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 "1q4khii0xbjwmkida0b35q8rmwhg325qizjwz6slkjhz250a85ji"))))
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 "0vsm38w83zf0djcrc5ymb1ysg88hmgq2w937ql7pqgvk5px8f2mi"))))
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 "1ws5gds453xgfili87r35rz1wn2i7jbqissq98csbiddpkgls8sx"))))
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 packages 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)))
741 (home-page "http://shiny.rstudio.com")
742 (synopsis "Easy interactive web applications with R")
744 "Makes it incredibly easy to build interactive web applications
745 with R. Automatic \"reactive\" binding between inputs and outputs and
746 extensive prebuilt widgets make it possible to build beautiful,
747 responsive, and powerful applications with minimal effort.")
748 (license license:artistic2.0)))
750 (define-public r-shinydashboard
752 (name "r-shinydashboard")
756 (uri (cran-uri "shinydashboard" version))
759 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
760 (build-system r-build-system)
761 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
762 ;; Regenerate it from the included sources.
764 `(#:modules ((guix build utils)
765 (guix build r-build-system)
768 (modify-phases %standard-phases
769 (add-after 'unpack 'generate-minified-javascript
771 (with-directory-excursion "inst/AdminLTE"
772 (delete-file "app.min.js")
773 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
774 (call-with-output-file "app.min.js"
776 (dump-port minified port))))))))))
778 `(("r-htmltools" ,r-htmltools)
779 ("r-promises" ,r-promises)
780 ("r-shiny" ,r-shiny)))
782 `(("uglify-js" ,uglify-js)))
783 (home-page "http://rstudio.github.io/shinydashboard/")
784 (synopsis "Create dashboards with shiny")
785 (description "This package provides an extension to the Shiny web
786 application framework for R, making it easy to create attractive dashboards.")
787 ;; This package includes software that was released under the Expat
788 ;; license, but the whole package is released under GPL version 2 or
790 (license license:gpl2+)))
792 (define-public r-shinyfiles
794 (name "r-shinyfiles")
799 (uri (cran-uri "shinyFiles" version))
802 "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i"))))
803 (properties `((upstream-name . "shinyFiles")))
804 (build-system r-build-system)
807 ("r-htmltools" ,r-htmltools)
808 ("r-jsonlite" ,r-jsonlite)
810 ("r-tibble" ,r-tibble)))
811 (home-page "https://github.com/thomasp85/shinyFiles")
812 (synopsis "Server-side file system viewer for Shiny")
814 "This package provides functionality for client-side navigation of the
815 server side file system in shiny apps. In case the app is running locally
816 this gives the user direct access to the file system without the need to
817 \"download\" files to a temporary location. Both file and folder selection as
818 well as file saving is available.")
819 (license license:gpl2+)))
821 (define-public r-crosstalk
828 (uri (cran-uri "crosstalk" version))
831 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
832 (build-system r-build-system)
834 `(("r-ggplot2" ,r-ggplot2)
835 ("r-htmltools" ,r-htmltools)
836 ("r-jsonlite" ,r-jsonlite)
837 ("r-lazyeval" ,r-lazyeval)
839 ("r-shiny" ,r-shiny)))
840 (home-page "https://rstudio.github.io/crosstalk/")
841 (synopsis "Inter-widget interactivity for HTML widgets")
843 "This package provides building blocks for allowing HTML widgets to
844 communicate with each other, with Shiny or without (i.e. static @code{.html}
845 files). It currently supports linked brushing and filtering.")
846 (license license:expat)))
848 (define-public r-rook
855 (uri (cran-uri "Rook" version))
858 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
859 (properties `((upstream-name . "Rook")))
860 (build-system r-build-system)
861 (propagated-inputs `(("r-brew" ,r-brew)))
862 (home-page "https://cran.r-project.org/web/packages/Rook")
863 (synopsis "Web server interface for R")
865 "This package contains the Rook specification and convenience software
866 for building and running Rook applications. A Rook application is an R
867 reference class object that implements a @code{call} method or an R closure
868 that takes exactly one argument, an environment, and returns a list with three
869 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
870 (license license:gpl2)))
872 (define-public r-miniui
879 (uri (cran-uri "miniUI" version))
882 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
883 (properties `((upstream-name . "miniUI")))
884 (build-system r-build-system)
886 `(("r-htmltools" ,r-htmltools)
887 ("r-shiny" ,r-shiny)))
888 (home-page "https://cran.r-project.org/web/packages/miniUI/")
889 (synopsis "Shiny UI widgets for small screens")
891 "This package provides UI widget and layout functions for writing Shiny apps that
892 work well on small screens.")
893 (license license:gpl3)))
895 (define-public r-feather
902 (uri (cran-uri "feather" version))
905 "0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa"))))
906 (build-system r-build-system)
910 ("r-tibble" ,r-tibble)))
911 (home-page "https://github.com/wesm/feather")
912 (synopsis "R Bindings to the Feather API")
913 (description "Read and write feather files, a lightweight binary columnar
914 data store designed for maximum speed.")
915 (license license:asl2.0)))
917 (define-public r-maps
924 (uri (cran-uri "maps" version))
927 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
928 (build-system r-build-system)
929 (home-page "https://cran.r-project.org/web/packages/maps")
930 (synopsis "Draw geographical maps")
931 (description "This package provides an R module for display of maps.
932 Projection code and larger maps are in separate packages (@code{mapproj} and
934 (license license:gpl2)))
936 (define-public r-mapproj
943 (uri (cran-uri "mapproj" version))
946 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
947 (build-system r-build-system)
948 (propagated-inputs `(("r-maps" ,r-maps)))
949 (home-page "https://cran.r-project.org/web/packages/mapproj")
950 (synopsis "Map projection in R")
951 (description "This package converts latitude/longitude into projected
953 (license (list license:gpl2 ; The R interface
954 (license:non-copyleft ; The C code
955 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
956 "Lucent Public License Version 1.02")))))
958 (define-public r-rgooglemaps
960 (name "r-rgooglemaps")
965 (uri (cran-uri "RgoogleMaps" version))
968 "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
969 (properties `((upstream-name . "RgoogleMaps")))
970 (build-system r-build-system)
971 (propagated-inputs `(("r-png" ,r-png)))
972 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
973 (synopsis "Use Google Maps in R")
974 (description "This package serves two purposes:
976 @item Provide a comfortable R interface to query the Google server for static
978 @item Use the map as a background image to overlay plots within R. This
979 requires proper coordinate scaling.
981 (license license:gpl2+)))
983 (define-public r-geosphere
990 (uri (cran-uri "geosphere" version))
993 "186qdm5niq7v3d4w4rngx71znsgi44hnam7698bsx9ar5mg5b6wx"))))
994 (build-system r-build-system)
995 (propagated-inputs `(("r-sp" ,r-sp)))
996 (home-page "https://cran.r-project.org/web/packages/geosphere")
997 (synopsis "Spherical trigonometry")
998 (description "This package computes spherical trigonometry for geographic
999 applications. That is, compute distances and related measures for angular
1000 (longitude/latitude) locations.")
1001 (license license:gpl3+)))
1003 (define-public r-ggmap
1010 (uri (cran-uri "ggmap" version))
1013 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1014 (build-system r-build-system)
1016 `(("r-bitops" ,r-bitops)
1017 ("r-digest" ,r-digest)
1018 ("r-dplyr" ,r-dplyr)
1019 ("r-ggplot2" ,r-ggplot2)
1023 ("r-magrittr" ,r-magrittr)
1026 ("r-purrr" ,r-purrr)
1027 ("r-rgooglemaps" ,r-rgooglemaps)
1028 ("r-rjson" ,r-rjson)
1029 ("r-scales" ,r-scales)
1030 ("r-stringr" ,r-stringr)
1031 ("r-tibble" ,r-tibble)
1032 ("r-tidyr" ,r-tidyr)))
1033 (home-page "https://github.com/dkahle/ggmap")
1034 (synopsis "Spatial visualization with ggplot2")
1035 (description "This package provides a collection of functions to visualize
1036 spatial data and models on top of static maps from various online sources (e.g
1037 Google Maps and Stamen Maps). It includes tools common to those tasks,
1038 including functions for geolocation and routing.")
1039 (license license:gpl2)))
1041 (define-public r-haven
1048 (uri (cran-uri "haven" version))
1051 "0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0"))))
1052 (build-system r-build-system)
1056 `(("r-forcats" ,r-forcats)
1059 ("r-readr" ,r-readr)
1060 ("r-tibble" ,r-tibble)))
1061 (home-page "https://haven.tidyverse.org")
1062 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1064 "This package lets you mport foreign statistical formats into R via the
1065 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1066 (license license:expat)))
1068 (define-public r-amap
1074 (uri (cran-uri "amap" version))
1077 "1qnl2x98x64iaipkx5126rsddq2sx5ml43h75xyiyn30yvbmlxyk"))))
1078 (build-system r-build-system)
1080 `(("gfortran" ,gfortran)))
1081 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1082 (synopsis "Another multidimensional analysis package")
1083 (description "This package provides tools for clustering and principal
1084 component analysis (with robust methods, and parallelized functions).")
1085 (license license:gpl2+)))
1087 (define-public r-ape
1094 (uri (cran-uri "ape" version))
1097 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1098 (build-system r-build-system)
1100 `(("r-lattice" ,r-lattice)
1102 ("r-rcpp" ,r-rcpp)))
1103 (home-page "http://ape-package.ird.fr/")
1104 (synopsis "Analyses of phylogenetics and evolution")
1106 "This package provides functions for reading, writing, plotting, and
1107 manipulating phylogenetic trees, analyses of comparative data in a
1108 phylogenetic framework, ancestral character analyses, analyses of
1109 diversification and macroevolution, computing distances from DNA sequences,
1110 and several other tools.")
1111 (license license:gpl2+)))
1113 (define-public r-abbyyr
1120 (uri (cran-uri "abbyyR" version))
1123 "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx"))))
1124 (properties `((upstream-name . "abbyyR")))
1125 (build-system r-build-system)
1127 `(("r-curl" ,r-curl)
1130 ("r-progress" ,r-progress)
1131 ("r-readr" ,r-readr)
1133 (home-page "https://github.com/soodoku/abbyyR")
1134 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1136 "This package provides tools to get text from images of text using Abbyy
1137 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1138 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1139 passports and get the results in a variety of formats including plain text and
1140 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1141 (license license:expat)))
1143 (define-public r-colorspace
1145 (name "r-colorspace")
1150 (uri (cran-uri "colorspace" version))
1152 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1153 (build-system r-build-system)
1154 (home-page "https://cran.r-project.org/web/packages/colorspace")
1155 (synopsis "Color space manipulation")
1157 "This package carries out a mapping between assorted color spaces
1158 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1159 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1160 colors are provided.")
1161 (license license:bsd-3)))
1163 (define-public r-glue
1170 (uri (cran-uri "glue" version))
1173 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1174 (build-system r-build-system)
1175 (home-page "https://github.com/tidyverse/glue")
1176 (synopsis "Interpreted string literals")
1178 "This package provides an implementation of interpreted string literals,
1179 inspired by Python's Literal String Interpolation (PEP-0498) and
1180 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1181 (license license:expat)))
1183 (define-public r-pastecs
1189 (uri (cran-uri "pastecs" version))
1192 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1193 (build-system r-build-system)
1195 `(("r-boot" ,r-boot)))
1196 (home-page "http://www.sciviews.org/pastecs")
1197 (synopsis "Analysis of space-time ecological series")
1199 "This package provides functions for regulation, decomposition and analysis
1200 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1201 initiative to bring PASSTEC 2000 functionalities to R.")
1202 (license license:gpl2+)))
1204 (define-public r-plogr
1211 (uri (cran-uri "plogr" version))
1214 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1215 (build-system r-build-system)
1216 (home-page "https://github.com/krlmlr/plogr")
1217 (synopsis "R bindings for the plog C++ logging library")
1219 "This package provides the header files for a stripped-down version of
1220 the plog header-only C++ logging library, and a method to log to R's standard
1222 (license license:expat)))
1224 (define-public r-pls
1231 (uri (cran-uri "pls" version))
1234 "0jw3zl5z06023zxr74phnvwax8m3i4a4i6lsqiq6j15aq9zq3zgq"))))
1235 (build-system r-build-system)
1236 (home-page "http://mevik.net/work/software/pls.html")
1237 (synopsis "Partial Least Squares and Principal Component Regression")
1239 "The pls package implements multivariate regression methods: Partial Least
1240 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1241 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1244 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1245 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1246 @item multi-response models (or @dfn{PLS2})
1247 @item flexible cross-validation
1248 @item Jackknife variance estimates of regression coefficients
1249 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1250 (R)MSEP, R², and correlation loadings
1251 @item formula interface, modelled after @code{lm()}, with methods for predict,
1252 print, summary, plot, update, etc.
1253 @item extraction functions for coefficients, scores, and loadings
1254 @item MSEP, RMSEP, and R² estimates
1255 @item multiplicative scatter correction (@dfn{MSC})
1257 (license license:gpl2)))
1266 (uri (cran-uri "ps" version))
1268 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1269 (build-system r-build-system)
1270 (home-page "http://ps.r-lib.org")
1271 (synopsis "List, query, and manipulate system processes")
1273 "The ps package implements an API to list, query, and manipulate system
1274 processes. Most of its code is based on the @code{psutil} Python package.")
1275 (license license:bsd-3)))
1277 (define-public r-pkgbuild
1284 (uri (cran-uri "pkgbuild" version))
1287 "0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9"))))
1288 (build-system r-build-system)
1290 `(("r-callr" ,r-callr)
1292 ("r-crayon" ,r-crayon)
1294 ("r-prettyunits" ,r-prettyunits)
1296 ("r-rprojroot" ,r-rprojroot)
1297 ("r-withr" ,r-withr)))
1298 (home-page "https://github.com/r-pkgs/pkgbuild")
1299 (synopsis "Find tools needed to build R packages")
1301 "This package provides functions used to build R packages. It locates
1302 compilers needed to build R packages on various platforms and ensures the PATH
1303 is configured appropriately so R can use them.")
1304 (license license:gpl3)))
1306 (define-public r-pkgload
1313 (uri (cran-uri "pkgload" version))
1316 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1317 (build-system r-build-system)
1319 `(("r-desc" ,r-desc)
1320 ("r-pkgbuild" ,r-pkgbuild)
1321 ("r-rlang" ,r-rlang)
1322 ("r-rprojroot" ,r-rprojroot)
1323 ("r-rstudioapi" ,r-rstudioapi)
1324 ("r-withr" ,r-withr)))
1325 (home-page "https://github.com/r-lib/pkgload")
1326 (synopsis "Simulate package installation and attach")
1328 "This package simulates the process of installing a package and then
1329 attaching it. This is a key part of the @code{devtools} package as it allows
1330 you to rapidly iterate while developing a package.")
1331 (license license:gpl3)))
1333 (define-public r-rcpp
1340 (uri (cran-uri "Rcpp" version))
1342 (base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7"))))
1343 (build-system r-build-system)
1345 `(("r-knitr" ,r-knitr))) ; for vignettes
1346 (home-page "http://www.rcpp.org")
1347 (synopsis "Seamless R and C++ integration")
1349 "The Rcpp package provides R functions as well as C++ classes which offer
1350 a seamless integration of R and C++. Many R data types and objects can be
1351 mapped back and forth to C++ equivalents which facilitates both writing of new
1352 code as well as easier integration of third-party libraries. Documentation
1353 about Rcpp is provided by several vignettes included in this package, via the
1354 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1355 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1356 @code{citation(\"Rcpp\")} for details on these last two.")
1357 (license license:gpl2+)))
1359 (define-public r-bindr
1366 (uri (cran-uri "bindr" version))
1369 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1370 (build-system r-build-system)
1371 (home-page "https://github.com/krlmlr/bindr")
1372 (synopsis "Parametrized active bindings")
1374 "This package provides a simple interface for creating active bindings
1375 where the bound function accepts additional arguments.")
1376 (license license:expat)))
1378 (define-public r-bindrcpp
1385 (uri (cran-uri "bindrcpp" version))
1388 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1389 (build-system r-build-system)
1391 `(("r-bindr" ,r-bindr)
1392 ("r-plogr" ,r-plogr)
1393 ("r-rcpp" ,r-rcpp)))
1394 (home-page "https://github.com/krlmlr/bindrcpp")
1395 (synopsis "Rcpp interface to active bindings")
1397 "This package provides an easy way to fill an environment with active
1398 bindings that call a C++ function.")
1399 (license license:expat)))
1401 (define-public r-auc
1408 (uri (cran-uri "AUC" version))
1411 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1412 (properties `((upstream-name . "AUC")))
1413 (build-system r-build-system)
1414 (home-page "https://cran.r-project.org/web/packages/AUC")
1415 (synopsis "Compute the area under the curve of selected measures")
1417 "This package includes functions to compute the area under the curve of
1418 selected measures: the area under the sensitivity curve (AUSEC), the area
1419 under the specificity curve (AUSPC), the area under the accuracy
1420 curve (AUACC), and the area under the receiver operating characteristic
1421 curve (AUROC). The curves can also be visualized. Support for partial areas
1423 (license license:gpl2+)))
1425 (define-public r-calibrate
1427 (name "r-calibrate")
1432 (uri (cran-uri "calibrate" version))
1435 "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
1436 (build-system r-build-system)
1438 `(("r-mass" ,r-mass)))
1439 (home-page "https://cran.r-project.org/web/packages/calibrate")
1440 (synopsis "Calibration of scatterplot and biplot axes")
1442 "This is a package for drawing calibrated scales with tick marks
1443 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1444 (license license:gpl2)))
1446 (define-public r-shape
1453 (uri (cran-uri "shape" version))
1456 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1457 (build-system r-build-system)
1458 (home-page "https://cran.r-project.org/web/packages/shape")
1459 (synopsis "Functions for plotting graphical shapes")
1461 "This package provides functions for plotting graphical shapes such as
1462 ellipses, circles, cylinders, arrows, ...")
1463 (license license:gpl3+)))
1465 (define-public r-globaloptions
1467 (name "r-globaloptions")
1472 (uri (cran-uri "GlobalOptions" version))
1475 "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn"))))
1476 (properties `((upstream-name . "GlobalOptions")))
1477 (build-system r-build-system)
1478 (home-page "https://github.com/jokergoo/GlobalOptions")
1479 (synopsis "Generate functions to get or set global options")
1481 "This package provides more controls on the option values such as
1482 validation and filtering on the values, making options invisible or private.")
1483 (license license:gpl2+)))
1485 (define-public r-circlize
1492 (uri (cran-uri "circlize" version))
1495 "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f"))))
1496 (build-system r-build-system)
1498 `(("r-colorspace" ,r-colorspace)
1499 ("r-globaloptions" ,r-globaloptions)
1500 ("r-shape" ,r-shape)))
1501 (home-page "https://github.com/jokergoo/circlize")
1502 (synopsis "Circular visualization")
1504 "Circular layout is an efficient way to visualise huge amounts of
1505 information. This package provides an implementation of circular layout
1506 generation in R as well as an enhancement of available software. Its
1507 flexibility is based on the usage of low-level graphics functions such that
1508 self-defined high-level graphics can be easily implemented by users for
1509 specific purposes. Together with the seamless connection between the powerful
1510 computational and visual environment in R, it gives users more convenience and
1511 freedom to design figures for better understanding complex patterns behind
1512 multi-dimensional data.")
1513 (license license:gpl2+)))
1515 (define-public r-powerlaw
1522 (uri (cran-uri "poweRlaw" version))
1525 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1526 (properties `((upstream-name . "poweRlaw")))
1527 (build-system r-build-system)
1529 `(("r-vgam" ,r-vgam)))
1530 (home-page "https://github.com/csgillespie/poweRlaw")
1531 (synopsis "Tools for the analysis of heavy tailed distributions")
1533 "This package provides an implementation of maximum likelihood estimators
1534 for a variety of heavy tailed distributions, including both the discrete and
1535 continuous power law distributions. Additionally, a goodness-of-fit based
1536 approach is used to estimate the lower cut-off for the scaling region.")
1537 ;; Any of these GPL versions.
1538 (license (list license:gpl2 license:gpl3))))
1540 (define-public r-compare
1547 (uri (cran-uri "compare" version))
1550 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1551 (build-system r-build-system)
1552 (home-page "https://cran.r-project.org/web/packages/compare")
1553 (synopsis "Comparing objects for differences")
1555 "This package provides functions to compare a model object to a
1556 comparison object. If the objects are not identical, the functions can be
1557 instructed to explore various modifications of the objects (e.g., sorting
1558 rows, dropping names) to see if the modified versions are identical.")
1559 (license license:gpl2+)))
1561 (define-public r-dendextend
1563 (name "r-dendextend")
1568 (uri (cran-uri "dendextend" version))
1571 "091jznl549d44w1h8kk1vwddzhijkyh0wpgkykd494fnc8rzpw48"))))
1572 (build-system r-build-system)
1575 ("r-ggplot2" ,r-ggplot2)
1576 ("r-magrittr" ,r-magrittr)
1577 ("r-viridis" ,r-viridis)
1578 ("r-whisker" ,r-whisker)))
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 "1rhwm0bdw30z3rvl0bn56xprjl3zrdy7150w4gl4bkvn2d6h9fav"))))
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
2075 (uri (cran-uri "lpSolve" version))
2078 "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
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 "15d5q5vpp4wx5rk5kjxjdxpwc8mkq5sbdz8gi07iscrvhzb5rzfr"))))
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 "0x16k0nixgbayh3g4didacn0gmnl5fdfxa0l323phphmimyj49zl"))))
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 "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa"))))
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 "0lyvi32aikkvwdj0y2hc13kmmi0cw1icg8z9lcw10l8326sxm0vf"))))
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 "0rdamj1j9z3kxmi27pc79v6mhh8rgxaxz4xz70ybf8kqh2x66cgm"))))
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 packages 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 "1ym97xl2icjpfkrici0wig29w06bb704hp51v7h5liygjlwpkhlc"))))
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 "1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92"))))
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 "123wmnykmlq9prqx1g9ij9vyqx25pib2jnqjrwy39rfmzbsypbx3"))))
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-pillar
3663 (uri (cran-uri "pillar" version))
3666 "1xnbb9sr5wn9dmp6m7cr4z7i6pmjvyabnfcx6x7i7mvdjmgvaf5k"))))
3667 (build-system r-build-system)
3670 ("r-crayon" ,r-crayon)
3671 ("r-fansi" ,r-fansi)
3672 ("r-rlang" ,r-rlang)
3673 ("r-utf8" ,r-utf8)))
3674 (home-page "https://github.com/r-lib/pillar")
3675 (synopsis "Coloured formatting for columns")
3677 "This package provides a @code{pillar} generic designed for formatting
3678 columns of data using the full range of colours provided by modern
3680 (license license:gpl3)))
3682 (define-public r-uuid
3689 (uri (cran-uri "uuid" version))
3692 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
3693 (build-system r-build-system)
3694 (home-page "http://www.rforge.net/uuid")
3695 (synopsis "Tools for generating and handling of UUIDs")
3697 "This package provides tools for generating and handling of
3698 @dfn{Universally Unique Identifiers} (UUIDs).")
3699 (license license:expat)))
3701 (define-public r-tinytex
3708 (uri (cran-uri "tinytex" version))
3711 "03ggxbd4y1ipcmjw5ixa6g6wg4ydargnln7g08bdrdi96zyyq1fh"))))
3712 (build-system r-build-system)
3714 `(("r-xfun" ,r-xfun)))
3715 (home-page "https://github.com/yihui/tinytex")
3716 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
3718 "This package provides helper functions to install and maintain the LaTeX
3719 distribution named TinyTeX, a lightweight, cross-platform, portable, and
3720 easy-to-maintain version of TeX Live. This package also contains helper
3721 functions to compile LaTeX documents, and install missing LaTeX packages
3723 (license license:expat)))
3725 (define-public r-metap
3732 (uri (cran-uri "metap" version))
3735 "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0"))))
3736 (build-system r-build-system)
3738 `(("r-lattice" ,r-lattice)
3739 ("r-rdpack" ,r-rdpack)))
3740 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3741 (synopsis "Meta-analysis of significance values")
3743 "The canonical way to perform meta-analysis involves using effect sizes.
3744 When they are not available this package provides a number of methods for
3745 meta-analysis of significance values including the methods of Edgington,
3746 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3747 published results; and a routine for graphical display.")
3748 (license license:gpl2)))
3750 (define-public r-network
3757 (uri (cran-uri "network" version))
3760 "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
3761 (build-system r-build-system)
3763 `(("r-magrittr" ,r-magrittr)
3764 ("r-tibble" ,r-tibble)))
3765 (home-page "https://statnet.org/")
3766 (synopsis "Classes for relational data")
3768 "This package provides tools to create and modify network objects. The
3769 @code{network} class can represent a range of relational data types, and
3770 supports arbitrary vertex/edge/graph attributes.")
3771 (license license:gpl2+)))
3773 (define-public r-statnet-common
3775 (name "r-statnet-common")
3780 (uri (cran-uri "statnet.common" version))
3783 "0q942g6kqmqxfss1cxb3yg8y5r1k1h5cyy99s1cfisrn6hqc6xhi"))))
3785 `((upstream-name . "statnet.common")))
3786 (build-system r-build-system)
3788 `(("r-coda" ,r-coda)))
3789 (home-page "https://statnet.org")
3790 (synopsis "R scripts and utilities used by the Statnet software")
3791 (description "This package provides non-statistical utilities used by the
3792 software developed by the Statnet Project.")
3793 (license license:gpl3)))
3795 (define-public r-sna
3802 (uri (cran-uri "sna" version))
3805 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
3806 (build-system r-build-system)
3808 `(("r-network" ,r-network)
3809 ("r-statnet-common" ,r-statnet-common)))
3810 (home-page "https://statnet.org")
3811 (synopsis "Tools for social network analysis")
3813 "This package provides a range of tools for social network analysis,
3814 including node and graph-level indices, structural distance and covariance
3815 methods, structural equivalence detection, network regression, random graph
3816 generation, and 2D/3D network visualization.")
3817 (license license:gpl2+)))
3819 (define-public r-ttr
3826 (uri (cran-uri "TTR" version))
3829 "18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb"))))
3830 (properties `((upstream-name . "TTR")))
3831 (build-system r-build-system)
3833 `(("r-curl" ,r-curl)
3836 (native-inputs `(("gfortran" ,gfortran)))
3837 (home-page "https://github.com/joshuaulrich/TTR")
3838 (synopsis "Technical trading rules")
3840 "This package provides functions and data to construct technical trading
3842 (license license:gpl2)))
3844 (define-public r-leaps
3851 (uri (cran-uri "leaps" version))
3854 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
3855 (build-system r-build-system)
3856 (native-inputs `(("gfortran" ,gfortran)))
3857 (home-page "https://cran.r-project.org/web/packages/leaps/")
3858 (synopsis "Regression subset selection")
3860 "This package provides tools for regression subset selection, including
3861 exhaustive search.")
3862 (license license:gpl2+)))
3864 (define-public r-splus2r
3871 (uri (cran-uri "splus2R" version))
3874 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
3875 (properties `((upstream-name . "splus2R")))
3876 (build-system r-build-system)
3877 (native-inputs `(("gfortran" ,gfortran)))
3878 (home-page "https://cran.r-project.org/web/packages/splus2R/")
3879 (synopsis "Supplemental S-PLUS functionality in R")
3881 "Currently there are many functions in S-PLUS that are missing in R. To
3882 facilitate the conversion of S-PLUS packages to R packages, this package
3883 provides some missing S-PLUS functionality in R.")
3884 (license license:gpl2)))
3886 (define-public r-ifultools
3888 (name "r-ifultools")
3893 (uri (cran-uri "ifultools" version))
3896 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
3897 (build-system r-build-system)
3899 `(("r-mass" ,r-mass)
3900 ("r-splus2r" ,r-splus2r)))
3901 (home-page "https://cran.r-project.org/web/packages/ifultools/")
3902 (synopsis "Insightful research tools")
3903 (description "This package provides C code used by the wmtsa, fractal, and
3905 (license license:gpl2)))
3907 (define-public r-sapa
3914 (uri (cran-uri "sapa" version))
3917 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
3918 (build-system r-build-system)
3920 `(("r-ifultools" ,r-ifultools)
3921 ("r-splus2r" ,r-splus2r)))
3922 (home-page "https://cran.r-project.org/web/packages/sapa/")
3923 (synopsis "Spectral analysis for physical applications")
3924 (description "This package provides software for the book Spectral
3925 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
3926 Cambridge University Press, 1993.")
3927 (license license:gpl2)))
3929 (define-public r-aggregation
3931 (name "r-aggregation")
3936 (uri (cran-uri "aggregation" version))
3939 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
3940 (build-system r-build-system)
3941 (home-page "https://cran.r-project.org/web/packages/aggregation/")
3942 (synopsis "Methods for p-value aggregation")
3944 "This package contains functionality for performing the following methods
3945 of p-value aggregation: Fisher's method, the Lancaster method (weighted
3946 Fisher's method), and Sidak correction.")
3947 (license license:gpl3)))
3949 (define-public r-quantmod
3956 (uri (cran-uri "quantmod" version))
3959 "1csljagnpkr1mmc18h70b64zbyj07kx972nip9dng39jfg7ilnyr"))))
3960 (build-system r-build-system)
3962 `(("r-curl" ,r-curl)
3966 (home-page "https://cran.r-project.org/web/packages/quantmod/")
3967 (synopsis "Quantitative financial modelling framework")
3968 (description "This package provides a quantitative financial modelling
3969 framework to allow users to specify, build, trade, and analyse quantitative
3970 financial trading strategies.")
3971 (license license:gpl3)))
3973 (define-public r-tseries
3980 (uri (cran-uri "tseries" version))
3983 "08kjw0bfj5gfcrxpblwqxwna8a5g9gnr7ya61qb02r263pyhm50j"))))
3984 (build-system r-build-system)
3986 `(("r-quadprog" ,r-quadprog)
3987 ("r-quantmod" ,r-quantmod)
3990 `(("gfortran" ,gfortran)))
3991 (home-page "https://cran.r-project.org/web/packages/tseries/")
3992 (synopsis "Time series analysis and computational finance")
3994 "This package provides functions relating to time series analysis and
3995 computational finance.")
3996 (license license:gpl2)))
3998 (define-public r-wmtsa
4005 (uri (cran-uri "wmtsa" version))
4008 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4009 (build-system r-build-system)
4011 `(("r-ifultools" ,r-ifultools)
4013 ("r-splus2r" ,r-splus2r)))
4014 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4015 (synopsis "Wavelet methods for time series analysis")
4017 "This package provides software to accompany the book \"Wavelet Methods
4018 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4019 University Press, 2000.")
4020 (license license:gpl2)))
4022 (define-public r-tsa
4029 (uri (cran-uri "TSA" version))
4032 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4033 (properties `((upstream-name . "TSA")))
4034 (build-system r-build-system)
4036 `(("r-leaps" ,r-leaps)
4037 ("r-locfit" ,r-locfit)
4038 ("r-mgcv" ,r-mgcv)))
4039 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4040 (synopsis "Time series analysis")
4042 "This package contains R functions and datasets detailed in the book
4043 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4044 Cryer and Kung-Sik Chan.")
4045 (license license:gpl2+)))
4047 (define-public r-extradistr
4049 (name "r-extradistr")
4054 (uri (cran-uri "extraDistr" version))
4057 "00lvqp5bb3iak5myiz4rqm887bkq9sdh7aybmz84mmfni6q01m28"))))
4058 (properties `((upstream-name . "extraDistr")))
4059 (build-system r-build-system)
4061 `(("r-rcpp" ,r-rcpp)))
4062 (home-page "https://github.com/twolodzko/extraDistr")
4063 (synopsis "Additional univariate and multivariate distributions")
4065 "This package implements density, distribution functions, quantile
4066 functions and random generation functions for a large number of univariate and
4067 multivariate distributions.")
4068 (license license:gpl2)))
4070 (define-public r-fractal
4077 (uri (cran-uri "fractal" version))
4080 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4081 (build-system r-build-system)
4083 `(("r-ifultools" ,r-ifultools)
4086 ("r-scatterplot3d" ,r-scatterplot3d)
4087 ("r-splus2r" ,r-splus2r)
4088 ("r-wmtsa" ,r-wmtsa)))
4089 (home-page "https://cran.r-project.org/web/packages/fractal/")
4090 (synopsis "Fractal time series modeling and analysis")
4092 "This package provides tools for stochastic fractal and deterministic
4093 chaotic time series analysis.")
4094 (license license:gpl2)))
4096 (define-public r-urca
4103 (uri (cran-uri "urca" version))
4106 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4107 (build-system r-build-system)
4108 (propagated-inputs `(("r-nlme" ,r-nlme)))
4109 (native-inputs `(("gfortran" ,gfortran)))
4110 (home-page "https://cran.r-project.org/web/packages/urca/")
4111 (synopsis "Unit root and cointegration tests for time series data")
4113 "This package provides unit root and cointegration tests encountered in
4114 applied econometric analysis.")
4115 (license license:gpl2+)))
4117 (define-public r-cubature
4124 (uri (cran-uri "cubature" version))
4127 "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"))))
4128 (build-system r-build-system)
4130 `(("r-rcpp" ,r-rcpp)))
4131 (home-page "https://github.com/bnaras/cubature")
4132 (synopsis "Adaptive multivariate integration over hypercubes")
4134 "This package is an R wrapper around the cubature C library for adaptive
4135 multivariate integration over hypercubes. This version provides both
4136 @code{hcubature} and @code{pcubature} routines in addition to a vector
4138 ;; The included cubature C library is released under GPLv2+, but the
4139 ;; wrapper declares the license to be GPLv3+.
4140 (license (list license:gpl2+ license:gpl3+))))
4142 (define-public r-trend
4149 (uri (cran-uri "trend" version))
4152 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4153 (build-system r-build-system)
4155 `(("r-extradistr" ,r-extradistr)))
4157 `(("gfortran" ,gfortran)))
4158 (home-page "https://cran.r-project.org/web/packages/trend/")
4159 (synopsis "Non-parametric trend tests and change-point detection")
4161 "The analysis of environmental data often requires the detection of
4162 trends and change-points. This package includes tests for trend
4163 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4164 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4165 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4166 correlation trend test), change-point detection (Lanzante's test procedures,
4167 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4168 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4169 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4170 sample Robust Rank-Order Distributional Test.")
4171 (license license:gpl3)))
4173 (define-public r-expm
4180 (uri (cran-uri "expm" version))
4183 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4184 (build-system r-build-system)
4185 (propagated-inputs `(("r-matrix" ,r-matrix)))
4186 (native-inputs `(("gfortran" ,gfortran)))
4187 (home-page "https://r-forge.r-project.org/projects/expm/")
4188 (synopsis "Tools for matrix exponentials and related quantities")
4190 "This package provides tools for the computation of the matrix
4191 exponential, logarithm, square root, and related quantities.")
4192 (license license:gpl2+)))
4194 (define-public r-complexplus
4196 (name "r-complexplus")
4201 (uri (cran-uri "complexplus" version))
4204 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4205 (build-system r-build-system)
4207 `(("r-expm" ,r-expm)
4208 ("r-matrix" ,r-matrix)))
4209 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4210 (synopsis "Functions of complex or real variables")
4212 "This package extends several functions to the complex domain, including
4213 the matrix exponential and logarithm, and the determinant.")
4214 (license license:gpl2)))
4216 (define-public r-phontools
4218 (name "r-phontools")
4223 (uri (cran-uri "phonTools" version))
4226 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4227 (properties `((upstream-name . "phonTools")))
4228 (build-system r-build-system)
4229 (home-page "http://www.santiagobarreda.com/rscripts.html")
4230 (synopsis "Tools for phonetic and acoustic analyses")
4232 "This package contains tools for the organization, display, and analysis
4233 of the sorts of data frequently encountered in phonetics research and
4234 experimentation, including the easy creation of IPA vowel plots, and the
4235 creation and manipulation of WAVE audio files.")
4236 (license license:bsd-2)))
4245 (uri (cran-uri "np" version))
4248 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4249 (build-system r-build-system)
4251 `(("r-boot" ,r-boot)
4252 ("r-cubature" ,r-cubature)
4253 ("r-quadprog" ,r-quadprog)
4254 ("r-quantreg" ,r-quantreg)))
4255 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4256 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4257 (description "This package provides non-parametric (and semi-parametric)
4258 kernel methods that seamlessly handle a mix of continuous, unordered, and
4259 ordered factor data types.")
4260 ;; Any version of the GPL.
4261 (license license:gpl3+)))
4263 (define-public r-powerplus
4265 (name "r-powerplus")
4270 (uri (cran-uri "powerplus" version))
4273 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4274 (build-system r-build-system)
4276 `(("r-complexplus" ,r-complexplus)
4279 ("r-matrix" ,r-matrix)
4280 ("r-phontools" ,r-phontools)))
4281 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4282 (synopsis "Exponentiation operations")
4284 "This package provides tools for the computation of matrix and scalar
4286 (license license:gpl2)))
4288 (define-public r-heatmaply
4290 (name "r-heatmaply")
4295 (uri (cran-uri "heatmaply" version))
4298 "0h8s5djzj4mrmaswlcaap6jbwxrkbzc43bbqik3qf8vrqz335w04"))))
4299 (build-system r-build-system)
4301 `(("r-assertthat" ,r-assertthat)
4302 ("r-colorspace" ,r-colorspace)
4303 ("r-dendextend" ,r-dendextend)
4304 ("r-ggplot2" ,r-ggplot2)
4305 ("r-gplots" ,r-gplots)
4306 ("r-htmlwidgets" ,r-htmlwidgets)
4307 ("r-knitr" ,r-knitr) ; needed for vignettes
4308 ("r-magrittr" ,r-magrittr)
4309 ("r-plotly" ,r-plotly)
4310 ("r-rcolorbrewer" ,r-rcolorbrewer)
4311 ("r-reshape2" ,r-reshape2)
4312 ("r-scales" ,r-scales)
4313 ("r-seriation" ,r-seriation)
4314 ("r-viridis" ,r-viridis)
4315 ("r-webshot" ,r-webshot)))
4316 (home-page "https://cran.r-project.org/package=heatmaply")
4317 (synopsis "Interactive cluster heat maps using plotly")
4319 "This package enables you to create interactive cluster heatmaps that can
4320 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4321 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4322 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4323 a popular graphical method for visualizing high-dimensional data, in which a
4324 table of numbers is encoded as a grid of colored cells. The rows and columns
4325 of the matrix are ordered to highlight patterns and are often accompanied by
4327 ;; Either version of the license.
