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, 2019 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>
18 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
20 ;;; This file is part of GNU Guix.
22 ;;; GNU Guix is free software; you can redistribute it and/or modify it
23 ;;; under the terms of the GNU General Public License as published by
24 ;;; the Free Software Foundation; either version 3 of the License, or (at
25 ;;; your option) any later version.
27 ;;; GNU Guix is distributed in the hope that it will be useful, but
28 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
29 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
30 ;;; GNU General Public License for more details.
32 ;;; You should have received a copy of the GNU General Public License
33 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
35 (define-module (gnu packages cran)
36 #:use-module ((guix licenses) #:prefix license:)
37 #:use-module (guix packages)
38 #:use-module (guix download)
39 #:use-module (guix git-download)
40 #:use-module (guix utils)
41 #:use-module (guix build-system r)
42 #:use-module (gnu packages algebra)
43 #:use-module (gnu packages base)
44 #:use-module (gnu packages bioinformatics)
45 #:use-module (gnu packages c)
46 #:use-module (gnu packages compression)
47 #:use-module (gnu packages curl)
48 #:use-module (gnu packages databases)
49 #:use-module (gnu packages fontutils)
50 #:use-module (gnu packages gcc)
51 #:use-module (gnu packages geo)
52 #:use-module (gnu packages ghostscript)
53 #:use-module (gnu packages gl)
54 #:use-module (gnu packages gnome)
55 #:use-module (gnu packages graph)
56 #:use-module (gnu packages gtk)
57 #:use-module (gnu packages haskell-xyz)
58 #:use-module (gnu packages icu4c)
59 #:use-module (gnu packages image)
60 #:use-module (gnu packages imagemagick)
61 #:use-module (gnu packages java)
62 #:use-module (gnu packages javascript)
63 #:use-module (gnu packages lisp)
64 #:use-module (gnu packages machine-learning)
65 #:use-module (gnu packages maths)
66 #:use-module (gnu packages mpi)
67 #:use-module (gnu packages multiprecision)
68 #:use-module (gnu packages networking)
69 #:use-module (gnu packages pcre)
70 #:use-module (gnu packages perl)
71 #:use-module (gnu packages pkg-config)
72 #:use-module (gnu packages python)
73 #:use-module (gnu packages python-xyz)
74 #:use-module (gnu packages statistics)
75 #:use-module (gnu packages tls)
76 #:use-module (gnu packages web)
77 #:use-module (gnu packages xorg))
79 (define-public r-clipr
86 (uri (cran-uri "clipr" version))
89 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
90 (build-system r-build-system)
91 (home-page "https://github.com/mdlincoln/clipr")
92 (synopsis "Read and write from the system clipboard")
94 "This package provides simple utility functions to read from and write to
95 the system clipboards.")
96 (license license:gpl3)))
98 (define-public r-ellipsis
105 (uri (cran-uri "ellipsis" version))
108 "01z9gq311nzwv3a0sa49jhm5ylqd59srip4vjkrf23hzgb5i9y0b"))))
109 (build-system r-build-system)
111 `(("r-rlang" ,r-rlang)))
112 (home-page "https://github.com/hadley/ellipsis")
113 (synopsis "Tools for working with additional arguments")
115 "In S3 generics, it's useful to take @code{...} so that methods can have
116 additional arguments. But this flexibility comes at a cost: misspelled
117 arguments will be silently ignored. The @code{ellipsis} package is an
118 experiment that allows a generic to warn if any arguments passed in @code{...}
120 (license license:gpl3)))
129 (uri (cran-uri "grr" version))
132 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
133 (build-system r-build-system)
134 (home-page "https://cran.r-project.org/web/packages/grr")
135 (synopsis "Alternative implementations of base R functions")
137 "This package provides alternative implementations of some base R
138 functions, including @code{sort}, @code{order}, and @code{match}. The
139 functions are simplified but can be faster or have other advantages.")
140 (license license:gpl3)))
142 (define-public r-matrix-utils
144 (name "r-matrix-utils")
149 (uri (cran-uri "Matrix.utils" version))
152 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
153 (properties `((upstream-name . "Matrix.utils")))
154 (build-system r-build-system)
157 ("r-matrix" ,r-matrix)))
158 (home-page "https://github.com/cvarrichio/Matrix.utils")
160 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
162 "This package implements data manipulation methods such as @code{cast},
163 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
165 (license license:gpl3)))
174 (uri (cran-uri "sys" version))
177 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
178 (build-system r-build-system)
179 (home-page "https://github.com/jeroen/sys")
180 (synopsis "Powerful and reliable tools for running system commands in R")
182 "This package provides drop-in replacements for the base @code{system2()}
183 function with fine control and consistent behavior across platforms. It
184 supports clean interruption, timeout, background tasks, and streaming STDIN /
185 STDOUT / STDERR over binary or text connections. The package also provides
186 functions for evaluating expressions inside a temporary fork. Such
187 evaluations have no side effects on the main R process, and support reliable
188 interrupts and timeouts. This provides the basis for a sandboxing
190 (license license:expat)))
192 (define-public r-askpass
199 (uri (cran-uri "askpass" version))
202 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
203 (build-system r-build-system)
204 (propagated-inputs `(("r-sys" ,r-sys)))
205 (home-page "https://github.com/jeroen/askpass")
206 (synopsis "Safe password entry for R")
208 "This package provides cross-platform utilities for prompting the user
209 for credentials or a passphrase, for example to authenticate with a server or
210 read a protected key.")
211 (license license:expat)))
213 (define-public r-vegan
220 (uri (cran-uri "vegan" version))
223 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
224 (build-system r-build-system)
226 `(("gfortran" ,gfortran)))
228 `(("r-cluster" ,r-cluster)
229 ("r-knitr" ,r-knitr) ; needed for vignettes
230 ("r-lattice" ,r-lattice)
233 ("r-permute" ,r-permute)))
234 (home-page "https://cran.r-project.org/web/packages/vegan")
235 (synopsis "Functions for community ecology")
237 "The vegan package provides tools for descriptive community ecology. It
238 has most basic functions of diversity analysis, community ordination and
239 dissimilarity analysis. Most of its multivariate tools can be used for other
240 data types as well.")
241 (license license:gpl2+)))
243 (define-public r-tidyverse
250 (uri (cran-uri "tidyverse" version))
253 "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"))))
254 (build-system r-build-system)
256 `(("r-broom" ,r-broom)
258 ("r-crayon" ,r-crayon)
259 ("r-dbplyr" ,r-dbplyr)
261 ("r-forcats" ,r-forcats)
262 ("r-ggplot2" ,r-ggplot2)
266 ("r-jsonlite" ,r-jsonlite)
267 ("r-lubridate" ,r-lubridate)
268 ("r-magrittr" ,r-magrittr)
269 ("r-modelr" ,r-modelr)
272 ("r-readxl" ,r-readxl)
273 ("r-reprex" ,r-reprex)
275 ("r-rstudioapi" ,r-rstudioapi)
277 ("r-stringr" ,r-stringr)
278 ("r-tibble" ,r-tibble)
281 (home-page "https://tidyverse.tidyverse.org")
282 (synopsis "Install and load packages from the \"Tidyverse\"")
284 "The @code{tidyverse} is a set of packages that work in harmony because
285 they share common data representations and API design. This package is
286 designed to make it easy to install and load multiple tidyverse packages in a
288 (license license:gpl3)))
290 (define-public r-rvest
297 (uri (cran-uri "rvest" version))
300 "0ji5lk8g1gbv4d9c4jg1fg6rgsqrrwkm05j1id7drdw9kqdifgj1"))))
301 (build-system r-build-system)
304 ("r-magrittr" ,r-magrittr)
305 ("r-selectr" ,r-selectr)
307 (home-page "https://github.com/hadley/rvest")
308 (synopsis "Simple web scraping for R")
310 "@code{r-rvest} helps you scrape information from web pages. It is
311 designed to work with @code{magrittr} to make it easy to express common web
312 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
313 (license license:gpl3)))
315 (define-public r-selectr
322 (uri (cran-uri "selectr" version))
325 "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b"))))
326 (build-system r-build-system)
328 `(("r-stringr" ,r-stringr)
330 (home-page "https://sjp.co.nz/projects/selectr/")
331 (synopsis "Translate CSS selectors to XPath expressions")
333 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
334 expression. This allows you to use CSS selectors when working with the XML
335 package as it can only evaluate XPath expressions. Also provided are
336 convenience functions useful for using CSS selectors on XML nodes. This
337 package is a port of the Python package @code{cssselect}.")
338 (license license:bsd-3)))
340 (define-public r-reprex
347 (uri (cran-uri "reprex" version))
350 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
351 (build-system r-build-system)
353 `(("r-callr" ,r-callr)
357 ("r-rmarkdown" ,r-rmarkdown)
358 ("r-whisker" ,r-whisker)
359 ("r-withr" ,r-withr)))
360 (home-page "https://github.com/tidyverse/reprex")
361 (synopsis "Prepare reproducible R code examples for sharing")
363 "This package provides a convenience wrapper that uses the
364 @code{rmarkdown} package to render small snippets of code to target formats
365 that include both code and output. The goal is to encourage the sharing of
366 small, reproducible, and runnable examples on code-oriented websites or email.
367 @code{reprex} also extracts clean, runnable R code from various common formats,
368 such as copy/paste from an R session.")
369 (license license:expat)))
371 (define-public r-callr
378 (uri (cran-uri "callr" version))
381 "12dbqzjngbyaqdyw0yq1blyfx8pagcvx1vqj2jm451hs25nhdrnh"))))
382 (build-system r-build-system)
385 ("r-processx" ,r-processx)))
386 (home-page "https://github.com/r-lib/callr#readme")
387 (synopsis "Call R from R")
389 "It is sometimes useful to perform a computation in a separate R process,
390 without affecting the current R process at all. This package does exactly
392 (license license:expat)))
394 (define-public r-readxl
401 (uri (cran-uri "readxl" version))
404 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
405 (build-system r-build-system)
407 `(("r-cellranger" ,r-cellranger)
408 ("r-progress" ,r-progress)
410 ("r-tibble" ,r-tibble)))
411 (home-page "https://readxl.tidyverse.org")
412 (synopsis "Read Excel files")
414 "This package lets you import Excel files into R. It supports
415 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
416 the embedded @code{RapidXML} C++ library.")
417 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
418 ;; 'rapidxml' which is Boost.
419 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
421 (define-public r-modelr
428 (uri (cran-uri "modelr" version))
431 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
432 (build-system r-build-system)
434 `(("r-broom" ,r-broom)
436 ("r-magrittr" ,r-magrittr)
439 ("r-tibble" ,r-tibble)
440 ("r-tidyr" ,r-tidyr)))
441 (home-page "https://github.com/tidyverse/modelr")
442 (synopsis "Helper functions for modelling in pipelines")
444 "Functions for modelling that help you seamlessly integrate modelling
445 into a pipeline of data manipulation and visualisation.")
446 (license license:gpl3)))
448 (define-public r-httpuv
454 (uri (cran-uri "httpuv" version))
457 "13ax0hs2lc39ilznh1zarwqdzahcbhb8adilrfik3xg0fkljpcwk"))))
458 (build-system r-build-system)
462 ("r-promises" ,r-promises)
465 (home-page "https://github.com/rstudio/httpuv")
466 (synopsis "HTTP and WebSocket server library for R")
468 "The httpuv package provides low-level socket and protocol support for
469 handling HTTP and WebSocket requests directly from within R. It is primarily
470 intended as a building block for other packages, rather than making it
471 particularly easy to create complete web applications using httpuv alone.")
472 ;; This package includes third-party code that was originally released
473 ;; under various non-copyleft licenses. Full licensing information can be
474 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
475 (license license:gpl3+)))
477 (define-public r-jsonlite
483 (uri (cran-uri "jsonlite" version))
486 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
487 (build-system r-build-system)
488 (home-page "http://arxiv.org/abs/1403.2805")
489 (synopsis "Robust, high performance JSON parser and generator for R")
491 "The jsonlite package provides a fast JSON parser and generator optimized
492 for statistical data and the web. It offers flexible, robust, high
493 performance tools for working with JSON in R and is particularly powerful for
494 building pipelines and interacting with a web API. In addition to converting
495 JSON data from/to R objects, jsonlite contains functions to stream, validate,
496 and prettify JSON data. The unit tests included with the package verify that
497 all edge cases are encoded and decoded consistently for use with dynamic data
498 in systems and applications.")
499 (license license:expat)))
501 (define-public r-servr
507 (uri (cran-uri "servr" version))
510 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
511 (build-system r-build-system)
513 `(("r-httpuv" ,r-httpuv)
514 ("r-jsonlite" ,r-jsonlite)
517 (home-page "https://github.com/yihui/servr")
518 (synopsis "Simple HTTP server to serve static files or dynamic documents")
520 "Servr provides an HTTP server in R to serve static files, or dynamic
521 documents that can be converted to HTML files (e.g., R Markdown) under a given
523 (license license:expat)))
525 (define-public r-htmltools
531 (uri (cran-uri "htmltools" version))
534 "06l17d8jkf438yk2mchpsp4j90bynnapz3nabh5vkcc324p5a62v"))))
535 (build-system r-build-system)
537 `(("r-digest" ,r-digest)
539 ("r-rlang" ,r-rlang)))
540 (home-page "https://cran.r-project.org/web/packages/htmltools")
541 (synopsis "R tools for HTML")
543 "This package provides tools for HTML generation and output in R.")
544 (license license:expat)))
546 (define-public r-htmlwidgets
548 (name "r-htmlwidgets")
552 (uri (cran-uri "htmlwidgets" version))
555 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
556 (build-system r-build-system)
558 `(("r-htmltools" ,r-htmltools)
559 ("r-jsonlite" ,r-jsonlite)
561 (home-page "https://github.com/ramnathv/htmlwidgets")
562 (synopsis "HTML Widgets for R")
564 "HTML widgets is a framework for creating HTML widgets that render in
565 various contexts including the R console, R Markdown documents, and Shiny web
567 (license license:expat)))
569 (define-public r-htmltable
576 (uri (cran-uri "htmlTable" version))
579 "0h6jslchlx1dzqqdb70c3n9xlapcym9ykycvr0hc4q3450y8qmvh"))))
580 (properties `((upstream-name . "htmlTable")))
581 (build-system r-build-system)
583 `(("r-checkmate" ,r-checkmate)
584 ("r-htmltools" ,r-htmltools)
585 ("r-htmlwidgets" ,r-htmlwidgets)
587 ("r-magrittr" ,r-magrittr)
588 ("r-rstudioapi" ,r-rstudioapi)
589 ("r-stringr" ,r-stringr)))
590 (home-page "http://gforge.se/packages/")
591 (synopsis "Advanced tables for Markdown/HTML")
593 "This package provides functions to build tables with advanced layout
594 elements such as row spanners, column spanners, table spanners, zebra
595 striping, and more. While allowing advanced layout, the underlying
596 CSS-structure is simple in order to maximize compatibility with word
597 processors such as LibreOffice. The package also contains a few text
598 formatting functions that help outputting text compatible with HTML or
600 (license license:gpl3+)))
602 (define-public r-curl
608 (uri (cran-uri "curl" version))
611 "0xh227gvb056wlipjxxbf555z1i1qcs7rr1igvs6k6645y9irrlp"))))
612 (build-system r-build-system)
615 (modify-phases %standard-phases
616 ;; The environment variable CURL_CA_BUNDLE is only respected when
617 ;; running Windows, so we disable the platform checks.
