides tools for multiple imputation of missing data in
2962 multilevel modeling. It includes a user-friendly interface to the packages
2963 pan and jomo, and several functions for visualization, data management and the
2964 analysis of multiply imputed data sets.")
2965 (license license:gpl2+)))
2967 (define-public r-mice
2974 (uri (cran-uri "mice" version))
2977 "0icydc312sbvzbp0r0mhs2r77a2ly2xvz5w5amirz3wdkvgyrk2g"))))
2978 (build-system r-build-system)
2980 `(("r-broom" ,r-broom)
2981 ("r-dplyr" ,r-dplyr)
2982 ("r-lattice" ,r-lattice)
2984 ("r-mitml" ,r-mitml)
2987 ("r-rlang" ,r-rlang)
2988 ("r-rpart" ,r-rpart)
2989 ("r-survival" ,r-survival)))
2990 (home-page "https://cran.r-project.org/web/packages/mice/")
2991 (synopsis "Multivariate imputation by chained equations")
2993 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
2994 implemented by the MICE algorithm as described in @url{Van Buuren and
2995 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
2996 variable has its own imputation model. Built-in imputation models are
2997 provided for continuous data (predictive mean matching, normal), binary
2998 data (logistic regression), unordered categorical data (polytomous logistic
2999 regression) and ordered categorical data (proportional odds). MICE can also
3000 impute continuous two-level data (normal model, pan, second-level variables).
3001 Passive imputation can be used to maintain consistency between variables.
3002 Various diagnostic plots are available to inspect the quality of the
3004 ;; Any of these two versions.
3005 (license (list license:gpl2 license:gpl3))))
3007 (define-public r-truncnorm
3009 (name "r-truncnorm")
3014 (uri (cran-uri "truncnorm" version))
3017 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3018 (build-system r-build-system)
3019 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3020 (synopsis "Truncated normal distribution")
3021 (description "This package provides functions for the truncated normal
3022 distribution with mean equal to @code{mean} and standard deviation equal to
3023 @code{sd}. It includes density, distribution, quantile, and expected value
3024 functions, as well as a random generation function.")
3025 (license license:gpl2)))
3027 (define-public r-rsolnp
3034 (uri (cran-uri "Rsolnp" version))
3037 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3038 (properties `((upstream-name . "Rsolnp")))
3039 (build-system r-build-system)
3041 `(("r-truncnorm" ,r-truncnorm)))
3042 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3043 (synopsis "General non-linear optimization")
3044 (description "The Rsolnp package implements a general non-linear augmented
3045 Lagrange multiplier method solver, a @dfn{sequential quadratic
3046 programming} (SQP) based solver).")
3047 ;; Any version of the GPL.
3048 (license license:gpl2+)))
3050 (define-public r-hardyweinberg
3052 (name "r-hardyweinberg")
3057 (uri (cran-uri "HardyWeinberg" version))
3060 "15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9"))))
3061 (properties `((upstream-name . "HardyWeinberg")))
3062 (build-system r-build-system)
3064 `(("r-mice" ,r-mice)
3066 ("r-rsolnp" ,r-rsolnp)))
3067 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3068 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3070 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3071 diallelic genetic marker data. All classical tests (chi-square, exact,
3072 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3073 included in the package, as well as functions for power computation and for
3074 the simulation of marker data under equilibrium and disequilibrium. Routines
3075 for dealing with markers on the X-chromosome are included. Functions for
3076 testing equilibrium in the presence of missing data by using multiple
3077 imputation are also provided. Implements several graphics for exploring the
3078 equilibrium status of a large set of diallelic markers: ternary plots with
3079 acceptance regions, log-ratio plots and Q-Q plots.")
3080 (license license:gpl2+)))
3089 (uri (cran-uri "sm" version))
3092 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3093 (build-system r-build-system)
3094 (native-inputs `(("gfortran" ,gfortran)))
3095 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3096 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3098 "This is software accompanying the book 'Applied Smoothing Techniques for
3099 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3100 University Press. It provides smoothing methods for nonparametric regression
3101 and density estimation")
3102 (license license:gpl2+)))
3104 (define-public r-venndiagram
3106 (name "r-venndiagram")
3110 (uri (cran-uri "VennDiagram" version))
3113 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3114 (properties `((upstream-name . "VennDiagram")))
3115 (build-system r-build-system)
3117 `(("r-futile-logger" ,r-futile-logger)))
3118 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3119 (synopsis "Generate High-Resolution Venn and Euler Plots")
3121 "This package provides a set of functions to generate high-resolution
3122 Venn and Euler plots. It includes handling for several special cases,
3123 including two-case scaling, and extensive customization of plot shape and
3125 (license license:gpl2+)))
3127 (define-public r-vioplot
3134 (uri (cran-uri "vioplot" version))
3137 "1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn"))))
3138 (build-system r-build-system)
3142 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3143 (synopsis "Violin plot")
3145 "This package provides a violin plot, which is a combination of a box
3146 plot and a kernel density plot.")
3147 (license license:bsd-3)))
3149 (define-public r-rsofia
3155 ;; This package has been removed from CRAN, so we can
3156 ;; only fetch it from the archives.
3157 (uri (string-append "https://cran.r-project.org/src/"
3158 "contrib/Archive/RSofia/RSofia_"
3162 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3163 (properties `((upstream-name . "RSofia")))
3164 (build-system r-build-system)
3166 `(("r-rcpp" ,r-rcpp)))
3167 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3168 (synopsis "Port of sofia-ml to R")
3169 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3170 suite of fast incremental algorithms for machine learning that can be used for
3171 training models for classification or ranking.")
3172 (license license:asl2.0)))
3174 (define-public r-xts
3181 (uri (cran-uri "xts" version))
3184 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3185 (build-system r-build-system)
3186 (propagated-inputs `(("r-zoo" ,r-zoo)))
3187 (home-page "https://github.com/joshuaulrich/xts")
3188 (synopsis "Extensible time series")
3190 "This package provides for uniform handling of R's different time-based
3191 data classes by extending @code{zoo}, maximizing native format information
3192 preservation and allowing for user-level customization and extension, while
3193 simplifying cross-class interoperability.")
3194 (license license:gpl2+)))
3196 (define-public r-performanceanalytics
3198 (name "r-performanceanalytics")
3203 (uri (cran-uri "PerformanceAnalytics" version))
3206 "01bgm57z079g6r505w3bj293zkbd49fwa8sg55z87vizwavipml6"))))
3208 `((upstream-name . "PerformanceAnalytics")))
3209 (build-system r-build-system)
3211 `(("r-quadprog" ,r-quadprog)
3214 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3215 (synopsis "Econometric tools for performance and risk analysis")
3216 (description "This is a collection of econometric functions for
3217 performance and risk analysis. This package aims to aid practitioners and
3218 researchers in utilizing the latest research in analysis of non-normal return
3219 streams. In general, it is most tested on return (rather than price) data on
3220 a regular scale, but most functions will work with irregular return data as
3221 well, and increasing numbers of functions will work with P&L or price data
3223 ;; Either version may be picked.
3224 (license (list license:gpl2 license:gpl3))))
3226 (define-public r-laeken
3233 (uri (cran-uri "laeken" version))
3236 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3237 (build-system r-build-system)
3239 `(("r-boot" ,r-boot)
3240 ("r-mass" ,r-mass)))
3241 (home-page "https://cran.r-project.org/web/packages/laeken/")
3242 (synopsis "Estimation of indicators on social exclusion and poverty")
3243 (description "This package provides tools for the estimation of indicators
3244 on social exclusion and poverty, as well as an implementation of Pareto tail
3245 modeling for empirical income distributions.")
3246 (license license:gpl2+)))
3248 (define-public r-vcd
3255 (uri (cran-uri "vcd" version))
3258 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3259 (build-system r-build-system)
3261 `(("r-colorspace" ,r-colorspace)
3262 ("r-lmtest" ,r-lmtest)
3263 ("r-mass" ,r-mass)))
3264 (home-page "https://cran.r-project.org/web/packages/vcd/")
3265 (synopsis "Visualizing categorical data")
3266 (description "This package provides visualization techniques, data sets,
3267 summary and inference procedures aimed particularly at categorical data.
3268 Special emphasis is given to highly extensible grid graphics. The package was
3269 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3270 Friendly and is now the main support package for a new book, \"Discrete Data
3271 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3272 (license license:gpl2)))
3274 (define-public r-ica
3281 (uri (cran-uri "ica" version))
3284 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3285 (build-system r-build-system)
3286 (home-page "https://cran.r-project.org/web/packages/ica/")
3287 (synopsis "Independent component analysis")
3288 (description "This package provides tools for @dfn{Independent Component
3289 Analysis} (ICA) using various algorithms: FastICA,
3290 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3291 of Eigenmatrices} (JADE).")
3292 (license license:gpl2+)))
3294 (define-public r-dtw
3301 (uri (cran-uri "dtw" version))
3304 "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
3305 (build-system r-build-system)
3306 (propagated-inputs `(("r-proxy" ,r-proxy)))
3307 (home-page "http://dtw.r-forge.r-project.org/")
3308 (synopsis "Dynamic Time Warping Algorithms")
3309 (description "This package provides a comprehensive implementation of
3310 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3311 optimal (least cumulative distance) alignment between points of two time
3312 series. Common DTW variants covered include local (slope) and global (window)
3313 constraints, subsequence matches, arbitrary distance definitions,
3314 normalizations, minimum variance matching, and so on.")
3315 (license license:gpl2+)))
3317 (define-public r-sdmtools
3320 (version "1.1-221.1")
3324 (uri (cran-uri "SDMTools" version))
3327 "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q"))))
3328 (properties `((upstream-name . "SDMTools")))
3329 (build-system r-build-system)
3330 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3331 (home-page "http://www.rforge.net/SDMTools/")
3332 (synopsis "Species distribution modelling tools")
3333 (description "This package provides a set of tools for post processing
3334 the outcomes of species distribution modeling exercises. It includes novel
3335 methods for comparing models and tracking changes in distributions through
3336 time. It further includes methods for visualizing outcomes, selecting
3337 thresholds, calculating measures of accuracy and landscape fragmentation
3339 (license license:gpl3+)))
3341 (define-public r-scatterplot3d
3343 (name "r-scatterplot3d")
3348 (uri (cran-uri "scatterplot3d" version))
3351 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3352 (build-system r-build-system)
3353 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3354 (synopsis "3D scatter plot")
3355 (description "This package provides an implementation of scatter plots for
3356 plotting. a three dimensional point cloud.")
3357 (license license:gpl2)))
3359 (define-public r-ggridges
3366 (uri (cran-uri "ggridges" version))
3369 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3370 (build-system r-build-system)
3372 `(("r-ggplot2" ,r-ggplot2)
3374 ("r-scales" ,r-scales)
3375 ("r-withr" ,r-withr)))
3376 (home-page "https://github.com/clauswilke/ggridges")
3377 (synopsis "Ridgeline plots in ggplot2")
3379 "Ridgeline plots provide a convenient way of visualizing changes in
3380 distributions over time or space. This package enables the creation of such
3381 plots in @code{ggplot2}.")
3382 (license license:gpl2)))
3384 (define-public r-ggjoy
3391 (uri (cran-uri "ggjoy" version))
3394 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3395 (build-system r-build-system)
3397 `(("r-ggplot2" ,r-ggplot2)
3398 ("r-ggridges" ,r-ggridges)))
3399 (home-page "https://github.com/clauswilke/ggjoy")
3400 (synopsis "Joyplots in ggplot2")
3401 (description "Joyplots provide a convenient way of visualizing changes in
3402 distributions over time or space. This package enables the creation of such
3403 plots in @code{ggplot2}.")
3404 (license license:gpl2)))
3406 (define-public r-cli
3413 (uri (cran-uri "cli" version))
3416 "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g"))))
3417 (build-system r-build-system)
3419 `(("r-assertthat" ,r-assertthat)
3420 ("r-crayon" ,r-crayon)))
3421 (home-page "https://github.com/r-lib/cli#readme")
3422 (synopsis "Helpers for developing command line interfaces")
3423 (description "This package provides a suite of tools designed to build
3424 attractive command line interfaces (CLIs). It includes tools for drawing
3425 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3426 (license license:expat)))
3428 (define-public r-argparser
3430 (name "r-argparser")
3435 (uri (cran-uri "argparser" version))
3438 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3439 (build-system r-build-system)
3440 (home-page "https://bitbucket.org/djhshih/argparser")
3441 (synopsis "Command-line argument parser")
3443 "This package provides a cross-platform command-line argument parser
3444 written purely in R with no external dependencies. It is useful with the
3445 Rscript front-end and facilitates turning an R script into an executable
3447 (license license:gpl3+)))
3449 (define-public r-debugme
3456 (uri (cran-uri "debugme" version))
3459 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3460 (build-system r-build-system)
3461 (propagated-inputs `(("r-crayon" ,r-crayon)))
3462 (home-page "https://github.com/r-lib/debugme#readme")
3463 (synopsis "Debug R packages")
3465 "This package allows the user to specify debug messages as special string
3466 constants, and control debugging of packages via environment variables.")
3467 (license license:expat)))
3469 (define-public r-processx
3476 (uri (cran-uri "processx" version))
3479 "1bhbfacx2z2d97pz5bch45nvbvywhx2zp049czlfbdivkzgxn8v1"))))
3480 (build-system r-build-system)
3484 (home-page "https://github.com/r-lib/processx3")
3485 (synopsis "Execute and control system processes")
3487 "This package provides portable tools to run system processes in the
3488 background. It can check if a background process is running; wait on a
3489 background process to finish; get the exit status of finished processes; kill
3490 background processes and their children; restart processes. It can read the
3491 standard output and error of the processes, using non-blocking connections.
3492 @code{processx} can poll a process for standard output or error, with a
3493 timeout. It can also poll several processes at once.")
3494 (license license:expat)))
3496 (define-public r-tsp
3503 (uri (cran-uri "TSP" version))
3506 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3507 (properties `((upstream-name . "TSP")))
3508 (build-system r-build-system)
3509 (propagated-inputs `(("r-foreach" ,r-foreach)))
3510 (home-page "https://cran.r-project.org/web/packages/TSP/")
3511 (synopsis "Traveling salesperson problem (TSP)")
3512 (description "This package provides basic infrastructure and some
3513 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3514 traveling salesman problem).")
3515 (license license:gpl3)))
3517 (define-public r-qap
3524 (uri (cran-uri "qap" version))
3527 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3528 (build-system r-build-system)
3529 (native-inputs `(("gfortran" ,gfortran)))
3530 (home-page "https://cran.r-project.org/web/packages/qap/")
3531 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3532 (description "This package implements heuristics for the @dfn{quadratic
3533 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3535 (license license:gpl3)))
3537 (define-public r-gclus
3544 (uri (cran-uri "gclus" version))
3547 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3548 (build-system r-build-system)
3549 (propagated-inputs `(("r-cluster" ,r-cluster)))
3550 (home-page "https://cran.r-project.org/web/packages/gclus/")
3551 (synopsis "Clustering graphics")
3552 (description "This package orders panels in scatterplot matrices and
3553 parallel coordinate displays by some merit index. It contains various indices
3554 of merit, ordering functions, and enhanced versions of @code{pairs} and
3555 @code{parcoord} which color panels according to their merit level.")
3556 (license license:gpl2+)))
3558 (define-public r-webshot
3565 (uri (cran-uri "webshot" version))
3568 "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr"))))
3569 (build-system r-build-system)
3571 `(("r-callr" ,r-callr)
3572 ("r-jsonlite" ,r-jsonlite)
3573 ("r-magrittr" ,r-magrittr)))
3574 (home-page "https://github.com/wch/webshot/")
3575 (synopsis "Take screenshots of web pages")
3577 "Webshot makes it easy to take screenshots of web pages from within R.
3578 It can also run Shiny applications locally and take screenshots of the
3579 application; and it can render and screenshot static as well as interactive R
3580 Markdown documents.")
3581 (license license:gpl2)))
3583 (define-public r-seriation
3585 (name "r-seriation")
3590 (uri (cran-uri "seriation" version))
3593 "0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6"))))
3594 (build-system r-build-system)
3596 `(("r-cluster" ,r-cluster)
3597 ("r-colorspace" ,r-colorspace)
3598 ("r-dendextend" ,r-dendextend)
3599 ("r-gclus" ,r-gclus)
3600 ("r-gplots" ,r-gplots)
3603 ("r-registry" ,r-registry)
3605 (native-inputs `(("gfortran" ,gfortran)))
3606 (home-page "http://s2.smu.edu/IDA/seriation/")
3607 (synopsis "Infrastructure for ordering objects using seriation")
3609 "This package provides infrastructure for seriation with an
3610 implementation of several seriation/sequencing techniques to reorder matrices,
3611 dissimilarity matrices, and dendrograms. It also provides (optimally)
3612 reordered heatmaps, color images and clustering visualizations like
3613 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3615 (license license:gpl3)))
3617 (define-public r-xfun
3624 (uri (cran-uri "xfun" version))
3627 "1gllyyjhkvswcwa15h1f3kb1l1drs2ifpxy4jjanmmhaj7wcmvy9"))))
3628 (build-system r-build-system)
3629 (home-page "https://github.com/yihui/xfun")
3630 (synopsis "Miscellaneous functions")
3632 "This package provides miscellaneous functions commonly used in other
3633 packages maintained by Yihui Xie.")
3634 (license license:expat)))
3636 (define-public r-utf8
3643 (uri (cran-uri "utf8" version))
3646 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
3647 (build-system r-build-system)
3648 (home-page "https://github.com/patperry/r-utf8")
3649 (synopsis "Unicode text processing")
3651 "This package provides tools to process and print UTF-8 encoded
3652 international text (Unicode). Input, validate, normalize, encode, format, and
3654 (license license:asl2.0)))
3656 (define-public r-zeallot
3663 (uri (cran-uri "zeallot" version))
3666 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
3667 (build-system r-build-system)
3668 (home-page "https://github.com/nteetor/zeallot")
3669 (synopsis "Multiple, unpacking, and destructuring assignment")
3671 "This package provides a @code{%<-%} operator to perform multiple,
3672 unpacking, and destructuring assignment in R. The operator unpacks the
3673 right-hand side of an assignment into multiple values and assigns these values
3674 to variables on the left-hand side of the assignment.")
3675 (license license:expat)))
3677 (define-public r-vctrs
3684 (uri (cran-uri "vctrs" version))
3687 "13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c"))))
3688 (build-system r-build-system)
3690 `(("r-backports" ,r-backports)
3691 ("r-digest" ,r-digest)
3693 ("r-rlang" ,r-rlang)
3694 ("r-zeallot" ,r-zeallot)))
3695 (home-page "https://github.com/r-lib/vctrs")
3696 (synopsis "Vector helpers")
3698 "There are three main goals to the @code{vctrs} package:
3701 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
3702 @code{length()} and @code{class()}. These definitions are paired with a
3703 framework for type-coercion and size-recycling.
3704 @item To define type- and size-stability as desirable function properties, use
3705 them to analyse existing base function, and to propose better alternatives.
3706 This work has been particularly motivated by thinking about the ideal
3707 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
3708 @item To provide a new @code{vctr} base class that makes it easy to create new
3709 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
3710 a few new @code{vctrs} generics, making implementation considerably simpler
3713 (license license:gpl3)))
3715 (define-public r-pillar
3722 (uri (cran-uri "pillar" version))
3725 "0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm"))))
3726 (build-system r-build-system)
3729 ("r-crayon" ,r-crayon)
3730 ("r-fansi" ,r-fansi)
3731 ("r-rlang" ,r-rlang)
3733 ("r-vctrs" ,r-vctrs)))
3734 (home-page "https://github.com/r-lib/pillar")
3735 (synopsis "Coloured formatting for columns")
3737 "This package provides a @code{pillar} generic designed for formatting
3738 columns of data using the full range of colours provided by modern
3740 (license license:gpl3)))
3742 (define-public r-uuid
3749 (uri (cran-uri "uuid" version))
3752 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
3753 (build-system r-build-system)
3754 (home-page "http://www.rforge.net/uuid")
3755 (synopsis "Tools for generating and handling of UUIDs")
3757 "This package provides tools for generating and handling of
3758 @dfn{Universally Unique Identifiers} (UUIDs).")
3759 (license license:expat)))
3761 (define-public r-tinytex
3768 (uri (cran-uri "tinytex" version))
3771 "1bbphyrbk2rnyi0jhw4hj2w4l84kyhb0km901qd5qnnl0cy6dzvb"))))
3772 (build-system r-build-system)
3774 `(("r-xfun" ,r-xfun)))
3775 (home-page "https://github.com/yihui/tinytex")
3776 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
3778 "This package provides helper functions to install and maintain the LaTeX
3779 distribution named TinyTeX, a lightweight, cross-platform, portable, and
3780 easy-to-maintain version of TeX Live. This package also contains helper
3781 functions to compile LaTeX documents, and install missing LaTeX packages
3783 (license license:expat)))
3785 (define-public r-metap
3792 (uri (cran-uri "metap" version))
3795 "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0"))))
3796 (build-system r-build-system)
3798 `(("r-lattice" ,r-lattice)
3799 ("r-rdpack" ,r-rdpack)))
3800 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3801 (synopsis "Meta-analysis of significance values")
3803 "The canonical way to perform meta-analysis involves using effect sizes.
3804 When they are not available this package provides a number of methods for
3805 meta-analysis of significance values including the methods of Edgington,
3806 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3807 published results; and a routine for graphical display.")
3808 (license license:gpl2)))
3810 (define-public r-network
3817 (uri (cran-uri "network" version))
3820 "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
3821 (build-system r-build-system)
3823 `(("r-magrittr" ,r-magrittr)
3824 ("r-tibble" ,r-tibble)))
3825 (home-page "https://statnet.org/")
3826 (synopsis "Classes for relational data")
3828 "This package provides tools to create and modify network objects. The
3829 @code{network} class can represent a range of relational data types, and
3830 supports arbitrary vertex/edge/graph attributes.")
3831 (license license:gpl2+)))
3833 (define-public r-statnet-common
3835 (name "r-statnet-common")
3840 (uri (cran-uri "statnet.common" version))
3843 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
3845 `((upstream-name . "statnet.common")))
3846 (build-system r-build-system)
3848 `(("r-coda" ,r-coda)))
3849 (home-page "https://statnet.org")
3850 (synopsis "R scripts and utilities used by the Statnet software")
3851 (description "This package provides non-statistical utilities used by the
3852 software developed by the Statnet Project.")
3853 (license license:gpl3)))
3855 (define-public r-sna
3862 (uri (cran-uri "sna" version))
3865 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
3866 (build-system r-build-system)
3868 `(("r-network" ,r-network)
3869 ("r-statnet-common" ,r-statnet-common)))
3870 (home-page "https://statnet.org")
3871 (synopsis "Tools for social network analysis")
3873 "This package provides a range of tools for social network analysis,
3874 including node and graph-level indices, structural distance and covariance
3875 methods, structural equivalence detection, network regression, random graph
3876 generation, and 2D/3D network visualization.")
3877 (license license:gpl2+)))
3879 (define-public r-ttr
3886 (uri (cran-uri "TTR" version))
3889 "18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb"))))
3890 (properties `((upstream-name . "TTR")))
3891 (build-system r-build-system)
3893 `(("r-curl" ,r-curl)
3896 (native-inputs `(("gfortran" ,gfortran)))
3897 (home-page "https://github.com/joshuaulrich/TTR")
3898 (synopsis "Technical trading rules")
3900 "This package provides functions and data to construct technical trading
3902 (license license:gpl2)))
3904 (define-public r-leaps
3911 (uri (cran-uri "leaps" version))
3914 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
3915 (build-system r-build-system)
3916 (native-inputs `(("gfortran" ,gfortran)))
3917 (home-page "https://cran.r-project.org/web/packages/leaps/")
3918 (synopsis "Regression subset selection")
3920 "This package provides tools for regression subset selection, including
3921 exhaustive search.")
3922 (license license:gpl2+)))
3924 (define-public r-splus2r
3931 (uri (cran-uri "splus2R" version))
3934 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
3935 (properties `((upstream-name . "splus2R")))
3936 (build-system r-build-system)
3937 (native-inputs `(("gfortran" ,gfortran)))
3938 (home-page "https://cran.r-project.org/web/packages/splus2R/")
3939 (synopsis "Supplemental S-PLUS functionality in R")
3941 "Currently there are many functions in S-PLUS that are missing in R. To
3942 facilitate the conversion of S-PLUS packages to R packages, this package
3943 provides some missing S-PLUS functionality in R.")
3944 (license license:gpl2)))
3946 (define-public r-ifultools
3948 (name "r-ifultools")
3953 (uri (cran-uri "ifultools" version))
3956 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
3957 (build-system r-build-system)
3959 `(("r-mass" ,r-mass)
3960 ("r-splus2r" ,r-splus2r)))
3961 (home-page "https://cran.r-project.org/web/packages/ifultools/")
3962 (synopsis "Insightful research tools")
3963 (description "This package provides C code used by the wmtsa, fractal, and
3965 (license license:gpl2)))
3967 (define-public r-sapa
3974 (uri (cran-uri "sapa" version))
3977 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
3978 (build-system r-build-system)
3980 `(("r-ifultools" ,r-ifultools)
3981 ("r-splus2r" ,r-splus2r)))
3982 (home-page "https://cran.r-project.org/web/packages/sapa/")
3983 (synopsis "Spectral analysis for physical applications")
3984 (description "This package provides software for the book Spectral
3985 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
3986 Cambridge University Press, 1993.")
3987 (license license:gpl2)))
3989 (define-public r-aggregation
3991 (name "r-aggregation")
3996 (uri (cran-uri "aggregation" version))
3999 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4000 (build-system r-build-system)
4001 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4002 (synopsis "Methods for p-value aggregation")
4004 "This package contains functionality for performing the following methods
4005 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4006 Fisher's method), and Sidak correction.")
4007 (license license:gpl3)))
4009 (define-public r-quantmod
4016 (uri (cran-uri "quantmod" version))
4019 "1csljagnpkr1mmc18h70b64zbyj07kx972nip9dng39jfg7ilnyr"))))
4020 (build-system r-build-system)
4022 `(("r-curl" ,r-curl)
4026 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4027 (synopsis "Quantitative financial modelling framework")
4028 (description "This package provides a quantitative financial modelling
4029 framework to allow users to specify, build, trade, and analyse quantitative
4030 financial trading strategies.")
4031 (license license:gpl3)))
4033 (define-public r-tseries
4040 (uri (cran-uri "tseries" version))
4043 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4044 (build-system r-build-system)
4046 `(("r-quadprog" ,r-quadprog)
4047 ("r-quantmod" ,r-quantmod)
4050 `(("gfortran" ,gfortran)))
4051 (home-page "https://cran.r-project.org/web/packages/tseries/")
4052 (synopsis "Time series analysis and computational finance")
4054 "This package provides functions relating to time series analysis and
4055 computational finance.")
4056 (license license:gpl2)))
4058 (define-public r-wmtsa
4065 (uri (cran-uri "wmtsa" version))
4068 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4069 (build-system r-build-system)
4071 `(("r-ifultools" ,r-ifultools)
4073 ("r-splus2r" ,r-splus2r)))
4074 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4075 (synopsis "Wavelet methods for time series analysis")
4077 "This package provides software to accompany the book \"Wavelet Methods
4078 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4079 University Press, 2000.")
4080 (license license:gpl2)))
4082 (define-public r-tsa
4089 (uri (cran-uri "TSA" version))
4092 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4093 (properties `((upstream-name . "TSA")))
4094 (build-system r-build-system)
4096 `(("r-leaps" ,r-leaps)
4097 ("r-locfit" ,r-locfit)
4098 ("r-mgcv" ,r-mgcv)))
4099 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4100 (synopsis "Time series analysis")
4102 "This package contains R functions and datasets detailed in the book
4103 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4104 Cryer and Kung-Sik Chan.")
4105 (license license:gpl2+)))
4107 (define-public r-extradistr
4109 (name "r-extradistr")
4114 (uri (cran-uri "extraDistr" version))
4117 "00lvqp5bb3iak5myiz4rqm887bkq9sdh7aybmz84mmfni6q01m28"))))
4118 (properties `((upstream-name . "extraDistr")))
4119 (build-system r-build-system)
4121 `(("r-rcpp" ,r-rcpp)))
4122 (home-page "https://github.com/twolodzko/extraDistr")
4123 (synopsis "Additional univariate and multivariate distributions")
4125 "This package implements density, distribution functions, quantile
4126 functions and random generation functions for a large number of univariate and
4127 multivariate distributions.")
4128 (license license:gpl2)))
4130 (define-public r-fractal
4137 (uri (cran-uri "fractal" version))
4140 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4141 (build-system r-build-system)
4143 `(("r-ifultools" ,r-ifultools)
4146 ("r-scatterplot3d" ,r-scatterplot3d)
4147 ("r-splus2r" ,r-splus2r)
4148 ("r-wmtsa" ,r-wmtsa)))
4149 (home-page "https://cran.r-project.org/web/packages/fractal/")
4150 (synopsis "Fractal time series modeling and analysis")
4152 "This package provides tools for stochastic fractal and deterministic
4153 chaotic time series analysis.")
4154 (license license:gpl2)))
4156 (define-public r-urca
4163 (uri (cran-uri "urca" version))
4166 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4167 (build-system r-build-system)
4168 (propagated-inputs `(("r-nlme" ,r-nlme)))
4169 (native-inputs `(("gfortran" ,gfortran)))
4170 (home-page "https://cran.r-project.org/web/packages/urca/")
4171 (synopsis "Unit root and cointegration tests for time series data")
4173 "This package provides unit root and cointegration tests encountered in
4174 applied econometric analysis.")
4175 (license license:gpl2+)))
4177 (define-public r-cubature
4184 (uri (cran-uri "cubature" version))
4187 "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"))))
4188 (build-system r-build-system)
4190 `(("r-rcpp" ,r-rcpp)))
4191 (home-page "https://github.com/bnaras/cubature")
4192 (synopsis "Adaptive multivariate integration over hypercubes")
4194 "This package is an R wrapper around the cubature C library for adaptive
4195 multivariate integration over hypercubes. This version provides both
4196 @code{hcubature} and @code{pcubature} routines in addition to a vector
4198 ;; The included cubature C library is released under GPLv2+, but the
4199 ;; wrapper declares the license to be GPLv3+.
4200 (license (list license:gpl2+ license:gpl3+))))
4202 (define-public r-trend
4209 (uri (cran-uri "trend" version))
4212 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4213 (build-system r-build-system)
4215 `(("r-extradistr" ,r-extradistr)))
4217 `(("gfortran" ,gfortran)))
4218 (home-page "https://cran.r-project.org/web/packages/trend/")
4219 (synopsis "Non-parametric trend tests and change-point detection")
4221 "The analysis of environmental data often requires the detection of
4222 trends and change-points. This package includes tests for trend
4223 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4224 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4225 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4226 correlation trend test), change-point detection (Lanzante's test procedures,
4227 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4228 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4229 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4230 sample Robust Rank-Order Distributional Test.")
4231 (license license:gpl3)))
4233 (define-public r-expm
4240 (uri (cran-uri "expm" version))
4243 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4244 (build-system r-build-system)
4245 (propagated-inputs `(("r-matrix" ,r-matrix)))
4246 (native-inputs `(("gfortran" ,gfortran)))
4247 (home-page "https://r-forge.r-project.org/projects/expm/")
4248 (synopsis "Tools for matrix exponentials and related quantities")
4250 "This package provides tools for the computation of the matrix
4251 exponential, logarithm, square root, and related quantities.")
4252 (license license:gpl2+)))
4254 (define-public r-complexplus
4256 (name "r-complexplus")
4261 (uri (cran-uri "complexplus" version))
4264 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4265 (build-system r-build-system)
4267 `(("r-expm" ,r-expm)
4268 ("r-matrix" ,r-matrix)))
4269 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4270 (synopsis "Functions of complex or real variables")
4272 "This package extends several functions to the complex domain, including
4273 the matrix exponential and logarithm, and the determinant.")
4274 (license license:gpl2)))
4276 (define-public r-phontools
4278 (name "r-phontools")
4283 (uri (cran-uri "phonTools" version))
4286 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4287 (properties `((upstream-name . "phonTools")))
4288 (build-system r-build-system)
4289 (home-page "http://www.santiagobarreda.com/rscripts.html")
4290 (synopsis "Tools for phonetic and acoustic analyses")
4292 "This package contains tools for the organization, display, and analysis
4293 of the sorts of data frequently encountered in phonetics research and
4294 experimentation, including the easy creation of IPA vowel plots, and the
4295 creation and manipulation of WAVE audio files.")
4296 (license license:bsd-2)))
4305 (uri (cran-uri "np" version))
4308 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4309 (build-system r-build-system)
4311 `(("r-boot" ,r-boot)
4312 ("r-cubature" ,r-cubature)
4313 ("r-quadprog" ,r-quadprog)
4314 ("r-quantreg" ,r-quantreg)))
4315 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4316 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4317 (description "This package provides non-parametric (and semi-parametric)
4318 kernel methods that seamlessly handle a mix of continuous, unordered, and
4319 ordered factor data types.")
4320 ;; Any version of the GPL.
4321 (license license:gpl3+)))
4323 (define-public r-powerplus
4325 (name "r-powerplus")
4330 (uri (cran-uri "powerplus" version))
4333 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4334 (build-system r-build-system)
4336 `(("r-complexplus" ,r-complexplus)
4339 ("r-matrix" ,r-matrix)
4340 ("r-phontools" ,r-phontools)))
4341 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4342 (synopsis "Exponentiation operations")
4344 "This package provides tools for the computation of matrix and scalar
4346 (license license:gpl2)))
4348 (define-public r-heatmaply
4350 (name "r-heatmaply")
4355 (uri (cran-uri "heatmaply" version))
4358 "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1"))))
4359 (build-system r-build-system)
4361 `(("r-assertthat" ,r-assertthat)
4362 ("r-colorspace" ,r-colorspace)
4363 ("r-dendextend" ,r-dendextend)
4364 ("r-ggplot2" ,r-ggplot2)
4365 ("r-htmlwidgets" ,r-htmlwidgets)
4366 ("r-magrittr" ,r-magrittr)
4367 ("r-plotly" ,r-plotly)
4368 ("r-rcolorbrewer" ,r-rcolorbrewer)
4369 ("r-reshape2" ,r-reshape2)
4370 ("r-scales" ,r-scales)
4371 ("r-seriation" ,r-seriation)
4372 ("r-viridis" ,r-viridis)
4373 ("r-webshot" ,r-webshot)))
4374 (home-page "https://cran.r-project.org/package=heatmaply")
4375 (synopsis "Interactive cluster heat maps using plotly")
4377 "This package enables you to create interactive cluster heatmaps that can
4378 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4379 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4380 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4381 a popular graphical method for visualizing high-dimensional data, in which a
4382 table of numbers is encoded as a grid of colored cells. The rows and columns
4383 of the matrix are ordered to highlight patterns and are often accompanied by
4385 ;; Either version of the license.
4386 (license (list license:gpl2 license:gpl3))))
4395 (uri (cran-uri "h5" version))
4398 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4399 (build-system r-build-system)
4404 `(("which" ,which)))
4406 `(("r-rcpp" ,r-rcpp)))
4407 (home-page "https://github.com/mannau/h5")
4408 (synopsis "Interface to the HDF5 Library")
4410 "This package provides an S4 interface to the HDF5 library supporting
4411 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4412 binary files in a language independent format. The HDF5 format can therefore
4413 be used as an alternative to R's save/load mechanism. Since h5 is able to
4414 access only subsets of stored data it can also handle data sets which do not
4416 (license license:bsd-2)))
4418 (define-public r-cgdsr
4425 (uri (cran-uri "cgdsr" version))
4428 "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23"))))
4429 (build-system r-build-system)
4431 `(("r-r-methodss3" ,r-r-methodss3)
4432 ("r-r-oo" ,r-r-oo)))
4433 (home-page "https://github.com/cBioPortal/cgdsr")
4434 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4436 "This package provides a basic set of R functions for querying the Cancer
4437 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4438 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4439 (license license:lgpl3)))
4441 (define-public r-import
4448 (uri (cran-uri "import" version))
4451 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4452 (build-system r-build-system)
4453 (home-page "https://github.com/smbache/import")
4454 (synopsis "Import mechanism for R")
4456 "This is an alternative mechanism for importing objects from packages.
4457 The syntax allows for importing multiple objects from a package with a single
4458 command in an expressive way. The import package bridges some of the gap
4459 between using @code{library} (or @code{require}) and direct (single-object)
4460 imports. Furthermore the imported objects are not placed in the current
4461 environment. It is also possible to import objects from stand-alone @code{.R}
4463 (license license:expat)))
4465 (define-public r-shinyace
4472 (uri (cran-uri "shinyAce" version))
4475 "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j"))))
4476 (properties `((upstream-name . "shinyAce")))
4477 (build-system r-build-system)
4479 `(("r-shiny" ,r-shiny)
4480 ("r-jsonlite" ,r-jsonlite)))
4481 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4482 (synopsis "Ace editor bindings for Shiny")
4484 "This package provides Ace editor bindings to enable a rich text editing
4485 environment within Shiny.")