4328 (license (list license:gpl2 license:gpl3))))
4337 (uri (cran-uri "h5" version))
4340 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4341 (build-system r-build-system)
4346 `(("which" ,which)))
4348 `(("r-rcpp" ,r-rcpp)))
4349 (home-page "https://github.com/mannau/h5")
4350 (synopsis "Interface to the HDF5 Library")
4352 "This package provides an S4 interface to the HDF5 library supporting
4353 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4354 binary files in a language independent format. The HDF5 format can therefore
4355 be used as an alternative to R's save/load mechanism. Since h5 is able to
4356 access only subsets of stored data it can also handle data sets which do not
4358 (license license:bsd-2)))
4360 (define-public r-cgdsr
4367 (uri (cran-uri "cgdsr" version))
4370 "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23"))))
4371 (build-system r-build-system)
4373 `(("r-r-methodss3" ,r-r-methodss3)
4374 ("r-r-oo" ,r-r-oo)))
4375 (home-page "https://github.com/cBioPortal/cgdsr")
4376 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4378 "This package provides a basic set of R functions for querying the Cancer
4379 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4380 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4381 (license license:lgpl3)))
4383 (define-public r-import
4390 (uri (cran-uri "import" version))
4393 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4394 (build-system r-build-system)
4395 (home-page "https://github.com/smbache/import")
4396 (synopsis "Import mechanism for R")
4398 "This is an alternative mechanism for importing objects from packages.
4399 The syntax allows for importing multiple objects from a package with a single
4400 command in an expressive way. The import package bridges some of the gap
4401 between using @code{library} (or @code{require}) and direct (single-object)
4402 imports. Furthermore the imported objects are not placed in the current
4403 environment. It is also possible to import objects from stand-alone @code{.R}
4405 (license license:expat)))
4407 (define-public r-shinyace
4414 (uri (cran-uri "shinyAce" version))
4417 "02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j"))))
4418 (properties `((upstream-name . "shinyAce")))
4419 (build-system r-build-system)
4421 `(("r-shiny" ,r-shiny)
4422 ("r-jsonlite" ,r-jsonlite)))
4423 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4424 (synopsis "Ace editor bindings for Shiny")
4426 "This package provides Ace editor bindings to enable a rich text editing
4427 environment within Shiny.")
4428 (license license:expat)))
4430 (define-public r-base64url
4432 (name "r-base64url")
4437 (uri (cran-uri "base64url" version))
4440 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4441 (build-system r-build-system)
4443 `(("r-backports" ,r-backports)))
4444 (home-page "https://github.com/mllg/base64url")
4445 (synopsis "Fast and URL-safe base64 encoder and decoder")
4447 "This package provides a URL-safe base64 encoder and decoder. In
4448 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4449 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4450 encoder does not fill the string with trailing @code{=}. The resulting
4451 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4452 and thus are safe to use in URLs or for file names. The package also comes
4453 with a simple base32 encoder/decoder suited for case insensitive file
4455 (license license:gpl3)))
4457 (define-public r-radiant-data
4459 (name "r-radiant-data")
4464 (uri (cran-uri "radiant.data" version))
4467 "17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn"))
4468 (modules '((guix build utils)))
4471 ;; Delete files that are under CC-NC-SA.
4472 (delete-file-recursively "inst/app/tools/help")
4474 (properties `((upstream-name . "radiant.data")))
4475 (build-system r-build-system)
4477 `(("r-base64enc" ,r-base64enc)
4478 ("r-broom" ,r-broom)
4481 ("r-dplyr" ,r-dplyr)
4484 ("r-ggplot2" ,r-ggplot2)
4485 ("r-gridextra" ,r-gridextra)
4486 ("r-import" ,r-import)
4487 ("r-jsonlite" ,r-jsonlite)
4488 ("r-knitr" ,r-knitr)
4489 ("r-lubridate" ,r-lubridate)
4490 ("r-magrittr" ,r-magrittr)
4491 ("r-markdown" ,r-markdown)
4492 ("r-plotly" ,r-plotly)
4493 ("r-psych" ,r-psych)
4494 ("r-readr" ,r-readr)
4495 ("r-readxl" ,r-readxl)
4496 ("r-rlang" ,r-rlang)
4497 ("r-rmarkdown" ,r-rmarkdown)
4498 ("r-rstudioapi" ,r-rstudioapi)
4499 ("r-scales" ,r-scales)
4500 ("r-shiny" ,r-shiny)
4501 ("r-shinyfiles" ,r-shinyfiles)
4502 ("r-shinyace" ,r-shinyace)
4503 ("r-stringi" ,r-stringi)
4504 ("r-tibble" ,r-tibble)
4505 ("r-tidyr" ,r-tidyr)
4506 ("r-writexl" ,r-writexl)))
4507 (home-page "https://github.com/radiant-rstats/radiant.data")
4508 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4510 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4511 visualizing, summarizing, transforming, and combining data. It also contains
4512 functionality to generate reproducible reports of the analyses conducted in
4514 (license license:agpl3)))
4516 (define-public r-algdesign
4518 (name "r-algdesign")
4523 (uri (cran-uri "AlgDesign" version))
4526 "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
4527 (properties `((upstream-name . "AlgDesign")))
4528 (build-system r-build-system)
4529 (home-page "https://github.com/jvbraun/AlgDesign")
4530 (synopsis "Algorithmic experimental design")
4532 "This package provides tools to calculate exact and approximate theory
4533 experimental designs for D, A, and I criteria. Very large designs may be
4534 created. Experimental designs may be blocked or blocked designs created from
4535 a candidate list, using several criteria. The blocking can be done when whole
4536 and within plot factors interact.")
4537 (license license:gpl2+)))
4539 (define-public r-signal
4546 (uri (cran-uri "signal" version))
4549 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
4550 (build-system r-build-system)
4551 (propagated-inputs `(("r-mass" ,r-mass)))
4552 (native-inputs `(("gfortran" ,gfortran)))
4553 (home-page "https://cran.r-project.org/web/packages/signal/")
4554 (synopsis "Signal processing")
4556 "This package provides a set of signal processing functions originally
4557 written for Matlab and GNU Octave. It includes filter generation utilities,
4558 filtering functions, resampling routines, and visualization of filter models.
4559 It also includes interpolation functions.")
4560 (license license:gpl2)))
4562 (define-public r-gsubfn
4569 (uri (cran-uri "gsubfn" version))
4572 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
4573 (build-system r-build-system)
4574 (propagated-inputs `(("r-proto" ,r-proto)))
4575 (home-page "http://gsubfn.googlecode.com")
4576 (synopsis "Utilities for strings and function arguments.")
4578 "This package provides @code{gsubfn} which is like @code{gsub} but can
4579 take a replacement function or certain other objects instead of the
4580 replacement string. Matches and back references are input to the replacement
4581 function and replaced by the function output. @code{gsubfn} can be used to
4582 split strings based on content rather than delimiters and for quasi-perl-style
4583 string interpolation. The package also has facilities for translating
4584 formulas to functions and allowing such formulas in function calls instead of
4586 (license license:gpl2+)))
4588 (define-public r-sqldf
4595 (uri (cran-uri "sqldf" version))
4598 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
4599 (build-system r-build-system)
4601 `(("r-chron" ,r-chron)
4603 ("r-gsubfn" ,r-gsubfn)
4604 ("r-proto" ,r-proto)
4605 ("r-rsqlite" ,r-rsqlite)))
4606 (home-page "https://github.com/ggrothendieck/sqldf")
4607 (synopsis "Manipulate R data frames using SQL")
4609 "The @code{sqldf} function is typically passed a single argument which is
4610 an SQL select statement where the table names are ordinary R data frame names.
4611 @code{sqldf} transparently sets up a database, imports the data frames into
4612 that database, performs the SQL statement and returns the result using a
4613 heuristic to determine which class to assign to each column of the returned
4614 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
4615 used to read filtered files into R even if the original files are larger than
4616 R itself can handle.")
4617 (license license:gpl2)))
4619 (define-public r-abind
4626 (uri (cran-uri "abind" version))
4629 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
4630 (build-system r-build-system)
4631 (home-page "https://cran.r-project.org/web/packages/abind/")
4632 (synopsis "Combine multidimensional arrays")
4634 "This package provides tools to combine multidimensional arrays into a
4635 single array. This is a generalization of @code{cbind} and @code{rbind}. It
4636 works with vectors, matrices, and higher-dimensional arrays. It also provides
4637 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
4638 extracting and replacing data in arrays.")
4639 (license license:lgpl2.0+)))
4641 (define-public r-prroc
4648 (uri (cran-uri "PRROC" version))
4651 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
4652 (properties `((upstream-name . "PRROC")))
4653 (build-system r-build-system)
4654 (home-page "https://cran.r-project.org/web/packages/PRROC/")
4655 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
4657 "This package computes the areas under the @dfn{precision-recall} (PR)
4658 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
4659 contrast to other implementations, the interpolation between points of the PR
4660 curve is done by a non-linear piecewise function. In addition to the areas
4661 under the curves, the curves themselves can also be computed and plotted by a
4662 specific S3-method.")
4663 (license license:gpl3)))
4665 (define-public r-vim
4672 (uri (cran-uri "VIM" version))
4675 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
4676 (properties `((upstream-name . "VIM")))
4677 (build-system r-build-system)
4680 ("r-colorspace" ,r-colorspace)
4681 ("r-data-table" ,r-data-table)
4682 ("r-e1071" ,r-e1071)
4683 ("r-laeken" ,r-laeken)
4686 ("r-ranger" ,r-ranger)
4688 ("r-robustbase" ,r-robustbase)
4691 (home-page "https://github.com/alexkowa/VIM")
4692 (synopsis "Visualization and imputation of missing values")
4694 "This package provides tools for the visualization of missing and/or
4695 imputed values are introduced, which can be used for exploring the data and
4696 the structure of the missing and/or imputed values. Depending on this
4697 structure of the missing values, the corresponding methods may help to
4698 identify the mechanism generating the missing values and allows to explore the
4699 data including missing values. In addition, the quality of imputation can be
4700 visually explored using various univariate, bivariate, multiple and
4701 multivariate plot methods.")
4702 (license license:gpl2+)))
4704 (define-public r-fnn
4711 (uri (cran-uri "FNN" version))
4714 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
4715 (properties `((upstream-name . "FNN")))
4716 (build-system r-build-system)
4717 (home-page "https://cran.r-project.org/web/packages/FNN")
4718 (synopsis "Fast nearest neighbor search algorithms and applications")
4720 "This package provides cover-tree and kd-tree fast k-nearest neighbor
4721 search algorithms. Related applications including KNN classification,
4722 regression and information measures are implemented.")
4723 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
4724 ;; later can be used.
4725 (license license:gpl2+)))
4727 (define-public r-smoother
4734 (uri (cran-uri "smoother" version))
4737 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
4738 (build-system r-build-system)
4740 `(("r-ttr" ,r-ttr)))
4741 (home-page "http://cran.r-project.org/web/packages/smoother")
4742 (synopsis "Functions relating to the smoothing of numerical data")
4744 "This package provides a collection of methods for smoothing numerical
4745 data, commencing with a port of the Matlab gaussian window smoothing function.
4746 In addition, several functions typically used in smoothing of financial data
4748 (license license:gpl2)))
4750 (define-public r-riverplot
4752 (name "r-riverplot")
4757 (uri (cran-uri "riverplot" version))
4760 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
4761 (build-system r-build-system)
4762 (home-page "https://logfc.wordpress.com")
4763 (synopsis "Sankey or ribbon plots")
4765 "Sankey plots are a type of diagram that is convenient to illustrate how
4766 flow of information, resources etc. separates and joins, much like observing
4767 how rivers split and merge. For example, they can be used to compare
4768 different clusterings. This package provides an implementation of Sankey
4770 (license license:gpl2+)))
4772 (define-public r-dyn
4779 (uri (cran-uri "dyn" version))
4782 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
4783 (build-system r-build-system)
4785 `(("r-zoo" ,r-zoo)))
4786 (home-page "https://cran.r-project.org/web/packages/dyn")
4787 (synopsis "Time series regression")
4789 "This package provides the dyn class interfaces @code{ts}, @code{irts},
4790 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
4791 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
4792 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
4793 @code{randomForest::randomForest()} and other regression functions, allowing
4794 those functions to be used with time series including specifications that may
4795 contain lags, diffs and missing values.")
4797 (license license:gpl2+)))
4799 (define-public r-catdap
4806 (uri (cran-uri "catdap" version))
4809 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
4810 (build-system r-build-system)
4812 `(("gfortran" ,gfortran)))
4813 (home-page "https://cran.r-project.org/web/packages/catdap/")
4814 (synopsis "Tools for categorical data analysis")
4816 "This package provides functions for analyzing multivariate data.
4817 Dependencies of the distribution of the specified variable (response
4818 variable) to other variables (explanatory variables) are derived and
4819 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
4820 (license license:gpl2+)))
4822 (define-public r-arules
4829 (uri (cran-uri "arules" version))
4832 "0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y"))))
4833 (build-system r-build-system)
4835 `(("r-matrix" ,r-matrix)))
4836 (home-page "https://github.com/mhahsler/arules")
4837 (synopsis "Mining association rules and frequent itemsets")
4839 "This package provides an infrastructure for representing, manipulating
4840 and analyzing transaction data and patterns (frequent itemsets and association rules).
4841 It also provides C implementations of the association mining algorithms Apriori
4843 (license license:gpl3)))
4845 (define-public r-parsedate
4847 (name "r-parsedate")
4852 (uri (cran-uri "parsedate" version))
4855 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
4856 (build-system r-build-system)
4858 `(("r-rematch2" ,r-rematch2)))
4859 (home-page "https://github.com/gaborcsardi/parsedate")
4861 "Recognize and parse dates in various formats")
4863 "This package provides three functions for dealing with dates:
4864 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
4865 time formats, @code{parse_date} parses dates in unspecified formats,
4866 and @code{format_iso_8601} formats a date in ISO 8601 format.")
4867 (license license:gpl2)))
4869 (define-public r-abc-data
4876 (uri (cran-uri "abc.data" version))
4879 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
4880 (properties `((upstream-name . "abc.data")))
4881 (build-system r-build-system)
4882 (home-page "https://cran.r-project.org/web/packages/abc.data/")
4883 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
4885 "This package contains data which are used by functions of the abc
4886 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
4887 algorithms for performing parameter estimation, model selection, and
4889 (license license:gpl3+)))
4891 (define-public r-abc
4898 (uri (cran-uri "abc" version))
4901 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
4902 (build-system r-build-system)
4904 `(("r-abc-data" ,r-abc-data)
4905 ("r-locfit" ,r-locfit)
4908 ("r-quantreg" ,r-quantreg)))
4909 (home-page "https://cran.r-project.org/web/packages/abc/")
4910 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
4912 "This package implements several @dfn{Approximate Bayesian
4913 Computation} (ABC) algorithms for performing parameter estimation, model
4914 selection, and goodness-of-fit. Cross-validation tools are also available for
4915 measuring the accuracy of ABC estimates, and to calculate the
4916 misclassification probabilities of different models.")
4917 (license license:gpl3+)))
4919 (define-public r-zip
4926 (uri (cran-uri "zip" version))
4929 "0cchbzp2s2qz7r4n9qdwgfgik5xzr0dzxmj25r8435i85k86ysi1"))))
4930 (build-system r-build-system)
4931 (home-page "https://github.com/gaborcsardi/zip")
4932 (synopsis "Cross-platform Zip compression")
4934 "This package provides a cross-platform Zip compression library for R.
4935 It is a replacement for the @code{zip} function, that does not require any
4936 additional external tools on any platform.")
4937 (license license:cc0)))
4939 (define-public r-openxlsx
4946 (uri (cran-uri "openxlsx" version))
4949 "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb"))))
4950 (build-system r-build-system)
4952 `(("r-rcpp" ,r-rcpp)
4954 (home-page "https://github.com/awalker89/openxlsx")
4955 (synopsis "Read, write and edit XLSX files")
4957 "This package simplifies the creation of Excel @code{.xlsx} files by
4958 providing a high level interface to writing, styling and editing worksheets.
4959 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
4960 and @code{XLConnect} packages with the added benefit of removing the
4961 dependency on Java.")
4962 (license license:gpl3)))
4964 (define-public r-rio
4971 (uri (cran-uri "rio" version))
4974 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
4975 (build-system r-build-system)
4977 `(("r-curl" ,r-curl)
4978 ("r-data-table" ,r-data-table)
4979 ("r-foreign" ,r-foreign)
4980 ("r-haven" ,r-haven)
4981 ("r-openxlsx" ,r-openxlsx)
4982 ("r-readxl" ,r-readxl)
4983 ("r-tibble" ,r-tibble)))
4984 (home-page "https://github.com/leeper/rio")
4985 (synopsis "Swiss-army knife for data I/O")
4987 "This package provides streamlined data import and export infrastructure
4988 by making assumptions that the user is probably willing to make: @code{import}
4989 and @code{export} determine the data structure from the file extension,
4990 reasonable defaults are used for data import and export (e.g.,
4991 @code{stringsAsFactors=FALSE}), web-based import is natively
4992 supported (including from SSL/HTTPS), compressed files can be read directly
4993 without explicit decompression, and fast import packages are used where
4994 appropriate. An additional convenience function, @code{convert}, provides a
4995 simple method for converting between file types.")
4996 (license license:gpl2)))
4998 (define-public r-maptools
5005 (uri (cran-uri "maptools" version))
5008 "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax"))))
5009 (build-system r-build-system)
5011 `(("r-foreign" ,r-foreign)
5012 ("r-lattice" ,r-lattice)
5014 (home-page "http://r-forge.r-project.org/projects/maptools/")
5015 (synopsis "Tools for reading and handling spatial objects")
5017 "This package provides a set of tools for manipulating and reading
5018 geographic data, in particular ESRI Shapefiles. It includes binary access to
5019 GSHHG shoreline files. The package also provides interface wrappers for
5020 exchanging spatial objects with other R packages.")
5021 ;; The C source files from shapelib are released under the Expat license.
5022 ;; The R code is released under GPL version 2 or later.
5023 (license (list license:gpl2+
5026 (define-public r-later
5033 (uri (cran-uri "later" version))
5036 "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb"))))
5037 (build-system r-build-system)
5041 ("r-rlang" ,r-rlang)))
5042 (home-page "https://github.com/r-lib/later")
5043 (synopsis "Utilities for delaying function execution")
5045 "This package provides tools to execute arbitrary R or C functions some
5046 time after the current time, after the R execution stack has emptied.")
5047 (license license:gpl2+)))
5049 (define-public r-promises
5056 (uri (cran-uri "promises" version))
5059 "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
5060 (build-system r-build-system)
5062 `(("r-later" ,r-later)
5063 ("r-magrittr" ,r-magrittr)
5066 ("r-rlang" ,r-rlang)))
5067 (home-page "https://rstudio.github.io/promises")
5068 (synopsis "Abstractions for promise-based asynchronous programming")
5070 "This package provides fundamental abstractions for doing asynchronous
5071 programming in R using promises. Asynchronous programming is useful for
5072 allowing a single R process to orchestrate multiple tasks in the background
5073 while also attending to something else. Semantics are similar to JavaScript
5074 promises, but with a syntax that is idiomatic R.")
5075 (license license:expat)))
5077 (define-public r-dosnow
5084 (uri (cran-uri "doSNOW" version))
5087 "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
5088 (properties `((upstream-name . "doSNOW")))
5089 (build-system r-build-system)
5091 `(("r-foreach" ,r-foreach)
5092 ("r-iterators" ,r-iterators)
5093 ("r-snow" ,r-snow)))
5094 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5095 (synopsis "Foreach parallel adaptor for the snow package")
5097 "This package provides a parallel backend for the @code{%dopar%} function
5098 using the @code{snow} package.")
5099 (license license:gpl2)))
5101 (define-public r-snowfall
5104 (version "1.84-6.1")
5107 (uri (cran-uri "snowfall" version))
5109 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5110 (build-system r-build-system)
5112 `(("r-snow" ,r-snow)))
5113 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5114 (synopsis "Easier cluster computing")
5115 (description "This package is a usability wrapper around snow for easier
5116 development of parallel R programs. This package offers e.g. extended error
5117 checks, and additional functions. All functions work in sequential mode, too,
5118 if no cluster is present or wished. The package is also designed as connector
5119 to the cluster management tool @code{sfCluster}, but can also used without
5121 (license license:gpl2+)))
5123 (define-public r-rappdirs
5130 (uri (cran-uri "rappdirs" version))
5133 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5134 (build-system r-build-system)
5135 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5136 (synopsis "Determine where to save data, caches, and logs")
5138 "This package provides an easy way to determine which directories on the
5139 user's computer should be used to save data, caches and logs. It is a port of
5140 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5141 (license license:expat)))
5143 (define-public r-learnr
5150 (uri (cran-uri "learnr" version))
5153 "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5"))))
5154 (build-system r-build-system)
5156 `(("r-evaluate" ,r-evaluate)
5157 ("r-htmltools" ,r-htmltools)
5158 ("r-htmlwidgets" ,r-htmlwidgets)
5159 ("r-jsonlite" ,r-jsonlite)
5160 ("r-knitr" ,r-knitr)
5161 ("r-markdown" ,r-markdown)
5162 ("r-rappdirs" ,r-rappdirs)
5163 ("r-rmarkdown" ,r-rmarkdown)
5164 ("r-rprojroot" ,r-rprojroot)
5165 ("r-shiny" ,r-shiny)
5166 ("r-withr" ,r-withr)))
5167 (home-page "https://rstudio.github.io/learnr/")
5168 (synopsis "Interactive tutorials for R")
5170 "This package provides tools to create interactive tutorials using R
5171 Markdown. Use a combination of narrative, figures, videos, exercises, and
5172 quizzes to create self-paced tutorials for learning about R and R packages.")
5173 (license license:asl2.0)))
5175 (define-public r-analytics
5177 (name "r-analytics")
5182 (uri (cran-uri "analytics" version))
5185 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5186 (build-system r-build-system)
5189 ("r-cluster" ,r-cluster)
5190 ("r-fractal" ,r-fractal)
5191 ("r-lmtest" ,r-lmtest)
5194 ("r-powerplus" ,r-powerplus)
5195 ("r-robust" ,r-robust)
5196 ("r-trend" ,r-trend)
5200 (home-page "https://cran.r-project.org/web/packages/analytics/")
5201 (synopsis "Collection of data analysis tools")
5203 "This package is a collection of data analysis tools. It includes tools
5204 for regression outlier detection in a fitted linear model, stationary
5205 bootstrap using a truncated geometric distribution, a comprehensive test for
5206 weak stationarity, column means by group, weighted biplots, and a heuristic to
5207 obtain a better initial configuration in non-metric MDS.")
5208 (license license:gpl2)))
5210 (define-public r-reticulate
5212 (name "r-reticulate")
5217 (uri (cran-uri "reticulate" version))
5220 "0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb"))))
5221 (build-system r-build-system)
5222 (inputs `(("python" ,python)))
5224 `(("r-jsonlite" ,r-jsonlite)
5225 ("r-matrix" ,r-matrix)
5226 ("r-rcpp" ,r-rcpp)))
5227 (home-page "https://github.com/rstudio/reticulate")
5228 (synopsis "R interface to Python")
5230 "This package provides an interface from R to Python modules, classes,
5231 and functions. When calling into Python, R data types are automatically
5232 converted to their equivalent Python types. When values are returned from
5233 Python to R they are converted back to R types.")
5234 (license license:asl2.0)))
5236 (define-public r-bibtex
5243 (uri (cran-uri "bibtex" version))
5246 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5247 (build-system r-build-system)
5248 (propagated-inputs `(("r-stringr" ,r-stringr)))
5249 (home-page "https://github.com/romainfrancois/bibtex")
5250 (synopsis "Bibtex parser")
5251 (description "This package provides a utility for R to parse a bibtex
5253 (license license:gpl2+)))
5255 (define-public r-ggseqlogo
5257 (name "r-ggseqlogo")
5262 (uri (cran-uri "ggseqlogo" version))
5265 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5266 (build-system r-build-system)
5267 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5268 (home-page "https://github.com/omarwagih/ggseqlogo")
5269 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5271 "The range of functions provided by this package makes it possible to
5272 draw highly versatile genomic sequence logos. Features include, but are not
5273 limited to, modifying colour schemes and fonts used to draw the logo,
5274 generating multiple logo plots, and aiding the visualisation with annotations.
5275 Sequence logos can easily be combined with other ggplot2 plots.")
5276 ;; Unspecified version of the LGPL.
5277 (license license:lgpl3+)))
5279 (define-public r-ggsci
5286 (uri (cran-uri "ggsci" version))
5289 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5290 (build-system r-build-system)
5292 `(("r-ggplot2" ,r-ggplot2)
5293 ("r-scales" ,r-scales)))
5294 (home-page "https://nanx.me/ggsci/")
5295 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5297 "This package provides a collection of ggplot2 color palettes inspired by
5298 plots in scientific journals, data visualization libraries, science fiction
5299 movies, and TV shows.")
5300 (license license:gpl3)))
5302 (define-public r-ggsignif
5309 (uri (cran-uri "ggsignif" version))
5312 "0z04g5kqdj66fyfxb5d2m7njkqd7idbiy4xgsnxdh5pbh3cr643x"))))
5313 (build-system r-build-system)
5315 `(("r-ggplot2" ,r-ggplot2)))
5316 (home-page "https://github.com/const-ae/ggsignif")
5317 (synopsis "Significance brackets for ggplot2")
5319 "Enrich your ggplots with group-wise comparisons. This package provides
5320 an easy way to indicate if two groups are significantly different. Commonly
5321 this is shown by a bracket on top connecting the groups of interest which
5322 itself is annotated with the level of significance. The package provides a
5323 single layer that takes the groups for comparison and the test as arguments
5324 and adds the annotation to the plot.")
5325 (license license:gpl3)))
5327 (define-public r-ggpubr
5334 (uri (cran-uri "ggpubr" version))
5337 "0rkpcjb1x7lvhj68aam5airbi534jqyiq12x5xk40a25iifhghq6"))))
5338 (build-system r-build-system)
5340 `(("r-cowplot" ,r-cowplot)
5341 ("r-dplyr" ,r-dplyr)
5342 ("r-ggplot2" ,r-ggplot2)
5343 ("r-ggrepel" ,r-ggrepel)
5344 ("r-ggsci" ,r-ggsci)
5345 ("r-ggsignif" ,r-ggsignif)
5347 ("r-gridextra" ,r-gridextra)
5348 ("r-magrittr" ,r-magrittr)
5349 ("r-polynom" ,r-polynom)
5350 ("r-purrr" ,r-purrr)
5351 ("r-scales" ,r-scales)
5352 ("r-tidyr" ,r-tidyr)))
5353 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5354 (synopsis "ggplot2-based publication-ready plots")
5356 "The ggplot2 package is an excellent and flexible package for elegant
5357 data visualization in R. However the default generated plots require some
5358 formatting before we can send them for publication. The ggpubr package
5359 provides some easy-to-use functions for creating and customizing ggplot2-based
5360 publication-ready plots.")
5361 (license license:gpl2)))
5363 (define-public r-ellipse
5370 (uri (cran-uri "ellipse" version))
5373 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5374 (build-system r-build-system)
5375 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5376 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5378 "This package contains various routines for drawing ellipses and
5379 ellipse-like confidence regions, implementing the plots described in Murdoch
5380 and Chow (1996), A graphical display of large correlation matrices, The
5381 American Statistician 50, 178-180. There are also routines implementing the
5382 profile plots described in Bates and Watts (1988), Nonlinear Regression
5383 Analysis and its Applications.")
5384 (license license:gpl2+)))
5386 (define-public r-flashclust
5388 (name "r-flashclust")
5393 (uri (cran-uri "flashClust" version))
5396 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5397 (properties `((upstream-name . "flashClust")))
5398 (build-system r-build-system)
5399 (native-inputs `(("gfortran" ,gfortran)))
5400 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5401 (synopsis "Implementation of optimal hierarchical clustering")
5403 "This package provides a fast implementation of hierarchical
5405 (license license:gpl2+)))
5407 (define-public r-factominer
5409 (name "r-factominer")
5414 (uri (cran-uri "FactoMineR" version))
5417 "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
5418 (properties `((upstream-name . "FactoMineR")))
5419 (build-system r-build-system)
5422 ("r-cluster" ,r-cluster)
5423 ("r-ellipse" ,r-ellipse)
5424 ("r-flashclust" ,r-flashclust)
5425 ("r-lattice" ,r-lattice)
5426 ("r-leaps" ,r-leaps)
5428 ("r-scatterplot3d" ,r-scatterplot3d)))
5429 (home-page "http://factominer.free.fr")
5430 (synopsis "Multivariate exploratory data analysis and data mining")
5432 "This package provides exploratory data analysis methods to summarize,
5433 visualize and describe datasets. The main principal component methods are
5434 available, those with the largest potential in terms of applications:
5435 principal component analysis (PCA) when variables are quantitative,
5436 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5437 variables are categorical, Multiple Factor Analysis when variables are
5438 structured in groups, etc. and hierarchical cluster analysis.")
5439 (license license:gpl2+)))
5441 (define-public r-factoextra
5443 (name "r-factoextra")
5448 (uri (cran-uri "factoextra" version))
5451 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
5452 (build-system r-build-system)
5454 `(("r-abind" ,r-abind)
5455 ("r-cluster" ,r-cluster)
5456 ("r-dendextend" ,r-dendextend)
5457 ("r-factominer" ,r-factominer)
5458 ("r-ggplot2" ,r-ggplot2)
5459 ("r-ggpubr" ,r-ggpubr)
5460 ("r-ggrepel" ,r-ggrepel)
5461 ("r-reshape2" ,r-reshape2)
5462 ("r-tidyr" ,r-tidyr)))
5463 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5464 (synopsis "Extract and visualize the results of multivariate data analyses")
5466 "This package provides some easy-to-use functions to extract and
5467 visualize the output of multivariate data analyses, including
5468 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5469 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5470 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5471 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5472 packages. It contains also functions for simplifying some clustering analysis
5473 steps and provides ggplot2-based elegant data visualization.")
5474 (license license:gpl2)))
5476 (define-public r-fansi
5483 (uri (cran-uri "fansi" version))
5486 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
5487 (build-system r-build-system)
5489 `(("r-knitr" ,r-knitr))) ; for vignettes
5490 (home-page "https://github.com/brodieG/fansi")
5491 (synopsis "ANSI control sequence aware string functions")
5493 "This package provides counterparts to R string manipulation functions
5494 that account for the effects of ANSI text formatting control sequences.")
5495 (license license:gpl2+)))
5497 (define-public r-nbclust
5504 (uri (cran-uri "NbClust" version))
5507 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
5508 (properties `((upstream-name . "NbClust")))
5509 (build-system r-build-system)
5510 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
5511 (synopsis "Determine the best number of clusters in a data set")
5513 "NbClust provides 30 indexes for determining the optimal number of
5514 clusters in a data set and offers the best clustering scheme from different
5515 results to the user.")
5516 (license license:gpl2)))
5518 (define-public r-hdf5r
5525 (uri (cran-uri "hdf5r" version))
5528 "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq"))))
5529 (build-system r-build-system)
5534 `(("r-bit64" ,r-bit64)
5536 (home-page "https://hhoeflin.github.io/hdf5r")
5537 (synopsis "Interface to the HDF5 binary data format")
5539 "HDF5 is a data model, library and file format for storing and managing
5540 large amounts of data. This package provides a nearly feature complete,
5541 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
5542 functionality is added so that HDF5 objects behave very similar to their
5543 corresponding R counterparts.")
5544 (license license:asl2.0)))
5546 (define-public r-itertools
5548 (name "r-itertools")
5553 (uri (cran-uri "itertools" version))
5556 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
5557 (build-system r-build-system)
5559 `(("r-iterators" ,r-iterators)))
5560 (home-page "https://cran.r-project.org/web/packages/itertools/")
5561 (synopsis "Iterator tools")
5563 "This package provides various tools for creating iterators, many
5564 patterned after functions in the Python @code{itertools} module, and others
5565 patterned after functions in the snow package.")
5566 (license license:gpl2)))
5568 (define-public r-polynom
5575 (uri (cran-uri "polynom" version))
5578 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
5579 (build-system r-build-system)
5580 (home-page "https://cran.r-project.org/web/packages/polynom/")
5581 (synopsis "Functions for univariate polynomial manipulations")
5583 "This package provides a collection of functions to implement a class for
5584 univariate polynomial manipulations.")
5585 (license license:gpl2)))
5587 (define-public r-gbrd
5594 (uri (cran-uri "gbRd" version))
5597 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
5598 (properties `((upstream-name . "gbRd")))
5599 (build-system r-build-system)
5600 (home-page "https://cran.r-project.org/web/packages/gbRd/")
5601 (synopsis "Utilities for processing Rd objects and files")
5603 "This package provides utilities for processing Rd objects and files.
5604 Extract argument descriptions and other parts of the help pages of
5606 (license license:gpl2+)))
5608 (define-public r-rjags
5615 (uri (cran-uri "rjags" version))
5618 "17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m"))))
5619 (build-system r-build-system)
5621 `(("r-coda" ,r-coda)))
5625 `(("pkg-config" ,pkg-config)))
5626 (home-page "http://mcmc-jags.sourceforge.net")
5627 (synopsis "Bayesian graphical models using MCMC")
5629 "This package provides an R interface to the JAGS MCMC library. JAGS is
5630 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
5631 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
5632 (license license:gpl2)))
5634 (define-public r-rdpack
5641 (uri (cran-uri "Rdpack" version))
5644 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
5645 (properties `((upstream-name . "Rdpack")))
5646 (build-system r-build-system)
5648 `(("r-bibtex" ,r-bibtex)
5649 ("r-gbrd" ,r-gbrd)))
5650 (home-page "https://github.com/GeoBosh/Rdpack")
5651 (synopsis "Update and manipulate Rd documentation objects")
5653 "This package provides functions for manipulation of R documentation
5654 objects, including functions @code{reprompt()} and @code{ereprompt()} for
5655 updating Rd documentation for functions, methods and classes; it also includes
5656 Rd macros for citations and import of references from bibtex files for use in
5657 Rd files and roxygen2 comments, as well as many functions for manipulation of
5658 references and Rd files.")
5659 (license license:gpl2+)))
5661 (define-public r-officer
5668 (uri (cran-uri "officer" version))
5671 "1m4b3mcn5j5q3nq0jp1nranh4rdb8vxcpabn6ryqk9m6709fvhjz"))))
5672 (build-system r-build-system)
5674 `(("r-base64enc" ,r-base64enc)
5675 ("r-digest" ,r-digest)
5676 ("r-htmltools" ,r-htmltools)
5677 ("r-magrittr" ,r-magrittr)
5680 ("r-rlang" ,r-rlang)
5684 (home-page "https://davidgohel.github.io/officer")
5685 (synopsis "Manipulation of Word and PowerPoint documents")
5687 "This package provides tools to access and manipulate Word and PowerPoint
5688 documents from R. The package focuses on tabular and graphical reporting from
5689 R; it also provides two functions that let users get document content into
5690 data objects. A set of functions lets add and remove images, tables and
5691 paragraphs of text in new or existing documents. When working with PowerPoint
5692 presentations, slides can be added or removed; shapes inside slides can also
5693 be added or removed. When working with Word documents, a cursor can be used
5694 to help insert or delete content at a specific location in the document.")
5695 (license license:gpl3)))
5697 (define-public r-abn
5704 (uri (cran-uri "abn" version))
5707 "1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm"))))
5708 (build-system r-build-system)
5712 `(("r-cairo" ,r-cairo)
5717 ("r-rcpparmadillo" ,r-rcpparmadillo)
5718 ("r-rjags" ,r-rjags)))
5719 (home-page "http://www.r-bayesian-networks.org")
5720 (synopsis "Modelling multivariate data with additive bayesian networks")
5722 "Bayesian network analysis is a form of probabilistic graphical models
5723 which derives from empirical data a directed acyclic graph, DAG, describing
5724 the dependency structure between random variables. An additive Bayesian
5725 network model consists of a form of a DAG where each node comprises a
5726 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
5727 equivalent to Bayesian multivariate regression using graphical modelling, they
5728 generalises the usual multivariable regression, GLM, to multiple dependent
5729 variables. This package provides routines to help determine optimal Bayesian
5730 network models for a given data set, where these models are used to identify
5731 statistical dependencies in messy, complex data.")
5732 (license license:gpl2+)))
5734 (define-public r-acd
5741 (uri (cran-uri "ACD" version))
5744 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
5745 (properties `((upstream-name . "ACD")))
5746 (build-system r-build-system)
5747 (home-page "https://cran.r-project.org/web/packages/ACD/")
5748 (synopsis "Categorical data analysis with complete or missing responses")
5750 "This package provides tools for categorical data analysis with complete
5751 or missing responses.")
5752 (license license:gpl2+)))
5754 (define-public r-acdm
5761 (uri (cran-uri "ACDm" version))
5764 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
5765 (properties `((upstream-name . "ACDm")))
5766 (build-system r-build-system)
5768 `(("r-dplyr" ,r-dplyr)
5769 ("r-ggplot2" ,r-ggplot2)
5771 ("r-rsolnp" ,r-rsolnp)
5773 (home-page "https://cran.r-project.org/web/packages/ACDm/")
5774 (synopsis "Tools for Autoregressive Conditional Duration Models")
5776 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
5777 and Russell, 1998) models. It creates trade, price or volume durations from
5778 transactions (tic) data, performs diurnal adjustments, fits various ACD models
5780 (license license:gpl2+)))
5782 (define-public r-overlap
5789 (uri (cran-uri "overlap" version))
5792 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
5793 (build-system r-build-system)
5794 (home-page "https://cran.r-project.org/web/packages/overlap/")
5795 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
5797 "This package provides functions to fit kernel density functions to data
5798 on temporal activity patterns of animals; estimate coefficients of overlapping
5799 of densities for two species; and calculate bootstrap estimates of confidence
5801 (license license:gpl3+)))
5803 (define-public r-snakecase
5805 (name "r-snakecase")
5810 (uri (cran-uri "snakecase" version))
5813 "1g6xai53dl24ws0mwhqrkcv583ziaq505cv3z8v5dhjgy98kilyj"))))
5814 (build-system r-build-system)
5816 `(("r-stringi" ,r-stringi)
5817 ("r-stringr" ,r-stringr)))
5818 (home-page "https://github.com/Tazinho/snakecase")
5819 (synopsis "Convert strings into any case")
5821 "This package provides a consistent, flexible and easy to use tool to
5822 parse and convert strings into cases like snake or camel among others.")