618 ;; This can be removed once the libcurl has been patched.
619 (add-after 'unpack 'allow-CURL_CA_BUNDLE
621 (substitute* "R/onload.R"
622 (("if \\(!grepl\\(\"mingw\".*")
624 (substitute* "src/handle.c"
625 (("#ifdef _WIN32") "#if 1"))
631 `(("pkg-config" ,pkg-config)))
632 (home-page "https://github.com/jeroenooms/curl")
633 (synopsis "HTTP client for R")
635 "The @code{curl()} and @code{curl_download()} functions provide highly
636 configurable drop-in replacements for base @code{url()} and
637 @code{download.file()} with better performance, support for encryption, gzip
638 compression, authentication, and other @code{libcurl} goodies. The core of
639 the package implements a framework for performing fully customized requests
640 where data can be processed either in memory, on disk, or streaming via the
641 callback or connection interfaces.")
642 (license license:expat)))
644 (define-public r-hwriter
651 (uri (cran-uri "hwriter" version))
654 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
655 (build-system r-build-system)
656 (home-page "https://cran.r-project.org/web/packages/hwriter")
657 (synopsis "Output R objects in HTML format")
659 "This package provides easy-to-use and versatile functions to output R
660 objects in HTML format.")
661 (license license:lgpl2.1+)))
663 (define-public r-rjson
670 (uri (cran-uri "rjson" version))
673 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
674 (build-system r-build-system)
675 (home-page "https://cran.r-project.org/web/packages/rjson")
676 (synopsis "JSON library for R")
678 "This package provides functions to convert R objects into JSON objects
680 (license license:gpl2+)))
682 (define-public r-shiny
690 (url "https://github.com/rstudio/shiny.git")
691 (commit (string-append "v" version))))
692 (file-name (git-file-name name version))
695 "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
696 (build-system r-build-system)
698 `(#:modules ((guix build r-build-system)
699 (guix build minify-build-system)
702 #:imported-modules (,@%r-build-system-modules
703 (guix build minify-build-system))
705 (modify-phases (@ (guix build r-build-system) %standard-phases)
706 (add-after 'unpack 'replace-bundled-minified-JavaScript
707 (lambda* (#:key inputs #:allow-other-keys)
708 (let ((replace-file (lambda (old new)
709 (format #t "replacing ~a with ~a\n" old new)
712 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
713 ;; contain just data. They are not minified code, so we don't
715 (with-directory-excursion "inst/www/shared"
716 (replace-file "bootstrap/shim/respond.min.js"
717 (string-append (assoc-ref inputs "js-respond")
718 "/share/javascript/respond.min.js"))
719 (replace-file "bootstrap/shim/html5shiv.min.js"
720 (string-append (assoc-ref inputs "js-html5shiv")
721 "/share/javascript/html5shiv.min.js"))
722 (replace-file "json2-min.js"
723 (string-append (assoc-ref inputs "js-json2")
724 "/share/javascript/json2.min.js"))
725 (replace-file "strftime/strftime-min.js"
726 (string-append (assoc-ref inputs "js-strftime")
727 "/share/javascript/strftime.min.js"))
728 (replace-file "highlight/highlight.pack.js"
729 (string-append (assoc-ref inputs "js-highlight")
730 "/share/javascript/highlight.min.js"))
731 (replace-file "datatables/js/jquery.dataTables.min.js"
732 (string-append (assoc-ref inputs "js-datatables")
733 "/share/javascript/jquery.dataTables.min.js"))
734 (replace-file "selectize/js/selectize.min.js"
735 (string-append (assoc-ref inputs "js-selectize")
736 "/share/javascript/selectize.min.js"))
737 (replace-file "selectize/js/es5-shim.min.js"
738 (string-append (assoc-ref inputs "js-es5-shim")
739 "/share/javascript/es5-shim.min.js"))
740 (for-each (match-lambda
743 (minify source #:target target)))
744 '(("jqueryui/jquery-ui.js" .
745 "jqueryui/jquery-ui.min.js")
746 ("datepicker/js/bootstrap-datepicker.js" .
747 "datepicker/js/bootstrap-datepicker.min.js")
748 ("ionrangeslider/js/ion.rangeSlider.js" .
749 "ionrangeslider/js/ion.rangeSlider.min.js")
750 ("bootstrap/js/bootstrap.js" .
751 "bootstrap/js/bootstrap.min.js")
758 `(("r-crayon" ,r-crayon)
759 ("r-httpuv" ,r-httpuv)
761 ("r-jsonlite" ,r-jsonlite)
762 ("r-xtable" ,r-xtable)
763 ("r-digest" ,r-digest)
764 ("r-htmltools" ,r-htmltools)
766 ("r-sourcetools" ,r-sourcetools)))
768 `(("js-datatables" ,js-datatables)
769 ("js-html5shiv" ,js-html5shiv)
770 ("js-json2" ,js-json2)
771 ("js-respond" ,js-respond)
772 ("js-selectize" ,js-selectize)
773 ("js-strftime" ,js-strftime)
774 ("js-highlight" ,js-highlight)
775 ("js-es5-shim" ,js-es5-shim)))
777 `(("uglify-js" ,uglify-js)))
778 (home-page "http://shiny.rstudio.com")
779 (synopsis "Easy interactive web applications with R")
781 "Makes it incredibly easy to build interactive web applications
782 with R. Automatic \"reactive\" binding between inputs and outputs and
783 extensive prebuilt widgets make it possible to build beautiful,
784 responsive, and powerful applications with minimal effort.")
785 (license license:artistic2.0)))
787 ;; This package includes minified JavaScript files. When upgrading please
788 ;; check that there are no new minified JavaScript files.
789 (define-public r-shinytree
796 (uri (cran-uri "shinyTree" version))
799 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
800 (modules '((guix build utils)))
803 ;; Delete minified JavaScript
804 (for-each delete-file
805 '("inst/www/jsTree-3.3.7/libs/require.js"
806 "inst/www/jsTree-3.3.7/libs/jquery.js"
807 "inst/www/jsTree-3.3.7/jstree.min.js"))
809 (properties `((upstream-name . "shinyTree")))
810 (build-system r-build-system)
812 `(#:modules ((guix build utils)
813 (guix build r-build-system)
817 (modify-phases %standard-phases
818 (add-after 'unpack 'replace-minified-javascript
819 (lambda* (#:key inputs #:allow-other-keys)
820 (with-directory-excursion "inst/www/jsTree-3.3.7/"
821 (symlink (string-append (assoc-ref inputs "js-requirejs")
822 "/share/javascript/require.min.js")
827 `((,(assoc-ref inputs "js-jquery")
831 (lambda (sources targets)
832 (for-each (lambda (source target)
833 (format #t "Processing ~a --> ~a~%"
835 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
836 (call-with-output-file target
838 (dump-port minified port)))))
842 `(("r-htmlwidgets" ,r-htmlwidgets)
843 ("r-jsonlite" ,r-jsonlite)
844 ("r-promises" ,r-promises)
846 ("r-stringr" ,r-stringr)))
848 `(("js-requirejs" ,js-requirejs)))
850 `(("uglify-js" ,uglify-js)
854 (uri "https://code.jquery.com/jquery-3.3.1.js")
857 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
858 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
859 (synopsis "jsTree bindings for Shiny")
861 "This package exposes R bindings to jsTree, a JavaScript library that
862 supports interactive trees, to enable rich, editable trees in Shiny.")
863 (license license:expat)))
865 (define-public r-shinydashboard
867 (name "r-shinydashboard")
871 (uri (cran-uri "shinydashboard" version))
874 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
875 (build-system r-build-system)
876 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
877 ;; Regenerate it from the included sources.
879 `(#:modules ((guix build utils)
880 (guix build r-build-system)
883 (modify-phases %standard-phases
884 (add-after 'unpack 'generate-minified-javascript
886 (with-directory-excursion "inst/AdminLTE"
887 (delete-file "app.min.js")
888 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
889 (call-with-output-file "app.min.js"
891 (dump-port minified port))))))))))
893 `(("r-htmltools" ,r-htmltools)
894 ("r-promises" ,r-promises)
895 ("r-shiny" ,r-shiny)))
897 `(("uglify-js" ,uglify-js)))
898 (home-page "http://rstudio.github.io/shinydashboard/")
899 (synopsis "Create dashboards with shiny")
900 (description "This package provides an extension to the Shiny web
901 application framework for R, making it easy to create attractive dashboards.")
902 ;; This package includes software that was released under the Expat
903 ;; license, but the whole package is released under GPL version 2 or
905 (license license:gpl2+)))
907 (define-public r-shinyfiles
909 (name "r-shinyfiles")
914 (uri (cran-uri "shinyFiles" version))
917 "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i"))))
918 (properties `((upstream-name . "shinyFiles")))
919 (build-system r-build-system)
922 ("r-htmltools" ,r-htmltools)
923 ("r-jsonlite" ,r-jsonlite)
925 ("r-tibble" ,r-tibble)))
926 (home-page "https://github.com/thomasp85/shinyFiles")
927 (synopsis "Server-side file system viewer for Shiny")
929 "This package provides functionality for client-side navigation of the
930 server side file system in shiny apps. In case the app is running locally
931 this gives the user direct access to the file system without the need to
932 \"download\" files to a temporary location. Both file and folder selection as
933 well as file saving is available.")
934 (license license:gpl2+)))
936 (define-public r-shinythemes
938 (name "r-shinythemes")
943 (uri (cran-uri "shinythemes" version))
946 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
947 (properties `((upstream-name . "shinythemes")))
948 (build-system r-build-system)
949 (propagated-inputs `(("r-shiny" ,r-shiny)))
950 (home-page "http://rstudio.github.io/shinythemes/")
951 (synopsis "Themes for Shiny")
953 "This package provides themes for use with Shiny. It includes several
954 Bootstrap themes, which are packaged for use with Shiny applications.")
955 ;; The package is released under version 3 of the GPL, but it includes
956 ;; source files that are covered by the Expat license. It also includes
957 ;; fonts under SIL or the ASL.
958 (license (list license:gpl3 license:expat
959 license:silofl1.1 license:asl2.0))))
961 ;; The package sources include minified variants of d3.js and non-minified
962 ;; source code of d3-jetpack.
970 (uri (cran-uri "d3r" version))
973 "0xl3im76lp7pd5lhp8jfyqdm4j4zvjrx5a5fl81xv2cf7x3n4f2a"))))
974 (build-system r-build-system)
976 `(#:modules ((guix build utils)
977 (guix build r-build-system)
981 (modify-phases %standard-phases
982 (add-after 'unpack 'process-javascript
983 (lambda* (#:key inputs #:allow-other-keys)
984 (with-directory-excursion "inst/www/d3/"
988 `((,(assoc-ref inputs "d3.v3.js")
990 (,(assoc-ref inputs "d3.v4.js")
992 (,(assoc-ref inputs "d3.v5.js")
993 "v5/dist/d3.min.js"))))
994 (lambda (sources targets)
995 (for-each (lambda (source target)
996 (format #t "Processing ~a --> ~a~%"
999 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1000 (call-with-output-file target
1002 (dump-port minified port)))))
1006 `(("r-dplyr" ,r-dplyr)
1007 ("r-htmltools" ,r-htmltools)
1008 ("r-tidyr" ,r-tidyr)))
1010 `(("uglify-js" ,uglify-js)
1014 (uri "https://d3js.org/d3.v3.js")
1017 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1021 (uri "https://d3js.org/d3.v4.js")
1024 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1028 (uri "https://d3js.org/d3.v5.js")
1031 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1032 (home-page "https://github.com/timelyportfolio/d3r")
1033 (synopsis "d3.js utilities for R")
1035 "This package provides a suite of functions to help ease the use of the
1036 d3.js visualization library in R. These helpers include
1037 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1038 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1039 R objects into the JSON format that the d3.js library expects.")
1040 (license license:bsd-3)))
1042 ;; We use the latest commit here because the last release was in 2016 while
1043 ;; the latest commit was in 2018.
1044 (define-public r-sankeyd3
1045 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1049 (version (git-version "0.3.2" revision commit))
1054 (url "https://github.com/fbreitwieser/sankeyD3.git")
1056 (file-name (git-file-name name version))
1059 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1060 (build-system r-build-system)
1063 ("r-htmlwidgets" ,r-htmlwidgets)
1064 ("r-shiny" ,r-shiny)
1065 ("r-magrittr" ,r-magrittr)))
1066 (home-page "https://github.com/fbreitwieser/sankeyD3")
1067 (synopsis "Sankey network graphs from R")
1069 "This package provides an R library to generate Sankey network graphs
1070 in R and Shiny via the D3 visualization library.")
1071 ;; The R code is licensed under GPLv3+. It includes the non-minified
1072 ;; JavaScript source code of d3-sankey, which is released under the
1073 ;; 3-clause BSD license.
1074 (license (list license:gpl3+ license:bsd-3)))))
1076 (define-public r-crosstalk
1078 (name "r-crosstalk")
1083 (uri (cran-uri "crosstalk" version))
1086 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
1087 (build-system r-build-system)
1089 `(("r-ggplot2" ,r-ggplot2)
1090 ("r-htmltools" ,r-htmltools)
1091 ("r-jsonlite" ,r-jsonlite)
1092 ("r-lazyeval" ,r-lazyeval)
1094 ("r-shiny" ,r-shiny)))
1095 (home-page "https://rstudio.github.io/crosstalk/")
1096 (synopsis "Inter-widget interactivity for HTML widgets")
1098 "This package provides building blocks for allowing HTML widgets to
1099 communicate with each other, with Shiny or without (i.e. static @code{.html}
1100 files). It currently supports linked brushing and filtering.")
1101 (license license:expat)))
1103 (define-public r-rook
1110 (uri (cran-uri "Rook" version))
1113 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1114 (properties `((upstream-name . "Rook")))
1115 (build-system r-build-system)
1116 (propagated-inputs `(("r-brew" ,r-brew)))
1117 (home-page "https://cran.r-project.org/web/packages/Rook")
1118 (synopsis "Web server interface for R")
1120 "This package contains the Rook specification and convenience software
1121 for building and running Rook applications. A Rook application is an R
1122 reference class object that implements a @code{call} method or an R closure
1123 that takes exactly one argument, an environment, and returns a list with three
1124 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1125 (license license:gpl2)))
1127 (define-public r-miniui
1134 (uri (cran-uri "miniUI" version))
1137 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1138 (properties `((upstream-name . "miniUI")))
1139 (build-system r-build-system)
1141 `(("r-htmltools" ,r-htmltools)
1142 ("r-shiny" ,r-shiny)))
1143 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1144 (synopsis "Shiny UI widgets for small screens")
1146 "This package provides UI widget and layout functions for writing Shiny apps that
1147 work well on small screens.")
1148 (license license:gpl3)))
1150 (define-public r-feather
1157 (uri (cran-uri "feather" version))
1160 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1161 (build-system r-build-system)
1165 ("r-tibble" ,r-tibble)))
1166 (home-page "https://github.com/wesm/feather")
1167 (synopsis "R Bindings to the Feather API")
1168 (description "Read and write feather files, a lightweight binary columnar
1169 data store designed for maximum speed.")