4486 (license license:expat)))
4488 (define-public r-base64url
4490 (name "r-base64url")
4495 (uri (cran-uri "base64url" version))
4498 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4499 (build-system r-build-system)
4501 `(("r-backports" ,r-backports)))
4502 (home-page "https://github.com/mllg/base64url")
4503 (synopsis "Fast and URL-safe base64 encoder and decoder")
4505 "This package provides a URL-safe base64 encoder and decoder. In
4506 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4507 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4508 encoder does not fill the string with trailing @code{=}. The resulting
4509 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4510 and thus are safe to use in URLs or for file names. The package also comes
4511 with a simple base32 encoder/decoder suited for case insensitive file
4513 (license license:gpl3)))
4515 (define-public r-radiant-data
4517 (name "r-radiant-data")
4522 (uri (cran-uri "radiant.data" version))
4525 "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn"))
4526 (modules '((guix build utils)))
4529 ;; Delete files that are under CC-NC-SA.
4530 (delete-file-recursively "inst/app/tools/help")
4532 (properties `((upstream-name . "radiant.data")))
4533 (build-system r-build-system)
4535 `(("r-base64enc" ,r-base64enc)
4536 ("r-broom" ,r-broom)
4539 ("r-dplyr" ,r-dplyr)
4542 ("r-ggplot2" ,r-ggplot2)
4543 ("r-gridextra" ,r-gridextra)
4544 ("r-import" ,r-import)
4545 ("r-jsonlite" ,r-jsonlite)
4546 ("r-knitr" ,r-knitr)
4547 ("r-lubridate" ,r-lubridate)
4548 ("r-magrittr" ,r-magrittr)
4549 ("r-markdown" ,r-markdown)
4550 ("r-plotly" ,r-plotly)
4551 ("r-psych" ,r-psych)
4552 ("r-readr" ,r-readr)
4553 ("r-readxl" ,r-readxl)
4554 ("r-rlang" ,r-rlang)
4555 ("r-rmarkdown" ,r-rmarkdown)
4556 ("r-rstudioapi" ,r-rstudioapi)
4557 ("r-scales" ,r-scales)
4558 ("r-shiny" ,r-shiny)
4559 ("r-shinyfiles" ,r-shinyfiles)
4560 ("r-shinyace" ,r-shinyace)
4561 ("r-stringi" ,r-stringi)
4562 ("r-tibble" ,r-tibble)
4563 ("r-tidyr" ,r-tidyr)
4564 ("r-writexl" ,r-writexl)))
4565 (home-page "https://github.com/radiant-rstats/radiant.data")
4566 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4568 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4569 visualizing, summarizing, transforming, and combining data. It also contains
4570 functionality to generate reproducible reports of the analyses conducted in
4572 (license license:agpl3)))
4574 (define-public r-algdesign
4576 (name "r-algdesign")
4581 (uri (cran-uri "AlgDesign" version))
4584 "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
4585 (properties `((upstream-name . "AlgDesign")))
4586 (build-system r-build-system)
4587 (home-page "https://github.com/jvbraun/AlgDesign")
4588 (synopsis "Algorithmic experimental design")
4590 "This package provides tools to calculate exact and approximate theory
4591 experimental designs for D, A, and I criteria. Very large designs may be
4592 created. Experimental designs may be blocked or blocked designs created from
4593 a candidate list, using several criteria. The blocking can be done when whole
4594 and within plot factors interact.")
4595 (license license:gpl2+)))
4597 (define-public r-signal
4604 (uri (cran-uri "signal" version))
4607 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
4608 (build-system r-build-system)
4609 (propagated-inputs `(("r-mass" ,r-mass)))
4610 (native-inputs `(("gfortran" ,gfortran)))
4611 (home-page "https://cran.r-project.org/web/packages/signal/")
4612 (synopsis "Signal processing")
4614 "This package provides a set of signal processing functions originally
4615 written for Matlab and GNU Octave. It includes filter generation utilities,
4616 filtering functions, resampling routines, and visualization of filter models.
4617 It also includes interpolation functions.")
4618 (license license:gpl2)))
4620 (define-public r-gsubfn
4627 (uri (cran-uri "gsubfn" version))
4630 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
4631 (build-system r-build-system)
4632 (propagated-inputs `(("r-proto" ,r-proto)))
4633 (home-page "http://gsubfn.googlecode.com")
4634 (synopsis "Utilities for strings and function arguments.")
4636 "This package provides @code{gsubfn} which is like @code{gsub} but can
4637 take a replacement function or certain other objects instead of the
4638 replacement string. Matches and back references are input to the replacement
4639 function and replaced by the function output. @code{gsubfn} can be used to
4640 split strings based on content rather than delimiters and for quasi-perl-style
4641 string interpolation. The package also has facilities for translating
4642 formulas to functions and allowing such formulas in function calls instead of
4644 (license license:gpl2+)))
4646 (define-public r-sqldf
4653 (uri (cran-uri "sqldf" version))
4656 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
4657 (build-system r-build-system)
4659 `(("r-chron" ,r-chron)
4661 ("r-gsubfn" ,r-gsubfn)
4662 ("r-proto" ,r-proto)
4663 ("r-rsqlite" ,r-rsqlite)))
4664 (home-page "https://github.com/ggrothendieck/sqldf")
4665 (synopsis "Manipulate R data frames using SQL")
4667 "The @code{sqldf} function is typically passed a single argument which is
4668 an SQL select statement where the table names are ordinary R data frame names.
4669 @code{sqldf} transparently sets up a database, imports the data frames into
4670 that database, performs the SQL statement and returns the result using a
4671 heuristic to determine which class to assign to each column of the returned
4672 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
4673 used to read filtered files into R even if the original files are larger than
4674 R itself can handle.")
4675 (license license:gpl2)))
4677 (define-public r-abind
4684 (uri (cran-uri "abind" version))
4687 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
4688 (build-system r-build-system)
4689 (home-page "https://cran.r-project.org/web/packages/abind/")
4690 (synopsis "Combine multidimensional arrays")
4692 "This package provides tools to combine multidimensional arrays into a
4693 single array. This is a generalization of @code{cbind} and @code{rbind}. It
4694 works with vectors, matrices, and higher-dimensional arrays. It also provides
4695 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
4696 extracting and replacing data in arrays.")
4697 (license license:lgpl2.0+)))
4699 (define-public r-prroc
4706 (uri (cran-uri "PRROC" version))
4709 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
4710 (properties `((upstream-name . "PRROC")))
4711 (build-system r-build-system)
4712 (home-page "https://cran.r-project.org/web/packages/PRROC/")
4713 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
4715 "This package computes the areas under the @dfn{precision-recall} (PR)
4716 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
4717 contrast to other implementations, the interpolation between points of the PR
4718 curve is done by a non-linear piecewise function. In addition to the areas
4719 under the curves, the curves themselves can also be computed and plotted by a
4720 specific S3-method.")
4721 (license license:gpl3)))
4723 (define-public r-vim
4730 (uri (cran-uri "VIM" version))
4733 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
4734 (properties `((upstream-name . "VIM")))
4735 (build-system r-build-system)
4738 ("r-colorspace" ,r-colorspace)
4739 ("r-data-table" ,r-data-table)
4740 ("r-e1071" ,r-e1071)
4741 ("r-laeken" ,r-laeken)
4744 ("r-ranger" ,r-ranger)
4746 ("r-robustbase" ,r-robustbase)
4749 (home-page "https://github.com/alexkowa/VIM")
4750 (synopsis "Visualization and imputation of missing values")
4752 "This package provides tools for the visualization of missing and/or
4753 imputed values are introduced, which can be used for exploring the data and
4754 the structure of the missing and/or imputed values. Depending on this
4755 structure of the missing values, the corresponding methods may help to
4756 identify the mechanism generating the missing values and allows to explore the
4757 data including missing values. In addition, the quality of imputation can be
4758 visually explored using various univariate, bivariate, multiple and
4759 multivariate plot methods.")
4760 (license license:gpl2+)))
4762 (define-public r-fnn
4769 (uri (cran-uri "FNN" version))
4772 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
4773 (properties `((upstream-name . "FNN")))
4774 (build-system r-build-system)
4775 (home-page "https://cran.r-project.org/web/packages/FNN")
4776 (synopsis "Fast nearest neighbor search algorithms and applications")
4778 "This package provides cover-tree and kd-tree fast k-nearest neighbor
4779 search algorithms. Related applications including KNN classification,
4780 regression and information measures are implemented.")
4781 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
4782 ;; later can be used.
4783 (license license:gpl2+)))
4785 (define-public r-smoother
4792 (uri (cran-uri "smoother" version))
4795 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
4796 (build-system r-build-system)
4798 `(("r-ttr" ,r-ttr)))
4799 (home-page "http://cran.r-project.org/web/packages/smoother")
4800 (synopsis "Functions relating to the smoothing of numerical data")
4802 "This package provides a collection of methods for smoothing numerical
4803 data, commencing with a port of the Matlab gaussian window smoothing function.
4804 In addition, several functions typically used in smoothing of financial data
4806 (license license:gpl2)))
4808 (define-public r-riverplot
4810 (name "r-riverplot")
4815 (uri (cran-uri "riverplot" version))
4818 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
4819 (build-system r-build-system)
4820 (home-page "https://logfc.wordpress.com")
4821 (synopsis "Sankey or ribbon plots")
4823 "Sankey plots are a type of diagram that is convenient to illustrate how
4824 flow of information, resources etc. separates and joins, much like observing
4825 how rivers split and merge. For example, they can be used to compare
4826 different clusterings. This package provides an implementation of Sankey
4828 (license license:gpl2+)))
4830 (define-public r-dyn
4837 (uri (cran-uri "dyn" version))
4840 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
4841 (build-system r-build-system)
4843 `(("r-zoo" ,r-zoo)))
4844 (home-page "https://cran.r-project.org/web/packages/dyn")
4845 (synopsis "Time series regression")
4847 "This package provides the dyn class interfaces @code{ts}, @code{irts},
4848 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
4849 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
4850 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
4851 @code{randomForest::randomForest()} and other regression functions, allowing
4852 those functions to be used with time series including specifications that may
4853 contain lags, diffs and missing values.")
4855 (license license:gpl2+)))
4857 (define-public r-catdap
4864 (uri (cran-uri "catdap" version))
4867 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
4868 (build-system r-build-system)
4870 `(("gfortran" ,gfortran)))
4871 (home-page "https://cran.r-project.org/web/packages/catdap/")
4872 (synopsis "Tools for categorical data analysis")
4874 "This package provides functions for analyzing multivariate data.
4875 Dependencies of the distribution of the specified variable (response
4876 variable) to other variables (explanatory variables) are derived and
4877 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
4878 (license license:gpl2+)))
4880 (define-public r-arules
4887 (uri (cran-uri "arules" version))
4890 "0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y"))))
4891 (build-system r-build-system)
4893 `(("r-matrix" ,r-matrix)))
4894 (home-page "https://github.com/mhahsler/arules")
4895 (synopsis "Mining association rules and frequent itemsets")
4897 "This package provides an infrastructure for representing, manipulating
4898 and analyzing transaction data and patterns (frequent itemsets and association rules).
4899 It also provides C implementations of the association mining algorithms Apriori
4901 (license license:gpl3)))
4903 (define-public r-parsedate
4905 (name "r-parsedate")
4910 (uri (cran-uri "parsedate" version))
4913 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
4914 (build-system r-build-system)
4916 `(("r-rematch2" ,r-rematch2)))
4917 (home-page "https://github.com/gaborcsardi/parsedate")
4919 "Recognize and parse dates in various formats")
4921 "This package provides three functions for dealing with dates:
4922 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
4923 time formats, @code{parse_date} parses dates in unspecified formats,
4924 and @code{format_iso_8601} formats a date in ISO 8601 format.")
4925 (license license:gpl2)))
4927 (define-public r-abc-data
4934 (uri (cran-uri "abc.data" version))
4937 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
4938 (properties `((upstream-name . "abc.data")))
4939 (build-system r-build-system)
4940 (home-page "https://cran.r-project.org/web/packages/abc.data/")
4941 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
4943 "This package contains data which are used by functions of the abc
4944 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
4945 algorithms for performing parameter estimation, model selection, and
4947 (license license:gpl3+)))
4949 (define-public r-abc
4956 (uri (cran-uri "abc" version))
4959 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
4960 (build-system r-build-system)
4962 `(("r-abc-data" ,r-abc-data)
4963 ("r-locfit" ,r-locfit)
4966 ("r-quantreg" ,r-quantreg)))
4967 (home-page "https://cran.r-project.org/web/packages/abc/")
4968 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
4970 "This package implements several @dfn{Approximate Bayesian
4971 Computation} (ABC) algorithms for performing parameter estimation, model
4972 selection, and goodness-of-fit. Cross-validation tools are also available for
4973 measuring the accuracy of ABC estimates, and to calculate the
4974 misclassification probabilities of different models.")
4975 (license license:gpl3+)))
4977 (define-public r-zip
4984 (uri (cran-uri "zip" version))
4987 "1xvgs7mhxi0sdp5ix4nisqm9lf8f75b7ip7b1hqpq9bzh0x6z8ix"))))
4988 (build-system r-build-system)
4989 (home-page "https://github.com/gaborcsardi/zip")
4990 (synopsis "Cross-platform Zip compression")
4992 "This package provides a cross-platform Zip compression library for R.
4993 It is a replacement for the @code{zip} function, that does not require any
4994 additional external tools on any platform.")
4995 (license license:cc0)))
4997 (define-public r-openxlsx
5004 (uri (cran-uri "openxlsx" version))
5007 "1lflygpi1z4rlb1c6g6wsmi334maiiy7jhpg6ph4sw8lpvg12w4b"))))
5008 (build-system r-build-system)
5010 `(("r-rcpp" ,r-rcpp)
5012 (home-page "https://github.com/awalker89/openxlsx")
5013 (synopsis "Read, write and edit XLSX files")
5015 "This package simplifies the creation of Excel @code{.xlsx} files by
5016 providing a high level interface to writing, styling and editing worksheets.
5017 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5018 and @code{XLConnect} packages with the added benefit of removing the
5019 dependency on Java.")
5020 (license license:gpl3)))
5022 (define-public r-rio
5029 (uri (cran-uri "rio" version))
5032 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5033 (build-system r-build-system)
5035 `(("r-curl" ,r-curl)
5036 ("r-data-table" ,r-data-table)
5037 ("r-foreign" ,r-foreign)
5038 ("r-haven" ,r-haven)
5039 ("r-openxlsx" ,r-openxlsx)
5040 ("r-readxl" ,r-readxl)
5041 ("r-tibble" ,r-tibble)))
5042 (home-page "https://github.com/leeper/rio")
5043 (synopsis "Swiss-army knife for data I/O")
5045 "This package provides streamlined data import and export infrastructure
5046 by making assumptions that the user is probably willing to make: @code{import}
5047 and @code{export} determine the data structure from the file extension,
5048 reasonable defaults are used for data import and export (e.g.,
5049 @code{stringsAsFactors=FALSE}), web-based import is natively
5050 supported (including from SSL/HTTPS), compressed files can be read directly
5051 without explicit decompression, and fast import packages are used where
5052 appropriate. An additional convenience function, @code{convert}, provides a
5053 simple method for converting between file types.")
5054 (license license:gpl2)))
5056 (define-public r-maptools
5063 (uri (cran-uri "maptools" version))
5066 "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax"))))
5067 (build-system r-build-system)
5069 `(("r-foreign" ,r-foreign)
5070 ("r-lattice" ,r-lattice)
5072 (home-page "http://r-forge.r-project.org/projects/maptools/")
5073 (synopsis "Tools for reading and handling spatial objects")
5075 "This package provides a set of tools for manipulating and reading
5076 geographic data, in particular ESRI Shapefiles. It includes binary access to
5077 GSHHG shoreline files. The package also provides interface wrappers for
5078 exchanging spatial objects with other R packages.")
5079 ;; The C source files from shapelib are released under the Expat license.
5080 ;; The R code is released under GPL version 2 or later.
5081 (license (list license:gpl2+
5084 (define-public r-later
5091 (uri (cran-uri "later" version))
5094 "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb"))))
5095 (build-system r-build-system)
5099 ("r-rlang" ,r-rlang)))
5100 (home-page "https://github.com/r-lib/later")
5101 (synopsis "Utilities for delaying function execution")
5103 "This package provides tools to execute arbitrary R or C functions some
5104 time after the current time, after the R execution stack has emptied.")
5105 (license license:gpl2+)))
5107 (define-public r-promises
5114 (uri (cran-uri "promises" version))
5117 "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
5118 (build-system r-build-system)
5120 `(("r-later" ,r-later)
5121 ("r-magrittr" ,r-magrittr)
5124 ("r-rlang" ,r-rlang)))
5125 (home-page "https://rstudio.github.io/promises")
5126 (synopsis "Abstractions for promise-based asynchronous programming")
5128 "This package provides fundamental abstractions for doing asynchronous
5129 programming in R using promises. Asynchronous programming is useful for
5130 allowing a single R process to orchestrate multiple tasks in the background
5131 while also attending to something else. Semantics are similar to JavaScript
5132 promises, but with a syntax that is idiomatic R.")
5133 (license license:expat)))
5135 (define-public r-dosnow
5142 (uri (cran-uri "doSNOW" version))
5145 "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
5146 (properties `((upstream-name . "doSNOW")))
5147 (build-system r-build-system)
5149 `(("r-foreach" ,r-foreach)
5150 ("r-iterators" ,r-iterators)
5151 ("r-snow" ,r-snow)))
5152 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5153 (synopsis "Foreach parallel adaptor for the snow package")
5155 "This package provides a parallel backend for the @code{%dopar%} function
5156 using the @code{snow} package.")
5157 (license license:gpl2)))
5159 (define-public r-snowfall
5162 (version "1.84-6.1")
5165 (uri (cran-uri "snowfall" version))
5167 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5168 (build-system r-build-system)
5170 `(("r-snow" ,r-snow)))
5171 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5172 (synopsis "Easier cluster computing")
5173 (description "This package is a usability wrapper around snow for easier
5174 development of parallel R programs. This package offers e.g. extended error
5175 checks, and additional functions. All functions work in sequential mode, too,
5176 if no cluster is present or wished. The package is also designed as connector
5177 to the cluster management tool @code{sfCluster}, but can also used without
5179 (license license:gpl2+)))
5181 (define-public r-rappdirs
5188 (uri (cran-uri "rappdirs" version))
5191 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5192 (build-system r-build-system)
5193 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5194 (synopsis "Determine where to save data, caches, and logs")
5196 "This package provides an easy way to determine which directories on the
5197 user's computer should be used to save data, caches and logs. It is a port of
5198 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5199 (license license:expat)))
5201 (define-public r-learnr
5208 (uri (cran-uri "learnr" version))
5211 "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5"))))
5212 (build-system r-build-system)
5214 `(("r-evaluate" ,r-evaluate)
5215 ("r-htmltools" ,r-htmltools)
5216 ("r-htmlwidgets" ,r-htmlwidgets)
5217 ("r-jsonlite" ,r-jsonlite)
5218 ("r-knitr" ,r-knitr)
5219 ("r-markdown" ,r-markdown)
5220 ("r-rappdirs" ,r-rappdirs)
5221 ("r-rmarkdown" ,r-rmarkdown)
5222 ("r-rprojroot" ,r-rprojroot)
5223 ("r-shiny" ,r-shiny)
5224 ("r-withr" ,r-withr)))
5225 (home-page "https://rstudio.github.io/learnr/")
5226 (synopsis "Interactive tutorials for R")
5228 "This package provides tools to create interactive tutorials using R
5229 Markdown. Use a combination of narrative, figures, videos, exercises, and
5230 quizzes to create self-paced tutorials for learning about R and R packages.")
5231 (license license:asl2.0)))
5233 (define-public r-analytics
5235 (name "r-analytics")
5240 (uri (cran-uri "analytics" version))
5243 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5244 (build-system r-build-system)
5247 ("r-cluster" ,r-cluster)
5248 ("r-fractal" ,r-fractal)
5249 ("r-lmtest" ,r-lmtest)
5252 ("r-powerplus" ,r-powerplus)
5253 ("r-robust" ,r-robust)
5254 ("r-trend" ,r-trend)
5258 (home-page "https://cran.r-project.org/web/packages/analytics/")
5259 (synopsis "Collection of data analysis tools")
5261 "This package is a collection of data analysis tools. It includes tools
5262 for regression outlier detection in a fitted linear model, stationary
5263 bootstrap using a truncated geometric distribution, a comprehensive test for
5264 weak stationarity, column means by group, weighted biplots, and a heuristic to
5265 obtain a better initial configuration in non-metric MDS.")
5266 (license license:gpl2)))
5268 (define-public r-reticulate
5270 (name "r-reticulate")
5275 (uri (cran-uri "reticulate" version))
5278 "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb"))))
5279 (build-system r-build-system)
5280 (inputs `(("python" ,python)))
5282 `(("r-jsonlite" ,r-jsonlite)
5283 ("r-matrix" ,r-matrix)
5284 ("r-rcpp" ,r-rcpp)))
5285 (home-page "https://github.com/rstudio/reticulate")
5286 (synopsis "R interface to Python")
5288 "This package provides an interface from R to Python modules, classes,
5289 and functions. When calling into Python, R data types are automatically
5290 converted to their equivalent Python types. When values are returned from
5291 Python to R they are converted back to R types.")
5292 (license license:asl2.0)))
5294 (define-public r-bibtex
5301 (uri (cran-uri "bibtex" version))
5304 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5305 (build-system r-build-system)
5306 (propagated-inputs `(("r-stringr" ,r-stringr)))
5307 (home-page "https://github.com/romainfrancois/bibtex")
5308 (synopsis "Bibtex parser")
5309 (description "This package provides a utility for R to parse a bibtex
5311 (license license:gpl2+)))
5313 (define-public r-ggseqlogo
5315 (name "r-ggseqlogo")
5320 (uri (cran-uri "ggseqlogo" version))
5323 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5324 (build-system r-build-system)
5325 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5326 (home-page "https://github.com/omarwagih/ggseqlogo")
5327 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5329 "The range of functions provided by this package makes it possible to
5330 draw highly versatile genomic sequence logos. Features include, but are not
5331 limited to, modifying colour schemes and fonts used to draw the logo,
5332 generating multiple logo plots, and aiding the visualisation with annotations.
5333 Sequence logos can easily be combined with other ggplot2 plots.")
5334 ;; Unspecified version of the LGPL.
5335 (license license:lgpl3+)))
5337 (define-public r-ggsci
5344 (uri (cran-uri "ggsci" version))
5347 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5348 (build-system r-build-system)
5350 `(("r-ggplot2" ,r-ggplot2)
5351 ("r-scales" ,r-scales)))
5352 (home-page "https://nanx.me/ggsci/")
5353 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5355 "This package provides a collection of ggplot2 color palettes inspired by
5356 plots in scientific journals, data visualization libraries, science fiction
5357 movies, and TV shows.")
5358 (license license:gpl3)))
5360 (define-public r-ggsignif
5367 (uri (cran-uri "ggsignif" version))
5370 "0z04g5kqdj66fyfxb5d2m7njkqd7idbiy4xgsnxdh5pbh3cr643x"))))
5371 (build-system r-build-system)
5373 `(("r-ggplot2" ,r-ggplot2)))
5374 (home-page "https://github.com/const-ae/ggsignif")
5375 (synopsis "Significance brackets for ggplot2")
5377 "Enrich your ggplots with group-wise comparisons. This package provides
5378 an easy way to indicate if two groups are significantly different. Commonly
5379 this is shown by a bracket on top connecting the groups of interest which
5380 itself is annotated with the level of significance. The package provides a
5381 single layer that takes the groups for comparison and the test as arguments
5382 and adds the annotation to the plot.")
5383 (license license:gpl3)))
5385 (define-public r-ggpubr
5392 (uri (cran-uri "ggpubr" version))
5395 "0rkpcjb1x7lvhj68aam5airbi534jqyiq12x5xk40a25iifhghq6"))))
5396 (build-system r-build-system)
5398 `(("r-cowplot" ,r-cowplot)
5399 ("r-dplyr" ,r-dplyr)
5400 ("r-ggplot2" ,r-ggplot2)
5401 ("r-ggrepel" ,r-ggrepel)
5402 ("r-ggsci" ,r-ggsci)
5403 ("r-ggsignif" ,r-ggsignif)
5405 ("r-gridextra" ,r-gridextra)
5406 ("r-magrittr" ,r-magrittr)
5407 ("r-polynom" ,r-polynom)
5408 ("r-purrr" ,r-purrr)
5409 ("r-scales" ,r-scales)
5410 ("r-tidyr" ,r-tidyr)))
5411 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5412 (synopsis "ggplot2-based publication-ready plots")
5414 "The ggplot2 package is an excellent and flexible package for elegant
5415 data visualization in R. However the default generated plots require some
5416 formatting before we can send them for publication. The ggpubr package
5417 provides some easy-to-use functions for creating and customizing ggplot2-based
5418 publication-ready plots.")
5419 (license license:gpl2)))
5421 (define-public r-ellipse
5428 (uri (cran-uri "ellipse" version))
5431 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5432 (build-system r-build-system)
5433 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5434 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5436 "This package contains various routines for drawing ellipses and
5437 ellipse-like confidence regions, implementing the plots described in Murdoch
5438 and Chow (1996), A graphical display of large correlation matrices, The
5439 American Statistician 50, 178-180. There are also routines implementing the
5440 profile plots described in Bates and Watts (1988), Nonlinear Regression
5441 Analysis and its Applications.")
5442 (license license:gpl2+)))
5444 (define-public r-flashclust
5446 (name "r-flashclust")
5451 (uri (cran-uri "flashClust" version))
5454 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5455 (properties `((upstream-name . "flashClust")))
5456 (build-system r-build-system)
5457 (native-inputs `(("gfortran" ,gfortran)))
5458 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5459 (synopsis "Implementation of optimal hierarchical clustering")
5461 "This package provides a fast implementation of hierarchical
5463 (license license:gpl2+)))
5465 (define-public r-factominer
5467 (name "r-factominer")
5472 (uri (cran-uri "FactoMineR" version))
5475 "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
5476 (properties `((upstream-name . "FactoMineR")))
5477 (build-system r-build-system)
5480 ("r-cluster" ,r-cluster)
5481 ("r-ellipse" ,r-ellipse)
5482 ("r-flashclust" ,r-flashclust)
5483 ("r-lattice" ,r-lattice)
5484 ("r-leaps" ,r-leaps)
5486 ("r-scatterplot3d" ,r-scatterplot3d)))
5487 (home-page "http://factominer.free.fr")
5488 (synopsis "Multivariate exploratory data analysis and data mining")
5490 "This package provides exploratory data analysis methods to summarize,
5491 visualize and describe datasets. The main principal component methods are
5492 available, those with the largest potential in terms of applications:
5493 principal component analysis (PCA) when variables are quantitative,
5494 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5495 variables are categorical, Multiple Factor Analysis when variables are
5496 structured in groups, etc. and hierarchical cluster analysis.")
5497 (license license:gpl2+)))
5499 (define-public r-factoextra
5501 (name "r-factoextra")
5506 (uri (cran-uri "factoextra" version))
5509 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
5510 (build-system r-build-system)
5512 `(("r-abind" ,r-abind)
5513 ("r-cluster" ,r-cluster)
5514 ("r-dendextend" ,r-dendextend)
5515 ("r-factominer" ,r-factominer)
5516 ("r-ggplot2" ,r-ggplot2)
5517 ("r-ggpubr" ,r-ggpubr)
5518 ("r-ggrepel" ,r-ggrepel)
5519 ("r-reshape2" ,r-reshape2)
5520 ("r-tidyr" ,r-tidyr)))
5521 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5522 (synopsis "Extract and visualize the results of multivariate data analyses")
5524 "This package provides some easy-to-use functions to extract and
5525 visualize the output of multivariate data analyses, including
5526 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5527 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5528 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5529 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5530 packages. It contains also functions for simplifying some clustering analysis
5531 steps and provides ggplot2-based elegant data visualization.")
5532 (license license:gpl2)))
5534 (define-public r-fansi
5541 (uri (cran-uri "fansi" version))
5544 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
5545 (build-system r-build-system)
5547 `(("r-knitr" ,r-knitr))) ; for vignettes
5548 (home-page "https://github.com/brodieG/fansi")
5549 (synopsis "ANSI control sequence aware string functions")
5551 "This package provides counterparts to R string manipulation functions
5552 that account for the effects of ANSI text formatting control sequences.")
5553 (license license:gpl2+)))
5555 (define-public r-nbclust
5562 (uri (cran-uri "NbClust" version))
5565 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
5566 (properties `((upstream-name . "NbClust")))
5567 (build-system r-build-system)
5568 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
5569 (synopsis "Determine the best number of clusters in a data set")
5571 "NbClust provides 30 indexes for determining the optimal number of
5572 clusters in a data set and offers the best clustering scheme from different
5573 results to the user.")
5574 (license license:gpl2)))
5576 (define-public r-hdf5r
5583 (uri (cran-uri "hdf5r" version))
5586 "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq"))))
5587 (build-system r-build-system)
5592 `(("r-bit64" ,r-bit64)
5594 (home-page "https://hhoeflin.github.io/hdf5r")
5595 (synopsis "Interface to the HDF5 binary data format")
5597 "HDF5 is a data model, library and file format for storing and managing
5598 large amounts of data. This package provides a nearly feature complete,
5599 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
5600 functionality is added so that HDF5 objects behave very similar to their
5601 corresponding R counterparts.")
5602 (license license:asl2.0)))
5604 (define-public r-itertools
5606 (name "r-itertools")
5611 (uri (cran-uri "itertools" version))
5614 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
5615 (build-system r-build-system)
5617 `(("r-iterators" ,r-iterators)))
5618 (home-page "https://cran.r-project.org/web/packages/itertools/")
5619 (synopsis "Iterator tools")
5621 "This package provides various tools for creating iterators, many
5622 patterned after functions in the Python @code{itertools} module, and others
5623 patterned after functions in the snow package.")
5624 (license license:gpl2)))
5626 (define-public r-polynom
5633 (uri (cran-uri "polynom" version))
5636 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
5637 (build-system r-build-system)
5638 (home-page "https://cran.r-project.org/web/packages/polynom/")
5639 (synopsis "Functions for univariate polynomial manipulations")
5641 "This package provides a collection of functions to implement a class for
5642 univariate polynomial manipulations.")
5643 (license license:gpl2)))
5645 (define-public r-gbrd
5652 (uri (cran-uri "gbRd" version))
5655 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
5656 (properties `((upstream-name . "gbRd")))
5657 (build-system r-build-system)
5658 (home-page "https://cran.r-project.org/web/packages/gbRd/")
5659 (synopsis "Utilities for processing Rd objects and files")
5661 "This package provides utilities for processing Rd objects and files.
5662 Extract argument descriptions and other parts of the help pages of
5664 (license license:gpl2+)))
5666 (define-public r-rjags
5673 (uri (cran-uri "rjags" version))
5676 "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m"))))
5677 (build-system r-build-system)
5679 `(("r-coda" ,r-coda)))
5683 `(("pkg-config" ,pkg-config)))
5684 (home-page "http://mcmc-jags.sourceforge.net")
5685 (synopsis "Bayesian graphical models using MCMC")
5687 "This package provides an R interface to the JAGS MCMC library. JAGS is
5688 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
5689 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
5690 (license license:gpl2)))
5692 (define-public r-rdpack
5699 (uri (cran-uri "Rdpack" version))
5702 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
5703 (properties `((upstream-name . "Rdpack")))
5704 (build-system r-build-system)
5706 `(("r-bibtex" ,r-bibtex)
5707 ("r-gbrd" ,r-gbrd)))
5708 (home-page "https://github.com/GeoBosh/Rdpack")
5709 (synopsis "Update and manipulate Rd documentation objects")
5711 "This package provides functions for manipulation of R documentation
5712 objects, including functions @code{reprompt()} and @code{ereprompt()} for
5713 updating Rd documentation for functions, methods and classes; it also includes
5714 Rd macros for citations and import of references from bibtex files for use in
5715 Rd files and roxygen2 comments, as well as many functions for manipulation of
5716 references and Rd files.")
5717 (license license:gpl2+)))
5719 (define-public r-officer
5726 (uri (cran-uri "officer" version))
5729 "1m4b3mcn5j5q3nq0jp1nranh4rdb8vxcpabn6ryqk9m6709fvhjz"))))
5730 (build-system r-build-system)
5732 `(("r-base64enc" ,r-base64enc)
5733 ("r-digest" ,r-digest)
5734 ("r-htmltools" ,r-htmltools)
5735 ("r-magrittr" ,r-magrittr)
5738 ("r-rlang" ,r-rlang)
5742 (home-page "https://davidgohel.github.io/officer")
5743 (synopsis "Manipulation of Word and PowerPoint documents")
5745 "This package provides tools to access and manipulate Word and PowerPoint
5746 documents from R. The package focuses on tabular and graphical reporting from
5747 R; it also provides two functions that let users get document content into
5748 data objects. A set of functions lets add and remove images, tables and
5749 paragraphs of text in new or existing documents. When working with PowerPoint
5750 presentations, slides can be added or removed; shapes inside slides can also
5751 be added or removed. When working with Word documents, a cursor can be used
5752 to help insert or delete content at a specific location in the document.")
5753 (license license:gpl3)))
5755 (define-public r-abn
5762 (uri (cran-uri "abn" version))
5765 "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm"))))
5766 (build-system r-build-system)
5770 `(("r-cairo" ,r-cairo)
5775 ("r-rcpparmadillo" ,r-rcpparmadillo)
5776 ("r-rjags" ,r-rjags)))
5777 (home-page "http://www.r-bayesian-networks.org")
5778 (synopsis "Modelling multivariate data with additive bayesian networks")
5780 "Bayesian network analysis is a form of probabilistic graphical models
5781 which derives from empirical data a directed acyclic graph, DAG, describing
5782 the dependency structure between random variables. An additive Bayesian
5783 network model consists of a form of a DAG where each node comprises a
5784 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
5785 equivalent to Bayesian multivariate regression using graphical modelling, they
5786 generalises the usual multivariable regression, GLM, to multiple dependent
5787 variables. This package provides routines to help determine optimal Bayesian
5788 network models for a given data set, where these models are used to identify
5789 statistical dependencies in messy, complex data.")
5790 (license license:gpl2+)))
5792 (define-public r-acd
5799 (uri (cran-uri "ACD" version))
5802 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
5803 (properties `((upstream-name . "ACD")))
5804 (build-system r-build-system)
5805 (home-page "https://cran.r-project.org/web/packages/ACD/")
5806 (synopsis "Categorical data analysis with complete or missing responses")
5808 "This package provides tools for categorical data analysis with complete
5809 or missing responses.")
5810 (license license:gpl2+)))
5812 (define-public r-acdm
5819 (uri (cran-uri "ACDm" version))
5822 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
5823 (properties `((upstream-name . "ACDm")))
5824 (build-system r-build-system)
5826 `(("r-dplyr" ,r-dplyr)
5827 ("r-ggplot2" ,r-ggplot2)
5829 ("r-rsolnp" ,r-rsolnp)
5831 (home-page "https://cran.r-project.org/web/packages/ACDm/")
5832 (synopsis "Tools for Autoregressive Conditional Duration Models")
5834 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
5835 and Russell, 1998) models. It creates trade, price or volume durations from
5836 transactions (tic) data, performs diurnal adjustments, fits various ACD models
5838 (license license:gpl2+)))
5840 (define-public r-overlap
5847 (uri (cran-uri "overlap" version))
5850 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
5851 (build-system r-build-system)
5852 (home-page "https://cran.r-project.org/web/packages/overlap/")
5853 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
5855 "This package provides functions to fit kernel density functions to data
5856 on temporal activity patterns of animals; estimate coefficients of overlapping
5857 of densities for two species; and calculate bootstrap estimates of confidence
5859 (license license:gpl3+)))
5861 (define-public r-snakecase
5863 (name "r-snakecase")
5868 (uri (cran-uri "snakecase" version))
5871 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
5872 (build-system r-build-system)
5874 `(("r-stringi" ,r-stringi)
5875 ("r-stringr" ,r-stringr)))
5876 (home-page "https://github.com/Tazinho/snakecase")
5877 (synopsis "Convert strings into any case")
5879 "This package provides a consistent, flexible and easy to use tool to
5880 parse and convert strings into cases like snake or camel among others.")
5881 (license license:gpl3)))
5883 (define-public r-prediction
5885 (name "r-prediction")
5890 (uri (cran-uri "prediction" version))
5893 "0kx7xbm2j6c8h6gk1iig4vfpg877psg16j74hl7zc2mv40sc6dy5"))))
5894 (build-system r-build-system)
5896 `(("r-data-table" ,r-data-table)))
5897 (home-page "https://github.com/leeper/prediction")
5898 (synopsis "Tidy, type-safe prediction methods")
5900 "This package provides the @code{prediction()} function, a type-safe
5901 alternative to @code{predict()} that always returns a data frame. The package
5902 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
5903 from the @code{stats} package, as well as numerous other model classes from
5904 other add-on packages.")
5905 (license license:expat)))
5907 (define-public r-insight
5914 (uri (cran-uri "insight" version))
5917 "1r288hc01cpyrk3nias30fw783z2vw20qr1k67vr65anh7mwm7vb"))))
5918 (build-system r-build-system)
5919 (home-page "https://easystats.github.io/insight/")
5920 (synopsis "Easy access to model information for various model objects")
5922 "This package provides a tool to provide an easy, intuitive and
5923 consistent access to information contained in various R models, like model
5924 formulas, model terms, information about random effects, data that was used to
5925 fit the model or data from response variables. The package mainly revolves
5926 around two types of functions: Functions that find (the names of) information,
5927 starting with @code{find_}, and functions that get the underlying data,
5928 starting with @code{get_}. The package has a consistent syntax and works with
5929 many different model objects, where otherwise functions to access these
5930 information are missing.")