5823 (license license:gpl3)))
5825 (define-public r-prediction
5827 (name "r-prediction")
5832 (uri (cran-uri "prediction" version))
5835 "0kx7xbm2j6c8h6gk1iig4vfpg877psg16j74hl7zc2mv40sc6dy5"))))
5836 (build-system r-build-system)
5838 `(("r-data-table" ,r-data-table)))
5839 (home-page "https://github.com/leeper/prediction")
5840 (synopsis "Tidy, type-safe prediction methods")
5842 "This package provides the @code{prediction()} function, a type-safe
5843 alternative to @code{predict()} that always returns a data frame. The package
5844 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
5845 from the @code{stats} package, as well as numerous other model classes from
5846 other add-on packages.")
5847 (license license:expat)))
5849 (define-public r-insight
5856 (uri (cran-uri "insight" version))
5859 "0fn9cd5qxqlpjv3d05mk66k5z5ll60x5la51mby5h7k4l6bqmsiz"))))
5860 (build-system r-build-system)
5861 (home-page "https://easystats.github.io/insight/")
5862 (synopsis "Easy access to model information for various model objects")
5864 "This package provides a tool to provide an easy, intuitive and
5865 consistent access to information contained in various R models, like model
5866 formulas, model terms, information about random effects, data that was used to
5867 fit the model or data from response variables. The package mainly revolves
5868 around two types of functions: Functions that find (the names of) information,
5869 starting with @code{find_}, and functions that get the underlying data,
5870 starting with @code{get_}. The package has a consistent syntax and works with
5871 many different model objects, where otherwise functions to access these
5872 information are missing.")
5873 (license license:gpl3)))
5875 (define-public r-sjlabelled
5877 (name "r-sjlabelled")
5882 (uri (cran-uri "sjlabelled" version))
5885 "00c0c22ynpihgf2bvmcfnkvqwqvxax2zzb7wldsmg2f7z5a32aa6"))))
5886 (build-system r-build-system)
5888 `(("r-dplyr" ,r-dplyr)
5889 ("r-haven" ,r-haven)
5890 ("r-insight" ,r-insight)
5891 ("r-magrittr" ,r-magrittr)
5892 ("r-purrr" ,r-purrr)
5893 ("r-rlang" ,r-rlang)))
5894 (home-page "https://github.com/strengejacke/sjlabelled")
5895 (synopsis "Labelled data utility functions")
5897 "This package provides a collection of functions dealing with labelled
5898 data, like reading and writing data between R and other statistical software
5899 packages. This includes easy ways to get, set or change value and variable
5900 label attributes, to convert labelled vectors into factors or numeric (and
5901 vice versa), or to deal with multiple declared missing values.")
5902 (license license:gpl3)))
5904 (define-public r-sjmisc
5911 (uri (cran-uri "sjmisc" version))
5914 "11iiap0w5v0dszgwx4pi3j1zf9vnlw1ml1wjvq1hg9iz1plgbfnc"))))
5915 (build-system r-build-system)
5917 `(("r-dplyr" ,r-dplyr)
5918 ("r-haven" ,r-haven)
5919 ("r-magrittr" ,r-magrittr)
5920 ("r-purrr" ,r-purrr)
5921 ("r-rlang" ,r-rlang)
5922 ("r-sjlabelled" ,r-sjlabelled)))
5923 (home-page "https://github.com/strengejacke/sjmisc")
5924 (synopsis "Data and variable transformation functions")
5926 "This package is a collection of miscellaneous utility functions,
5927 supporting data transformation tasks like recoding, dichotomizing or grouping
5928 variables, setting and replacing missing values. The data transformation
5929 functions also support labelled data, and all integrate seamlessly into a
5930 tidyverse workflow.")
5931 (license license:gpl3)))
5933 (define-public r-nortest
5940 (uri (cran-uri "nortest" version))
5943 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
5944 (build-system r-build-system)
5945 (home-page "https://cran.r-project.org/web/packages/nortest/")
5946 (synopsis "Tests for normality")
5948 "This package provides five omnibus tests for testing the composite
5949 hypothesis of normality.")
5950 (license license:gpl2+)))
5952 (define-public r-moonbook
5959 (uri (cran-uri "moonBook" version))
5962 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
5963 (properties `((upstream-name . "moonBook")))
5964 (build-system r-build-system)
5966 `(("r-magrittr" ,r-magrittr)
5967 ("r-nortest" ,r-nortest)
5968 ("r-purrr" ,r-purrr)
5969 ("r-sjmisc" ,r-sjmisc)
5970 ("r-stringr" ,r-stringr)
5971 ("r-survival" ,r-survival)))
5972 (home-page "https://github.com/cardiomoon/moonBook")
5973 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
5975 "This package provides several analysis-related functions for the book
5976 entitled \"R statistics and graph for medical articles\" (written in Korean),
5977 version 1, by Keon-Woong Moon with Korean demographic data with several plot
5979 (license license:gpl2)))
5981 (define-public r-flextable
5983 (name "r-flextable")
5988 (uri (cran-uri "flextable" version))
5991 "0sabdvkdlx5i1nr7nz68cappwsibzsjxpmiz3yp948ckbfmkdb27"))))
5992 (build-system r-build-system)
5994 `(("r-base64enc" ,r-base64enc)
5995 ("r-data-table" ,r-data-table)
5996 ("r-gdtools" ,r-gdtools)
5997 ("r-htmltools" ,r-htmltools)
5998 ("r-knitr" ,r-knitr)
5999 ("r-officer" ,r-officer)
6000 ("r-rlang" ,r-rlang)
6001 ("r-rmarkdown" ,r-rmarkdown)
6002 ("r-xml2" ,r-xml2)))
6003 (home-page "https://davidgohel.github.io/flextable")
6004 (synopsis "Functions for tabular reporting")
6006 "This package provides tools to create pretty tables for HTML documents
6007 and other formats. Functions are provided to let users create tables, modify
6008 and format their content. It extends the @code{officer} package and can be
6009 used within R markdown documents when rendering to HTML and to Word
6011 (license license:gpl3)))
6013 (define-public r-writexl
6020 (uri (cran-uri "writexl" version))
6023 "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"))))
6024 (build-system r-build-system)
6025 (inputs `(("zlib" ,zlib)))
6026 (home-page "https://github.com/ropensci/writexl")
6027 (synopsis "Export data frames to xlsx format")
6029 "This package provides a data frame to xlsx exporter based on
6031 (license license:bsd-2)))
6033 (define-public r-biasedurn
6035 (name "r-biasedurn")
6040 (uri (cran-uri "BiasedUrn" version))
6043 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6044 (properties `((upstream-name . "BiasedUrn")))
6045 (build-system r-build-system)
6046 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6047 (synopsis "Biased Urn model distributions")
6049 "This package provides statistical models of biased sampling in the form
6050 of univariate and multivariate noncentral hypergeometric distributions,
6051 including Wallenius' noncentral hypergeometric distribution and Fisher's
6052 noncentral hypergeometric distribution (also called extended hypergeometric
6054 (license license:gpl3)))
6056 (define-public r-goplot
6063 (uri (cran-uri "GOplot" version))
6066 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6067 (properties `((upstream-name . "GOplot")))
6068 (build-system r-build-system)
6070 `(("r-ggdendro" ,r-ggdendro)
6071 ("r-ggplot2" ,r-ggplot2)
6072 ("r-gridextra" ,r-gridextra)
6073 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6074 (home-page "https://github.com/wencke/wencke.github.io")
6075 (synopsis "Visualization of functional analysis data")
6077 "This package provides an implementation of multilayered visualizations
6078 for enhanced graphical representation of functional analysis data. It
6079 combines and integrates omics data derived from expression and functional
6080 annotation enrichment analyses. Its plotting functions have been developed
6081 with an hierarchical structure in mind: starting from a general overview to
6082 identify the most enriched categories (modified bar plot, bubble plot) to a
6083 more detailed one displaying different types of relevant information for the
6084 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6085 Venn diagram, heatmap).")
6086 (license license:gpl2)))
6088 (define-public r-getopt
6095 (uri (cran-uri "getopt" version))
6098 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6099 (build-system r-build-system)
6100 (home-page "https://github.com/trevorld/getopt")
6101 (synopsis "Command-line option processor for R")
6103 "This package is designed to be used with Rscript to write shebang
6104 scripts that accept short and long options. Many users will prefer to
6105 use the packages @code{optparse} or @code{argparse} which add extra
6106 features like automatically generated help options and usage texts,
6107 support for default values, positional argument support, etc.")
6108 (license license:gpl2+)))
6110 (define-public r-findpython
6112 (name "r-findpython")
6117 (uri (cran-uri "findpython" version))
6120 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6121 (build-system r-build-system)
6122 (home-page "https://github.com/trevorld/findpython")
6123 (synopsis "Functions to find an acceptable Python binary")
6125 "This package was designed to find an acceptable Python binary that
6126 matches version and feature constraints.")
6127 (license license:expat)))
6129 ;; This in not the same as "r-argparser"
6130 (define-public r-argparse
6137 (uri (cran-uri "argparse" version))
6140 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6141 (build-system r-build-system)
6142 (inputs `(("python" ,python)))
6144 `(("r-findpython" ,r-findpython)
6145 ("r-jsonlite" ,r-jsonlite)
6147 (home-page "https://github.com/trevorld/argparse")
6148 (synopsis "Command line optional and positional argument parser")
6150 "This package provides a command line parser to be used with Rscript to
6151 write shebang scripts that gracefully accept positional and optional arguments
6152 and automatically generate usage notices.")
6153 (license license:gpl2+)))
6155 (define-public r-hash
6162 (uri (cran-uri "hash" version))
6165 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6166 (build-system r-build-system)
6167 (home-page "https://cran.r-project.org/web/packages/hash/")
6168 (synopsis "Implementation of hash/associated arrays/dictionaries")
6170 "This package implements a data structure similar to hashes in Perl and
6171 dictionaries in Python but with a purposefully R flavor. For objects of
6172 appreciable size, access using hashes outperforms native named lists and
6174 (license license:gpl2+)))
6176 (define-public r-orddom
6183 (uri (cran-uri "orddom" version))
6186 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6187 (build-system r-build-system)
6188 (propagated-inputs `(("r-psych" ,r-psych)))
6189 (home-page "https://cran.r-project.org/web/packages/orddom/")
6190 (synopsis "Ordinal dominance statistics")
6192 "This package provides tools to compute ordinal, statistics and effect
6193 sizes as an alternative to mean comparison: Cliff's delta or success rate
6194 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6195 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6196 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6197 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6198 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6199 Group (Non-)Overlap considerations.")
6200 (license license:gpl2)))
6202 (define-public r-doby
6209 (uri (cran-uri "doBy" version))
6212 "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb"))))
6213 (properties `((upstream-name . "doBy")))
6214 (build-system r-build-system)
6216 `(("r-dplyr" ,r-dplyr)
6217 ("r-magrittr" ,r-magrittr)
6219 ("r-matrix" ,r-matrix)
6220 ("r-plyr" ,r-plyr)))
6221 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6222 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6224 "This package contains:
6227 @item facilities for working with grouped data: @code{do}
6228 something to data stratified @code{by} some variables.
6229 @item implementations of least-squares means, general linear contrasts, and
6230 @item miscellaneous other utilities.
6232 (license license:gpl2+)))
6234 (define-public r-refgenome
6236 (name "r-refgenome")
6241 (uri (cran-uri "refGenome" version))
6244 "1s4lxv5pqk6d0f0a9iclgv88yl346fwvzgraxh0gwpbym1yhh787"))))
6245 (properties `((upstream-name . "refGenome")))
6246 (build-system r-build-system)
6250 ("r-rsqlite" ,r-rsqlite)))
6251 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6253 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6255 "This package contains functionality for importing and managing of
6256 downloaded genome annotation data from the Ensembl genome browser (European
6257 Bioinformatics Institute) and from the UCSC genome browser (University of
6258 California, Santa Cruz) and annotation routines for genomic positions and
6259 splice site positions.")
6260 (license license:gpl2)))
6262 (define-public r-basix
6269 (uri (cran-uri "BASIX" version))
6272 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6273 (properties `((upstream-name . "BASIX")))
6274 (build-system r-build-system)
6275 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6276 (synopsis "Efficient C/C++ toolset for R")
6278 "BASIX provides some efficient C/C++ implementations of native R
6279 procedures to speed up calculations in R.")
6280 (license license:gpl2)))
6282 (define-public r-blockfest
6284 (name "r-blockfest")
6289 (uri (cran-uri "BlockFeST" version))
6292 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6293 (properties `((upstream-name . "BlockFeST")))
6294 (build-system r-build-system)
6295 (propagated-inputs `(("r-basix" ,r-basix)))
6296 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6297 (synopsis "Bayesian calculation of region-specific fixation index")
6299 "This package provides an R implementation of an extension of the
6300 BayeScan software for codominant markers, adding the option to group
6301 individual SNPs into pre-defined blocks. A typical application of this new
6302 approach is the identification of genomic regions, genes, or gene sets
6303 containing one or more SNPs that evolved under directional selection.")
6304 (license license:gpl2)))
6306 (define-public r-proc
6313 (uri (cran-uri "pROC" version))
6316 "0ki1pvj5iaki81crapvwqllg5avn5qlvv62axnsdkdcmv9xc3wg0"))))
6317 (properties `((upstream-name . "pROC")))
6318 (build-system r-build-system)
6320 `(("r-plyr" ,r-plyr)
6321 ("r-rcpp" ,r-rcpp)))
6322 (home-page "http://expasy.org/tools/pROC/")
6323 (synopsis "Display and analyze ROC curves")
6325 "This package provides tools for visualizing, smoothing and comparing
6326 receiver operating characteristic (ROC curves). The area under the
6327 curve (AUC) can be compared with statistical tests based on U-statistics or
6328 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6329 (license license:gpl3+)))
6331 (define-public r-rootsolve
6333 (name "r-rootsolve")
6338 (uri (cran-uri "rootSolve" version))
6341 "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8"))))
6342 (properties `((upstream-name . "rootSolve")))
6343 (build-system r-build-system)
6344 (native-inputs `(("gfortran" ,gfortran)))
6345 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6346 (synopsis "Tools for the analysis of ordinary differential equations")
6348 "This package provides routines to find the root of nonlinear functions,
6349 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6350 differential equations} (ODE). It includes routines that:
6353 @item generate gradient and jacobian matrices (full and banded),
6354 @item find roots of non-linear equations by the Newton-Raphson method,
6355 @item estimate steady-state conditions of a system of (differential) equations
6356 in full, banded or sparse form, using the Newton-Raphson method, or by
6357 dynamically running,
6358 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6359 and 3-D partial differential equations, that have been converted to ordinary
6360 differential equations by numerical differencing (using the method-of-lines
6363 (license license:gpl2+)))
6365 (define-public r-abcanalysis
6367 (name "r-abcanalysis")
6372 (uri (cran-uri "ABCanalysis" version))
6374 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6375 (properties `((upstream-name . "ABCanalysis")))
6376 (build-system r-build-system)
6377 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6378 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6379 (synopsis "Computed ABC Analysis")
6381 "Multivariate data sets often differ in several factors or derived statistical
6382 parameters, which have to be selected for a valid interpretation. Basing this
6383 selection on traditional statistical limits leads occasionally to the perception
6384 of losing information from a data set. This package provides tools to calculate
6385 these limits on the basis of the mathematical properties of the distribution of
6386 the analyzed items.")
6387 (license license:gpl3)))
6389 (define-public r-slam
6396 (uri (cran-uri "slam" version))
6398 (base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4"))))
6399 (build-system r-build-system)
6400 (home-page "https://cran.r-project.org/web/packages/slam/")
6401 (synopsis "Sparse lightweight arrays and matrices")
6403 "This package contains data structures and algorithms for sparse arrays and matrices,
6404 based on index arrays and simple triplet representations, respectively.")
6405 (license license:gpl2)))
6407 (define-public r-manipulatewidget
6409 (name "r-manipulatewidget")
6414 (uri (cran-uri "manipulateWidget" version))
6416 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6418 `((upstream-name . "manipulateWidget")))
6419 (build-system r-build-system)
6421 `(("r-base64enc" ,r-base64enc)
6422 ("r-codetools" ,r-codetools)
6423 ("r-htmltools" ,r-htmltools)
6424 ("r-htmlwidgets" ,r-htmlwidgets)
6425 ("r-knitr" ,r-knitr)
6426 ("r-miniui" ,r-miniui)
6427 ("r-shiny" ,r-shiny)
6428 ("r-webshot" ,r-webshot)))
6429 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6430 (synopsis "Add even more interactivity to interactive charts")
6432 "This package lets you create in just a few lines of R code a nice user interface to
6433 modify the data or the graphical parameters of one or multiple interactive
6434 charts. It is useful to quickly explore visually some data or for package
6435 developers to generate user interfaces easy to maintain.")
6436 (license license:gpl2+)))
6445 (uri (cran-uri "A3" version))
6447 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6448 (properties `((upstream-name . "A3")))
6449 (build-system r-build-system)
6451 `(("r-pbapply" ,r-pbapply)
6452 ("r-xtable" ,r-xtable)))
6453 (home-page "https://cran.r-project.org/web/packages/A3/")
6454 (synopsis "Error metrics for predictive models")
6456 "This package supplies tools for tabulating and analyzing the results of predictive
6457 models. The methods employed are applicable to virtually any predictive model
6458 and make comparisons between different methodologies straightforward.")
6459 (license license:gpl2+)))
6461 (define-public r-infotheo
6468 (uri (cran-uri "infotheo" version))
6471 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
6472 (build-system r-build-system)
6473 (home-page "http://homepage.meyerp.com/software")
6474 (synopsis "Information-theoretic measures")
6476 "This package implements various measures of information theory based on
6477 several entropy estimators.")
6478 (license license:gpl3+)))
6480 (define-public r-abcoptim
6487 (uri (cran-uri "ABCoptim" version))
6489 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
6490 (properties `((upstream-name . "ABCoptim")))
6491 (build-system r-build-system)
6492 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
6493 (home-page "https://github.com/gvegayon/ABCoptim/")
6494 (synopsis "Optimization of Artificial Bee Colony algorithm")
6496 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
6497 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
6498 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
6499 algorithms, and uses only common control parameters such as colony size and
6500 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
6501 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
6502 This version is a work-in-progress and is written in R code.")
6503 (license license:expat)))
6505 (define-public r-abcp2
6512 (uri (cran-uri "ABCp2" version))
6514 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
6515 (properties `((upstream-name . "ABCp2")))
6516 (build-system r-build-system)
6517 (propagated-inputs `(("r-mass" ,r-mass)))
6518 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
6519 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
6521 "This package tests the goodness of fit of a distribution of offspring to the Normal,
6522 Poisson, and Gamma distribution and estimates the proportional paternity of the
6523 second male (P2) based on the best fit distribution.")
6524 (license license:gpl2)))
6526 (define-public r-abcrf
6533 (uri (cran-uri "abcrf" version))
6535 (base32 "06vy3inikrr9hv36q4djhrgzi9zizdfnhz17wpra8kadmr7qj441"))))
6536 (build-system r-build-system)
6538 `(("r-mass" ,r-mass)
6539 ("r-matrixstats" ,r-matrixstats)
6540 ("r-ranger" ,r-ranger)
6542 ("r-rcpparmadillo" ,r-rcpparmadillo)
6543 ("r-readr" ,r-readr)
6544 ("r-stringr" ,r-stringr)))
6545 (home-page "https://cran.r-project.org/web/packages/abcrf/")
6546 (synopsis "Approximate bayesian computation via random forests")
6548 "This package performs approximate bayesian computation (ABC) model choice and
6549 parameter inference via random forests. This machine learning tool named random
6550 forests (RF) can conduct selection among the highly complex models covered by
6552 (license license:gpl2+)))
6554 (define-public r-abctools
6561 (uri (cran-uri "abctools" version))
6563 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
6564 (build-system r-build-system)
6567 ("r-abind" ,r-abind)
6568 ("r-hmisc" ,r-hmisc)
6569 ("r-plyr" ,r-plyr)))
6570 (home-page "https://github.com/dennisprangle/abctools/")
6571 (synopsis "Tools for ABC analyses")
6573 "This @code{r-abctools} package provides tools for approximate Bayesian computation
6574 including summary statistic selection and assessing coverage. This includes
6575 recent dimension reduction algorithms to tune the choice of summary statistics,
6576 and coverage methods to tune the choice of threshold.")
6577 (license license:gpl2+)))
6579 (define-public r-ggstance
6586 (uri (cran-uri "ggstance" version))
6588 (base32 "0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh"))))
6589 (build-system r-build-system)
6591 `(("r-ggplot2" ,r-ggplot2)
6593 ("r-rlang" ,r-rlang)
6594 ("r-withr" ,r-withr)))
6595 (home-page "https://cran.r-project.org/web/packages/ggstance/")
6596 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
6598 "This package is a @code{r-ggplot2} extension that provides flipped components:
6600 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
6601 @item vertical versions of @code{r-ggplot2} positions.
6603 (license license:gpl3)))
6605 (define-public r-mosaiccore
6607 (name "r-mosaiccore")
6612 (uri (cran-uri "mosaicCore" version))
6614 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
6615 (properties `((upstream-name . "mosaicCore")))
6616 (build-system r-build-system)
6618 `(("r-dplyr" ,r-dplyr)
6619 ("r-lazyeval" ,r-lazyeval)
6621 ("r-rlang" ,r-rlang)
6622 ("r-tidyr" ,r-tidyr)))
6623 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
6624 (synopsis "Common utilities for mosaic family packages")
6626 "Common utilities used in other Mosaic family packages are collected here.")
6627 (license license:gpl2+)))
6629 (define-public r-ggformula
6631 (name "r-ggformula")
6636 (uri (cran-uri "ggformula" version))
6638 (base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx"))))
6639 (build-system r-build-system)
6641 `(("r-ggplot2" ,r-ggplot2)
6642 ("r-ggstance" ,r-ggstance)
6643 ("r-magrittr" ,r-magrittr)
6644 ("r-mosaiccore" ,r-mosaiccore)
6645 ("r-rlang" ,r-rlang)
6646 ("r-stringr" ,r-stringr)
6647 ("r-tibble" ,r-tibble)
6648 ("r-tidyr" ,r-tidyr)))
6649 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
6650 (synopsis "Formula interface for the @code{r-ggplot2}")
6652 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
6653 gf_density(), and so on, bring the formula interface to ggplot(). This captures
6654 and extends the excellent simplicity of the lattice-graphics formula interface,
6655 while providing the intuitive capabilities of @code{r-ggplot2}.")
6656 (license license:expat)))
6658 (define-public r-mosaicdata
6660 (name "r-mosaicdata")
6665 (uri (cran-uri "mosaicData" version))
6667 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
6668 (properties `((upstream-name . "mosaicData")))
6669 (build-system r-build-system)
6670 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
6671 (synopsis "Data sets for project Mosaic")
6673 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
6674 used to teach mathematics, statistics, computation and modeling.")
6675 (license license:gpl2+)))
6677 (define-public r-raster
6684 (uri (cran-uri "raster" version))
6687 "1lmhf7p7is8ai7lv7zsj2rdzf83j7ccl4x7a9vwxxa824zy4bkf4"))))
6688 (build-system r-build-system)
6690 `(("r-rcpp" ,r-rcpp)
6692 (home-page "https://www.rspatial.org/")
6693 (synopsis "Geographic data analysis and modeling")
6695 "The package implements basic and high-level functions for reading,
6696 writing, manipulating, analyzing and modeling of gridded spatial data.
6697 Processing of very large files is supported.")
6698 (license license:gpl3+)))
6700 (define-public r-mosaic
6707 (uri (cran-uri "mosaic" version))
6709 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
6710 (build-system r-build-system)
6712 `(("r-broom" ,r-broom)
6713 ("r-dplyr" ,r-dplyr)
6714 ("r-ggdendro" ,r-ggdendro)
6715 ("r-ggformula" ,r-ggformula)
6716 ("r-ggplot2" ,r-ggplot2)
6717 ("r-ggrepel" ,r-ggrepel)
6719 ("r-gridextra" ,r-gridextra)
6720 ("r-lattice" ,r-lattice)
6721 ("r-latticeextra" ,r-latticeextra)
6722 ("r-lazyeval" ,r-lazyeval)
6724 ("r-matrix" ,r-matrix)
6725 ("r-mosaiccore" ,r-mosaiccore)
6726 ("r-mosaicdata" ,r-mosaicdata)
6727 ("r-readr" ,r-readr)
6728 ("r-tidyr" ,r-tidyr)))
6729 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
6730 (synopsis "Mathematics, statistics, and computation teaching utilities")
6732 "This package contain data sets and utilities from
6733 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
6734 statistics, computation and modeling. Project MOSAIC is a community of
6735 educators working to tie together aspects of quantitative work that students
6736 in science, technology, engineering and mathematics will need in their
6737 professional lives, but which are usually taught in isolation, if at all.")
6738 (license license:gpl2+)))
6740 (define-public r-abd
6747 (uri (cran-uri "abd" version))
6749 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
6750 (build-system r-build-system)
6752 `(("r-lattice" ,r-lattice)
6753 ("r-mosaic" ,r-mosaic)
6754 ("r-nlme" ,r-nlme)))
6755 (home-page "https://cran.r-project.org/web/packages/abd/")
6756 (synopsis "Analysis of biological data")
6758 "The @code{r-abd} package contains data sets and sample code for the Analysis of
6759 biological data by Michael Whitlock and Dolph Schluter.")
6760 (license license:gpl2)))
6762 (define-public r-svgui
6769 (uri (cran-uri "svGUI" version))
6771 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
6772 (properties `((upstream-name . "svGUI")))
6773 (build-system r-build-system)
6774 (home-page "https://github.com/SciViews/svGUI/")
6775 (synopsis "Functions for managing GUI clients in R")
6777 "The SciViews @code{svGUI} package eases the management of Graphical User
6778 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
6779 centralizes info about GUI elements currently used, and it dispatches GUI
6780 calls to the particular toolkits in use in function of the context.")
6781 (license license:gpl2)))
6783 (define-public r-svdialogs
6785 (name "r-svdialogs")
6790 (uri (cran-uri "svDialogs" version))
6792 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
6793 (properties `((upstream-name . "svDialogs")))
6794 (build-system r-build-system)
6797 ("zenity" ,zenity)))
6799 `(("r-rstudioapi" ,r-rstudioapi)
6800 ("r-svgui" ,r-svgui)))
6801 (home-page "https://github.com/SciViews/svDialogs/")
6802 (synopsis "Portable dialog boxes")
6804 "This package helps to construct standard dialog boxes for your GUI, including
6805 message boxes, input boxes, list, file or directory selection, and others. In
6806 case R cannot display GUI dialog boxes, a simpler command line version of these
6807 interactive elements is also provided as a fallback solution.")
6808 (license license:gpl2)))
6810 (define-public r-abe
6817 (uri (cran-uri "abe" version))
6820 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
6821 (build-system r-build-system)
6822 (home-page "https://cran.r-project.org/web/packages/abe/")
6823 (synopsis "Augmented backward elimination")
6825 "This package performs augmented backward elimination and checks the
6826 stability of the obtained model. Augmented backward elimination combines
6827 significance or information based criteria with the change in estimate to
6828 either select the optimal model for prediction purposes or to serve as a tool
6829 to obtain a practically sound, highly interpretable model.")
6830 (license license:gpl2+)))
6832 (define-public r-abf2
6839 (uri (cran-uri "abf2" version))
6841 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
6842 (build-system r-build-system)
6843 (home-page "https://cran.r-project.org/web/packages/abf2/")
6844 (synopsis "Load gap-free axon @code{r-abf2} files")
6846 "This package loads electrophysiology data from ABF2 files, as created by
6847 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
6848 mode are currently supported.")
6849 (license license:artistic2.0)))
6851 (define-public r-abhgenotyper
6853 (name "r-abhgenotyper")
6858 (uri (cran-uri "ABHgenotypeR" version))
6860 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
6861 (properties `((upstream-name . "ABHgenotypeR")))
6862 (build-system r-build-system)
6864 `(("r-ggplot2" ,r-ggplot2)
6865 ("r-reshape2" ,r-reshape2)))
6866 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
6867 (synopsis "Visualize and manipulate ABH genotypes")
6869 "The @code{r-abhgenotyper} package provides simple imputation,
6870 error-correction and plotting capacities for genotype data. The package is
6871 supposed to serve as an intermediate but independent analysis tool between the
6872 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
6873 not found in either TASSEL or @code{r-qtl} in addition to visualization of
6874 genotypes as \"graphical genotypes\".")
6875 (license license:gpl3)))
6877 (define-public r-furrr
6884 (uri (cran-uri "furrr" version))
6887 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
6888 (build-system r-build-system)
6890 `(("r-future" ,r-future)
6891 ("r-globals" ,r-globals)
6892 ("r-purrr" ,r-purrr)
6893 ("r-rlang" ,r-rlang)))
6894 (home-page "https://github.com/DavisVaughan/furrr")
6895 (synopsis "Apply mapping functions in parallel using futures")
6897 "This package provides implementations of the family of @code{map()}
6898 functions from the @code{purrr} package that can be resolved using any
6899 @code{future}-supported backend, e.g. parallel on the local machine or
6900 distributed on a compute cluster.")
6901 (license license:lgpl2.1+)))
6903 (define-public r-abjutils
6910 (uri (cran-uri "abjutils" version))
6912 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
6913 (build-system r-build-system)
6915 `(("r-devtools" ,r-devtools)
6916 ("r-dplyr" ,r-dplyr)
6917 ("r-furrr" ,r-furrr)
6918 ("r-future" ,r-future)
6921 ("r-magrittr" ,r-magrittr)
6922 ("r-progress" ,r-progress)
6923 ("r-purrr" ,r-purrr)
6924 ("r-readr" ,r-readr)
6925 ("r-rlang" ,r-rlang)
6926 ("r-rstudioapi" ,r-rstudioapi)
6927 ("r-scales" ,r-scales)
6928 ("r-stringi" ,r-stringi)
6929 ("r-stringr" ,r-stringr)
6930 ("r-tibble" ,r-tibble)
6931 ("r-tidyr" ,r-tidyr)))
6932 (home-page "https://github.com/abjur/abjutils/")
6933 (synopsis "Collection of tools for jurimetrical analysis")
6935 "This package implements general purpose tools, such as functions for
6936 sampling and basic manipulation of Brazilian lawsuits identification number.
6937 It also implements functions for text cleaning, such as accentuation
6939 (license license:expat)))
6941 (define-public r-abnormality
6943 (name "r-abnormality")
6948 (uri (cran-uri "abnormality" version))
6950 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
6951 (build-system r-build-system)
6953 `(("r-mass" ,r-mass)
6954 ("r-matrix" ,r-matrix)))
6955 (home-page "https://cran.r-project.org/web/packages/abnormality/")
6956 (synopsis "Measure a subject's abnormality with respect to a reference population")
6958 "This package contains functions to implement the methodology and
6959 considerations laid out by Marks et al. in the article \"Measuring abnormality
6960 in high dimensional spaces: applications in biomechanical gait analysis\".
6961 Using high-dimensional datasets to measure a subject's overall level of
6962 abnormality as compared to a reference population is often needed in outcomes
6964 (license license:expat)))
6966 (define-public r-abodoutlier
6968 (name "r-abodoutlier")
6973 (uri (cran-uri "abodOutlier" version))
6975 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
6976 (properties `((upstream-name . "abodOutlier")))
6977 (build-system r-build-system)
6979 `(("r-cluster" ,r-cluster)))
6980 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
6981 (synopsis "Angle-based outlier detection")
6983 "This package performs angle-based outlier detection on a given data
6984 frame. It offers three methods to process data:
6986 @item full but slow implementation using all the data that has cubic
6988 @item a fully randomized method;
6989 @item a method using k-nearest neighbours.
6991 These algorithms are well suited for high dimensional data outlier
6993 (license license:expat)))
6995 (define-public r-abps
7002 (uri (cran-uri "ABPS" version))
7004 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7005 (properties `((upstream-name . "ABPS")))
7006 (build-system r-build-system)
7007 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7008 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7009 (synopsis "Abnormal blood profile score to detect blood doping")
7011 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7012 The ABPS is a part of the Athlete biological passport program of the World
7013 anti-doping agency, which combines several blood parameters into a single
7014 score in order to detect blood doping. The package also contains functions to
7015 calculate other scores used in anti-doping programs, such as the ratio of
7016 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7017 (license license:gpl2+)))
7019 (define-public r-parmigene
7021 (name "r-parmigene")
7026 (uri (cran-uri "parmigene" version))
7029 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7030 (build-system r-build-system)
7031 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7032 (synopsis "Mutual information estimation for gene network reconstruction")
7034 "This package provides a parallel estimation of the mutual information
7035 based on entropy estimates from k-nearest neighbors distances and algorithms
7036 for the reconstruction of gene regulatory networks.")
7037 (license license:agpl3+)))
7039 (define-public r-pscl
7046 (uri (cran-uri "pscl" version))
7048 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7049 (build-system r-build-system)
7051 `(("r-mass" ,r-mass)))
7052 (home-page "https://github.com/atahk/pscl/")
7053 (synopsis "Political science computational laboratory")
7055 "The @code{pscl} is an R package providing classes and methods for:
7057 @item Bayesian analysis of roll call data (item-response models);
7058 @item elementary Bayesian statistics;
7059 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7061 @item utility functions.
7063 (license license:gpl2)))
7065 (define-public r-accelmissing
7067 (name "r-accelmissing")
7072 (uri (cran-uri "accelmissing" version))
7074 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7075 (build-system r-build-system)
7077 `(("r-mice" ,r-mice)
7078 ("r-pscl" ,r-pscl)))
7079 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7080 (synopsis "Missing value imputation for accelerometer data")
7082 "This package provides a statistical method to impute the missing values in
7083 accelerometer data. The methodology includes both parametric and
7084 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7085 model. It also provides multiple functions to preprocess the accelerometer data
7086 previous to the missing data imputation. These include detecting the wearing
7087 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7088 (license license:gpl2+)))
7090 (define-public r-mhsmm
7097 (uri (cran-uri "mhsmm" version))
7099 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7100 (build-system r-build-system)
7101 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7102 (home-page "https://github.com/jaredo/mhsmm/")
7103 (synopsis "Inference for hidden Markov and semi-Markov models")
7105 "The @code{r-mhsmm} package implements estimation and prediction methods for
7106 hidden Markov and semi-Markov models for multiple observation sequences. Such
7107 techniques are of interest when observed data is thought to be dependent on some
7108 unobserved (or hidden) state. Also, this package is suitable for equidistant
7109 time series data, with multivariate and/or missing data. Allows user defined
7110 emission distributions.")
7111 (license license:gpl2+)))
7113 (define-public r-nleqslv
7120 (uri (cran-uri "nleqslv" version))
7122 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7123 (build-system r-build-system)
7124 (native-inputs `(("gfortran" ,gfortran)))
7125 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7126 (synopsis "Solve systems of nonlinear equations")
7128 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7129 Broyden or a Newton method with a choice of global strategies such as line
7130 search and trust region. There are options for using a numerical or user
7131 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7132 singular or ill-conditioned Jacobian.")
7133 (license license:gpl2+)))
7135 (define-public r-physicalactivity
7137 (name "r-physicalactivity")
7142 (uri (cran-uri "PhysicalActivity" version))
7144 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7146 `((upstream-name . "PhysicalActivity")))
7147 (build-system r-build-system)
7148 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7149 (synopsis "Procesing accelerometer data for physical activity measurement")
7151 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7152 for classification of monitor wear and nonwear time intervals in accelerometer
7153 data collected to assess physical activity. The package also contains functions
7154 for making plots of accelerometer data and obtaining the summary of various
7155 information including daily monitor wear time and the mean monitor wear time
7156 during valid days. The revised package version 0.2-1 improved the functions
7157 regarding speed, robustness and add better support for time zones and daylight
7158 saving. In addition, several functions were added:
7160 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7161 @item the @code{markPAI} can categorize physical activity intensity level based
7162 on user-defined cut-points of accelerometer counts.
7164 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7165 @code{queryActigraph} functions.")
7166 (license license:gpl3+)))
7168 (define-public r-acc
7175 (uri (cran-uri "acc" version))
7177 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7178 (build-system r-build-system)
7180 `(("r-circlize" ,r-circlize)
7182 ("r-ggplot2" ,r-ggplot2)
7183 ("r-iterators" ,r-iterators)
7184 ("r-mhsmm" ,r-mhsmm)
7185 ("r-nleqslv" ,r-nleqslv)
7186 ("r-physicalactivity" ,r-physicalactivity)
7188 ("r-r-utils" ,r-r-utils)
7190 ("r-rcpparmadillo" ,r-rcpparmadillo)
7191 ("r-rsqlite" ,r-rsqlite)
7193 (home-page "https://cran.r-project.org/web/packages/acc/")
7194 (synopsis "Exploring accelerometer data")
7196 "This package processes accelerometer data from uni-axial and tri-axial devices
7197 and generates data summaries. Also, includes functions to plot, analyze, and
7198 simulate accelerometer data.")
7199 (license license:gpl2+)))
7201 (define-public r-rbenchmark
7203 (name "r-rbenchmark")
7208 (uri (cran-uri "rbenchmark" version))
7210 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7211 (build-system r-build-system)
7212 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7213 (synopsis "Benchmarking routine for R")
7215 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7216 and is intended to facilitate benchmarking of arbitrary R code. The library
7217 consists of just one function, benchmark, which is a simple wrapper around
7218 system.time. Given a specification of the benchmarking process (counts of
7219 replications, evaluation environment) and an arbitrary number of expressions,
7220 benchmark evaluates each of the expressions in the specified environment,
7221 replicating the evaluation as many times as specified, and returning the results
7222 conveniently wrapped into a data frame.")