1170 (license license:asl2.0)))
1172 (define-public r-maps
1179 (uri (cran-uri "maps" version))
1182 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1183 (build-system r-build-system)
1184 (home-page "https://cran.r-project.org/web/packages/maps")
1185 (synopsis "Draw geographical maps")
1186 (description "This package provides an R module for display of maps.
1187 Projection code and larger maps are in separate packages (@code{mapproj} and
1189 (license license:gpl2)))
1191 (define-public r-mapproj
1198 (uri (cran-uri "mapproj" version))
1201 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
1202 (build-system r-build-system)
1203 (propagated-inputs `(("r-maps" ,r-maps)))
1204 (home-page "https://cran.r-project.org/web/packages/mapproj")
1205 (synopsis "Map projection in R")
1206 (description "This package converts latitude/longitude into projected
1208 (license (list license:gpl2 ; The R interface
1209 (license:non-copyleft ; The C code
1210 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1211 "Lucent Public License Version 1.02")))))
1213 (define-public r-rgooglemaps
1215 (name "r-rgooglemaps")
1220 (uri (cran-uri "RgoogleMaps" version))
1223 "0sbklacc4jl5524ixhc11mh6smrzdz4l9pji6cn402i6zdn9z05x"))))
1224 (properties `((upstream-name . "RgoogleMaps")))
1225 (build-system r-build-system)
1226 (propagated-inputs `(("r-png" ,r-png)))
1227 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1228 (synopsis "Use Google Maps in R")
1229 (description "This package serves two purposes:
1231 @item Provide a comfortable R interface to query the Google server for static
1233 @item Use the map as a background image to overlay plots within R. This
1234 requires proper coordinate scaling.
1236 (license license:gpl2+)))
1238 (define-public r-geosphere
1240 (name "r-geosphere")
1245 (uri (cran-uri "geosphere" version))
1248 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1249 (build-system r-build-system)
1250 (propagated-inputs `(("r-sp" ,r-sp)))
1251 (home-page "https://cran.r-project.org/web/packages/geosphere")
1252 (synopsis "Spherical trigonometry")
1253 (description "This package computes spherical trigonometry for geographic
1254 applications. That is, compute distances and related measures for angular
1255 (longitude/latitude) locations.")
1256 (license license:gpl3+)))
1258 (define-public r-ggmap
1265 (uri (cran-uri "ggmap" version))
1268 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1269 (build-system r-build-system)
1271 `(("r-bitops" ,r-bitops)
1272 ("r-digest" ,r-digest)
1273 ("r-dplyr" ,r-dplyr)
1274 ("r-ggplot2" ,r-ggplot2)
1278 ("r-magrittr" ,r-magrittr)
1281 ("r-purrr" ,r-purrr)
1282 ("r-rgooglemaps" ,r-rgooglemaps)
1283 ("r-rjson" ,r-rjson)
1284 ("r-scales" ,r-scales)
1285 ("r-stringr" ,r-stringr)
1286 ("r-tibble" ,r-tibble)
1287 ("r-tidyr" ,r-tidyr)))
1288 (home-page "https://github.com/dkahle/ggmap")
1289 (synopsis "Spatial visualization with ggplot2")
1290 (description "This package provides a collection of functions to visualize
1291 spatial data and models on top of static maps from various online sources (e.g
1292 Google Maps and Stamen Maps). It includes tools common to those tasks,
1293 including functions for geolocation and routing.")
1294 (license license:gpl2)))
1296 (define-public r-haven
1303 (uri (cran-uri "haven" version))
1306 "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h"))))
1307 (build-system r-build-system)
1311 `(("r-forcats" ,r-forcats)
1314 ("r-readr" ,r-readr)
1315 ("r-tibble" ,r-tibble)))
1316 (home-page "https://haven.tidyverse.org")
1317 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1319 "This package lets you mport foreign statistical formats into R via the
1320 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1321 (license license:expat)))
1323 (define-public r-amap
1329 (uri (cran-uri "amap" version))
1332 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
1333 (build-system r-build-system)
1335 `(("gfortran" ,gfortran)))
1336 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1337 (synopsis "Another multidimensional analysis package")
1338 (description "This package provides tools for clustering and principal
1339 component analysis (with robust methods, and parallelized functions).")
1340 (license license:gpl2+)))
1342 (define-public r-ape
1349 (uri (cran-uri "ape" version))
1352 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1353 (build-system r-build-system)
1355 `(("r-lattice" ,r-lattice)
1357 ("r-rcpp" ,r-rcpp)))
1358 (home-page "http://ape-package.ird.fr/")
1359 (synopsis "Analyses of phylogenetics and evolution")
1361 "This package provides functions for reading, writing, plotting, and
1362 manipulating phylogenetic trees, analyses of comparative data in a
1363 phylogenetic framework, ancestral character analyses, analyses of
1364 diversification and macroevolution, computing distances from DNA sequences,
1365 and several other tools.")
1366 (license license:gpl2+)))
1368 (define-public r-abbyyr
1375 (uri (cran-uri "abbyyR" version))
1378 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1379 (properties `((upstream-name . "abbyyR")))
1380 (build-system r-build-system)
1382 `(("r-curl" ,r-curl)
1385 ("r-progress" ,r-progress)
1386 ("r-readr" ,r-readr)
1388 (home-page "https://github.com/soodoku/abbyyR")
1389 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1391 "This package provides tools to get text from images of text using Abbyy
1392 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1393 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1394 passports and get the results in a variety of formats including plain text and
1395 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1396 (license license:expat)))
1398 (define-public r-colorspace
1400 (name "r-colorspace")
1405 (uri (cran-uri "colorspace" version))
1407 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1408 (build-system r-build-system)
1409 (home-page "https://cran.r-project.org/web/packages/colorspace")
1410 (synopsis "Color space manipulation")
1412 "This package carries out a mapping between assorted color spaces
1413 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1414 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1415 colors are provided.")
1416 (license license:bsd-3)))
1418 (define-public r-glue
1425 (uri (cran-uri "glue" version))
1428 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1429 (build-system r-build-system)
1430 (home-page "https://github.com/tidyverse/glue")
1431 (synopsis "Interpreted string literals")
1433 "This package provides an implementation of interpreted string literals,
1434 inspired by Python's Literal String Interpolation (PEP-0498) and
1435 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1436 (license license:expat)))
1438 (define-public r-pastecs
1444 (uri (cran-uri "pastecs" version))
1447 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1448 (build-system r-build-system)
1450 `(("r-boot" ,r-boot)))
1451 (home-page "http://www.sciviews.org/pastecs")
1452 (synopsis "Analysis of space-time ecological series")
1454 "This package provides functions for regulation, decomposition and analysis
1455 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1456 initiative to bring PASSTEC 2000 functionalities to R.")
1457 (license license:gpl2+)))
1459 (define-public r-plogr
1466 (uri (cran-uri "plogr" version))
1469 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1470 (build-system r-build-system)
1471 (home-page "https://github.com/krlmlr/plogr")
1472 (synopsis "R bindings for the plog C++ logging library")
1474 "This package provides the header files for a stripped-down version of
1475 the plog header-only C++ logging library, and a method to log to R's standard
1477 (license license:expat)))
1479 (define-public r-pls
1486 (uri (cran-uri "pls" version))
1488 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1489 (build-system r-build-system)
1490 (home-page "http://mevik.net/work/software/pls.html")
1491 (synopsis "Partial Least Squares and Principal Component Regression")
1493 "The pls package implements multivariate regression methods: Partial Least
1494 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1495 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1498 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1499 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1500 @item multi-response models (or @dfn{PLS2})
1501 @item flexible cross-validation
1502 @item Jackknife variance estimates of regression coefficients
1503 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1504 (R)MSEP, R², and correlation loadings
1505 @item formula interface, modelled after @code{lm()}, with methods for predict,
1506 print, summary, plot, update, etc.
1507 @item extraction functions for coefficients, scores, and loadings
1508 @item MSEP, RMSEP, and R² estimates
1509 @item multiplicative scatter correction (@dfn{MSC})
1511 (license license:gpl2)))
1520 (uri (cran-uri "ps" version))
1522 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1523 (build-system r-build-system)
1524 (home-page "http://ps.r-lib.org")
1525 (synopsis "List, query, and manipulate system processes")
1527 "The ps package implements an API to list, query, and manipulate system
1528 processes. Most of its code is based on the @code{psutil} Python package.")
1529 (license license:bsd-3)))
1531 (define-public r-pkgbuild
1538 (uri (cran-uri "pkgbuild" version))
1540 (base32 "0xnlz6ivhkbmncg9hfw5p69lm4rjy3wn5lyxmygxyf4rrfnnqwxx"))))
1541 (build-system r-build-system)
1543 `(("r-callr" ,r-callr)
1545 ("r-crayon" ,r-crayon)
1547 ("r-prettyunits" ,r-prettyunits)
1549 ("r-rprojroot" ,r-rprojroot)
1550 ("r-withr" ,r-withr)))
1551 (home-page "https://github.com/r-pkgs/pkgbuild")
1552 (synopsis "Find tools needed to build R packages")
1554 "This package provides functions used to build R packages. It locates
1555 compilers needed to build R packages on various platforms and ensures the PATH
1556 is configured appropriately so R can use them.")
1557 (license license:gpl3)))
1559 (define-public r-pkgload
1566 (uri (cran-uri "pkgload" version))
1569 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1570 (build-system r-build-system)
1572 `(("r-desc" ,r-desc)
1573 ("r-pkgbuild" ,r-pkgbuild)
1574 ("r-rlang" ,r-rlang)
1575 ("r-rprojroot" ,r-rprojroot)
1576 ("r-rstudioapi" ,r-rstudioapi)
1577 ("r-withr" ,r-withr)))
1578 (home-page "https://github.com/r-lib/pkgload")
1579 (synopsis "Simulate package installation and attach")
1581 "This package simulates the process of installing a package and then
1582 attaching it. This is a key part of the @code{devtools} package as it allows
1583 you to rapidly iterate while developing a package.")
1584 (license license:gpl3)))
1586 (define-public r-rcpp
1593 (uri (cran-uri "Rcpp" version))
1595 (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd"))))
1596 (build-system r-build-system)
1598 `(("r-knitr" ,r-knitr))) ; for vignettes
1599 (home-page "http://www.rcpp.org")
1600 (synopsis "Seamless R and C++ integration")
1602 "The Rcpp package provides R functions as well as C++ classes which offer
1603 a seamless integration of R and C++. Many R data types and objects can be
1604 mapped back and forth to C++ equivalents which facilitates both writing of new
1605 code as well as easier integration of third-party libraries. Documentation
1606 about Rcpp is provided by several vignettes included in this package, via the
1607 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1608 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1609 @code{citation(\"Rcpp\")} for details on these last two.")
1610 (license license:gpl2+)))
1612 (define-public r-bindr
1619 (uri (cran-uri "bindr" version))
1622 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1623 (build-system r-build-system)
1624 (home-page "https://github.com/krlmlr/bindr")
1625 (synopsis "Parametrized active bindings")
1627 "This package provides a simple interface for creating active bindings
1628 where the bound function accepts additional arguments.")
1629 (license license:expat)))
1631 (define-public r-bindrcpp
1638 (uri (cran-uri "bindrcpp" version))
1641 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1642 (build-system r-build-system)
1644 `(("r-bindr" ,r-bindr)
1645 ("r-plogr" ,r-plogr)
1646 ("r-rcpp" ,r-rcpp)))
1647 (home-page "https://github.com/krlmlr/bindrcpp")
1648 (synopsis "Rcpp interface to active bindings")
1650 "This package provides an easy way to fill an environment with active
1651 bindings that call a C++ function.")
1652 (license license:expat)))
1654 (define-public r-auc
1661 (uri (cran-uri "AUC" version))
1664 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1665 (properties `((upstream-name . "AUC")))
1666 (build-system r-build-system)
1667 (home-page "https://cran.r-project.org/web/packages/AUC")
1668 (synopsis "Compute the area under the curve of selected measures")
1670 "This package includes functions to compute the area under the curve of
1671 selected measures: the area under the sensitivity curve (AUSEC), the area
1672 under the specificity curve (AUSPC), the area under the accuracy
1673 curve (AUACC), and the area under the receiver operating characteristic
1674 curve (AUROC). The curves can also be visualized. Support for partial areas
1676 (license license:gpl2+)))
1678 (define-public r-calibrate
1680 (name "r-calibrate")
1685 (uri (cran-uri "calibrate" version))
1687 (base32 "1s423nr176l2sc66wp7hzgqkv7c2bq8d2bjrrvrrm5qa9y3zdx1k"))))
1688 (build-system r-build-system)
1690 `(("r-mass" ,r-mass)))
1691 (home-page "https://cran.r-project.org/web/packages/calibrate")
1692 (synopsis "Calibration of scatterplot and biplot axes")
1694 "This is a package for drawing calibrated scales with tick marks
1695 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1696 (license license:gpl2)))
1698 (define-public r-shape
1705 (uri (cran-uri "shape" version))
1708 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1709 (build-system r-build-system)
1710 (home-page "https://cran.r-project.org/web/packages/shape")
1711 (synopsis "Functions for plotting graphical shapes")
1713 "This package provides functions for plotting graphical shapes such as
1714 ellipses, circles, cylinders, arrows, ...")
1715 (license license:gpl3+)))
1717 (define-public r-globaloptions
1719 (name "r-globaloptions")
1724 (uri (cran-uri "GlobalOptions" version))
1726 (base32 "0x89hfz80avq4zcskxl71i4zi0mgniqqxfrvz050aa2189wfyja2"))))
1727 (properties `((upstream-name . "GlobalOptions")))
1728 (build-system r-build-system)
1729 (home-page "https://github.com/jokergoo/GlobalOptions")
1730 (synopsis "Generate functions to get or set global options")
1732 "This package provides more controls on the option values such as
1733 validation and filtering on the values, making options invisible or private.")
1734 (license license:gpl2+)))
1736 (define-public r-circlize
1743 (uri (cran-uri "circlize" version))
1746 "0jvr9hmxyhg0zx101iiqkrg8wfaj86kp62xpv42n2j9fkn5r1mi2"))))
1747 (build-system r-build-system)
1749 `(("r-colorspace" ,r-colorspace)
1750 ("r-globaloptions" ,r-globaloptions)
1751 ("r-shape" ,r-shape)))
1752 (home-page "https://github.com/jokergoo/circlize")
1753 (synopsis "Circular visualization")
1755 "Circular layout is an efficient way to visualise huge amounts of
1756 information. This package provides an implementation of circular layout
1757 generation in R as well as an enhancement of available software. Its
1758 flexibility is based on the usage of low-level graphics functions such that
1759 self-defined high-level graphics can be easily implemented by users for
1760 specific purposes. Together with the seamless connection between the powerful
1761 computational and visual environment in R, it gives users more convenience and
1762 freedom to design figures for better understanding complex patterns behind
1763 multi-dimensional data.")