5931 (license license:gpl3)))
5933 (define-public r-sjlabelled
5935 (name "r-sjlabelled")
5940 (uri (cran-uri "sjlabelled" version))
5943 "0rnmlwpp41h04dzfjd5ncvzjzs43slaimb4v2in1axznv3haafyc"))))
5944 (build-system r-build-system)
5946 `(("r-haven" ,r-haven)
5947 ("r-insight" ,r-insight)
5948 ("r-magrittr" ,r-magrittr)
5949 ("r-purrr" ,r-purrr)
5950 ("r-rlang" ,r-rlang)
5951 ("r-tidyselect" ,r-tidyselect)))
5952 (home-page "https://github.com/strengejacke/sjlabelled")
5953 (synopsis "Labelled data utility functions")
5955 "This package provides a collection of functions dealing with labelled
5956 data, like reading and writing data between R and other statistical software
5957 packages. This includes easy ways to get, set or change value and variable
5958 label attributes, to convert labelled vectors into factors or numeric (and
5959 vice versa), or to deal with multiple declared missing values.")
5960 (license license:gpl3)))
5962 (define-public r-sjmisc
5969 (uri (cran-uri "sjmisc" version))
5972 "11iiap0w5v0dszgwx4pi3j1zf9vnlw1ml1wjvq1hg9iz1plgbfnc"))))
5973 (build-system r-build-system)
5975 `(("r-dplyr" ,r-dplyr)
5976 ("r-haven" ,r-haven)
5977 ("r-magrittr" ,r-magrittr)
5978 ("r-purrr" ,r-purrr)
5979 ("r-rlang" ,r-rlang)
5980 ("r-sjlabelled" ,r-sjlabelled)))
5981 (home-page "https://github.com/strengejacke/sjmisc")
5982 (synopsis "Data and variable transformation functions")
5984 "This package is a collection of miscellaneous utility functions,
5985 supporting data transformation tasks like recoding, dichotomizing or grouping
5986 variables, setting and replacing missing values. The data transformation
5987 functions also support labelled data, and all integrate seamlessly into a
5988 tidyverse workflow.")
5989 (license license:gpl3)))
5991 (define-public r-nortest
5998 (uri (cran-uri "nortest" version))
6001 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6002 (build-system r-build-system)
6003 (home-page "https://cran.r-project.org/web/packages/nortest/")
6004 (synopsis "Tests for normality")
6006 "This package provides five omnibus tests for testing the composite
6007 hypothesis of normality.")
6008 (license license:gpl2+)))
6010 (define-public r-moonbook
6017 (uri (cran-uri "moonBook" version))
6020 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6021 (properties `((upstream-name . "moonBook")))
6022 (build-system r-build-system)
6024 `(("r-magrittr" ,r-magrittr)
6025 ("r-nortest" ,r-nortest)
6026 ("r-purrr" ,r-purrr)
6027 ("r-sjmisc" ,r-sjmisc)
6028 ("r-stringr" ,r-stringr)
6029 ("r-survival" ,r-survival)))
6030 (home-page "https://github.com/cardiomoon/moonBook")
6031 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6033 "This package provides several analysis-related functions for the book
6034 entitled \"R statistics and graph for medical articles\" (written in Korean),
6035 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6037 (license license:gpl2)))
6039 (define-public r-flextable
6041 (name "r-flextable")
6046 (uri (cran-uri "flextable" version))
6049 "0h6ylgz1mn61d2kh1bym8hfl3r7nf4z092lmjsaav3h1ki3avrnl"))))
6050 (build-system r-build-system)
6052 `(("r-base64enc" ,r-base64enc)
6053 ("r-data-table" ,r-data-table)
6054 ("r-gdtools" ,r-gdtools)
6055 ("r-htmltools" ,r-htmltools)
6056 ("r-knitr" ,r-knitr)
6057 ("r-officer" ,r-officer)
6058 ("r-rlang" ,r-rlang)
6059 ("r-rmarkdown" ,r-rmarkdown)
6060 ("r-xml2" ,r-xml2)))
6061 (home-page "https://davidgohel.github.io/flextable")
6062 (synopsis "Functions for tabular reporting")
6064 "This package provides tools to create pretty tables for HTML documents
6065 and other formats. Functions are provided to let users create tables, modify
6066 and format their content. It extends the @code{officer} package and can be
6067 used within R markdown documents when rendering to HTML and to Word
6069 (license license:gpl3)))
6071 (define-public r-writexl
6078 (uri (cran-uri "writexl" version))
6081 "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"))))
6082 (build-system r-build-system)
6083 (inputs `(("zlib" ,zlib)))
6084 (home-page "https://github.com/ropensci/writexl")
6085 (synopsis "Export data frames to xlsx format")
6087 "This package provides a data frame to xlsx exporter based on
6089 (license license:bsd-2)))
6091 (define-public r-biasedurn
6093 (name "r-biasedurn")
6098 (uri (cran-uri "BiasedUrn" version))
6101 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6102 (properties `((upstream-name . "BiasedUrn")))
6103 (build-system r-build-system)
6104 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6105 (synopsis "Biased Urn model distributions")
6107 "This package provides statistical models of biased sampling in the form
6108 of univariate and multivariate noncentral hypergeometric distributions,
6109 including Wallenius' noncentral hypergeometric distribution and Fisher's
6110 noncentral hypergeometric distribution (also called extended hypergeometric
6112 (license license:gpl3)))
6114 (define-public r-goplot
6121 (uri (cran-uri "GOplot" version))
6124 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6125 (properties `((upstream-name . "GOplot")))
6126 (build-system r-build-system)
6128 `(("r-ggdendro" ,r-ggdendro)
6129 ("r-ggplot2" ,r-ggplot2)
6130 ("r-gridextra" ,r-gridextra)
6131 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6132 (home-page "https://github.com/wencke/wencke.github.io")
6133 (synopsis "Visualization of functional analysis data")
6135 "This package provides an implementation of multilayered visualizations
6136 for enhanced graphical representation of functional analysis data. It
6137 combines and integrates omics data derived from expression and functional
6138 annotation enrichment analyses. Its plotting functions have been developed
6139 with an hierarchical structure in mind: starting from a general overview to
6140 identify the most enriched categories (modified bar plot, bubble plot) to a
6141 more detailed one displaying different types of relevant information for the
6142 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6143 Venn diagram, heatmap).")
6144 (license license:gpl2)))
6146 (define-public r-getopt
6153 (uri (cran-uri "getopt" version))
6156 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6157 (build-system r-build-system)
6158 (home-page "https://github.com/trevorld/getopt")
6159 (synopsis "Command-line option processor for R")
6161 "This package is designed to be used with Rscript to write shebang
6162 scripts that accept short and long options. Many users will prefer to
6163 use the packages @code{optparse} or @code{argparse} which add extra
6164 features like automatically generated help options and usage texts,
6165 support for default values, positional argument support, etc.")
6166 (license license:gpl2+)))
6168 (define-public r-findpython
6170 (name "r-findpython")
6175 (uri (cran-uri "findpython" version))
6178 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6179 (build-system r-build-system)
6180 (home-page "https://github.com/trevorld/findpython")
6181 (synopsis "Functions to find an acceptable Python binary")
6183 "This package was designed to find an acceptable Python binary that
6184 matches version and feature constraints.")
6185 (license license:expat)))
6187 ;; This in not the same as "r-argparser"
6188 (define-public r-argparse
6195 (uri (cran-uri "argparse" version))
6198 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6199 (build-system r-build-system)
6200 (inputs `(("python" ,python)))
6202 `(("r-findpython" ,r-findpython)
6203 ("r-jsonlite" ,r-jsonlite)
6205 (home-page "https://github.com/trevorld/argparse")
6206 (synopsis "Command line optional and positional argument parser")
6208 "This package provides a command line parser to be used with Rscript to
6209 write shebang scripts that gracefully accept positional and optional arguments
6210 and automatically generate usage notices.")
6211 (license license:gpl2+)))
6213 (define-public r-hash
6220 (uri (cran-uri "hash" version))
6223 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6224 (build-system r-build-system)
6225 (home-page "https://cran.r-project.org/web/packages/hash/")
6226 (synopsis "Implementation of hash/associated arrays/dictionaries")
6228 "This package implements a data structure similar to hashes in Perl and
6229 dictionaries in Python but with a purposefully R flavor. For objects of
6230 appreciable size, access using hashes outperforms native named lists and
6232 (license license:gpl2+)))
6234 (define-public r-orddom
6241 (uri (cran-uri "orddom" version))
6244 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6245 (build-system r-build-system)
6246 (propagated-inputs `(("r-psych" ,r-psych)))
6247 (home-page "https://cran.r-project.org/web/packages/orddom/")
6248 (synopsis "Ordinal dominance statistics")
6250 "This package provides tools to compute ordinal, statistics and effect
6251 sizes as an alternative to mean comparison: Cliff's delta or success rate
6252 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6253 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6254 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6255 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6256 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6257 Group (Non-)Overlap considerations.")
6258 (license license:gpl2)))
6260 (define-public r-doby
6267 (uri (cran-uri "doBy" version))
6270 "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb"))))
6271 (properties `((upstream-name . "doBy")))
6272 (build-system r-build-system)
6274 `(("r-dplyr" ,r-dplyr)
6275 ("r-magrittr" ,r-magrittr)
6277 ("r-matrix" ,r-matrix)
6278 ("r-plyr" ,r-plyr)))
6279 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6280 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6282 "This package contains:
6285 @item facilities for working with grouped data: @code{do}
6286 something to data stratified @code{by} some variables.
6287 @item implementations of least-squares means, general linear contrasts, and
6288 @item miscellaneous other utilities.
6290 (license license:gpl2+)))
6292 (define-public r-refgenome
6294 (name "r-refgenome")
6299 (uri (cran-uri "refGenome" version))
6302 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6303 (properties `((upstream-name . "refGenome")))
6304 (build-system r-build-system)
6308 ("r-rsqlite" ,r-rsqlite)))
6309 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6311 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6313 "This package contains functionality for importing and managing of
6314 downloaded genome annotation data from the Ensembl genome browser (European
6315 Bioinformatics Institute) and from the UCSC genome browser (University of
6316 California, Santa Cruz) and annotation routines for genomic positions and
6317 splice site positions.")
6318 (license license:gpl2)))
6320 (define-public r-basix
6327 (uri (cran-uri "BASIX" version))
6330 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6331 (properties `((upstream-name . "BASIX")))
6332 (build-system r-build-system)
6333 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6334 (synopsis "Efficient C/C++ toolset for R")
6336 "BASIX provides some efficient C/C++ implementations of native R
6337 procedures to speed up calculations in R.")
6338 (license license:gpl2)))
6340 (define-public r-blockfest
6342 (name "r-blockfest")
6347 (uri (cran-uri "BlockFeST" version))
6350 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6351 (properties `((upstream-name . "BlockFeST")))
6352 (build-system r-build-system)
6353 (propagated-inputs `(("r-basix" ,r-basix)))
6354 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6355 (synopsis "Bayesian calculation of region-specific fixation index")
6357 "This package provides an R implementation of an extension of the
6358 BayeScan software for codominant markers, adding the option to group
6359 individual SNPs into pre-defined blocks. A typical application of this new
6360 approach is the identification of genomic regions, genes, or gene sets
6361 containing one or more SNPs that evolved under directional selection.")
6362 (license license:gpl2)))
6364 (define-public r-proc
6371 (uri (cran-uri "pROC" version))
6374 "1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
6375 (properties `((upstream-name . "pROC")))
6376 (build-system r-build-system)
6378 `(("r-plyr" ,r-plyr)
6379 ("r-rcpp" ,r-rcpp)))
6380 (home-page "http://expasy.org/tools/pROC/")
6381 (synopsis "Display and analyze ROC curves")
6383 "This package provides tools for visualizing, smoothing and comparing
6384 receiver operating characteristic (ROC curves). The area under the
6385 curve (AUC) can be compared with statistical tests based on U-statistics or
6386 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6387 (license license:gpl3+)))
6389 (define-public r-rootsolve
6391 (name "r-rootsolve")
6396 (uri (cran-uri "rootSolve" version))
6399 "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8"))))
6400 (properties `((upstream-name . "rootSolve")))
6401 (build-system r-build-system)
6402 (native-inputs `(("gfortran" ,gfortran)))
6403 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6404 (synopsis "Tools for the analysis of ordinary differential equations")
6406 "This package provides routines to find the root of nonlinear functions,
6407 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6408 differential equations} (ODE). It includes routines that:
6411 @item generate gradient and jacobian matrices (full and banded),
6412 @item find roots of non-linear equations by the Newton-Raphson method,
6413 @item estimate steady-state conditions of a system of (differential) equations
6414 in full, banded or sparse form, using the Newton-Raphson method, or by
6415 dynamically running,
6416 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6417 and 3-D partial differential equations, that have been converted to ordinary
6418 differential equations by numerical differencing (using the method-of-lines
6421 (license license:gpl2+)))
6423 (define-public r-abcanalysis
6425 (name "r-abcanalysis")
6430 (uri (cran-uri "ABCanalysis" version))
6432 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6433 (properties `((upstream-name . "ABCanalysis")))
6434 (build-system r-build-system)
6435 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6436 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6437 (synopsis "Computed ABC Analysis")
6439 "Multivariate data sets often differ in several factors or derived statistical
6440 parameters, which have to be selected for a valid interpretation. Basing this
6441 selection on traditional statistical limits leads occasionally to the perception
6442 of losing information from a data set. This package provides tools to calculate
6443 these limits on the basis of the mathematical properties of the distribution of
6444 the analyzed items.")
6445 (license license:gpl3)))
6447 (define-public r-slam
6454 (uri (cran-uri "slam" version))
6456 (base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4"))))
6457 (build-system r-build-system)
6458 (home-page "https://cran.r-project.org/web/packages/slam/")
6459 (synopsis "Sparse lightweight arrays and matrices")
6461 "This package contains data structures and algorithms for sparse arrays and matrices,
6462 based on index arrays and simple triplet representations, respectively.")
6463 (license license:gpl2)))
6465 (define-public r-manipulatewidget
6467 (name "r-manipulatewidget")
6472 (uri (cran-uri "manipulateWidget" version))
6474 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6476 `((upstream-name . "manipulateWidget")))
6477 (build-system r-build-system)
6479 `(("r-base64enc" ,r-base64enc)
6480 ("r-codetools" ,r-codetools)
6481 ("r-htmltools" ,r-htmltools)
6482 ("r-htmlwidgets" ,r-htmlwidgets)
6483 ("r-knitr" ,r-knitr)
6484 ("r-miniui" ,r-miniui)
6485 ("r-shiny" ,r-shiny)
6486 ("r-webshot" ,r-webshot)))
6487 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6488 (synopsis "Add even more interactivity to interactive charts")
6490 "This package lets you create in just a few lines of R code a nice user interface to
6491 modify the data or the graphical parameters of one or multiple interactive
6492 charts. It is useful to quickly explore visually some data or for package
6493 developers to generate user interfaces easy to maintain.")
6494 (license license:gpl2+)))
6503 (uri (cran-uri "A3" version))
6505 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6506 (properties `((upstream-name . "A3")))
6507 (build-system r-build-system)
6509 `(("r-pbapply" ,r-pbapply)
6510 ("r-xtable" ,r-xtable)))
6511 (home-page "https://cran.r-project.org/web/packages/A3/")
6512 (synopsis "Error metrics for predictive models")
6514 "This package supplies tools for tabulating and analyzing the results of predictive
6515 models. The methods employed are applicable to virtually any predictive model
6516 and make comparisons between different methodologies straightforward.")
6517 (license license:gpl2+)))
6519 (define-public r-infotheo
6526 (uri (cran-uri "infotheo" version))
6529 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
6530 (build-system r-build-system)
6531 (home-page "http://homepage.meyerp.com/software")
6532 (synopsis "Information-theoretic measures")
6534 "This package implements various measures of information theory based on
6535 several entropy estimators.")
6536 (license license:gpl3+)))
6538 (define-public r-abcoptim
6545 (uri (cran-uri "ABCoptim" version))
6547 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
6548 (properties `((upstream-name . "ABCoptim")))
6549 (build-system r-build-system)
6550 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
6551 (home-page "https://github.com/gvegayon/ABCoptim/")
6552 (synopsis "Optimization of Artificial Bee Colony algorithm")
6554 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
6555 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
6556 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
6557 algorithms, and uses only common control parameters such as colony size and
6558 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
6559 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
6560 This version is a work-in-progress and is written in R code.")
6561 (license license:expat)))
6563 (define-public r-abcp2
6570 (uri (cran-uri "ABCp2" version))
6572 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
6573 (properties `((upstream-name . "ABCp2")))
6574 (build-system r-build-system)
6575 (propagated-inputs `(("r-mass" ,r-mass)))
6576 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
6577 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
6579 "This package tests the goodness of fit of a distribution of offspring to the Normal,
6580 Poisson, and Gamma distribution and estimates the proportional paternity of the
6581 second male (P2) based on the best fit distribution.")
6582 (license license:gpl2)))
6584 (define-public r-abcrf
6591 (uri (cran-uri "abcrf" version))
6593 (base32 "06vy3inikrr9hv36q4djhrgzi9zizdfnhz17wpra8kadmr7qj441"))))
6594 (build-system r-build-system)
6596 `(("r-mass" ,r-mass)
6597 ("r-matrixstats" ,r-matrixstats)
6598 ("r-ranger" ,r-ranger)
6600 ("r-rcpparmadillo" ,r-rcpparmadillo)
6601 ("r-readr" ,r-readr)
6602 ("r-stringr" ,r-stringr)))
6603 (home-page "https://cran.r-project.org/web/packages/abcrf/")
6604 (synopsis "Approximate bayesian computation via random forests")
6606 "This package performs approximate bayesian computation (ABC) model choice and
6607 parameter inference via random forests. This machine learning tool named random
6608 forests (RF) can conduct selection among the highly complex models covered by
6610 (license license:gpl2+)))
6612 (define-public r-abctools
6619 (uri (cran-uri "abctools" version))
6621 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
6622 (build-system r-build-system)
6625 ("r-abind" ,r-abind)
6626 ("r-hmisc" ,r-hmisc)
6627 ("r-plyr" ,r-plyr)))
6628 (home-page "https://github.com/dennisprangle/abctools/")
6629 (synopsis "Tools for ABC analyses")
6631 "This @code{r-abctools} package provides tools for approximate Bayesian computation
6632 including summary statistic selection and assessing coverage. This includes
6633 recent dimension reduction algorithms to tune the choice of summary statistics,
6634 and coverage methods to tune the choice of threshold.")
6635 (license license:gpl2+)))
6637 (define-public r-ggstance
6644 (uri (cran-uri "ggstance" version))
6646 (base32 "0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh"))))
6647 (build-system r-build-system)
6649 `(("r-ggplot2" ,r-ggplot2)
6651 ("r-rlang" ,r-rlang)
6652 ("r-withr" ,r-withr)))
6653 (home-page "https://cran.r-project.org/web/packages/ggstance/")
6654 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
6656 "This package is a @code{r-ggplot2} extension that provides flipped components:
6658 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
6659 @item vertical versions of @code{r-ggplot2} positions.
6661 (license license:gpl3)))
6663 (define-public r-mosaiccore
6665 (name "r-mosaiccore")
6670 (uri (cran-uri "mosaicCore" version))
6672 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
6673 (properties `((upstream-name . "mosaicCore")))
6674 (build-system r-build-system)
6676 `(("r-dplyr" ,r-dplyr)
6677 ("r-lazyeval" ,r-lazyeval)
6679 ("r-rlang" ,r-rlang)
6680 ("r-tidyr" ,r-tidyr)))
6681 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
6682 (synopsis "Common utilities for mosaic family packages")
6684 "Common utilities used in other Mosaic family packages are collected here.")
6685 (license license:gpl2+)))
6687 (define-public r-ggformula
6689 (name "r-ggformula")
6694 (uri (cran-uri "ggformula" version))
6696 (base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx"))))
6697 (build-system r-build-system)
6699 `(("r-ggplot2" ,r-ggplot2)
6700 ("r-ggstance" ,r-ggstance)
6701 ("r-magrittr" ,r-magrittr)
6702 ("r-mosaiccore" ,r-mosaiccore)
6703 ("r-rlang" ,r-rlang)
6704 ("r-stringr" ,r-stringr)
6705 ("r-tibble" ,r-tibble)
6706 ("r-tidyr" ,r-tidyr)))
6707 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
6708 (synopsis "Formula interface for the @code{r-ggplot2}")
6710 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
6711 gf_density(), and so on, bring the formula interface to ggplot(). This captures
6712 and extends the excellent simplicity of the lattice-graphics formula interface,
6713 while providing the intuitive capabilities of @code{r-ggplot2}.")
6714 (license license:expat)))
6716 (define-public r-mosaicdata
6718 (name "r-mosaicdata")
6723 (uri (cran-uri "mosaicData" version))
6725 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
6726 (properties `((upstream-name . "mosaicData")))
6727 (build-system r-build-system)
6728 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
6729 (synopsis "Data sets for project Mosaic")
6731 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
6732 used to teach mathematics, statistics, computation and modeling.")
6733 (license license:gpl2+)))
6735 (define-public r-raster
6742 (uri (cran-uri "raster" version))
6745 "0ljrymsp4zzaxdj1l0mw0a6hi88m5h0h920ixfzrg0szbyxqd0yk"))))
6746 (build-system r-build-system)
6748 `(("r-rcpp" ,r-rcpp)
6750 (home-page "https://www.rspatial.org/")
6751 (synopsis "Geographic data analysis and modeling")
6753 "The package implements basic and high-level functions for reading,
6754 writing, manipulating, analyzing and modeling of gridded spatial data.
6755 Processing of very large files is supported.")
6756 (license license:gpl3+)))
6758 (define-public r-mosaic
6765 (uri (cran-uri "mosaic" version))
6767 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
6768 (build-system r-build-system)
6770 `(("r-broom" ,r-broom)
6771 ("r-dplyr" ,r-dplyr)
6772 ("r-ggdendro" ,r-ggdendro)
6773 ("r-ggformula" ,r-ggformula)
6774 ("r-ggplot2" ,r-ggplot2)
6775 ("r-ggrepel" ,r-ggrepel)
6777 ("r-gridextra" ,r-gridextra)
6778 ("r-lattice" ,r-lattice)
6779 ("r-latticeextra" ,r-latticeextra)
6780 ("r-lazyeval" ,r-lazyeval)
6782 ("r-matrix" ,r-matrix)
6783 ("r-mosaiccore" ,r-mosaiccore)
6784 ("r-mosaicdata" ,r-mosaicdata)
6785 ("r-readr" ,r-readr)
6786 ("r-tidyr" ,r-tidyr)))
6787 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
6788 (synopsis "Mathematics, statistics, and computation teaching utilities")
6790 "This package contain data sets and utilities from
6791 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
6792 statistics, computation and modeling. Project MOSAIC is a community of
6793 educators working to tie together aspects of quantitative work that students
6794 in science, technology, engineering and mathematics will need in their
6795 professional lives, but which are usually taught in isolation, if at all.")
6796 (license license:gpl2+)))
6798 (define-public r-abd
6805 (uri (cran-uri "abd" version))
6807 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
6808 (build-system r-build-system)
6810 `(("r-lattice" ,r-lattice)
6811 ("r-mosaic" ,r-mosaic)
6812 ("r-nlme" ,r-nlme)))
6813 (home-page "https://cran.r-project.org/web/packages/abd/")
6814 (synopsis "Analysis of biological data")
6816 "The @code{r-abd} package contains data sets and sample code for the Analysis of
6817 biological data by Michael Whitlock and Dolph Schluter.")
6818 (license license:gpl2)))
6820 (define-public r-svgui
6827 (uri (cran-uri "svGUI" version))
6829 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
6830 (properties `((upstream-name . "svGUI")))
6831 (build-system r-build-system)
6832 (home-page "https://github.com/SciViews/svGUI/")
6833 (synopsis "Functions for managing GUI clients in R")
6835 "The SciViews @code{svGUI} package eases the management of Graphical User
6836 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
6837 centralizes info about GUI elements currently used, and it dispatches GUI
6838 calls to the particular toolkits in use in function of the context.")
6839 (license license:gpl2)))
6841 (define-public r-svdialogs
6843 (name "r-svdialogs")
6848 (uri (cran-uri "svDialogs" version))
6850 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
6851 (properties `((upstream-name . "svDialogs")))
6852 (build-system r-build-system)
6855 ("zenity" ,zenity)))
6857 `(("r-rstudioapi" ,r-rstudioapi)
6858 ("r-svgui" ,r-svgui)))
6859 (home-page "https://github.com/SciViews/svDialogs/")
6860 (synopsis "Portable dialog boxes")
6862 "This package helps to construct standard dialog boxes for your GUI, including
6863 message boxes, input boxes, list, file or directory selection, and others. In
6864 case R cannot display GUI dialog boxes, a simpler command line version of these
6865 interactive elements is also provided as a fallback solution.")
6866 (license license:gpl2)))
6868 (define-public r-abe
6875 (uri (cran-uri "abe" version))
6878 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
6879 (build-system r-build-system)
6880 (home-page "https://cran.r-project.org/web/packages/abe/")
6881 (synopsis "Augmented backward elimination")
6883 "This package performs augmented backward elimination and checks the
6884 stability of the obtained model. Augmented backward elimination combines
6885 significance or information based criteria with the change in estimate to
6886 either select the optimal model for prediction purposes or to serve as a tool
6887 to obtain a practically sound, highly interpretable model.")
6888 (license license:gpl2+)))
6890 (define-public r-abf2
6897 (uri (cran-uri "abf2" version))
6899 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
6900 (build-system r-build-system)
6901 (home-page "https://cran.r-project.org/web/packages/abf2/")
6902 (synopsis "Load gap-free axon @code{r-abf2} files")
6904 "This package loads electrophysiology data from ABF2 files, as created by
6905 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
6906 mode are currently supported.")
6907 (license license:artistic2.0)))
6909 (define-public r-abhgenotyper
6911 (name "r-abhgenotyper")
6916 (uri (cran-uri "ABHgenotypeR" version))
6918 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
6919 (properties `((upstream-name . "ABHgenotypeR")))
6920 (build-system r-build-system)
6922 `(("r-ggplot2" ,r-ggplot2)
6923 ("r-reshape2" ,r-reshape2)))
6924 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
6925 (synopsis "Visualize and manipulate ABH genotypes")
6927 "The @code{r-abhgenotyper} package provides simple imputation,
6928 error-correction and plotting capacities for genotype data. The package is
6929 supposed to serve as an intermediate but independent analysis tool between the
6930 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
6931 not found in either TASSEL or @code{r-qtl} in addition to visualization of
6932 genotypes as \"graphical genotypes\".")
6933 (license license:gpl3)))
6935 (define-public r-furrr
6942 (uri (cran-uri "furrr" version))
6945 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
6946 (build-system r-build-system)
6948 `(("r-future" ,r-future)
6949 ("r-globals" ,r-globals)
6950 ("r-purrr" ,r-purrr)
6951 ("r-rlang" ,r-rlang)))
6952 (home-page "https://github.com/DavisVaughan/furrr")
6953 (synopsis "Apply mapping functions in parallel using futures")
6955 "This package provides implementations of the family of @code{map()}
6956 functions from the @code{purrr} package that can be resolved using any
6957 @code{future}-supported backend, e.g. parallel on the local machine or
6958 distributed on a compute cluster.")
6959 (license license:lgpl2.1+)))
6961 (define-public r-abjutils
6968 (uri (cran-uri "abjutils" version))
6970 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
6971 (build-system r-build-system)
6973 `(("r-devtools" ,r-devtools)
6974 ("r-dplyr" ,r-dplyr)
6975 ("r-furrr" ,r-furrr)
6976 ("r-future" ,r-future)
6979 ("r-magrittr" ,r-magrittr)
6980 ("r-progress" ,r-progress)
6981 ("r-purrr" ,r-purrr)
6982 ("r-readr" ,r-readr)
6983 ("r-rlang" ,r-rlang)
6984 ("r-rstudioapi" ,r-rstudioapi)
6985 ("r-scales" ,r-scales)
6986 ("r-stringi" ,r-stringi)
6987 ("r-stringr" ,r-stringr)
6988 ("r-tibble" ,r-tibble)
6989 ("r-tidyr" ,r-tidyr)))
6990 (home-page "https://github.com/abjur/abjutils/")
6991 (synopsis "Collection of tools for jurimetrical analysis")
6993 "This package implements general purpose tools, such as functions for
6994 sampling and basic manipulation of Brazilian lawsuits identification number.
6995 It also implements functions for text cleaning, such as accentuation
6997 (license license:expat)))
6999 (define-public r-abnormality
7001 (name "r-abnormality")
7006 (uri (cran-uri "abnormality" version))
7008 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7009 (build-system r-build-system)
7011 `(("r-mass" ,r-mass)
7012 ("r-matrix" ,r-matrix)))
7013 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7014 (synopsis "Measure a subject's abnormality with respect to a reference population")
7016 "This package contains functions to implement the methodology and
7017 considerations laid out by Marks et al. in the article \"Measuring abnormality
7018 in high dimensional spaces: applications in biomechanical gait analysis\".
7019 Using high-dimensional datasets to measure a subject's overall level of
7020 abnormality as compared to a reference population is often needed in outcomes
7022 (license license:expat)))
7024 (define-public r-abodoutlier
7026 (name "r-abodoutlier")
7031 (uri (cran-uri "abodOutlier" version))
7033 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7034 (properties `((upstream-name . "abodOutlier")))
7035 (build-system r-build-system)
7037 `(("r-cluster" ,r-cluster)))
7038 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7039 (synopsis "Angle-based outlier detection")
7041 "This package performs angle-based outlier detection on a given data
7042 frame. It offers three methods to process data:
7044 @item full but slow implementation using all the data that has cubic
7046 @item a fully randomized method;
7047 @item a method using k-nearest neighbours.
7049 These algorithms are well suited for high dimensional data outlier
7051 (license license:expat)))
7053 (define-public r-abps
7060 (uri (cran-uri "ABPS" version))
7062 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7063 (properties `((upstream-name . "ABPS")))
7064 (build-system r-build-system)
7065 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7066 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7067 (synopsis "Abnormal blood profile score to detect blood doping")
7069 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7070 The ABPS is a part of the Athlete biological passport program of the World
7071 anti-doping agency, which combines several blood parameters into a single
7072 score in order to detect blood doping. The package also contains functions to
7073 calculate other scores used in anti-doping programs, such as the ratio of
7074 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7075 (license license:gpl2+)))
7077 (define-public r-parmigene
7079 (name "r-parmigene")
7084 (uri (cran-uri "parmigene" version))
7087 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7088 (build-system r-build-system)
7089 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7090 (synopsis "Mutual information estimation for gene network reconstruction")
7092 "This package provides a parallel estimation of the mutual information
7093 based on entropy estimates from k-nearest neighbors distances and algorithms
7094 for the reconstruction of gene regulatory networks.")
7095 (license license:agpl3+)))
7097 (define-public r-pscl
7104 (uri (cran-uri "pscl" version))
7106 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7107 (build-system r-build-system)
7109 `(("r-mass" ,r-mass)))
7110 (home-page "https://github.com/atahk/pscl/")
7111 (synopsis "Political science computational laboratory")
7113 "The @code{pscl} is an R package providing classes and methods for:
7115 @item Bayesian analysis of roll call data (item-response models);
7116 @item elementary Bayesian statistics;
7117 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7119 @item utility functions.
7121 (license license:gpl2)))
7123 (define-public r-accelmissing
7125 (name "r-accelmissing")
7130 (uri (cran-uri "accelmissing" version))
7132 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7133 (build-system r-build-system)
7135 `(("r-mice" ,r-mice)
7136 ("r-pscl" ,r-pscl)))
7137 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7138 (synopsis "Missing value imputation for accelerometer data")
7140 "This package provides a statistical method to impute the missing values in
7141 accelerometer data. The methodology includes both parametric and
7142 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7143 model. It also provides multiple functions to preprocess the accelerometer data
7144 previous to the missing data imputation. These include detecting the wearing
7145 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7146 (license license:gpl2+)))
7148 (define-public r-mhsmm
7155 (uri (cran-uri "mhsmm" version))
7157 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7158 (build-system r-build-system)
7159 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7160 (home-page "https://github.com/jaredo/mhsmm/")
7161 (synopsis "Inference for hidden Markov and semi-Markov models")
7163 "The @code{r-mhsmm} package implements estimation and prediction methods for
7164 hidden Markov and semi-Markov models for multiple observation sequences. Such
7165 techniques are of interest when observed data is thought to be dependent on some
7166 unobserved (or hidden) state. Also, this package is suitable for equidistant
7167 time series data, with multivariate and/or missing data. Allows user defined
7168 emission distributions.")
7169 (license license:gpl2+)))
7171 (define-public r-nleqslv
7178 (uri (cran-uri "nleqslv" version))
7180 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7181 (build-system r-build-system)
7182 (native-inputs `(("gfortran" ,gfortran)))
7183 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7184 (synopsis "Solve systems of nonlinear equations")
7186 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7187 Broyden or a Newton method with a choice of global strategies such as line
7188 search and trust region. There are options for using a numerical or user
7189 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7190 singular or ill-conditioned Jacobian.")
7191 (license license:gpl2+)))
7193 (define-public r-physicalactivity
7195 (name "r-physicalactivity")
7200 (uri (cran-uri "PhysicalActivity" version))
7202 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7204 `((upstream-name . "PhysicalActivity")))
7205 (build-system r-build-system)
7206 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7207 (synopsis "Procesing accelerometer data for physical activity measurement")
7209 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7210 for classification of monitor wear and nonwear time intervals in accelerometer
7211 data collected to assess physical activity. The package also contains functions
7212 for making plots of accelerometer data and obtaining the summary of various
7213 information including daily monitor wear time and the mean monitor wear time
7214 during valid days. The revised package version 0.2-1 improved the functions
7215 regarding speed, robustness and add better support for time zones and daylight
7216 saving. In addition, several functions were added:
7218 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7219 @item the @code{markPAI} can categorize physical activity intensity level based
7220 on user-defined cut-points of accelerometer counts.
7222 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7223 @code{queryActigraph} functions.")
7224 (license license:gpl3+)))
7226 (define-public r-acc
7233 (uri (cran-uri "acc" version))
7235 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7236 (build-system r-build-system)
7238 `(("r-circlize" ,r-circlize)
7240 ("r-ggplot2" ,r-ggplot2)
7241 ("r-iterators" ,r-iterators)
7242 ("r-mhsmm" ,r-mhsmm)
7243 ("r-nleqslv" ,r-nleqslv)
7244 ("r-physicalactivity" ,r-physicalactivity)
7246 ("r-r-utils" ,r-r-utils)
7248 ("r-rcpparmadillo" ,r-rcpparmadillo)
7249 ("r-rsqlite" ,r-rsqlite)
7251 (home-page "https://cran.r-project.org/web/packages/acc/")
7252 (synopsis "Exploring accelerometer data")
7254 "This package processes accelerometer data from uni-axial and tri-axial devices
7255 and generates data summaries. Also, includes functions to plot, analyze, and
7256 simulate accelerometer data.")
7257 (license license:gpl2+)))
7259 (define-public r-rbenchmark
7261 (name "r-rbenchmark")
7266 (uri (cran-uri "rbenchmark" version))
7268 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7269 (build-system r-build-system)
7270 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7271 (synopsis "Benchmarking routine for R")
7273 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7274 and is intended to facilitate benchmarking of arbitrary R code. The library
7275 consists of just one function, benchmark, which is a simple wrapper around
7276 system.time. Given a specification of the benchmarking process (counts of
7277 replications, evaluation environment) and an arbitrary number of expressions,
7278 benchmark evaluates each of the expressions in the specified environment,
7279 replicating the evaluation as many times as specified, and returning the results
7280 conveniently wrapped into a data frame.")
7281 (license license:gpl2+)))
7283 (define-public r-mitools
7290 (uri (cran-uri "mitools" version))
7293 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7294 (build-system r-build-system)
7295 (propagated-inputs `(("r-dbi" ,r-dbi)))
7296 (home-page "https://cran.r-project.org/web/packages/mitools/")
7297 (synopsis "Tools for multiple imputation of missing data")
7299 "This package provides tools to perform analyses and combine results from
7300 multiple-imputation datasets.")
7301 (license license:gpl2)))
7303 (define-public r-magick
7310 (uri (cran-uri "magick" version))
7313 "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m"))))
7314 (build-system r-build-system)
7316 `(("imagemagick" ,imagemagick)
7319 `(("r-curl" ,r-curl)
7320 ("r-magrittr" ,r-magrittr)
7321 ("r-rcpp" ,r-rcpp)))
7323 `(("pkg-config" ,pkg-config)))
7324 (home-page "https://github.com/ropensci/magick")
7325 (synopsis "Advanced graphics and image-processing in R")
7327 "This package provides bindings to ImageMagick, a comprehensive image
7328 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7329 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7330 operations are vectorized via the Magick++ STL meaning they operate either on
7331 a single frame or a series of frames for working with layers, collages, or
7332 animation. In RStudio, images are automatically previewed when printed to the
7333 console, resulting in an interactive editing environment.")
7334 (license license:expat)))
7336 (define-public r-survey
7343 (uri (cran-uri "survey" version))
7346 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7347 (build-system r-build-system)
7349 `(("r-lattice" ,r-lattice)
7350 ("r-matrix" ,r-matrix)
7351 ("r-minqa" ,r-minqa)
7352 ("r-mitools" ,r-mitools)
7353 ("r-numderiv" ,r-numderiv)
7354 ("r-survival" ,r-survival)))
7355 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7356 (synopsis "Analysis of complex survey samples")
7358 "This package provides tools for the analysis of complex survey samples.