7223 (license license:gpl2+)))
7225 (define-public r-mitools
7232 (uri (cran-uri "mitools" version))
7235 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7236 (build-system r-build-system)
7237 (propagated-inputs `(("r-dbi" ,r-dbi)))
7238 (home-page "https://cran.r-project.org/web/packages/mitools/")
7239 (synopsis "Tools for multiple imputation of missing data")
7241 "This package provides tools to perform analyses and combine results from
7242 multiple-imputation datasets.")
7243 (license license:gpl2)))
7245 (define-public r-magick
7252 (uri (cran-uri "magick" version))
7255 "18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m"))))
7256 (build-system r-build-system)
7258 `(("imagemagick" ,imagemagick)
7261 `(("r-curl" ,r-curl)
7262 ("r-magrittr" ,r-magrittr)
7263 ("r-rcpp" ,r-rcpp)))
7265 `(("pkg-config" ,pkg-config)))
7266 (home-page "https://github.com/ropensci/magick")
7267 (synopsis "Advanced graphics and image-processing in R")
7269 "This package provides bindings to ImageMagick, a comprehensive image
7270 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7271 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7272 operations are vectorized via the Magick++ STL meaning they operate either on
7273 a single frame or a series of frames for working with layers, collages, or
7274 animation. In RStudio, images are automatically previewed when printed to the
7275 console, resulting in an interactive editing environment.")
7276 (license license:expat)))
7278 (define-public r-survey
7285 (uri (cran-uri "survey" version))
7288 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7289 (build-system r-build-system)
7291 `(("r-lattice" ,r-lattice)
7292 ("r-matrix" ,r-matrix)
7293 ("r-minqa" ,r-minqa)
7294 ("r-mitools" ,r-mitools)
7295 ("r-numderiv" ,r-numderiv)
7296 ("r-survival" ,r-survival)))
7297 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7298 (synopsis "Analysis of complex survey samples")
7300 "This package provides tools for the analysis of complex survey samples.
7301 The provided features include: summary statistics, two-sample tests, rank
7302 tests, generalised linear models, cumulative link models, Cox models,
7303 loglinear models, and general maximum pseudolikelihood estimation for
7304 multistage stratified, cluster-sampled, unequally weighted survey samples;
7305 variances by Taylor series linearisation or replicate weights;
7306 post-stratification, calibration, and raking; two-phase subsampling designs;
7307 graphics; PPS sampling without replacement; principal components, and factor
7309 ;; Either version of the GPL.
7310 (license (list license:gpl2 license:gpl3))))
7312 (define-public r-dvmisc
7319 (uri (cran-uri "dvmisc" version))
7321 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7322 (build-system r-build-system)
7324 `(("r-cubature" ,r-cubature)
7325 ("r-data-table" ,r-data-table)
7326 ("r-dplyr" ,r-dplyr)
7327 ("r-ggplot2" ,r-ggplot2)
7329 ("r-mvtnorm" ,r-mvtnorm)
7330 ("r-pracma" ,r-pracma)
7331 ("r-purrr" ,r-purrr)
7332 ("r-rbenchmark" ,r-rbenchmark)
7334 ("r-survey" ,r-survey)))
7335 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7336 (synopsis "Faster computation of common statistics and miscellaneous functions")
7338 "This package implements faster versions of base R functions (e.g. mean, standard
7339 deviation, covariance, weighted mean), mostly written in C++, along with
7340 miscellaneous functions for various purposes (e.g. create the histogram with
7341 fitted probability density function or probability mass function curve, create
7342 the body mass index groups, assess the linearity assumption in logistic
7344 (license license:gpl2)))
7346 (define-public r-accelerometry
7348 (name "r-accelerometry")
7353 (uri (cran-uri "accelerometry" version))
7355 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7356 (build-system r-build-system)
7358 `(("r-dvmisc" ,r-dvmisc)
7359 ("r-rcpp" ,r-rcpp)))
7360 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7361 (synopsis "Functions for processing accelerometer data")
7363 "This package provides a collection of functions that perform operations on
7364 time-series accelerometer data, such as identify the non-wear time, flag minutes
7365 that are part of an activity bout, and find the maximum 10-minute average count
7366 value. The functions are generally very flexible, allowing for a variety of
7367 algorithms to be implemented.")
7368 (license license:gpl3)))
7370 (define-public r-absim
7377 (uri (cran-uri "AbSim" version))
7379 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7380 (properties `((upstream-name . "AbSim")))
7381 (build-system r-build-system)
7384 ("r-powerlaw" ,r-powerlaw)))
7385 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7386 (synopsis "Time resolved simulations of antibody repertoires")
7388 "This package provides simulation methods for the evolution of antibody repertoires.
7389 The heavy and light chain variable region of both human and C57BL/6 mice can
7390 be simulated in a time-dependent fashion. Both single lineages using one set of
7391 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7392 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7393 Upon completion, the main loop of the algorithm begins, with each iteration
7394 representing one simulated time step. Various mutation events are possible at
7395 each time step, contributing to a diverse final repertoire.")
7396 (license license:gpl2)))
7398 (define-public r-quic
7405 (uri (cran-uri "QUIC" version))
7407 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7408 (properties `((upstream-name . "QUIC")))
7409 (build-system r-build-system)
7410 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7411 (synopsis "Regularized sparse inverse covariance matrix estimation")
7413 "This package implements the regularized Gaussian maximum likelihood
7414 estimation of the inverse of a covariance matrix. It uses Newton's method and
7415 coordinate descent to solve the regularized inverse covariance matrix
7416 estimation problem.")
7417 ;; The project home page states that the release is under GPLv3 or later.
7418 ;; The CRAN page only says GPL-3.
7419 (license license:gpl3+)))
7421 (define-public r-abundant
7428 (uri (cran-uri "abundant" version))
7430 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7431 (build-system r-build-system)
7433 `(("r-quic" ,r-quic)))
7434 (home-page "https://cran.r-project.org/web/packages/abundant/")
7435 (synopsis "Abundant regression and high-dimensional principal fitted components")
7437 "This package provides tools to fit and predict with the high-dimensional
7438 principal fitted components model. This model is described by Cook, Forzani,
7439 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7440 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7441 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7442 (license license:gpl2+)))
7444 (define-public r-ac3net
7451 (uri (cran-uri "Ac3net" version))
7453 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7454 (properties `((upstream-name . "Ac3net")))
7455 (build-system r-build-system)
7457 `(("r-data-table" ,r-data-table)))
7458 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
7459 (synopsis "Inferring directional conservative causal core gene networks")
7460 (description "This package infers directional Conservative causal core
7461 (gene) networks (C3NET). This is a version of the algorithm C3NET with
7462 directional network.")
7463 (license license:gpl3+)))
7465 (define-public r-aca
7472 (uri (cran-uri "ACA" version))
7474 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
7475 (properties `((upstream-name . "ACA")))
7476 (build-system r-build-system)
7477 (home-page "https://cran.r-project.org/web/packages/ACA/")
7478 (synopsis "Abrupt change-point or aberration detection in point series")
7480 "This package offers an interactive function for the detection of breakpoints in
7482 ;; Any version of the GPL
7483 (license (list license:gpl2+ license:gpl3+))))
7485 (define-public r-acceptancesampling
7487 (name "r-acceptancesampling")
7492 (uri (cran-uri "AcceptanceSampling" version))
7494 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
7496 `((upstream-name . "AcceptanceSampling")))
7497 (build-system r-build-system)
7498 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
7499 (synopsis "Creation and evaluation of acceptance sampling plans")
7501 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
7502 acceptance sampling plans. Acceptance sampling is a methodology commonly used
7503 in quality control and improvement. International standards of acceptance
7504 sampling provide sampling plans for specific circumstances. The aim of this
7505 package is to provide an easy-to-use interface to visualize single, double or
7506 multiple sampling plans. In addition, methods have been provided to enable the
7507 user to assess sampling plans against pre-specified levels of performance, as
7508 measured by the probability of acceptance for a given level of quality in the
7510 (license license:gpl3+)))
7512 (define-public r-acclma
7519 (uri (cran-uri "ACCLMA" version))
7521 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
7522 (properties `((upstream-name . "ACCLMA")))
7523 (build-system r-build-system)
7524 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
7525 (synopsis "ACC & LMA graph plotting")
7527 "This package contains a function that imports data from a @acronym{CSV,
7528 Comma-Separated Values} file, or uses manually entered data from the format (x,
7529 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
7530 Curve} vs @acronym{LOI, Line of Independence} graph and
7531 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
7532 function is @code{plotLMA} (source file, header) that takes a data set and plots the
7533 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
7534 string) was passed, a manual data entry window is opened. The header parameter
7535 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
7536 a header row or not. The dataset should contain only one independent variable
7537 (x) and one dependent variable (y) and can contain a weight for each
7539 (license license:gpl2)))
7541 (define-public r-aspi
7548 (uri (cran-uri "aspi" version))
7550 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
7551 (build-system r-build-system)
7553 "https://cran.r-project.org/web/packages/aspi/")
7555 "Analysis of symmetry of parasitic infections")
7557 "This package provides tools for the analysis and visualization of bilateral
7558 asymmetry in parasitic infections.")
7559 (license license:gpl3+)))
7561 (define-public r-sandwich
7568 (uri (cran-uri "sandwich" version))
7571 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
7572 (build-system r-build-system)
7574 `(("r-zoo" ,r-zoo)))
7575 (home-page "https://cran.r-project.org/web/packages/sandwich/")
7576 (synopsis "Robust Covariance Matrix Estimators")
7578 "This package provides model-robust standard error estimators for
7579 cross-sectional, time series, clustered, panel, and longitudinal data.")
7580 ;; Either version of the license.
7581 (license (list license:gpl2 license:gpl3))))
7583 (define-public r-th-data
7590 (uri (cran-uri "TH.data" version))
7593 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
7594 (properties `((upstream-name . "TH.data")))
7595 (build-system r-build-system)
7597 `(("r-mass" ,r-mass)
7598 ("r-survival" ,r-survival)))
7599 (home-page "https://cran.r-project.org/web/packages/TH.data/")
7600 (synopsis "Shared data sets")
7602 "This package contains supporting data sets that are used in other
7603 packages maintained by Torsten Hothorn.")
7604 (license license:gpl3)))
7606 (define-public r-multcomp
7613 (uri (cran-uri "multcomp" version))
7616 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
7617 (build-system r-build-system)
7619 `(("r-codetools" ,r-codetools)
7620 ("r-mvtnorm" ,r-mvtnorm)
7621 ("r-sandwich" ,r-sandwich)
7622 ("r-survival" ,r-survival)
7623 ("r-th-data" ,r-th-data)))
7624 (home-page "https://cran.r-project.org/web/packages/multcomp/")
7625 (synopsis "Simultaneous inference in general parametric models")
7627 "Simultaneous tests and confidence intervals for general linear
7628 hypotheses in parametric models, including linear, generalized linear, linear
7629 mixed effects, and survival models. The package includes demos reproducing
7630 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
7631 Hothorn, Westfall, 2010, CRC Press).")
7632 (license license:gpl2)))
7634 (define-public r-emmeans
7641 (uri (cran-uri "emmeans" version))
7644 "09gxphan34c615y4lhjdqkg5cz4ih9b1r3bb4chs3mwmiav1rxqn"))))
7645 (build-system r-build-system)
7647 `(("r-estimability" ,r-estimability)
7648 ("r-mvtnorm" ,r-mvtnorm)
7649 ("r-numderiv" ,r-numderiv)
7651 ("r-xtable" ,r-xtable)))
7652 (home-page "https://github.com/rvlenth/emmeans")
7653 (synopsis "Estimated marginal means, aka least-squares means")
7655 "This package provides tools to obtain @dfn{estimated marginal
7656 means} (EMMs) for many linear, generalized linear, and mixed models. It can
7657 be used to compute contrasts or linear functions of EMMs, trends, and
7658 comparisons of slopes.")
7659 ;; Either version of the license.
7660 (license (list license:gpl2 license:gpl3))))
7662 (define-public r-pwr
7669 (uri (cran-uri "pwr" version))
7672 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
7673 (build-system r-build-system)
7675 `(("r-knitr" ,r-knitr)))
7676 (home-page "https://github.com/heliosdrm/pwr")
7677 (synopsis "Basic functions for power analysis")
7679 "This package provides power analysis functions along the lines of
7681 (license license:gpl3+)))
7683 (define-public r-libcoin
7690 (uri (cran-uri "libcoin" version))
7693 "1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i"))))
7694 (build-system r-build-system)
7695 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7696 (home-page "https://cran.r-project.org/web/packages/libcoin")
7697 (synopsis "Linear test statistics for permutation inference")
7699 "This package provides basic infrastructure for linear test statistics
7700 and permutation inference in the framework of Strasser and Weber (1999).")
7701 (license license:gpl2)))
7703 (define-public r-coin
7710 (uri (cran-uri "coin" version))
7713 "1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd"))))
7714 (build-system r-build-system)
7716 `(("r-libcoin" ,r-libcoin)
7717 ("r-matrixstats" ,r-matrixstats)
7718 ("r-modeltools" ,r-modeltools)
7719 ("r-multcomp" ,r-multcomp)
7720 ("r-mvtnorm" ,r-mvtnorm)
7721 ("r-survival" ,r-survival)))
7722 (home-page "http://coin.r-forge.r-project.org")
7723 (synopsis "Conditional inference procedures in a permutation test framework")
7725 "This package provides conditional inference procedures for the general
7726 independence problem including two-sample, K-sample (non-parametric ANOVA),
7727 correlation, censored, ordered and multivariate problems.")
7728 (license license:gpl2)))
7730 (define-public r-bayesplot
7732 (name "r-bayesplot")
7737 (uri (cran-uri "bayesplot" version))
7740 "0in9cq2ybpa7njrwqx4l6nc8i01cjswsvzwlyiw465pi74aapr57"))))
7741 (build-system r-build-system)
7743 `(("pandoc" ,ghc-pandoc)
7744 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
7746 `(("r-dplyr" ,r-dplyr)
7747 ("r-ggplot2" ,r-ggplot2)
7748 ("r-ggridges" ,r-ggridges)
7749 ("r-reshape2" ,r-reshape2)
7750 ("r-rlang" ,r-rlang)))
7751 (home-page "http://mc-stan.org/bayesplot")
7752 (synopsis "Plotting for Bayesian models")
7754 "This package provides plotting functions for posterior analysis, model
7755 checking, and MCMC diagnostics. The package is designed not only to provide
7756 convenient functionality for users, but also a common set of functions that
7757 can be easily used by developers working on a variety of R packages for
7758 Bayesian modeling.")
7759 (license license:gpl3+)))
7761 (define-public r-tmb
7768 (uri (cran-uri "TMB" version))
7771 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
7772 (properties `((upstream-name . "TMB")))
7773 (build-system r-build-system)
7775 `(("r-matrix" ,r-matrix)
7776 ("r-rcppeigen" ,r-rcppeigen)))
7777 (home-page "http://tmb-project.org")
7778 (synopsis "Template model builder: a general random effect tool")
7780 "With this tool, a user should be able to quickly implement complex
7781 random effect models through simple C++ templates. The package combines
7782 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
7783 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
7784 from R) to obtain an efficient implementation of the applied Laplace
7785 approximation with exact derivatives. Key features are: Automatic sparseness
7786 detection, parallelism through BLAS and parallel user templates.")
7787 (license license:gpl2)))
7789 (define-public r-sjstats
7796 (uri (cran-uri "sjstats" version))
7799 "012hp9m17xzjnsfvjjz2wdfgxm3irsrfx0zmahfnfmgdrwxd5vk5"))))
7800 (build-system r-build-system)
7802 `(("r-broom" ,r-broom)
7803 ("r-dplyr" ,r-dplyr)
7804 ("r-emmeans" ,r-emmeans)
7805 ("r-insight" ,r-insight)
7807 ("r-magrittr" ,r-magrittr)
7809 ("r-matrix" ,r-matrix)
7810 ("r-modelr" ,r-modelr)
7811 ("r-purrr" ,r-purrr)
7812 ("r-rlang" ,r-rlang)
7813 ("r-sjlabelled" ,r-sjlabelled)
7814 ("r-sjmisc" ,r-sjmisc)
7815 ("r-tidyr" ,r-tidyr)))
7816 (home-page "https://github.com/strengejacke/sjstats")
7817 (synopsis "Functions for common statistical computations")
7819 "This package provides a collection of convenient functions for common
7820 statistical computations, which are not directly provided by R's @code{base}
7821 or @code{stats} packages. This package aims at providing, first, shortcuts
7822 for statistical measures, which otherwise could only be calculated with
7823 additional effort. Second, these shortcut functions are generic, and can be
7824 applied not only to vectors, but also to other objects as well. The focus of
7825 most functions lies on summary statistics or fit measures for regression
7826 models, including generalized linear models, mixed effects models and Bayesian
7828 (license license:gpl3)))
7830 (define-public r-glmmtmb
7837 (uri (cran-uri "glmmTMB" version))
7840 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
7841 (properties `((upstream-name . "glmmTMB")))
7842 (build-system r-build-system)
7844 `(("r-lme4" ,r-lme4)
7845 ("r-matrix" ,r-matrix)
7847 ("r-rcppeigen" ,r-rcppeigen)
7850 `(("r-knitr" ,r-knitr))) ; for vignettes
7851 (home-page "https://github.com/glmmTMB")
7852 (synopsis "Generalized linear mixed models")
7854 "Fit linear and generalized linear mixed models with various extensions,
7855 including zero-inflation. The models are fitted using maximum likelihood
7856 estimation via the Template Model Builder. Random effects are assumed to be
7857 Gaussian on the scale of the linear predictor and are integrated out using the
7858 Laplace approximation. Gradients are calculated using automatic
7860 (license license:agpl3+)))
7862 (define-public r-bayestestr
7864 (name "r-bayestestr")
7869 (uri (cran-uri "bayestestR" version))
7872 "1m6gj55z3shm3m3mgqj8nk73wij67y617sl04rbj400wz9qrhfva"))))
7873 (properties `((upstream-name . "bayestestR")))
7874 (build-system r-build-system)
7876 `(("r-insight" ,r-insight)))
7877 (home-page "https://github.com/easystats/bayestestR")
7878 (synopsis "Describe Bayesian models and posterior distributions")
7880 "This package provides utilities to understand and describe posterior
7881 distributions and Bayesian models. It includes point-estimates such as
7882 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
7883 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
7884 ROPE percentage and pd).")
7885 (license license:gpl3)))
7887 (define-public r-performance
7889 (name "r-performance")
7894 (uri (cran-uri "performance" version))
7897 "19lfx25hkavzbycrh6hq4v24a0dz4s60ryq6jyihjlxgrb9g7cnw"))))
7898 (build-system r-build-system)
7900 `(("r-bayestestr" ,r-bayestestr)
7901 ("r-insight" ,r-insight)))
7902 (home-page "https://easystats.github.io/performance/")
7903 (synopsis "Assessment of regression models performance")
7905 "This package provides utilities for computing measures to assess model
7906 quality, which are not directly provided by R's @code{base} or @code{stats}
7907 packages. These include e.g. measures like r-squared, intraclass correlation
7908 coefficient, root mean squared error or functions to check models for
7909 overdispersion, singularity or zero-inflation and more. Functions apply to a
7910 large variety of regression models, including generalized linear models, mixed
7911 effects models and Bayesian models.")
7912 (license license:gpl3)))
7914 (define-public r-ggeffects
7916 (name "r-ggeffects")
7921 (uri (cran-uri "ggeffects" version))
7924 "1bbr44yk1j8pz4kcbw1cqrzcnbih9n6rsgf96a6py5094qcal2qd"))))
7925 (build-system r-build-system)
7927 `(("r-dplyr" ,r-dplyr)
7928 ("r-insight" ,r-insight)
7929 ("r-magrittr" ,r-magrittr)
7931 ("r-purrr" ,r-purrr)
7932 ("r-rlang" ,r-rlang)
7933 ("r-scales" ,r-scales)
7934 ("r-sjlabelled" ,r-sjlabelled)
7935 ("r-sjmisc" ,r-sjmisc)))
7936 (home-page "https://github.com/strengejacke/ggeffects")
7937 (synopsis "Create tidy data frames of marginal effects for ggplot")
7939 "This package provides tools to compute marginal effects from statistical
7940 models and return the result as tidy data frames. These data frames are ready
7941 to use with the @code{ggplot2} package. Marginal effects can be calculated
7942 for many different models. Interaction terms, splines and polynomial terms
7943 are also supported. The two main functions are @code{ggpredict()} and
7944 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
7945 results using @code{ggplot2}.")
7946 (license license:gpl3)))
7948 (define-public r-sjplot
7955 (uri (cran-uri "sjPlot" version))
7958 "0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy"))))
7959 (properties `((upstream-name . "sjPlot")))
7960 (build-system r-build-system)
7962 `(("r-bayestestr" ,r-bayestestr)
7963 ("r-broom" ,r-broom)
7964 ("r-dplyr" ,r-dplyr)
7965 ("r-forcats" ,r-forcats)
7966 ("r-ggeffects" ,r-ggeffects)
7967 ("r-ggplot2" ,r-ggplot2)
7968 ("r-glmmtmb" ,r-glmmtmb)
7969 ("r-insight" ,r-insight)
7970 ("r-knitr" ,r-knitr)
7972 ("r-magrittr" ,r-magrittr)
7974 ("r-modelr" ,r-modelr)
7976 ("r-performance" ,r-performance)
7977 ("r-psych" ,r-psych)
7978 ("r-purrr" ,r-purrr)
7979 ("r-rlang" ,r-rlang)
7980 ("r-scales" ,r-scales)
7981 ("r-sjlabelled" ,r-sjlabelled)
7982 ("r-sjmisc" ,r-sjmisc)
7983 ("r-sjstats" ,r-sjstats)
7984 ("r-tidyr" ,r-tidyr)))
7985 (home-page "https://strengejacke.github.io/sjPlot/")
7986 (synopsis "Data visualization for statistics in social science")
7988 "This package represents a collection of plotting and table output
7989 functions for data visualization. Results of various statistical
7990 analyses (that are commonly used in social sciences) can be visualized using
7991 this package, including simple and cross tabulated frequencies, histograms,
7992 box plots, (generalized) linear models, mixed effects models, principal
7993 component analysis and correlation matrices, cluster analyses, scatter plots,
7994 stacked scales, effects plots of regression models (including interaction
7995 terms) and much more. This package supports labelled data.")
7996 (license license:gpl3)))
7998 (define-public r-ini
8005 (uri (cran-uri "ini" version))
8008 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8009 (build-system r-build-system)
8010 (home-page "https://github.com/dvdscripter/ini")
8011 (synopsis "Read and write configuration files")
8013 "This package provides tools to parse simple @code{.ini} configuration
8014 files to an structured list. Users can manipulate this resulting list with
8015 @code{lapply()} functions. This same structured list can be used to write
8016 back to file after modifications.")
8017 (license license:gpl3)))
8026 (uri (cran-uri "gh" version))
8029 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8030 (build-system r-build-system)
8032 `(("r-httr" ,r-httr)
8034 ("r-jsonlite" ,r-jsonlite)))
8035 (home-page "https://github.com/r-lib/gh#readme")
8036 (synopsis "Access the GitHub API via R")
8038 "This package provides a minimal R client to access the GitHub API.")
8039 (license license:expat)))
8048 (uri (cran-uri "fs" version))
8051 "1p6y0ar5kidwv0f5vzhj7yaw5802rpqwdma2ij3vrvjf9f7l9z1s"))))
8052 (build-system r-build-system)
8054 `(("r-rcpp" ,r-rcpp)))
8056 `(("pkg-config" ,pkg-config)))
8057 (home-page "http://fs.r-lib.org")
8058 (synopsis "Cross-platform file system operations based on libuv")
8060 "This package provides a cross-platform interface to file system
8061 operations, built on top of the libuv C library.")
8062 (license license:gpl3)))
8064 (define-public r-clisymbols
8066 (name "r-clisymbols")
8071 (uri (cran-uri "clisymbols" version))
8074 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8075 (build-system r-build-system)
8076 (home-page "https://github.com/gaborcsardi/clisymbols")
8077 (synopsis "Unicode symbols at the R prompt")
8079 "This package provides a small subset of Unicode symbols, that are useful
8080 when building command line applications. They fall back to alternatives on
8081 terminals that do not support Unicode.")
8082 (license license:expat)))
8084 (define-public r-usethis
8091 (uri (cran-uri "usethis" version))
8094 "0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag"))))
8095 (build-system r-build-system)
8097 `(("r-clipr" ,r-clipr)
8098 ("r-clisymbols" ,r-clisymbols)
8099 ("r-crayon" ,r-crayon)
8104 ("r-git2r" ,r-git2r)
8106 ("r-purrr" ,r-purrr)
8107 ("r-rlang" ,r-rlang)
8108 ("r-rprojroot" ,r-rprojroot)
8109 ("r-rstudioapi" ,r-rstudioapi)
8110 ("r-whisker" ,r-whisker)
8111 ("r-withr" ,r-withr)
8112 ("r-yaml" ,r-yaml)))
8113 (home-page "https://github.com/r-lib/usethis")
8114 (synopsis "Automate R package and project setup")
8116 "This package helps you to automate R package and project setup tasks
8117 that are otherwise performed manually. This includes setting up unit testing,
8118 test coverage, continuous integration, Git, GitHub integration, licenses,
8119 Rcpp, RStudio projects, and more.")
8120 (license license:gpl3)))
8122 (define-public r-sessioninfo
8124 (name "r-sessioninfo")
8129 (uri (cran-uri "sessioninfo" version))
8132 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8133 (build-system r-build-system)
8136 ("r-withr" ,r-withr)))
8137 (home-page "https://github.com/r-lib/sessioninfo#readme")
8138 (synopsis "R session information")
8140 "This package provides tools to query and print information about the
8141 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8142 more information about packages, and where they were installed from.")
8143 (license license:gpl2)))
8145 (define-public r-remotes
8152 (uri (cran-uri "remotes" version))
8155 "1jbn4kjimcr82zv5lnqxqa2487a96vn6jxf7wc6gnpxr6k06d61p"))))
8156 (build-system r-build-system)
8157 (home-page "https://github.com/r-lib/remotes#readme")
8158 (synopsis "R package installation from remote repositories")
8160 "Download and install R packages stored in GitHub, BitBucket, or plain
8161 subversion or git repositories. This package is a lightweight replacement of
8162 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8163 the code was copied over from @code{devtools}.")
8164 (license license:gpl2+)))
8166 (define-public r-xopen
8173 (uri (cran-uri "xopen" version))
8176 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8177 (build-system r-build-system)
8179 `(("r-processx" ,r-processx)))
8180 (home-page "https://github.com/r-lib/xopen#readme")
8181 (synopsis "Open system files, URLs, anything")
8183 "This package provides a cross-platform solution to open files,
8184 directories or URLs with their associated programs.")
8185 (license license:expat)))
8187 (define-public r-rcmdcheck
8189 (name "r-rcmdcheck")
8194 (uri (cran-uri "rcmdcheck" version))
8197 "0ys1nd7690mhwzslyzg8fq1wxr28nz8g6av5iykkrshb8lkxg7ly"))))
8198 (build-system r-build-system)
8200 `(("r-callr" ,r-callr)
8202 ("r-crayon" ,r-crayon)
8204 ("r-digest" ,r-digest)
8205 ("r-pkgbuild" ,r-pkgbuild)
8206 ("r-prettyunits" ,r-prettyunits)
8208 ("r-rprojroot" ,r-rprojroot)
8209 ("r-sessioninfo" ,r-sessioninfo)
8210 ("r-withr" ,r-withr)
8211 ("r-xopen" ,r-xopen)))
8212 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8213 (synopsis "Run R CMD check from R and capture results")
8215 "Run @code{R CMD check} from R programmatically, and capture the results
8216 of the individual checks.")
8217 (license license:expat)))
8219 (define-public r-rapportools
8221 (name "r-rapportools")
8226 (uri (cran-uri "rapportools" version))
8229 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8230 (build-system r-build-system)
8232 `(("r-pander" ,r-pander)
8234 ("r-reshape" ,r-reshape)))
8235 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8236 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8238 "This package provides helper functions that act as wrappers to more
8239 advanced statistical methods with the advantage of having sane defaults for
8241 (license license:agpl3+)))
8243 (define-public r-pander
8250 (uri (cran-uri "pander" version))
8253 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8254 (build-system r-build-system)
8256 `(("r-digest" ,r-digest)
8257 ("r-rcpp" ,r-rcpp)))
8258 (home-page "https://rapporter.github.io/pander")
8259 (synopsis "Render R objects into Pandoc's markdown")
8261 "The main aim of the pander R package is to provide a minimal and easy
8262 tool for rendering R objects into Pandoc's markdown. The package is also
8263 capable of exporting/converting complex Pandoc documents (reports) in various
8265 ;; This package is licensed under either the AGPLv3+ or the very rarely
8267 (license license:agpl3+)))
8269 (define-public r-summarytools
8271 (name "r-summarytools")
8276 (uri (cran-uri "summarytools" version))
8279 "1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f"))))
8280 (build-system r-build-system)
8282 `(("r-checkmate" ,r-checkmate)
8283 ("r-dplyr" ,r-dplyr)
8284 ("r-htmltools" ,r-htmltools)
8285 ("r-lubridate" ,r-lubridate)
8286 ("r-magick" ,r-magick)
8287 ("r-matrixstats" ,r-matrixstats)
8288 ("r-pander" ,r-pander)
8290 ("r-rapportools" ,r-rapportools)
8291 ("r-rcurl" ,r-rcurl)
8292 ("r-tibble" ,r-tibble)
8293 ("r-tidyr" ,r-tidyr)))
8294 (home-page "https://github.com/dcomtois/summarytools")
8295 (synopsis "Tools to quickly and neatly summarize data")
8297 "This package provides tools for data frame summaries, cross-tabulations,
8298 weight-enabled frequency tables and common univariate statistics in concise
8299 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8300 good point-of-entry for exploring data, both for experienced and new R
8302 (license license:gpl2)))
8304 (define-public r-lsei
8311 (uri (cran-uri "lsei" version))
8314 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8315 (build-system r-build-system)
8317 `(("gfortran" ,gfortran)))
8318 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8319 (synopsis "Solve regression problems under equality/inequality constraints")
8321 "It contains functions that solve least squares linear regression
8322 problems under linear equality/inequality constraints. Functions for solving
8323 quadratic programming problems are also available, which transform such
8324 problems into least squares ones first.")
8325 (license license:gpl2+)))
8327 (define-public r-npsurv
8334 (uri (cran-uri "npsurv" version))
8337 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8338 (build-system r-build-system)
8340 `(("r-lsei" ,r-lsei)))
8341 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8342 (synopsis "Nonparametric survival analysis")
8344 "This package contains functions for non-parametric survival analysis of
8345 exact and interval-censored observations.")
8346 (license license:gpl2+)))
8348 (define-public r-clusteval
8350 (name "r-clusteval")
8355 (uri (cran-uri "clusteval" version))
8358 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8359 (build-system r-build-system)
8361 `(("r-mvtnorm" ,r-mvtnorm)
8362 ("r-rcpp" ,r-rcpp)))
8363 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8364 (synopsis "Evaluation of clustering algorithms")
8366 "This R package provides a suite of tools to evaluate clustering
8367 algorithms, clusterings, and individual clusters.")
8368 (license license:expat)))
8370 (define-public r-tweedie
8377 (uri (cran-uri "tweedie" version))
8380 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8381 (build-system r-build-system)
8382 (native-inputs `(("gfortran" ,gfortran)))
8383 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8384 (synopsis "Evaluation of Tweedie exponential family models")
8386 "Maximum likelihood computations for Tweedie families, including the
8387 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8388 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8389 and related methods.")
8390 (license license:gpl2+)))
8392 (define-public r-rcppgsl
8399 (uri (cran-uri "RcppGSL" version))
8402 "16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m"))))
8403 (properties `((upstream-name . "RcppGSL")))
8404 (build-system r-build-system)
8406 `(("r-rcpp" ,r-rcpp)
8409 `(("r-knitr" ,r-knitr))) ; for vignettes
8410 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8411 (synopsis "Rcpp integration for GSL vectors and matrices")
8413 "The GNU Scientific Library (or GSL) is a collection of numerical
8414 routines for scientific computing. It is particularly useful for C and C++
8415 programs as it provides a standard C interface to a wide range of mathematical
8416 routines. There are over 1000 functions in total with an extensive test
8417 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8418 structures and R using concepts from Rcpp which is itself a package that eases
8419 the interfaces between R and C++.")
8420 (license license:gpl2+)))
8422 (define-public r-mvabund
8429 (uri (cran-uri "mvabund" version))
8432 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
8433 (build-system r-build-system)
8435 `(("r-mass" ,r-mass)
8437 ("r-rcppgsl" ,r-rcppgsl)
8438 ("r-statmod" ,r-statmod)
8439 ("r-tweedie" ,r-tweedie)))
8440 (home-page "https://cran.r-project.org/web/packages/mvabund/")
8441 (synopsis "Statistical methods for analysing multivariate abundance data")
8443 "This package provides a set of tools for displaying, modeling and
8444 analysing multivariate abundance data in community ecology.")
8445 (license license:lgpl2.1+)))
8447 (define-public r-afex
8454 (uri (cran-uri "afex" version))
8457 "0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7"))))
8458 (build-system r-build-system)
8462 ("r-lmertest" ,r-lmertest)
8463 ("r-pbkrtest" ,r-pbkrtest)
8464 ("r-reshape2" ,r-reshape2)))
8465 (home-page "https://afex.singmann.science/")
8466 (synopsis "Analysis of factorial experiments")
8468 "This package provides convenience functions for analyzing factorial
8469 experiments using ANOVA or mixed models.")
8470 (license license:gpl2+)))
8472 (define-public r-lmertest
8479 (uri (cran-uri "lmerTest" version))
8482 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
8483 (properties `((upstream-name . "lmerTest")))
8484 (build-system r-build-system)
8486 `(("r-ggplot2" ,r-ggplot2)
8489 ("r-numderiv" ,r-numderiv)))
8490 (home-page "https://github.com/runehaubo/lmerTestR")
8491 (synopsis "Tests in linear mixed effects models")
8493 "This package provides p-values in type I, II or III anova and summary
8494 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
8495 method. A Kenward-Roger method is also available via the @code{pbkrtest}
8496 package. Model selection methods include step, drop1 and anova-like tables
8497 for random effects (ranova). Methods for Least-Square means (LS-means) and
8498 tests of linear contrasts of fixed effects are also available.")
8499 (license license:gpl2+)))
8501 (define-public r-r2glmm
8508 (uri (cran-uri "r2glmm" version))
8511 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
8512 (build-system r-build-system)
8514 `(("r-afex" ,r-afex)
8515 ("r-data-table" ,r-data-table)
8516 ("r-dplyr" ,r-dplyr)
8517 ("r-ggplot2" ,r-ggplot2)
8518 ("r-gridextra" ,r-gridextra)
8519 ("r-lmertest" ,r-lmertest)
8521 ("r-matrix" ,r-matrix)
8523 ("r-pbkrtest" ,r-pbkrtest)))
8524 (home-page "https://github.com/bcjaeger/r2glmm")
8525 (synopsis "Compute R squared for mixed (multilevel) models")
8527 "This package computes model and semi partial R squared with confidence
8528 limits for the linear and generalized linear mixed model (LMM and GLMM). The
8529 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
8530 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
8532 (license license:gpl2)))
8534 (define-public r-weights
8541 (uri (cran-uri "weights" version))
8544 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
8545 (build-system r-build-system)
8547 `(("r-gdata" ,r-gdata)
8548 ("r-hmisc" ,r-hmisc)
8549 ("r-mice" ,r-mice)))
8551 "https://cran.r-project.org/web/packages/weights/")
8552 (synopsis "Weighting and weighted statistics")
8553 (description "This package Provides a variety of functions for producing
8554 simple weighted statistics, such as weighted Pearson's correlations, partial
8555 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
8556 includes some software for quickly recoding survey data and plotting point
8557 estimates from interaction terms in regressions (and multiply imputed
8558 regressions). NOTE: Weighted partial correlation calculations pulled to
8560 (license license:gpl2+)))
8562 (define-public r-rcppannoy
8564 (name "r-rcppannoy")
8569 (uri (cran-uri "RcppAnnoy" version))
8572 "1ik50ancfgcvh03n4jsqwjk8lf056rbgd70q4l4didmvh5kcyjd1"))))
8573 (properties `((upstream-name . "RcppAnnoy")))
8574 (build-system r-build-system)
8576 `(("r-rcpp" ,r-rcpp)))
8578 `(("r-knitr" ,r-knitr))) ; for vignettes
8579 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
8580 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
8582 "Annoy is a small C++ library for Approximate Nearest Neighbors written
8583 for efficient memory usage as well an ability to load from and save to disk.
8584 This package provides an R interface.")
8585 ;; Annoy is released under ASL 2.0, but this wrapper is released under
8587 (license (list license:gpl2+ license:asl2.0))))
8589 (define-public r-rcpphnsw
8596 (uri (cran-uri "RcppHNSW" version))
8599 "158a069n42pbnjrlmvqsr6bm2cfp9hxpnk3nhp3dwi9qjlq4r9bm"))))
8600 (properties `((upstream-name . "RcppHNSW")))
8601 (build-system r-build-system)
8602 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8603 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
8604 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
8606 "Hnswlib is a C++ library for approximate nearest neighbors. This
8607 package provides a minimal R interface by relying on the Rcpp package.")
8608 ;; hnswlib is released under Version 2.0 of the Apache License.