1764 (license license:gpl2+)))
1766 (define-public r-powerlaw
1773 (uri (cran-uri "poweRlaw" version))
1776 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1777 (properties `((upstream-name . "poweRlaw")))
1778 (build-system r-build-system)
1780 `(("r-vgam" ,r-vgam)))
1781 (home-page "https://github.com/csgillespie/poweRlaw")
1782 (synopsis "Tools for the analysis of heavy tailed distributions")
1784 "This package provides an implementation of maximum likelihood estimators
1785 for a variety of heavy tailed distributions, including both the discrete and
1786 continuous power law distributions. Additionally, a goodness-of-fit based
1787 approach is used to estimate the lower cut-off for the scaling region.")
1788 ;; Any of these GPL versions.
1789 (license (list license:gpl2 license:gpl3))))
1791 (define-public r-compare
1798 (uri (cran-uri "compare" version))
1801 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1802 (build-system r-build-system)
1803 (home-page "https://cran.r-project.org/web/packages/compare")
1804 (synopsis "Comparing objects for differences")
1806 "This package provides functions to compare a model object to a
1807 comparison object. If the objects are not identical, the functions can be
1808 instructed to explore various modifications of the objects (e.g., sorting
1809 rows, dropping names) to see if the modified versions are identical.")
1810 (license license:gpl2+)))
1812 (define-public r-dendextend
1814 (name "r-dendextend")
1819 (uri (cran-uri "dendextend" version))
1822 "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl"))))
1823 (build-system r-build-system)
1825 `(("r-ggplot2" ,r-ggplot2)
1826 ("r-magrittr" ,r-magrittr)
1827 ("r-viridis" ,r-viridis)))
1828 (home-page "https://cran.r-project.org/web/packages/dendextend")
1829 (synopsis "Extending 'dendrogram' functionality in R")
1831 "This package offers a set of functions for extending @code{dendrogram}
1832 objects in R, letting you visualize and compare trees of hierarchical
1833 clusterings. You can adjust a tree's graphical parameters (the color, size,
1834 type, etc of its branches, nodes and labels) and visually and statistically
1835 compare different dendrograms to one another.")
1836 ;; Any of these versions
1837 (license (list license:gpl2 license:gpl3))))
1839 (define-public r-getoptlong
1841 (name "r-getoptlong")
1846 (uri (cran-uri "GetoptLong" version))
1849 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1850 (properties `((upstream-name . "GetoptLong")))
1851 (build-system r-build-system)
1855 `(("r-globaloptions" ,r-globaloptions)
1856 ("r-rjson" ,r-rjson)))
1857 (home-page "https://github.com/jokergoo/GetoptLong")
1858 (synopsis "Parsing command-line arguments and variable interpolation")
1860 "This is yet another command-line argument parser which wraps the
1861 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1862 use in R. It also provides a simple way for variable interpolation in R.")
1863 (license license:gpl2+)))
1865 (define-public r-fastmatch
1867 (name "r-fastmatch")
1872 (uri (cran-uri "fastmatch" version))
1875 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1876 (build-system r-build-system)
1877 (home-page "http://www.rforge.net/fastmatch")
1878 (synopsis "Fast match function")
1880 "This package provides a fast @code{match} replacement for cases that
1881 require repeated look-ups. It is slightly faster that R's built-in
1882 @code{match} function on first match against a table, but extremely fast on
1883 any subsequent lookup as it keeps the hash table in memory.")
1884 (license license:gpl2)))
1893 (uri (cran-uri "ff" version))
1896 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1897 (build-system r-build-system)
1898 (propagated-inputs `(("r-bit" ,r-bit)))
1899 (home-page "http://ff.r-forge.r-project.org/")
1900 (synopsis "Memory-efficient storage of large data on disk and access functions")
1902 "This package provides data structures that are stored on disk but
1903 behave (almost) as if they were in RAM by transparently mapping only a section
1905 ;; error Architecture not supported.
1906 (supported-systems (delete "aarch64-linux" %supported-systems))
1907 (license license:gpl2)))
1909 (define-public r-ffbase
1916 (uri (cran-uri "ffbase" version))
1919 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
1920 (build-system r-build-system)
1923 ("r-fastmatch" ,r-fastmatch)
1925 (home-page "http://github.com/edwindj/ffbase")
1926 (synopsis "Basic statistical functions for package 'ff'")
1928 "This package extends the out of memory vectors of @code{ff} with
1929 statistical functions and other utilities to ease their usage.")
1930 (license license:gpl3)))
1932 (define-public r-prettyunits
1934 (name "r-prettyunits")
1939 (uri (cran-uri "prettyunits" version))
1942 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
1943 (build-system r-build-system)
1945 `(("r-assertthat" ,r-assertthat)
1946 ("r-magrittr" ,r-magrittr)))
1947 (home-page "https://github.com/gaborcsardi/prettyunits")
1948 (synopsis "Pretty, human readable formatting of quantities")
1950 "This package provides tools for pretty, human readable formatting of
1952 (license license:expat)))
1954 (define-public r-reshape
1961 (uri (cran-uri "reshape" version))
1964 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
1965 (build-system r-build-system)
1967 `(("r-plyr" ,r-plyr)
1968 ("r-rcpp" ,r-rcpp)))
1969 (home-page "http://had.co.nz/reshape")
1970 (synopsis "Flexibly reshape data")
1972 "Flexibly restructure and aggregate data using just two functions:
1973 @code{melt} and @code{cast}. This package provides them.")
1974 (license license:expat)))
1976 (define-public r-progress
1983 (uri (cran-uri "progress" version))
1986 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
1987 (build-system r-build-system)
1989 `(("r-crayon" ,r-crayon)
1991 ("r-prettyunits" ,r-prettyunits)
1993 (home-page "https://github.com/gaborcsardi/progress")
1994 (synopsis "Terminal progress bars")
1996 "This package provides configurable progress bars. They may include
1997 percentage, elapsed time, and/or the estimated completion time. They work in
1998 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
1999 package also provides a C++ API, that works with or without Rcpp.")
2000 (license license:expat)))
2002 (define-public r-ggally
2009 (uri (cran-uri "GGally" version))
2012 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
2013 (properties `((upstream-name . "GGally")))
2014 (build-system r-build-system)
2016 `(("libressl" ,libressl)))
2018 `(("r-ggplot2" ,r-ggplot2)
2019 ("r-gtable" ,r-gtable)
2021 ("r-progress" ,r-progress)
2022 ("r-rcolorbrewer" ,r-rcolorbrewer)
2023 ("r-reshape" ,r-reshape)
2024 ("r-rlang" ,r-rlang)))
2025 (home-page "https://ggobi.github.io/ggally")
2026 (synopsis "Extension to ggplot2")
2028 "The R package ggplot2 is a plotting system based on the grammar of
2029 graphics. GGally extends ggplot2 by adding several functions to reduce the
2030 complexity of combining geometric objects with transformed data. Some of
2031 these functions include a pairwise plot matrix, a two group pairwise plot
2032 matrix, a parallel coordinates plot, a survival plot, and several functions to
2034 (license license:gpl2+)))
2036 (define-public r-proxy
2043 (uri (cran-uri "proxy" version))
2046 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
2047 (build-system r-build-system)
2048 (home-page "https://cran.r-project.org/web/packages/proxy")
2049 (synopsis "Distance and similarity measures")
2051 "This package provides an extensible framework for the efficient
2052 calculation of auto- and cross-proximities, along with implementations of the
2053 most popular ones.")
2054 (license license:gpl2)))
2063 (uri (cran-uri "sp" version))
2066 "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p"))))
2067 (build-system r-build-system)
2069 `(("r-lattice" ,r-lattice)))
2070 (home-page "https://cran.r-project.org/web/packages/sp")
2071 (synopsis "Classes and methods for spatial data")
2073 "This package provides classes and methods for spatial data; the classes
2074 document where the spatial location information resides, for 2D or 3D data.
2075 Utility functions are provided, e.g. for plotting data as maps, spatial
2076 selection, as well as methods for retrieving coordinates, for subsetting,
2077 print, summary, etc.")
2078 (license license:gpl2+)))
2080 (define-public r-rmtstat
2087 (uri (cran-uri "RMTstat" version))
2090 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2091 (properties `((upstream-name . "RMTstat")))
2092 (build-system r-build-system)
2093 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2094 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2096 "This package provides functions for working with the Tracy-Widom laws
2097 and other distributions related to the eigenvalues of large Wishart
2099 (license license:bsd-3)))
2101 (define-public r-rmpi
2107 (uri (cran-uri "Rmpi" version))
2110 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2111 (properties `((upstream-name . "Rmpi")))
2112 (build-system r-build-system)
2114 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2115 #:phases (modify-phases %standard-phases
2116 (add-before 'install 'mpi-setup
2119 `(("openmpi" ,openmpi)))
2121 `(("pkg-config" ,pkg-config)))
2122 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2123 (synopsis "R interface to message-passing interface (MPI)")
2125 "This package provides an interface (wrapper) to MPI APIs. It also
2126 provides an interactive R manager and worker environment.")
2127 (license license:gpl2+)))
2129 (define-public r-lmoments
2136 (uri (cran-uri "Lmoments" version))
2139 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2140 (properties `((upstream-name . "Lmoments")))
2141 (build-system r-build-system)
2143 `(("r-rcpp" ,r-rcpp)
2144 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2145 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2146 (synopsis "L-moments and quantile mixtures")
2148 "This package contains functions to estimate L-moments and trimmed
2149 L-moments from the data. It also contains functions to estimate the
2150 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2151 quantile mixture from L-moments and trimmed L-moments.")
2152 (license license:gpl2)))
2154 (define-public r-distillery
2156 (name "r-distillery")
2161 (uri (cran-uri "distillery" version))
2164 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2165 (build-system r-build-system)
2166 (home-page "http://www.ral.ucar.edu/staff/ericg")
2167 (synopsis "Functions for confidence intervals and object information")
2169 "This package provides some very simple method functions for confidence
2170 interval calculation and to distill pertinent information from a potentially
2171 complex object; primarily used in common with the packages extRemes and
2173 (license license:gpl2+)))
2175 (define-public r-extremes
2182 (uri (cran-uri "extRemes" version))
2185 "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic"))))
2186 (properties `((upstream-name . "extRemes")))
2187 (build-system r-build-system)
2189 `(("r-distillery" ,r-distillery)
2190 ("r-lmoments" ,r-lmoments)))
2191 (home-page "http://www.assessment.ucar.edu/toolkit/")
2192 (synopsis "Extreme value analysis")
2194 "ExtRemes is a suite of functions for carrying out analyses on the
2195 extreme values of a process of interest; be they block maxima over long blocks
2196 or excesses over a high threshold.")
2197 (license license:gpl2+)))
2199 (define-public r-lmtest
2206 (uri (cran-uri "lmtest" version))
2209 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2210 (build-system r-build-system)
2212 `(("r-zoo" ,r-zoo)))
2214 `(("gfortran" ,gfortran)))
2215 (home-page "https://cran.r-project.org/web/packages/lmtest")
2216 (synopsis "Testing linear regression models")
2218 "This package provides a collection of tests, data sets, and examples for
2219 diagnostic checking in linear regression models. Furthermore, some generic
2220 tools for inference in parametric models are provided.")
2221 ;; Either version is okay
2222 (license (list license:gpl2 license:gpl3))))
2224 (define-public r-idr
2230 (uri (cran-uri "idr" version))
2233 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2234 (build-system r-build-system)
2235 (home-page "https://cran.r-project.org/web/packages/idr/")
2236 (synopsis "Irreproducible discovery rate")
2238 "This is a package for estimating the copula mixture model and plotting
2239 correspondence curves in \"Measuring reproducibility of high-throughput
2240 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2241 by Li, Brown, Huang, and Bickel")
2242 (license license:gpl2+)))
2244 (define-public r-inline
2250 (uri (cran-uri "inline" version))
2253 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2254 (build-system r-build-system)
2255 (home-page "https://cran.r-project.org/web/packages/inline")
2256 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2258 "This package provides functionality to dynamically define R functions
2259 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2260 @code{.Call} calling conventions.")
2261 ;; Any version of the LGPL.
2262 (license license:lgpl3+)))
2264 (define-public r-bbmle
2271 (uri (cran-uri "bbmle" version))
2274 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2275 (build-system r-build-system)
2277 `(("r-lattice" ,r-lattice)
2279 ("r-numderiv" ,r-numderiv)))
2280 (home-page "https://cran.r-project.org/web/packages/bbmle")
2281 (synopsis "Tools for General Maximum Likelihood Estimation")
2283 "This package provides methods and functions for fitting maximum
2284 likelihood models in R. This package modifies and extends the @code{mle}
2285 classes in the @code{stats4} package.")
2286 ;; Any version of the GPL
2287 (license license:gpl2+)))
2289 (define-public r-emdbook
2296 (uri (cran-uri "emdbook" version))
2299 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2300 (build-system r-build-system)
2302 `(("r-bbmle" ,r-bbmle)
2304 ("r-lattice" ,r-lattice)
2307 ("r-rcpp" ,r-rcpp)))
2308 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2309 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2311 "This package provides auxiliary functions and data sets for \"Ecological
2312 Models and Data\", a book presenting maximum likelihood estimation and related
2313 topics for ecologists (ISBN 978-0-691-12522-0).")
2315 (license (list license:gpl2 license:gpl3))))
2317 (define-public r-lpsolve
2320 (version "5.6.13.3")
2324 (uri (cran-uri "lpSolve" version))
2327 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2328 (properties `((upstream-name . "lpSolve")))
2329 (build-system r-build-system)
2330 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2331 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2333 "Lp_solve is software for solving linear, integer and mixed integer
2334 programs. This implementation supplies a \"wrapper\" function in C and some R
2335 functions that solve general linear/integer problems, assignment problems, and
2336 transportation problems.")
2337 (license license:lgpl2.0)))
2339 (define-public r-limsolve
2346 (uri (cran-uri "limSolve" version))
2349 "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
2350 (properties `((upstream-name . "limSolve")))
2351 (build-system r-build-system)
2353 `(("r-lpsolve" ,r-lpsolve)
2355 ("r-quadprog" ,r-quadprog)))
2356 (native-inputs `(("gfortran" ,gfortran)))
2357 (home-page "https://cran.r-project.org/web/packages/limSolve")
2358 (synopsis "Solving linear inverse models")
2360 "This package provides functions that:
2363 @item find the minimum/maximum of a linear or quadratic function,
2364 @item sample an underdetermined or overdetermined system,
2365 @item solve a linear system Ax=B for the unknown x.
2368 It includes banded and tridiagonal linear systems. The package calls Fortran
2369 functions from LINPACK.")
2371 (license (list license:gpl2+ license:gpl3+))))
2373 (define-public r-fitdistrplus
2375 (name "r-fitdistrplus")
2380 (uri (cran-uri "fitdistrplus" version))
2383 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2384 (build-system r-build-system)
2386 `(("r-mass" ,r-mass)
2387 ("r-npsurv" ,r-npsurv)
2388 ("r-survival" ,r-survival)))
2389 (home-page "http://riskassessment.r-forge.r-project.org")
2390 (synopsis "Fitting a parametric distribution from data")
2392 "This package extends the @code{fitdistr} function of the MASS package
2393 with several functions to help the fit of a parametric distribution to
2394 non-censored or censored data. Censored data may contain left-censored,
2395 right-censored and interval-censored values, with several lower and upper
2396 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2397 provides moment matching (MME), quantile matching (QME) and maximum
2398 goodness-of-fit estimation (MGE) methods (available only for non-censored
2399 data). Weighted versions of MLE, MME and QME are available.")