7359 The provided features include: summary statistics, two-sample tests, rank
7360 tests, generalised linear models, cumulative link models, Cox models,
7361 loglinear models, and general maximum pseudolikelihood estimation for
7362 multistage stratified, cluster-sampled, unequally weighted survey samples;
7363 variances by Taylor series linearisation or replicate weights;
7364 post-stratification, calibration, and raking; two-phase subsampling designs;
7365 graphics; PPS sampling without replacement; principal components, and factor
7367 ;; Either version of the GPL.
7368 (license (list license:gpl2 license:gpl3))))
7370 (define-public r-dvmisc
7377 (uri (cran-uri "dvmisc" version))
7379 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7380 (build-system r-build-system)
7382 `(("r-cubature" ,r-cubature)
7383 ("r-data-table" ,r-data-table)
7384 ("r-dplyr" ,r-dplyr)
7385 ("r-ggplot2" ,r-ggplot2)
7387 ("r-mvtnorm" ,r-mvtnorm)
7388 ("r-pracma" ,r-pracma)
7389 ("r-purrr" ,r-purrr)
7390 ("r-rbenchmark" ,r-rbenchmark)
7392 ("r-survey" ,r-survey)))
7393 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7394 (synopsis "Faster computation of common statistics and miscellaneous functions")
7396 "This package implements faster versions of base R functions (e.g. mean, standard
7397 deviation, covariance, weighted mean), mostly written in C++, along with
7398 miscellaneous functions for various purposes (e.g. create the histogram with
7399 fitted probability density function or probability mass function curve, create
7400 the body mass index groups, assess the linearity assumption in logistic
7402 (license license:gpl2)))
7404 (define-public r-accelerometry
7406 (name "r-accelerometry")
7411 (uri (cran-uri "accelerometry" version))
7413 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7414 (build-system r-build-system)
7416 `(("r-dvmisc" ,r-dvmisc)
7417 ("r-rcpp" ,r-rcpp)))
7418 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7419 (synopsis "Functions for processing accelerometer data")
7421 "This package provides a collection of functions that perform operations on
7422 time-series accelerometer data, such as identify the non-wear time, flag minutes
7423 that are part of an activity bout, and find the maximum 10-minute average count
7424 value. The functions are generally very flexible, allowing for a variety of
7425 algorithms to be implemented.")
7426 (license license:gpl3)))
7428 (define-public r-absim
7435 (uri (cran-uri "AbSim" version))
7437 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7438 (properties `((upstream-name . "AbSim")))
7439 (build-system r-build-system)
7442 ("r-powerlaw" ,r-powerlaw)))
7443 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7444 (synopsis "Time resolved simulations of antibody repertoires")
7446 "This package provides simulation methods for the evolution of antibody repertoires.
7447 The heavy and light chain variable region of both human and C57BL/6 mice can
7448 be simulated in a time-dependent fashion. Both single lineages using one set of
7449 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7450 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7451 Upon completion, the main loop of the algorithm begins, with each iteration
7452 representing one simulated time step. Various mutation events are possible at
7453 each time step, contributing to a diverse final repertoire.")
7454 (license license:gpl2)))
7456 (define-public r-quic
7463 (uri (cran-uri "QUIC" version))
7465 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7466 (properties `((upstream-name . "QUIC")))
7467 (build-system r-build-system)
7468 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7469 (synopsis "Regularized sparse inverse covariance matrix estimation")
7471 "This package implements the regularized Gaussian maximum likelihood
7472 estimation of the inverse of a covariance matrix. It uses Newton's method and
7473 coordinate descent to solve the regularized inverse covariance matrix
7474 estimation problem.")
7475 ;; The project home page states that the release is under GPLv3 or later.
7476 ;; The CRAN page only says GPL-3.
7477 (license license:gpl3+)))
7479 (define-public r-abundant
7486 (uri (cran-uri "abundant" version))
7488 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7489 (build-system r-build-system)
7491 `(("r-quic" ,r-quic)))
7492 (home-page "https://cran.r-project.org/web/packages/abundant/")
7493 (synopsis "Abundant regression and high-dimensional principal fitted components")
7495 "This package provides tools to fit and predict with the high-dimensional
7496 principal fitted components model. This model is described by Cook, Forzani,
7497 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7498 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7499 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7500 (license license:gpl2+)))
7502 (define-public r-ac3net
7509 (uri (cran-uri "Ac3net" version))
7511 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7512 (properties `((upstream-name . "Ac3net")))
7513 (build-system r-build-system)
7515 `(("r-data-table" ,r-data-table)))
7516 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
7517 (synopsis "Inferring directional conservative causal core gene networks")
7518 (description "This package infers directional Conservative causal core
7519 (gene) networks (C3NET). This is a version of the algorithm C3NET with
7520 directional network.")
7521 (license license:gpl3+)))
7523 (define-public r-aca
7530 (uri (cran-uri "ACA" version))
7532 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
7533 (properties `((upstream-name . "ACA")))
7534 (build-system r-build-system)
7535 (home-page "https://cran.r-project.org/web/packages/ACA/")
7536 (synopsis "Abrupt change-point or aberration detection in point series")
7538 "This package offers an interactive function for the detection of breakpoints in
7540 ;; Any version of the GPL
7541 (license (list license:gpl2+ license:gpl3+))))
7543 (define-public r-acceptancesampling
7545 (name "r-acceptancesampling")
7550 (uri (cran-uri "AcceptanceSampling" version))
7552 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
7554 `((upstream-name . "AcceptanceSampling")))
7555 (build-system r-build-system)
7556 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
7557 (synopsis "Creation and evaluation of acceptance sampling plans")
7559 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
7560 acceptance sampling plans. Acceptance sampling is a methodology commonly used
7561 in quality control and improvement. International standards of acceptance
7562 sampling provide sampling plans for specific circumstances. The aim of this
7563 package is to provide an easy-to-use interface to visualize single, double or
7564 multiple sampling plans. In addition, methods have been provided to enable the
7565 user to assess sampling plans against pre-specified levels of performance, as
7566 measured by the probability of acceptance for a given level of quality in the
7568 (license license:gpl3+)))
7570 (define-public r-acclma
7577 (uri (cran-uri "ACCLMA" version))
7579 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
7580 (properties `((upstream-name . "ACCLMA")))
7581 (build-system r-build-system)
7582 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
7583 (synopsis "ACC & LMA graph plotting")
7585 "This package contains a function that imports data from a @acronym{CSV,
7586 Comma-Separated Values} file, or uses manually entered data from the format (x,
7587 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
7588 Curve} vs @acronym{LOI, Line of Independence} graph and
7589 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
7590 function is @code{plotLMA} (source file, header) that takes a data set and plots the
7591 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
7592 string) was passed, a manual data entry window is opened. The header parameter
7593 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
7594 a header row or not. The dataset should contain only one independent variable
7595 (x) and one dependent variable (y) and can contain a weight for each
7597 (license license:gpl2)))
7599 (define-public r-aspi
7606 (uri (cran-uri "aspi" version))
7608 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
7609 (build-system r-build-system)
7611 "https://cran.r-project.org/web/packages/aspi/")
7613 "Analysis of symmetry of parasitic infections")
7615 "This package provides tools for the analysis and visualization of bilateral
7616 asymmetry in parasitic infections.")
7617 (license license:gpl3+)))
7619 (define-public r-sandwich
7626 (uri (cran-uri "sandwich" version))
7629 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
7630 (build-system r-build-system)
7632 `(("r-zoo" ,r-zoo)))
7633 (home-page "https://cran.r-project.org/web/packages/sandwich/")
7634 (synopsis "Robust Covariance Matrix Estimators")
7636 "This package provides model-robust standard error estimators for
7637 cross-sectional, time series, clustered, panel, and longitudinal data.")
7638 ;; Either version of the license.
7639 (license (list license:gpl2 license:gpl3))))
7641 (define-public r-th-data
7648 (uri (cran-uri "TH.data" version))
7651 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
7652 (properties `((upstream-name . "TH.data")))
7653 (build-system r-build-system)
7655 `(("r-mass" ,r-mass)
7656 ("r-survival" ,r-survival)))
7657 (home-page "https://cran.r-project.org/web/packages/TH.data/")
7658 (synopsis "Shared data sets")
7660 "This package contains supporting data sets that are used in other
7661 packages maintained by Torsten Hothorn.")
7662 (license license:gpl3)))
7664 (define-public r-multcomp
7671 (uri (cran-uri "multcomp" version))
7674 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
7675 (build-system r-build-system)
7677 `(("r-codetools" ,r-codetools)
7678 ("r-mvtnorm" ,r-mvtnorm)
7679 ("r-sandwich" ,r-sandwich)
7680 ("r-survival" ,r-survival)
7681 ("r-th-data" ,r-th-data)))
7682 (home-page "https://cran.r-project.org/web/packages/multcomp/")
7683 (synopsis "Simultaneous inference in general parametric models")
7685 "Simultaneous tests and confidence intervals for general linear
7686 hypotheses in parametric models, including linear, generalized linear, linear
7687 mixed effects, and survival models. The package includes demos reproducing
7688 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
7689 Hothorn, Westfall, 2010, CRC Press).")
7690 (license license:gpl2)))
7692 (define-public r-emmeans
7699 (uri (cran-uri "emmeans" version))
7702 "09gxphan34c615y4lhjdqkg5cz4ih9b1r3bb4chs3mwmiav1rxqn"))))
7703 (build-system r-build-system)
7705 `(("r-estimability" ,r-estimability)
7706 ("r-mvtnorm" ,r-mvtnorm)
7707 ("r-numderiv" ,r-numderiv)
7709 ("r-xtable" ,r-xtable)))
7710 (home-page "https://github.com/rvlenth/emmeans")
7711 (synopsis "Estimated marginal means, aka least-squares means")
7713 "This package provides tools to obtain @dfn{estimated marginal
7714 means} (EMMs) for many linear, generalized linear, and mixed models. It can
7715 be used to compute contrasts or linear functions of EMMs, trends, and
7716 comparisons of slopes.")
7717 ;; Either version of the license.
7718 (license (list license:gpl2 license:gpl3))))
7720 (define-public r-pwr
7727 (uri (cran-uri "pwr" version))
7730 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
7731 (build-system r-build-system)
7733 `(("r-knitr" ,r-knitr)))
7734 (home-page "https://github.com/heliosdrm/pwr")
7735 (synopsis "Basic functions for power analysis")
7737 "This package provides power analysis functions along the lines of
7739 (license license:gpl3+)))
7741 (define-public r-libcoin
7748 (uri (cran-uri "libcoin" version))
7751 "1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i"))))
7752 (build-system r-build-system)
7753 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7754 (home-page "https://cran.r-project.org/web/packages/libcoin")
7755 (synopsis "Linear test statistics for permutation inference")
7757 "This package provides basic infrastructure for linear test statistics
7758 and permutation inference in the framework of Strasser and Weber (1999).")
7759 (license license:gpl2)))
7761 (define-public r-coin
7768 (uri (cran-uri "coin" version))
7771 "1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd"))))
7772 (build-system r-build-system)
7774 `(("r-libcoin" ,r-libcoin)
7775 ("r-matrixstats" ,r-matrixstats)
7776 ("r-modeltools" ,r-modeltools)
7777 ("r-multcomp" ,r-multcomp)
7778 ("r-mvtnorm" ,r-mvtnorm)
7779 ("r-survival" ,r-survival)))
7780 (home-page "http://coin.r-forge.r-project.org")
7781 (synopsis "Conditional inference procedures in a permutation test framework")
7783 "This package provides conditional inference procedures for the general
7784 independence problem including two-sample, K-sample (non-parametric ANOVA),
7785 correlation, censored, ordered and multivariate problems.")
7786 (license license:gpl2)))
7788 (define-public r-bayesplot
7790 (name "r-bayesplot")
7795 (uri (cran-uri "bayesplot" version))
7798 "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
7799 (build-system r-build-system)
7801 `(("pandoc" ,ghc-pandoc)
7802 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
7804 `(("r-dplyr" ,r-dplyr)
7805 ("r-ggplot2" ,r-ggplot2)
7806 ("r-ggridges" ,r-ggridges)
7808 ("r-reshape2" ,r-reshape2)
7809 ("r-rlang" ,r-rlang)
7810 ("r-tibble" ,r-tibble)
7811 ("r-tidyselect" ,r-tidyselect)))
7812 (home-page "http://mc-stan.org/bayesplot")
7813 (synopsis "Plotting for Bayesian models")
7815 "This package provides plotting functions for posterior analysis, model
7816 checking, and MCMC diagnostics. The package is designed not only to provide
7817 convenient functionality for users, but also a common set of functions that
7818 can be easily used by developers working on a variety of R packages for
7819 Bayesian modeling.")
7820 (license license:gpl3+)))
7822 (define-public r-tmb
7829 (uri (cran-uri "TMB" version))
7832 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
7833 (properties `((upstream-name . "TMB")))
7834 (build-system r-build-system)
7836 `(("r-matrix" ,r-matrix)
7837 ("r-rcppeigen" ,r-rcppeigen)))
7838 (home-page "http://tmb-project.org")
7839 (synopsis "Template model builder: a general random effect tool")
7841 "With this tool, a user should be able to quickly implement complex
7842 random effect models through simple C++ templates. The package combines
7843 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
7844 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
7845 from R) to obtain an efficient implementation of the applied Laplace
7846 approximation with exact derivatives. Key features are: Automatic sparseness
7847 detection, parallelism through BLAS and parallel user templates.")
7848 (license license:gpl2)))
7850 (define-public r-sjstats
7857 (uri (cran-uri "sjstats" version))
7860 "1x9ybvz84vgaabmqp4z6crbv5q6kqjg6msk1spbr11zx9dbj06ca"))))
7861 (build-system r-build-system)
7863 `(("r-bayestestr" ,r-bayestestr)
7864 ("r-broom" ,r-broom)
7865 ("r-dplyr" ,r-dplyr)
7866 ("r-emmeans" ,r-emmeans)
7867 ("r-insight" ,r-insight)
7869 ("r-magrittr" ,r-magrittr)
7871 ("r-modelr" ,r-modelr)
7872 ("r-performance" ,r-performance)
7873 ("r-purrr" ,r-purrr)
7874 ("r-rlang" ,r-rlang)
7875 ("r-sjlabelled" ,r-sjlabelled)
7876 ("r-sjmisc" ,r-sjmisc)
7877 ("r-tidyr" ,r-tidyr)))
7878 (home-page "https://github.com/strengejacke/sjstats")
7879 (synopsis "Functions for common statistical computations")
7881 "This package provides a collection of convenient functions for common
7882 statistical computations, which are not directly provided by R's @code{base}
7883 or @code{stats} packages. This package aims at providing, first, shortcuts
7884 for statistical measures, which otherwise could only be calculated with
7885 additional effort. Second, these shortcut functions are generic, and can be
7886 applied not only to vectors, but also to other objects as well. The focus of
7887 most functions lies on summary statistics or fit measures for regression
7888 models, including generalized linear models, mixed effects models and Bayesian
7890 (license license:gpl3)))
7892 (define-public r-glmmtmb
7899 (uri (cran-uri "glmmTMB" version))
7902 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
7903 (properties `((upstream-name . "glmmTMB")))
7904 (build-system r-build-system)
7906 `(("r-lme4" ,r-lme4)
7907 ("r-matrix" ,r-matrix)
7909 ("r-rcppeigen" ,r-rcppeigen)
7912 `(("r-knitr" ,r-knitr))) ; for vignettes
7913 (home-page "https://github.com/glmmTMB")
7914 (synopsis "Generalized linear mixed models")
7916 "Fit linear and generalized linear mixed models with various extensions,
7917 including zero-inflation. The models are fitted using maximum likelihood
7918 estimation via the Template Model Builder. Random effects are assumed to be
7919 Gaussian on the scale of the linear predictor and are integrated out using the
7920 Laplace approximation. Gradients are calculated using automatic
7922 (license license:agpl3+)))
7924 (define-public r-bayestestr
7926 (name "r-bayestestr")
7931 (uri (cran-uri "bayestestR" version))
7934 "0729j4fdxkkvmh99nmny38dywidzgmipdjqbi2ljxygsn4jg7ysy"))))
7935 (properties `((upstream-name . "bayestestR")))
7936 (build-system r-build-system)
7938 `(("r-insight" ,r-insight)))
7939 (home-page "https://github.com/easystats/bayestestR")
7940 (synopsis "Describe Bayesian models and posterior distributions")
7942 "This package provides utilities to understand and describe posterior
7943 distributions and Bayesian models. It includes point-estimates such as
7944 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
7945 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
7946 ROPE percentage and pd).")
7947 (license license:gpl3)))
7949 (define-public r-performance
7951 (name "r-performance")
7956 (uri (cran-uri "performance" version))
7959 "1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
7960 (build-system r-build-system)
7962 `(("r-bayestestr" ,r-bayestestr)
7963 ("r-insight" ,r-insight)))
7964 (home-page "https://easystats.github.io/performance/")
7965 (synopsis "Assessment of regression models performance")
7967 "This package provides utilities for computing measures to assess model
7968 quality, which are not directly provided by R's @code{base} or @code{stats}
7969 packages. These include e.g. measures like r-squared, intraclass correlation
7970 coefficient, root mean squared error or functions to check models for
7971 overdispersion, singularity or zero-inflation and more. Functions apply to a
7972 large variety of regression models, including generalized linear models, mixed
7973 effects models and Bayesian models.")
7974 (license license:gpl3)))
7976 (define-public r-ggeffects
7978 (name "r-ggeffects")
7983 (uri (cran-uri "ggeffects" version))
7986 "0gmqzjk8k8q6j4q6asv9f3b1fv4qrw5w8xa48ha3y98shzm5np9k"))))
7987 (build-system r-build-system)
7989 `(("r-dplyr" ,r-dplyr)
7990 ("r-insight" ,r-insight)
7991 ("r-magrittr" ,r-magrittr)
7993 ("r-purrr" ,r-purrr)
7994 ("r-rlang" ,r-rlang)
7995 ("r-scales" ,r-scales)
7996 ("r-sjlabelled" ,r-sjlabelled)
7997 ("r-sjmisc" ,r-sjmisc)))
7998 (home-page "https://github.com/strengejacke/ggeffects")
7999 (synopsis "Create tidy data frames of marginal effects for ggplot")
8001 "This package provides tools to compute marginal effects from statistical
8002 models and return the result as tidy data frames. These data frames are ready
8003 to use with the @code{ggplot2} package. Marginal effects can be calculated
8004 for many different models. Interaction terms, splines and polynomial terms
8005 are also supported. The two main functions are @code{ggpredict()} and
8006 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8007 results using @code{ggplot2}.")
8008 (license license:gpl3)))
8010 (define-public r-sjplot
8017 (uri (cran-uri "sjPlot" version))
8020 "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy"))))
8021 (properties `((upstream-name . "sjPlot")))
8022 (build-system r-build-system)
8024 `(("r-bayestestr" ,r-bayestestr)
8025 ("r-broom" ,r-broom)
8026 ("r-dplyr" ,r-dplyr)
8027 ("r-forcats" ,r-forcats)
8028 ("r-ggeffects" ,r-ggeffects)
8029 ("r-ggplot2" ,r-ggplot2)
8030 ("r-glmmtmb" ,r-glmmtmb)
8031 ("r-insight" ,r-insight)
8032 ("r-knitr" ,r-knitr)
8034 ("r-magrittr" ,r-magrittr)
8036 ("r-modelr" ,r-modelr)
8038 ("r-performance" ,r-performance)
8039 ("r-psych" ,r-psych)
8040 ("r-purrr" ,r-purrr)
8041 ("r-rlang" ,r-rlang)
8042 ("r-scales" ,r-scales)
8043 ("r-sjlabelled" ,r-sjlabelled)
8044 ("r-sjmisc" ,r-sjmisc)
8045 ("r-sjstats" ,r-sjstats)
8046 ("r-tidyr" ,r-tidyr)))
8047 (home-page "https://strengejacke.github.io/sjPlot/")
8048 (synopsis "Data visualization for statistics in social science")
8050 "This package represents a collection of plotting and table output
8051 functions for data visualization. Results of various statistical
8052 analyses (that are commonly used in social sciences) can be visualized using
8053 this package, including simple and cross tabulated frequencies, histograms,
8054 box plots, (generalized) linear models, mixed effects models, principal
8055 component analysis and correlation matrices, cluster analyses, scatter plots,
8056 stacked scales, effects plots of regression models (including interaction
8057 terms) and much more. This package supports labelled data.")
8058 (license license:gpl3)))
8060 (define-public r-ini
8067 (uri (cran-uri "ini" version))
8070 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8071 (build-system r-build-system)
8072 (home-page "https://github.com/dvdscripter/ini")
8073 (synopsis "Read and write configuration files")
8075 "This package provides tools to parse simple @code{.ini} configuration
8076 files to an structured list. Users can manipulate this resulting list with
8077 @code{lapply()} functions. This same structured list can be used to write
8078 back to file after modifications.")
8079 (license license:gpl3)))
8088 (uri (cran-uri "gh" version))
8091 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8092 (build-system r-build-system)
8094 `(("r-httr" ,r-httr)
8096 ("r-jsonlite" ,r-jsonlite)))
8097 (home-page "https://github.com/r-lib/gh#readme")
8098 (synopsis "Access the GitHub API via R")
8100 "This package provides a minimal R client to access the GitHub API.")
8101 (license license:expat)))
8110 (uri (cran-uri "fs" version))
8113 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8114 (build-system r-build-system)
8116 `(("r-rcpp" ,r-rcpp)))
8118 `(("pkg-config" ,pkg-config)))
8119 (home-page "http://fs.r-lib.org")
8120 (synopsis "Cross-platform file system operations based on libuv")
8122 "This package provides a cross-platform interface to file system
8123 operations, built on top of the libuv C library.")
8124 (license license:gpl3)))
8126 (define-public r-clisymbols
8128 (name "r-clisymbols")
8133 (uri (cran-uri "clisymbols" version))
8136 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8137 (build-system r-build-system)
8138 (home-page "https://github.com/gaborcsardi/clisymbols")
8139 (synopsis "Unicode symbols at the R prompt")
8141 "This package provides a small subset of Unicode symbols, that are useful
8142 when building command line applications. They fall back to alternatives on
8143 terminals that do not support Unicode.")
8144 (license license:expat)))
8146 (define-public r-usethis
8153 (uri (cran-uri "usethis" version))
8156 "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag"))))
8157 (build-system r-build-system)
8159 `(("r-clipr" ,r-clipr)
8160 ("r-clisymbols" ,r-clisymbols)
8161 ("r-crayon" ,r-crayon)
8166 ("r-git2r" ,r-git2r)
8168 ("r-purrr" ,r-purrr)
8169 ("r-rlang" ,r-rlang)
8170 ("r-rprojroot" ,r-rprojroot)
8171 ("r-rstudioapi" ,r-rstudioapi)
8172 ("r-whisker" ,r-whisker)
8173 ("r-withr" ,r-withr)
8174 ("r-yaml" ,r-yaml)))
8175 (home-page "https://github.com/r-lib/usethis")
8176 (synopsis "Automate R package and project setup")
8178 "This package helps you to automate R package and project setup tasks
8179 that are otherwise performed manually. This includes setting up unit testing,
8180 test coverage, continuous integration, Git, GitHub integration, licenses,
8181 Rcpp, RStudio projects, and more.")
8182 (license license:gpl3)))
8184 (define-public r-sessioninfo
8186 (name "r-sessioninfo")
8191 (uri (cran-uri "sessioninfo" version))
8194 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8195 (build-system r-build-system)
8198 ("r-withr" ,r-withr)))
8199 (home-page "https://github.com/r-lib/sessioninfo#readme")
8200 (synopsis "R session information")
8202 "This package provides tools to query and print information about the
8203 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8204 more information about packages, and where they were installed from.")
8205 (license license:gpl2)))
8207 (define-public r-remotes
8214 (uri (cran-uri "remotes" version))
8217 "1jbn4kjimcr82zv5lnqxqa2487a96vn6jxf7wc6gnpxr6k06d61p"))))
8218 (build-system r-build-system)
8219 (home-page "https://github.com/r-lib/remotes#readme")
8220 (synopsis "R package installation from remote repositories")
8222 "Download and install R packages stored in GitHub, BitBucket, or plain
8223 subversion or git repositories. This package is a lightweight replacement of
8224 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8225 the code was copied over from @code{devtools}.")
8226 (license license:gpl2+)))
8228 (define-public r-xopen
8235 (uri (cran-uri "xopen" version))
8238 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8239 (build-system r-build-system)
8241 `(("r-processx" ,r-processx)))
8242 (home-page "https://github.com/r-lib/xopen#readme")
8243 (synopsis "Open system files, URLs, anything")
8245 "This package provides a cross-platform solution to open files,
8246 directories or URLs with their associated programs.")
8247 (license license:expat)))
8249 (define-public r-rcmdcheck
8251 (name "r-rcmdcheck")
8256 (uri (cran-uri "rcmdcheck" version))
8259 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8260 (build-system r-build-system)
8262 `(("r-callr" ,r-callr)
8264 ("r-crayon" ,r-crayon)
8266 ("r-digest" ,r-digest)
8267 ("r-pkgbuild" ,r-pkgbuild)
8268 ("r-prettyunits" ,r-prettyunits)
8270 ("r-rprojroot" ,r-rprojroot)
8271 ("r-sessioninfo" ,r-sessioninfo)
8272 ("r-withr" ,r-withr)
8273 ("r-xopen" ,r-xopen)))
8274 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8275 (synopsis "Run R CMD check from R and capture results")
8277 "Run @code{R CMD check} from R programmatically, and capture the results
8278 of the individual checks.")
8279 (license license:expat)))
8281 (define-public r-rapportools
8283 (name "r-rapportools")
8288 (uri (cran-uri "rapportools" version))
8291 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8292 (build-system r-build-system)
8294 `(("r-pander" ,r-pander)
8296 ("r-reshape" ,r-reshape)))
8297 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8298 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8300 "This package provides helper functions that act as wrappers to more
8301 advanced statistical methods with the advantage of having sane defaults for
8303 (license license:agpl3+)))
8305 (define-public r-pander
8312 (uri (cran-uri "pander" version))
8315 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8316 (build-system r-build-system)
8318 `(("r-digest" ,r-digest)
8319 ("r-rcpp" ,r-rcpp)))
8320 (home-page "https://rapporter.github.io/pander")
8321 (synopsis "Render R objects into Pandoc's markdown")
8323 "The main aim of the pander R package is to provide a minimal and easy
8324 tool for rendering R objects into Pandoc's markdown. The package is also
8325 capable of exporting/converting complex Pandoc documents (reports) in various
8327 ;; This package is licensed under either the AGPLv3+ or the very rarely
8329 (license license:agpl3+)))
8331 (define-public r-summarytools
8333 (name "r-summarytools")
8338 (uri (cran-uri "summarytools" version))
8341 "1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f"))))
8342 (build-system r-build-system)
8344 `(("r-checkmate" ,r-checkmate)
8345 ("r-dplyr" ,r-dplyr)
8346 ("r-htmltools" ,r-htmltools)
8347 ("r-lubridate" ,r-lubridate)
8348 ("r-magick" ,r-magick)
8349 ("r-matrixstats" ,r-matrixstats)
8350 ("r-pander" ,r-pander)
8352 ("r-rapportools" ,r-rapportools)
8353 ("r-rcurl" ,r-rcurl)
8354 ("r-tibble" ,r-tibble)
8355 ("r-tidyr" ,r-tidyr)))
8356 (home-page "https://github.com/dcomtois/summarytools")
8357 (synopsis "Tools to quickly and neatly summarize data")
8359 "This package provides tools for data frame summaries, cross-tabulations,
8360 weight-enabled frequency tables and common univariate statistics in concise
8361 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8362 good point-of-entry for exploring data, both for experienced and new R
8364 (license license:gpl2)))
8366 (define-public r-lsei
8373 (uri (cran-uri "lsei" version))
8376 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8377 (build-system r-build-system)
8379 `(("gfortran" ,gfortran)))
8380 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8381 (synopsis "Solve regression problems under equality/inequality constraints")
8383 "It contains functions that solve least squares linear regression
8384 problems under linear equality/inequality constraints. Functions for solving
8385 quadratic programming problems are also available, which transform such
8386 problems into least squares ones first.")
8387 (license license:gpl2+)))
8389 (define-public r-npsurv
8396 (uri (cran-uri "npsurv" version))
8399 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8400 (build-system r-build-system)
8402 `(("r-lsei" ,r-lsei)))
8403 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8404 (synopsis "Nonparametric survival analysis")
8406 "This package contains functions for non-parametric survival analysis of
8407 exact and interval-censored observations.")
8408 (license license:gpl2+)))
8410 (define-public r-clusteval
8412 (name "r-clusteval")
8417 (uri (cran-uri "clusteval" version))
8420 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8421 (build-system r-build-system)
8423 `(("r-mvtnorm" ,r-mvtnorm)
8424 ("r-rcpp" ,r-rcpp)))
8425 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8426 (synopsis "Evaluation of clustering algorithms")
8428 "This R package provides a suite of tools to evaluate clustering
8429 algorithms, clusterings, and individual clusters.")
8430 (license license:expat)))
8432 (define-public r-tweedie
8439 (uri (cran-uri "tweedie" version))
8442 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8443 (build-system r-build-system)
8444 (native-inputs `(("gfortran" ,gfortran)))
8445 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8446 (synopsis "Evaluation of Tweedie exponential family models")
8448 "Maximum likelihood computations for Tweedie families, including the
8449 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8450 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8451 and related methods.")
8452 (license license:gpl2+)))
8454 (define-public r-rcppgsl
8461 (uri (cran-uri "RcppGSL" version))
8464 "16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m"))))
8465 (properties `((upstream-name . "RcppGSL")))
8466 (build-system r-build-system)
8468 `(("r-rcpp" ,r-rcpp)
8471 `(("r-knitr" ,r-knitr))) ; for vignettes
8472 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8473 (synopsis "Rcpp integration for GSL vectors and matrices")
8475 "The GNU Scientific Library (or GSL) is a collection of numerical
8476 routines for scientific computing. It is particularly useful for C and C++
8477 programs as it provides a standard C interface to a wide range of mathematical
8478 routines. There are over 1000 functions in total with an extensive test
8479 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8480 structures and R using concepts from Rcpp which is itself a package that eases
8481 the interfaces between R and C++.")
8482 (license license:gpl2+)))
8484 (define-public r-mvabund
8491 (uri (cran-uri "mvabund" version))
8494 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
8495 (build-system r-build-system)
8497 `(("r-mass" ,r-mass)
8499 ("r-rcppgsl" ,r-rcppgsl)
8500 ("r-statmod" ,r-statmod)
8501 ("r-tweedie" ,r-tweedie)))
8502 (home-page "https://cran.r-project.org/web/packages/mvabund/")
8503 (synopsis "Statistical methods for analysing multivariate abundance data")
8505 "This package provides a set of tools for displaying, modeling and
8506 analysing multivariate abundance data in community ecology.")
8507 (license license:lgpl2.1+)))
8509 (define-public r-afex
8516 (uri (cran-uri "afex" version))
8519 "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7"))))
8520 (build-system r-build-system)
8524 ("r-lmertest" ,r-lmertest)
8525 ("r-pbkrtest" ,r-pbkrtest)
8526 ("r-reshape2" ,r-reshape2)))
8527 (home-page "https://afex.singmann.science/")
8528 (synopsis "Analysis of factorial experiments")
8530 "This package provides convenience functions for analyzing factorial
8531 experiments using ANOVA or mixed models.")
8532 (license license:gpl2+)))
8534 (define-public r-lmertest
8541 (uri (cran-uri "lmerTest" version))
8544 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
8545 (properties `((upstream-name . "lmerTest")))
8546 (build-system r-build-system)
8548 `(("r-ggplot2" ,r-ggplot2)
8551 ("r-numderiv" ,r-numderiv)))
8552 (home-page "https://github.com/runehaubo/lmerTestR")
8553 (synopsis "Tests in linear mixed effects models")
8555 "This package provides p-values in type I, II or III anova and summary
8556 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
8557 method. A Kenward-Roger method is also available via the @code{pbkrtest}
8558 package. Model selection methods include step, drop1 and anova-like tables
8559 for random effects (ranova). Methods for Least-Square means (LS-means) and
8560 tests of linear contrasts of fixed effects are also available.")
8561 (license license:gpl2+)))
8563 (define-public r-r2glmm
8570 (uri (cran-uri "r2glmm" version))
8573 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
8574 (build-system r-build-system)
8576 `(("r-afex" ,r-afex)
8577 ("r-data-table" ,r-data-table)
8578 ("r-dplyr" ,r-dplyr)
8579 ("r-ggplot2" ,r-ggplot2)
8580 ("r-gridextra" ,r-gridextra)
8581 ("r-lmertest" ,r-lmertest)
8583 ("r-matrix" ,r-matrix)
8585 ("r-pbkrtest" ,r-pbkrtest)))
8586 (home-page "https://github.com/bcjaeger/r2glmm")
8587 (synopsis "Compute R squared for mixed (multilevel) models")
8589 "This package computes model and semi partial R squared with confidence
8590 limits for the linear and generalized linear mixed model (LMM and GLMM). The
8591 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
8592 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
8594 (license license:gpl2)))
8596 (define-public r-weights
8603 (uri (cran-uri "weights" version))
8606 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
8607 (build-system r-build-system)
8609 `(("r-gdata" ,r-gdata)
8610 ("r-hmisc" ,r-hmisc)
8611 ("r-mice" ,r-mice)))
8613 "https://cran.r-project.org/web/packages/weights/")
8614 (synopsis "Weighting and weighted statistics")
8615 (description "This package Provides a variety of functions for producing
8616 simple weighted statistics, such as weighted Pearson's correlations, partial
8617 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
8618 includes some software for quickly recoding survey data and plotting point
8619 estimates from interaction terms in regressions (and multiply imputed
8620 regressions). NOTE: Weighted partial correlation calculations pulled to
8622 (license license:gpl2+)))
8624 (define-public r-rcppannoy
8626 (name "r-rcppannoy")
8631 (uri (cran-uri "RcppAnnoy" version))
8634 "1b0fmip9c4i0my1yjrvqy8jxfiiqcggq2kms135q0b53njxnqwwg"))))
8635 (properties `((upstream-name . "RcppAnnoy")))
8636 (build-system r-build-system)
8638 `(("r-rcpp" ,r-rcpp)))
8640 `(("r-knitr" ,r-knitr))) ; for vignettes
8641 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
8642 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
8644 "Annoy is a small C++ library for Approximate Nearest Neighbors written
8645 for efficient memory usage as well an ability to load from and save to disk.
8646 This package provides an R interface.")
8647 ;; Annoy is released under ASL 2.0, but this wrapper is released under
8649 (license (list license:gpl2+ license:asl2.0))))
8651 (define-public r-rcpphnsw
8658 (uri (cran-uri "RcppHNSW" version))
8661 "158a069n42pbnjrlmvqsr6bm2cfp9hxpnk3nhp3dwi9qjlq4r9bm"))))
8662 (properties `((upstream-name . "RcppHNSW")))
8663 (build-system r-build-system)
8664 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8665 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
8666 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
8668 "Hnswlib is a C++ library for approximate nearest neighbors. This
8669 package provides a minimal R interface by relying on the Rcpp package.")
8670 ;; hnswlib is released under Version 2.0 of the Apache License.
8671 (license (list license:gpl3 license:asl2.0))))
8673 (define-public r-ncdf4
8680 (uri (cran-uri "ncdf4" version))
8683 "083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd"))))
8684 (build-system r-build-system)
8686 `(("netcdf" ,netcdf)
8688 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
8689 (synopsis "R interface to Unidata netCDF format data files")
8691 "This package provides a high-level R interface to data files written
8692 using Unidata's netCDF library (version 4 or earlier), which are binary data
8693 files that are portable across platforms and include metadata information in
8694 addition to the data sets. Using this package, netCDF files can be opened and
8695 data sets read in easily. It is also easy to create new netCDF dimensions,
8696 variables, and files, in either version 3 or 4 format, and manipulate existing
8698 (license license:gpl3+)))
8700 (define-public r-biocmanager
8702 (name "r-biocmanager")
8707 (uri (cran-uri "BiocManager" version))
8710 "0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah"))))
8711 (properties `((upstream-name . "BiocManager")))
8712 (build-system r-build-system)
8713 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
8714 (synopsis "Access the Bioconductor project package repository")
8716 "This package provides a convenient tool to install and update
8717 Bioconductor packages.")
8718 (license license:artistic2.0)))
8720 (define-public r-rgl
8723 (version "0.100.19")
8727 (uri (cran-uri "rgl" version))
8730 "09bhvx8aq104yzysfgd7wlnq4vrvmnd4jzgj0c32whjfal10fqsh"))))
8731 (build-system r-build-system)
8733 `(("pkg-config" ,pkg-config)))
8735 `(("freetype" ,freetype)
8739 ("ghc-pandoc" ,ghc-pandoc)
8742 `(("r-crosstalk" ,r-crosstalk)
8743 ("r-htmltools" ,r-htmltools)
8744 ("r-htmlwidgets" ,r-htmlwidgets)
8745 ("r-jsonlite" ,r-jsonlite)
8746 ("r-knitr" ,r-knitr)
8747 ("r-magrittr" ,r-magrittr)
8748 ("r-manipulatewidget" ,r-manipulatewidget)
8749 ("r-shiny" ,r-shiny)))
8750 (home-page "https://r-forge.r-project.org/projects/rgl/")
8751 (synopsis "3D visualization using OpenGL")
8753 "This package provides medium to high level functions for 3D interactive graphics,
8754 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
8755 as functions for constructing representations of geometric
8756 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
8757 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
8758 image formats, including PNG, Postscript, SVG, PGF.")