8609 (license (list license:gpl3 license:asl2.0))))
8611 (define-public r-ncdf4
8618 (uri (cran-uri "ncdf4" version))
8621 "083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd"))))
8622 (build-system r-build-system)
8624 `(("netcdf" ,netcdf)
8626 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
8627 (synopsis "R interface to Unidata netCDF format data files")
8629 "This package provides a high-level R interface to data files written
8630 using Unidata's netCDF library (version 4 or earlier), which are binary data
8631 files that are portable across platforms and include metadata information in
8632 addition to the data sets. Using this package, netCDF files can be opened and
8633 data sets read in easily. It is also easy to create new netCDF dimensions,
8634 variables, and files, in either version 3 or 4 format, and manipulate existing
8636 (license license:gpl3+)))
8638 (define-public r-biocmanager
8640 (name "r-biocmanager")
8645 (uri (cran-uri "BiocManager" version))
8648 "0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah"))))
8649 (properties `((upstream-name . "BiocManager")))
8650 (build-system r-build-system)
8651 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
8652 (synopsis "Access the Bioconductor project package repository")
8654 "This package provides a convenient tool to install and update
8655 Bioconductor packages.")
8656 (license license:artistic2.0)))
8658 (define-public r-rgl
8661 (version "0.100.19")
8665 (uri (cran-uri "rgl" version))
8668 "09bhvx8aq104yzysfgd7wlnq4vrvmnd4jzgj0c32whjfal10fqsh"))))
8669 (build-system r-build-system)
8671 `(("pkg-config" ,pkg-config)))
8673 `(("freetype" ,freetype)
8677 ("ghc-pandoc" ,ghc-pandoc)
8680 `(("r-crosstalk" ,r-crosstalk)
8681 ("r-htmltools" ,r-htmltools)
8682 ("r-htmlwidgets" ,r-htmlwidgets)
8683 ("r-jsonlite" ,r-jsonlite)
8684 ("r-knitr" ,r-knitr)
8685 ("r-magrittr" ,r-magrittr)
8686 ("r-manipulatewidget" ,r-manipulatewidget)
8687 ("r-shiny" ,r-shiny)))
8688 (home-page "https://r-forge.r-project.org/projects/rgl/")
8689 (synopsis "3D visualization using OpenGL")
8691 "This package provides medium to high level functions for 3D interactive graphics,
8692 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
8693 as functions for constructing representations of geometric
8694 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
8695 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
8696 image formats, including PNG, Postscript, SVG, PGF.")
8697 ;; Any version of the GPL.
8698 (license (list license:gpl2+ license:gpl3+))))
8700 (define-public r-multicool
8702 (name "r-multicool")
8707 (uri (cran-uri "multicool" version))
8710 "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
8711 (build-system r-build-system)
8712 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8713 (home-page "https://cran.r-project.org/web/packages/multicool/")
8714 (synopsis "Permutations of multisets in cool-lex order")
8716 "This package provides a set of tools to permute multisets without loops
8717 or hash tables and to generate integer partitions. Cool-lex order is similar
8718 to colexicographical order.")
8719 (license license:gpl2)))
8721 (define-public r-misc3d
8728 (uri (cran-uri "misc3d" version))
8731 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
8732 (build-system r-build-system)
8733 (home-page "https://cran.r-project.org/web/packages/misc3d/")
8734 (synopsis "Miscellaneous 3D Plots")
8736 "This package provides a collection of miscellaneous 3d plots, including
8738 ;; Any version of the GPL.
8739 (license (list license:gpl2+ license:gpl3+))))
8748 (uri (cran-uri "ks" version))
8751 "0d5i8458s8ri9pcx2jm003z1ajk7ha3pmw1sr6lgn6a8d7wgmvqb"))))
8752 (build-system r-build-system)
8755 ("r-kernlab" ,r-kernlab)
8756 ("r-kernsmooth" ,r-kernsmooth)
8757 ("r-matrix" ,r-matrix)
8758 ("r-mclust" ,r-mclust)
8760 ("r-multicool" ,r-multicool)
8761 ("r-mvtnorm" ,r-mvtnorm)))
8762 (home-page "http://www.mvstat.net/tduong/")
8763 (synopsis "Kernel smoothing")
8765 "This package provides kernel smoothers for univariate and multivariate
8766 data, including density functions, density derivatives, cumulative
8767 distributions, modal clustering, discriminant analysis, and two-sample
8768 hypothesis testing.")
8769 ;; Either version of the GPL.
8770 (license (list license:gpl2 license:gpl3))))
8772 (define-public r-feature
8779 (uri (cran-uri "feature" version))
8782 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
8783 (build-system r-build-system)
8786 ("r-misc3d" ,r-misc3d)
8788 (home-page "http://www.mvstat.net/tduong/")
8789 (synopsis "Inferential feature significance for kernel density estimation")
8791 "The feature package contains functions to display and compute kernel
8792 density estimates, significant gradient and significant curvature regions.
8793 Significant gradient and/or curvature regions often correspond to significant
8794 features (e.g. local modes).")
8795 ;; Either version of the GPL.
8796 (license (list license:gpl2 license:gpl3))))
8798 (define-public r-arm
8805 (uri (cran-uri "arm" version))
8808 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
8809 (build-system r-build-system)
8811 `(("r-abind" ,r-abind)
8815 ("r-matrix" ,r-matrix)
8816 ("r-nlme" ,r-nlme)))
8817 (home-page "https://cran.r-project.org/web/packages/arm/")
8818 (synopsis "Data analysis using regression and multilevel/hierarchical models")
8820 "This package provides functions to accompany A. Gelman and J. Hill,
8821 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
8822 University Press, 2007.")
8823 (license license:gpl3+)))
8825 (define-public r-circular
8832 (uri (cran-uri "circular" version))
8835 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
8836 (build-system r-build-system)
8838 `(("r-boot" ,r-boot)
8839 ("r-mvtnorm" ,r-mvtnorm)))
8841 `(("gfortran" ,gfortran)))
8842 (home-page "https://cran.r-project.org/web/packages/circular/")
8843 (synopsis "Circular statistics")
8845 "This package provides tools for circular statistics, from \"Topics in
8846 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
8848 (license license:gpl2+)))
8850 (define-public r-activity
8857 (uri (cran-uri "activity" version))
8860 "11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs"))))
8861 (build-system r-build-system)
8863 `(("r-circular" ,r-circular)
8864 ("r-pbapply" ,r-pbapply)))
8865 (home-page "https://cran.r-project.org/web/packages/activity/")
8866 (synopsis "Animal activity statistics")
8868 "This package provides functions to fit kernel density functions to
8869 animal activity time data; plot activity distributions; quantify overall
8870 levels of activity; statistically compare activity metrics through
8871 bootstrapping; and evaluate variation in linear variables with time (or other
8872 circular variables).")
8873 (license license:gpl3)))
8875 (define-public r-ouch
8882 (uri (cran-uri "ouch" version))
8885 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
8886 (build-system r-build-system)
8887 (propagated-inputs `(("r-subplex" ,r-subplex)))
8888 (home-page "http://kingaa.github.io/ouch/")
8889 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
8891 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
8892 for evolution along a phylogenetic tree.")
8893 (license license:gpl2+)))
8895 (define-public r-fmsb
8902 (uri (cran-uri "fmsb" version))
8905 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
8906 (build-system r-build-system)
8907 (home-page "http://minato.sip21c.org/msb/")
8908 (synopsis "Functions for medical statistics book with demographic data")
8910 "This package provides several utility functions for the book entitled
8911 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
8912 Japan, 2007) with Japanese demographic data and some demographic analysis
8913 related functions.")
8914 (license license:gpl2+)))
8916 (define-public r-stabledist
8918 (name "r-stabledist")
8923 (uri (cran-uri "stabledist" version))
8926 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
8927 (build-system r-build-system)
8928 (home-page "http://www.rmetrics.org")
8929 (synopsis "Stable distribution functions")
8931 "This package provides density, probability and quantile functions, and
8932 random number generation for (skew) stable distributions, using the
8933 parametrizations of Nolan.")
8934 (license license:gpl2+)))
8936 (define-public r-gsl
8943 (uri (cran-uri "gsl" version))
8946 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
8947 (build-system r-build-system)
8950 (home-page "https://cran.r-project.org/web/packages/gsl")
8951 (synopsis "Wrapper for the GNU Scientific Library")
8953 "This package provides an R wrapper for the special functions and quasi
8954 random number generators of the GNU Scientific Library.")
8955 (license license:gpl2+)))
8957 (define-public r-adgoftest
8959 (name "r-adgoftest")
8964 (uri (cran-uri "ADGofTest" version))
8967 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
8968 (properties `((upstream-name . "ADGofTest")))
8969 (build-system r-build-system)
8970 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
8971 (synopsis "Anderson-Darling GoF test")
8973 "This package provides an implementation of the Anderson-Darling GoF test
8974 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
8975 Anderson-Darling Distribution\".")
8976 ;; Any version of the GPL.
8977 (license license:gpl3+)))
8979 (define-public r-softimpute
8981 (name "r-softimpute")
8986 (uri (cran-uri "softImpute" version))
8989 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
8990 (properties `((upstream-name . "softImpute")))
8991 (build-system r-build-system)
8993 `(("r-matrix" ,r-matrix)))
8995 `(("gfortran" ,gfortran)))
8996 (home-page "https://cran.r-project.org/web/packages/softImpute")
8997 (synopsis "Matrix completion via iterative soft-thresholded SVD")
8999 "This package provides iterative methods for matrix completion that use
9000 nuclear-norm regularization. The package includes procedures for centering
9001 and scaling rows, columns or both, and for computing low-rank @dfn{single
9002 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9004 (license license:gpl2)))
9006 (define-public r-fftwtools
9008 (name "r-fftwtools")
9013 (uri (cran-uri "fftwtools" version))
9016 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9017 (build-system r-build-system)
9018 (inputs `(("fftw" ,fftw)))
9019 (home-page "https://github.com/krahim/fftwtools")
9020 (synopsis "Wrapper for FFTW3")
9022 "This package provides a wrapper for several FFTW functions. It provides
9023 access to the two-dimensional FFT, the multivariate FFT, and the
9024 one-dimensional real to complex FFT using the FFTW3 library. The package
9025 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9026 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9027 The FFT functions have a parameter that allows them to not return the
9028 redundant complex conjugate when the input is real data.")
9029 (license license:gpl2+)))
9031 (define-public r-tiff
9038 (uri (cran-uri "tiff" version))
9041 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9042 (build-system r-build-system)
9044 `(("libtiff" ,libtiff)
9045 ("libjpeg" ,libjpeg)
9047 (home-page "http://www.rforge.net/tiff/")
9048 (synopsis "Read and write TIFF images")
9050 "This package provides an easy and simple way to read, write and display
9051 bitmap images stored in the TIFF format. It can read and write both files and
9052 in-memory raw vectors.")
9053 ;; Either of these two license versions.
9054 (license (list license:gpl2 license:gpl3))))
9056 (define-public r-waveslim
9063 (uri (cran-uri "waveslim" version))
9066 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9067 (build-system r-build-system)
9069 `(("gfortran" ,gfortran)))
9070 (home-page "http://waveslim.blogspot.com")
9071 (synopsis "Basic wavelet routines for signal processing")
9073 "This package provides basic wavelet routines for time series (1D),
9074 image (2D) and array (3D) analysis. The code provided here is based on
9075 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9076 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9077 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9078 pairs (Selesnick 2001, 2002).")
9079 (license license:bsd-3)))
9081 (define-public r-wordcloud
9083 (name "r-wordcloud")
9088 (uri (cran-uri "wordcloud" version))
9091 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9092 (build-system r-build-system)
9094 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9095 ("r-rcpp" ,r-rcpp)))
9096 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9097 (synopsis "Word clouds")
9099 "This package provides functionality to create pretty word clouds,
9100 visualize differences and similarity between documents, and avoid
9101 over-plotting in scatter plots with text.")
9102 (license license:lgpl2.1)))
9104 (define-public r-colorramps
9106 (name "r-colorramps")
9111 (uri (cran-uri "colorRamps" version))
9114 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9115 (properties `((upstream-name . "colorRamps")))
9116 (build-system r-build-system)
9117 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9118 (synopsis "Build color tables")
9119 (description "This package provides features to build gradient color
9121 ;; Any version of the GPL
9122 (license license:gpl3+)))
9124 (define-public r-tidytree
9131 (uri (cran-uri "tidytree" version))
9134 "04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w"))))
9135 (build-system r-build-system)
9138 ("r-dplyr" ,r-dplyr)
9139 ("r-lazyeval" ,r-lazyeval)
9140 ("r-magrittr" ,r-magrittr)
9141 ("r-rlang" ,r-rlang)
9142 ("r-tibble" ,r-tibble)))
9143 (home-page "https://github.com/GuangchuangYu/tidytree")
9144 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9146 "Phylogenetic trees generally contain multiple components including nodes,
9147 edges, branches and associated data. This package provides an approach to
9148 convert tree objects to tidy data frames. It also provides tidy interfaces to
9149 manipulate tree data.")
9150 (license license:artistic2.0)))
9152 (define-public r-rvcheck
9159 (uri (cran-uri "rvcheck" version))
9162 "1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b"))))
9163 (build-system r-build-system)
9165 `(("r-rlang" ,r-rlang)))
9166 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9167 (synopsis "R package version check")
9169 "This package provides tools to check the latest release version of R and
9170 R packages (on CRAN, Bioconductor or Github).")
9171 (license license:artistic2.0)))
9173 (define-public r-docopt
9180 (uri (cran-uri "docopt" version))
9183 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9184 (build-system r-build-system)
9185 (home-page "https://github.com/docopt/docopt.R")
9186 (synopsis "Command-line interface specification language")
9188 "This package enables you to define a command-line interface by just
9189 giving it a description in the specific format.")
9190 (license license:expat)))
9192 (define-public r-sparsesvd
9194 (name "r-sparsesvd")
9199 (uri (cran-uri "sparsesvd" version))
9202 "1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam"))))
9203 (build-system r-build-system)
9204 (propagated-inputs `(("r-matrix" ,r-matrix)))
9205 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9206 (synopsis "Sparse truncated singular value decomposition")
9208 "This package provides a Wrapper around the SVDLIBC library
9209 for (truncated) singular value decomposition of a sparse matrix. Currently,
9210 only sparse real matrices in Matrix package format are supported.")
9211 ;; SVDLIBC is released under BSD-2. The R interface is released under
9213 (license (list license:bsd-3 license:bsd-2))))
9215 (define-public r-densityclust
9217 (name "r-densityclust")
9222 (uri (cran-uri "densityClust" version))
9225 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9226 (properties `((upstream-name . "densityClust")))
9227 (build-system r-build-system)
9230 ("r-ggplot2" ,r-ggplot2)
9231 ("r-ggrepel" ,r-ggrepel)
9232 ("r-gridextra" ,r-gridextra)
9233 ("r-rcolorbrewer" ,r-rcolorbrewer)
9235 ("r-rtsne" ,r-rtsne)))
9236 (home-page "https://cran.r-project.org/web/packages/densityClust")
9237 (synopsis "Clustering by fast search and find of density peaks")
9239 "This package provides an improved implementation (based on k-nearest
9240 neighbors) of the density peak clustering algorithm, originally described by
9241 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9242 large datasets (> 100,000 samples) very efficiently.")
9243 (license license:gpl2+)))
9245 (define-public r-combinat
9252 (uri (cran-uri "combinat" version))
9255 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9256 (build-system r-build-system)
9257 (home-page "https://cran.r-project.org/web/packages/combinat")
9258 (synopsis "Combinatorics utilities")
9259 (description "This package provides assorted routines for combinatorics.")
9260 (license license:gpl2)))
9262 (define-public r-qlcmatrix
9264 (name "r-qlcmatrix")
9269 (uri (cran-uri "qlcMatrix" version))
9272 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9273 (properties `((upstream-name . "qlcMatrix")))
9274 (build-system r-build-system)
9276 `(("r-docopt" ,r-docopt)
9277 ("r-matrix" ,r-matrix)
9279 ("r-sparsesvd" ,r-sparsesvd)))
9280 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9281 (synopsis "Sparse matrix functions for quantitative language comparison")
9283 "This package provides an extension of the functionality of the Matrix
9284 package for using sparse matrices. Some of the functions are very general,
9285 while other are highly specific for the special data format used for
9286 @dfn{quantitative language comparison} (QLC).")
9287 (license license:gpl3)))
9289 (define-public r-ddrtree
9296 (uri (cran-uri "DDRTree" version))
9299 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9300 (properties `((upstream-name . "DDRTree")))
9301 (build-system r-build-system)
9304 ("r-irlba" ,r-irlba)
9306 ("r-rcppeigen" ,r-rcppeigen)))
9307 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9308 (synopsis "Learning principal graphs with DDRTree")
9310 "This package provides an implementation of the framework of
9311 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9312 dimensional space while constructs a principal tree which passes through the
9313 middle of the data simultaneously. DDRTree shows superiority to
9314 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9315 intrinsic structure of single cell genomics data. In general, it could be
9316 used to reconstruct the temporal progression as well as the bifurcation
9317 structure of any data type.")
9318 (license license:asl2.0)))
9320 (define-public r-corpcor
9327 (uri (cran-uri "corpcor" version))
9330 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9331 (build-system r-build-system)
9332 (home-page "http://strimmerlab.org/software/corpcor/")
9333 (synopsis "Efficient estimation of covariance and (partial) correlation")
9335 "This package implements a James-Stein-type shrinkage estimator for the
9336 covariance matrix, with separate shrinkage for variances and correlations.
9337 Furthermore, functions are available for fast singular value decomposition,
9338 for computing the pseudoinverse, and for checking the rank and positive
9339 definiteness of a matrix.")
9340 (license license:gpl3+)))
9342 (define-public r-rspectra
9349 (uri (cran-uri "RSpectra" version))
9352 "12w5vnz39gyciza0fl7fw4f9i9kjw763h3mvk1sxd97c5dsn26jg"))))
9353 (properties `((upstream-name . "RSpectra")))
9354 (build-system r-build-system)
9356 `(("r-matrix" ,r-matrix)
9358 ("r-rcppeigen" ,r-rcppeigen)))
9359 (home-page "https://github.com/yixuan/RSpectra")
9360 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
9362 "This package provides an R interface to the Spectra library for
9363 large-scale eigenvalue and SVD problems. It is typically used to compute a
9364 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
9365 which is usually more efficient than @code{eigen()} if k << n.")
9367 (license license:mpl2.0)))
9369 (define-public r-vbsr
9376 (uri (cran-uri "vbsr" version))
9379 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
9380 (build-system r-build-system)
9381 (home-page "https://cran.r-project.org/web/packages/vbsr")
9382 (synopsis "Variational Bayes spike regression regularized linear models")
9384 "This package provides an efficient algorithm for solving ultra-sparse
9385 regularized regression models using a variational Bayes algorithm with a spike
9386 prior. The algorithm is solved on a path, with coordinate updates, and is
9387 capable of generating very sparse models. Very general model
9388 diagnostics for controlling type-1 errors are also provided.")
9389 (license license:gpl2)))
9391 (define-public r-flare
9398 (uri (cran-uri "flare" version))
9401 "0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1"))))
9402 (build-system r-build-system)
9404 `(("r-igraph" ,r-igraph)
9405 ("r-lattice" ,r-lattice)
9407 ("r-matrix" ,r-matrix)))
9408 (home-page "https://cran.r-project.org/web/packages/flare")
9409 (synopsis "Family of Lasso regression implementations")
9411 "This packages provides implementations of a family of Lasso variants
9412 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
9413 high dimensional sparse linear models.")
9414 (license license:gpl2)))
9416 (define-public r-lassopv
9423 (uri (cran-uri "lassopv" version))
9426 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
9427 (build-system r-build-system)
9428 (propagated-inputs `(("r-lars" ,r-lars)))
9429 (home-page "https://github.com/lingfeiwang/lassopv")
9430 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
9432 "This package enables you to estimate the p-values for predictors x
9433 against target variable y in Lasso regression, using the regularization
9434 strength when each predictor enters the active set of regularization path for
9435 the first time as the statistic.")
9436 (license license:gpl3)))
9438 (define-public r-splitstackshape
9440 (name "r-splitstackshape")
9445 (uri (cran-uri "splitstackshape" version))
9448 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
9449 (build-system r-build-system)
9451 `(("r-data-table" ,r-data-table)))
9452 (home-page "https://github.com/mrdwab/splitstackshape")
9453 (synopsis "Stack and reshape datasets after splitting concatenated values")
9455 "Online data collection tools like Google Forms often export
9456 multiple-response questions with data concatenated in cells. The
9457 @code{concat.split} (cSplit) family of functions provided by this package
9458 splits such data into separate cells. This package also includes functions to
9459 stack groups of columns and to reshape wide data, even when the data are
9460 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
9461 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
9463 (license license:gpl3)))
9465 (define-public r-tfmpvalue
9467 (name "r-tfmpvalue")
9472 (uri (cran-uri "TFMPvalue" version))
9475 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
9476 (properties `((upstream-name . "TFMPvalue")))
9477 (build-system r-build-system)
9478 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9479 (home-page "https://github.com/ge11232002/TFMPvalue")
9480 (synopsis "P-value computation for position weight matrices")
9482 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
9483 identification from sequence/alignments, we are interested in the significance
9484 of certain match scores. TFMPvalue provides the accurate calculation of a
9485 p-value with a score threshold for position weight matrices, or the score with
9486 a given p-value. It is an interface to code originally made available by
9487 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
9488 Touzet and Varre (2007).")
9489 (license license:gpl2)))
9491 (define-public r-rnifti
9498 (uri (cran-uri "RNifti" version))
9501 "07sfzps4yg5zdhbxh6i4rbjvbjvvf2d8i9jcf64ywbmi557sw1zv"))))
9502 (properties `((upstream-name . "RNifti")))
9503 (build-system r-build-system)
9504 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9505 (home-page "https://github.com/jonclayden/RNifti")
9506 (synopsis "Fast R and C++ access to NIfTI images")
9508 "This package provides very fast read and write access to images stored
9509 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
9510 compiled C and interpreted R code. It also provides a C/C++ API that can be
9511 used by other packages.")
9512 (license license:gpl2)))
9514 (define-public r-shades
9521 (uri (cran-uri "shades" version))
9524 "0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv"))))
9525 (build-system r-build-system)
9526 (home-page "https://github.com/jonclayden/shades")
9527 (synopsis "Simple color manipulation")
9529 "This package provides functions for easily manipulating colors,
9530 creating color scales and calculating color distances.")
9531 (license license:bsd-3)))
9533 (define-public r-ore
9540 (uri (cran-uri "ore" version))
9543 "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m"))))
9544 (build-system r-build-system)
9545 (home-page "https://github.com/jonclayden/ore")
9546 (synopsis "R interface to the Onigmo regular expression library")
9548 "This package provides an alternative to R's built-in functionality for
9549 handling regular expressions, based on the Onigmo library. It offers
9550 first-class compiled regex objects, partial matching and function-based
9551 substitutions, amongst other features.")
9552 (license license:bsd-3)))
9554 (define-public r-reportr
9561 (uri (cran-uri "reportr" version))
9564 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
9565 (build-system r-build-system)
9566 (propagated-inputs `(("r-ore" ,r-ore)))
9567 (home-page "https://github.com/jonclayden/reportr")
9568 (synopsis "General message and error reporting system")
9570 "This package provides a system for reporting messages, which offers
9571 certain useful features over the standard R system, such as the incorporation
9572 of output consolidation, message filtering, assertions, expression
9573 substitution, automatic generation of stack traces for debugging, and
9574 conditional reporting based on the current \"output level\".")
9575 (license license:gpl2)))
9577 (define-public r-tractor-base
9579 (name "r-tractor-base")
9584 (uri (cran-uri "tractor.base" version))
9587 "0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj"))))
9588 (properties `((upstream-name . "tractor.base")))
9589 (build-system r-build-system)
9592 ("r-reportr" ,r-reportr)
9593 ("r-rnifti" ,r-rnifti)
9594 ("r-shades" ,r-shades)))
9595 (home-page "http://www.tractor-mri.org.uk")
9596 (synopsis "Read, manipulate and visualize magnetic resonance images")
9598 "This package provides functions for working with magnetic resonance
9599 images. It supports reading and writing of popular file formats (DICOM,
9600 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
9601 visualization; flexible image manipulation; metadata and sparse image
9603 (license license:gpl2)))
9605 (define-public r-grimport
9612 (uri (cran-uri "grImport" version))
9615 "19d05ygpiv47lfzhfih35pdfll0axbrgd6p86l59mmg2d0j0s8bd"))))
9616 (properties `((upstream-name . "grImport")))
9617 (build-system r-build-system)
9619 `(("ghostscript" ,ghostscript)))
9621 `(("r-xml" ,r-xml)))
9622 (home-page "https://cran.r-project.org/web/packages/grImport")
9623 (synopsis "Convert, import, and draw PostScript pictures")
9625 "This package provides functions for converting, importing, and drawing
9626 PostScript pictures in R plots.")
9627 (license license:gpl2+)))
9629 (define-public r-grimport2
9631 (name "r-grimport2")
9636 (uri (cran-uri "grImport2" version))
9639 "1hwx287pp936f0wbcicplwmhz96ip00wq09dp7bvz80lqcmr8nyx"))))
9640 (properties `((upstream-name . "grImport2")))
9641 (build-system r-build-system)
9643 `(("r-base64enc" ,r-base64enc)
9647 (home-page "https://cran.r-project.org/web/packages/grImport2/")
9648 (synopsis "Import SVG graphics")
9650 "This package provides functions for importing external vector images and
9651 drawing them as part of R plots. This package is different from the
9652 @code{grImport} package because, where that package imports PostScript format
9653 images, this package imports SVG format images. Furthermore, this package
9654 imports a specific subset of SVG, so external images must be preprocessed
9655 using a package like @code{rsvg} to produce SVG that this package can import.
9656 SVG features that are not supported by R graphics, such as gradient fills, can
9657 be imported and then exported via the @code{gridSVG} package.")
9658 (license license:gpl2+)))
9660 (define-public r-kohonen
9667 (uri (cran-uri "kohonen" version))
9670 "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"))))
9671 (build-system r-build-system)
9673 `(("r-mass" ,r-mass)
9674 ("r-rcpp" ,r-rcpp)))
9675 (home-page "https://cran.r-project.org/web/packages/kohonen")
9676 (synopsis "Supervised and unsupervised self-organising maps")
9678 "This package provides functions to train @dfn{self-organising
9679 maps} (SOMs). Also interrogation of the maps and prediction using trained
9680 maps are supported. The name of the package refers to Teuvo Kohonen, the
9681 inventor of the SOM.")
9682 (license license:gpl2+)))
9684 (define-public r-nnls
9691 (uri (cran-uri "nnls" version))
9694 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
9695 (build-system r-build-system)
9696 (native-inputs `(("gfortran" ,gfortran)))
9697 (home-page "https://cran.r-project.org/web/packages/nnls")
9698 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
9700 "This package provides an R interface to the Lawson-Hanson implementation
9701 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
9702 the combination of non-negative and non-positive constraints.")
9703 (license license:gpl2+)))
9705 (define-public r-iso
9712 (uri (cran-uri "Iso" version))
9715 "0lljc99sdzdqj6d56qbsggibr6pkdwkh821bj70ianikyvmdc1y0"))))
9716 (properties `((upstream-name . "Iso")))
9717 (build-system r-build-system)
9718 (native-inputs `(("gfortran" ,gfortran)))
9719 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
9720 (synopsis "Functions to perform isotonic regression")
9722 "This package provides support for linear order and unimodal
9723 order (univariate) isotonic regression and bivariate isotonic regression with
9724 linear order on both variables.")
9725 (license license:gpl2+)))
9727 (define-public r-chemometricswithr
9729 (name "r-chemometricswithr")
9734 (uri (cran-uri "ChemometricsWithR" version))
9737 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
9739 `((upstream-name . "ChemometricsWithR")))
9740 (build-system r-build-system)
9742 `(("r-devtools" ,r-devtools)
9743 ("r-kohonen" ,r-kohonen)
9746 (home-page "https://github.com/rwehrens/CWR")
9747 (synopsis "Chemometrics with R")
9749 "This package provides functions and scripts used in the book
9750 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
9751 Life Sciences\" by Ron Wehrens, Springer (2011).")
9752 (license license:gpl2+)))
9754 (define-public r-als
9761 (uri (cran-uri "ALS" version))
9764 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
9765 (properties `((upstream-name . "ALS")))
9766 (build-system r-build-system)
9769 ("r-nnls" ,r-nnls)))
9770 (home-page "https://cran.r-project.org/web/packages/ALS")
9771 (synopsis "Multivariate curve resolution alternating least squares")
9773 "Alternating least squares is often used to resolve components
9774 contributing to data with a bilinear structure; the basic technique may be
9775 extended to alternating constrained least squares. This package provides an
9776 implementation of @dfn{multivariate curve resolution alternating least
9779 Commonly applied constraints include unimodality, non-negativity, and
9780 normalization of components. Several data matrices may be decomposed
9781 simultaneously by assuming that one of the two matrices in the bilinear
9782 decomposition is shared between datasets.")
9783 (license license:gpl2+)))
9785 (define-public r-strucchange
9787 (name "r-strucchange")
9792 (uri (cran-uri "strucchange" version))
9795 "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl"))))
9796 (build-system r-build-system)
9798 `(("r-sandwich" ,r-sandwich)
9800 (home-page "https://cran.r-project.org/web/packages/strucchange")
9801 (synopsis "Testing, monitoring, and dating structural changes")
9803 "This package provides tools for testing, monitoring and dating
9804 structural changes in (linear) regression models. It features tests/methods
9805 from the generalized fluctuation test framework as well as from the F
9806 test (Chow test) framework. This includes methods to fit, plot and test
9807 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
9808 statistics, respectively. It is possible to monitor incoming data online
9809 using fluctuation processes. Finally, the breakpoints in regression models
9810 with structural changes can be estimated together with confidence intervals.
9811 Emphasis is always given to methods for visualizing the data.")
9812 ;; Either of these two GPL versions
9813 (license (list license:gpl2 license:gpl3))))
9815 (define-public r-pixmap
9822 (uri (cran-uri "pixmap" version))
9825 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
9826 (build-system r-build-system)
9827 (home-page "https://cran.r-project.org/web/packages/pixmap")
9828 (synopsis "Tools for bitmap images")
9830 "This package provides functions for importing, exporting, plotting and
9831 other manipulations of bitmapped images.")
9832 (license license:gpl2)))
9834 (define-public r-rapidjsonr
9836 (name "r-rapidjsonr")
9841 (uri (cran-uri "rapidjsonr" version))
9844 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
9845 (build-system r-build-system)
9846 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
9847 (synopsis "JSON parser")
9849 "This package provides JSON parsing capability through the Rapidjson
9851 (license license:expat)))
9853 (define-public r-ontologyindex
9855 (name "r-ontologyindex")
9860 (uri (cran-uri "ontologyIndex" version))
9863 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
9864 (properties `((upstream-name . "ontologyIndex")))
9865 (build-system r-build-system)
9866 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
9867 (synopsis "Functions for processing ontologies in R")
9869 "This package provides functions for reading ontologies into R as lists
9870 and manipulating sets of ontological terms.")
9871 (license license:gpl2+)))
9873 (define-public r-bigrquery
9875 (name "r-bigrquery")
9880 (uri (cran-uri "bigrquery" version))
9883 "0h2nzyn1w0padpl61l467j7vlkc2wair7sh6p26p94z4zfsnv0i1"))))
9884 (build-system r-build-system)
9886 `(("r-assertthat" ,r-assertthat)
9887 ("r-bit64" ,r-bit64)
9892 ("r-jsonlite" ,r-jsonlite)
9893 ("r-prettyunits" ,r-prettyunits)
9894 ("r-progress" ,r-progress)
9895 ("r-rapidjsonr" ,r-rapidjsonr)
9897 ("r-tibble" ,r-tibble)))
9898 (home-page "https://github.com/rstats-db/bigrquery")
9899 (synopsis "R interface to Google's BigQuery API")
9901 "This package provides an R interface to Google's BigQuery database.")
9902 (license license:gpl3)))
9904 (define-public r-gmp
9907 (version "0.5-13.5")
9911 (uri (cran-uri "gmp" version))
9914 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
9915 (build-system r-build-system)
9918 (modify-phases %standard-phases
9919 (add-after 'unpack 'set-CC
9920 (lambda _ (setenv "CC" "gcc") #t)))))
9921 (inputs `(("gmp" ,gmp)))
9922 (home-page "https://cran.r-project.org/web/packages/gmp")
9923 (synopsis "Multiple precision arithmetic")
9925 "This package supports multiple precision arithmetic (big integers and
9926 rationals, prime number tests, matrix computation), \"arithmetic without
9927 limitations\" using the GNU Multiple Precision library.")
9928 ;; Any version of the GPL.
9929 (license license:gpl3+)))
9931 (define-public r-rmpfr
9938 (uri (cran-uri "Rmpfr" version))
9941 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
9942 (properties `((upstream-name . "Rmpfr")))
9943 (build-system r-build-system)
9947 `(("r-gmp" ,r-gmp)))
9948 (home-page "http://rmpfr.r-forge.r-project.org/")
9949 (synopsis "R bindings to the MPFR library")
9951 "This package supports arithmetic (via S4 classes and methods) for
9952 arbitrary precision floating point numbers, including transcendental
9953 functions. To this end, the package interfaces with the @dfn{Multiple
9954 Precision Floating-Point Reliable} (MPFR) library.")
9955 (license license:gpl2+)))
9957 (define-public r-assertive-base
9959 (name "r-assertive-base")
9964 (uri (cran-uri "assertive.base" version))
9967 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
9969 `((upstream-name . "assertive.base")))
9970 (build-system r-build-system)
9971 (home-page "https://bitbucket.org/richierocks/assertive.base")
9972 (synopsis "Core of the assertive package")
9974 "This package provides a minimal set of predicates and assertions used by
9975 the assertive package. This is mainly for use by other package developers who
9976 want to include run-time testing features in their own packages.")
9977 (license license:gpl3+)))
9979 (define-public r-assertive-properties
9981 (name "r-assertive-properties")
9986 (uri (cran-uri "assertive.properties" version))
9989 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
9991 `((upstream-name . "assertive.properties")))
9992 (build-system r-build-system)
9994 `(("r-assertive-base" ,r-assertive-base)))
9995 (home-page "https://bitbucket.org/richierocks/assertive.properties")
9996 (synopsis "Assertions to check properties of variables")
9998 "This package provides a set of predicates and assertions for checking
9999 the properties of variables, such as length, names and attributes. This is
10000 mainly for use by other package developers who want to include run-time
10001 testing features in their own packages.")
10002 (license license:gpl3+)))
10004 (define-public r-assertive-numbers
10006 (name "r-assertive-numbers")
10011 (uri (cran-uri "assertive.numbers" version))
10014 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10016 `((upstream-name . "assertive.numbers")))
10017 (build-system r-build-system)
10019 `(("r-assertive-base" ,r-assertive-base)))
10020 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10021 (synopsis "Assertions to check properties of numbers")
10023 "This package provides a set of predicates and assertions for checking
10024 the properties of numbers. This is mainly for use by other package developers
10025 who want to include run-time testing features in their own packages.")
10026 (license license:gpl3+)))
10028 (define-public r-assertive-sets
10030 (name "r-assertive-sets")
10035 (uri (cran-uri "assertive.sets" version))
10038 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10040 `((upstream-name . "assertive.sets")))
10041 (build-system r-build-system)
10043 `(("r-assertive-base" ,r-assertive-base)))
10044 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10045 (synopsis "Assertions to check properties of sets")
10047 "This package provides a set of predicates and assertions for checking
10048 the properties of sets. This is mainly for use by other package developers
10049 who want to include run-time testing features in their own packages.")
10050 (license license:gpl3+)))
10052 (define-public r-assertive-matrices
10054 (name "r-assertive-matrices")
10059 (uri (cran-uri "assertive.matrices" version))
10062 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10064 `((upstream-name . "assertive.matrices")))
10065 (build-system r-build-system)
10067 `(("r-assertive-base" ,r-assertive-base)))
10068 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10069 (synopsis "Assertions to check properties of matrices")
10071 "This package provides a set of predicates and assertions for checking
10072 the properties of matrices. This is mainly for use by other package
10073 developers who want to include run-time testing features in their own
10075 (license license:gpl3+)))
10077 (define-public r-assertive-models
10079 (name "r-assertive-models")
10084 (uri (cran-uri "assertive.models" version))
10087 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10089 `((upstream-name . "assertive.models")))
10090 (build-system r-build-system)
10092 `(("r-assertive-base" ,r-assertive-base)))
10093 (home-page "https://bitbucket.org/richierocks/assertive.models")
10094 (synopsis "Assertions to check properties of models")
10096 "This package provides a set of predicates and assertions for checking
10097 the properties of models. This is mainly for use by other package developers
10098 who want to include run-time testing features in their own packages.")
10099 (license license:gpl3+)))
10101 (define-public r-assertive-reflection
10103 (name "r-assertive-reflection")
10108 (uri (cran-uri "assertive.reflection" version))
10111 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10113 `((upstream-name . "assertive.reflection")))
10114 (build-system r-build-system)
10116 `(("r-assertive-base" ,r-assertive-base)))
10117 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10118 (synopsis "Assertions for checking the state of R")
10120 "This package provides a set of predicates and assertions for checking
10121 the state and capabilities of R, the operating system it is running on, and
10122 the IDE being used. This is mainly for use by other package developers who
10123 want to include run-time testing features in their own packages.")
10124 (license license:gpl3+)))
10126 (define-public r-assertive-types
10128 (name "r-assertive-types")
10133 (uri (cran-uri "assertive.types" version))
10136 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10138 `((upstream-name . "assertive.types")))
10139 (build-system r-build-system)
10141 `(("r-assertive-base" ,r-assertive-base)
10142 ("r-assertive-properties" ,r-assertive-properties)
10143 ("r-codetools" ,r-codetools)))
10144 (home-page "https://bitbucket.org/richierocks/assertive.types")
10145 (synopsis "Assertions to check types of variables")
10147 "This package provides a set of predicates and assertions for checking
10148 the types of variables. This is mainly for use by other package developers
10149 who want to include run-time testing features in their own packages.")
10150 (license license:gpl3+)))
10152 (define-public r-assertive-files
10154 (name "r-assertive-files")
10159 (uri (cran-uri "assertive.files" version))
10162 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10164 `((upstream-name . "assertive.files")))
10165 (build-system r-build-system)
10167 `(("r-assertive-base" ,r-assertive-base)
10168 ("r-assertive-numbers" ,r-assertive-numbers)))
10169 (home-page "https://bitbucket.org/richierocks/assertive.files")
10170 (synopsis "Assertions to check properties of files")
10172 "This package provides a set of predicates and assertions for checking
10173 the properties of files and connections. This is mainly for use by other
10174 package developers who want to include run-time testing features in their own
10176 (license license:gpl3+)))
10178 (define-public r-assertive-code
10180 (name "r-assertive-code")
10185 (uri (cran-uri "assertive.code" version))
10188 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10190 `((upstream-name . "assertive.code")))
10191 (build-system r-build-system)
10193 `(("r-assertive-base" ,r-assertive-base)
10194 ("r-assertive-properties" ,r-assertive-properties)
10195 ("r-assertive-types" ,r-assertive-types)))
10196 (home-page "https://bitbucket.org/richierocks/assertive.code")
10197 (synopsis "Assertions to check properties of code")
10199 "This package provides a set of predicates and assertions for checking
10200 the properties of code. This is mainly for use by other package developers
10201 who want to include run-time testing features in their own packages.")