2400 (license license:gpl2+)))
2402 (define-public r-energy
2409 (uri (cran-uri "energy" version))
2412 "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
2413 (build-system r-build-system)
2415 `(("r-boot" ,r-boot)
2416 ("r-rcpp" ,r-rcpp)))
2417 (home-page "https://cran.r-project.org/web/packages/energy")
2418 (synopsis "Multivariate inference via the energy of data")
2420 "This package provides e-statistics (energy) tests and statistics for
2421 multivariate and univariate inference, including distance correlation,
2422 one-sample, two-sample, and multi-sample tests for comparing multivariate
2423 distributions, are implemented. Measuring and testing multivariate
2424 independence based on distance correlation, partial distance correlation,
2425 multivariate goodness-of-fit tests, clustering based on energy distance,
2426 testing for multivariate normality, distance components (disco) for
2427 non-parametric analysis of structured data, and other energy
2428 statistics/methods are implemented.")
2429 (license license:gpl2+)))
2431 (define-public r-suppdists
2433 (name "r-suppdists")
2438 (uri (cran-uri "SuppDists" version))
2441 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2442 (properties `((upstream-name . "SuppDists")))
2443 (build-system r-build-system)
2444 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2445 (synopsis "Supplementary distributions")
2447 "This package provides ten distributions supplementing those built into
2448 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2449 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2450 coefficient, Johnson distributions, normal scores and generalized
2451 hypergeometric distributions. In addition two random number generators of
2452 George Marsaglia are included.")
2453 (license license:gpl2+)))
2455 (define-public r-ksamples
2462 (uri (cran-uri "kSamples" version))
2465 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2466 (properties `((upstream-name . "kSamples")))
2467 (build-system r-build-system)
2469 `(("r-suppdists" ,r-suppdists)))
2470 (home-page "https://cran.r-project.org/web/packages/kSamples")
2471 (synopsis "K-Sample rank tests and their combinations")
2473 "This package provides tools to compares k samples using the
2474 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2475 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2476 test. It computes asymptotic, simulated or (limited) exact P-values, all
2477 valid under randomization, with or without ties, or conditionally under random
2478 sampling from populations, given the observed tie pattern. Except for Steel's
2479 test and the JT test it also combines these tests across several blocks of
2481 (license license:gpl2+)))
2483 (define-public r-cvst
2490 (uri (cran-uri "CVST" version))
2493 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2494 (properties `((upstream-name . "CVST")))
2495 (build-system r-build-system)
2497 `(("r-kernlab" ,r-kernlab)
2498 ("r-matrix" ,r-matrix)))
2499 (home-page "https://cran.r-project.org/web/packages/CVST")
2500 (synopsis "Fast cross-validation via sequential testing")
2502 "This package implements the fast cross-validation via sequential
2503 testing (CVST) procedure. CVST is an improved cross-validation procedure
2504 which uses non-parametric testing coupled with sequential analysis to
2505 determine the best parameter set on linearly increasing subsets of the data.
2506 Additionally to the CVST the package contains an implementation of the
2507 ordinary k-fold cross-validation with a flexible and powerful set of helper
2508 objects and methods to handle the overall model selection process. The
2509 implementations of the Cochran's Q test with permutations and the sequential
2510 testing framework of Wald are generic and can therefore also be used in other
2512 (license license:gpl2+)))
2514 (define-public r-squarem
2517 (version "2017.10-1")
2521 (uri (cran-uri "SQUAREM" version))
2524 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2525 (properties `((upstream-name . "SQUAREM")))
2526 (build-system r-build-system)
2527 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2528 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2530 "This package provides algorithms for accelerating the convergence of
2531 slow, monotone sequences from smooth, contraction mapping such as the EM
2532 algorithm. It can be used to accelerate any smooth, linearly convergent
2533 acceleration scheme. A tutorial style introduction to this package is
2534 available in a vignette.")
2535 (license license:gpl2+)))
2537 (define-public r-lava
2544 (uri (cran-uri "lava" version))
2547 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2548 (build-system r-build-system)
2550 `(("r-numderiv" ,r-numderiv)
2551 ("r-squarem" ,r-squarem)
2552 ("r-survival" ,r-survival)))
2553 (home-page "https://github.com/kkholst/lava")
2554 (synopsis "Latent variable models")
2556 "This package provides tools for the estimation and simulation of latent
2558 (license license:gpl3)))
2560 (define-public r-drr
2567 (uri (cran-uri "DRR" version))
2570 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2571 (properties `((upstream-name . "DRR")))
2572 (build-system r-build-system)
2574 `(("r-cvst" ,r-cvst)
2575 ("r-kernlab" ,r-kernlab)
2576 ("r-matrix" ,r-matrix)))
2577 (home-page "https://cran.r-project.org/web/packages/DRR")
2578 (synopsis "Dimensionality reduction via regression")
2580 "This package provides an implementation of dimensionality reduction via
2581 regression using Kernel Ridge Regression.")
2582 (license license:gpl3)))
2584 (define-public r-prodlim
2587 (version "2018.04.18")
2591 (uri (cran-uri "prodlim" version))
2594 "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb"))))
2595 (build-system r-build-system)
2597 `(("r-kernsmooth" ,r-kernsmooth)
2600 ("r-survival" ,r-survival)))
2601 (home-page "https://cran.r-project.org/web/packages/prodlim")
2602 (synopsis "Product-limit estimation for censored event history analysis")
2604 "This package provides a fast and user-friendly implementation of
2605 nonparametric estimators for censored event history (survival) analysis with
2606 the Kaplan-Meier and Aalen-Johansen methods.")
2607 (license license:gpl2+)))
2609 (define-public r-dimred
2616 (uri (cran-uri "dimRed" version))
2619 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2620 (properties `((upstream-name . "dimRed")))
2621 (build-system r-build-system)
2624 ("r-magrittr" ,r-magrittr)))
2625 (home-page "https://github.com/gdkrmr/dimRed")
2626 (synopsis "Framework for dimensionality reduction")
2628 "This package provides a collection of dimensionality reduction
2629 techniques from R packages and provides a common interface for calling the
2631 (license license:gpl3)))
2633 (define-public r-timedate
2636 (version "3043.102")
2640 (uri (cran-uri "timeDate" version))
2643 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2644 (properties `((upstream-name . "timeDate")))
2645 (build-system r-build-system)
2646 (home-page "https://www.rmetrics.org")
2647 (synopsis "Chronological and calendar objects")
2649 "This package provides an environment for teaching \"Financial
2650 Engineering and Computational Finance\" and for managing chronological and
2652 (license license:gpl2+)))
2654 (define-public r-magic
2661 (uri (cran-uri "magic" version))
2664 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2665 (build-system r-build-system)
2667 `(("r-abind" ,r-abind)))
2668 (home-page "https://github.com/RobinHankin/magic.git")
2669 (synopsis "Create and investigate magic squares")
2671 "This package provides a collection of efficient, vectorized algorithms
2672 for the creation and investigation of magic squares and hypercubes, including
2673 a variety of functions for the manipulation and analysis of arbitrarily
2674 dimensioned arrays.")
2675 (license license:gpl2)))
2677 (define-public r-rmysql
2684 (uri (cran-uri "RMySQL" version))
2687 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2688 (properties `((upstream-name . "RMySQL")))
2689 (build-system r-build-system)
2691 `(("mariadb" ,mariadb "lib")
2692 ("mariadb-dev" ,mariadb "dev")
2695 `(("r-dbi" ,r-dbi)))
2696 (home-page "https://github.com/r-dbi/RMySQL")
2697 (synopsis "Database interface and MySQL driver for R")
2699 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2700 package contains an old implementation based on legacy code from S-PLUS which
2701 is being phased out. A modern MySQL client based on Rcpp is available from
2702 the RMariaDB package.")
2703 (license license:gpl2)))
2705 (define-public r-rpostgresql
2707 (name "r-rpostgresql")
2712 (uri (cran-uri "RPostgreSQL" version))
2715 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2716 (properties `((upstream-name . "RPostgreSQL")))
2717 (build-system r-build-system)
2719 `(("postgresql" ,postgresql)))
2721 `(("r-dbi" ,r-dbi)))
2722 (home-page "https://github.com/tomoakin/RPostgreSQL")
2723 (synopsis "R interface to the PostgreSQL database system")
2725 "This package provides a Database Interface (DBI) compliant driver for R
2726 to access PostgreSQL database systems.")
2727 ;; The whole package is released under GPL version 2. It includes code
2728 ;; under the PostgreSQL license.
2729 (license license:gpl2)))
2731 (define-public r-linprog
2738 (uri (cran-uri "linprog" version))
2741 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2742 (build-system r-build-system)
2743 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2744 (home-page "http://linprog.r-forge.r-project.org/")
2745 (synopsis "Linear programming and optimization")
2747 "This package can be used to solve Linear Programming / Linear
2748 Optimization problems by using the simplex algorithm.")
2749 (license license:gpl2+)))
2751 (define-public r-geometry
2758 (uri (cran-uri "geometry" version))
2761 "1mx5n5mw63nij4n6crs9165mlls4fnh1ipw5ch467rjsidgl0mg8"))))
2762 (build-system r-build-system)
2764 `(("r-magic" ,r-magic)
2765 ("r-linprog" ,r-linprog)
2766 ("r-lpsolve" ,r-lpsolve)
2768 ("r-rcppprogress" ,r-rcppprogress)))
2769 (home-page "http://geometry.r-forge.r-project.org/")
2770 (synopsis "Mesh generation and surface tesselation")
2772 "This package makes the qhull library available in R, in a similar manner
2773 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2774 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2775 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2776 and higher dimensions. It implements the Quickhull algorithm for computing
2777 the convex hull. Qhull does not support constrained Delaunay triangulations,
2778 or mesh generation of non-convex objects, but the package does include some R
2779 functions that allow for this. Currently the package only gives access to
2780 Delaunay triangulation and convex hull computation.")
2781 ;; The Qhull sources are included and are distributed under a custom
2782 ;; non-copyleft license. The R sources are released under GPL version 2.
2783 (license (list license:gpl2
2784 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2786 (define-public r-ddalpha
2793 (uri (cran-uri "ddalpha" version))
2796 "1vzs0cvl6xw3h9i00rg3hs02xwgxcnh8326y10kxmhs3qq4m7nb2"))))
2797 (build-system r-build-system)
2800 ("r-class" ,r-class)
2801 ("r-geometry" ,r-geometry)
2804 ("r-robustbase" ,r-robustbase)
2805 ("r-sfsmisc" ,r-sfsmisc)))
2807 `(("gfortran" ,gfortran)))
2808 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2809 (synopsis "Depth-Based classification and calculation of data depth")
2811 "This package contains procedures for depth-based supervised learning,
2812 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2813 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2814 statistical depth function to a compact low-dimensional space, where the final
2815 classification is done. It also offers an extension to functional data and
2816 routines for calculating certain notions of statistical depth functions. 50
2817 multivariate and 5 functional classification problems are included.")
2818 (license license:gpl2)))
2820 (define-public r-gower
2827 (uri (cran-uri "gower" version))
2830 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2831 (build-system r-build-system)
2832 (home-page "https://github.com/markvanderloo/gower")
2833 (synopsis "Gower's distance")
2835 "This package provides tools to compute Gower's distance (or similarity)
2836 coefficient between records, and to compute the top-n matches between records.
2837 Core algorithms are executed in parallel on systems supporting OpenMP.")
2838 (license license:gpl3)))
2840 (define-public r-rcpproll
2847 (uri (cran-uri "RcppRoll" version))
2850 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2851 (properties `((upstream-name . "RcppRoll")))
2852 (build-system r-build-system)
2854 `(("r-rcpp" ,r-rcpp)))
2855 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2856 (synopsis "Efficient rolling and windowed operations")
2858 "This package provides fast and efficient routines for common rolling /
2859 windowed operations. Routines for the efficient computation of windowed mean,
2860 median, sum, product, minimum, maximum, standard deviation and variance are
2862 (license license:gpl2+)))
2864 (define-public r-ipred
2871 (uri (cran-uri "ipred" version))
2874 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2875 (build-system r-build-system)
2877 `(("r-class" ,r-class)
2880 ("r-prodlim" ,r-prodlim)
2881 ("r-rpart" ,r-rpart)
2882 ("r-survival" ,r-survival)))
2883 (home-page "https://cran.r-project.org/web/packages/ipred")
2884 (synopsis "Improved predictors")
2886 "This package provides improved predictive models by indirect
2887 classification and bagging for classification, regression and survival
2888 problems as well as resampling based estimators of prediction error.")
2889 (license license:gpl2+)))
2891 (define-public r-psych
2898 (uri (cran-uri "psych" version))
2901 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
2902 (build-system r-build-system)
2904 `(("r-foreign" ,r-foreign)
2905 ("r-lattice" ,r-lattice)
2906 ("r-mnormt" ,r-mnormt)
2907 ("r-nlme" ,r-nlme)))
2908 (home-page "https://cran.r-project.org/web/packages/psych/")
2909 (synopsis "Procedures for psychological, psychometric, and personality research")
2911 "This package provides a general purpose toolbox for personality,
2912 psychometric theory and experimental psychology. Functions are primarily for
2913 multivariate analysis and scale construction using factor analysis, principal
2914 component analysis, cluster analysis and reliability analysis, although others
2915 provide basic descriptive statistics. Item Response Theory is done using
2916 factor analysis of tetrachoric and polychoric correlations. Functions for
2917 analyzing data at multiple levels include within and between group statistics,
2918 including correlations and factor analysis. Functions for simulating and
2919 testing particular item and test structures are included. Several functions
2920 serve as a useful front end for structural equation modeling. Graphical
2921 displays of path diagrams, factor analysis and structural equation models are
2922 created using basic graphics.")
2923 (license license:gpl2+)))
2925 (define-public r-generics
2932 (uri (cran-uri "generics" version))
2935 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
2936 (build-system r-build-system)
2937 (home-page "https://github.com/r-lib/generics")
2938 (synopsis "Common S3 generics not provided by base R methods")
2940 "In order to reduce potential package dependencies and conflicts,
2941 generics provides a number of commonly used S3 generics that are not provided
2942 by base R methods related to model fitting.")
2943 (license license:gpl2)))
2945 (define-public r-broom
2952 (uri (cran-uri "broom" version))
2955 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
2956 (build-system r-build-system)
2958 `(("r-backports" ,r-backports)
2959 ("r-dplyr" ,r-dplyr)
2960 ("r-generics" ,r-generics)
2962 ("r-purrr" ,r-purrr)
2963 ("r-reshape2" ,r-reshape2)
2964 ("r-stringr" ,r-stringr)
2965 ("r-tibble" ,r-tibble)
2966 ("r-tidyr" ,r-tidyr)))
2967 (home-page "https://github.com/tidyverse/broom")
2968 (synopsis "Convert statistical analysis objects into tidy data frames")
2970 "This package provides tools to convert statistical analysis objects from
2971 R into tidy data frames, so that they can more easily be combined, reshaped
2972 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
2973 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
2974 summarizes a model's statistical findings such as coefficients of a
2975 regression; @code{augment}, which adds columns to the original data such as
2976 predictions, residuals and cluster assignments; and @code{glance}, which
2977 provides a one-row summary of model-level statistics.")