8759 ;; Any version of the GPL.
8760 (license (list license:gpl2+ license:gpl3+))))
8762 (define-public r-multicool
8764 (name "r-multicool")
8769 (uri (cran-uri "multicool" version))
8772 "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
8773 (build-system r-build-system)
8774 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8775 (home-page "https://cran.r-project.org/web/packages/multicool/")
8776 (synopsis "Permutations of multisets in cool-lex order")
8778 "This package provides a set of tools to permute multisets without loops
8779 or hash tables and to generate integer partitions. Cool-lex order is similar
8780 to colexicographical order.")
8781 (license license:gpl2)))
8783 (define-public r-misc3d
8790 (uri (cran-uri "misc3d" version))
8793 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
8794 (build-system r-build-system)
8795 (home-page "https://cran.r-project.org/web/packages/misc3d/")
8796 (synopsis "Miscellaneous 3D Plots")
8798 "This package provides a collection of miscellaneous 3d plots, including
8800 ;; Any version of the GPL.
8801 (license (list license:gpl2+ license:gpl3+))))
8810 (uri (cran-uri "ks" version))
8813 "06ymx244yknmpl6935l4pafqbm4gcbpnhqg7rinql6rrfr9mcrag"))))
8814 (build-system r-build-system)
8817 ("r-kernlab" ,r-kernlab)
8818 ("r-kernsmooth" ,r-kernsmooth)
8819 ("r-matrix" ,r-matrix)
8820 ("r-mclust" ,r-mclust)
8822 ("r-multicool" ,r-multicool)
8823 ("r-mvtnorm" ,r-mvtnorm)))
8824 (home-page "http://www.mvstat.net/tduong/")
8825 (synopsis "Kernel smoothing")
8827 "This package provides kernel smoothers for univariate and multivariate
8828 data, including density functions, density derivatives, cumulative
8829 distributions, modal clustering, discriminant analysis, and two-sample
8830 hypothesis testing.")
8831 ;; Either version of the GPL.
8832 (license (list license:gpl2 license:gpl3))))
8834 (define-public r-feature
8841 (uri (cran-uri "feature" version))
8844 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
8845 (build-system r-build-system)
8848 ("r-misc3d" ,r-misc3d)
8850 (home-page "http://www.mvstat.net/tduong/")
8851 (synopsis "Inferential feature significance for kernel density estimation")
8853 "The feature package contains functions to display and compute kernel
8854 density estimates, significant gradient and significant curvature regions.
8855 Significant gradient and/or curvature regions often correspond to significant
8856 features (e.g. local modes).")
8857 ;; Either version of the GPL.
8858 (license (list license:gpl2 license:gpl3))))
8860 (define-public r-arm
8867 (uri (cran-uri "arm" version))
8870 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
8871 (build-system r-build-system)
8873 `(("r-abind" ,r-abind)
8877 ("r-matrix" ,r-matrix)
8878 ("r-nlme" ,r-nlme)))
8879 (home-page "https://cran.r-project.org/web/packages/arm/")
8880 (synopsis "Data analysis using regression and multilevel/hierarchical models")
8882 "This package provides functions to accompany A. Gelman and J. Hill,
8883 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
8884 University Press, 2007.")
8885 (license license:gpl3+)))
8887 (define-public r-circular
8894 (uri (cran-uri "circular" version))
8897 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
8898 (build-system r-build-system)
8900 `(("r-boot" ,r-boot)
8901 ("r-mvtnorm" ,r-mvtnorm)))
8903 `(("gfortran" ,gfortran)))
8904 (home-page "https://cran.r-project.org/web/packages/circular/")
8905 (synopsis "Circular statistics")
8907 "This package provides tools for circular statistics, from \"Topics in
8908 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
8910 (license license:gpl2+)))
8912 (define-public r-activity
8919 (uri (cran-uri "activity" version))
8922 "11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs"))))
8923 (build-system r-build-system)
8925 `(("r-circular" ,r-circular)
8926 ("r-pbapply" ,r-pbapply)))
8927 (home-page "https://cran.r-project.org/web/packages/activity/")
8928 (synopsis "Animal activity statistics")
8930 "This package provides functions to fit kernel density functions to
8931 animal activity time data; plot activity distributions; quantify overall
8932 levels of activity; statistically compare activity metrics through
8933 bootstrapping; and evaluate variation in linear variables with time (or other
8934 circular variables).")
8935 (license license:gpl3)))
8937 (define-public r-ouch
8944 (uri (cran-uri "ouch" version))
8947 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
8948 (build-system r-build-system)
8949 (propagated-inputs `(("r-subplex" ,r-subplex)))
8950 (home-page "http://kingaa.github.io/ouch/")
8951 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
8953 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
8954 for evolution along a phylogenetic tree.")
8955 (license license:gpl2+)))
8957 (define-public r-fmsb
8964 (uri (cran-uri "fmsb" version))
8967 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
8968 (build-system r-build-system)
8969 (home-page "http://minato.sip21c.org/msb/")
8970 (synopsis "Functions for medical statistics book with demographic data")
8972 "This package provides several utility functions for the book entitled
8973 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
8974 Japan, 2007) with Japanese demographic data and some demographic analysis
8975 related functions.")
8976 (license license:gpl2+)))
8978 (define-public r-stabledist
8980 (name "r-stabledist")
8985 (uri (cran-uri "stabledist" version))
8988 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
8989 (build-system r-build-system)
8990 (home-page "http://www.rmetrics.org")
8991 (synopsis "Stable distribution functions")
8993 "This package provides density, probability and quantile functions, and
8994 random number generation for (skew) stable distributions, using the
8995 parametrizations of Nolan.")
8996 (license license:gpl2+)))
8998 (define-public r-gsl
9005 (uri (cran-uri "gsl" version))
9008 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9009 (build-system r-build-system)
9012 (home-page "https://cran.r-project.org/web/packages/gsl")
9013 (synopsis "Wrapper for the GNU Scientific Library")
9015 "This package provides an R wrapper for the special functions and quasi
9016 random number generators of the GNU Scientific Library.")
9017 (license license:gpl2+)))
9019 (define-public r-adgoftest
9021 (name "r-adgoftest")
9026 (uri (cran-uri "ADGofTest" version))
9029 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9030 (properties `((upstream-name . "ADGofTest")))
9031 (build-system r-build-system)
9032 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9033 (synopsis "Anderson-Darling GoF test")
9035 "This package provides an implementation of the Anderson-Darling GoF test
9036 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9037 Anderson-Darling Distribution\".")
9038 ;; Any version of the GPL.
9039 (license license:gpl3+)))
9041 (define-public r-softimpute
9043 (name "r-softimpute")
9048 (uri (cran-uri "softImpute" version))
9051 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9052 (properties `((upstream-name . "softImpute")))
9053 (build-system r-build-system)
9055 `(("r-matrix" ,r-matrix)))
9057 `(("gfortran" ,gfortran)))
9058 (home-page "https://cran.r-project.org/web/packages/softImpute")
9059 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9061 "This package provides iterative methods for matrix completion that use
9062 nuclear-norm regularization. The package includes procedures for centering
9063 and scaling rows, columns or both, and for computing low-rank @dfn{single
9064 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9066 (license license:gpl2)))
9068 (define-public r-fftwtools
9070 (name "r-fftwtools")
9075 (uri (cran-uri "fftwtools" version))
9078 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9079 (build-system r-build-system)
9080 (inputs `(("fftw" ,fftw)))
9081 (home-page "https://github.com/krahim/fftwtools")
9082 (synopsis "Wrapper for FFTW3")
9084 "This package provides a wrapper for several FFTW functions. It provides
9085 access to the two-dimensional FFT, the multivariate FFT, and the
9086 one-dimensional real to complex FFT using the FFTW3 library. The package
9087 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9088 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9089 The FFT functions have a parameter that allows them to not return the
9090 redundant complex conjugate when the input is real data.")
9091 (license license:gpl2+)))
9093 (define-public r-tiff
9100 (uri (cran-uri "tiff" version))
9103 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9104 (build-system r-build-system)
9106 `(("libtiff" ,libtiff)
9107 ("libjpeg" ,libjpeg)
9109 (home-page "http://www.rforge.net/tiff/")
9110 (synopsis "Read and write TIFF images")
9112 "This package provides an easy and simple way to read, write and display
9113 bitmap images stored in the TIFF format. It can read and write both files and
9114 in-memory raw vectors.")
9115 ;; Either of these two license versions.
9116 (license (list license:gpl2 license:gpl3))))
9118 (define-public r-waveslim
9125 (uri (cran-uri "waveslim" version))
9128 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9129 (build-system r-build-system)
9131 `(("gfortran" ,gfortran)))
9132 (home-page "http://waveslim.blogspot.com")
9133 (synopsis "Basic wavelet routines for signal processing")
9135 "This package provides basic wavelet routines for time series (1D),
9136 image (2D) and array (3D) analysis. The code provided here is based on
9137 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9138 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9139 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9140 pairs (Selesnick 2001, 2002).")
9141 (license license:bsd-3)))
9143 (define-public r-wordcloud
9145 (name "r-wordcloud")
9150 (uri (cran-uri "wordcloud" version))
9153 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9154 (build-system r-build-system)
9156 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9157 ("r-rcpp" ,r-rcpp)))
9158 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9159 (synopsis "Word clouds")
9161 "This package provides functionality to create pretty word clouds,
9162 visualize differences and similarity between documents, and avoid
9163 over-plotting in scatter plots with text.")
9164 (license license:lgpl2.1)))
9166 (define-public r-colorramps
9168 (name "r-colorramps")
9173 (uri (cran-uri "colorRamps" version))
9176 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9177 (properties `((upstream-name . "colorRamps")))
9178 (build-system r-build-system)
9179 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9180 (synopsis "Build color tables")
9181 (description "This package provides features to build gradient color
9183 ;; Any version of the GPL
9184 (license license:gpl3+)))
9186 (define-public r-tidytree
9193 (uri (cran-uri "tidytree" version))
9196 "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w"))))
9197 (build-system r-build-system)
9200 ("r-dplyr" ,r-dplyr)
9201 ("r-lazyeval" ,r-lazyeval)
9202 ("r-magrittr" ,r-magrittr)
9203 ("r-rlang" ,r-rlang)
9204 ("r-tibble" ,r-tibble)))
9205 (home-page "https://github.com/GuangchuangYu/tidytree")
9206 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9208 "Phylogenetic trees generally contain multiple components including nodes,
9209 edges, branches and associated data. This package provides an approach to
9210 convert tree objects to tidy data frames. It also provides tidy interfaces to
9211 manipulate tree data.")
9212 (license license:artistic2.0)))
9214 (define-public r-rvcheck
9221 (uri (cran-uri "rvcheck" version))
9224 "1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b"))))
9225 (build-system r-build-system)
9227 `(("r-rlang" ,r-rlang)))
9228 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9229 (synopsis "R package version check")
9231 "This package provides tools to check the latest release version of R and
9232 R packages (on CRAN, Bioconductor or Github).")
9233 (license license:artistic2.0)))
9235 (define-public r-docopt
9242 (uri (cran-uri "docopt" version))
9245 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9246 (build-system r-build-system)
9247 (home-page "https://github.com/docopt/docopt.R")
9248 (synopsis "Command-line interface specification language")
9250 "This package enables you to define a command-line interface by just
9251 giving it a description in the specific format.")
9252 (license license:expat)))
9254 (define-public r-sparsesvd
9256 (name "r-sparsesvd")
9261 (uri (cran-uri "sparsesvd" version))
9264 "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam"))))
9265 (build-system r-build-system)
9266 (propagated-inputs `(("r-matrix" ,r-matrix)))
9267 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9268 (synopsis "Sparse truncated singular value decomposition")
9270 "This package provides a Wrapper around the SVDLIBC library
9271 for (truncated) singular value decomposition of a sparse matrix. Currently,
9272 only sparse real matrices in Matrix package format are supported.")
9273 ;; SVDLIBC is released under BSD-2. The R interface is released under
9275 (license (list license:bsd-3 license:bsd-2))))
9277 (define-public r-densityclust
9279 (name "r-densityclust")
9284 (uri (cran-uri "densityClust" version))
9287 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9288 (properties `((upstream-name . "densityClust")))
9289 (build-system r-build-system)
9292 ("r-ggplot2" ,r-ggplot2)
9293 ("r-ggrepel" ,r-ggrepel)
9294 ("r-gridextra" ,r-gridextra)
9295 ("r-rcolorbrewer" ,r-rcolorbrewer)
9297 ("r-rtsne" ,r-rtsne)))
9298 (home-page "https://cran.r-project.org/web/packages/densityClust")
9299 (synopsis "Clustering by fast search and find of density peaks")
9301 "This package provides an improved implementation (based on k-nearest
9302 neighbors) of the density peak clustering algorithm, originally described by
9303 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9304 large datasets (> 100,000 samples) very efficiently.")
9305 (license license:gpl2+)))
9307 (define-public r-combinat
9314 (uri (cran-uri "combinat" version))
9317 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9318 (build-system r-build-system)
9319 (home-page "https://cran.r-project.org/web/packages/combinat")
9320 (synopsis "Combinatorics utilities")
9321 (description "This package provides assorted routines for combinatorics.")
9322 (license license:gpl2)))
9324 (define-public r-qlcmatrix
9326 (name "r-qlcmatrix")
9331 (uri (cran-uri "qlcMatrix" version))
9334 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9335 (properties `((upstream-name . "qlcMatrix")))
9336 (build-system r-build-system)
9338 `(("r-docopt" ,r-docopt)
9339 ("r-matrix" ,r-matrix)
9341 ("r-sparsesvd" ,r-sparsesvd)))
9342 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9343 (synopsis "Sparse matrix functions for quantitative language comparison")
9345 "This package provides an extension of the functionality of the Matrix
9346 package for using sparse matrices. Some of the functions are very general,
9347 while other are highly specific for the special data format used for
9348 @dfn{quantitative language comparison} (QLC).")
9349 (license license:gpl3)))
9351 (define-public r-ddrtree
9358 (uri (cran-uri "DDRTree" version))
9361 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9362 (properties `((upstream-name . "DDRTree")))
9363 (build-system r-build-system)
9366 ("r-irlba" ,r-irlba)
9368 ("r-rcppeigen" ,r-rcppeigen)))
9369 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9370 (synopsis "Learning principal graphs with DDRTree")
9372 "This package provides an implementation of the framework of
9373 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9374 dimensional space while constructs a principal tree which passes through the
9375 middle of the data simultaneously. DDRTree shows superiority to
9376 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9377 intrinsic structure of single cell genomics data. In general, it could be
9378 used to reconstruct the temporal progression as well as the bifurcation
9379 structure of any data type.")
9380 (license license:asl2.0)))
9382 (define-public r-corpcor
9389 (uri (cran-uri "corpcor" version))
9392 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9393 (build-system r-build-system)
9394 (home-page "http://strimmerlab.org/software/corpcor/")
9395 (synopsis "Efficient estimation of covariance and (partial) correlation")
9397 "This package implements a James-Stein-type shrinkage estimator for the
9398 covariance matrix, with separate shrinkage for variances and correlations.
9399 Furthermore, functions are available for fast singular value decomposition,
9400 for computing the pseudoinverse, and for checking the rank and positive
9401 definiteness of a matrix.")
9402 (license license:gpl3+)))
9404 (define-public r-rspectra
9411 (uri (cran-uri "RSpectra" version))
9414 "12w5vnz39gyciza0fl7fw4f9i9kjw763h3mvk1sxd97c5dsn26jg"))))
9415 (properties `((upstream-name . "RSpectra")))
9416 (build-system r-build-system)
9418 `(("r-matrix" ,r-matrix)
9420 ("r-rcppeigen" ,r-rcppeigen)))
9421 (home-page "https://github.com/yixuan/RSpectra")
9422 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
9424 "This package provides an R interface to the Spectra library for
9425 large-scale eigenvalue and SVD problems. It is typically used to compute a
9426 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
9427 which is usually more efficient than @code{eigen()} if k << n.")
9429 (license license:mpl2.0)))
9431 (define-public r-vbsr
9438 (uri (cran-uri "vbsr" version))
9441 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
9442 (build-system r-build-system)
9443 (home-page "https://cran.r-project.org/web/packages/vbsr")
9444 (synopsis "Variational Bayes spike regression regularized linear models")
9446 "This package provides an efficient algorithm for solving ultra-sparse
9447 regularized regression models using a variational Bayes algorithm with a spike
9448 prior. The algorithm is solved on a path, with coordinate updates, and is
9449 capable of generating very sparse models. Very general model
9450 diagnostics for controlling type-1 errors are also provided.")
9451 (license license:gpl2)))
9453 (define-public r-flare
9460 (uri (cran-uri "flare" version))
9463 "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1"))))
9464 (build-system r-build-system)
9466 `(("r-igraph" ,r-igraph)
9467 ("r-lattice" ,r-lattice)
9469 ("r-matrix" ,r-matrix)))
9470 (home-page "https://cran.r-project.org/web/packages/flare")
9471 (synopsis "Family of Lasso regression implementations")
9473 "This package provides implementations of a family of Lasso variants
9474 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
9475 high dimensional sparse linear models.")
9476 (license license:gpl2)))
9478 (define-public r-lassopv
9485 (uri (cran-uri "lassopv" version))
9488 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
9489 (build-system r-build-system)
9490 (propagated-inputs `(("r-lars" ,r-lars)))
9491 (home-page "https://github.com/lingfeiwang/lassopv")
9492 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
9494 "This package enables you to estimate the p-values for predictors x
9495 against target variable y in Lasso regression, using the regularization
9496 strength when each predictor enters the active set of regularization path for
9497 the first time as the statistic.")
9498 (license license:gpl3)))
9500 (define-public r-splitstackshape
9502 (name "r-splitstackshape")
9507 (uri (cran-uri "splitstackshape" version))
9510 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
9511 (build-system r-build-system)
9513 `(("r-data-table" ,r-data-table)))
9514 (home-page "https://github.com/mrdwab/splitstackshape")
9515 (synopsis "Stack and reshape datasets after splitting concatenated values")
9517 "Online data collection tools like Google Forms often export
9518 multiple-response questions with data concatenated in cells. The
9519 @code{concat.split} (cSplit) family of functions provided by this package
9520 splits such data into separate cells. This package also includes functions to
9521 stack groups of columns and to reshape wide data, even when the data are
9522 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
9523 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
9525 (license license:gpl3)))
9527 (define-public r-tfmpvalue
9529 (name "r-tfmpvalue")
9534 (uri (cran-uri "TFMPvalue" version))
9537 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
9538 (properties `((upstream-name . "TFMPvalue")))
9539 (build-system r-build-system)
9540 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9541 (home-page "https://github.com/ge11232002/TFMPvalue")
9542 (synopsis "P-value computation for position weight matrices")
9544 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
9545 identification from sequence/alignments, we are interested in the significance
9546 of certain match scores. TFMPvalue provides the accurate calculation of a
9547 p-value with a score threshold for position weight matrices, or the score with
9548 a given p-value. It is an interface to code originally made available by
9549 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
9550 Touzet and Varre (2007).")
9551 (license license:gpl2)))
9553 (define-public r-rnifti
9560 (uri (cran-uri "RNifti" version))
9563 "07sfzps4yg5zdhbxh6i4rbjvbjvvf2d8i9jcf64ywbmi557sw1zv"))))
9564 (properties `((upstream-name . "RNifti")))
9565 (build-system r-build-system)
9566 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9567 (home-page "https://github.com/jonclayden/RNifti")
9568 (synopsis "Fast R and C++ access to NIfTI images")
9570 "This package provides very fast read and write access to images stored
9571 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
9572 compiled C and interpreted R code. It also provides a C/C++ API that can be
9573 used by other packages.")
9574 (license license:gpl2)))
9576 (define-public r-shades
9583 (uri (cran-uri "shades" version))
9586 "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv"))))
9587 (build-system r-build-system)
9588 (home-page "https://github.com/jonclayden/shades")
9589 (synopsis "Simple color manipulation")
9591 "This package provides functions for easily manipulating colors,
9592 creating color scales and calculating color distances.")
9593 (license license:bsd-3)))
9595 (define-public r-ore
9602 (uri (cran-uri "ore" version))
9605 "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m"))))
9606 (build-system r-build-system)
9607 (home-page "https://github.com/jonclayden/ore")
9608 (synopsis "R interface to the Onigmo regular expression library")
9610 "This package provides an alternative to R's built-in functionality for
9611 handling regular expressions, based on the Onigmo library. It offers
9612 first-class compiled regex objects, partial matching and function-based
9613 substitutions, amongst other features.")
9614 (license license:bsd-3)))
9616 (define-public r-reportr
9623 (uri (cran-uri "reportr" version))
9626 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
9627 (build-system r-build-system)
9628 (propagated-inputs `(("r-ore" ,r-ore)))
9629 (home-page "https://github.com/jonclayden/reportr")
9630 (synopsis "General message and error reporting system")
9632 "This package provides a system for reporting messages, which offers
9633 certain useful features over the standard R system, such as the incorporation
9634 of output consolidation, message filtering, assertions, expression
9635 substitution, automatic generation of stack traces for debugging, and
9636 conditional reporting based on the current \"output level\".")
9637 (license license:gpl2)))
9639 (define-public r-tractor-base
9641 (name "r-tractor-base")
9646 (uri (cran-uri "tractor.base" version))
9649 "0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj"))))
9650 (properties `((upstream-name . "tractor.base")))
9651 (build-system r-build-system)
9654 ("r-reportr" ,r-reportr)
9655 ("r-rnifti" ,r-rnifti)
9656 ("r-shades" ,r-shades)))
9657 (home-page "http://www.tractor-mri.org.uk")
9658 (synopsis "Read, manipulate and visualize magnetic resonance images")
9660 "This package provides functions for working with magnetic resonance
9661 images. It supports reading and writing of popular file formats (DICOM,
9662 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
9663 visualization; flexible image manipulation; metadata and sparse image
9665 (license license:gpl2)))
9667 (define-public r-grimport
9674 (uri (cran-uri "grImport" version))
9677 "0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16"))))
9678 (properties `((upstream-name . "grImport")))
9679 (build-system r-build-system)
9681 `(("ghostscript" ,ghostscript)))
9683 `(("r-xml" ,r-xml)))
9684 (home-page "https://cran.r-project.org/web/packages/grImport")
9685 (synopsis "Convert, import, and draw PostScript pictures")
9687 "This package provides functions for converting, importing, and drawing
9688 PostScript pictures in R plots.")
9689 (license license:gpl2+)))
9691 (define-public r-grimport2
9693 (name "r-grimport2")
9698 (uri (cran-uri "grImport2" version))
9701 "0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls"))))
9702 (properties `((upstream-name . "grImport2")))
9703 (build-system r-build-system)
9705 `(("r-base64enc" ,r-base64enc)
9709 (home-page "https://cran.r-project.org/web/packages/grImport2/")
9710 (synopsis "Import SVG graphics")
9712 "This package provides functions for importing external vector images and
9713 drawing them as part of R plots. This package is different from the
9714 @code{grImport} package because, where that package imports PostScript format
9715 images, this package imports SVG format images. Furthermore, this package
9716 imports a specific subset of SVG, so external images must be preprocessed
9717 using a package like @code{rsvg} to produce SVG that this package can import.
9718 SVG features that are not supported by R graphics, such as gradient fills, can
9719 be imported and then exported via the @code{gridSVG} package.")
9720 (license license:gpl2+)))
9722 (define-public r-kohonen
9729 (uri (cran-uri "kohonen" version))
9732 "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"))))
9733 (build-system r-build-system)
9735 `(("r-mass" ,r-mass)
9736 ("r-rcpp" ,r-rcpp)))
9737 (home-page "https://cran.r-project.org/web/packages/kohonen")
9738 (synopsis "Supervised and unsupervised self-organising maps")
9740 "This package provides functions to train @dfn{self-organising
9741 maps} (SOMs). Also interrogation of the maps and prediction using trained
9742 maps are supported. The name of the package refers to Teuvo Kohonen, the
9743 inventor of the SOM.")
9744 (license license:gpl2+)))
9746 (define-public r-nnls
9753 (uri (cran-uri "nnls" version))
9756 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
9757 (build-system r-build-system)
9758 (native-inputs `(("gfortran" ,gfortran)))
9759 (home-page "https://cran.r-project.org/web/packages/nnls")
9760 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
9762 "This package provides an R interface to the Lawson-Hanson implementation
9763 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
9764 the combination of non-negative and non-positive constraints.")
9765 (license license:gpl2+)))
9767 (define-public r-iso
9774 (uri (cran-uri "Iso" version))
9777 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
9778 (properties `((upstream-name . "Iso")))
9779 (build-system r-build-system)
9780 (native-inputs `(("gfortran" ,gfortran)))
9781 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
9782 (synopsis "Functions to perform isotonic regression")
9784 "This package provides support for linear order and unimodal
9785 order (univariate) isotonic regression and bivariate isotonic regression with
9786 linear order on both variables.")
9787 (license license:gpl2+)))
9789 (define-public r-chemometricswithr
9791 (name "r-chemometricswithr")
9796 (uri (cran-uri "ChemometricsWithR" version))
9799 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
9801 `((upstream-name . "ChemometricsWithR")))
9802 (build-system r-build-system)
9804 `(("r-devtools" ,r-devtools)
9805 ("r-kohonen" ,r-kohonen)
9808 (home-page "https://github.com/rwehrens/CWR")
9809 (synopsis "Chemometrics with R")
9811 "This package provides functions and scripts used in the book
9812 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
9813 Life Sciences\" by Ron Wehrens, Springer (2011).")
9814 (license license:gpl2+)))
9816 (define-public r-als
9823 (uri (cran-uri "ALS" version))
9826 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
9827 (properties `((upstream-name . "ALS")))
9828 (build-system r-build-system)
9831 ("r-nnls" ,r-nnls)))
9832 (home-page "https://cran.r-project.org/web/packages/ALS")
9833 (synopsis "Multivariate curve resolution alternating least squares")
9835 "Alternating least squares is often used to resolve components
9836 contributing to data with a bilinear structure; the basic technique may be
9837 extended to alternating constrained least squares. This package provides an
9838 implementation of @dfn{multivariate curve resolution alternating least
9841 Commonly applied constraints include unimodality, non-negativity, and
9842 normalization of components. Several data matrices may be decomposed
9843 simultaneously by assuming that one of the two matrices in the bilinear
9844 decomposition is shared between datasets.")
9845 (license license:gpl2+)))
9847 (define-public r-strucchange
9849 (name "r-strucchange")
9854 (uri (cran-uri "strucchange" version))
9857 "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl"))))
9858 (build-system r-build-system)
9860 `(("r-sandwich" ,r-sandwich)
9862 (home-page "https://cran.r-project.org/web/packages/strucchange")
9863 (synopsis "Testing, monitoring, and dating structural changes")
9865 "This package provides tools for testing, monitoring and dating
9866 structural changes in (linear) regression models. It features tests/methods
9867 from the generalized fluctuation test framework as well as from the F
9868 test (Chow test) framework. This includes methods to fit, plot and test
9869 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
9870 statistics, respectively. It is possible to monitor incoming data online
9871 using fluctuation processes. Finally, the breakpoints in regression models
9872 with structural changes can be estimated together with confidence intervals.
9873 Emphasis is always given to methods for visualizing the data.")
9874 ;; Either of these two GPL versions
9875 (license (list license:gpl2 license:gpl3))))
9877 (define-public r-pixmap
9884 (uri (cran-uri "pixmap" version))
9887 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
9888 (build-system r-build-system)
9889 (home-page "https://cran.r-project.org/web/packages/pixmap")
9890 (synopsis "Tools for bitmap images")
9892 "This package provides functions for importing, exporting, plotting and
9893 other manipulations of bitmapped images.")
9894 (license license:gpl2)))
9896 (define-public r-rapidjsonr
9898 (name "r-rapidjsonr")
9903 (uri (cran-uri "rapidjsonr" version))
9906 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
9907 (build-system r-build-system)
9908 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
9909 (synopsis "JSON parser")
9911 "This package provides JSON parsing capability through the Rapidjson
9913 (license license:expat)))
9915 (define-public r-ontologyindex
9917 (name "r-ontologyindex")
9922 (uri (cran-uri "ontologyIndex" version))
9925 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
9926 (properties `((upstream-name . "ontologyIndex")))
9927 (build-system r-build-system)
9928 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
9929 (synopsis "Functions for processing ontologies in R")
9931 "This package provides functions for reading ontologies into R as lists
9932 and manipulating sets of ontological terms.")
9933 (license license:gpl2+)))
9935 (define-public r-bigrquery
9937 (name "r-bigrquery")
9942 (uri (cran-uri "bigrquery" version))
9945 "1if39xkr231xmjq10fx2g7bgg4jgfd3wzx1p9g3pq4hbf2s6x0is"))))
9946 (build-system r-build-system)
9948 `(("r-assertthat" ,r-assertthat)
9949 ("r-bit64" ,r-bit64)
9954 ("r-jsonlite" ,r-jsonlite)
9955 ("r-prettyunits" ,r-prettyunits)
9956 ("r-progress" ,r-progress)
9957 ("r-rapidjsonr" ,r-rapidjsonr)
9959 ("r-tibble" ,r-tibble)))
9960 (home-page "https://github.com/rstats-db/bigrquery")
9961 (synopsis "R interface to Google's BigQuery API")
9963 "This package provides an R interface to Google's BigQuery database.")
9964 (license license:gpl3)))
9966 (define-public r-gmp
9969 (version "0.5-13.5")
9973 (uri (cran-uri "gmp" version))
9976 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
9977 (build-system r-build-system)
9980 (modify-phases %standard-phases
9981 (add-after 'unpack 'set-CC
9982 (lambda _ (setenv "CC" "gcc") #t)))))
9983 (inputs `(("gmp" ,gmp)))
9984 (home-page "https://cran.r-project.org/web/packages/gmp")
9985 (synopsis "Multiple precision arithmetic")
9987 "This package supports multiple precision arithmetic (big integers and
9988 rationals, prime number tests, matrix computation), \"arithmetic without
9989 limitations\" using the GNU Multiple Precision library.")
9990 ;; Any version of the GPL.
9991 (license license:gpl3+)))
9993 (define-public r-rmpfr
10000 (uri (cran-uri "Rmpfr" version))
10003 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10004 (properties `((upstream-name . "Rmpfr")))
10005 (build-system r-build-system)
10009 `(("r-gmp" ,r-gmp)))
10010 (home-page "http://rmpfr.r-forge.r-project.org/")
10011 (synopsis "R bindings to the MPFR library")
10013 "This package supports arithmetic (via S4 classes and methods) for
10014 arbitrary precision floating point numbers, including transcendental
10015 functions. To this end, the package interfaces with the @dfn{Multiple
10016 Precision Floating-Point Reliable} (MPFR) library.")
10017 (license license:gpl2+)))
10019 (define-public r-assertive-base
10021 (name "r-assertive-base")
10026 (uri (cran-uri "assertive.base" version))
10029 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10031 `((upstream-name . "assertive.base")))
10032 (build-system r-build-system)
10033 (home-page "https://bitbucket.org/richierocks/assertive.base")
10034 (synopsis "Core of the assertive package")
10036 "This package provides a minimal set of predicates and assertions used by
10037 the assertive package. This is mainly for use by other package developers who
10038 want to include run-time testing features in their own packages.")
10039 (license license:gpl3+)))
10041 (define-public r-assertive-properties
10043 (name "r-assertive-properties")
10048 (uri (cran-uri "assertive.properties" version))
10051 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10053 `((upstream-name . "assertive.properties")))
10054 (build-system r-build-system)
10056 `(("r-assertive-base" ,r-assertive-base)))
10057 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10058 (synopsis "Assertions to check properties of variables")
10060 "This package provides a set of predicates and assertions for checking
10061 the properties of variables, such as length, names and attributes. This is
10062 mainly for use by other package developers who want to include run-time
10063 testing features in their own packages.")
10064 (license license:gpl3+)))
10066 (define-public r-assertive-numbers
10068 (name "r-assertive-numbers")
10073 (uri (cran-uri "assertive.numbers" version))
10076 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10078 `((upstream-name . "assertive.numbers")))
10079 (build-system r-build-system)
10081 `(("r-assertive-base" ,r-assertive-base)))
10082 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10083 (synopsis "Assertions to check properties of numbers")
10085 "This package provides a set of predicates and assertions for checking
10086 the properties of numbers. This is mainly for use by other package developers
10087 who want to include run-time testing features in their own packages.")
10088 (license license:gpl3+)))
10090 (define-public r-assertive-sets
10092 (name "r-assertive-sets")
10097 (uri (cran-uri "assertive.sets" version))
10100 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10102 `((upstream-name . "assertive.sets")))
10103 (build-system r-build-system)
10105 `(("r-assertive-base" ,r-assertive-base)))
10106 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10107 (synopsis "Assertions to check properties of sets")
10109 "This package provides a set of predicates and assertions for checking
10110 the properties of sets. This is mainly for use by other package developers
10111 who want to include run-time testing features in their own packages.")
10112 (license license:gpl3+)))
10114 (define-public r-assertive-matrices
10116 (name "r-assertive-matrices")
10121 (uri (cran-uri "assertive.matrices" version))
10124 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10126 `((upstream-name . "assertive.matrices")))
10127 (build-system r-build-system)
10129 `(("r-assertive-base" ,r-assertive-base)))
10130 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10131 (synopsis "Assertions to check properties of matrices")
10133 "This package provides a set of predicates and assertions for checking
10134 the properties of matrices. This is mainly for use by other package
10135 developers who want to include run-time testing features in their own
10137 (license license:gpl3+)))
10139 (define-public r-assertive-models
10141 (name "r-assertive-models")
10146 (uri (cran-uri "assertive.models" version))
10149 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10151 `((upstream-name . "assertive.models")))
10152 (build-system r-build-system)
10154 `(("r-assertive-base" ,r-assertive-base)))
10155 (home-page "https://bitbucket.org/richierocks/assertive.models")
10156 (synopsis "Assertions to check properties of models")
10158 "This package provides a set of predicates and assertions for checking
10159 the properties of models. This is mainly for use by other package developers
10160 who want to include run-time testing features in their own packages.")
10161 (license license:gpl3+)))
10163 (define-public r-assertive-reflection
10165 (name "r-assertive-reflection")
10170 (uri (cran-uri "assertive.reflection" version))
10173 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10175 `((upstream-name . "assertive.reflection")))
10176 (build-system r-build-system)
10178 `(("r-assertive-base" ,r-assertive-base)))
10179 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10180 (synopsis "Assertions for checking the state of R")
10182 "This package provides a set of predicates and assertions for checking
10183 the state and capabilities of R, the operating system it is running on, and
10184 the IDE being used. This is mainly for use by other package developers who
10185 want to include run-time testing features in their own packages.")
10186 (license license:gpl3+)))
10188 (define-public r-assertive-types
10190 (name "r-assertive-types")
10195 (uri (cran-uri "assertive.types" version))
10198 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10200 `((upstream-name . "assertive.types")))
10201 (build-system r-build-system)
10203 `(("r-assertive-base" ,r-assertive-base)
10204 ("r-assertive-properties" ,r-assertive-properties)
10205 ("r-codetools" ,r-codetools)))
10206 (home-page "https://bitbucket.org/richierocks/assertive.types")
10207 (synopsis "Assertions to check types of variables")
10209 "This package provides a set of predicates and assertions for checking
10210 the types of variables. This is mainly for use by other package developers
10211 who want to include run-time testing features in their own packages.")
10212 (license license:gpl3+)))
10214 (define-public r-assertive-files
10216 (name "r-assertive-files")
10221 (uri (cran-uri "assertive.files" version))
10224 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10226 `((upstream-name . "assertive.files")))
10227 (build-system r-build-system)
10229 `(("r-assertive-base" ,r-assertive-base)
10230 ("r-assertive-numbers" ,r-assertive-numbers)))
10231 (home-page "https://bitbucket.org/richierocks/assertive.files")
10232 (synopsis "Assertions to check properties of files")
10234 "This package provides a set of predicates and assertions for checking
10235 the properties of files and connections. This is mainly for use by other
10236 package developers who want to include run-time testing features in their own
10238 (license license:gpl3+)))
10240 (define-public r-assertive-code
10242 (name "r-assertive-code")
10247 (uri (cran-uri "assertive.code" version))
10250 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10252 `((upstream-name . "assertive.code")))
10253 (build-system r-build-system)
10255 `(("r-assertive-base" ,r-assertive-base)
10256 ("r-assertive-properties" ,r-assertive-properties)
10257 ("r-assertive-types" ,r-assertive-types)))
10258 (home-page "https://bitbucket.org/richierocks/assertive.code")
10259 (synopsis "Assertions to check properties of code")
10261 "This package provides a set of predicates and assertions for checking
10262 the properties of code. This is mainly for use by other package developers
10263 who want to include run-time testing features in their own packages.")