10202 (license license:gpl3+)))
10204 (define-public r-assertive-datetimes
10206 (name "r-assertive-datetimes")
10211 (uri (cran-uri "assertive.datetimes" version))
10214 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10216 `((upstream-name . "assertive.datetimes")))
10217 (build-system r-build-system)
10219 `(("r-assertive-base" ,r-assertive-base)
10220 ("r-assertive-types" ,r-assertive-types)))
10221 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10222 (synopsis "Assertions to check properties of dates and times")
10224 "This package provides a set of predicates and assertions for checking
10225 the properties of dates and times. This is mainly for use by other package
10226 developers who want to include run-time testing features in their own
10228 (license license:gpl3+)))
10230 (define-public r-assertive-strings
10232 (name "r-assertive-strings")
10237 (uri (cran-uri "assertive.strings" version))
10240 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10242 `((upstream-name . "assertive.strings")))
10243 (build-system r-build-system)
10245 `(("r-assertive-base" ,r-assertive-base)
10246 ("r-assertive-types" ,r-assertive-types)
10247 ("r-stringi" ,r-stringi)))
10248 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10249 (synopsis "Assertions to check properties of strings")
10251 "This package provides a set of predicates and assertions for checking
10252 the properties of strings. This is mainly for use by other package developers
10253 who want to include run-time testing features in their own packages.")
10254 (license license:gpl3+)))
10256 (define-public r-assertive-data-us
10258 (name "r-assertive-data-us")
10263 (uri (cran-uri "assertive.data.us" version))
10266 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10268 `((upstream-name . "assertive.data.us")))
10269 (build-system r-build-system)
10271 `(("r-assertive-base" ,r-assertive-base)
10272 ("r-assertive-strings" ,r-assertive-strings)))
10273 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10274 (synopsis "Assertions to check properties of strings")
10276 "This package provides a set of predicates and assertions for checking
10277 the properties of US-specific complex data types. This is mainly for use by
10278 other package developers who want to include run-time testing features in
10279 their own packages.")
10280 (license license:gpl3+)))
10282 (define-public r-assertive-data-uk
10284 (name "r-assertive-data-uk")
10289 (uri (cran-uri "assertive.data.uk" version))
10292 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10294 `((upstream-name . "assertive.data.uk")))
10295 (build-system r-build-system)
10297 `(("r-assertive-base" ,r-assertive-base)
10298 ("r-assertive-strings" ,r-assertive-strings)))
10299 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10300 (synopsis "Assertions to check properties of strings")
10302 "This package provides a set of predicates and assertions for checking
10303 the properties of UK-specific complex data types. This is mainly for use by
10304 other package developers who want to include run-time testing features in
10305 their own packages.")
10306 (license license:gpl3+)))
10308 (define-public r-assertive-data
10310 (name "r-assertive-data")
10315 (uri (cran-uri "assertive.data" version))
10318 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
10320 `((upstream-name . "assertive.data")))
10321 (build-system r-build-system)
10323 `(("r-assertive-base" ,r-assertive-base)
10324 ("r-assertive-strings" ,r-assertive-strings)))
10325 (home-page "https://bitbucket.org/richierocks/assertive.data")
10326 (synopsis "Assertions to check properties of data")
10328 "This package provides a set of predicates and assertions for checking
10329 the properties of (country independent) complex data types. This is mainly
10330 for use by other package developers who want to include run-time testing
10331 features in their own packages.")
10332 (license license:gpl3+)))
10334 (define-public r-assertive
10336 (name "r-assertive")
10341 (uri (cran-uri "assertive" version))
10344 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
10345 (build-system r-build-system)
10347 `(("r-assertive-base" ,r-assertive-base)
10348 ("r-assertive-code" ,r-assertive-code)
10349 ("r-assertive-data" ,r-assertive-data)
10350 ("r-assertive-data-uk" ,r-assertive-data-uk)
10351 ("r-assertive-data-us" ,r-assertive-data-us)
10352 ("r-assertive-datetimes" ,r-assertive-datetimes)
10353 ("r-assertive-files" ,r-assertive-files)
10354 ("r-assertive-matrices" ,r-assertive-matrices)
10355 ("r-assertive-models" ,r-assertive-models)
10356 ("r-assertive-numbers" ,r-assertive-numbers)
10357 ("r-assertive-properties" ,r-assertive-properties)
10358 ("r-assertive-reflection" ,r-assertive-reflection)
10359 ("r-assertive-sets" ,r-assertive-sets)
10360 ("r-assertive-strings" ,r-assertive-strings)
10361 ("r-assertive-types" ,r-assertive-types)
10362 ("r-knitr" ,r-knitr)))
10363 (home-page "https://bitbucket.org/richierocks/assertive")
10364 (synopsis "Readable check functions to ensure code integrity")
10366 "This package provides lots of predicates (@code{is_*} functions) to
10367 check the state of your variables, and assertions (@code{assert_*} functions)
10368 to throw errors if they aren't in the right form.")
10369 (license license:gpl3+)))
10371 (define-public r-dotcall64
10373 (name "r-dotcall64")
10378 (uri (cran-uri "dotCall64" version))
10381 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
10382 (properties `((upstream-name . "dotCall64")))
10383 (build-system r-build-system)
10384 (native-inputs `(("gfortran" ,gfortran)))
10385 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
10386 (synopsis "Enhanced foreign function interface supporting long vectors")
10388 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
10389 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
10390 supports long vectors, arguments of type 64-bit integer, and provides a
10391 mechanism to avoid unnecessary copies of read-only and write-only arguments.
10392 This makes it a convenient and fast interface to C/C++ and Fortran code.")
10393 (license license:gpl2+)))
10395 (define-public r-spam
10402 (uri (cran-uri "spam" version))
10405 "024dgfnjfxvsiymbzrhadinamj6qy509f4sbd1zxql8ymkyxn7vi"))))
10406 (build-system r-build-system)
10408 `(("r-dotcall64" ,r-dotcall64)))
10409 (native-inputs `(("gfortran" ,gfortran)))
10410 (home-page "https://www.math.uzh.ch/pages/spam/")
10411 (synopsis "Sparse matrix algebra")
10413 "This package provides a set of functions for sparse matrix algebra.
10414 Differences with other sparse matrix packages are:
10417 @item it only supports (essentially) one sparse matrix format;
10418 @item it is based on transparent and simple structure(s);
10419 @item it is tailored for MCMC calculations within G(M)RF;
10420 @item and it is fast and scalable (with the extension package @code{spam64}).
10422 ;; Either of these licenses
10423 (license (list license:bsd-3 license:lgpl2.0))))
10425 (define-public r-fields
10432 (uri (cran-uri "fields" version))
10435 "0hsr6r0zyv8zqkfyd9fmjk6v901m2r8pmswvsmps6w5zvpi0p5kw"))))
10436 (build-system r-build-system)
10438 `(("r-maps" ,r-maps)
10439 ("r-spam" ,r-spam)))
10441 `(("gfortran" ,gfortran)))
10442 (home-page "http://www.image.ucar.edu/fields")
10443 (synopsis "Tools for spatial data")
10445 "This is a package for curve, surface and function fitting with an
10446 emphasis on splines, spatial data and spatial statistics. The major methods
10447 include cubic, and thin plate splines, Kriging, and compactly supported
10448 covariance functions for large data sets.")
10449 (license license:gpl2+)))
10451 (define-public r-spatialextremes
10453 (name "r-spatialextremes")
10458 (uri (cran-uri "SpatialExtremes" version))
10461 "1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050"))))
10463 `((upstream-name . "SpatialExtremes")))
10464 (build-system r-build-system)
10466 `(("r-fields" ,r-fields)
10467 ("r-maps" ,r-maps)))
10468 (home-page "http://spatialextremes.r-forge.r-project.org/")
10469 (synopsis "Modelling spatial extremes")
10471 "This package provides tools for the statistical modelling of spatial
10472 extremes using max-stable processes, copula or Bayesian hierarchical models.
10473 More precisely, this package allows (conditional) simulations from various
10474 parametric max-stable models, analysis of the extremal spatial dependence, the
10475 fitting of such processes using composite likelihoods or least square (simple
10476 max-stable processes only), model checking and selection and prediction.")
10477 (license license:gpl2+)))
10479 (define-public r-drc
10486 (uri (cran-uri "drc" version))
10489 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
10490 (build-system r-build-system)
10493 ("r-gtools" ,r-gtools)
10495 ("r-multcomp" ,r-multcomp)
10496 ("r-plotrix" ,r-plotrix)
10497 ("r-scales" ,r-scales)))
10498 (home-page "https://cran.r-project.org/web/packages/drc")
10499 (synopsis "Analysis of dose-response curves")
10501 "This package provides a suite of flexible and versatile model fitting
10502 and after-fitting functions for the analysis of dose-response data.")
10503 (license license:gpl2+)))
10505 (define-public r-rmeta
10512 (uri (cran-uri "rmeta" version))
10515 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
10516 (build-system r-build-system)
10517 (home-page "https://cran.r-project.org/web/packages/rmeta")
10518 (synopsis "Tools for meta-analysis")
10520 "This package provides functions for simple fixed and random effects
10521 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
10522 draws standard summary plots, funnel plots, and computes summaries and tests
10523 for association and heterogeneity.")
10524 (license license:gpl2)))
10526 (define-public r-bootstrap
10528 (name "r-bootstrap")
10533 (uri (cran-uri "bootstrap" version))
10536 "08lmsy7k8wsgv89yc904c6fidcymr1ma2ry4fl0p69p21v4iiwa4"))))
10537 (build-system r-build-system)
10538 (native-inputs `(("gfortran" ,gfortran)))
10539 (home-page "https://cran.r-project.org/web/packages/bootstrap")
10540 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
10542 "This package provides software and data for the book \"An Introduction
10543 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
10544 This package is primarily provided for projects already based on it, and for
10545 support of the book. New projects should preferentially use the recommended
10546 package \"boot\".")
10547 (license license:bsd-3)))
10549 (define-public r-survivalroc
10551 (name "r-survivalroc")
10556 (uri (cran-uri "survivalROC" version))
10559 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
10560 (properties `((upstream-name . "survivalROC")))
10561 (build-system r-build-system)
10562 (home-page "https://cran.r-project.org/web/packages/survivalROC")
10563 (synopsis "Time-dependent ROC curve estimation from censored survival data")
10565 "Compute time-dependent ROC curve from censored survival data using
10566 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
10567 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
10568 (license license:gpl2+)))
10570 (define-public r-longitudinal
10572 (name "r-longitudinal")
10577 (uri (cran-uri "longitudinal" version))
10580 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
10581 (build-system r-build-system)
10582 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
10583 (home-page "http://strimmerlab.org/software/longitudinal/")
10584 (synopsis "Analysis of multiple time course data")
10586 "This package contains general data structures and functions for
10587 longitudinal data with multiple variables, repeated measurements, and
10588 irregularly spaced time points. It also implements a shrinkage estimator of
10589 dynamical correlation and dynamical covariance.")
10590 (license license:gpl3+)))
10592 (define-public r-genenet
10599 (uri (cran-uri "GeneNet" version))
10602 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
10603 (properties `((upstream-name . "GeneNet")))
10604 (build-system r-build-system)
10606 `(("r-corpcor" ,r-corpcor)
10607 ("r-fdrtool" ,r-fdrtool)
10608 ("r-longitudinal" ,r-longitudinal)))
10609 (home-page "http://strimmerlab.org/software/genenet/")
10610 (synopsis "Modeling and inferring gene networks")
10612 "This package analyzes gene expression (time series) data with focus on
10613 the inference of gene networks. In particular, GeneNet implements the methods
10614 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
10615 for learning large-scale gene association networks (including assignment of
10616 putative directions).")
10617 (license license:gpl3+)))
10619 (define-public r-rbamtools
10621 (name "r-rbamtools")
10622 (version "2.16.11.2")
10626 (uri (cran-uri "rbamtools" version))
10629 "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj"))))
10630 (build-system r-build-system)
10631 (inputs `(("zlib" ,zlib)))
10633 `(("r-refgenome" ,r-refgenome)))
10634 (home-page "https://cran.r-project.org/web/packages/rbamtools")
10635 (synopsis "Read and write BAM (binary alignment) files")
10637 "This package provides an R interface to functions of the SAMtools
10639 (license license:artistic2.0)))
10641 (define-public r-protviz
10648 (uri (cran-uri "protViz" version))
10651 "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1"))))
10652 (properties `((upstream-name . "protViz")))
10653 (build-system r-build-system)
10656 ("python-2" ,python-2)))
10657 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10658 (home-page "https://github.com/protViz/protViz/")
10659 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
10661 "This package helps with quality checks, visualizations and analysis of
10662 mass spectrometry data, coming from proteomics experiments. The package is
10663 developed, tested and used at the Functional Genomics Center Zurich, where it
10664 is used mainly for prototyping, teaching, and having fun with proteomics data.
10665 But it can also be used to do data analysis for small scale data sets.")
10666 (license license:gpl3)))
10668 (define-public r-cmprsk
10675 (uri (cran-uri "cmprsk" version))
10678 "1imr3wpnj4g57n2x4ryahl4lk8lvq9y2r7319zv3k82mznha8bcm"))))
10679 (build-system r-build-system)
10681 `(("r-survival" ,r-survival)))
10683 `(("gfortran" ,gfortran)))
10684 (home-page "https://cran.r-project.org/web/packages/cmprsk")
10685 (synopsis "Subdistribution analysis of competing risks")
10687 "This package provides tool for estimation, testing and regression
10688 modeling of subdistribution functions in competing risks, as described in
10689 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
10690 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
10691 A proportional hazards model for the subdistribution of a competing risk,
10692 JASA, 94:496-509.")
10693 (license license:gpl2+)))
10695 (define-public r-etm
10702 (uri (cran-uri "etm" version))
10705 "0ws103b3pmli0z4xbyfxkly2wnnnxnnwc0r66qjjqjrlvm7pffl1"))))
10706 (build-system r-build-system)
10708 `(("r-data-table" ,r-data-table)
10709 ("r-lattice" ,r-lattice)
10711 ("r-rcpparmadillo" ,r-rcpparmadillo)
10712 ("r-survival" ,r-survival)))
10713 (home-page "https://cran.r-project.org/web/packages/etm")
10714 (synopsis "Empirical transition matrix")
10716 "The @dfn{empirical transition matrix} (etm) package permits to estimate
10717 the matrix of transition probabilities for any time-inhomogeneous multistate
10718 model with finite state space using the Aalen-Johansen estimator.")
10719 (license license:expat)))
10721 (define-public r-epi
10728 (uri (cran-uri "Epi" version))
10731 "1z3959761ryv54y6vsrxxvhrwzz50xrxn55pqh5y7lrxh91zdsvl"))))
10732 (properties `((upstream-name . "Epi")))
10733 (build-system r-build-system)
10735 `(("r-cmprsk" ,r-cmprsk)
10736 ("r-data-table" ,r-data-table)
10739 ("r-matrix" ,r-matrix)
10741 ("r-numderiv" ,r-numderiv)
10743 ("r-survival" ,r-survival)
10745 (home-page "http://BendixCarstensen.com/Epi/")
10746 (synopsis "Statistical analysis in epidemiology")
10748 "This package provides functions for demographic and epidemiological
10749 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
10750 particular representation, manipulation and simulation of multistate data -
10751 the Lexis suite of functions, which includes interfaces to the @code{mstate},
10752 @code{etm} and @code{cmprsk} packages. It also contains functions for
10753 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
10754 data and some useful functions for tabulation and plotting, as well as a
10755 number of epidemiological data sets.")
10756 (license license:gpl2)))
10758 (define-public r-ppls
10761 (version "1.6-1.1")
10765 (uri (cran-uri "ppls" version))
10768 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
10769 (build-system r-build-system)
10770 (propagated-inputs `(("r-mass" ,r-mass)))
10771 (home-page "https://cran.r-project.org/web/packages/ppls")
10772 (synopsis "Penalized partial least squares")
10774 "This package contains linear and nonlinear regression methods based on
10775 partial least squares and penalization techniques. Model parameters are
10776 selected via cross-validation, and confidence intervals ans tests for the
10777 regression coefficients can be conducted via jackknifing.")
10778 (license license:gpl2+)))
10780 (define-public r-huge
10787 (uri (cran-uri "huge" version))
10790 "1j93gvi1jyq3ld9jhdqhrpm2is54rk3ilmf3yw7fx6gva0y6hjqd"))))
10791 (build-system r-build-system)
10793 `(("r-igraph" ,r-igraph)
10795 ("r-matrix" ,r-matrix)
10797 ("r-rcppeigen" ,r-rcppeigen)))
10798 (home-page "https://cran.r-project.org/web/packages/huge")
10799 (synopsis "High-dimensional undirected graph estimation")
10801 "This package provides a general framework for high-dimensional
10802 undirected graph estimation. It integrates data preprocessing, neighborhood
10803 screening, graph estimation, and model selection techniques into a pipeline.")
10804 (license license:gpl2)))
10806 (define-public r-parcor
10813 (uri (cran-uri "parcor" version))
10816 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
10817 (build-system r-build-system)
10820 ("r-genenet" ,r-genenet)
10821 ("r-glmnet" ,r-glmnet)
10823 ("r-ppls" ,r-ppls)))
10824 (home-page "https://cran.r-project.org/web/packages/parcor")
10825 (synopsis "Regularized estimation of partial correlation matrices")
10827 "This package estimates the matrix of partial correlations based on
10828 different regularized regression methods: lasso, adaptive lasso, PLS, and
10829 Ridge Regression. In addition, the package provides model selection for
10830 lasso, adaptive lasso and Ridge regression based on cross-validation.")
10831 (license license:gpl2+)))
10833 (define-public r-mcmc
10840 (uri (cran-uri "mcmc" version))
10843 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
10844 (build-system r-build-system)
10845 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
10846 (synopsis "Markov chain Monte Carlo")
10848 "This package simulates continuous distributions of random vectors using
10849 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
10850 function that evaluates the log unnormalized density. Algorithms are random
10851 walk Metropolis algorithm (function @code{metrop}), simulated
10852 tempering (function @code{temper}), and morphometric random walk
10853 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
10854 by change of variable.")
10855 (license license:expat)))
10857 (define-public r-listenv
10864 (uri (cran-uri "listenv" version))
10867 "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1"))))
10868 (build-system r-build-system)
10870 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
10871 (home-page "https://github.com/HenrikBengtsson/listenv")
10872 (synopsis "Environments behaving (almost) as lists")
10874 "This package implements list environments. List environments are
10875 environments that have list-like properties. For instance, the elements of a
10876 list environment are ordered and can be accessed and iterated over using index
10878 (license license:lgpl2.1+)))
10880 (define-public r-globals
10887 (uri (cran-uri "globals" version))
10890 "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br"))))
10891 (build-system r-build-system)
10893 `(("r-codetools" ,r-codetools)))
10894 (home-page "https://github.com/HenrikBengtsson/globals")
10895 (synopsis "Identify global objects in R expressions")
10897 "This package provides tools to identify global (\"unknown\" or \"free\")
10898 objects in R expressions by code inspection using various strategies, e.g.
10899 conservative or liberal. The objective of this package is to make it as
10900 simple as possible to identify global objects for the purpose of exporting
10901 them in distributed compute environments.")
10902 (license license:lgpl2.1+)))
10904 (define-public r-future
10911 (uri (cran-uri "future" version))
10914 "12hq7hsfydlscwrb37ns9a8561bzpsp82nn7jrcyj0ydk610nipm"))))
10915 (build-system r-build-system)
10917 `(("r-digest" ,r-digest)
10918 ("r-globals" ,r-globals)
10919 ("r-listenv" ,r-listenv)))
10921 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
10922 (home-page "https://github.com/HenrikBengtsson/future")
10923 (synopsis "Unified parallel and distributed processing in R")
10925 "The purpose of this package is to provide a lightweight and unified
10926 Future API for sequential and parallel processing of R expression via futures.
10927 This package implements sequential, multicore, multisession, and cluster
10928 futures. With these, R expressions can be evaluated on the local machine, in
10929 parallel a set of local machines, or distributed on a mix of local and remote
10930 machines. Extensions to this package implement additional backends for
10931 processing futures via compute cluster schedulers etc. Because of its unified
10932 API, there is no need to modify any code in order to switch from sequential on
10933 the local machine to, say, distributed processing on a remote compute cluster.")
10934 (license license:lgpl2.1+)))
10936 (define-public r-future-apply
10938 (name "r-future-apply")
10943 (uri (cran-uri "future.apply" version))
10946 "00ma43ma3byrf9vfqqn9g8sn18c71ryhk7lpza5h7817f1kibw1h"))))
10947 (properties `((upstream-name . "future.apply")))
10948 (build-system r-build-system)
10950 `(("r-future" ,r-future)
10951 ("r-globals" ,r-globals)))
10953 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
10954 (home-page "https://github.com/HenrikBengtsson/future.apply")
10955 (synopsis "Apply function to elements in parallel using futures")
10957 "This package provides implementations of @code{apply()},
10958 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
10959 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
10960 can be resolved using any future-supported backend, e.g. parallel on the local
10961 machine or distributed on a compute cluster.")
10962 (license license:gpl2+)))
10964 (define-public r-rsvd
10971 (uri (cran-uri "rsvd" version))
10974 "0vjhrvnkl9rmvl8sv2kac5sd10z3fgxymb676ynxzc2pmhydy3an"))))
10975 (build-system r-build-system)
10977 `(("r-matrix" ,r-matrix)))
10978 (home-page "https://github.com/erichson/rSVD")
10979 (synopsis "Randomized singular value decomposition")
10981 "Low-rank matrix decompositions are fundamental tools and widely used for
10982 data analysis, dimension reduction, and data compression. Classically, highly
10983 accurate deterministic matrix algorithms are used for this task. However, the
10984 emergence of large-scale data has severely challenged our computational
10985 ability to analyze big data. The concept of randomness has been demonstrated
10986 as an effective strategy to quickly produce approximate answers to familiar
10987 problems such as the @dfn{singular value decomposition} (SVD). This package
10988 provides several randomized matrix algorithms such as the randomized singular
10989 value decomposition (@code{rsvd}), randomized principal component
10990 analysis (@code{rpca}), randomized robust principal component
10991 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
10992 and the randomized CUR decomposition (@code{rcur}). In addition several plot
10993 functions are provided.")
10994 (license license:gpl3+)))
10996 (define-public r-sloop
11003 (uri (cran-uri "sloop" version))
11006 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11007 (build-system r-build-system)
11009 `(("r-codetools" ,r-codetools)
11010 ("r-crayon" ,r-crayon)
11011 ("r-purrr" ,r-purrr)
11012 ("r-rlang" ,r-rlang)
11013 ("r-tibble" ,r-tibble)))
11014 (home-page "https://github.com/r-lib/sloop")
11015 (synopsis "Helpers for object-oriented programming in R")
11017 "This package provides a collection of helper functions designed to
11018 help you to better understand object oriented programming in R, particularly
11020 (license license:gpl3)))
11022 (define-public r-capushe
11029 (uri (cran-uri "capushe" version))
11032 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11033 (build-system r-build-system)
11034 (propagated-inputs `(("r-mass" ,r-mass)))
11035 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11036 (synopsis "Calibrating penalities using slope heuristics")
11038 "This package provides tools for the calibration of penalized criteria
11039 for model selection. The calibration methods available are based on the slope
11041 (license license:gpl2+)))
11043 (define-public r-dorng
11050 (uri (cran-uri "doRNG" version))
11053 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11054 (properties `((upstream-name . "doRNG")))
11055 (build-system r-build-system)
11057 `(("r-foreach" ,r-foreach)
11058 ("r-iterators" ,r-iterators)
11059 ("r-pkgmaker" ,r-pkgmaker)
11060 ("r-rngtools" ,r-rngtools)))
11061 (home-page "https://renozao.github.io/doRNG/")
11062 (synopsis "Generic reproducible parallel backend for foreach loops")
11064 "This package provides functions to perform reproducible parallel
11065 @code{foreach} loops, using independent random streams as generated by
11066 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11067 convert standard @code{%dopar%} loops into fully reproducible loops,
11068 independently of the number of workers, the task scheduling strategy, or the
11069 chosen parallel environment and associated foreach backend.")
11070 (license license:gpl2+)))
11072 (define-public r-blockmodeling
11074 (name "r-blockmodeling")
11079 (uri (cran-uri "blockmodeling" version))
11082 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11083 (build-system r-build-system)
11085 `(("r-doparallel" ,r-doparallel)
11086 ("r-dorng" ,r-dorng)
11087 ("r-foreach" ,r-foreach)
11088 ("r-matrix" ,r-matrix)))
11089 (native-inputs `(("gfortran" ,gfortran)))
11090 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11091 (synopsis "Generalized and classical blockmodeling of valued networks")
11093 "This package is primarily meant as an implementation of generalized
11094 blockmodeling for valued networks. In addition, measures of similarity or
11095 dissimilarity based on structural equivalence and regular equivalence (REGE
11096 algorithms) can be computed and partitioned matrices can be plotted.")
11097 (license license:gpl2+)))
11099 (define-public r-upsetr
11106 (uri (cran-uri "UpSetR" version))
11109 "08vj7l92b8fpqyqwxshll2mhk3yhgyr74axvr2lf29z78bapymhz"))))
11110 (properties `((upstream-name . "UpSetR")))
11111 (build-system r-build-system)
11113 `(("r-ggplot2" ,r-ggplot2)
11114 ("r-gridextra" ,r-gridextra)
11116 ("r-scales" ,r-scales)))
11117 (home-page "https://github.com/hms-dbmi/UpSetR")
11118 (synopsis "Visualize intersecting sets")
11120 "This package provides a more scalable alternative to Venn and Euler
11121 diagrams for visualizing intersecting sets. Create visualizations of
11122 intersecting sets using a novel matrix design, along with visualizations of
11123 several common set, element and attribute related tasks.")
11124 (license license:expat)))
11126 ;; This package includes a JavaScript file, which is not minified. When
11127 ;; upgrading please check that there are no new minified JavaScript files.
11128 (define-public r-shinybs
11135 (uri (cran-uri "shinyBS" version))
11138 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11139 (properties `((upstream-name . "shinyBS")))
11140 (build-system r-build-system)
11141 ;; The tests spawn Shiny browser apps. They cannot be run
11142 ;; non-interactively.
11143 (arguments '(#:tests? #f))
11145 `(("r-htmltools" ,r-htmltools)
11146 ("r-shiny" ,r-shiny)))
11147 (home-page "https://ebailey78.github.io/shinyBS/")
11148 (synopsis "Twitter Bootstrap components for Shiny")
11150 "This package adds additional Twitter Bootstrap components to Shiny.")
11151 (license license:gpl3)))
11153 (define-public r-outliers
11155 (name "r-outliers")
11160 (uri (cran-uri "outliers" version))
11163 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11164 (build-system r-build-system)
11165 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11166 (synopsis "Tests for outliers")
11168 "This package provides a collection of some tests commonly used for
11169 identifying outliers.")
11170 (license license:gpl2+)))
11172 (define-public r-bayesm
11179 (uri (cran-uri "bayesm" version))
11182 "0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
11183 (build-system r-build-system)
11185 `(("r-rcpp" ,r-rcpp)
11186 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11187 (home-page "http://www.perossi.org/home/bsm-1")
11188 (synopsis "Bayesian inference for marketing/micro-econometrics")
11190 "This package covers many important models used in marketing and
11191 micro-econometrics applications, including Bayes Regression (univariate or
11192 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11193 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11194 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11195 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11196 Estimation with normal base, Hierarchical Linear Models with normal prior and
11197 covariates, Hierarchical Linear Models with a mixture of normals prior and
11198 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11199 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11200 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11201 analysis of choice-based conjoint data, Bayesian treatment of linear
11202 instrumental variables models, Analysis of Multivariate Ordinal survey data
11203 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11204 Coefficient Logit Models.")
11205 (license license:gpl2+)))
11207 (define-public r-tensora
11214 (uri (cran-uri "tensorA" version))
11217 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11218 (properties `((upstream-name . "tensorA")))
11219 (build-system r-build-system)
11220 (home-page "http://www.stat.boogaart.de/tensorA")
11221 (synopsis "Advanced tensor arithmetic with named indices")
11223 "This package provides convenience functions for advanced linear algebra
11224 with tensors and computation with datasets of tensors on a higher level
11225 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11226 co- and contravariate indices, and parallel computations on sequences of
11228 (license license:gpl2+)))
11230 (define-public r-rarpack
11237 (uri (cran-uri "rARPACK" version))
11240 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11241 (properties `((upstream-name . "rARPACK")))
11242 (build-system r-build-system)
11243 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11244 (home-page "https://github.com/yixuan/rARPACK")
11245 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11247 "This package was previously an R wrapper of the ARPACK library, and now
11248 a shell of the R package RSpectra, an R interface to the Spectra library for
11249 solving large scale eigenvalue/vector problems. The current version of
11250 rARPACK simply imports and exports the functions provided by RSpectra. New
11251 users of rARPACK are advised to switch to the RSpectra package.")
11252 (license license:bsd-3)))
11254 (define-public r-compositions
11256 (name "r-compositions")
11261 (uri (cran-uri "compositions" version))
11264 "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i"))))
11265 (build-system r-build-system)
11267 `(("r-bayesm" ,r-bayesm)
11268 ("r-energy" ,r-energy)
11269 ("r-robustbase" ,r-robustbase)
11270 ("r-tensora" ,r-tensora)))
11271 (home-page "http://www.stat.boogaart.de/compositions")
11272 (synopsis "Compositional data analysis")
11274 "This package provides functions for the consistent analysis of
11275 compositional data (e.g. portions of substances) and positive
11276 numbers (e.g. concentrations).")
11277 (license license:gpl2+)))
11279 (define-public r-cobs
11286 (uri (cran-uri "cobs" version))
11289 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11290 (build-system r-build-system)
11292 `(("r-quantreg" ,r-quantreg)
11293 ("r-sparsem" ,r-sparsem)))
11294 (home-page "https://cran.r-project.org/web/packages/cobs")
11295 (synopsis "Constrained B-Splines (sparse matrix based)")
11297 "This package provides qualitatively constrained (regression) smoothing
11298 splines via linear programming and sparse matrices.")
11299 (license license:gpl2+)))
11301 (define-public r-drimpute
11303 (name "r-drimpute")
11308 (uri (cran-uri "DrImpute" version))
11311 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11312 (properties `((upstream-name . "DrImpute")))
11313 (build-system r-build-system)
11315 `(("r-rcpp" ,r-rcpp)
11316 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11317 (home-page "https://github.com/ikwak2/DrImpute")
11318 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11320 "This is an R package for imputing dropout events. Many statistical
11321 methods in cell type identification, visualization and lineage reconstruction
11322 do not account for dropout events. DrImpute can improve the performance of
11323 such software by imputing dropout events.")
11324 (license license:gpl3)))
11326 (define-public r-gamlss-dist
11328 (name "r-gamlss-dist")
11333 (uri (cran-uri "gamlss.dist" version))
11336 "0154pm1f3g77krj0gxh9icz207pshdrxihb6gjv1k5aph8y69zc7"))))
11337 (properties `((upstream-name . "gamlss.dist")))
11338 (build-system r-build-system)
11339 (propagated-inputs `(("r-mass" ,r-mass)))
11340 (home-page "http://www.gamlss.org/")
11341 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
11343 "This package provides a set of distributions which can be used for
11344 modelling the response variables in Generalized Additive Models for Location
11345 Scale and Shape. The distributions can be continuous, discrete or mixed
11346 distributions. Extra distributions can be created, by transforming, any
11347 continuous distribution defined on the real line, to a distribution defined on
11348 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
11349 transformation, respectively.")
11350 ;; Either version of the GPL.
11351 (license (list license:gpl2 license:gpl3))))
11353 ;; This package includes JavaScript files, which are not minified. When
11354 ;; upgrading please check that there are no new minified JavaScript files.
11355 (define-public r-shinyjs
11362 (uri (cran-uri "shinyjs" version))
11365 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
11366 (build-system r-build-system)
11368 `(("r-digest" ,r-digest)
11369 ("r-htmltools" ,r-htmltools)
11370 ("r-jsonlite" ,r-jsonlite)
11371 ("r-shiny" ,r-shiny)))
11372 (home-page "https://deanattali.com/shinyjs")
11373 (synopsis "Improve the user experience of your Shiny apps")
11375 "Perform common useful JavaScript operations in Shiny apps that will
11376 greatly improve your apps without having to know any JavaScript. Examples
11377 include: hiding an element, disabling an input, resetting an input back to its
11378 original value, delaying code execution by a few seconds, and many more useful
11379 functions for both the end user and the developer. Shinyjs can also be used
11380 to easily call your own custom JavaScript functions from R.")
11381 (license license:agpl3+)))
11383 ;; This package includes minified JavaScript files. When upgrading please
11384 ;; check that there are no new minified JavaScript files.
11385 (define-public r-colourpicker
11387 (name "r-colourpicker")
11392 (uri (cran-uri "colourpicker" version))
11395 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
11396 (build-system r-build-system)
11398 `(#:modules ((guix build utils)
11399 (guix build r-build-system)
11403 (modify-phases %standard-phases
11404 (add-after 'unpack 'process-javascript
11405 (lambda* (#:key inputs #:allow-other-keys)
11406 (with-directory-excursion "inst"
11410 `((,(assoc-ref inputs "js-salvattore")
11411 "examples/colourInput/www/salvattore.min.js")
11412 (,(assoc-ref inputs "js-jquery")
11413 "htmlwidgets/lib/jquery/jquery.min.js")
11414 ("www/shared/colourpicker/js/colourpicker.js"
11415 "www/shared/colourpicker/js/colourpicker.min.js"))))
11416 (lambda (sources targets)
11417 (for-each (lambda (source target)
11418 (format #t "Processing ~a --> ~a~%"
11420 (delete-file target)
11421 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
11422 (call-with-output-file target
11424 (dump-port minified port)))))
11425 sources targets))))
11428 `(("r-ggplot2" ,r-ggplot2)
11429 ("r-htmltools" ,r-htmltools)
11430 ("r-htmlwidgets" ,r-htmlwidgets)
11431 ("r-jsonlite" ,r-jsonlite)
11432 ("r-miniui" ,r-miniui)
11433 ("r-shiny" ,r-shiny)
11434 ("r-shinyjs" ,r-shinyjs)))
11436 `(("uglify-js" ,uglify-js)
11440 (uri "https://code.jquery.com/jquery-3.3.1.js")
11443 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
11447 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
11450 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
11451 (home-page "https://github.com/daattali/colourpicker")
11452 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
11454 "This package provides a color picker that can be used as an input in
11455 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
11456 custom color palettes, and many more options. A plot color helper tool is
11457 available as an RStudio Addin, which helps you pick colors to use in your
11458 plots. A more generic color picker RStudio Addin is also provided to let you
11459 select colors to use in your R code.")
11460 (license license:expat)))
11462 (define-public r-ggextra
11469 (uri (cran-uri "ggExtra" version))
11472 "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
11473 (properties `((upstream-name . "ggExtra")))
11474 (build-system r-build-system)
11476 `(("r-colourpicker" ,r-colourpicker)
11477 ("r-ggplot2" ,r-ggplot2)
11478 ("r-gtable" ,r-gtable)
11479 ("r-miniui" ,r-miniui)
11480 ("r-scales" ,r-scales)
11481 ("r-shiny" ,r-shiny)
11482 ("r-shinyjs" ,r-shinyjs)))
11483 (home-page "https://github.com/daattali/ggExtra")
11484 (synopsis "Marginal histograms for ggplot2 and other enhancements")
11486 "This package is a collection of functions and layers to enhance ggplot2.
11487 The flagship function is @code{ggMarginal()}, which can be used to add
11488 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
11489 (license license:expat)))
11491 (define-public r-minpack-lm
11493 (name "r-minpack-lm")
11498 (uri (cran-uri "minpack.lm" version))
11501 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
11502 (properties `((upstream-name . "minpack.lm")))
11503 (build-system r-build-system)
11504 (native-inputs `(("gfortran" ,gfortran)))
11505 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
11506 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
11508 "The @code{nls.lm} function provides an R interface to @code{lmder} and
11509 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
11510 problems by a modification of the Levenberg-Marquardt algorithm, with support
11511 for lower and upper parameter bounds. The implementation can be used via
11512 @code{nls}-like calls using the @code{nlsLM} function.")
11513 (license license:gpl3)))
11515 (define-public r-moments
11522 (uri (cran-uri "moments" version))
11525 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
11526 (build-system r-build-system)
11527 (home-page "https://cran.r-project.org/web/packages/moments")
11528 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
11530 "This package provides functions to calculate: moments, Pearson's
11531 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
11532 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
11533 (license license:gpl2+)))
11535 (define-public r-msir
11542 (uri (cran-uri "msir" version))
11545 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
11546 (build-system r-build-system)
11548 `(("r-mclust" ,r-mclust)))
11549 (home-page "https://cran.r-project.org/web/packages/msir")
11550 (synopsis "Model-based sliced inverse regression")
11552 "This is an R package for dimension reduction based on finite Gaussian
11553 mixture modeling of inverse regression.")
11554 (license license:gpl2+)))
11556 (define-public r-pbivnorm
11558 (name "r-pbivnorm")
11563 (uri (cran-uri "pbivnorm" version))
11566 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
11567 (build-system r-build-system)
11568 (native-inputs `(("gfortran" ,gfortran)))
11569 (home-page "https://github.com/brentonk/pbivnorm")
11570 (synopsis "Vectorized bivariate normal CDF")
11572 "This package provides a vectorized R function for calculating
11573 probabilities from a standard bivariate normal CDF.")