2978 (license license:expat)))
2980 (define-public r-recipes
2987 (uri (cran-uri "recipes" version))
2990 "1gw8x7vqj7k18mfpiqinyfwzv9i5r0pb51k7xcfxsjap6m9nks98"))))
2991 (build-system r-build-system)
2993 `(("r-dplyr" ,r-dplyr)
2994 ("r-generics" ,r-generics)
2996 ("r-gower" ,r-gower)
2997 ("r-ipred" ,r-ipred)
2998 ("r-lubridate" ,r-lubridate)
2999 ("r-magrittr" ,r-magrittr)
3000 ("r-matrix" ,r-matrix)
3001 ("r-purrr" ,r-purrr)
3002 ("r-rlang" ,r-rlang)
3003 ("r-tibble" ,r-tibble)
3004 ("r-tidyr" ,r-tidyr)
3005 ("r-tidyselect" ,r-tidyselect)
3006 ("r-timedate" ,r-timedate)
3007 ("r-withr" ,r-withr)))
3008 (home-page "https://github.com/topepo/recipes")
3009 (synopsis "Preprocessing tools to create design matrices")
3011 "Recipes is an extensible framework to create and preprocess design
3012 matrices. Recipes consist of one or more data manipulation and analysis
3013 \"steps\". Statistical parameters for the steps can be estimated from an
3014 initial data set and then applied to other data sets. The resulting design
3015 matrices can then be used as inputs into statistical or machine learning
3017 (license license:gpl2)))
3019 (define-public r-pdist
3026 (uri (cran-uri "pdist" version))
3029 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3030 (build-system r-build-system)
3031 (home-page "https://github.com/jeffwong/pdist")
3032 (synopsis "Partitioned distance function")
3034 "Pdist computes the euclidean distance between rows of a matrix X and
3035 rows of another matrix Y. Previously, this could be done by binding the two
3036 matrices together and calling @code{dist}, but this creates unnecessary
3037 computation by computing the distances between a row of X and another row of
3038 X, and likewise for Y. Pdist strictly computes distances across the two
3039 matrices, not within the same matrix, making computations significantly faster
3040 for certain use cases.")
3041 (license license:gpl3+)))
3043 (define-public r-ggrepel
3050 (uri (cran-uri "ggrepel" version))
3053 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
3054 (build-system r-build-system)
3056 `(("r-ggplot2" ,r-ggplot2)
3058 ("r-scales" ,r-scales)))
3059 (home-page "http://github.com/slowkow/ggrepel")
3060 (synopsis "Repulsive text and label geometries for ggplot2")
3062 "This package provides text and label geometries for ggplot2 that help to
3063 avoid overlapping text labels. Labels repel away from each other and away
3064 from the data points.")
3065 (license license:gpl3)))
3067 (define-public r-corrplot
3074 (uri (cran-uri "corrplot" version))
3077 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3078 (build-system r-build-system)
3079 (home-page "https://github.com/taiyun/corrplot")
3080 (synopsis "Visualization of a correlation matrix")
3082 "This package provides a graphical display of a correlation matrix or
3083 general matrix. It also contains some algorithms to do matrix reordering. In
3084 addition, corrplot is good at details, including choosing color, text labels,
3085 color labels, layout, etc.")
3086 ;; Any version of the GPL
3087 (license license:gpl2+)))
3089 (define-public r-stringdist
3091 (name "r-stringdist")
3096 (uri (cran-uri "stringdist" version))
3098 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3099 (build-system r-build-system)
3100 (home-page "https://github.com/markvanderloo/stringdist")
3101 (synopsis "Approximate string matching and string distance functions")
3103 "This package implements an approximate string matching version of R's
3104 native @code{match} function. It can calculate various string distances based
3105 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3106 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3107 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3108 can be computed between character vectors while taking proper care of encoding
3109 or between integer vectors representing generic sequences.")
3110 (license license:gpl3+)))
3112 (define-public r-ucminf
3119 (uri (cran-uri "ucminf" version))
3122 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3123 (build-system r-build-system)
3124 (native-inputs `(("gfortran" ,gfortran)))
3125 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3126 (synopsis "General-purpose unconstrained non-linear optimization")
3128 "This package provides an implementation of an algorithm for
3129 general-purpose unconstrained non-linear optimization. The algorithm is of
3130 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3131 search with a trust region type monitoring of the input to the line search
3132 algorithm. The interface of @code{ucminf} is designed for easy interchange
3133 with the package @code{optim}.")
3134 (license license:gpl2+)))
3136 (define-public r-ordinal
3139 (version "2019.4-25")
3143 (uri (cran-uri "ordinal" version))
3146 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
3147 (build-system r-build-system)
3149 `(("r-mass" ,r-mass)
3150 ("r-matrix" ,r-matrix)
3151 ("r-numderiv" ,r-numderiv)
3152 ("r-ucminf" ,r-ucminf)))
3153 (home-page "https://github.com/runehaubo/ordinal")
3154 (synopsis "Regression models for ordinal data")
3156 "This package provides an implementation of cumulative link (mixed)
3157 models also known as ordered regression models, proportional odds models,
3158 proportional hazards models for grouped survival times and ordered models.
3159 Estimation is via maximum likelihood and mixed models are fitted with the
3160 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3161 (license license:gpl2+)))
3163 (define-public r-jomo
3170 (uri (cran-uri "jomo" version))
3173 "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr"))))
3174 (build-system r-build-system)
3176 `(("r-lme4" ,r-lme4)
3178 ("r-ordinal" ,r-ordinal)
3179 ("r-survival" ,r-survival)))
3180 (home-page "https://cran.r-project.org/web/packages/jomo/")
3181 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3183 "Similarly to Schafer's package pan, jomo is a package for multilevel
3184 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3185 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3186 possibility of handling binary and categorical data through latent normal
3187 variables, the option to use cluster-specific covariance matrices and to
3188 impute compatibly with the substantive model.")
3189 (license license:gpl2)))
3191 (define-public r-pan
3198 (uri (cran-uri "pan" version))
3201 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3202 (build-system r-build-system)
3203 (native-inputs `(("gfortran" ,gfortran)))
3204 (home-page "https://cran.r-project.org/web/packages/pan/")
3205 (synopsis "Multiple imputation for multivariate panel or clustered data")
3207 "This package implements multiple imputation for multivariate panel or
3209 (license license:gpl3)))
3211 (define-public r-mitml
3218 (uri (cran-uri "mitml" version))
3221 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3222 (build-system r-build-system)
3224 `(("r-haven" ,r-haven)
3227 (home-page "https://cran.r-project.org/web/packages/mitml/")
3228 (synopsis "Tools for multiple imputation in multilevel modeling")
3230 "This package provides tools for multiple imputation of missing data in
3231 multilevel modeling. It includes a user-friendly interface to the packages
3232 pan and jomo, and several functions for visualization, data management and the
3233 analysis of multiply imputed data sets.")
3234 (license license:gpl2+)))
3236 (define-public r-mice
3243 (uri (cran-uri "mice" version))
3246 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
3247 (build-system r-build-system)
3249 `(("r-broom" ,r-broom)
3250 ("r-dplyr" ,r-dplyr)
3251 ("r-lattice" ,r-lattice)
3253 ("r-mitml" ,r-mitml)
3256 ("r-rlang" ,r-rlang)
3257 ("r-rpart" ,r-rpart)
3258 ("r-survival" ,r-survival)))
3259 (home-page "https://cran.r-project.org/web/packages/mice/")
3260 (synopsis "Multivariate imputation by chained equations")
3262 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3263 implemented by the MICE algorithm as described in @url{Van Buuren and
3264 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3265 variable has its own imputation model. Built-in imputation models are
3266 provided for continuous data (predictive mean matching, normal), binary
3267 data (logistic regression), unordered categorical data (polytomous logistic
3268 regression) and ordered categorical data (proportional odds). MICE can also
3269 impute continuous two-level data (normal model, pan, second-level variables).
3270 Passive imputation can be used to maintain consistency between variables.
3271 Various diagnostic plots are available to inspect the quality of the
3273 ;; Any of these two versions.
3274 (license (list license:gpl2 license:gpl3))))
3276 (define-public r-truncnorm
3278 (name "r-truncnorm")
3283 (uri (cran-uri "truncnorm" version))
3286 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3287 (build-system r-build-system)
3288 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3289 (synopsis "Truncated normal distribution")
3290 (description "This package provides functions for the truncated normal
3291 distribution with mean equal to @code{mean} and standard deviation equal to
3292 @code{sd}. It includes density, distribution, quantile, and expected value
3293 functions, as well as a random generation function.")
3294 (license license:gpl2)))
3296 (define-public r-rsolnp
3303 (uri (cran-uri "Rsolnp" version))
3306 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3307 (properties `((upstream-name . "Rsolnp")))
3308 (build-system r-build-system)
3310 `(("r-truncnorm" ,r-truncnorm)))
3311 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3312 (synopsis "General non-linear optimization")
3313 (description "The Rsolnp package implements a general non-linear augmented
3314 Lagrange multiplier method solver, a @dfn{sequential quadratic
3315 programming} (SQP) based solver).")
3316 ;; Any version of the GPL.
3317 (license license:gpl2+)))
3319 (define-public r-hardyweinberg
3321 (name "r-hardyweinberg")
3326 (uri (cran-uri "HardyWeinberg" version))
3329 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3330 (properties `((upstream-name . "HardyWeinberg")))
3331 (build-system r-build-system)
3333 `(("r-mice" ,r-mice)
3335 ("r-rsolnp" ,r-rsolnp)))
3336 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3337 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3339 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3340 diallelic genetic marker data. All classical tests (chi-square, exact,
3341 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3342 included in the package, as well as functions for power computation and for
3343 the simulation of marker data under equilibrium and disequilibrium. Routines
3344 for dealing with markers on the X-chromosome are included. Functions for
3345 testing equilibrium in the presence of missing data by using multiple
3346 imputation are also provided. Implements several graphics for exploring the
3347 equilibrium status of a large set of diallelic markers: ternary plots with
3348 acceptance regions, log-ratio plots and Q-Q plots.")
3349 (license license:gpl2+)))
3358 (uri (cran-uri "sm" version))
3361 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3362 (build-system r-build-system)
3363 (native-inputs `(("gfortran" ,gfortran)))
3364 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3365 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3367 "This is software accompanying the book 'Applied Smoothing Techniques for
3368 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3369 University Press. It provides smoothing methods for nonparametric regression
3370 and density estimation")
3371 (license license:gpl2+)))
3373 (define-public r-venndiagram
3375 (name "r-venndiagram")
3379 (uri (cran-uri "VennDiagram" version))
3382 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3383 (properties `((upstream-name . "VennDiagram")))
3384 (build-system r-build-system)
3386 `(("r-futile-logger" ,r-futile-logger)))
3387 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3388 (synopsis "Generate High-Resolution Venn and Euler Plots")
3390 "This package provides a set of functions to generate high-resolution
3391 Venn and Euler plots. It includes handling for several special cases,
3392 including two-case scaling, and extensive customization of plot shape and
3394 (license license:gpl2+)))
3396 (define-public r-vioplot
3403 (uri (cran-uri "vioplot" version))
3406 "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv"))))
3407 (build-system r-build-system)
3411 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3412 (synopsis "Violin plot")
3414 "This package provides a violin plot, which is a combination of a box
3415 plot and a kernel density plot.")
3416 (license license:bsd-3)))
3418 (define-public r-rsofia
3424 ;; This package has been removed from CRAN, so we can
3425 ;; only fetch it from the archives.
3426 (uri (string-append "https://cran.r-project.org/src/"
3427 "contrib/Archive/RSofia/RSofia_"
3431 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3432 (properties `((upstream-name . "RSofia")))
3433 (build-system r-build-system)
3435 `(("r-rcpp" ,r-rcpp)))
3436 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3437 (synopsis "Port of sofia-ml to R")
3438 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3439 suite of fast incremental algorithms for machine learning that can be used for
3440 training models for classification or ranking.")
3441 (license license:asl2.0)))
3443 (define-public r-xts
3450 (uri (cran-uri "xts" version))
3453 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3454 (build-system r-build-system)
3455 (propagated-inputs `(("r-zoo" ,r-zoo)))
3456 (home-page "https://github.com/joshuaulrich/xts")
3457 (synopsis "Extensible time series")
3459 "This package provides for uniform handling of R's different time-based
3460 data classes by extending @code{zoo}, maximizing native format information
3461 preservation and allowing for user-level customization and extension, while
3462 simplifying cross-class interoperability.")
3463 (license license:gpl2+)))
3465 (define-public r-performanceanalytics
3467 (name "r-performanceanalytics")
3472 (uri (cran-uri "PerformanceAnalytics" version))
3475 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3477 `((upstream-name . "PerformanceAnalytics")))
3478 (build-system r-build-system)
3480 `(("r-quadprog" ,r-quadprog)
3483 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3484 (synopsis "Econometric tools for performance and risk analysis")
3485 (description "This is a collection of econometric functions for
3486 performance and risk analysis. This package aims to aid practitioners and
3487 researchers in utilizing the latest research in analysis of non-normal return
3488 streams. In general, it is most tested on return (rather than price) data on
3489 a regular scale, but most functions will work with irregular return data as
3490 well, and increasing numbers of functions will work with P&L or price data
3492 ;; Either version may be picked.
3493 (license (list license:gpl2 license:gpl3))))
3495 (define-public r-laeken
3502 (uri (cran-uri "laeken" version))
3505 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3506 (build-system r-build-system)
3508 `(("r-boot" ,r-boot)
3509 ("r-mass" ,r-mass)))
3510 (home-page "https://cran.r-project.org/web/packages/laeken/")
3511 (synopsis "Estimation of indicators on social exclusion and poverty")
3512 (description "This package provides tools for the estimation of indicators
3513 on social exclusion and poverty, as well as an implementation of Pareto tail
3514 modeling for empirical income distributions.")
3515 (license license:gpl2+)))
3517 (define-public r-vcd
3524 (uri (cran-uri "vcd" version))
3527 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3528 (build-system r-build-system)
3530 `(("r-colorspace" ,r-colorspace)
3531 ("r-lmtest" ,r-lmtest)
3532 ("r-mass" ,r-mass)))
3533 (home-page "https://cran.r-project.org/web/packages/vcd/")
3534 (synopsis "Visualizing categorical data")
3535 (description "This package provides visualization techniques, data sets,
3536 summary and inference procedures aimed particularly at categorical data.
3537 Special emphasis is given to highly extensible grid graphics. The package was
3538 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3539 Friendly and is now the main support package for a new book, \"Discrete Data
3540 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3541 (license license:gpl2)))
3543 (define-public r-ica
3550 (uri (cran-uri "ica" version))
3553 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3554 (build-system r-build-system)
3555 (home-page "https://cran.r-project.org/web/packages/ica/")
3556 (synopsis "Independent component analysis")
3557 (description "This package provides tools for @dfn{Independent Component
3558 Analysis} (ICA) using various algorithms: FastICA,
3559 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3560 of Eigenmatrices} (JADE).")