10264 (license license:gpl3+)))
10266 (define-public r-assertive-datetimes
10268 (name "r-assertive-datetimes")
10273 (uri (cran-uri "assertive.datetimes" version))
10276 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10278 `((upstream-name . "assertive.datetimes")))
10279 (build-system r-build-system)
10281 `(("r-assertive-base" ,r-assertive-base)
10282 ("r-assertive-types" ,r-assertive-types)))
10283 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10284 (synopsis "Assertions to check properties of dates and times")
10286 "This package provides a set of predicates and assertions for checking
10287 the properties of dates and times. This is mainly for use by other package
10288 developers who want to include run-time testing features in their own
10290 (license license:gpl3+)))
10292 (define-public r-assertive-strings
10294 (name "r-assertive-strings")
10299 (uri (cran-uri "assertive.strings" version))
10302 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10304 `((upstream-name . "assertive.strings")))
10305 (build-system r-build-system)
10307 `(("r-assertive-base" ,r-assertive-base)
10308 ("r-assertive-types" ,r-assertive-types)
10309 ("r-stringi" ,r-stringi)))
10310 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10311 (synopsis "Assertions to check properties of strings")
10313 "This package provides a set of predicates and assertions for checking
10314 the properties of strings. This is mainly for use by other package developers
10315 who want to include run-time testing features in their own packages.")
10316 (license license:gpl3+)))
10318 (define-public r-assertive-data-us
10320 (name "r-assertive-data-us")
10325 (uri (cran-uri "assertive.data.us" version))
10328 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10330 `((upstream-name . "assertive.data.us")))
10331 (build-system r-build-system)
10333 `(("r-assertive-base" ,r-assertive-base)
10334 ("r-assertive-strings" ,r-assertive-strings)))
10335 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10336 (synopsis "Assertions to check properties of strings")
10338 "This package provides a set of predicates and assertions for checking
10339 the properties of US-specific complex data types. This is mainly for use by
10340 other package developers who want to include run-time testing features in
10341 their own packages.")
10342 (license license:gpl3+)))
10344 (define-public r-assertive-data-uk
10346 (name "r-assertive-data-uk")
10351 (uri (cran-uri "assertive.data.uk" version))
10354 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10356 `((upstream-name . "assertive.data.uk")))
10357 (build-system r-build-system)
10359 `(("r-assertive-base" ,r-assertive-base)
10360 ("r-assertive-strings" ,r-assertive-strings)))
10361 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10362 (synopsis "Assertions to check properties of strings")
10364 "This package provides a set of predicates and assertions for checking
10365 the properties of UK-specific complex data types. This is mainly for use by
10366 other package developers who want to include run-time testing features in
10367 their own packages.")
10368 (license license:gpl3+)))
10370 (define-public r-assertive-data
10372 (name "r-assertive-data")
10377 (uri (cran-uri "assertive.data" version))
10380 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
10382 `((upstream-name . "assertive.data")))
10383 (build-system r-build-system)
10385 `(("r-assertive-base" ,r-assertive-base)
10386 ("r-assertive-strings" ,r-assertive-strings)))
10387 (home-page "https://bitbucket.org/richierocks/assertive.data")
10388 (synopsis "Assertions to check properties of data")
10390 "This package provides a set of predicates and assertions for checking
10391 the properties of (country independent) complex data types. This is mainly
10392 for use by other package developers who want to include run-time testing
10393 features in their own packages.")
10394 (license license:gpl3+)))
10396 (define-public r-assertive
10398 (name "r-assertive")
10403 (uri (cran-uri "assertive" version))
10406 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
10407 (build-system r-build-system)
10409 `(("r-assertive-base" ,r-assertive-base)
10410 ("r-assertive-code" ,r-assertive-code)
10411 ("r-assertive-data" ,r-assertive-data)
10412 ("r-assertive-data-uk" ,r-assertive-data-uk)
10413 ("r-assertive-data-us" ,r-assertive-data-us)
10414 ("r-assertive-datetimes" ,r-assertive-datetimes)
10415 ("r-assertive-files" ,r-assertive-files)
10416 ("r-assertive-matrices" ,r-assertive-matrices)
10417 ("r-assertive-models" ,r-assertive-models)
10418 ("r-assertive-numbers" ,r-assertive-numbers)
10419 ("r-assertive-properties" ,r-assertive-properties)
10420 ("r-assertive-reflection" ,r-assertive-reflection)
10421 ("r-assertive-sets" ,r-assertive-sets)
10422 ("r-assertive-strings" ,r-assertive-strings)
10423 ("r-assertive-types" ,r-assertive-types)
10424 ("r-knitr" ,r-knitr)))
10425 (home-page "https://bitbucket.org/richierocks/assertive")
10426 (synopsis "Readable check functions to ensure code integrity")
10428 "This package provides lots of predicates (@code{is_*} functions) to
10429 check the state of your variables, and assertions (@code{assert_*} functions)
10430 to throw errors if they aren't in the right form.")
10431 (license license:gpl3+)))
10433 (define-public r-dotcall64
10435 (name "r-dotcall64")
10440 (uri (cran-uri "dotCall64" version))
10443 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
10444 (properties `((upstream-name . "dotCall64")))
10445 (build-system r-build-system)
10446 (native-inputs `(("gfortran" ,gfortran)))
10447 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
10448 (synopsis "Enhanced foreign function interface supporting long vectors")
10450 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
10451 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
10452 supports long vectors, arguments of type 64-bit integer, and provides a
10453 mechanism to avoid unnecessary copies of read-only and write-only arguments.
10454 This makes it a convenient and fast interface to C/C++ and Fortran code.")
10455 (license license:gpl2+)))
10457 (define-public r-spam
10464 (uri (cran-uri "spam" version))
10467 "024dgfnjfxvsiymbzrhadinamj6qy509f4sbd1zxql8ymkyxn7vi"))))
10468 (build-system r-build-system)
10470 `(("r-dotcall64" ,r-dotcall64)))
10471 (native-inputs `(("gfortran" ,gfortran)))
10472 (home-page "https://www.math.uzh.ch/pages/spam/")
10473 (synopsis "Sparse matrix algebra")
10475 "This package provides a set of functions for sparse matrix algebra.
10476 Differences with other sparse matrix packages are:
10479 @item it only supports (essentially) one sparse matrix format;
10480 @item it is based on transparent and simple structure(s);
10481 @item it is tailored for MCMC calculations within G(M)RF;
10482 @item and it is fast and scalable (with the extension package @code{spam64}).
10484 ;; Either of these licenses
10485 (license (list license:bsd-3 license:lgpl2.0))))
10487 (define-public r-fields
10494 (uri (cran-uri "fields" version))
10497 "1q9x68dczjym56v7x90x4x5br59vj3dww6w8v42zd3yl17h7c1h1"))))
10498 (build-system r-build-system)
10500 `(("r-maps" ,r-maps)
10501 ("r-spam" ,r-spam)))
10503 `(("gfortran" ,gfortran)))
10504 (home-page "http://www.image.ucar.edu/fields")
10505 (synopsis "Tools for spatial data")
10507 "This is a package for curve, surface and function fitting with an
10508 emphasis on splines, spatial data and spatial statistics. The major methods
10509 include cubic, and thin plate splines, Kriging, and compactly supported
10510 covariance functions for large data sets.")
10511 (license license:gpl2+)))
10513 (define-public r-spatialextremes
10515 (name "r-spatialextremes")
10520 (uri (cran-uri "SpatialExtremes" version))
10523 "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050"))))
10525 `((upstream-name . "SpatialExtremes")))
10526 (build-system r-build-system)
10528 `(("r-fields" ,r-fields)
10529 ("r-maps" ,r-maps)))
10530 (home-page "http://spatialextremes.r-forge.r-project.org/")
10531 (synopsis "Modelling spatial extremes")
10533 "This package provides tools for the statistical modelling of spatial
10534 extremes using max-stable processes, copula or Bayesian hierarchical models.
10535 More precisely, this package allows (conditional) simulations from various
10536 parametric max-stable models, analysis of the extremal spatial dependence, the
10537 fitting of such processes using composite likelihoods or least square (simple
10538 max-stable processes only), model checking and selection and prediction.")
10539 (license license:gpl2+)))
10541 (define-public r-drc
10548 (uri (cran-uri "drc" version))
10551 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
10552 (build-system r-build-system)
10555 ("r-gtools" ,r-gtools)
10557 ("r-multcomp" ,r-multcomp)
10558 ("r-plotrix" ,r-plotrix)
10559 ("r-scales" ,r-scales)))
10560 (home-page "https://cran.r-project.org/web/packages/drc")
10561 (synopsis "Analysis of dose-response curves")
10563 "This package provides a suite of flexible and versatile model fitting
10564 and after-fitting functions for the analysis of dose-response data.")
10565 (license license:gpl2+)))
10567 (define-public r-rmeta
10574 (uri (cran-uri "rmeta" version))
10577 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
10578 (build-system r-build-system)
10579 (home-page "https://cran.r-project.org/web/packages/rmeta")
10580 (synopsis "Tools for meta-analysis")
10582 "This package provides functions for simple fixed and random effects
10583 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
10584 draws standard summary plots, funnel plots, and computes summaries and tests
10585 for association and heterogeneity.")
10586 (license license:gpl2)))
10588 (define-public r-bootstrap
10590 (name "r-bootstrap")
10595 (uri (cran-uri "bootstrap" version))
10598 "08lmsy7k8wsgv89yc904c6fidcymr1ma2ry4fl0p69p21v4iiwa4"))))
10599 (build-system r-build-system)
10600 (native-inputs `(("gfortran" ,gfortran)))
10601 (home-page "https://cran.r-project.org/web/packages/bootstrap")
10602 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
10604 "This package provides software and data for the book \"An Introduction
10605 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
10606 This package is primarily provided for projects already based on it, and for
10607 support of the book. New projects should preferentially use the recommended
10608 package \"boot\".")
10609 (license license:bsd-3)))
10611 (define-public r-survivalroc
10613 (name "r-survivalroc")
10618 (uri (cran-uri "survivalROC" version))
10621 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
10622 (properties `((upstream-name . "survivalROC")))
10623 (build-system r-build-system)
10624 (home-page "https://cran.r-project.org/web/packages/survivalROC")
10625 (synopsis "Time-dependent ROC curve estimation from censored survival data")
10627 "Compute time-dependent ROC curve from censored survival data using
10628 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
10629 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
10630 (license license:gpl2+)))
10632 (define-public r-longitudinal
10634 (name "r-longitudinal")
10639 (uri (cran-uri "longitudinal" version))
10642 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
10643 (build-system r-build-system)
10644 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
10645 (home-page "http://strimmerlab.org/software/longitudinal/")
10646 (synopsis "Analysis of multiple time course data")
10648 "This package contains general data structures and functions for
10649 longitudinal data with multiple variables, repeated measurements, and
10650 irregularly spaced time points. It also implements a shrinkage estimator of
10651 dynamical correlation and dynamical covariance.")
10652 (license license:gpl3+)))
10654 (define-public r-genenet
10661 (uri (cran-uri "GeneNet" version))
10664 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
10665 (properties `((upstream-name . "GeneNet")))
10666 (build-system r-build-system)
10668 `(("r-corpcor" ,r-corpcor)
10669 ("r-fdrtool" ,r-fdrtool)
10670 ("r-longitudinal" ,r-longitudinal)))
10671 (home-page "http://strimmerlab.org/software/genenet/")
10672 (synopsis "Modeling and inferring gene networks")
10674 "This package analyzes gene expression (time series) data with focus on
10675 the inference of gene networks. In particular, GeneNet implements the methods
10676 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
10677 for learning large-scale gene association networks (including assignment of
10678 putative directions).")
10679 (license license:gpl3+)))
10681 (define-public r-rbamtools
10683 (name "r-rbamtools")
10684 (version "2.16.11.2")
10688 (uri (cran-uri "rbamtools" version))
10691 "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj"))))
10692 (build-system r-build-system)
10693 (inputs `(("zlib" ,zlib)))
10695 `(("r-refgenome" ,r-refgenome)))
10696 (home-page "https://cran.r-project.org/web/packages/rbamtools")
10697 (synopsis "Read and write BAM (binary alignment) files")
10699 "This package provides an R interface to functions of the SAMtools
10701 (license license:artistic2.0)))
10703 (define-public r-protviz
10710 (uri (cran-uri "protViz" version))
10713 "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1"))))
10714 (properties `((upstream-name . "protViz")))
10715 (build-system r-build-system)
10718 ("python-2" ,python-2)))
10719 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10720 (home-page "https://github.com/protViz/protViz/")
10721 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
10723 "This package helps with quality checks, visualizations and analysis of
10724 mass spectrometry data, coming from proteomics experiments. The package is
10725 developed, tested and used at the Functional Genomics Center Zurich, where it
10726 is used mainly for prototyping, teaching, and having fun with proteomics data.
10727 But it can also be used to do data analysis for small scale data sets.")
10728 (license license:gpl3)))
10730 (define-public r-cmprsk
10737 (uri (cran-uri "cmprsk" version))
10740 "1nacbzx950ygaqgnj0949skhwpzar5i3xlscd44jsimk2gsppx6z"))))
10741 (build-system r-build-system)
10743 `(("r-survival" ,r-survival)))
10745 `(("gfortran" ,gfortran)))
10746 (home-page "https://cran.r-project.org/web/packages/cmprsk")
10747 (synopsis "Subdistribution analysis of competing risks")
10749 "This package provides tool for estimation, testing and regression
10750 modeling of subdistribution functions in competing risks, as described in
10751 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
10752 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
10753 A proportional hazards model for the subdistribution of a competing risk,
10754 JASA, 94:496-509.")
10755 (license license:gpl2+)))
10757 (define-public r-etm
10764 (uri (cran-uri "etm" version))
10767 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
10768 (build-system r-build-system)
10770 `(("r-data-table" ,r-data-table)
10771 ("r-lattice" ,r-lattice)
10773 ("r-rcpparmadillo" ,r-rcpparmadillo)
10774 ("r-survival" ,r-survival)))
10775 (home-page "https://cran.r-project.org/web/packages/etm")
10776 (synopsis "Empirical transition matrix")
10778 "The @dfn{empirical transition matrix} (etm) package permits to estimate
10779 the matrix of transition probabilities for any time-inhomogeneous multistate
10780 model with finite state space using the Aalen-Johansen estimator.")
10781 (license license:expat)))
10783 (define-public r-epi
10790 (uri (cran-uri "Epi" version))
10793 "1lanr9x0c6w22406p56j7cwk6wck8njq6pscb4gzc613d68zj1lk"))))
10794 (properties `((upstream-name . "Epi")))
10795 (build-system r-build-system)
10797 `(("r-cmprsk" ,r-cmprsk)
10798 ("r-data-table" ,r-data-table)
10801 ("r-matrix" ,r-matrix)
10803 ("r-numderiv" ,r-numderiv)
10805 ("r-survival" ,r-survival)
10807 (home-page "http://BendixCarstensen.com/Epi/")
10808 (synopsis "Statistical analysis in epidemiology")
10810 "This package provides functions for demographic and epidemiological
10811 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
10812 particular representation, manipulation and simulation of multistate data -
10813 the Lexis suite of functions, which includes interfaces to the @code{mstate},
10814 @code{etm} and @code{cmprsk} packages. It also contains functions for
10815 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
10816 data and some useful functions for tabulation and plotting, as well as a
10817 number of epidemiological data sets.")
10818 (license license:gpl2)))
10820 (define-public r-ppls
10823 (version "1.6-1.1")
10827 (uri (cran-uri "ppls" version))
10830 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
10831 (build-system r-build-system)
10832 (propagated-inputs `(("r-mass" ,r-mass)))
10833 (home-page "https://cran.r-project.org/web/packages/ppls")
10834 (synopsis "Penalized partial least squares")
10836 "This package contains linear and nonlinear regression methods based on
10837 partial least squares and penalization techniques. Model parameters are
10838 selected via cross-validation, and confidence intervals ans tests for the
10839 regression coefficients can be conducted via jackknifing.")
10840 (license license:gpl2+)))
10842 (define-public r-huge
10849 (uri (cran-uri "huge" version))
10852 "1j93gvi1jyq3ld9jhdqhrpm2is54rk3ilmf3yw7fx6gva0y6hjqd"))))
10853 (build-system r-build-system)
10855 `(("r-igraph" ,r-igraph)
10857 ("r-matrix" ,r-matrix)
10859 ("r-rcppeigen" ,r-rcppeigen)))
10860 (home-page "https://cran.r-project.org/web/packages/huge")
10861 (synopsis "High-dimensional undirected graph estimation")
10863 "This package provides a general framework for high-dimensional
10864 undirected graph estimation. It integrates data preprocessing, neighborhood
10865 screening, graph estimation, and model selection techniques into a pipeline.")
10866 (license license:gpl2)))
10868 (define-public r-parcor
10875 (uri (cran-uri "parcor" version))
10878 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
10879 (build-system r-build-system)
10882 ("r-genenet" ,r-genenet)
10883 ("r-glmnet" ,r-glmnet)
10885 ("r-ppls" ,r-ppls)))
10886 (home-page "https://cran.r-project.org/web/packages/parcor")
10887 (synopsis "Regularized estimation of partial correlation matrices")
10889 "This package estimates the matrix of partial correlations based on
10890 different regularized regression methods: lasso, adaptive lasso, PLS, and
10891 Ridge Regression. In addition, the package provides model selection for
10892 lasso, adaptive lasso and Ridge regression based on cross-validation.")
10893 (license license:gpl2+)))
10895 (define-public r-mcmc
10902 (uri (cran-uri "mcmc" version))
10905 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
10906 (build-system r-build-system)
10907 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
10908 (synopsis "Markov chain Monte Carlo")
10910 "This package simulates continuous distributions of random vectors using
10911 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
10912 function that evaluates the log unnormalized density. Algorithms are random
10913 walk Metropolis algorithm (function @code{metrop}), simulated
10914 tempering (function @code{temper}), and morphometric random walk
10915 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
10916 by change of variable.")
10917 (license license:expat)))
10919 (define-public r-listenv
10926 (uri (cran-uri "listenv" version))
10929 "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1"))))
10930 (build-system r-build-system)
10932 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
10933 (home-page "https://github.com/HenrikBengtsson/listenv")
10934 (synopsis "Environments behaving (almost) as lists")
10936 "This package implements list environments. List environments are
10937 environments that have list-like properties. For instance, the elements of a
10938 list environment are ordered and can be accessed and iterated over using index
10940 (license license:lgpl2.1+)))
10942 (define-public r-globals
10949 (uri (cran-uri "globals" version))
10952 "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br"))))
10953 (build-system r-build-system)
10955 `(("r-codetools" ,r-codetools)))
10956 (home-page "https://github.com/HenrikBengtsson/globals")
10957 (synopsis "Identify global objects in R expressions")
10959 "This package provides tools to identify global (\"unknown\" or \"free\")
10960 objects in R expressions by code inspection using various strategies, e.g.
10961 conservative or liberal. The objective of this package is to make it as
10962 simple as possible to identify global objects for the purpose of exporting
10963 them in distributed compute environments.")
10964 (license license:lgpl2.1+)))
10966 (define-public r-future
10973 (uri (cran-uri "future" version))
10976 "0h8ng2a6vg4axd5f75xcb3ip9d95zi22fa048dq2bzlnncwlznjz"))))
10977 (build-system r-build-system)
10979 `(("r-digest" ,r-digest)
10980 ("r-globals" ,r-globals)
10981 ("r-listenv" ,r-listenv)))
10983 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
10984 (home-page "https://github.com/HenrikBengtsson/future")
10985 (synopsis "Unified parallel and distributed processing in R")
10987 "The purpose of this package is to provide a lightweight and unified
10988 Future API for sequential and parallel processing of R expression via futures.
10989 This package implements sequential, multicore, multisession, and cluster
10990 futures. With these, R expressions can be evaluated on the local machine, in
10991 parallel a set of local machines, or distributed on a mix of local and remote
10992 machines. Extensions to this package implement additional backends for
10993 processing futures via compute cluster schedulers etc. Because of its unified
10994 API, there is no need to modify any code in order to switch from sequential on
10995 the local machine to, say, distributed processing on a remote compute cluster.")
10996 (license license:lgpl2.1+)))
10998 (define-public r-future-apply
11000 (name "r-future-apply")
11005 (uri (cran-uri "future.apply" version))
11008 "00ma43ma3byrf9vfqqn9g8sn18c71ryhk7lpza5h7817f1kibw1h"))))
11009 (properties `((upstream-name . "future.apply")))
11010 (build-system r-build-system)
11012 `(("r-future" ,r-future)
11013 ("r-globals" ,r-globals)))
11015 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11016 (home-page "https://github.com/HenrikBengtsson/future.apply")
11017 (synopsis "Apply function to elements in parallel using futures")
11019 "This package provides implementations of @code{apply()},
11020 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11021 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11022 can be resolved using any future-supported backend, e.g. parallel on the local
11023 machine or distributed on a compute cluster.")
11024 (license license:gpl2+)))
11026 (define-public r-rsvd
11033 (uri (cran-uri "rsvd" version))
11036 "1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
11037 (build-system r-build-system)
11039 `(("r-matrix" ,r-matrix)))
11040 (home-page "https://github.com/erichson/rSVD")
11041 (synopsis "Randomized singular value decomposition")
11043 "Low-rank matrix decompositions are fundamental tools and widely used for
11044 data analysis, dimension reduction, and data compression. Classically, highly
11045 accurate deterministic matrix algorithms are used for this task. However, the
11046 emergence of large-scale data has severely challenged our computational
11047 ability to analyze big data. The concept of randomness has been demonstrated
11048 as an effective strategy to quickly produce approximate answers to familiar
11049 problems such as the @dfn{singular value decomposition} (SVD). This package
11050 provides several randomized matrix algorithms such as the randomized singular
11051 value decomposition (@code{rsvd}), randomized principal component
11052 analysis (@code{rpca}), randomized robust principal component
11053 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11054 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11055 functions are provided.")
11056 (license license:gpl3+)))
11058 (define-public r-sloop
11065 (uri (cran-uri "sloop" version))
11068 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11069 (build-system r-build-system)
11071 `(("r-codetools" ,r-codetools)
11072 ("r-crayon" ,r-crayon)
11073 ("r-purrr" ,r-purrr)
11074 ("r-rlang" ,r-rlang)
11075 ("r-tibble" ,r-tibble)))
11076 (home-page "https://github.com/r-lib/sloop")
11077 (synopsis "Helpers for object-oriented programming in R")
11079 "This package provides a collection of helper functions designed to
11080 help you to better understand object oriented programming in R, particularly
11082 (license license:gpl3)))
11084 (define-public r-capushe
11091 (uri (cran-uri "capushe" version))
11094 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11095 (build-system r-build-system)
11096 (propagated-inputs `(("r-mass" ,r-mass)))
11097 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11098 (synopsis "Calibrating penalties using slope heuristics")
11100 "This package provides tools for the calibration of penalized criteria
11101 for model selection. The calibration methods available are based on the slope
11103 (license license:gpl2+)))
11105 (define-public r-dorng
11112 (uri (cran-uri "doRNG" version))
11115 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11116 (properties `((upstream-name . "doRNG")))
11117 (build-system r-build-system)
11119 `(("r-foreach" ,r-foreach)
11120 ("r-iterators" ,r-iterators)
11121 ("r-pkgmaker" ,r-pkgmaker)
11122 ("r-rngtools" ,r-rngtools)))
11123 (home-page "https://renozao.github.io/doRNG/")
11124 (synopsis "Generic reproducible parallel backend for foreach loops")
11126 "This package provides functions to perform reproducible parallel
11127 @code{foreach} loops, using independent random streams as generated by
11128 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11129 convert standard @code{%dopar%} loops into fully reproducible loops,
11130 independently of the number of workers, the task scheduling strategy, or the
11131 chosen parallel environment and associated foreach backend.")
11132 (license license:gpl2+)))
11134 (define-public r-blockmodeling
11136 (name "r-blockmodeling")
11141 (uri (cran-uri "blockmodeling" version))
11144 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11145 (build-system r-build-system)
11147 `(("r-doparallel" ,r-doparallel)
11148 ("r-dorng" ,r-dorng)
11149 ("r-foreach" ,r-foreach)
11150 ("r-matrix" ,r-matrix)))
11151 (native-inputs `(("gfortran" ,gfortran)))
11152 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11153 (synopsis "Generalized and classical blockmodeling of valued networks")
11155 "This package is primarily meant as an implementation of generalized
11156 blockmodeling for valued networks. In addition, measures of similarity or
11157 dissimilarity based on structural equivalence and regular equivalence (REGE
11158 algorithms) can be computed and partitioned matrices can be plotted.")
11159 (license license:gpl2+)))
11161 (define-public r-upsetr
11168 (uri (cran-uri "UpSetR" version))
11171 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11172 (properties `((upstream-name . "UpSetR")))
11173 (build-system r-build-system)
11175 `(("r-ggplot2" ,r-ggplot2)
11176 ("r-gridextra" ,r-gridextra)
11178 ("r-scales" ,r-scales)))
11179 (home-page "https://github.com/hms-dbmi/UpSetR")
11180 (synopsis "Visualize intersecting sets")
11182 "This package provides a more scalable alternative to Venn and Euler
11183 diagrams for visualizing intersecting sets. Create visualizations of
11184 intersecting sets using a novel matrix design, along with visualizations of
11185 several common set, element and attribute related tasks.")
11186 (license license:expat)))
11188 ;; This package includes a JavaScript file, which is not minified. When
11189 ;; upgrading please check that there are no new minified JavaScript files.
11190 (define-public r-shinybs
11197 (uri (cran-uri "shinyBS" version))
11200 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11201 (properties `((upstream-name . "shinyBS")))
11202 (build-system r-build-system)
11203 ;; The tests spawn Shiny browser apps. They cannot be run
11204 ;; non-interactively.
11205 (arguments '(#:tests? #f))
11207 `(("r-htmltools" ,r-htmltools)
11208 ("r-shiny" ,r-shiny)))
11209 (home-page "https://ebailey78.github.io/shinyBS/")
11210 (synopsis "Twitter Bootstrap components for Shiny")
11212 "This package adds additional Twitter Bootstrap components to Shiny.")
11213 (license license:gpl3)))
11215 (define-public r-outliers
11217 (name "r-outliers")
11222 (uri (cran-uri "outliers" version))
11225 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11226 (build-system r-build-system)
11227 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11228 (synopsis "Tests for outliers")
11230 "This package provides a collection of some tests commonly used for
11231 identifying outliers.")
11232 (license license:gpl2+)))
11234 (define-public r-bayesm
11241 (uri (cran-uri "bayesm" version))
11244 "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
11245 (build-system r-build-system)
11247 `(("r-rcpp" ,r-rcpp)
11248 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11249 (home-page "http://www.perossi.org/home/bsm-1")
11250 (synopsis "Bayesian inference for marketing/micro-econometrics")
11252 "This package covers many important models used in marketing and
11253 micro-econometrics applications, including Bayes Regression (univariate or
11254 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11255 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11256 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11257 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11258 Estimation with normal base, Hierarchical Linear Models with normal prior and
11259 covariates, Hierarchical Linear Models with a mixture of normals prior and
11260 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11261 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11262 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11263 analysis of choice-based conjoint data, Bayesian treatment of linear
11264 instrumental variables models, Analysis of Multivariate Ordinal survey data
11265 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11266 Coefficient Logit Models.")
11267 (license license:gpl2+)))
11269 (define-public r-tensora
11276 (uri (cran-uri "tensorA" version))
11279 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11280 (properties `((upstream-name . "tensorA")))
11281 (build-system r-build-system)
11282 (home-page "http://www.stat.boogaart.de/tensorA")
11283 (synopsis "Advanced tensor arithmetic with named indices")
11285 "This package provides convenience functions for advanced linear algebra
11286 with tensors and computation with datasets of tensors on a higher level
11287 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11288 co- and contravariate indices, and parallel computations on sequences of
11290 (license license:gpl2+)))
11292 (define-public r-rarpack
11299 (uri (cran-uri "rARPACK" version))
11302 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11303 (properties `((upstream-name . "rARPACK")))
11304 (build-system r-build-system)
11305 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11306 (home-page "https://github.com/yixuan/rARPACK")
11307 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11309 "This package was previously an R wrapper of the ARPACK library, and now
11310 a shell of the R package RSpectra, an R interface to the Spectra library for
11311 solving large scale eigenvalue/vector problems. The current version of
11312 rARPACK simply imports and exports the functions provided by RSpectra. New
11313 users of rARPACK are advised to switch to the RSpectra package.")
11314 (license license:bsd-3)))
11316 (define-public r-compositions
11318 (name "r-compositions")
11323 (uri (cran-uri "compositions" version))
11326 "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i"))))
11327 (build-system r-build-system)
11329 `(("r-bayesm" ,r-bayesm)
11330 ("r-energy" ,r-energy)
11331 ("r-robustbase" ,r-robustbase)
11332 ("r-tensora" ,r-tensora)))
11333 (home-page "http://www.stat.boogaart.de/compositions")
11334 (synopsis "Compositional data analysis")
11336 "This package provides functions for the consistent analysis of
11337 compositional data (e.g. portions of substances) and positive
11338 numbers (e.g. concentrations).")
11339 (license license:gpl2+)))
11341 (define-public r-cobs
11348 (uri (cran-uri "cobs" version))
11351 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11352 (build-system r-build-system)
11354 `(("r-quantreg" ,r-quantreg)
11355 ("r-sparsem" ,r-sparsem)))
11356 (home-page "https://cran.r-project.org/web/packages/cobs")
11357 (synopsis "Constrained B-Splines (sparse matrix based)")
11359 "This package provides qualitatively constrained (regression) smoothing
11360 splines via linear programming and sparse matrices.")
11361 (license license:gpl2+)))
11363 (define-public r-drimpute
11365 (name "r-drimpute")
11370 (uri (cran-uri "DrImpute" version))
11373 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11374 (properties `((upstream-name . "DrImpute")))
11375 (build-system r-build-system)
11377 `(("r-rcpp" ,r-rcpp)
11378 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11379 (home-page "https://github.com/ikwak2/DrImpute")
11380 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11382 "This is an R package for imputing dropout events. Many statistical
11383 methods in cell type identification, visualization and lineage reconstruction
11384 do not account for dropout events. DrImpute can improve the performance of
11385 such software by imputing dropout events.")
11386 (license license:gpl3)))
11388 (define-public r-gamlss-dist
11390 (name "r-gamlss-dist")
11395 (uri (cran-uri "gamlss.dist" version))
11398 "0zi87lgigr83l35zqq1y1g4cdq6ssjamripzz7yis74aznh6qg1l"))))
11399 (properties `((upstream-name . "gamlss.dist")))
11400 (build-system r-build-system)
11401 (propagated-inputs `(("r-mass" ,r-mass)))
11402 (home-page "http://www.gamlss.org/")
11403 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
11405 "This package provides a set of distributions which can be used for
11406 modelling the response variables in Generalized Additive Models for Location
11407 Scale and Shape. The distributions can be continuous, discrete or mixed
11408 distributions. Extra distributions can be created, by transforming, any
11409 continuous distribution defined on the real line, to a distribution defined on
11410 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
11411 transformation, respectively.")
11412 ;; Either version of the GPL.
11413 (license (list license:gpl2 license:gpl3))))
11415 ;; This package includes JavaScript files, which are not minified. When
11416 ;; upgrading please check that there are no new minified JavaScript files.
11417 (define-public r-shinyjs
11424 (uri (cran-uri "shinyjs" version))
11427 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
11428 (build-system r-build-system)
11430 `(("r-digest" ,r-digest)
11431 ("r-htmltools" ,r-htmltools)
11432 ("r-jsonlite" ,r-jsonlite)
11433 ("r-shiny" ,r-shiny)))
11434 (home-page "https://deanattali.com/shinyjs")
11435 (synopsis "Improve the user experience of your Shiny apps")
11437 "Perform common useful JavaScript operations in Shiny apps that will
11438 greatly improve your apps without having to know any JavaScript. Examples
11439 include: hiding an element, disabling an input, resetting an input back to its
11440 original value, delaying code execution by a few seconds, and many more useful
11441 functions for both the end user and the developer. Shinyjs can also be used
11442 to easily call your own custom JavaScript functions from R.")
11443 (license license:agpl3+)))
11445 ;; This package includes minified JavaScript files. When upgrading please
11446 ;; check that there are no new minified JavaScript files.
11447 (define-public r-colourpicker
11449 (name "r-colourpicker")
11454 (uri (cran-uri "colourpicker" version))
11457 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
11458 (build-system r-build-system)
11460 `(#:modules ((guix build utils)
11461 (guix build r-build-system)
11465 (modify-phases %standard-phases
11466 (add-after 'unpack 'process-javascript
11467 (lambda* (#:key inputs #:allow-other-keys)
11468 (with-directory-excursion "inst"
11472 `((,(assoc-ref inputs "js-salvattore")
11473 "examples/colourInput/www/salvattore.min.js")
11474 (,(assoc-ref inputs "js-jquery")
11475 "htmlwidgets/lib/jquery/jquery.min.js")
11476 ("www/shared/colourpicker/js/colourpicker.js"
11477 "www/shared/colourpicker/js/colourpicker.min.js"))))
11478 (lambda (sources targets)
11479 (for-each (lambda (source target)
11480 (format #t "Processing ~a --> ~a~%"
11482 (delete-file target)
11483 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
11484 (call-with-output-file target
11486 (dump-port minified port)))))
11487 sources targets))))
11490 `(("r-ggplot2" ,r-ggplot2)
11491 ("r-htmltools" ,r-htmltools)
11492 ("r-htmlwidgets" ,r-htmlwidgets)
11493 ("r-jsonlite" ,r-jsonlite)
11494 ("r-miniui" ,r-miniui)
11495 ("r-shiny" ,r-shiny)
11496 ("r-shinyjs" ,r-shinyjs)))
11498 `(("uglify-js" ,uglify-js)
11502 (uri "https://code.jquery.com/jquery-3.3.1.js")
11505 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
11509 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
11512 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
11513 (home-page "https://github.com/daattali/colourpicker")
11514 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
11516 "This package provides a color picker that can be used as an input in
11517 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
11518 custom color palettes, and many more options. A plot color helper tool is
11519 available as an RStudio Addin, which helps you pick colors to use in your
11520 plots. A more generic color picker RStudio Addin is also provided to let you
11521 select colors to use in your R code.")
11522 (license license:expat)))
11524 (define-public r-ggextra
11531 (uri (cran-uri "ggExtra" version))
11534 "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
11535 (properties `((upstream-name . "ggExtra")))
11536 (build-system r-build-system)
11538 `(("r-colourpicker" ,r-colourpicker)
11539 ("r-ggplot2" ,r-ggplot2)
11540 ("r-gtable" ,r-gtable)
11541 ("r-miniui" ,r-miniui)
11542 ("r-scales" ,r-scales)
11543 ("r-shiny" ,r-shiny)
11544 ("r-shinyjs" ,r-shinyjs)))
11545 (home-page "https://github.com/daattali/ggExtra")
11546 (synopsis "Marginal histograms for ggplot2 and other enhancements")
11548 "This package is a collection of functions and layers to enhance ggplot2.
11549 The flagship function is @code{ggMarginal()}, which can be used to add
11550 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
11551 (license license:expat)))
11553 (define-public r-minpack-lm
11555 (name "r-minpack-lm")
11560 (uri (cran-uri "minpack.lm" version))
11563 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
11564 (properties `((upstream-name . "minpack.lm")))
11565 (build-system r-build-system)
11566 (native-inputs `(("gfortran" ,gfortran)))
11567 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
11568 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
11570 "The @code{nls.lm} function provides an R interface to @code{lmder} and
11571 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
11572 problems by a modification of the Levenberg-Marquardt algorithm, with support
11573 for lower and upper parameter bounds. The implementation can be used via
11574 @code{nls}-like calls using the @code{nlsLM} function.")
11575 (license license:gpl3)))
11577 (define-public r-moments
11584 (uri (cran-uri "moments" version))
11587 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
11588 (build-system r-build-system)
11589 (home-page "https://cran.r-project.org/web/packages/moments")
11590 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
11592 "This package provides functions to calculate: moments, Pearson's
11593 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
11594 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
11595 (license license:gpl2+)))
11597 (define-public r-msir
11604 (uri (cran-uri "msir" version))
11607 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
11608 (build-system r-build-system)
11610 `(("r-mclust" ,r-mclust)))
11611 (home-page "https://cran.r-project.org/web/packages/msir")
11612 (synopsis "Model-based sliced inverse regression")
11614 "This is an R package for dimension reduction based on finite Gaussian
11615 mixture modeling of inverse regression.")
11616 (license license:gpl2+)))
11618 (define-public r-pbivnorm
11620 (name "r-pbivnorm")
11625 (uri (cran-uri "pbivnorm" version))
11628 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
11629 (build-system r-build-system)
11630 (native-inputs `(("gfortran" ,gfortran)))
11631 (home-page "https://github.com/brentonk/pbivnorm")
11632 (synopsis "Vectorized bivariate normal CDF")
11634 "This package provides a vectorized R function for calculating
11635 probabilities from a standard bivariate normal CDF.")
11636 (license license:gpl2+)))
11638 (define-public r-lavaan
11645 (uri (cran-uri "lavaan" version))
11648 "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
11649 (build-system r-build-system)
11651 `(("r-mass" ,r-mass)
11652 ("r-mnormt" ,r-mnormt)
11653 ("r-numderiv" ,r-numderiv)
11654 ("r-pbivnorm" ,r-pbivnorm)))
11655 (home-page "http://lavaan.ugent.be")
11656 (synopsis "Latent variable analysis")
11658 "This package provides tools to fit a variety of latent variable models,
11659 including confirmatory factor analysis, structural equation modeling and
11660 latent growth curve models.")