11574 (license license:gpl2+)))
11576 (define-public r-lavaan
11583 (uri (cran-uri "lavaan" version))
11586 "0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
11587 (build-system r-build-system)
11589 `(("r-mass" ,r-mass)
11590 ("r-mnormt" ,r-mnormt)
11591 ("r-numderiv" ,r-numderiv)
11592 ("r-pbivnorm" ,r-pbivnorm)))
11593 (home-page "http://lavaan.ugent.be")
11594 (synopsis "Latent variable analysis")
11596 "This package provides tools to fit a variety of latent variable models,
11597 including confirmatory factor analysis, structural equation modeling and
11598 latent growth curve models.")
11599 (license license:gpl2+)))
11601 (define-public r-nonnest2
11603 (name "r-nonnest2")
11608 (uri (cran-uri "nonnest2" version))
11611 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
11612 (build-system r-build-system)
11614 `(("r-compquadform" ,r-compquadform)
11615 ("r-lavaan" ,r-lavaan)
11616 ("r-mvtnorm" ,r-mvtnorm)
11617 ("r-sandwich" ,r-sandwich)))
11618 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
11619 (synopsis "Tests of non-nested models")
11621 "This package allows for testing of non-nested models. It includes tests
11622 of model distinguishability and of model fit that can be applied to both
11623 nested and non-nested models. The package also includes functionality to
11624 obtain confidence intervals associated with AIC and BIC.")
11625 ;; Either version of the GPL.
11626 (license (list license:gpl2 license:gpl3))))
11628 (define-public r-penalized
11630 (name "r-penalized")
11635 (uri (cran-uri "penalized" version))
11638 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
11639 (build-system r-build-system)
11641 `(("r-rcpp" ,r-rcpp)
11642 ("r-rcpparmadillo" ,r-rcpparmadillo)
11643 ("r-survival" ,r-survival)))
11644 (home-page "https://cran.r-project.org/web/packages/penalized/")
11645 (synopsis "Penalized estimation in GLMs and in the Cox model")
11647 "This package provides tools for fitting possibly high dimensional
11648 penalized regression models. The penalty structure can be any combination of
11649 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
11650 constraint on the regression coefficients. The supported regression models
11651 are linear, logistic and Poisson regression and the Cox Proportional Hazards
11652 model. Cross-validation routines allow optimization of the tuning
11654 (license license:gpl2+)))
11656 (define-public r-zim
11663 (uri (cran-uri "ZIM" version))
11666 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
11667 (properties `((upstream-name . "ZIM")))
11668 (build-system r-build-system)
11669 (propagated-inputs `(("r-mass" ,r-mass)))
11670 (home-page "https://github.com/biostatstudio/ZIM")
11671 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
11673 "Analyze count time series with excess zeros. Two types of statistical
11674 models are supported: Markov regression and state-space models. They are also
11675 known as observation-driven and parameter-driven models respectively in the
11676 time series literature. The functions used for Markov regression or
11677 observation-driven models can also be used to fit ordinary regression models
11678 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
11679 negative binomial (ZINB) assumption. The package also contains miscellaneous
11680 functions to compute density, distribution, quantile, and generate random
11681 numbers from ZIP and ZINB distributions.")
11682 (license license:gpl3)))
11684 (define-public r-nor1mix
11691 (uri (cran-uri "nor1mix" version))
11694 "1bvk888qml9qr7q703s7qzgm0sqfchcjdjqwqllm5vrjx0cnapj3"))))
11695 (build-system r-build-system)
11696 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
11697 (synopsis "Normal (1-d) mixture models")
11699 "This package provides S3 classes and methods for one-dimensional normal
11700 mixture models, for, e.g., density estimation or clustering algorithms
11701 research and teaching; it provides the widely used Marron-Wand densities. It
11702 also provides tools for efficient random number generation and graphics.")
11703 (license license:gpl2+)))
11705 (define-public r-beanplot
11707 (name "r-beanplot")
11712 (uri (cran-uri "beanplot" version))
11715 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
11716 (build-system r-build-system)
11717 (home-page "https://cran.r-project.org/web/packages/beanplot/")
11718 (synopsis "Visualization via beanplots")
11720 "This package provides beanplots, an alternative to
11721 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
11723 (license license:gpl2)))
11725 (define-public r-pbdzmq
11732 (uri (cran-uri "pbdZMQ" version))
11735 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
11736 (properties `((upstream-name . "pbdZMQ")))
11737 (build-system r-build-system)
11739 `(("zeromq" ,zeromq)
11742 `(("pkg-config" ,pkg-config)))
11743 (home-page "https://pbdr.org/")
11744 (synopsis "R interface to ZeroMQ")
11746 "ZeroMQ is a well-known library for high-performance asynchronous
11747 messaging in scalable, distributed applications. This package provides high
11748 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
11749 interactive client/server programming frameworks. A few wrapper functions
11750 compatible with @code{rzmq} are also provided.")
11751 (license license:gpl3)))
11753 (define-public r-repr
11760 (uri (cran-uri "repr" version))
11763 "0j8z4sl67fgnbywkhgg0bns68mbgf9iqnw4qiym2rjy1b08fpclq"))))
11764 (build-system r-build-system)
11766 `(("r-base64enc" ,r-base64enc)
11767 ("r-htmltools" ,r-htmltools)
11768 ("r-jsonlite" ,r-jsonlite)
11769 ("r-pillar" ,r-pillar)))
11770 (home-page "https://cran.r-project.org/web/packages/repr/")
11771 (synopsis "Serializable representations")
11773 "This package provides string and binary representations of objects for
11774 several formats and MIME types.")
11775 (license license:gpl3)))
11777 (define-public r-irdisplay
11779 (name "r-irdisplay")
11784 (uri (cran-uri "IRdisplay" version))
11787 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
11788 (properties `((upstream-name . "IRdisplay")))
11789 (build-system r-build-system)
11791 `(("r-repr" ,r-repr)))
11792 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
11793 (synopsis "Jupyter display machinery")
11795 "This package provides an interface to the rich display capabilities of
11796 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
11797 running IRkernel session.")
11798 (license license:expat)))
11800 (define-public r-irkernel
11802 (name "r-irkernel")
11807 (uri (cran-uri "IRkernel" version))
11810 "1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s"))))
11811 (properties `((upstream-name . "IRkernel")))
11812 (build-system r-build-system)
11815 (modify-phases %standard-phases
11816 (add-after 'install 'install-kernelspec
11817 (lambda* (#:key outputs #:allow-other-keys)
11818 (let ((out (assoc-ref outputs "out")))
11819 (setenv "HOME" "/tmp")
11820 (invoke "jupyter" "kernelspec" "install"
11823 (string-append out "/site-library/IRkernel/kernelspec"))
11826 `(("jupyter" ,jupyter)))
11828 `(("r-crayon" ,r-crayon)
11829 ("r-digest" ,r-digest)
11830 ("r-evaluate" ,r-evaluate)
11831 ("r-irdisplay" ,r-irdisplay)
11832 ("r-jsonlite" ,r-jsonlite)
11833 ("r-pbdzmq" ,r-pbdzmq)
11835 ("r-uuid" ,r-uuid)))
11836 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
11837 (synopsis "Native R kernel for Jupyter")
11839 "The R kernel for the Jupyter environment executes R code which the
11840 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
11842 (license license:expat)))
11844 (define-public r-gmodels
11851 (uri (cran-uri "gmodels" version))
11854 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
11855 (build-system r-build-system)
11857 `(("r-gdata" ,r-gdata)
11858 ("r-mass" ,r-mass)))
11859 (home-page "https://cran.r-project.org/web/packages/gmodels/")
11860 (synopsis "Various R programming tools for model fitting")
11862 "This package provides various R programming tools for model fitting.")
11863 (license license:gpl2)))
11865 (define-public r-apcluster
11867 (name "r-apcluster")
11872 (uri (cran-uri "apcluster" version))
11875 "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
11876 (build-system r-build-system)
11878 `(("r-matrix" ,r-matrix)
11879 ("r-rcpp" ,r-rcpp)))
11880 (home-page "https://cran.r-project.org/web/packages/apcluster/")
11881 (synopsis "Affinity propagation clustering")
11883 "This package implements affinity propagation clustering introduced by
11884 Frey and Dueck (2007). The package further provides leveraged affinity
11885 propagation and an algorithm for exemplar-based agglomerative clustering that
11886 can also be used to join clusters obtained from affinity propagation. Various
11887 plotting functions are available for analyzing clustering results.")
11888 (license license:gpl2+)))
11890 (define-public r-valr
11897 (uri (cran-uri "valr" version))
11900 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
11901 (build-system r-build-system)
11903 `(("r-broom" ,r-broom)
11904 ("r-dplyr" ,r-dplyr)
11905 ("r-ggplot2" ,r-ggplot2)
11907 ("r-readr" ,r-readr)
11908 ("r-rlang" ,r-rlang)
11909 ("r-stringr" ,r-stringr)
11910 ("r-tibble" ,r-tibble)))
11911 (home-page "http://github.com/rnabioco/valr")
11912 (synopsis "Genome interval arithmetic in R")
11914 "This package enables you to read and manipulate genome intervals and
11915 signals. It provides functionality similar to command-line tool suites within
11916 R, enabling interactive analysis and visualization of genome-scale data.")
11917 (license license:expat)))
11919 (define-public r-rematch2
11921 (name "r-rematch2")
11926 (uri (cran-uri "rematch2" version))
11929 "16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
11930 (build-system r-build-system)
11932 `(("r-tibble" ,r-tibble)))
11933 (home-page "https://github.com/r-lib/rematch2")
11934 (synopsis "Tidy output from regular expression matching")
11936 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
11937 return the match results in tidy data frames.")
11938 (license license:expat)))
11940 (define-public r-picante
11947 (uri (cran-uri "picante" version))
11950 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
11951 (build-system r-build-system)
11955 ("r-vegan" ,r-vegan)))
11956 (home-page "https://cran.r-project.org/web/packages/picante/")
11957 (synopsis "Integrating phylogenies and ecology")
11959 "This package provides functions for phylocom integration, community
11960 analyses, null-models, traits and evolution. It implements numerous
11961 ecophylogenetic approaches including measures of community phylogenetic and
11962 trait diversity, phylogenetic signal, estimation of trait values for
11963 unobserved taxa, null models for community and phylogeny randomizations, and
11964 utility functions for data input/output and phylogeny plotting. A full
11965 description of package functionality and methods are provided by Kembel et
11967 (license license:gpl2)))
11969 (define-public r-reinforcelearn
11971 (name "r-reinforcelearn")
11976 (uri (cran-uri "reinforcelearn" version))
11979 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
11980 (build-system r-build-system)
11982 `(("r-checkmate" ,r-checkmate)
11984 ("r-purrr" ,r-purrr)
11986 (home-page "https://markusdumke.github.io/reinforcelearn")
11987 (synopsis "Reinforcement learning")
11989 "This package implements reinforcement learning environments and
11990 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
11991 can be used with function approximation, eligibility traces (Singh & Sutton,
11992 1996) and experience replay (Mnih et al., 2013).")
11993 (license license:expat)))
11995 (define-public r-lemon
12002 (uri (cran-uri "lemon" version))
12005 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12006 (build-system r-build-system)
12008 `(("r-ggplot2" ,r-ggplot2)
12009 ("r-gridextra" ,r-gridextra)
12010 ("r-gtable" ,r-gtable)
12011 ("r-knitr" ,r-knitr)
12012 ("r-lattice" ,r-lattice)
12014 ("r-scales" ,r-scales)))
12015 (home-page "https://github.com/stefanedwards/lemon")
12016 (synopsis "Freshen up your ggplot2 plots")
12018 "This package provides functions for working with legends and axis lines
12019 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12021 (license license:gpl3)))
12023 (define-public r-wgaim
12030 (uri (cran-uri "wgaim" version))
12033 "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg"))))
12034 (build-system r-build-system)
12036 `(("r-lattice" ,r-lattice)
12038 (home-page "https://cran.r-project.org/web/packages/wgaim")
12039 (synopsis "Whole genome average interval mapping for QTL detection")
12041 "This package integrates sophisticated mixed modelling methods with a
12042 whole genome approach to detecting significant QTL in linkage maps.")
12043 (license license:gpl2+)))
12045 (define-public r-bedr
12052 (uri (cran-uri "bedr" version))
12055 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12056 (build-system r-build-system)
12058 `(("r-data-table" ,r-data-table)
12059 ("r-r-utils" ,r-r-utils)
12060 ("r-testthat" ,r-testthat)
12061 ("r-venndiagram" ,r-venndiagram)
12064 ("bedtools" ,bedtools)
12065 ("htslib" ,htslib))) ; for tabix
12067 `(("r-knitr" ,r-knitr))) ; for vignettes
12068 (home-page "https://cran.r-project.org/web/packages/bedr")
12069 (synopsis "Genomic region processing")
12071 "This package is for genomic regions processing using command line tools
12072 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12073 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12074 The bedr package's API enhances access to these tools as well as offers
12075 additional utilities for genomic regions processing.")
12076 (license license:gpl2)))
12078 (define-public r-partitions
12080 (name "r-partitions")
12085 (uri (cran-uri "partitions" version))
12088 "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx"))))
12089 (build-system r-build-system)
12092 ("r-polynom" ,r-polynom)))
12093 (home-page "https://cran.r-project.org/web/packages/partitions")
12094 (synopsis "Additive partitions of integers")
12096 "This package provides tools to enumerates the partitions, unequal
12097 partitions, and restricted partitions of an integer; the three corresponding
12098 partition functions are also given.")
12099 ;; Any version of the GPL
12100 (license license:gpl2+)))
12102 (define-public r-brobdingnag
12104 (name "r-brobdingnag")
12109 (uri (cran-uri "Brobdingnag" version))
12112 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12113 (properties `((upstream-name . "Brobdingnag")))
12114 (build-system r-build-system)
12115 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12116 (synopsis "Very large numbers in R")
12118 "This package handles very large numbers in R. Real numbers are held
12119 using their natural logarithms, plus a logical flag indicating sign. The
12120 package includes a vignette that gives a step-by-step introduction to using S4
12122 ;; Any version of the GPL
12123 (license license:gpl2+)))
12125 (define-public r-untb
12132 (uri (cran-uri "untb" version))
12135 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12136 (build-system r-build-system)
12138 `(("r-brobdingnag" ,r-brobdingnag)
12139 ("r-partitions" ,r-partitions)
12140 ("r-polynom" ,r-polynom)))
12141 (home-page "https://github.com/RobinHankin/untb.git")
12142 (synopsis "Ecological drift under the UNTB")
12144 "This package provides numerical simulations, and visualizations, of
12145 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12146 (license license:gpl2+)))
12148 (define-public r-stepwise
12150 (name "r-stepwise")
12155 (uri (cran-uri "stepwise" version))
12158 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12159 (build-system r-build-system)
12160 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12161 (synopsis "Stepwise detection of recombination breakpoints")
12163 "This package provides a stepwise approach to identifying recombination
12164 breakpoints in a genomic sequence alignment.")
12165 (license license:gpl2+)))
12167 (define-public r-snpmaxsel
12169 (name "r-snpmaxsel")
12174 (uri (cran-uri "SNPmaxsel" version))
12177 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12178 (properties `((upstream-name . "SNPmaxsel")))
12179 (build-system r-build-system)
12181 `(("r-combinat" ,r-combinat)
12182 ("r-mvtnorm" ,r-mvtnorm)))
12183 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12184 (synopsis "Maximally selected statistics for SNP data")
12186 "This package implements asymptotic methods related to maximally selected
12187 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12189 (license license:gpl2+)))
12191 (define-public r-acsnminer
12193 (name "r-acsnminer")
12194 (version "0.16.8.25")
12197 (uri (cran-uri "ACSNMineR" version))
12200 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12201 (properties `((upstream-name . "ACSNMineR")))
12202 (build-system r-build-system)
12204 `(("r-ggplot2" ,r-ggplot2)
12205 ("r-gridextra" ,r-gridextra)))
12206 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12207 (synopsis "Gene enrichment analysis")
12209 "This package provides tools to compute and represent gene set enrichment
12210 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12211 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12212 enrichment can be run with hypergeometric test or Fisher exact test, and can
12213 use multiple corrections. Visualization of data can be done either by
12214 barplots or heatmaps.")
12215 (license license:gpl2+)))
12217 (define-public r-seqinr
12224 (uri (cran-uri "seqinr" version))
12227 "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
12228 (build-system r-build-system)
12230 `(("r-ade4" ,r-ade4)
12231 ("r-segmented" ,r-segmented)))
12234 (home-page "http://seqinr.r-forge.r-project.org/")
12235 (synopsis "Biological sequences retrieval and analysis")
12237 "This package provides tools for exploratory data analysis and data
12238 visualization of biological sequence (DNA and protein) data. It also includes
12239 utilities for sequence data management under the ACNUC system.")
12240 (license license:gpl2+)))
12242 (define-public r-units
12249 (uri (cran-uri "units" version))
12252 "0kx640h60s3zzkdr302asap7diap6vri6d41scnx507yvkcqiph3"))))
12253 (build-system r-build-system)
12255 `(("udunits" ,udunits)))
12257 `(("r-rcpp" ,r-rcpp)))
12258 (home-page "https://github.com/r-quantities/units/")
12259 (synopsis "Measurement Units for R Vectors")
12261 "This package provides support for measurement units in R vectors,
12262 matrices and arrays: automatic propagation, conversion, derivation and
12263 simplification of units; raising errors in case of unit incompatibility. It
12264 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12266 (license license:gpl2)))
12268 (define-public r-classint
12270 (name "r-classint")
12275 (uri (cran-uri "classInt" version))
12278 "0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9"))))
12279 (properties `((upstream-name . "classInt")))
12280 (build-system r-build-system)
12282 `(("r-class" ,r-class)
12283 ("r-e1071" ,r-e1071)
12284 ("r-kernsmooth" ,r-kernsmooth)))
12285 (native-inputs `(("gfortran" ,gfortran)))
12286 (home-page "https://github.com/r-spatial/classInt/")
12287 (synopsis "Choose univariate class intervals")
12289 "This package provides selected commonly used methods for choosing
12290 univariate class intervals for mapping or other graphics purposes.")
12291 (license license:gpl2+)))
12293 (define-public r-spdata
12300 (uri (cran-uri "spData" version))
12303 "162cqb331ki43jx4r8lpkjpn2l712figd896rnawg9j1jmjyl96y"))))
12304 (properties `((upstream-name . "spData")))
12305 (build-system r-build-system)
12306 (home-page "https://github.com/Nowosad/spData")
12307 (synopsis "Datasets for spatial analysis")
12309 "This a package containing diverse spatial datasets for demonstrating,
12310 benchmarking and teaching spatial data analysis. It includes R data of class
12311 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
12312 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
12313 of the datasets are designed to illustrate specific analysis techniques.
12314 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
12315 illustrate point pattern analysis techniques.")
12316 (license license:cc0)))
12318 (define-public r-learnbayes
12320 (name "r-learnbayes")
12325 (uri (cran-uri "LearnBayes" version))
12328 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
12329 (properties `((upstream-name . "LearnBayes")))
12330 (build-system r-build-system)
12331 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
12332 (synopsis "Functions for learning Bayesian inference")
12334 "This package provides a collection of functions helpful in learning the
12335 basic tenets of Bayesian statistical inference. It contains functions for
12336 summarizing basic one and two parameter posterior distributions and predictive
12337 distributions. It contains MCMC algorithms for summarizing posterior
12338 distributions defined by the user. It also contains functions for regression
12339 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
12341 (license license:gpl2+)))
12343 (define-public r-deldir
12350 (uri (cran-uri "deldir" version))
12353 "0549kj0hlkdyvm5axsm3np30wg53fm2pxybijzw0avlgsd2y2n2q"))))
12354 (build-system r-build-system)
12355 (native-inputs `(("gfortran" ,gfortran)))
12356 (home-page "https://cran.r-project.org/web/packages/deldir")
12357 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
12359 "This package provides tools for calculating the Delaunay triangulation
12360 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
12361 of a planar point set. It plots triangulations and tessellations in various
12362 ways, clips tessellations to sub-windows, calculates perimeters of
12363 tessellations, and summarizes information about the tiles of the
12365 (license license:gpl2+)))
12367 (define-public r-sf
12374 (uri (cran-uri "sf" version))
12377 "0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1"))))
12378 (build-system r-build-system)
12385 `(("r-classint" ,r-classint)
12387 ("r-magrittr" ,r-magrittr)
12389 ("r-units" ,r-units)))
12390 (native-inputs `(("pkg-config" ,pkg-config)))
12391 (home-page "https://github.com/r-spatial/sf/")
12392 (synopsis "Simple features for R")
12394 "This package provides support for simple features, a standardized way to
12395 encode spatial vector data. It binds to GDAL for reading and writing data, to
12396 GEOS for geometrical operations, and to PROJ for projection conversions and
12397 datum transformations.")
12398 ;; Either of these licenses
12399 (license (list license:gpl2 license:expat))))
12401 (define-public r-spdep
12408 (uri (cran-uri "spdep" version))
12411 "06mk81kc1ml2wjc8wwwgr0wasjcr4mwrxpfa8vfc373bmnha635s"))))
12412 (build-system r-build-system)
12414 `(("r-boot" ,r-boot)
12416 ("r-deldir" ,r-deldir)
12418 ("r-gmodels" ,r-gmodels)
12419 ("r-learnbayes" ,r-learnbayes)
12421 ("r-matrix" ,r-matrix)
12425 ("r-spdata" ,r-spdata)))
12426 (home-page "https://github.com/r-spatial/spdep/")
12427 (synopsis "Spatial dependence: weighting schemes, statistics and models")
12429 "This package provides a collection of functions to create spatial
12430 weights matrix objects from polygon contiguities, from point patterns by
12431 distance and tessellations, for summarizing these objects, and for permitting
12432 their use in spatial data analysis, including regional aggregation by minimum
12434 (license license:gpl2+)))
12436 (define-public r-adegenet
12438 (name "r-adegenet")
12443 (uri (cran-uri "adegenet" version))
12446 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
12447 (build-system r-build-system)
12449 `(("r-ade4" ,r-ade4)
12452 ("r-dplyr" ,r-dplyr)
12453 ("r-ggplot2" ,r-ggplot2)
12454 ("r-igraph" ,r-igraph)
12456 ("r-reshape2" ,r-reshape2)
12457 ("r-seqinr" ,r-seqinr)
12458 ("r-shiny" ,r-shiny)
12459 ("r-spdep" ,r-spdep)
12460 ("r-vegan" ,r-vegan)))
12461 (home-page "https://github.com/thibautjombart/adegenet")
12462 (synopsis "Exploratory analysis of genetic and genomic data")
12464 "This package provides a toolset for the exploration of genetic and
12465 genomic data. Adegenet provides formal (S4) classes for storing and handling
12466 various genetic data, including genetic markers with varying ploidy and
12467 hierarchical population structure (@code{genind} class), alleles counts by
12468 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
12469 also implements original multivariate methods (DAPC, sPCA), graphics,
12470 statistical tests, simulation tools, distance and similarity measures, and
12471 several spatial methods. A range of both empirical and simulated datasets is
12472 also provided to illustrate various methods.")
12473 (license license:gpl2+)))
12475 (define-public r-pegas
12482 (uri (cran-uri "pegas" version))
12485 "0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx"))))
12486 (build-system r-build-system)
12488 `(("r-adegenet" ,r-adegenet)
12490 (home-page "http://ape-package.ird.fr/pegas.html")
12491 (synopsis "Population and evolutionary genetics analysis system")
12493 "This package provides functions for reading, writing, plotting,
12494 analysing, and manipulating allelic and haplotypic data, including from VCF
12495 files, and for the analysis of population nucleotide sequences and
12496 micro-satellites including coalescent analyses, linkage disequilibrium,
12497 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
12498 minimum spanning tree and network, and median-joining networks.")
12499 (license license:gpl2+)))
12501 (define-public r-rmetasim
12503 (name "r-rmetasim")
12508 (uri (cran-uri "rmetasim" version))
12511 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
12512 (build-system r-build-system)
12514 `(("r-ade4" ,r-ade4)
12515 ("r-adegenet" ,r-adegenet)
12516 ("r-gtools" ,r-gtools)
12517 ("r-pegas" ,r-pegas)))
12518 (home-page "https://cran.r-project.org/web/packages/rmetasim")
12519 (synopsis "Individual-based population genetic simulation environment")
12521 "This package provides an interface between R and the metasim simulation
12522 engine. The simulation environment is documented in: Strand, A.(2002),
12523 Metasim 1.0: an individual-based environment for simulating population
12524 genetics of complex population dynamics.")
12526 (license license:gpl2+)))
12528 (define-public r-genetics
12530 (name "r-genetics")
12531 (version "1.3.8.1.2")
12535 (uri (cran-uri "genetics" version))
12538 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
12539 (build-system r-build-system)
12541 `(("r-combinat" ,r-combinat)
12542 ("r-gdata" ,r-gdata)
12543 ("r-gtools" ,r-gtools)
12545 ("r-mvtnorm" ,r-mvtnorm)))
12546 (home-page "https://cran.r-project.org/web/packages/genetics/")
12547 (synopsis "Population genetics")
12549 "This package provides classes and methods for handling genetic data.
12550 It includes classes to represent genotypes and haplotypes at single markers up
12551 to multiple markers on multiple chromosomes. Function include allele
12552 frequencies, flagging homo/heterozygotes, flagging carriers of certain
12553 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
12554 and testing for linkage disequilibrium, ...")
12555 ;; Any GPL version.
12556 (license license:gpl2+)))
12558 (define-public r-snp-plotter
12560 (name "r-snp-plotter")
12565 (uri (cran-uri "snp.plotter" version))
12568 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
12569 (properties `((upstream-name . "snp.plotter")))
12570 (build-system r-build-system)
12571 (propagated-inputs `(("r-genetics" ,r-genetics)))
12572 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
12573 (synopsis "Plot p-values using single SNP and/or haplotype data")
12575 "This package helps you create plots of p-values using single SNP and/or
12576 haplotype data. Main features of the package include options to display a
12577 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
12578 datasets simultaneously. Plots can be created using global and/or individual
12579 haplotype p-values along with single SNP p-values. Images are created as
12580 either PDF/EPS files.")
12581 (license license:gpl2+)))
12583 (define-public r-polspline
12585 (name "r-polspline")
12590 (uri (cran-uri "polspline" version))
12593 "0g4s5nwi13yfs6b169yw8vrs48nvjyc014k2v7ybcxarl8z81va0"))))
12594 (build-system r-build-system)
12595 (native-inputs `(("gfortran" ,gfortran)))
12596 (home-page "https://cran.r-project.org/web/packages/polspline/")
12597 (synopsis "Polynomial spline routines")
12599 "This package provides routines for the polynomial spline fitting
12600 routines hazard regression, hazard estimation with flexible tails, logspline,
12601 lspec, polyclass, and polymars.")
12602 (license license:gpl2+)))
12604 (define-public r-rms
12607 (version "5.1-3.1")
12611 (uri (cran-uri "rms" version))
12614 "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9"))))
12615 (build-system r-build-system)
12617 `(("r-ggplot2" ,r-ggplot2)
12618 ("r-hmisc" ,r-hmisc)
12619 ("r-htmltable" ,r-htmltable)
12620 ("r-htmltools" ,r-htmltools)
12621 ("r-lattice" ,r-lattice)
12622 ("r-multcomp" ,r-multcomp)
12624 ("r-polspline" ,r-polspline)
12625 ("r-quantreg" ,r-quantreg)
12626 ("r-rpart" ,r-rpart)
12627 ("r-sparsem" ,r-sparsem)
12628 ("r-survival" ,r-survival)))
12629 (native-inputs `(("gfortran" ,gfortran)))
12630 (home-page "http://biostat.mc.vanderbilt.edu/rms")
12631 (synopsis "Regression modeling strategies")
12633 "This is a package for regression modeling, testing, estimation,
12634 validation, graphics, prediction, and typesetting by storing enhanced model
12635 design attributes in the fit. The rms package is a collection of functions
12636 that assist with and streamline modeling. It also contains functions for
12637 binary and ordinal logistic regression models, ordinal models for continuous Y
12638 with a variety of distribution families, and the Buckley-James multiple
12639 regression model for right-censored responses, and implements penalized
12640 maximum likelihood estimation for logistic and ordinary linear models. The
12641 package works with almost any regression model, but it was especially written
12642 to work with binary or ordinal regression models, Cox regression, accelerated
12643 failure time models, ordinary linear models, the Buckley-James model,
12644 generalized least squares for serially or spatially correlated observations,
12645 generalized linear models, and quantile regression.")
12646 (license license:gpl2+)))
12648 (define-public r-haplo-stats
12650 (name "r-haplo-stats")
12655 (uri (cran-uri "haplo.stats" version))
12658 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
12659 (properties `((upstream-name . "haplo.stats")))
12660 (build-system r-build-system)
12662 `(("r-rms" ,r-rms)))
12664 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
12665 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
12666 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
12668 "This package provides routines for the analysis of indirectly measured
12669 haplotypes. The statistical methods assume that all subjects are unrelated
12670 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
12671 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
12672 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
12673 examples in the vignette.")
12674 (license license:gpl2+)))
12676 (define-public r-bqtl
12683 (uri (cran-uri "bqtl" version))
12686 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
12687 (build-system r-build-system)
12688 (native-inputs `(("gfortran" ,gfortran)))
12689 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
12690 (synopsis "Bayesian QTL mapping toolkit")
12692 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
12693 lines. It includes maximum likelihood and Bayesian tools.")
12694 (license license:gpl2+)))
12696 (define-public r-ibdreg
12703 (uri (cran-uri "ibdreg" version))
12706 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
12707 (build-system r-build-system)
12708 (home-page "https://www.mayo.edu/research/labs/\
12709 statistical-genetics-genetic-epidemiology/software")
12710 (synopsis "Regression methods for IBD linkage with covariates")
12712 "This package provides a method to test genetic linkage with covariates
12713 by regression methods with response IBD sharing for relative pairs. Account
12714 for correlations of IBD statistics and covariates for relative pairs within
12715 the same pedigree.")
12716 (license license:gpl2+)))
12718 (define-public r-dlmap
12725 (uri (cran-uri "dlmap" version))
12728 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
12729 (build-system r-build-system)
12731 `(("r-ibdreg" ,r-ibdreg)
12735 ("r-wgaim" ,r-wgaim)))
12736 (home-page "https://cran.r-project.org/web/packages/dlmap/")
12737 (synopsis "Detection localization mapping for QTL")
12739 "This is package for QTL mapping in a mixed model framework with separate
12740 detection and localization stages. The first stage detects the number of QTL
12741 on each chromosome based on the genetic variation due to grouped markers on
12742 the chromosome; the second stage uses this information to determine the most
12743 likely QTL positions. The mixed model can accommodate general fixed and
12744 random effects, including spatial effects in field trials and pedigree
12745 effects. It is applicable to backcrosses, doubled haploids, recombinant
12746 inbred lines, F2 intercrosses, and association mapping populations.")
12747 (license license:gpl2)))
12749 (define-public r-ldheatmap
12751 (name "r-ldheatmap")
12756 (uri (cran-uri "LDheatmap" version))
12759 "0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s"))))
12760 (properties `((upstream-name . "LDheatmap")))
12761 (build-system r-build-system)
12763 `(("r-genetics" ,r-genetics)
12764 ("r-snpstats" ,r-snpstats)))
12765 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
12766 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
12768 "This package provides tools to produce a graphical display, as a heat
12769 map, of measures of pairwise linkage disequilibria between SNPs. Users may
12770 optionally include the physical locations or genetic map distances of each SNP
12772 (license license:gpl3)))
12774 (define-public r-hwde
12781 (uri (cran-uri "hwde" version))
12784 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
12785 (build-system r-build-system)
12786 (home-page "https://cran.r-project.org/web/packages/hwde/")
12787 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
12789 "This package fits models for genotypic disequilibria, as described in
12790 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
12791 terms are available that account for first order interactions between loci.
12792 It also implements, for a single locus in a single population, a conditional
12793 exact test for Hardy-Weinberg equilibrium.")
12794 (license license:gpl2+)))
12796 (define-public r-tdthap
12803 (uri (cran-uri "tdthap" version))
12806 "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r"))))
12807 (build-system r-build-system)
12808 (home-page "https://cran.r-project.org/web/packages/tdthap/")
12809 (synopsis "TDT tests for extended haplotypes")
12811 "Functions and examples are provided for transmission/disequilibrium
12812 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
12813 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
12814 (license license:artistic2.0)))
12816 (define-public r-sparql
12822 (uri (cran-uri "SPARQL" version))
12825 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
12826 (properties `((upstream-name . "SPARQL")))
12827 (build-system r-build-system)
12829 `(("r-rcurl" ,r-rcurl)
12831 (home-page "https://cran.r-project.org/web/packages/SPARQL")
12832 (synopsis "SPARQL client for R")
12833 (description "This package provides an interface to use SPARQL to pose
12834 SELECT or UPDATE queries to an end-point.")
12835 ;; The only license indication is found in the DESCRIPTION file,
12836 ;; which states GPL-3. So we cannot assume GPLv3+.
12837 (license license:gpl3)))
12839 (define-public r-bookdown
12841 (name "r-bookdown")
12845 (uri (cran-uri "bookdown" version))
12848 "0vg1s1w0l9pm95asqb21yf39mfk1nc9rdhmlys9xwr7p7i7rsz32"))))
12849 (build-system r-build-system)
12851 `(("r-htmltools" ,r-htmltools)
12852 ("r-knitr" ,r-knitr)
12853 ("r-rmarkdown" ,r-rmarkdown)
12854 ("r-tinytex" ,r-tinytex)
12856 ("r-xfun" ,r-xfun)))
12857 (home-page "https://github.com/rstudio/bookdown")
12858 (synopsis "Authoring books and technical documents with R markdown")
12859 (description "This package provides output formats and utilities for
12860 authoring books and technical documents with R Markdown.")
12861 (license license:gpl3)))
12863 (define-public r-optparse
12865 (name "r-optparse")
12870 (uri (cran-uri "optparse" version))
12873 "0zrp6jakjhawrwfri270ym83vj5a7nvjk0w6b41z41ahw2da99dm"))))
12874 (build-system r-build-system)
12876 `(("r-getopt" ,r-getopt)))
12877 (home-page "https://github.com/trevorld/optparse")
12878 (synopsis "Command line option parser")
12880 "This package provides a command line parser inspired by Python's
12881 @code{optparse} library to be used with Rscript to write shebang scripts
12882 that accept short and long options.")
12883 (license license:gpl2+)))
12885 (define-public r-wgcna
12892 (uri (cran-uri "WGCNA" version))
12895 "09387w85lxvwr8ax2i2h602b4dgfv4wbvsl9aj1q0b1vfs4rkk69"))))
12896 (properties `((upstream-name . "WGCNA")))
12897 (build-system r-build-system)
12899 `(("r-annotationdbi" ,r-annotationdbi)
12900 ("r-doparallel" ,r-doparallel)
12901 ("r-dynamictreecut" ,r-dynamictreecut)
12902 ("r-fastcluster" ,r-fastcluster)
12903 ("r-foreach" ,r-foreach)
12904 ("r-go-db" ,r-go-db)
12905 ("r-hmisc" ,r-hmisc)
12906 ("r-impute" ,r-impute)
12908 ("r-robust" ,r-robust)
12909 ("r-survival" ,r-survival)
12910 ("r-matrixstats" ,r-matrixstats)
12911 ("r-preprocesscore" ,r-preprocesscore)))
12913 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
12914 (synopsis "Weighted correlation network analysis")
12916 "This package provides functions necessary to perform Weighted
12917 Correlation Network Analysis on high-dimensional data. It includes functions
12918 for rudimentary data cleaning, construction and summarization of correlation
12919 networks, module identification and functions for relating both variables and
12920 modules to sample traits. It also includes a number of utility functions for
12921 data manipulation and visualization.")
12922 (license license:gpl2+)))
12924 (define-public r-kernlab
12931 (uri (cran-uri "kernlab" version))
12934 "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
12935 (build-system r-build-system)
12936 (home-page "https://cran.r-project.org/web/packages/kernlab")
12937 (synopsis "Kernel-based machine learning tools")
12939 "This package provides kernel-based machine learning methods for
12940 classification, regression, clustering, novelty detection, quantile regression
12941 and dimensionality reduction. Among other methods @code{kernlab} includes
12942 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
12944 (license license:gpl2)))
12946 (define-public r-hierfstat
12948 (name "r-hierfstat")
12949 (version "0.04-22")
12953 (uri (cran-uri "hierfstat" version))
12956 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
12957 (build-system r-build-system)
12959 `(("r-ade4" ,r-ade4)
12960 ("r-adegenet" ,r-adegenet)
12961 ("r-gtools" ,r-gtools)))
12962 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
12963 (synopsis "Estimation and tests of hierarchical F-statistics")
12965 "This package allows the estimation of hierarchical F-statistics from
12966 haploid or diploid genetic data with any numbers of levels in the hierarchy,
12967 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
12968 are also given to test via randomisations the significance of each F and
12969 variance components, using the likelihood-ratio statistics G.")
12970 (license license:gpl2+)))
12972 (define-public r-hapassoc
12974 (name "r-hapassoc")
12979 (uri (cran-uri "hapassoc" version))
12982 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
12983 (build-system r-build-system)
12984 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
12985 (synopsis "Inference of trait associations with SNP haplotypes")
12987 "Hapassoc performs likelihood inference of trait associations with
12988 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
12989 functions are developed primarily for data collected in cohort or
12990 cross-sectional studies. They can accommodate uncertain haplotype phase and
12991 handle missing genotypes at some SNPs.")
12992 (license license:gpl2)))
12994 (define-public r-sampling
12996 (name "r-sampling")
13001 (uri (cran-uri "sampling" version))
13004 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13005 (build-system r-build-system)
13007 `(("r-lpsolve" ,r-lpsolve)
13008 ("r-mass" ,r-mass)))
13009 (home-page "https://cran.r-project.org/web/packages/sampling/")
13010 (synopsis "Survey sampling")
13012 "This package provides functions for drawing and calibrating samples.")
13013 (license license:gpl2+)))
13015 (define-public r-r2html
13022 (uri (cran-uri "R2HTML" version))
13025 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13026 (properties `((upstream-name . "R2HTML")))
13027 (build-system r-build-system)
13028 (home-page "https://github.com/nalimilan/R2HTML")
13029 (synopsis "HTML export for R objects")
13031 "This package includes HTML functions and methods to write in an HTML
13032 file. Thus, making HTML reports is easy. It includes a function that allows
13033 redirection on the fly, which appears to be very useful for teaching purposes,
13034 as the student can keep a copy of the produced output to keep all that they
13035 did during the course. The package comes with a vignette describing how to
13036 write HTML reports for statistical analysis. Finally, a driver for Sweave
13037 allows to parse HTML flat files containing R code and to automatically write
13038 the corresponding outputs (tables and graphs).")