3561 (license license:gpl2+)))
3563 (define-public r-dtw
3570 (uri (cran-uri "dtw" version))
3573 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
3574 (build-system r-build-system)
3575 (propagated-inputs `(("r-proxy" ,r-proxy)))
3576 (home-page "http://dtw.r-forge.r-project.org/")
3577 (synopsis "Dynamic Time Warping Algorithms")
3578 (description "This package provides a comprehensive implementation of
3579 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3580 optimal (least cumulative distance) alignment between points of two time
3581 series. Common DTW variants covered include local (slope) and global (window)
3582 constraints, subsequence matches, arbitrary distance definitions,
3583 normalizations, minimum variance matching, and so on.")
3584 (license license:gpl2+)))
3586 (define-public r-sdmtools
3589 (version "1.1-221.1")
3593 (uri (cran-uri "SDMTools" version))
3596 "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q"))))
3597 (properties `((upstream-name . "SDMTools")))
3598 (build-system r-build-system)
3599 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3600 (home-page "http://www.rforge.net/SDMTools/")
3601 (synopsis "Species distribution modelling tools")
3602 (description "This package provides a set of tools for post processing
3603 the outcomes of species distribution modeling exercises. It includes novel
3604 methods for comparing models and tracking changes in distributions through
3605 time. It further includes methods for visualizing outcomes, selecting
3606 thresholds, calculating measures of accuracy and landscape fragmentation
3608 (license license:gpl3+)))
3610 (define-public r-scatterplot3d
3612 (name "r-scatterplot3d")
3617 (uri (cran-uri "scatterplot3d" version))
3620 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3621 (build-system r-build-system)
3622 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3623 (synopsis "3D scatter plot")
3624 (description "This package provides an implementation of scatter plots for
3625 plotting. a three dimensional point cloud.")
3626 (license license:gpl2)))
3628 (define-public r-ggridges
3635 (uri (cran-uri "ggridges" version))
3638 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3639 (build-system r-build-system)
3641 `(("r-ggplot2" ,r-ggplot2)
3643 ("r-scales" ,r-scales)
3644 ("r-withr" ,r-withr)))
3645 (home-page "https://github.com/clauswilke/ggridges")
3646 (synopsis "Ridgeline plots in ggplot2")
3648 "Ridgeline plots provide a convenient way of visualizing changes in
3649 distributions over time or space. This package enables the creation of such
3650 plots in @code{ggplot2}.")
3651 (license license:gpl2)))
3653 (define-public r-ggjoy
3660 (uri (cran-uri "ggjoy" version))
3663 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3664 (build-system r-build-system)
3666 `(("r-ggplot2" ,r-ggplot2)
3667 ("r-ggridges" ,r-ggridges)))
3668 (home-page "https://github.com/clauswilke/ggjoy")
3669 (synopsis "Joyplots in ggplot2")
3670 (description "Joyplots provide a convenient way of visualizing changes in
3671 distributions over time or space. This package enables the creation of such
3672 plots in @code{ggplot2}.")
3673 (license license:gpl2)))
3675 (define-public r-cli
3682 (uri (cran-uri "cli" version))
3685 "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g"))))
3686 (build-system r-build-system)
3688 `(("r-assertthat" ,r-assertthat)
3689 ("r-crayon" ,r-crayon)))
3690 (home-page "https://github.com/r-lib/cli#readme")
3691 (synopsis "Helpers for developing command line interfaces")
3692 (description "This package provides a suite of tools designed to build
3693 attractive command line interfaces (CLIs). It includes tools for drawing
3694 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3695 (license license:expat)))
3697 (define-public r-argparser
3699 (name "r-argparser")
3704 (uri (cran-uri "argparser" version))
3707 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3708 (build-system r-build-system)
3709 (home-page "https://bitbucket.org/djhshih/argparser")
3710 (synopsis "Command-line argument parser")
3712 "This package provides a cross-platform command-line argument parser
3713 written purely in R with no external dependencies. It is useful with the
3714 Rscript front-end and facilitates turning an R script into an executable
3716 (license license:gpl3+)))
3718 (define-public r-debugme
3725 (uri (cran-uri "debugme" version))
3728 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3729 (build-system r-build-system)
3730 (propagated-inputs `(("r-crayon" ,r-crayon)))
3731 (home-page "https://github.com/r-lib/debugme#readme")
3732 (synopsis "Debug R packages")
3734 "This package allows the user to specify debug messages as special string
3735 constants, and control debugging of packages via environment variables.")
3736 (license license:expat)))
3738 (define-public r-processx
3745 (uri (cran-uri "processx" version))
3748 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3749 (build-system r-build-system)
3753 (home-page "https://github.com/r-lib/processx3")
3754 (synopsis "Execute and control system processes")
3756 "This package provides portable tools to run system processes in the
3757 background. It can check if a background process is running; wait on a
3758 background process to finish; get the exit status of finished processes; kill
3759 background processes and their children; restart processes. It can read the
3760 standard output and error of the processes, using non-blocking connections.
3761 @code{processx} can poll a process for standard output or error, with a
3762 timeout. It can also poll several processes at once.")
3763 (license license:expat)))
3765 (define-public r-tsp
3772 (uri (cran-uri "TSP" version))
3775 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3776 (properties `((upstream-name . "TSP")))
3777 (build-system r-build-system)
3778 (propagated-inputs `(("r-foreach" ,r-foreach)))
3779 (home-page "https://cran.r-project.org/web/packages/TSP/")
3780 (synopsis "Traveling salesperson problem (TSP)")
3781 (description "This package provides basic infrastructure and some
3782 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3783 traveling salesman problem).")
3784 (license license:gpl3)))
3786 (define-public r-qap
3793 (uri (cran-uri "qap" version))
3796 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3797 (build-system r-build-system)
3798 (native-inputs `(("gfortran" ,gfortran)))
3799 (home-page "https://cran.r-project.org/web/packages/qap/")
3800 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3801 (description "This package implements heuristics for the @dfn{quadratic
3802 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3804 (license license:gpl3)))
3806 (define-public r-gclus
3813 (uri (cran-uri "gclus" version))
3816 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3817 (build-system r-build-system)
3818 (propagated-inputs `(("r-cluster" ,r-cluster)))
3819 (home-page "https://cran.r-project.org/web/packages/gclus/")
3820 (synopsis "Clustering graphics")
3821 (description "This package orders panels in scatterplot matrices and
3822 parallel coordinate displays by some merit index. It contains various indices
3823 of merit, ordering functions, and enhanced versions of @code{pairs} and
3824 @code{parcoord} which color panels according to their merit level.")
3825 (license license:gpl2+)))
3827 (define-public r-webshot
3834 (uri (cran-uri "webshot" version))
3837 "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr"))))
3838 (build-system r-build-system)
3840 `(("r-callr" ,r-callr)
3841 ("r-jsonlite" ,r-jsonlite)
3842 ("r-magrittr" ,r-magrittr)))
3843 (home-page "https://github.com/wch/webshot/")
3844 (synopsis "Take screenshots of web pages")
3846 "Webshot makes it easy to take screenshots of web pages from within R.
3847 It can also run Shiny applications locally and take screenshots of the
3848 application; and it can render and screenshot static as well as interactive R
3849 Markdown documents.")
3850 (license license:gpl2)))
3852 (define-public r-seriation
3854 (name "r-seriation")
3859 (uri (cran-uri "seriation" version))
3862 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
3863 (build-system r-build-system)
3865 `(("r-cluster" ,r-cluster)
3866 ("r-colorspace" ,r-colorspace)
3867 ("r-dendextend" ,r-dendextend)
3868 ("r-gclus" ,r-gclus)
3869 ("r-gplots" ,r-gplots)
3872 ("r-registry" ,r-registry)
3874 (native-inputs `(("gfortran" ,gfortran)))
3875 (home-page "http://s2.smu.edu/IDA/seriation/")
3876 (synopsis "Infrastructure for ordering objects using seriation")
3878 "This package provides infrastructure for seriation with an
3879 implementation of several seriation/sequencing techniques to reorder matrices,
3880 dissimilarity matrices, and dendrograms. It also provides (optimally)
3881 reordered heatmaps, color images and clustering visualizations like
3882 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3884 (license license:gpl3)))
3886 (define-public r-xfun
3893 (uri (cran-uri "xfun" version))
3895 (base32 "065ygh046ah43p5aqyrkv2vkxcnvnb4j7blfdygysg6hmqzp4pbv"))))
3896 (build-system r-build-system)
3897 (home-page "https://github.com/yihui/xfun")
3898 (synopsis "Miscellaneous functions")
3900 "This package provides miscellaneous functions commonly used in other
3901 packages maintained by Yihui Xie.")
3902 (license license:expat)))
3904 (define-public r-utf8
3911 (uri (cran-uri "utf8" version))
3914 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
3915 (build-system r-build-system)
3916 (home-page "https://github.com/patperry/r-utf8")
3917 (synopsis "Unicode text processing")
3919 "This package provides tools to process and print UTF-8 encoded
3920 international text (Unicode). Input, validate, normalize, encode, format, and
3922 (license license:asl2.0)))
3924 (define-public r-zeallot
3931 (uri (cran-uri "zeallot" version))
3934 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
3935 (build-system r-build-system)
3936 (home-page "https://github.com/nteetor/zeallot")
3937 (synopsis "Multiple, unpacking, and destructuring assignment")
3939 "This package provides a @code{%<-%} operator to perform multiple,
3940 unpacking, and destructuring assignment in R. The operator unpacks the
3941 right-hand side of an assignment into multiple values and assigns these values
3942 to variables on the left-hand side of the assignment.")
3943 (license license:expat)))
3945 (define-public r-vctrs
3952 (uri (cran-uri "vctrs" version))
3955 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
3956 (build-system r-build-system)
3958 `(("r-backports" ,r-backports)
3959 ("r-digest" ,r-digest)
3960 ("r-ellipsis" ,r-ellipsis)
3962 ("r-rlang" ,r-rlang)
3963 ("r-zeallot" ,r-zeallot)))
3964 (home-page "https://github.com/r-lib/vctrs")
3965 (synopsis "Vector helpers")
3967 "There are three main goals to the @code{vctrs} package:
3970 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
3971 @code{length()} and @code{class()}. These definitions are paired with a
3972 framework for type-coercion and size-recycling.
3973 @item To define type- and size-stability as desirable function properties, use
3974 them to analyse existing base function, and to propose better alternatives.
3975 This work has been particularly motivated by thinking about the ideal
3976 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
3977 @item To provide a new @code{vctr} base class that makes it easy to create new
3978 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
3979 a few new @code{vctrs} generics, making implementation considerably simpler
3982 (license license:gpl3)))
3984 (define-public r-pillar
3991 (uri (cran-uri "pillar" version))
3994 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
3995 (build-system r-build-system)
3998 ("r-crayon" ,r-crayon)
3999 ("r-fansi" ,r-fansi)
4000 ("r-rlang" ,r-rlang)
4002 ("r-vctrs" ,r-vctrs)))
4003 (home-page "https://github.com/r-lib/pillar")
4004 (synopsis "Coloured formatting for columns")
4006 "This package provides a @code{pillar} generic designed for formatting
4007 columns of data using the full range of colours provided by modern
4009 (license license:gpl3)))
4011 (define-public r-uuid
4018 (uri (cran-uri "uuid" version))
4021 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
4022 (build-system r-build-system)
4023 (home-page "http://www.rforge.net/uuid")
4024 (synopsis "Tools for generating and handling of UUIDs")
4026 "This package provides tools for generating and handling of
4027 @dfn{Universally Unique Identifiers} (UUIDs).")
4028 (license license:expat)))
4030 (define-public r-tinytex
4037 (uri (cran-uri "tinytex" version))
4040 "1dadq9l0527v038b1k1dyfs0dklsgxnmplls3qhqprfgskif8mga"))))
4041 (build-system r-build-system)
4043 `(("r-xfun" ,r-xfun)))
4044 (home-page "https://github.com/yihui/tinytex")
4045 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4047 "This package provides helper functions to install and maintain the LaTeX
4048 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4049 easy-to-maintain version of TeX Live. This package also contains helper
4050 functions to compile LaTeX documents, and install missing LaTeX packages
4052 (license license:expat)))
4054 (define-public r-metap
4061 (uri (cran-uri "metap" version))
4064 "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0"))))
4065 (build-system r-build-system)
4067 `(("r-lattice" ,r-lattice)
4068 ("r-rdpack" ,r-rdpack)))
4069 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
4070 (synopsis "Meta-analysis of significance values")
4072 "The canonical way to perform meta-analysis involves using effect sizes.
4073 When they are not available this package provides a number of methods for
4074 meta-analysis of significance values including the methods of Edgington,
4075 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
4076 published results; and a routine for graphical display.")
4077 (license license:gpl2)))
4079 (define-public r-network
4086 (uri (cran-uri "network" version))
4089 "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
4090 (build-system r-build-system)
4092 `(("r-magrittr" ,r-magrittr)
4093 ("r-tibble" ,r-tibble)))
4094 (home-page "https://statnet.org/")
4095 (synopsis "Classes for relational data")
4097 "This package provides tools to create and modify network objects. The
4098 @code{network} class can represent a range of relational data types, and
4099 supports arbitrary vertex/edge/graph attributes.")
4100 (license license:gpl2+)))
4102 (define-public r-statnet-common
4104 (name "r-statnet-common")
4109 (uri (cran-uri "statnet.common" version))
4112 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4114 `((upstream-name . "statnet.common")))
4115 (build-system r-build-system)
4117 `(("r-coda" ,r-coda)))
4118 (home-page "https://statnet.org")
4119 (synopsis "R scripts and utilities used by the Statnet software")
4120 (description "This package provides non-statistical utilities used by the
4121 software developed by the Statnet Project.")
4122 (license license:gpl3)))
4124 (define-public r-sna
4131 (uri (cran-uri "sna" version))
4134 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
4135 (build-system r-build-system)
4137 `(("r-network" ,r-network)
4138 ("r-statnet-common" ,r-statnet-common)))
4139 (home-page "https://statnet.org")
4140 (synopsis "Tools for social network analysis")
4142 "This package provides a range of tools for social network analysis,
4143 including node and graph-level indices, structural distance and covariance
4144 methods, structural equivalence detection, network regression, random graph
4145 generation, and 2D/3D network visualization.")
4146 (license license:gpl2+)))
4148 (define-public r-ttr
4155 (uri (cran-uri "TTR" version))
4158 "0fxipnyxaz55n4camrk9cs71x9w4dsmjrihysv8i1s6khf825rg6"))))
4159 (properties `((upstream-name . "TTR")))
4160 (build-system r-build-system)
4162 `(("r-curl" ,r-curl)
4165 (home-page "https://github.com/joshuaulrich/TTR")
4166 (synopsis "Technical trading rules")
4168 "This package provides functions and data to construct technical trading
4170 (license license:gpl2)))
4172 (define-public r-leaps
4179 (uri (cran-uri "leaps" version))
4182 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4183 (build-system r-build-system)
4184 (native-inputs `(("gfortran" ,gfortran)))
4185 (home-page "https://cran.r-project.org/web/packages/leaps/")
4186 (synopsis "Regression subset selection")
4188 "This package provides tools for regression subset selection, including
4189 exhaustive search.")