11661 (license license:gpl2+)))
11663 (define-public r-nonnest2
11665 (name "r-nonnest2")
11670 (uri (cran-uri "nonnest2" version))
11673 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
11674 (build-system r-build-system)
11676 `(("r-compquadform" ,r-compquadform)
11677 ("r-lavaan" ,r-lavaan)
11678 ("r-mvtnorm" ,r-mvtnorm)
11679 ("r-sandwich" ,r-sandwich)))
11680 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
11681 (synopsis "Tests of non-nested models")
11683 "This package allows for testing of non-nested models. It includes tests
11684 of model distinguishability and of model fit that can be applied to both
11685 nested and non-nested models. The package also includes functionality to
11686 obtain confidence intervals associated with AIC and BIC.")
11687 ;; Either version of the GPL.
11688 (license (list license:gpl2 license:gpl3))))
11690 (define-public r-penalized
11692 (name "r-penalized")
11697 (uri (cran-uri "penalized" version))
11700 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
11701 (build-system r-build-system)
11703 `(("r-rcpp" ,r-rcpp)
11704 ("r-rcpparmadillo" ,r-rcpparmadillo)
11705 ("r-survival" ,r-survival)))
11706 (home-page "https://cran.r-project.org/web/packages/penalized/")
11707 (synopsis "Penalized estimation in GLMs and in the Cox model")
11709 "This package provides tools for fitting possibly high dimensional
11710 penalized regression models. The penalty structure can be any combination of
11711 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
11712 constraint on the regression coefficients. The supported regression models
11713 are linear, logistic and Poisson regression and the Cox Proportional Hazards
11714 model. Cross-validation routines allow optimization of the tuning
11716 (license license:gpl2+)))
11718 (define-public r-zim
11725 (uri (cran-uri "ZIM" version))
11728 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
11729 (properties `((upstream-name . "ZIM")))
11730 (build-system r-build-system)
11731 (propagated-inputs `(("r-mass" ,r-mass)))
11732 (home-page "https://github.com/biostatstudio/ZIM")
11733 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
11735 "Analyze count time series with excess zeros. Two types of statistical
11736 models are supported: Markov regression and state-space models. They are also
11737 known as observation-driven and parameter-driven models respectively in the
11738 time series literature. The functions used for Markov regression or
11739 observation-driven models can also be used to fit ordinary regression models
11740 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
11741 negative binomial (ZINB) assumption. The package also contains miscellaneous
11742 functions to compute density, distribution, quantile, and generate random
11743 numbers from ZIP and ZINB distributions.")
11744 (license license:gpl3)))
11746 (define-public r-nor1mix
11753 (uri (cran-uri "nor1mix" version))
11756 "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3"))))
11757 (build-system r-build-system)
11758 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
11759 (synopsis "Normal (1-d) mixture models")
11761 "This package provides S3 classes and methods for one-dimensional normal
11762 mixture models, for, e.g., density estimation or clustering algorithms
11763 research and teaching; it provides the widely used Marron-Wand densities. It
11764 also provides tools for efficient random number generation and graphics.")
11765 (license license:gpl2+)))
11767 (define-public r-beanplot
11769 (name "r-beanplot")
11774 (uri (cran-uri "beanplot" version))
11777 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
11778 (build-system r-build-system)
11779 (home-page "https://cran.r-project.org/web/packages/beanplot/")
11780 (synopsis "Visualization via beanplots")
11782 "This package provides beanplots, an alternative to
11783 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
11785 (license license:gpl2)))
11787 (define-public r-pbdzmq
11794 (uri (cran-uri "pbdZMQ" version))
11797 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
11798 (properties `((upstream-name . "pbdZMQ")))
11799 (build-system r-build-system)
11801 `(("zeromq" ,zeromq)
11804 `(("pkg-config" ,pkg-config)))
11805 (home-page "https://pbdr.org/")
11806 (synopsis "R interface to ZeroMQ")
11808 "ZeroMQ is a well-known library for high-performance asynchronous
11809 messaging in scalable, distributed applications. This package provides high
11810 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
11811 interactive client/server programming frameworks. A few wrapper functions
11812 compatible with @code{rzmq} are also provided.")
11813 (license license:gpl3)))
11815 (define-public r-repr
11822 (uri (cran-uri "repr" version))
11825 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
11826 (build-system r-build-system)
11828 `(("r-base64enc" ,r-base64enc)
11829 ("r-htmltools" ,r-htmltools)
11830 ("r-jsonlite" ,r-jsonlite)
11831 ("r-pillar" ,r-pillar)))
11832 (home-page "https://cran.r-project.org/web/packages/repr/")
11833 (synopsis "Serializable representations")
11835 "This package provides string and binary representations of objects for
11836 several formats and MIME types.")
11837 (license license:gpl3)))
11839 (define-public r-irdisplay
11841 (name "r-irdisplay")
11846 (uri (cran-uri "IRdisplay" version))
11849 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
11850 (properties `((upstream-name . "IRdisplay")))
11851 (build-system r-build-system)
11853 `(("r-repr" ,r-repr)))
11854 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
11855 (synopsis "Jupyter display machinery")
11857 "This package provides an interface to the rich display capabilities of
11858 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
11859 running IRkernel session.")
11860 (license license:expat)))
11862 (define-public r-irkernel
11864 (name "r-irkernel")
11869 (uri (cran-uri "IRkernel" version))
11872 "1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s"))))
11873 (properties `((upstream-name . "IRkernel")))
11874 (build-system r-build-system)
11877 (modify-phases %standard-phases
11878 (add-after 'install 'install-kernelspec
11879 (lambda* (#:key outputs #:allow-other-keys)
11880 (let ((out (assoc-ref outputs "out")))
11881 (setenv "HOME" "/tmp")
11882 (invoke "jupyter" "kernelspec" "install"
11885 (string-append out "/site-library/IRkernel/kernelspec"))
11888 `(("jupyter" ,jupyter)))
11890 `(("r-crayon" ,r-crayon)
11891 ("r-digest" ,r-digest)
11892 ("r-evaluate" ,r-evaluate)
11893 ("r-irdisplay" ,r-irdisplay)
11894 ("r-jsonlite" ,r-jsonlite)
11895 ("r-pbdzmq" ,r-pbdzmq)
11897 ("r-uuid" ,r-uuid)))
11898 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
11899 (synopsis "Native R kernel for Jupyter")
11901 "The R kernel for the Jupyter environment executes R code which the
11902 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
11904 (license license:expat)))
11906 (define-public r-gmodels
11913 (uri (cran-uri "gmodels" version))
11916 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
11917 (build-system r-build-system)
11919 `(("r-gdata" ,r-gdata)
11920 ("r-mass" ,r-mass)))
11921 (home-page "https://cran.r-project.org/web/packages/gmodels/")
11922 (synopsis "Various R programming tools for model fitting")
11924 "This package provides various R programming tools for model fitting.")
11925 (license license:gpl2)))
11927 (define-public r-apcluster
11929 (name "r-apcluster")
11934 (uri (cran-uri "apcluster" version))
11937 "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
11938 (build-system r-build-system)
11940 `(("r-matrix" ,r-matrix)
11941 ("r-rcpp" ,r-rcpp)))
11942 (home-page "https://cran.r-project.org/web/packages/apcluster/")
11943 (synopsis "Affinity propagation clustering")
11945 "This package implements affinity propagation clustering introduced by
11946 Frey and Dueck (2007). The package further provides leveraged affinity
11947 propagation and an algorithm for exemplar-based agglomerative clustering that
11948 can also be used to join clusters obtained from affinity propagation. Various
11949 plotting functions are available for analyzing clustering results.")
11950 (license license:gpl2+)))
11952 (define-public r-valr
11959 (uri (cran-uri "valr" version))
11962 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
11963 (build-system r-build-system)
11965 `(("r-broom" ,r-broom)
11966 ("r-dplyr" ,r-dplyr)
11967 ("r-ggplot2" ,r-ggplot2)
11969 ("r-readr" ,r-readr)
11970 ("r-rlang" ,r-rlang)
11971 ("r-stringr" ,r-stringr)
11972 ("r-tibble" ,r-tibble)))
11973 (home-page "http://github.com/rnabioco/valr")
11974 (synopsis "Genome interval arithmetic in R")
11976 "This package enables you to read and manipulate genome intervals and
11977 signals. It provides functionality similar to command-line tool suites within
11978 R, enabling interactive analysis and visualization of genome-scale data.")
11979 (license license:expat)))
11981 (define-public r-rematch2
11983 (name "r-rematch2")
11988 (uri (cran-uri "rematch2" version))
11991 "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
11992 (build-system r-build-system)
11994 `(("r-tibble" ,r-tibble)))
11995 (home-page "https://github.com/r-lib/rematch2")
11996 (synopsis "Tidy output from regular expression matching")
11998 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
11999 return the match results in tidy data frames.")
12000 (license license:expat)))
12002 (define-public r-picante
12009 (uri (cran-uri "picante" version))
12012 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12013 (build-system r-build-system)
12017 ("r-vegan" ,r-vegan)))
12018 (home-page "https://cran.r-project.org/web/packages/picante/")
12019 (synopsis "Integrating phylogenies and ecology")
12021 "This package provides functions for phylocom integration, community
12022 analyses, null-models, traits and evolution. It implements numerous
12023 ecophylogenetic approaches including measures of community phylogenetic and
12024 trait diversity, phylogenetic signal, estimation of trait values for
12025 unobserved taxa, null models for community and phylogeny randomizations, and
12026 utility functions for data input/output and phylogeny plotting. A full
12027 description of package functionality and methods are provided by Kembel et
12029 (license license:gpl2)))
12031 (define-public r-reinforcelearn
12033 (name "r-reinforcelearn")
12038 (uri (cran-uri "reinforcelearn" version))
12041 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12042 (build-system r-build-system)
12044 `(("r-checkmate" ,r-checkmate)
12046 ("r-purrr" ,r-purrr)
12048 (home-page "https://markusdumke.github.io/reinforcelearn")
12049 (synopsis "Reinforcement learning")
12051 "This package implements reinforcement learning environments and
12052 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12053 can be used with function approximation, eligibility traces (Singh & Sutton,
12054 1996) and experience replay (Mnih et al., 2013).")
12055 (license license:expat)))
12057 (define-public r-lemon
12064 (uri (cran-uri "lemon" version))
12067 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12068 (build-system r-build-system)
12070 `(("r-ggplot2" ,r-ggplot2)
12071 ("r-gridextra" ,r-gridextra)
12072 ("r-gtable" ,r-gtable)
12073 ("r-knitr" ,r-knitr)
12074 ("r-lattice" ,r-lattice)
12076 ("r-scales" ,r-scales)))
12077 (home-page "https://github.com/stefanedwards/lemon")
12078 (synopsis "Freshen up your ggplot2 plots")
12080 "This package provides functions for working with legends and axis lines
12081 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12083 (license license:gpl3)))
12085 (define-public r-wgaim
12092 (uri (cran-uri "wgaim" version))
12095 "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg"))))
12096 (build-system r-build-system)
12098 `(("r-lattice" ,r-lattice)
12100 (home-page "https://cran.r-project.org/web/packages/wgaim")
12101 (synopsis "Whole genome average interval mapping for QTL detection")
12103 "This package integrates sophisticated mixed modelling methods with a
12104 whole genome approach to detecting significant QTL in linkage maps.")
12105 (license license:gpl2+)))
12107 (define-public r-bedr
12114 (uri (cran-uri "bedr" version))
12117 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12118 (build-system r-build-system)
12120 `(("r-data-table" ,r-data-table)
12121 ("r-r-utils" ,r-r-utils)
12122 ("r-testthat" ,r-testthat)
12123 ("r-venndiagram" ,r-venndiagram)
12126 ("bedtools" ,bedtools)
12127 ("htslib" ,htslib))) ; for tabix
12129 `(("r-knitr" ,r-knitr))) ; for vignettes
12130 (home-page "https://cran.r-project.org/web/packages/bedr")
12131 (synopsis "Genomic region processing")
12133 "This package is for genomic regions processing using command line tools
12134 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12135 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12136 The bedr package's API enhances access to these tools as well as offers
12137 additional utilities for genomic regions processing.")
12138 (license license:gpl2)))
12140 (define-public r-partitions
12142 (name "r-partitions")
12147 (uri (cran-uri "partitions" version))
12150 "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx"))))
12151 (build-system r-build-system)
12154 ("r-polynom" ,r-polynom)))
12155 (home-page "https://cran.r-project.org/web/packages/partitions")
12156 (synopsis "Additive partitions of integers")
12158 "This package provides tools to enumerates the partitions, unequal
12159 partitions, and restricted partitions of an integer; the three corresponding
12160 partition functions are also given.")
12161 ;; Any version of the GPL
12162 (license license:gpl2+)))
12164 (define-public r-brobdingnag
12166 (name "r-brobdingnag")
12171 (uri (cran-uri "Brobdingnag" version))
12174 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12175 (properties `((upstream-name . "Brobdingnag")))
12176 (build-system r-build-system)
12177 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12178 (synopsis "Very large numbers in R")
12180 "This package handles very large numbers in R. Real numbers are held
12181 using their natural logarithms, plus a logical flag indicating sign. The
12182 package includes a vignette that gives a step-by-step introduction to using S4
12184 ;; Any version of the GPL
12185 (license license:gpl2+)))
12187 (define-public r-untb
12194 (uri (cran-uri "untb" version))
12197 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12198 (build-system r-build-system)
12200 `(("r-brobdingnag" ,r-brobdingnag)
12201 ("r-partitions" ,r-partitions)
12202 ("r-polynom" ,r-polynom)))
12203 (home-page "https://github.com/RobinHankin/untb.git")
12204 (synopsis "Ecological drift under the UNTB")
12206 "This package provides numerical simulations, and visualizations, of
12207 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12208 (license license:gpl2+)))
12210 (define-public r-stepwise
12212 (name "r-stepwise")
12217 (uri (cran-uri "stepwise" version))
12220 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12221 (build-system r-build-system)
12222 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12223 (synopsis "Stepwise detection of recombination breakpoints")
12225 "This package provides a stepwise approach to identifying recombination
12226 breakpoints in a genomic sequence alignment.")
12227 (license license:gpl2+)))
12229 (define-public r-snpmaxsel
12231 (name "r-snpmaxsel")
12236 (uri (cran-uri "SNPmaxsel" version))
12239 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12240 (properties `((upstream-name . "SNPmaxsel")))
12241 (build-system r-build-system)
12243 `(("r-combinat" ,r-combinat)
12244 ("r-mvtnorm" ,r-mvtnorm)))
12245 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12246 (synopsis "Maximally selected statistics for SNP data")
12248 "This package implements asymptotic methods related to maximally selected
12249 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12251 (license license:gpl2+)))
12253 (define-public r-acsnminer
12255 (name "r-acsnminer")
12256 (version "0.16.8.25")
12259 (uri (cran-uri "ACSNMineR" version))
12262 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12263 (properties `((upstream-name . "ACSNMineR")))
12264 (build-system r-build-system)
12266 `(("r-ggplot2" ,r-ggplot2)
12267 ("r-gridextra" ,r-gridextra)))
12268 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12269 (synopsis "Gene enrichment analysis")
12271 "This package provides tools to compute and represent gene set enrichment
12272 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12273 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12274 enrichment can be run with hypergeometric test or Fisher exact test, and can
12275 use multiple corrections. Visualization of data can be done either by
12276 barplots or heatmaps.")
12277 (license license:gpl2+)))
12279 (define-public r-seqinr
12286 (uri (cran-uri "seqinr" version))
12289 "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
12290 (build-system r-build-system)
12292 `(("r-ade4" ,r-ade4)
12293 ("r-segmented" ,r-segmented)))
12296 (home-page "http://seqinr.r-forge.r-project.org/")
12297 (synopsis "Biological sequences retrieval and analysis")
12299 "This package provides tools for exploratory data analysis and data
12300 visualization of biological sequence (DNA and protein) data. It also includes
12301 utilities for sequence data management under the ACNUC system.")
12302 (license license:gpl2+)))
12304 (define-public r-units
12311 (uri (cran-uri "units" version))
12314 "0kx640h60s3zzkdr302asap7diap6vri6d41scnx507yvkcqiph3"))))
12315 (build-system r-build-system)
12317 `(("udunits" ,udunits)))
12319 `(("r-rcpp" ,r-rcpp)))
12320 (home-page "https://github.com/r-quantities/units/")
12321 (synopsis "Measurement Units for R Vectors")
12323 "This package provides support for measurement units in R vectors,
12324 matrices and arrays: automatic propagation, conversion, derivation and
12325 simplification of units; raising errors in case of unit incompatibility. It
12326 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12328 (license license:gpl2)))
12330 (define-public r-classint
12332 (name "r-classint")
12337 (uri (cran-uri "classInt" version))
12340 "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9"))))
12341 (properties `((upstream-name . "classInt")))
12342 (build-system r-build-system)
12344 `(("r-class" ,r-class)
12345 ("r-e1071" ,r-e1071)
12346 ("r-kernsmooth" ,r-kernsmooth)))
12347 (native-inputs `(("gfortran" ,gfortran)))
12348 (home-page "https://github.com/r-spatial/classInt/")
12349 (synopsis "Choose univariate class intervals")
12351 "This package provides selected commonly used methods for choosing
12352 univariate class intervals for mapping or other graphics purposes.")
12353 (license license:gpl2+)))
12355 (define-public r-spdata
12362 (uri (cran-uri "spData" version))
12365 "162cqb331ki43jx4r8lpkjpn2l712figd896rnawg9j1jmjyl96y"))))
12366 (properties `((upstream-name . "spData")))
12367 (build-system r-build-system)
12368 (home-page "https://github.com/Nowosad/spData")
12369 (synopsis "Datasets for spatial analysis")
12371 "This a package containing diverse spatial datasets for demonstrating,
12372 benchmarking and teaching spatial data analysis. It includes R data of class
12373 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
12374 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
12375 of the datasets are designed to illustrate specific analysis techniques.
12376 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
12377 illustrate point pattern analysis techniques.")
12378 (license license:cc0)))
12380 (define-public r-learnbayes
12382 (name "r-learnbayes")
12387 (uri (cran-uri "LearnBayes" version))
12390 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
12391 (properties `((upstream-name . "LearnBayes")))
12392 (build-system r-build-system)
12393 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
12394 (synopsis "Functions for learning Bayesian inference")
12396 "This package provides a collection of functions helpful in learning the
12397 basic tenets of Bayesian statistical inference. It contains functions for
12398 summarizing basic one and two parameter posterior distributions and predictive
12399 distributions. It contains MCMC algorithms for summarizing posterior
12400 distributions defined by the user. It also contains functions for regression
12401 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
12403 (license license:gpl2+)))
12405 (define-public r-deldir
12412 (uri (cran-uri "deldir" version))
12415 "0549kj0hlkdyvm5axsm3np30wg53fm2pxybijzw0avlgsd2y2n2q"))))
12416 (build-system r-build-system)
12417 (native-inputs `(("gfortran" ,gfortran)))
12418 (home-page "https://cran.r-project.org/web/packages/deldir")
12419 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
12421 "This package provides tools for calculating the Delaunay triangulation
12422 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
12423 of a planar point set. It plots triangulations and tessellations in various
12424 ways, clips tessellations to sub-windows, calculates perimeters of
12425 tessellations, and summarizes information about the tiles of the
12427 (license license:gpl2+)))
12429 (define-public r-sf
12436 (uri (cran-uri "sf" version))
12439 "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1"))))
12440 (build-system r-build-system)
12447 `(("r-classint" ,r-classint)
12449 ("r-magrittr" ,r-magrittr)
12451 ("r-units" ,r-units)))
12452 (native-inputs `(("pkg-config" ,pkg-config)))
12453 (home-page "https://github.com/r-spatial/sf/")
12454 (synopsis "Simple features for R")
12456 "This package provides support for simple features, a standardized way to
12457 encode spatial vector data. It binds to GDAL for reading and writing data, to
12458 GEOS for geometrical operations, and to PROJ for projection conversions and
12459 datum transformations.")
12460 ;; Either of these licenses
12461 (license (list license:gpl2 license:expat))))
12463 (define-public r-spdep
12470 (uri (cran-uri "spdep" version))
12473 "06mk81kc1ml2wjc8wwwgr0wasjcr4mwrxpfa8vfc373bmnha635s"))))
12474 (build-system r-build-system)
12476 `(("r-boot" ,r-boot)
12478 ("r-deldir" ,r-deldir)
12480 ("r-gmodels" ,r-gmodels)
12481 ("r-learnbayes" ,r-learnbayes)
12483 ("r-matrix" ,r-matrix)
12487 ("r-spdata" ,r-spdata)))
12488 (home-page "https://github.com/r-spatial/spdep/")
12489 (synopsis "Spatial dependence: weighting schemes, statistics and models")
12491 "This package provides a collection of functions to create spatial
12492 weights matrix objects from polygon contiguities, from point patterns by
12493 distance and tessellations, for summarizing these objects, and for permitting
12494 their use in spatial data analysis, including regional aggregation by minimum
12496 (license license:gpl2+)))
12498 (define-public r-adegenet
12500 (name "r-adegenet")
12505 (uri (cran-uri "adegenet" version))
12508 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
12509 (build-system r-build-system)
12511 `(("r-ade4" ,r-ade4)
12514 ("r-dplyr" ,r-dplyr)
12515 ("r-ggplot2" ,r-ggplot2)
12516 ("r-igraph" ,r-igraph)
12518 ("r-reshape2" ,r-reshape2)
12519 ("r-seqinr" ,r-seqinr)
12520 ("r-shiny" ,r-shiny)
12521 ("r-spdep" ,r-spdep)
12522 ("r-vegan" ,r-vegan)))
12523 (home-page "https://github.com/thibautjombart/adegenet")
12524 (synopsis "Exploratory analysis of genetic and genomic data")
12526 "This package provides a toolset for the exploration of genetic and
12527 genomic data. Adegenet provides formal (S4) classes for storing and handling
12528 various genetic data, including genetic markers with varying ploidy and
12529 hierarchical population structure (@code{genind} class), alleles counts by
12530 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
12531 also implements original multivariate methods (DAPC, sPCA), graphics,
12532 statistical tests, simulation tools, distance and similarity measures, and
12533 several spatial methods. A range of both empirical and simulated datasets is
12534 also provided to illustrate various methods.")
12535 (license license:gpl2+)))
12537 (define-public r-pegas
12544 (uri (cran-uri "pegas" version))
12547 "0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx"))))
12548 (build-system r-build-system)
12550 `(("r-adegenet" ,r-adegenet)
12552 (home-page "http://ape-package.ird.fr/pegas.html")
12553 (synopsis "Population and evolutionary genetics analysis system")
12555 "This package provides functions for reading, writing, plotting,
12556 analysing, and manipulating allelic and haplotypic data, including from VCF
12557 files, and for the analysis of population nucleotide sequences and
12558 micro-satellites including coalescent analyses, linkage disequilibrium,
12559 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
12560 minimum spanning tree and network, and median-joining networks.")
12561 (license license:gpl2+)))
12563 (define-public r-rmetasim
12565 (name "r-rmetasim")
12570 (uri (cran-uri "rmetasim" version))
12573 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
12574 (build-system r-build-system)
12576 `(("r-ade4" ,r-ade4)
12577 ("r-adegenet" ,r-adegenet)
12578 ("r-gtools" ,r-gtools)
12579 ("r-pegas" ,r-pegas)))
12580 (home-page "https://cran.r-project.org/web/packages/rmetasim")
12581 (synopsis "Individual-based population genetic simulation environment")
12583 "This package provides an interface between R and the metasim simulation
12584 engine. The simulation environment is documented in: Strand, A.(2002),
12585 Metasim 1.0: an individual-based environment for simulating population
12586 genetics of complex population dynamics.")
12588 (license license:gpl2+)))
12590 (define-public r-genetics
12592 (name "r-genetics")
12593 (version "1.3.8.1.2")
12597 (uri (cran-uri "genetics" version))
12600 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
12601 (build-system r-build-system)
12603 `(("r-combinat" ,r-combinat)
12604 ("r-gdata" ,r-gdata)
12605 ("r-gtools" ,r-gtools)
12607 ("r-mvtnorm" ,r-mvtnorm)))
12608 (home-page "https://cran.r-project.org/web/packages/genetics/")
12609 (synopsis "Population genetics")
12611 "This package provides classes and methods for handling genetic data.
12612 It includes classes to represent genotypes and haplotypes at single markers up
12613 to multiple markers on multiple chromosomes. Function include allele
12614 frequencies, flagging homo/heterozygotes, flagging carriers of certain
12615 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
12616 and testing for linkage disequilibrium, ...")
12617 ;; Any GPL version.
12618 (license license:gpl2+)))
12620 (define-public r-snp-plotter
12622 (name "r-snp-plotter")
12627 (uri (cran-uri "snp.plotter" version))
12630 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
12631 (properties `((upstream-name . "snp.plotter")))
12632 (build-system r-build-system)
12633 (propagated-inputs `(("r-genetics" ,r-genetics)))
12634 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
12635 (synopsis "Plot p-values using single SNP and/or haplotype data")
12637 "This package helps you create plots of p-values using single SNP and/or
12638 haplotype data. Main features of the package include options to display a
12639 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
12640 datasets simultaneously. Plots can be created using global and/or individual
12641 haplotype p-values along with single SNP p-values. Images are created as
12642 either PDF/EPS files.")
12643 (license license:gpl2+)))
12645 (define-public r-polspline
12647 (name "r-polspline")
12652 (uri (cran-uri "polspline" version))
12655 "0g4s5nwi13yfs6b169yw8vrs48nvjyc014k2v7ybcxarl8z81va0"))))
12656 (build-system r-build-system)
12657 (native-inputs `(("gfortran" ,gfortran)))
12658 (home-page "https://cran.r-project.org/web/packages/polspline/")
12659 (synopsis "Polynomial spline routines")
12661 "This package provides routines for the polynomial spline fitting
12662 routines hazard regression, hazard estimation with flexible tails, logspline,
12663 lspec, polyclass, and polymars.")
12664 (license license:gpl2+)))
12666 (define-public r-rms
12669 (version "5.1-3.1")
12673 (uri (cran-uri "rms" version))
12676 "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9"))))
12677 (build-system r-build-system)
12679 `(("r-ggplot2" ,r-ggplot2)
12680 ("r-hmisc" ,r-hmisc)
12681 ("r-htmltable" ,r-htmltable)
12682 ("r-htmltools" ,r-htmltools)
12683 ("r-lattice" ,r-lattice)
12684 ("r-multcomp" ,r-multcomp)
12686 ("r-polspline" ,r-polspline)
12687 ("r-quantreg" ,r-quantreg)
12688 ("r-rpart" ,r-rpart)
12689 ("r-sparsem" ,r-sparsem)
12690 ("r-survival" ,r-survival)))
12691 (native-inputs `(("gfortran" ,gfortran)))
12692 (home-page "http://biostat.mc.vanderbilt.edu/rms")
12693 (synopsis "Regression modeling strategies")
12695 "This is a package for regression modeling, testing, estimation,
12696 validation, graphics, prediction, and typesetting by storing enhanced model
12697 design attributes in the fit. The rms package is a collection of functions
12698 that assist with and streamline modeling. It also contains functions for
12699 binary and ordinal logistic regression models, ordinal models for continuous Y
12700 with a variety of distribution families, and the Buckley-James multiple
12701 regression model for right-censored responses, and implements penalized
12702 maximum likelihood estimation for logistic and ordinary linear models. The
12703 package works with almost any regression model, but it was especially written
12704 to work with binary or ordinal regression models, Cox regression, accelerated
12705 failure time models, ordinary linear models, the Buckley-James model,
12706 generalized least squares for serially or spatially correlated observations,
12707 generalized linear models, and quantile regression.")
12708 (license license:gpl2+)))
12710 (define-public r-haplo-stats
12712 (name "r-haplo-stats")
12717 (uri (cran-uri "haplo.stats" version))
12720 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
12721 (properties `((upstream-name . "haplo.stats")))
12722 (build-system r-build-system)
12724 `(("r-rms" ,r-rms)))
12726 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
12727 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
12728 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
12730 "This package provides routines for the analysis of indirectly measured
12731 haplotypes. The statistical methods assume that all subjects are unrelated
12732 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
12733 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
12734 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
12735 examples in the vignette.")
12736 (license license:gpl2+)))
12738 (define-public r-bqtl
12745 (uri (cran-uri "bqtl" version))
12748 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
12749 (build-system r-build-system)
12750 (native-inputs `(("gfortran" ,gfortran)))
12751 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
12752 (synopsis "Bayesian QTL mapping toolkit")
12754 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
12755 lines. It includes maximum likelihood and Bayesian tools.")
12756 (license license:gpl2+)))
12758 (define-public r-ibdreg
12765 (uri (cran-uri "ibdreg" version))
12768 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
12769 (build-system r-build-system)
12770 (home-page "https://www.mayo.edu/research/labs/\
12771 statistical-genetics-genetic-epidemiology/software")
12772 (synopsis "Regression methods for IBD linkage with covariates")
12774 "This package provides a method to test genetic linkage with covariates
12775 by regression methods with response IBD sharing for relative pairs. Account
12776 for correlations of IBD statistics and covariates for relative pairs within
12777 the same pedigree.")
12778 (license license:gpl2+)))
12780 (define-public r-dlmap
12787 (uri (cran-uri "dlmap" version))
12790 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
12791 (build-system r-build-system)
12793 `(("r-ibdreg" ,r-ibdreg)
12797 ("r-wgaim" ,r-wgaim)))
12798 (home-page "https://cran.r-project.org/web/packages/dlmap/")
12799 (synopsis "Detection localization mapping for QTL")
12801 "This is package for QTL mapping in a mixed model framework with separate
12802 detection and localization stages. The first stage detects the number of QTL
12803 on each chromosome based on the genetic variation due to grouped markers on
12804 the chromosome; the second stage uses this information to determine the most
12805 likely QTL positions. The mixed model can accommodate general fixed and
12806 random effects, including spatial effects in field trials and pedigree
12807 effects. It is applicable to backcrosses, doubled haploids, recombinant
12808 inbred lines, F2 intercrosses, and association mapping populations.")
12809 (license license:gpl2)))
12811 (define-public r-ldheatmap
12813 (name "r-ldheatmap")
12818 (uri (cran-uri "LDheatmap" version))
12821 "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s"))))
12822 (properties `((upstream-name . "LDheatmap")))
12823 (build-system r-build-system)
12825 `(("r-genetics" ,r-genetics)
12826 ("r-snpstats" ,r-snpstats)))
12827 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
12828 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
12830 "This package provides tools to produce a graphical display, as a heat
12831 map, of measures of pairwise linkage disequilibria between SNPs. Users may
12832 optionally include the physical locations or genetic map distances of each SNP
12834 (license license:gpl3)))
12836 (define-public r-hwde
12843 (uri (cran-uri "hwde" version))
12846 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
12847 (build-system r-build-system)
12848 (home-page "https://cran.r-project.org/web/packages/hwde/")
12849 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
12851 "This package fits models for genotypic disequilibria, as described in
12852 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
12853 terms are available that account for first order interactions between loci.
12854 It also implements, for a single locus in a single population, a conditional
12855 exact test for Hardy-Weinberg equilibrium.")
12856 (license license:gpl2+)))
12858 (define-public r-tdthap
12865 (uri (cran-uri "tdthap" version))
12868 "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r"))))
12869 (build-system r-build-system)
12870 (home-page "https://cran.r-project.org/web/packages/tdthap/")
12871 (synopsis "TDT tests for extended haplotypes")
12873 "Functions and examples are provided for transmission/disequilibrium
12874 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
12875 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
12876 (license license:artistic2.0)))
12878 (define-public r-sparql
12884 (uri (cran-uri "SPARQL" version))
12887 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
12888 (properties `((upstream-name . "SPARQL")))
12889 (build-system r-build-system)
12891 `(("r-rcurl" ,r-rcurl)
12893 (home-page "https://cran.r-project.org/web/packages/SPARQL")
12894 (synopsis "SPARQL client for R")
12895 (description "This package provides an interface to use SPARQL to pose
12896 SELECT or UPDATE queries to an end-point.")
12897 ;; The only license indication is found in the DESCRIPTION file,
12898 ;; which states GPL-3. So we cannot assume GPLv3+.
12899 (license license:gpl3)))
12901 (define-public r-bookdown
12903 (name "r-bookdown")
12907 (uri (cran-uri "bookdown" version))
12910 "0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r"))))
12911 (build-system r-build-system)
12913 `(("r-htmltools" ,r-htmltools)
12914 ("r-knitr" ,r-knitr)
12915 ("r-rmarkdown" ,r-rmarkdown)
12916 ("r-tinytex" ,r-tinytex)
12918 ("pandoc" ,ghc-pandoc)))
12919 (home-page "https://github.com/rstudio/bookdown")
12920 (synopsis "Authoring books and technical documents with R markdown")
12921 (description "This package provides output formats and utilities for
12922 authoring books and technical documents with R Markdown.")
12923 (license license:gpl3)))
12925 (define-public r-optparse
12927 (name "r-optparse")
12932 (uri (cran-uri "optparse" version))
12935 "0zrp6jakjhawrwfri270ym83vj5a7nvjk0w6b41z41ahw2da99dm"))))
12936 (build-system r-build-system)
12938 `(("r-getopt" ,r-getopt)))
12939 (home-page "https://github.com/trevorld/optparse")
12940 (synopsis "Command line option parser")
12942 "This package provides a command line parser inspired by Python's
12943 @code{optparse} library to be used with Rscript to write shebang scripts
12944 that accept short and long options.")
12945 (license license:gpl2+)))
12947 (define-public r-wgcna
12954 (uri (cran-uri "WGCNA" version))
12957 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
12958 (properties `((upstream-name . "WGCNA")))
12959 (build-system r-build-system)
12961 `(("r-annotationdbi" ,r-annotationdbi)
12962 ("r-doparallel" ,r-doparallel)
12963 ("r-dynamictreecut" ,r-dynamictreecut)
12964 ("r-fastcluster" ,r-fastcluster)
12965 ("r-foreach" ,r-foreach)
12966 ("r-go-db" ,r-go-db)
12967 ("r-hmisc" ,r-hmisc)
12968 ("r-impute" ,r-impute)
12970 ("r-robust" ,r-robust)
12971 ("r-survival" ,r-survival)
12972 ("r-matrixstats" ,r-matrixstats)
12973 ("r-preprocesscore" ,r-preprocesscore)))
12975 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
12976 (synopsis "Weighted correlation network analysis")
12978 "This package provides functions necessary to perform Weighted
12979 Correlation Network Analysis on high-dimensional data. It includes functions
12980 for rudimentary data cleaning, construction and summarization of correlation
12981 networks, module identification and functions for relating both variables and
12982 modules to sample traits. It also includes a number of utility functions for
12983 data manipulation and visualization.")
12984 (license license:gpl2+)))
12986 (define-public r-kernlab
12993 (uri (cran-uri "kernlab" version))
12996 "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
12997 (build-system r-build-system)
12998 (home-page "https://cran.r-project.org/web/packages/kernlab")
12999 (synopsis "Kernel-based machine learning tools")
13001 "This package provides kernel-based machine learning methods for
13002 classification, regression, clustering, novelty detection, quantile regression
13003 and dimensionality reduction. Among other methods @code{kernlab} includes
13004 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13006 (license license:gpl2)))
13008 (define-public r-hierfstat
13010 (name "r-hierfstat")
13011 (version "0.04-22")
13015 (uri (cran-uri "hierfstat" version))
13018 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13019 (build-system r-build-system)
13021 `(("r-ade4" ,r-ade4)
13022 ("r-adegenet" ,r-adegenet)
13023 ("r-gtools" ,r-gtools)))
13024 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13025 (synopsis "Estimation and tests of hierarchical F-statistics")
13027 "This package allows the estimation of hierarchical F-statistics from
13028 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13029 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13030 are also given to test via randomisations the significance of each F and
13031 variance components, using the likelihood-ratio statistics G.")
13032 (license license:gpl2+)))
13034 (define-public r-hapassoc
13036 (name "r-hapassoc")
13041 (uri (cran-uri "hapassoc" version))
13044 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13045 (build-system r-build-system)
13046 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13047 (synopsis "Inference of trait associations with SNP haplotypes")
13049 "Hapassoc performs likelihood inference of trait associations with
13050 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13051 functions are developed primarily for data collected in cohort or
13052 cross-sectional studies. They can accommodate uncertain haplotype phase and
13053 handle missing genotypes at some SNPs.")
13054 (license license:gpl2)))
13056 (define-public r-sampling
13058 (name "r-sampling")
13063 (uri (cran-uri "sampling" version))
13066 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13067 (build-system r-build-system)
13069 `(("r-lpsolve" ,r-lpsolve)
13070 ("r-mass" ,r-mass)))
13071 (home-page "https://cran.r-project.org/web/packages/sampling/")
13072 (synopsis "Survey sampling")
13074 "This package provides functions for drawing and calibrating samples.")
13075 (license license:gpl2+)))
13077 (define-public r-r2html
13084 (uri (cran-uri "R2HTML" version))
13087 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13088 (properties `((upstream-name . "R2HTML")))
13089 (build-system r-build-system)
13090 (home-page "https://github.com/nalimilan/R2HTML")
13091 (synopsis "HTML export for R objects")
13093 "This package includes HTML functions and methods to write in an HTML
13094 file. Thus, making HTML reports is easy. It includes a function that allows
13095 redirection on the fly, which appears to be very useful for teaching purposes,
13096 as the student can keep a copy of the produced output to keep all that they
13097 did during the course. The package comes with a vignette describing how to
13098 write HTML reports for statistical analysis. Finally, a driver for Sweave
13099 allows to parse HTML flat files containing R code and to automatically write
13100 the corresponding outputs (tables and graphs).")