13039 (license license:gpl2+)))
13041 (define-public r-rjava
13048 (uri (cran-uri "rJava" version))
13051 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13052 (properties `((upstream-name . "rJava")))
13053 (build-system r-build-system)
13055 `(#:modules ((guix build utils)
13056 (guix build r-build-system)
13059 (modify-phases %standard-phases
13060 (add-after 'unpack 'set-JAVA_HOME
13061 (lambda* (#:key inputs #:allow-other-keys)
13062 (let ((jdk (assoc-ref inputs "jdk")))
13063 (setenv "JAVA_HOME" jdk)
13064 (setenv "JAVA" (which "java"))
13065 (setenv "JAR" (which "jar"))
13066 (setenv "JAVAC" (which "javac"))
13067 (setenv "JAVAH" (which "javah"))
13068 (setenv "JAVA_CPPFLAGS"
13069 (string-append "-I" jdk "/include "
13070 "-I" jdk "/include/linux"))
13071 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13072 ((lib) (setenv "JAVA_LIBS" lib))
13073 (_ (error "Could not find libjvm.so"))))
13077 ("jdk" ,icedtea-8 "jdk")
13080 (home-page "http://www.rforge.net/rJava/")
13081 (synopsis "Low-Level R to Java interface")
13083 "This package provides a low-level interface to the Java VM very much
13084 like .C/.Call and friends. It allows the creation of objects, calling methods
13085 and accessing fields.")
13086 (license license:gpl2)))
13088 (define-public r-svmisc
13095 (uri (cran-uri "svMisc" version))
13098 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13099 (properties `((upstream-name . "svMisc")))
13100 (build-system r-build-system)
13101 (home-page "https://github.com/SciViews/svMisc")
13102 (synopsis "Miscellaneous functions for SciViews")
13104 "This package provides miscellaneous functions for SciViews or general
13105 use, including tools to manage a temporary environment attached to the search
13106 path for temporary variables you do not want to @code{save()} or
13107 @code{load()}; test the current platform; showing progress bars, etc.")
13108 (license license:gpl2)))
13110 (define-public r-xyz
13117 (uri (cran-uri "xyz" version))
13120 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13121 (build-system r-build-system)
13123 `(("r-rcpp" ,r-rcpp)))
13124 (home-page "https://cran.r-project.org/web/packages/xyz/")
13125 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13127 "High dimensional interaction search by brute force requires a quadratic
13128 computational cost in the number of variables. The xyz algorithm provably
13129 finds strong interactions in almost linear time. For details of the algorithm
13130 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13131 interaction search in high-dimensional data.")
13132 ;; Any version of the GPL.
13133 (license license:gpl2+)))
13135 (define-public r-rttf2pt1
13137 (name "r-rttf2pt1")
13142 (uri (cran-uri "Rttf2pt1" version))
13145 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13146 (properties `((upstream-name . "Rttf2pt1")))
13147 (build-system r-build-system)
13148 (home-page "https://github.com/wch/Rttf2pt1")
13149 (synopsis "Font conversion utility")
13151 "This package contains the program @code{ttf2pt1}, for use with the
13152 @code{extrafont} package.")
13153 ;; Most of the files are covered under the Expat license. Some files are
13154 ;; covered under BSD-3. Deviations for individual files are recorded in
13155 ;; the LICENSE file.
13156 (license (list license:bsd-3 license:expat
13157 (license:non-copyleft "file://LICENSE")))))
13159 (define-public r-extrafontdb
13161 (name "r-extrafontdb")
13166 (uri (cran-uri "extrafontdb" version))
13169 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13170 (build-system r-build-system)
13171 (home-page "https://github.com/wch/extrafontdb")
13172 (synopsis "Database for the extrafont package")
13174 "This package holds the database for the @code{extrafont} package.")
13175 (license license:gpl2)))
13177 (define-public r-extrafont
13179 (name "r-extrafont")
13184 (uri (cran-uri "extrafont" version))
13187 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13188 (build-system r-build-system)
13190 `(("r-extrafontdb" ,r-extrafontdb)
13191 ("r-rttf2pt1" ,r-rttf2pt1)))
13192 (home-page "https://github.com/wch/extrafont")
13193 (synopsis "Tools for using fonts in R")
13195 "The extrafont package makes it easier to use fonts other than the basic
13196 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13197 used with PDF or PostScript output files. There are two hurdles for using
13198 fonts in PDF (or Postscript) output files:
13201 @item Making R aware of the font and the dimensions of the characters.
13202 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13203 properly on a device that doesn't have the font. This is usually needed if
13204 you want to print the PDF file or share it with others.
13207 The extrafont package makes both of these things easier.")
13208 (license license:gpl2)))
13210 (define-public r-xkcd
13217 (uri (cran-uri "xkcd" version))
13220 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13221 (build-system r-build-system)
13223 `(("r-extrafont" ,r-extrafont)
13224 ("r-ggplot2" ,r-ggplot2)
13225 ("r-hmisc" ,r-hmisc)))
13226 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13227 (synopsis "Plot ggplot2 graphics in the XKCD style")
13229 "This package provides the means to plot ggplot2 graphs in the style of
13230 the XKCD web comic.")
13231 (license license:gpl3)))
13233 (define-public r-msigdbr
13240 (uri (cran-uri "msigdbr" version))
13243 "1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg"))))
13244 (build-system r-build-system)
13246 `(("r-dplyr" ,r-dplyr)
13247 ("r-magrittr" ,r-magrittr)
13248 ("r-rlang" ,r-rlang)
13249 ("r-tibble" ,r-tibble)))
13250 (home-page "https://github.com/igordot/msigdbr")
13251 (synopsis "MSigDB gene sets for multiple organisms")
13253 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13254 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13255 software in a standard R data frame with key-value pairs. Included are the
13256 original human gene symbols and Entrez IDs as well as the equivalents for
13257 various frequently studied model organisms such as mouse, rat, pig, fly, and
13259 ;; The package is covered under the Expat license, but the upstream MSigDB
13260 ;; files are made available under the Creative Commons Attribution 4.0
13261 ;; International license.
13262 (license (list license:expat license:cc-by4.0))))
13264 (define-public r-gridgraphics
13266 (name "r-gridgraphics")
13271 (uri (cran-uri "gridGraphics" version))
13274 "1dwws704jw2yhcdihyynh06jq0a2bnq9gy3z41yqr2i8vmxkwlfi"))))
13275 (properties `((upstream-name . "gridGraphics")))
13276 (build-system r-build-system)
13277 (home-page "https://github.com/pmur002/gridgraphics")
13278 (synopsis "Redraw base graphics using @code{grid} graphics")
13280 "This package provides functions to convert a page of plots drawn with
13281 the @code{graphics} package into identical output drawn with the @code{grid}
13282 package. The result looks like the original @code{graphics}-based plot, but
13283 consists of @code{grid} grobs and viewports that can then be manipulated with
13284 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13285 (license license:gpl2+)))
13287 (define-public r-farver
13294 (uri (cran-uri "farver" version))
13297 "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0"))))
13298 (build-system r-build-system)
13299 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13300 (home-page "https://github.com/thomasp85/farver")
13301 (synopsis "Vectorized color conversion and comparison")
13303 "The encoding of color can be handled in many different ways, using
13304 different color spaces. As different color spaces have different uses,
13305 efficient conversion between these representations are important. This
13306 package provides a set of functions that gives access to very fast color space
13307 conversion and comparisons implemented in C++, and offers 100-fold speed
13308 improvements over the @code{convertColor} function in the @code{grDevices}
13310 (license license:expat)))
13312 (define-public r-ggplotify
13314 (name "r-ggplotify")
13319 (uri (cran-uri "ggplotify" version))
13322 "14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby"))))
13323 (build-system r-build-system)
13325 `(("r-ggplot2" ,r-ggplot2)
13326 ("r-gridgraphics" ,r-gridgraphics)
13327 ("r-rvcheck" ,r-rvcheck)))
13328 (home-page "https://github.com/GuangchuangYu/ggplotify")
13329 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
13331 "This package provides tools to convert plot function calls (using
13332 expression or formula) to @code{grob} or @code{ggplot} objects that are
13333 compatible with the @code{grid} and @code{ggplot2} environment. With this
13334 package, we are able to e.g. use @code{cowplot} to align plots produced by
13335 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
13336 converting them to @code{ggplot} objects.")
13337 (license license:artistic2.0)))
13339 (define-public r-triebeard
13341 (name "r-triebeard")
13346 (uri (cran-uri "triebeard" version))
13349 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
13350 (build-system r-build-system)
13351 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13352 (home-page "https://github.com/Ironholds/triebeard/")
13353 (synopsis "Radix trees in Rcpp")
13355 "Radix trees, or tries, are key-value data structures optimized for
13356 efficient lookups, similar in purpose to hash tables. This package provides
13357 an implementation of radix trees for use in R programming and in developing
13358 packages with Rcpp.")
13359 (license license:expat)))
13361 (define-public r-tweenr
13368 (uri (cran-uri "tweenr" version))
13371 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
13372 (build-system r-build-system)
13374 `(("r-farver" ,r-farver)
13375 ("r-magrittr" ,r-magrittr)
13377 ("r-rlang" ,r-rlang)))
13378 (home-page "https://github.com/thomasp85/tweenr")
13379 (synopsis "Interpolate data for smooth animations")
13381 "In order to create smooth animation between states of data, tweening is
13382 necessary. This package provides a range of functions for creating tweened
13383 data that can be used as basis for animation. Furthermore it adds a number of
13384 vectorized interpolaters for common R data types such as numeric, date and
13386 (license license:expat)))
13388 (define-public r-polyclip
13390 (name "r-polyclip")
13395 (uri (cran-uri "polyclip" version))
13398 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
13399 (build-system r-build-system)
13400 (native-inputs `(("pkg-config" ,pkg-config)))
13401 (home-page "http://www.angusj.com/delphi/clipper.php")
13402 (synopsis "Polygon clipping")
13404 "This package provides an R port of the library Clipper. It performs
13405 polygon clipping operations (intersection, union, set minus, set difference)
13406 for polygonal regions of arbitrary complexity, including holes. It computes
13407 offset polygons (spatial buffer zones, morphological dilations, Minkowski
13408 dilations) for polygonal regions and polygonal lines. It computes the
13409 Minkowski Sum of general polygons. There is a function for removing
13410 self-intersections from polygon data.")
13411 (license license:boost1.0)))
13413 (define-public r-urltools
13415 (name "r-urltools")
13420 (uri (cran-uri "urltools" version))
13423 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
13424 (build-system r-build-system)
13426 `(("r-rcpp" ,r-rcpp)
13427 ("r-triebeard" ,r-triebeard)))
13428 (home-page "https://github.com/Ironholds/urltools/")
13429 (synopsis "Vectorized tools for URL handling and parsing")
13431 "This package provides a toolkit for all URL-handling needs, including
13432 encoding and decoding, parsing, parameter extraction and modification. All
13433 functions are designed to be both fast and entirely vectorized. It is
13434 intended to be useful for people dealing with web-related datasets, such as
13435 server-side logs, although may be useful for other situations involving large
13437 (license license:expat)))
13439 (define-public r-ggforce
13446 (uri (cran-uri "ggforce" version))
13449 "0snxx9zhcccxa7pz9pf3bjqmcmv9mz4m47v81hklnhm25jj40xg2"))))
13450 (build-system r-build-system)
13452 `(("r-ggplot2" ,r-ggplot2)
13453 ("r-gtable" ,r-gtable)
13455 ("r-polyclip" ,r-polyclip)
13457 ("r-rcppeigen" ,r-rcppeigen)
13458 ("r-rlang" ,r-rlang)
13459 ("r-scales" ,r-scales)
13460 ("r-tweenr" ,r-tweenr)))
13461 (home-page "https://ggforce.data-imaginist.com")
13462 (synopsis "Accelerating ggplot2")
13464 "The aim of the ggplot2 package is to aid in visual data investigations.
13465 This focus has led to a lack of facilities for composing specialized plots.
13466 Thi package aims to be a collection of mainly new statistics and geometries
13467 that fills this gap.")
13468 (license license:expat)))
13470 (define-public r-europepmc
13472 (name "r-europepmc")
13477 (uri (cran-uri "europepmc" version))
13480 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
13481 (build-system r-build-system)
13483 `(("r-dplyr" ,r-dplyr)
13485 ("r-jsonlite" ,r-jsonlite)
13487 ("r-progress" ,r-progress)
13488 ("r-purrr" ,r-purrr)
13489 ("r-urltools" ,r-urltools)
13490 ("r-xml2" ,r-xml2)))
13491 (home-page "https://github.com/ropensci/europepmc/")
13492 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
13494 "This package provides an R Client for the
13495 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
13496 Service}. It gives access to both metadata on life science literature and
13497 open access full texts. Europe PMC indexes all PubMed content and other
13498 literature sources including Agricola, a bibliographic database of citations
13499 to the agricultural literature, or Biological Patents. In addition to
13500 bibliographic metadata, the client allows users to fetch citations and
13501 reference lists. Links between life-science literature and other EBI
13502 databases, including ENA, PDB or ChEMBL are also accessible.")
13503 (license license:gpl3)))
13505 (define-public r-ggraph
13512 (uri (cran-uri "ggraph" version))
13515 "0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c"))))
13516 (build-system r-build-system)
13518 `(("r-digest" ,r-digest)
13519 ("r-dplyr" ,r-dplyr)
13520 ("r-ggforce" ,r-ggforce)
13521 ("r-ggplot2" ,r-ggplot2)
13522 ("r-ggrepel" ,r-ggrepel)
13523 ("r-gtable" ,r-gtable)
13524 ("r-igraph" ,r-igraph)
13528 ("r-scales" ,r-scales)
13529 ("r-viridis" ,r-viridis)))
13530 (home-page "https://cran.r-project.org/web/packages/ggraph/")
13531 (synopsis "Implementation of grammar of graphics for graphs and networks")
13533 "The grammar of graphics as implemented in ggplot2 is a poor fit for
13534 graph and network visualizations due to its reliance on tabular data input.
13535 The ggraph package is an extension of the ggplot2 API tailored to graph
13536 visualizations and provides the same flexible approach to building up plots
13538 (license license:gpl3)))
13540 (define-public r-varselrf
13542 (name "r-varselrf")
13547 (uri (cran-uri "varSelRF" version))
13550 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
13551 (properties `((upstream-name . "varSelRF")))
13552 (build-system r-build-system)
13554 `(("r-randomforest" ,r-randomforest)))
13555 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
13556 (synopsis "Variable selection using random forests")
13558 "This package provides tools for the variable selection from random
13559 forests using both backwards variable elimination (for the selection of small
13560 sets of non-redundant variables) and selection based on the importance
13561 spectrum (somewhat similar to scree plots; for the selection of large,
13562 potentially highly-correlated variables). The main applications are in
13563 high-dimensional data (e.g., microarray data, and other genomics and
13564 proteomics applications).")
13565 (license license:gpl2+)))
13567 (define-public r-pamr
13574 (uri (cran-uri "pamr" version))
13577 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
13578 (build-system r-build-system)
13580 `(("r-cluster" ,r-cluster)
13581 ("r-survival" ,r-survival)))
13582 (native-inputs `(("gfortran" ,gfortran)))
13583 (home-page "https://cran.r-project.org/web/packages/pamr/")
13584 (synopsis "Prediction Analysis for Microarrays")
13586 "This package provides some functions for sample classification in
13588 (license license:gpl2)))
13590 (define-public r-rda
13593 (version "1.0.2-2.1")
13597 (uri (cran-uri "rda" version))
13600 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
13601 (build-system r-build-system)
13602 (home-page "https://cran.r-project.org/web/packages/rda/")
13603 (synopsis "Shrunken centroids regularized discriminant analysis")
13605 "This package provides tools for shrunken centroids regularized
13606 discriminant analysis for the purpose of classifying high dimensional data.")
13607 (license license:gpl2+)))
13609 (define-public r-ggvis
13616 (uri (cran-uri "ggvis" version))
13619 "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk"))))
13620 (build-system r-build-system)
13622 `(("r-assertthat" ,r-assertthat)
13623 ("r-dplyr" ,r-dplyr)
13624 ("r-htmltools" ,r-htmltools)
13625 ("r-jsonlite" ,r-jsonlite)
13626 ("r-lazyeval" ,r-lazyeval)
13627 ("r-magrittr" ,r-magrittr)
13628 ("r-shiny" ,r-shiny)))
13629 (home-page "https://ggvis.rstudio.com/")
13630 (synopsis "Interactive grammar of graphics")
13632 "This package is a data visualization package for R providing an
13633 implementation of an interactive grammar of graphics, taking the best parts of
13634 ggplot2, combining them with the reactive framework of Shiny and drawing web
13635 graphics using Vega.")
13636 (license license:gpl2)))
13638 (define-public r-gbm
13645 (uri (cran-uri "gbm" version))
13648 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
13649 (build-system r-build-system)
13651 `(("r-gridextra" ,r-gridextra)
13652 ("r-lattice" ,r-lattice)
13653 ("r-survival" ,r-survival)))
13654 (home-page "https://github.com/gbm-developers/gbm")
13655 (synopsis "Generalized boosted regression models")
13657 "This package is an implementation of extensions to Freund and Schapire's
13658 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
13659 regression methods for least squares, absolute loss, t-distribution loss,
13660 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
13661 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
13662 and Learning to Rank measures (LambdaMart).")
13663 (license license:gpl2+)))
13665 (define-public r-threejs
13672 (uri (cran-uri "threejs" version))
13675 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
13676 (build-system r-build-system)
13678 `(#:modules ((guix build utils)
13679 (guix build r-build-system)
13683 (modify-phases %standard-phases
13684 (add-after 'unpack 'process-javascript
13685 (lambda* (#:key inputs #:allow-other-keys)
13686 (with-directory-excursion "inst"
13690 `((,(assoc-ref inputs "js-jquery")
13691 "htmlwidgets/lib/jquery/jquery.min.js")
13692 (,(assoc-ref inputs "js-threejs-85")
13693 "htmlwidgets/lib/threejs-85/three.min.js"))))
13694 (lambda (sources targets)
13695 (for-each (lambda (source target)
13696 (format #t "Processing ~a --> ~a~%"
13698 (delete-file target)
13699 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
13700 (call-with-output-file target
13702 (dump-port minified port)))))
13703 sources targets))))
13706 `(("r-base64enc" ,r-base64enc)
13707 ("r-crosstalk" ,r-crosstalk)
13708 ("r-htmlwidgets" ,r-htmlwidgets)
13709 ("r-igraph" ,r-igraph)))
13711 `(("uglify-js" ,uglify-js)
13715 (uri "https://code.jquery.com/jquery-3.3.1.js")
13718 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
13722 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
13725 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
13726 (home-page "https://bwlewis.github.io/rthreejs")
13727 (synopsis "Interactive 3D scatter plots, networks and globes")
13729 "Create interactive 3D scatter plots, network plots, and globes in R
13730 using the three.js visualization library.")
13731 (license license:expat)))
13733 (define-public r-mlbench
13740 (uri (cran-uri "mlbench" version))
13743 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
13744 (build-system r-build-system)
13745 (home-page "https://cran.r-project.org/web/packages/mlbench/")
13746 (synopsis "Machine learning benchmark problems")
13748 "This package provides a collection of artificial and real-world machine
13749 learning benchmark problems, including, e.g., several data sets from the UCI
13751 (license license:gpl2)))
13753 (define-public r-mpm
13760 (uri (cran-uri "mpm" version))
13763 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
13764 (build-system r-build-system)
13766 `(("r-kernsmooth" ,r-kernsmooth)
13767 ("r-mass" ,r-mass)))
13768 (home-page "http://mpm.r-forge.r-project.org")
13769 (synopsis "Multivariate projection methods")
13771 "This is a package for exploratory graphical analysis of multivariate
13772 data, specifically gene expression data with different projection methods:
13773 principal component analysis, correspondence analysis, spectral map
13775 (license license:gpl2+)))
13777 (define-public r-png
13783 (uri (cran-uri "png" version))
13786 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
13787 (build-system r-build-system)
13789 `(("libpng" ,libpng)
13791 (home-page "http://www.rforge.net/png/")
13792 (synopsis "Read and write PNG images")
13794 "This package provides an easy and simple way to read, write and display
13795 bitmap images stored in the PNG format. It can read and write both files and
13796 in-memory raw vectors.")
13797 ;; Any of these GPL versions.
13798 (license (list license:gpl2 license:gpl3))))
13800 (define-public r-ggcorrplot
13802 (name "r-ggcorrplot")
13807 (uri (cran-uri "ggcorrplot" version))
13810 "12sxvd9kjgszpbk35m7fj1wv7x40bp79c0g0by1xax70r3495h93"))))
13811 (build-system r-build-system)
13813 `(("r-ggplot2" ,r-ggplot2)
13814 ("r-reshape2" ,r-reshape2)))
13815 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
13816 (synopsis "Visualization of a correlation matrix using ggplot2")
13818 "The ggcorrplot package can be used to visualize easily a correlation
13819 matrix using ggplot2. It provides a solution for reordering the correlation
13820 matrix and displays the significance level on the plot. It also includes a
13821 function for computing a matrix of correlation p-values.")
13822 (license license:gpl2)))
13824 (define-public r-flexdashboard
13826 (name "r-flexdashboard")
13827 (version "0.5.1.1")
13831 (uri (cran-uri "flexdashboard" version))
13834 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
13835 (build-system r-build-system)
13837 `(#:modules ((guix build utils)
13838 (guix build r-build-system)
13842 (ice-9 textual-ports))
13844 (modify-phases %standard-phases
13845 (add-after 'unpack 'process-javascript
13846 (lambda* (#:key inputs #:allow-other-keys)
13847 (with-directory-excursion "inst"
13848 ;; Concatenate all components of prism.js
13849 (let ((contents (string-join
13850 (map (lambda (name)
13851 (call-with-input-file
13852 (assoc-ref inputs name)
13856 "js-prism-line-numbers"))
13858 (call-with-output-file "prism-src.js"
13859 (cut display contents <>)))
13863 `(("www/stickytableheaders/jquery.stickytableheaders.js"
13864 "www/stickytableheaders/jquery.stickytableheaders.min.js")
13866 "www/sly/sly.min.js")
13868 "www/prism/prism.js")
13869 (,(assoc-ref inputs "js-raphael")
13870 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
13871 (,(assoc-ref inputs "js-featherlight")
13872 "www/featherlight/featherlight.min.js"))))
13873 (lambda (sources targets)
13874 (for-each (lambda (source target)
13875 (format #t "Processing ~a --> ~a~%"
13877 (delete-file target)
13878 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
13879 (call-with-output-file target
13881 (dump-port minified port)))))
13882 sources targets))))
13885 `(("r-htmltools" ,r-htmltools)
13886 ("r-htmlwidgets" ,r-htmlwidgets)
13887 ("r-jsonlite" ,r-jsonlite)
13888 ("r-knitr" ,r-knitr)
13889 ("r-rmarkdown" ,r-rmarkdown)
13890 ("r-shiny" ,r-shiny)))
13892 `(("uglify-js" ,uglify-js)
13896 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
13899 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
13903 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
13906 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
13910 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
13913 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
13914 ("js-prism-line-numbers"
13917 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
13920 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
13924 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
13927 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
13928 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
13929 (synopsis "R Markdown format for flexible dashboards")
13931 "This package provides an R Markdown format for converting an R Markdown
13932 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
13933 of its components to the containing web page.")
13934 (license license:expat)))
13936 (define-public r-preseqr
13943 (uri (cran-uri "preseqR" version))
13946 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
13947 (properties `((upstream-name . "preseqR")))
13948 (build-system r-build-system)
13950 `(("r-polynom" ,r-polynom)))
13951 (home-page "https://cran.r-project.org/web/packages/preseqR/")
13952 (synopsis "Predicting species accumulation curves")
13954 "This package can be used to predict the r-species accumulation
13955 curve (r-SAC), which is the number of species represented at least r times as
13956 a function of the sampling effort. When r = 1, the curve is known as the
13957 species accumulation curve, or the library complexity curve in high-throughput
13958 genomic sequencing. The package includes both parametric and nonparametric
13959 methods, as described by Deng C, et al. (2018).")
13960 (license license:gpl3)))
13962 (define-public r-mapplots
13964 (name "r-mapplots")
13969 (uri (cran-uri "mapplots" version))
13972 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
13973 (build-system r-build-system)
13974 (home-page "https://cran.r-project.org/web/packages/mapplots/")
13975 (synopsis "Data visualization on maps")
13977 "This package helps you create simple maps; add sub-plots like pie plots
13978 to a map or any other plot; format, plot and export gridded data. The package
13979 was developed for displaying fisheries data but most functions can be used for
13980 more generic data visualisation.")
13981 (license license:gpl2+)))
13983 (define-public r-pmcmr
13990 (uri (cran-uri "PMCMR" version))
13993 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
13994 (properties `((upstream-name . "PMCMR")))
13995 (build-system r-build-system)
13996 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
13997 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
13999 "This is a deprecated package for calculating pairwise multiple
14000 comparisons of mean rank sums. This package is superseded by the novel
14001 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14002 compatibility of reverse depending packages for some time.")
14003 (license license:gpl3+)))
14005 (define-public r-downloader
14007 (name "r-downloader")
14012 (uri (cran-uri "downloader" version))
14015 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14016 (build-system r-build-system)
14018 `(("r-digest" ,r-digest)))
14019 (home-page "https://github.com/wch/downloader")
14020 (synopsis "Download files over HTTP and HTTPS")
14022 "This package provides a wrapper for the @code{download.file} function,
14023 making it possible to download files over HTTPS across platforms. The
14024 @code{RCurl} package provides this functionality (and much more) but has
14025 external dependencies. This package has is implemented purely in R.")
14026 (license license:gpl2)))
14028 (define-public r-rex
14035 (uri (cran-uri "rex" version))
14038 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14039 (build-system r-build-system)
14041 `(("r-lazyeval" ,r-lazyeval)
14042 ("r-magrittr" ,r-magrittr)))
14043 (home-page "https://github.com/kevinushey/rex")
14044 (synopsis "Friendly regular expressions")
14046 "This package provides a friendly interface for the construction of
14047 regular expressions. Regular expressions are a very powerful feature, however
14048 they are often difficult to interpret. Rex allows you to build complex
14049 regular expressions from human readable expressions")
14050 (license license:expat)))
14052 (define-public r-sctransform
14054 (name "r-sctransform")
14059 (uri (cran-uri "sctransform" version))
14062 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14063 (build-system r-build-system)
14065 `(("r-future" ,r-future)
14066 ("r-future-apply" ,r-future-apply)
14067 ("r-ggplot2" ,r-ggplot2)
14068 ("r-gridextra" ,r-gridextra)
14070 ("r-matrix" ,r-matrix)
14072 ("r-rcppeigen" ,r-rcppeigen)
14073 ("r-reshape2" ,r-reshape2)))
14074 (home-page "https://github.com/ChristophH/sctransform")
14075 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14077 "This package provides a normalization method for single-cell UMI count
14078 data using a variance stabilizing transformation. The transformation is based
14079 on a negative binomial regression model with regularized parameters. As part
14080 of the same regression framework, this package also provides functions for
14081 batch correction, and data correction.")
14082 (license license:gpl3)))
14084 (define-public r-styler
14091 (uri (cran-uri "styler" version))
14094 "1z24mi88snbz1avjw9phq0lzmigddvycc56s83nxzr9w9z85mh05"))))
14095 (build-system r-build-system)
14097 `(("r-backports" ,r-backports)
14099 ("r-magrittr" ,r-magrittr)
14100 ("r-purrr" ,r-purrr)
14101 ("r-rematch2" ,r-rematch2)
14102 ("r-rlang" ,r-rlang)
14103 ("r-rprojroot" ,r-rprojroot)
14104 ("r-tibble" ,r-tibble)
14105 ("r-withr" ,r-withr)
14106 ("r-xfun" ,r-xfun)))
14107 (home-page "https://github.com/r-lib/styler")
14108 (synopsis "Non-invasive pretty printing of R code")
14110 "This is a package for pretty-printing R code without changing the user's
14111 formatting intent.")
14112 (license license:gpl3)))
14114 (define-public r-scrime
14121 (uri (cran-uri "scrime" version))
14124 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14125 (build-system r-build-system)
14126 (home-page "https://cran.r-project.org/web/packages/scrime/")
14127 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14129 "This package provides tools for the analysis of high-dimensional data
14130 developed/implemented at the group \"Statistical Complexity Reduction In
14131 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14132 the functions can also be applied to other types of categorical data.")
14133 (license license:gpl2)))
14135 (define-public r-blme
14142 (uri (cran-uri "blme" version))
14145 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14146 (build-system r-build-system)
14147 (propagated-inputs `(("r-lme4" ,r-lme4)))
14148 (home-page "https://github.com/vdorie/blme")
14149 (synopsis "Bayesian linear mixed-effects models")
14151 "This package provides tools for maximum a posteriori estimation for
14152 linear and generalized linear mixed-effects models in a Bayesian setting. It
14153 extends the lme4 package.")
14154 (license license:gpl2+)))
14156 (define-public r-batchtools
14158 (name "r-batchtools")
14163 (uri (cran-uri "batchtools" version))
14166 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14167 (build-system r-build-system)
14169 `(("r-backports" ,r-backports)
14170 ("r-base64url" ,r-base64url)
14172 ("r-checkmate" ,r-checkmate)
14173 ("r-data-table" ,r-data-table)
14174 ("r-digest" ,r-digest)
14176 ("r-progress" ,r-progress)
14178 ("r-rappdirs" ,r-rappdirs)
14179 ("r-stringi" ,r-stringi)
14180 ("r-withr" ,r-withr)))
14181 (home-page "https://github.com/mllg/batchtools")
14182 (synopsis "Tools for computation on batch systems")
14184 "As a successor of the packages BatchJobs and BatchExperiments, this
14185 package provides a parallel implementation of the Map function for high
14186 performance computing systems managed by various schedulers. A multicore and
14187 socket mode allow the parallelization on a local machines, and multiple
14188 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14189 the package provides an abstraction mechanism to define large-scale computer
14190 experiments in a well-organized and reproducible way.")
14191 (license license:lgpl3)))
14193 (define-public r-clue
14200 (uri (cran-uri "clue" version))
14203 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
14204 (build-system r-build-system)
14205 (propagated-inputs `(("r-cluster" ,r-cluster)))
14206 (home-page "https://cran.r-project.org/web/packages/clue/")
14207 (synopsis "Tools for analyzing cluster ensembles")
14208 (description "Cluster ensembles are collections of individual solutions to
14209 a given clustering problem which are useful or necessary to consider in a wide
14210 range of applications. This R package provides an extensible computational
14211 environment for creating and analyzing cluster ensembles, with basic data
14212 structures for representing partitions and hierarchies, and facilities for
14213 computing on them, including methods for measuring proximity and obtaining
14214 consensus and secondary clusterings.")
14215 (license license:gpl2)))
14217 (define-public r-sitmo
14224 (uri (cran-uri "sitmo" version))
14227 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
14228 (build-system r-build-system)
14229 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14230 (home-page "https://github.com/coatless/sitmo/")
14231 (synopsis "Parallel pseudo random number generator header files")
14233 "This package provides two high quality and fast PPRNGs that may be used
14234 in an OpenMP parallel environment. In addition, there is a generator for one
14235 dimensional low-discrepancy sequence.")
14236 (license license:expat)))
14238 (define-public r-dqrng
14245 (uri (cran-uri "dqrng" version))
14248 "07fgs08w0afgz36lh90g5gi7rc93j2c0cqc9wvakch05f178wis4"))))
14249 (build-system r-build-system)
14253 ("r-sitmo" ,r-sitmo)))
14254 (home-page "https://www.daqana.org/dqrng")
14255 (synopsis "Fast pseudo random number generators")
14257 "Several fast random number generators are provided as C++ header-only
14258 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
14259 Additionally, fast functions for generating random numbers according to a
14260 uniform, normal and exponential distribution are included. The latter two use
14261 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
14262 functions are exported to R and as a C++ interface and are enabled for use
14263 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
14264 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
14265 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
14266 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
14267 ;; whole is distributed under the terms of the AGPL 3.
14268 (license license:agpl3)))
14270 (define-public r-dalex
14277 (uri (cran-uri "DALEX" version))
14280 "13l435l88r6wqaypxbf8jszc8wv5la1c3ahcxif2jcqlj4b1dks6"))))
14281 (properties `((upstream-name . "DALEX")))
14282 (build-system r-build-system)
14283 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
14284 (home-page "https://pbiecek.github.io/DALEX/")
14285 (synopsis "Descriptive machine learning explanations")
14287 "Machine Learning models are widely used and have various applications in
14288 classification or regression. Models created with boosting, bagging, stacking
14289 or similar techniques are often used due to their high performance, but such
14290 black-box models usually lack interpretability. The DALEX package contains
14291 various explainers that help to understand the link between input variables
14292 and model output.")
14293 ;; Any version of the GPL
14294 (license license:gpl3+)))
14296 (define-public r-enrichr
14303 (uri (cran-uri "enrichR" version))
14306 "0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn"))))
14307 (properties `((upstream-name . "enrichR")))
14308 (build-system r-build-system)
14310 `(("r-httr" ,r-httr)
14311 ("r-rjson" ,r-rjson)))
14312 (home-page "https://cran.r-project.org/web/packages/enrichR/")
14313 (synopsis "R Interface to Enrichr database for analyzing gene sets")
14315 "This package provides an R interface to all Enrichr databases, a
14316 web-based tool for analyzing gene sets and returns any enrichment of common
14317 annotated biological functions.")
14318 (license license:gpl2+)))
14320 (define-public r-plot3d
14327 (uri (cran-uri "plot3D" version))
14330 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
14331 (properties `((upstream-name . "plot3D")))
14332 (build-system r-build-system)
14333 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
14334 (home-page "https://cran.r-project.org/web/packages/plot3D")
14335 (synopsis "Plot multi-dimensional data")
14337 "This package provides functions for viewing 2D and 3D data, including
14338 perspective plots, slice plots, surface plots, scatter plots, etc. It
14339 includes data sets from oceanography.")
14340 (license license:gpl3+)))
14342 (define-public r-ggfortify
14344 (name "r-ggfortify")
14349 (uri (cran-uri "ggfortify" version))
14352 "1clyha9f9ygma64xbgi78lxsp1203f2ashqhhdpm71nr6w91bm88"))))
14353 (build-system r-build-system)
14355 `(("r-dplyr" ,r-dplyr)
14356 ("r-ggplot2" ,r-ggplot2)
14357 ("r-gridextra" ,r-gridextra)
14358 ("r-scales" ,r-scales)
14359 ("r-stringr" ,r-stringr)
14360 ("r-tibble" ,r-tibble)
14361 ("r-tidyr" ,r-tidyr)))
14362 (home-page "https://github.com/sinhrks/ggfortify")
14363 (synopsis "Data visualization tools for statistical analysis results")
14365 "This package provides unified plotting tools for statistics commonly
14366 used, such as GLM, time series, PCA families, clustering and survival
14367 analysis. The package offers a single plotting interface for these analysis
14368 results and plots in a unified style using the @code{ggplot2} package.")
14369 (license license:gpl2)))
14371 (define-public r-refmanager
14373 (name "r-refmanager")
14378 (uri (cran-uri "RefManageR" version))
14381 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
14382 (properties `((upstream-name . "RefManageR")))
14383 (build-system r-build-system)
14385 `(("r-bibtex" ,r-bibtex)
14387 ("r-jsonlite" ,r-jsonlite)
14388 ("r-lubridate" ,r-lubridate)
14390 ("r-stringr" ,r-stringr)
14391 ("r-xml2" ,r-xml2)))
14392 (home-page "https://github.com/ropensci/RefManageR/")
14393 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
14395 "This package provides tools for importing and working with bibliographic
14396 references. It greatly enhances the @code{bibentry} class by providing a
14397 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
14398 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
14399 by various formats for name lists (author by last names, translator by full
14400 names, etc.). Entries can be updated, combined, sorted, printed in a number
14401 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
14402 into R and converted to @code{BibEntry} objects.")
14403 ;; Any of these licenses may be picked.
14404 (license (list license:gpl2 license:gpl3 license:bsd-3))))
14406 (define-public r-citr
14413 (uri (cran-uri "citr" version))
14416 "0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g"))))
14417 (build-system r-build-system)
14419 `(("r-assertthat" ,r-assertthat)
14420 ("r-bibtex" ,r-bibtex)
14423 ("r-miniui" ,r-miniui)
14424 ("r-refmanager" ,r-refmanager)
14425 ("r-rstudioapi" ,r-rstudioapi)
14426 ("r-shiny" ,r-shiny)
14427 ("r-shinyjs" ,r-shinyjs)
14428 ("r-yaml" ,r-yaml)))
14429 (home-page "https://github.com/crsh/citr")
14430 (synopsis "RStudio add-in to insert Markdown citations")
14432 "This package provides functions and an RStudio add-in that search a
14433 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
14434 the current document.")
14435 (license license:expat)))
14437 (define-public r-xgboost
14444 (uri (cran-uri "xgboost" version))
14447 "0plhx63wcm4syslzmjfv6bdgaqn96fnav048hrj0vxk4dzgfp8sq"))))
14448 (build-system r-build-system)
14450 `(("r-data-table" ,r-data-table)
14451 ("r-magrittr" ,r-magrittr)
14452 ("r-matrix" ,r-matrix)
14453 ("r-stringi" ,r-stringi)))
14454 (home-page "https://github.com/dmlc/xgboost")
14455 (synopsis "Extreme gradient boosting")
14457 "This package provides an R interface to Extreme Gradient Boosting, which
14458 is an efficient implementation of the gradient boosting framework from Chen
14459 and Guestrin (2016). The package includes efficient linear model solver and
14460 tree learning algorithms. The package can automatically do parallel
14461 computation on a single machine. It supports various objective functions,
14462 including regression, classification and ranking. The package is made to be
14463 extensible, so that users are also allowed to define their own objectives
14465 (license license:asl2.0)))