13101 (license license:gpl2+)))
13103 (define-public r-rjava
13110 (uri (cran-uri "rJava" version))
13113 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13114 (properties `((upstream-name . "rJava")))
13115 (build-system r-build-system)
13117 `(#:modules ((guix build utils)
13118 (guix build r-build-system)
13121 (modify-phases %standard-phases
13122 (add-after 'unpack 'set-JAVA_HOME
13123 (lambda* (#:key inputs #:allow-other-keys)
13124 (let ((jdk (assoc-ref inputs "jdk")))
13125 (setenv "JAVA_HOME" jdk)
13126 (setenv "JAVA" (which "java"))
13127 (setenv "JAR" (which "jar"))
13128 (setenv "JAVAC" (which "javac"))
13129 (setenv "JAVAH" (which "javah"))
13130 (setenv "JAVA_CPPFLAGS"
13131 (string-append "-I" jdk "/include "
13132 "-I" jdk "/include/linux"))
13133 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13134 ((lib) (setenv "JAVA_LIBS" lib))
13135 (_ (error "Could not find libjvm.so"))))
13139 ("jdk" ,icedtea-8 "jdk")
13142 (home-page "http://www.rforge.net/rJava/")
13143 (synopsis "Low-Level R to Java interface")
13145 "This package provides a low-level interface to the Java VM very much
13146 like .C/.Call and friends. It allows the creation of objects, calling methods
13147 and accessing fields.")
13148 (license license:gpl2)))
13150 (define-public r-svmisc
13157 (uri (cran-uri "svMisc" version))
13160 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13161 (properties `((upstream-name . "svMisc")))
13162 (build-system r-build-system)
13163 (home-page "https://github.com/SciViews/svMisc")
13164 (synopsis "Miscellaneous functions for SciViews")
13166 "This package provides miscellaneous functions for SciViews or general
13167 use, including tools to manage a temporary environment attached to the search
13168 path for temporary variables you do not want to @code{save()} or
13169 @code{load()}; test the current platform; showing progress bars, etc.")
13170 (license license:gpl2)))
13172 (define-public r-xyz
13179 (uri (cran-uri "xyz" version))
13182 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13183 (build-system r-build-system)
13185 `(("r-rcpp" ,r-rcpp)))
13186 (home-page "https://cran.r-project.org/web/packages/xyz/")
13187 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13189 "High dimensional interaction search by brute force requires a quadratic
13190 computational cost in the number of variables. The xyz algorithm provably
13191 finds strong interactions in almost linear time. For details of the algorithm
13192 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13193 interaction search in high-dimensional data.")
13194 ;; Any version of the GPL.
13195 (license license:gpl2+)))
13197 (define-public r-rttf2pt1
13199 (name "r-rttf2pt1")
13204 (uri (cran-uri "Rttf2pt1" version))
13207 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13208 (properties `((upstream-name . "Rttf2pt1")))
13209 (build-system r-build-system)
13210 (home-page "https://github.com/wch/Rttf2pt1")
13211 (synopsis "Font conversion utility")
13213 "This package contains the program @code{ttf2pt1}, for use with the
13214 @code{extrafont} package.")
13215 ;; Most of the files are covered under the Expat license. Some files are
13216 ;; covered under BSD-3. Deviations for individual files are recorded in
13217 ;; the LICENSE file.
13218 (license (list license:bsd-3 license:expat
13219 (license:non-copyleft "file://LICENSE")))))
13221 (define-public r-extrafontdb
13223 (name "r-extrafontdb")
13228 (uri (cran-uri "extrafontdb" version))
13231 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13232 (build-system r-build-system)
13233 (home-page "https://github.com/wch/extrafontdb")
13234 (synopsis "Database for the extrafont package")
13236 "This package holds the database for the @code{extrafont} package.")
13237 (license license:gpl2)))
13239 (define-public r-extrafont
13241 (name "r-extrafont")
13246 (uri (cran-uri "extrafont" version))
13249 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13250 (build-system r-build-system)
13252 `(("r-extrafontdb" ,r-extrafontdb)
13253 ("r-rttf2pt1" ,r-rttf2pt1)))
13254 (home-page "https://github.com/wch/extrafont")
13255 (synopsis "Tools for using fonts in R")
13257 "The extrafont package makes it easier to use fonts other than the basic
13258 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13259 used with PDF or PostScript output files. There are two hurdles for using
13260 fonts in PDF (or Postscript) output files:
13263 @item Making R aware of the font and the dimensions of the characters.
13264 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13265 properly on a device that doesn't have the font. This is usually needed if
13266 you want to print the PDF file or share it with others.
13269 The extrafont package makes both of these things easier.")
13270 (license license:gpl2)))
13272 (define-public r-xkcd
13279 (uri (cran-uri "xkcd" version))
13282 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13283 (build-system r-build-system)
13285 `(("r-extrafont" ,r-extrafont)
13286 ("r-ggplot2" ,r-ggplot2)
13287 ("r-hmisc" ,r-hmisc)))
13288 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13289 (synopsis "Plot ggplot2 graphics in the XKCD style")
13291 "This package provides the means to plot ggplot2 graphs in the style of
13292 the XKCD web comic.")
13293 (license license:gpl3)))
13295 (define-public r-msigdbr
13302 (uri (cran-uri "msigdbr" version))
13305 "1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg"))))
13306 (build-system r-build-system)
13308 `(("r-dplyr" ,r-dplyr)
13309 ("r-magrittr" ,r-magrittr)
13310 ("r-rlang" ,r-rlang)
13311 ("r-tibble" ,r-tibble)))
13312 (home-page "https://github.com/igordot/msigdbr")
13313 (synopsis "MSigDB gene sets for multiple organisms")
13315 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13316 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13317 software in a standard R data frame with key-value pairs. Included are the
13318 original human gene symbols and Entrez IDs as well as the equivalents for
13319 various frequently studied model organisms such as mouse, rat, pig, fly, and
13321 ;; The package is covered under the Expat license, but the upstream MSigDB
13322 ;; files are made available under the Creative Commons Attribution 4.0
13323 ;; International license.
13324 (license (list license:expat license:cc-by4.0))))
13326 (define-public r-gridgraphics
13328 (name "r-gridgraphics")
13333 (uri (cran-uri "gridGraphics" version))
13336 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13337 (properties `((upstream-name . "gridGraphics")))
13338 (build-system r-build-system)
13339 (home-page "https://github.com/pmur002/gridgraphics")
13340 (synopsis "Redraw base graphics using @code{grid} graphics")
13342 "This package provides functions to convert a page of plots drawn with
13343 the @code{graphics} package into identical output drawn with the @code{grid}
13344 package. The result looks like the original @code{graphics}-based plot, but
13345 consists of @code{grid} grobs and viewports that can then be manipulated with
13346 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13347 (license license:gpl2+)))
13349 (define-public r-farver
13356 (uri (cran-uri "farver" version))
13359 "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0"))))
13360 (build-system r-build-system)
13361 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13362 (home-page "https://github.com/thomasp85/farver")
13363 (synopsis "Vectorized color conversion and comparison")
13365 "The encoding of color can be handled in many different ways, using
13366 different color spaces. As different color spaces have different uses,
13367 efficient conversion between these representations are important. This
13368 package provides a set of functions that gives access to very fast color space
13369 conversion and comparisons implemented in C++, and offers 100-fold speed
13370 improvements over the @code{convertColor} function in the @code{grDevices}
13372 (license license:expat)))
13374 (define-public r-ggplotify
13376 (name "r-ggplotify")
13381 (uri (cran-uri "ggplotify" version))
13384 "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby"))))
13385 (build-system r-build-system)
13387 `(("r-ggplot2" ,r-ggplot2)
13388 ("r-gridgraphics" ,r-gridgraphics)
13389 ("r-rvcheck" ,r-rvcheck)))
13390 (home-page "https://github.com/GuangchuangYu/ggplotify")
13391 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
13393 "This package provides tools to convert plot function calls (using
13394 expression or formula) to @code{grob} or @code{ggplot} objects that are
13395 compatible with the @code{grid} and @code{ggplot2} environment. With this
13396 package, we are able to e.g. use @code{cowplot} to align plots produced by
13397 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
13398 converting them to @code{ggplot} objects.")
13399 (license license:artistic2.0)))
13401 (define-public r-triebeard
13403 (name "r-triebeard")
13408 (uri (cran-uri "triebeard" version))
13411 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
13412 (build-system r-build-system)
13413 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13414 (home-page "https://github.com/Ironholds/triebeard/")
13415 (synopsis "Radix trees in Rcpp")
13417 "Radix trees, or tries, are key-value data structures optimized for
13418 efficient lookups, similar in purpose to hash tables. This package provides
13419 an implementation of radix trees for use in R programming and in developing
13420 packages with Rcpp.")
13421 (license license:expat)))
13423 (define-public r-tweenr
13430 (uri (cran-uri "tweenr" version))
13433 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
13434 (build-system r-build-system)
13436 `(("r-farver" ,r-farver)
13437 ("r-magrittr" ,r-magrittr)
13439 ("r-rlang" ,r-rlang)))
13440 (home-page "https://github.com/thomasp85/tweenr")
13441 (synopsis "Interpolate data for smooth animations")
13443 "In order to create smooth animation between states of data, tweening is
13444 necessary. This package provides a range of functions for creating tweened
13445 data that can be used as basis for animation. Furthermore it adds a number of
13446 vectorized interpolaters for common R data types such as numeric, date and
13448 (license license:expat)))
13450 (define-public r-polyclip
13452 (name "r-polyclip")
13457 (uri (cran-uri "polyclip" version))
13460 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
13461 (build-system r-build-system)
13462 (native-inputs `(("pkg-config" ,pkg-config)))
13463 (home-page "http://www.angusj.com/delphi/clipper.php")
13464 (synopsis "Polygon clipping")
13466 "This package provides an R port of the library Clipper. It performs
13467 polygon clipping operations (intersection, union, set minus, set difference)
13468 for polygonal regions of arbitrary complexity, including holes. It computes
13469 offset polygons (spatial buffer zones, morphological dilations, Minkowski
13470 dilations) for polygonal regions and polygonal lines. It computes the
13471 Minkowski Sum of general polygons. There is a function for removing
13472 self-intersections from polygon data.")
13473 (license license:boost1.0)))
13475 (define-public r-urltools
13477 (name "r-urltools")
13482 (uri (cran-uri "urltools" version))
13485 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
13486 (build-system r-build-system)
13488 `(("r-rcpp" ,r-rcpp)
13489 ("r-triebeard" ,r-triebeard)))
13490 (home-page "https://github.com/Ironholds/urltools/")
13491 (synopsis "Vectorized tools for URL handling and parsing")
13493 "This package provides a toolkit for all URL-handling needs, including
13494 encoding and decoding, parsing, parameter extraction and modification. All
13495 functions are designed to be both fast and entirely vectorized. It is
13496 intended to be useful for people dealing with web-related datasets, such as
13497 server-side logs, although may be useful for other situations involving large
13499 (license license:expat)))
13501 (define-public r-ggforce
13508 (uri (cran-uri "ggforce" version))
13511 "0snxx9zhcccxa7pz9pf3bjqmcmv9mz4m47v81hklnhm25jj40xg2"))))
13512 (build-system r-build-system)
13514 `(("r-ggplot2" ,r-ggplot2)
13515 ("r-gtable" ,r-gtable)
13517 ("r-polyclip" ,r-polyclip)
13519 ("r-rcppeigen" ,r-rcppeigen)
13520 ("r-rlang" ,r-rlang)
13521 ("r-scales" ,r-scales)
13522 ("r-tweenr" ,r-tweenr)))
13523 (home-page "https://ggforce.data-imaginist.com")
13524 (synopsis "Accelerating ggplot2")
13526 "The aim of the ggplot2 package is to aid in visual data investigations.
13527 This focus has led to a lack of facilities for composing specialized plots.
13528 Thi package aims to be a collection of mainly new statistics and geometries
13529 that fills this gap.")
13530 (license license:expat)))
13532 (define-public r-europepmc
13534 (name "r-europepmc")
13539 (uri (cran-uri "europepmc" version))
13542 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
13543 (build-system r-build-system)
13545 `(("r-dplyr" ,r-dplyr)
13547 ("r-jsonlite" ,r-jsonlite)
13549 ("r-progress" ,r-progress)
13550 ("r-purrr" ,r-purrr)
13551 ("r-urltools" ,r-urltools)
13552 ("r-xml2" ,r-xml2)))
13553 (home-page "https://github.com/ropensci/europepmc/")
13554 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
13556 "This package provides an R Client for the
13557 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
13558 Service}. It gives access to both metadata on life science literature and
13559 open access full texts. Europe PMC indexes all PubMed content and other
13560 literature sources including Agricola, a bibliographic database of citations
13561 to the agricultural literature, or Biological Patents. In addition to
13562 bibliographic metadata, the client allows users to fetch citations and
13563 reference lists. Links between life-science literature and other EBI
13564 databases, including ENA, PDB or ChEMBL are also accessible.")
13565 (license license:gpl3)))
13567 (define-public r-ggraph
13574 (uri (cran-uri "ggraph" version))
13577 "0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c"))))
13578 (build-system r-build-system)
13580 `(("r-digest" ,r-digest)
13581 ("r-dplyr" ,r-dplyr)
13582 ("r-ggforce" ,r-ggforce)
13583 ("r-ggplot2" ,r-ggplot2)
13584 ("r-ggrepel" ,r-ggrepel)
13585 ("r-gtable" ,r-gtable)
13586 ("r-igraph" ,r-igraph)
13590 ("r-scales" ,r-scales)
13591 ("r-viridis" ,r-viridis)))
13592 (home-page "https://cran.r-project.org/web/packages/ggraph/")
13593 (synopsis "Implementation of grammar of graphics for graphs and networks")
13595 "The grammar of graphics as implemented in ggplot2 is a poor fit for
13596 graph and network visualizations due to its reliance on tabular data input.
13597 The ggraph package is an extension of the ggplot2 API tailored to graph
13598 visualizations and provides the same flexible approach to building up plots
13600 (license license:gpl3)))
13602 (define-public r-varselrf
13604 (name "r-varselrf")
13609 (uri (cran-uri "varSelRF" version))
13612 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
13613 (properties `((upstream-name . "varSelRF")))
13614 (build-system r-build-system)
13616 `(("r-randomforest" ,r-randomforest)))
13617 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
13618 (synopsis "Variable selection using random forests")
13620 "This package provides tools for the variable selection from random
13621 forests using both backwards variable elimination (for the selection of small
13622 sets of non-redundant variables) and selection based on the importance
13623 spectrum (somewhat similar to scree plots; for the selection of large,
13624 potentially highly-correlated variables). The main applications are in
13625 high-dimensional data (e.g., microarray data, and other genomics and
13626 proteomics applications).")
13627 (license license:gpl2+)))
13629 (define-public r-pamr
13636 (uri (cran-uri "pamr" version))
13639 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
13640 (build-system r-build-system)
13642 `(("r-cluster" ,r-cluster)
13643 ("r-survival" ,r-survival)))
13644 (native-inputs `(("gfortran" ,gfortran)))
13645 (home-page "https://cran.r-project.org/web/packages/pamr/")
13646 (synopsis "Prediction Analysis for Microarrays")
13648 "This package provides some functions for sample classification in
13650 (license license:gpl2)))
13652 (define-public r-rda
13655 (version "1.0.2-2.1")
13659 (uri (cran-uri "rda" version))
13662 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
13663 (build-system r-build-system)
13664 (home-page "https://cran.r-project.org/web/packages/rda/")
13665 (synopsis "Shrunken centroids regularized discriminant analysis")
13667 "This package provides tools for shrunken centroids regularized
13668 discriminant analysis for the purpose of classifying high dimensional data.")
13669 (license license:gpl2+)))
13671 (define-public r-ggvis
13678 (uri (cran-uri "ggvis" version))
13681 "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk"))))
13682 (build-system r-build-system)
13684 `(("r-assertthat" ,r-assertthat)
13685 ("r-dplyr" ,r-dplyr)
13686 ("r-htmltools" ,r-htmltools)
13687 ("r-jsonlite" ,r-jsonlite)
13688 ("r-lazyeval" ,r-lazyeval)
13689 ("r-magrittr" ,r-magrittr)
13690 ("r-shiny" ,r-shiny)))
13691 (home-page "https://ggvis.rstudio.com/")
13692 (synopsis "Interactive grammar of graphics")
13694 "This package is a data visualization package for R providing an
13695 implementation of an interactive grammar of graphics, taking the best parts of
13696 ggplot2, combining them with the reactive framework of Shiny and drawing web
13697 graphics using Vega.")
13698 (license license:gpl2)))
13700 (define-public r-gbm
13707 (uri (cran-uri "gbm" version))
13710 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
13711 (build-system r-build-system)
13713 `(("r-gridextra" ,r-gridextra)
13714 ("r-lattice" ,r-lattice)
13715 ("r-survival" ,r-survival)))
13716 (home-page "https://github.com/gbm-developers/gbm")
13717 (synopsis "Generalized boosted regression models")
13719 "This package is an implementation of extensions to Freund and Schapire's
13720 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
13721 regression methods for least squares, absolute loss, t-distribution loss,
13722 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
13723 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
13724 and Learning to Rank measures (LambdaMart).")
13725 (license license:gpl2+)))
13727 (define-public r-threejs
13734 (uri (cran-uri "threejs" version))
13737 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
13738 (build-system r-build-system)
13740 `(#:modules ((guix build utils)
13741 (guix build r-build-system)
13745 (modify-phases %standard-phases
13746 (add-after 'unpack 'process-javascript
13747 (lambda* (#:key inputs #:allow-other-keys)
13748 (with-directory-excursion "inst"
13752 `((,(assoc-ref inputs "js-jquery")
13753 "htmlwidgets/lib/jquery/jquery.min.js")
13754 (,(assoc-ref inputs "js-threejs-85")
13755 "htmlwidgets/lib/threejs-85/three.min.js"))))
13756 (lambda (sources targets)
13757 (for-each (lambda (source target)
13758 (format #t "Processing ~a --> ~a~%"
13760 (delete-file target)
13761 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
13762 (call-with-output-file target
13764 (dump-port minified port)))))
13765 sources targets))))
13768 `(("r-base64enc" ,r-base64enc)
13769 ("r-crosstalk" ,r-crosstalk)
13770 ("r-htmlwidgets" ,r-htmlwidgets)
13771 ("r-igraph" ,r-igraph)))
13773 `(("uglify-js" ,uglify-js)
13777 (uri "https://code.jquery.com/jquery-3.3.1.js")
13780 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
13784 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
13787 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
13788 (home-page "https://bwlewis.github.io/rthreejs")
13789 (synopsis "Interactive 3D scatter plots, networks and globes")
13791 "Create interactive 3D scatter plots, network plots, and globes in R
13792 using the three.js visualization library.")
13793 (license license:expat)))
13795 (define-public r-mlbench
13802 (uri (cran-uri "mlbench" version))
13805 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
13806 (build-system r-build-system)
13807 (home-page "https://cran.r-project.org/web/packages/mlbench/")
13808 (synopsis "Machine learning benchmark problems")
13810 "This package provides a collection of artificial and real-world machine
13811 learning benchmark problems, including, e.g., several data sets from the UCI
13813 (license license:gpl2)))
13815 (define-public r-mpm
13822 (uri (cran-uri "mpm" version))
13825 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
13826 (build-system r-build-system)
13828 `(("r-kernsmooth" ,r-kernsmooth)
13829 ("r-mass" ,r-mass)))
13830 (home-page "http://mpm.r-forge.r-project.org")
13831 (synopsis "Multivariate projection methods")
13833 "This is a package for exploratory graphical analysis of multivariate
13834 data, specifically gene expression data with different projection methods:
13835 principal component analysis, correspondence analysis, spectral map
13837 (license license:gpl2+)))
13839 (define-public r-png
13845 (uri (cran-uri "png" version))
13848 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
13849 (build-system r-build-system)
13851 `(("libpng" ,libpng)
13853 (home-page "http://www.rforge.net/png/")
13854 (synopsis "Read and write PNG images")
13856 "This package provides an easy and simple way to read, write and display
13857 bitmap images stored in the PNG format. It can read and write both files and
13858 in-memory raw vectors.")
13859 ;; Any of these GPL versions.
13860 (license (list license:gpl2 license:gpl3))))
13862 (define-public r-ggcorrplot
13864 (name "r-ggcorrplot")
13869 (uri (cran-uri "ggcorrplot" version))
13872 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
13873 (build-system r-build-system)
13875 `(("r-ggplot2" ,r-ggplot2)
13876 ("r-reshape2" ,r-reshape2)))
13877 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
13878 (synopsis "Visualization of a correlation matrix using ggplot2")
13880 "The ggcorrplot package can be used to visualize easily a correlation
13881 matrix using ggplot2. It provides a solution for reordering the correlation
13882 matrix and displays the significance level on the plot. It also includes a
13883 function for computing a matrix of correlation p-values.")
13884 (license license:gpl2)))
13886 (define-public r-flexdashboard
13888 (name "r-flexdashboard")
13889 (version "0.5.1.1")
13893 (uri (cran-uri "flexdashboard" version))
13896 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
13897 (build-system r-build-system)
13899 `(#:modules ((guix build utils)
13900 (guix build r-build-system)
13904 (ice-9 textual-ports))
13906 (modify-phases %standard-phases
13907 (add-after 'unpack 'process-javascript
13908 (lambda* (#:key inputs #:allow-other-keys)
13909 (with-directory-excursion "inst"
13910 ;; Concatenate all components of prism.js
13911 (let ((contents (string-join
13912 (map (lambda (name)
13913 (call-with-input-file
13914 (assoc-ref inputs name)
13918 "js-prism-line-numbers"))
13920 (call-with-output-file "prism-src.js"
13921 (cut display contents <>)))
13925 `(("www/stickytableheaders/jquery.stickytableheaders.js"
13926 "www/stickytableheaders/jquery.stickytableheaders.min.js")
13928 "www/sly/sly.min.js")
13930 "www/prism/prism.js")
13931 (,(assoc-ref inputs "js-raphael")
13932 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
13933 (,(assoc-ref inputs "js-featherlight")
13934 "www/featherlight/featherlight.min.js"))))
13935 (lambda (sources targets)
13936 (for-each (lambda (source target)
13937 (format #t "Processing ~a --> ~a~%"
13939 (delete-file target)
13940 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
13941 (call-with-output-file target
13943 (dump-port minified port)))))
13944 sources targets))))
13947 `(("r-htmltools" ,r-htmltools)
13948 ("r-htmlwidgets" ,r-htmlwidgets)
13949 ("r-jsonlite" ,r-jsonlite)
13950 ("r-knitr" ,r-knitr)
13951 ("r-rmarkdown" ,r-rmarkdown)
13952 ("r-shiny" ,r-shiny)))
13954 `(("uglify-js" ,uglify-js)
13958 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
13961 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
13965 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
13968 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
13972 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
13975 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
13976 ("js-prism-line-numbers"
13979 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
13982 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
13986 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
13989 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
13990 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
13991 (synopsis "R Markdown format for flexible dashboards")
13993 "This package provides an R Markdown format for converting an R Markdown
13994 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
13995 of its components to the containing web page.")
13996 (license license:expat)))
13998 (define-public r-preseqr
14005 (uri (cran-uri "preseqR" version))
14008 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14009 (properties `((upstream-name . "preseqR")))
14010 (build-system r-build-system)
14012 `(("r-polynom" ,r-polynom)))
14013 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14014 (synopsis "Predicting species accumulation curves")
14016 "This package can be used to predict the r-species accumulation
14017 curve (r-SAC), which is the number of species represented at least r times as
14018 a function of the sampling effort. When r = 1, the curve is known as the
14019 species accumulation curve, or the library complexity curve in high-throughput
14020 genomic sequencing. The package includes both parametric and nonparametric
14021 methods, as described by Deng C, et al. (2018).")
14022 (license license:gpl3)))
14024 (define-public r-mapplots
14026 (name "r-mapplots")
14031 (uri (cran-uri "mapplots" version))
14034 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14035 (build-system r-build-system)
14036 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14037 (synopsis "Data visualization on maps")
14039 "This package helps you create simple maps; add sub-plots like pie plots
14040 to a map or any other plot; format, plot and export gridded data. The package
14041 was developed for displaying fisheries data but most functions can be used for
14042 more generic data visualisation.")
14043 (license license:gpl2+)))
14045 (define-public r-pmcmr
14052 (uri (cran-uri "PMCMR" version))
14055 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14056 (properties `((upstream-name . "PMCMR")))
14057 (build-system r-build-system)
14058 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14059 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14061 "This is a deprecated package for calculating pairwise multiple
14062 comparisons of mean rank sums. This package is superseded by the novel
14063 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14064 compatibility of reverse depending packages for some time.")
14065 (license license:gpl3+)))
14067 (define-public r-downloader
14069 (name "r-downloader")
14074 (uri (cran-uri "downloader" version))
14077 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14078 (build-system r-build-system)
14080 `(("r-digest" ,r-digest)))
14081 (home-page "https://github.com/wch/downloader")
14082 (synopsis "Download files over HTTP and HTTPS")
14084 "This package provides a wrapper for the @code{download.file} function,
14085 making it possible to download files over HTTPS across platforms. The
14086 @code{RCurl} package provides this functionality (and much more) but has
14087 external dependencies. This package has is implemented purely in R.")
14088 (license license:gpl2)))
14090 (define-public r-rex
14097 (uri (cran-uri "rex" version))
14100 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14101 (build-system r-build-system)
14103 `(("r-lazyeval" ,r-lazyeval)
14104 ("r-magrittr" ,r-magrittr)))
14105 (home-page "https://github.com/kevinushey/rex")
14106 (synopsis "Friendly regular expressions")
14108 "This package provides a friendly interface for the construction of
14109 regular expressions. Regular expressions are a very powerful feature, however
14110 they are often difficult to interpret. Rex allows you to build complex
14111 regular expressions from human readable expressions")
14112 (license license:expat)))
14114 (define-public r-sctransform
14116 (name "r-sctransform")
14121 (uri (cran-uri "sctransform" version))
14124 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14125 (build-system r-build-system)
14127 `(("r-future" ,r-future)
14128 ("r-future-apply" ,r-future-apply)
14129 ("r-ggplot2" ,r-ggplot2)
14130 ("r-gridextra" ,r-gridextra)
14132 ("r-matrix" ,r-matrix)
14134 ("r-rcppeigen" ,r-rcppeigen)
14135 ("r-reshape2" ,r-reshape2)))
14136 (home-page "https://github.com/ChristophH/sctransform")
14137 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14139 "This package provides a normalization method for single-cell UMI count
14140 data using a variance stabilizing transformation. The transformation is based
14141 on a negative binomial regression model with regularized parameters. As part
14142 of the same regression framework, this package also provides functions for
14143 batch correction, and data correction.")
14144 (license license:gpl3)))
14146 (define-public r-styler
14153 (uri (cran-uri "styler" version))
14156 "1k660lpjvd64gnf6bndcb1cq3qxsvik928kcn6271zmkhja5rgyb"))))
14157 (build-system r-build-system)
14159 `(("r-backports" ,r-backports)
14161 ("r-magrittr" ,r-magrittr)
14162 ("r-purrr" ,r-purrr)
14163 ("r-rematch2" ,r-rematch2)
14164 ("r-rlang" ,r-rlang)
14165 ("r-rprojroot" ,r-rprojroot)
14166 ("r-tibble" ,r-tibble)
14167 ("r-withr" ,r-withr)
14168 ("r-xfun" ,r-xfun)))
14169 (home-page "https://github.com/r-lib/styler")
14170 (synopsis "Non-invasive pretty printing of R code")
14172 "This is a package for pretty-printing R code without changing the user's
14173 formatting intent.")
14174 (license license:gpl3)))
14176 (define-public r-scrime
14183 (uri (cran-uri "scrime" version))
14186 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14187 (build-system r-build-system)
14188 (home-page "https://cran.r-project.org/web/packages/scrime/")
14189 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14191 "This package provides tools for the analysis of high-dimensional data
14192 developed/implemented at the group \"Statistical Complexity Reduction In
14193 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14194 the functions can also be applied to other types of categorical data.")
14195 (license license:gpl2)))
14197 (define-public r-blme
14204 (uri (cran-uri "blme" version))
14207 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14208 (build-system r-build-system)
14209 (propagated-inputs `(("r-lme4" ,r-lme4)))
14210 (home-page "https://github.com/vdorie/blme")
14211 (synopsis "Bayesian linear mixed-effects models")
14213 "This package provides tools for maximum a posteriori estimation for
14214 linear and generalized linear mixed-effects models in a Bayesian setting. It
14215 extends the lme4 package.")
14216 (license license:gpl2+)))
14218 (define-public r-batchtools
14220 (name "r-batchtools")
14225 (uri (cran-uri "batchtools" version))
14228 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14229 (build-system r-build-system)
14231 `(("r-backports" ,r-backports)
14232 ("r-base64url" ,r-base64url)
14234 ("r-checkmate" ,r-checkmate)
14235 ("r-data-table" ,r-data-table)
14236 ("r-digest" ,r-digest)
14238 ("r-progress" ,r-progress)
14240 ("r-rappdirs" ,r-rappdirs)
14241 ("r-stringi" ,r-stringi)
14242 ("r-withr" ,r-withr)))
14243 (home-page "https://github.com/mllg/batchtools")
14244 (synopsis "Tools for computation on batch systems")
14246 "As a successor of the packages BatchJobs and BatchExperiments, this
14247 package provides a parallel implementation of the Map function for high
14248 performance computing systems managed by various schedulers. A multicore and
14249 socket mode allow the parallelization on a local machines, and multiple
14250 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14251 the package provides an abstraction mechanism to define large-scale computer
14252 experiments in a well-organized and reproducible way.")
14253 (license license:lgpl3)))
14255 (define-public r-clue
14262 (uri (cran-uri "clue" version))
14265 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
14266 (build-system r-build-system)
14267 (propagated-inputs `(("r-cluster" ,r-cluster)))
14268 (home-page "https://cran.r-project.org/web/packages/clue/")
14269 (synopsis "Tools for analyzing cluster ensembles")
14270 (description "Cluster ensembles are collections of individual solutions to
14271 a given clustering problem which are useful or necessary to consider in a wide
14272 range of applications. This R package provides an extensible computational
14273 environment for creating and analyzing cluster ensembles, with basic data
14274 structures for representing partitions and hierarchies, and facilities for
14275 computing on them, including methods for measuring proximity and obtaining
14276 consensus and secondary clusterings.")
14277 (license license:gpl2)))
14279 (define-public r-sitmo
14286 (uri (cran-uri "sitmo" version))
14289 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
14290 (build-system r-build-system)
14291 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14292 (home-page "https://github.com/coatless/sitmo/")
14293 (synopsis "Parallel pseudo random number generator header files")
14295 "This package provides two high quality and fast PPRNGs that may be used
14296 in an OpenMP parallel environment. In addition, there is a generator for one
14297 dimensional low-discrepancy sequence.")
14298 (license license:expat)))
14300 (define-public r-dqrng
14307 (uri (cran-uri "dqrng" version))
14310 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
14311 (build-system r-build-system)
14315 ("r-sitmo" ,r-sitmo)))
14316 (home-page "https://www.daqana.org/dqrng")
14317 (synopsis "Fast pseudo random number generators")
14319 "Several fast random number generators are provided as C++ header-only
14320 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
14321 Additionally, fast functions for generating random numbers according to a
14322 uniform, normal and exponential distribution are included. The latter two use
14323 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
14324 functions are exported to R and as a C++ interface and are enabled for use
14325 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
14326 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
14327 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
14328 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
14329 ;; whole is distributed under the terms of the AGPL 3.
14330 (license license:agpl3)))
14332 (define-public r-dalex
14339 (uri (cran-uri "DALEX" version))
14342 "1mr8lqq8s4aacmh7xdhmkmv8vsjqjczlqlaw27xnsljgj2kgq87a"))))
14343 (properties `((upstream-name . "DALEX")))
14344 (build-system r-build-system)
14345 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
14346 (home-page "https://pbiecek.github.io/DALEX/")
14347 (synopsis "Descriptive machine learning explanations")
14349 "Machine Learning models are widely used and have various applications in
14350 classification or regression. Models created with boosting, bagging, stacking
14351 or similar techniques are often used due to their high performance, but such
14352 black-box models usually lack interpretability. The DALEX package contains
14353 various explainers that help to understand the link between input variables
14354 and model output.")
14355 ;; Any version of the GPL
14356 (license license:gpl3+)))
14358 (define-public r-enrichr
14365 (uri (cran-uri "enrichR" version))
14368 "0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn"))))
14369 (properties `((upstream-name . "enrichR")))
14370 (build-system r-build-system)
14372 `(("r-httr" ,r-httr)
14373 ("r-rjson" ,r-rjson)))
14374 (home-page "https://cran.r-project.org/web/packages/enrichR/")
14375 (synopsis "R Interface to Enrichr database for analyzing gene sets")
14377 "This package provides an R interface to all Enrichr databases, a
14378 web-based tool for analyzing gene sets and returns any enrichment of common
14379 annotated biological functions.")
14380 (license license:gpl2+)))
14382 (define-public r-plot3d
14389 (uri (cran-uri "plot3D" version))
14392 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
14393 (properties `((upstream-name . "plot3D")))
14394 (build-system r-build-system)
14395 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
14396 (home-page "https://cran.r-project.org/web/packages/plot3D")
14397 (synopsis "Plot multi-dimensional data")
14399 "This package provides functions for viewing 2D and 3D data, including
14400 perspective plots, slice plots, surface plots, scatter plots, etc. It
14401 includes data sets from oceanography.")
14402 (license license:gpl3+)))
14404 (define-public r-ggfortify
14406 (name "r-ggfortify")
14411 (uri (cran-uri "ggfortify" version))
14414 "1wk9j0xg5hj9i1vf62qjiphv8cbsgq7y6baay3pfl3wyb2dwgci0"))))
14415 (build-system r-build-system)
14417 `(("r-dplyr" ,r-dplyr)
14418 ("r-ggplot2" ,r-ggplot2)
14419 ("r-gridextra" ,r-gridextra)
14420 ("r-scales" ,r-scales)
14421 ("r-stringr" ,r-stringr)
14422 ("r-tibble" ,r-tibble)
14423 ("r-tidyr" ,r-tidyr)))
14424 (home-page "https://github.com/sinhrks/ggfortify")
14425 (synopsis "Data visualization tools for statistical analysis results")
14427 "This package provides unified plotting tools for statistics commonly
14428 used, such as GLM, time series, PCA families, clustering and survival
14429 analysis. The package offers a single plotting interface for these analysis
14430 results and plots in a unified style using the @code{ggplot2} package.")
14431 (license license:gpl2)))
14433 (define-public r-refmanager
14435 (name "r-refmanager")
14440 (uri (cran-uri "RefManageR" version))
14443 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
14444 (properties `((upstream-name . "RefManageR")))
14445 (build-system r-build-system)
14447 `(("r-bibtex" ,r-bibtex)
14449 ("r-jsonlite" ,r-jsonlite)
14450 ("r-lubridate" ,r-lubridate)
14452 ("r-stringr" ,r-stringr)
14453 ("r-xml2" ,r-xml2)))
14454 (home-page "https://github.com/ropensci/RefManageR/")
14455 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
14457 "This package provides tools for importing and working with bibliographic
14458 references. It greatly enhances the @code{bibentry} class by providing a
14459 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
14460 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
14461 by various formats for name lists (author by last names, translator by full
14462 names, etc.). Entries can be updated, combined, sorted, printed in a number
14463 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
14464 into R and converted to @code{BibEntry} objects.")
14465 ;; Any of these licenses may be picked.
14466 (license (list license:gpl2 license:gpl3 license:bsd-3))))
14468 (define-public r-citr
14475 (uri (cran-uri "citr" version))
14478 "0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g"))))
14479 (build-system r-build-system)
14481 `(("r-assertthat" ,r-assertthat)
14482 ("r-bibtex" ,r-bibtex)
14485 ("r-miniui" ,r-miniui)
14486 ("r-refmanager" ,r-refmanager)
14487 ("r-rstudioapi" ,r-rstudioapi)
14488 ("r-shiny" ,r-shiny)
14489 ("r-shinyjs" ,r-shinyjs)
14490 ("r-yaml" ,r-yaml)))
14491 (home-page "https://github.com/crsh/citr")
14492 (synopsis "RStudio add-in to insert Markdown citations")
14494 "This package provides functions and an RStudio add-in that search a
14495 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
14496 the current document.")
14497 (license license:expat)))
14499 (define-public r-xgboost
14506 (uri (cran-uri "xgboost" version))
14509 "0plhx63wcm4syslzmjfv6bdgaqn96fnav048hrj0vxk4dzgfp8sq"))))
14510 (build-system r-build-system)
14512 `(("r-data-table" ,r-data-table)
14513 ("r-magrittr" ,r-magrittr)
14514 ("r-matrix" ,r-matrix)
14515 ("r-stringi" ,r-stringi)))
14516 (home-page "https://github.com/dmlc/xgboost")
14517 (synopsis "Extreme gradient boosting")
14519 "This package provides an R interface to Extreme Gradient Boosting, which
14520 is an efficient implementation of the gradient boosting framework from Chen
14521 and Guestrin (2016). The package includes efficient linear model solver and
14522 tree learning algorithms. The package can automatically do parallel
14523 computation on a single machine. It supports various objective functions,
14524 including regression, classification and ranking. The package is made to be
14525 extensible, so that users are also allowed to define their own objectives
14527 (license license:asl2.0)))