4190 (license license:gpl2+)))
4192 (define-public r-splus2r
4199 (uri (cran-uri "splus2R" version))
4202 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4203 (properties `((upstream-name . "splus2R")))
4204 (build-system r-build-system)
4205 (native-inputs `(("gfortran" ,gfortran)))
4206 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4207 (synopsis "Supplemental S-PLUS functionality in R")
4209 "Currently there are many functions in S-PLUS that are missing in R. To
4210 facilitate the conversion of S-PLUS packages to R packages, this package
4211 provides some missing S-PLUS functionality in R.")
4212 (license license:gpl2)))
4214 (define-public r-ifultools
4216 (name "r-ifultools")
4221 (uri (cran-uri "ifultools" version))
4224 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4225 (build-system r-build-system)
4227 `(("r-mass" ,r-mass)
4228 ("r-splus2r" ,r-splus2r)))
4229 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4230 (synopsis "Insightful research tools")
4231 (description "This package provides C code used by the wmtsa, fractal, and
4233 (license license:gpl2)))
4235 (define-public r-sapa
4242 (uri (cran-uri "sapa" version))
4245 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4246 (build-system r-build-system)
4248 `(("r-ifultools" ,r-ifultools)
4249 ("r-splus2r" ,r-splus2r)))
4250 (home-page "https://cran.r-project.org/web/packages/sapa/")
4251 (synopsis "Spectral analysis for physical applications")
4252 (description "This package provides software for the book Spectral
4253 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4254 Cambridge University Press, 1993.")
4255 (license license:gpl2)))
4257 (define-public r-aggregation
4259 (name "r-aggregation")
4264 (uri (cran-uri "aggregation" version))
4267 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4268 (build-system r-build-system)
4269 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4270 (synopsis "Methods for p-value aggregation")
4272 "This package contains functionality for performing the following methods
4273 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4274 Fisher's method), and Sidak correction.")
4275 (license license:gpl3)))
4277 (define-public r-quantmod
4284 (uri (cran-uri "quantmod" version))
4287 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4288 (build-system r-build-system)
4290 `(("r-curl" ,r-curl)
4294 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4295 (synopsis "Quantitative financial modelling framework")
4296 (description "This package provides a quantitative financial modelling
4297 framework to allow users to specify, build, trade, and analyse quantitative
4298 financial trading strategies.")
4299 (license license:gpl3)))
4301 (define-public r-tseries
4308 (uri (cran-uri "tseries" version))
4311 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4312 (build-system r-build-system)
4314 `(("r-quadprog" ,r-quadprog)
4315 ("r-quantmod" ,r-quantmod)
4318 `(("gfortran" ,gfortran)))
4319 (home-page "https://cran.r-project.org/web/packages/tseries/")
4320 (synopsis "Time series analysis and computational finance")
4322 "This package provides functions relating to time series analysis and
4323 computational finance.")
4324 (license license:gpl2)))
4326 (define-public r-wmtsa
4333 (uri (cran-uri "wmtsa" version))
4336 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4337 (build-system r-build-system)
4339 `(("r-ifultools" ,r-ifultools)
4341 ("r-splus2r" ,r-splus2r)))
4342 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4343 (synopsis "Wavelet methods for time series analysis")
4345 "This package provides software to accompany the book \"Wavelet Methods
4346 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4347 University Press, 2000.")
4348 (license license:gpl2)))
4350 (define-public r-tsa
4357 (uri (cran-uri "TSA" version))
4360 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4361 (properties `((upstream-name . "TSA")))
4362 (build-system r-build-system)
4364 `(("r-leaps" ,r-leaps)
4365 ("r-locfit" ,r-locfit)
4366 ("r-mgcv" ,r-mgcv)))
4367 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4368 (synopsis "Time series analysis")
4370 "This package contains R functions and datasets detailed in the book
4371 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4372 Cryer and Kung-Sik Chan.")
4373 (license license:gpl2+)))
4375 (define-public r-extradistr
4377 (name "r-extradistr")
4382 (uri (cran-uri "extraDistr" version))
4385 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4386 (properties `((upstream-name . "extraDistr")))
4387 (build-system r-build-system)
4389 `(("r-rcpp" ,r-rcpp)))
4390 (home-page "https://github.com/twolodzko/extraDistr")
4391 (synopsis "Additional univariate and multivariate distributions")
4393 "This package implements density, distribution functions, quantile
4394 functions and random generation functions for a large number of univariate and
4395 multivariate distributions.")
4396 (license license:gpl2)))
4398 (define-public r-fractal
4405 (uri (cran-uri "fractal" version))
4408 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4409 (build-system r-build-system)
4411 `(("r-ifultools" ,r-ifultools)
4414 ("r-scatterplot3d" ,r-scatterplot3d)
4415 ("r-splus2r" ,r-splus2r)
4416 ("r-wmtsa" ,r-wmtsa)))
4417 (home-page "https://cran.r-project.org/web/packages/fractal/")
4418 (synopsis "Fractal time series modeling and analysis")
4420 "This package provides tools for stochastic fractal and deterministic
4421 chaotic time series analysis.")
4422 (license license:gpl2)))
4424 (define-public r-urca
4431 (uri (cran-uri "urca" version))
4434 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4435 (build-system r-build-system)
4436 (propagated-inputs `(("r-nlme" ,r-nlme)))
4437 (native-inputs `(("gfortran" ,gfortran)))
4438 (home-page "https://cran.r-project.org/web/packages/urca/")
4439 (synopsis "Unit root and cointegration tests for time series data")
4441 "This package provides unit root and cointegration tests encountered in
4442 applied econometric analysis.")
4443 (license license:gpl2+)))
4445 (define-public r-cubature
4452 (uri (cran-uri "cubature" version))
4455 "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"))))
4456 (build-system r-build-system)
4458 `(("r-rcpp" ,r-rcpp)))
4459 (home-page "https://github.com/bnaras/cubature")
4460 (synopsis "Adaptive multivariate integration over hypercubes")
4462 "This package is an R wrapper around the cubature C library for adaptive
4463 multivariate integration over hypercubes. This version provides both
4464 @code{hcubature} and @code{pcubature} routines in addition to a vector
4466 ;; The included cubature C library is released under GPLv2+, but the
4467 ;; wrapper declares the license to be GPLv3+.
4468 (license (list license:gpl2+ license:gpl3+))))
4470 (define-public r-trend
4477 (uri (cran-uri "trend" version))
4480 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4481 (build-system r-build-system)
4483 `(("r-extradistr" ,r-extradistr)))
4485 `(("gfortran" ,gfortran)))
4486 (home-page "https://cran.r-project.org/web/packages/trend/")
4487 (synopsis "Non-parametric trend tests and change-point detection")
4489 "The analysis of environmental data often requires the detection of
4490 trends and change-points. This package includes tests for trend
4491 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4492 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4493 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4494 correlation trend test), change-point detection (Lanzante's test procedures,
4495 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4496 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4497 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4498 sample Robust Rank-Order Distributional Test.")
4499 (license license:gpl3)))
4501 (define-public r-expm
4508 (uri (cran-uri "expm" version))
4511 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4512 (build-system r-build-system)
4513 (propagated-inputs `(("r-matrix" ,r-matrix)))
4514 (native-inputs `(("gfortran" ,gfortran)))
4515 (home-page "https://r-forge.r-project.org/projects/expm/")
4516 (synopsis "Tools for matrix exponentials and related quantities")
4518 "This package provides tools for the computation of the matrix
4519 exponential, logarithm, square root, and related quantities.")
4520 (license license:gpl2+)))
4522 (define-public r-complexplus
4524 (name "r-complexplus")
4529 (uri (cran-uri "complexplus" version))
4532 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4533 (build-system r-build-system)
4535 `(("r-expm" ,r-expm)
4536 ("r-matrix" ,r-matrix)))
4537 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4538 (synopsis "Functions of complex or real variables")
4540 "This package extends several functions to the complex domain, including
4541 the matrix exponential and logarithm, and the determinant.")
4542 (license license:gpl2)))
4544 (define-public r-phontools
4546 (name "r-phontools")
4551 (uri (cran-uri "phonTools" version))
4554 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4555 (properties `((upstream-name . "phonTools")))
4556 (build-system r-build-system)
4557 (home-page "http://www.santiagobarreda.com/rscripts.html")
4558 (synopsis "Tools for phonetic and acoustic analyses")
4560 "This package contains tools for the organization, display, and analysis
4561 of the sorts of data frequently encountered in phonetics research and
4562 experimentation, including the easy creation of IPA vowel plots, and the
4563 creation and manipulation of WAVE audio files.")
4564 (license license:bsd-2)))
4573 (uri (cran-uri "np" version))
4576 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4577 (build-system r-build-system)
4579 `(("r-boot" ,r-boot)
4580 ("r-cubature" ,r-cubature)
4581 ("r-quadprog" ,r-quadprog)
4582 ("r-quantreg" ,r-quantreg)))
4583 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4584 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4585 (description "This package provides non-parametric (and semi-parametric)
4586 kernel methods that seamlessly handle a mix of continuous, unordered, and
4587 ordered factor data types.")
4588 ;; Any version of the GPL.
4589 (license license:gpl3+)))
4591 (define-public r-powerplus
4593 (name "r-powerplus")
4598 (uri (cran-uri "powerplus" version))
4601 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4602 (build-system r-build-system)
4604 `(("r-complexplus" ,r-complexplus)
4607 ("r-matrix" ,r-matrix)
4608 ("r-phontools" ,r-phontools)))
4609 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4610 (synopsis "Exponentiation operations")
4612 "This package provides tools for the computation of matrix and scalar
4614 (license license:gpl2)))
4616 (define-public r-heatmaply
4618 (name "r-heatmaply")
4623 (uri (cran-uri "heatmaply" version))
4626 "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1"))))
4627 (build-system r-build-system)
4629 `(("r-assertthat" ,r-assertthat)
4630 ("r-colorspace" ,r-colorspace)
4631 ("r-dendextend" ,r-dendextend)
4632 ("r-ggplot2" ,r-ggplot2)
4633 ("r-htmlwidgets" ,r-htmlwidgets)
4634 ("r-magrittr" ,r-magrittr)
4635 ("r-plotly" ,r-plotly)
4636 ("r-rcolorbrewer" ,r-rcolorbrewer)
4637 ("r-reshape2" ,r-reshape2)
4638 ("r-scales" ,r-scales)
4639 ("r-seriation" ,r-seriation)
4640 ("r-viridis" ,r-viridis)
4641 ("r-webshot" ,r-webshot)))
4642 (home-page "https://cran.r-project.org/package=heatmaply")
4643 (synopsis "Interactive cluster heat maps using plotly")
4645 "This package enables you to create interactive cluster heatmaps that can
4646 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4647 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4648 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4649 a popular graphical method for visualizing high-dimensional data, in which a
4650 table of numbers is encoded as a grid of colored cells. The rows and columns
4651 of the matrix are ordered to highlight patterns and are often accompanied by
4653 ;; Either version of the license.
4654 (license (list license:gpl2 license:gpl3))))
4663 (uri (cran-uri "h5" version))
4666 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4667 (build-system r-build-system)
4672 `(("which" ,which)))
4674 `(("r-rcpp" ,r-rcpp)))
4675 (home-page "https://github.com/mannau/h5")
4676 (synopsis "Interface to the HDF5 Library")
4678 "This package provides an S4 interface to the HDF5 library supporting
4679 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4680 binary files in a language independent format. The HDF5 format can therefore
4681 be used as an alternative to R's save/load mechanism. Since h5 is able to
4682 access only subsets of stored data it can also handle data sets which do not
4684 (license license:bsd-2)))
4686 (define-public r-cgdsr
4693 (uri (cran-uri "cgdsr" version))
4696 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4697 (build-system r-build-system)
4699 `(("r-httr" ,r-httr)
4700 ("r-r-methodss3" ,r-r-methodss3)
4701 ("r-r-oo" ,r-r-oo)))
4702 (home-page "https://github.com/cBioPortal/cgdsr")
4703 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4705 "This package provides a basic set of R functions for querying the Cancer
4706 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4707 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4708 (license license:lgpl3)))
4710 (define-public r-import
4717 (uri (cran-uri "import" version))
4720 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4721 (build-system r-build-system)
4722 (home-page "https://github.com/smbache/import")
4723 (synopsis "Import mechanism for R")
4725 "This is an alternative mechanism for importing objects from packages.
4726 The syntax allows for importing multiple objects from a package with a single
4727 command in an expressive way. The import package bridges some of the gap
4728 between using @code{library} (or @code{require}) and direct (single-object)
4729 imports. Furthermore the imported objects are not placed in the current
4730 environment. It is also possible to import objects from stand-alone @code{.R}
4732 (license license:expat)))
4734 (define-public r-shinyace
4741 (uri (cran-uri "shinyAce" version))
4744 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
4745 (properties `((upstream-name . "shinyAce")))
4746 (build-system r-build-system)
4748 `(("r-shiny" ,r-shiny)
4749 ("r-jsonlite" ,r-jsonlite)))
4750 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4751 (synopsis "Ace editor bindings for Shiny")
4753 "This package provides Ace editor bindings to enable a rich text editing
4754 environment within Shiny.")
4755 (license license:expat)))
4757 (define-public r-base64url
4759 (name "r-base64url")
4764 (uri (cran-uri "base64url" version))
4767 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4768 (build-system r-build-system)
4770 `(("r-backports" ,r-backports)))
4771 (home-page "https://github.com/mllg/base64url")
4772 (synopsis "Fast and URL-safe base64 encoder and decoder")
4774 "This package provides a URL-safe base64 encoder and decoder. In
4775 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4776 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4777 encoder does not fill the string with trailing @code{=}. The resulting
4778 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4779 and thus are safe to use in URLs or for file names. The package also comes
4780 with a simple base32 encoder/decoder suited for case insensitive file
4782 (license license:gpl3)))
4784 (define-public r-radiant-data
4786 (name "r-radiant-data")
4791 (uri (cran-uri "radiant.data" version))
4794 "08x7zasxf429m021482p86lx3zc6dqz2mih0id8s34isg4gafapg"))
4795 (modules '((guix build utils)))
4798 ;; Delete files that are under CC-NC-SA.
4799 (delete-file-recursively "inst/app/tools/help")
4801 (properties `((upstream-name . "radiant.data")))
4802 (build-system r-build-system)
4804 `(("r-base64enc" ,r-base64enc)
4805 ("r-broom" ,r-broom)
4808 ("r-dplyr" ,r-dplyr)
4811 ("r-ggplot2" ,r-ggplot2)
4812 ("r-gridextra" ,r-gridextra)
4813 ("r-import" ,r-import)
4814 ("r-jsonlite" ,r-jsonlite)
4815 ("r-knitr" ,r-knitr)
4816 ("r-lubridate" ,r-lubridate)
4817 ("r-magrittr" ,r-magrittr)
4818 ("r-markdown" ,r-markdown)
4819 ("r-plotly" ,r-plotly)
4820 ("r-psych" ,r-psych)
4821 ("r-readr" ,r-readr)
4822 ("r-readxl" ,r-readxl)
4823 ("r-rlang" ,r-rlang)
4824 ("r-rmarkdown" ,r-rmarkdown)
4825 ("r-rstudioapi" ,r-rstudioapi)
4826 ("r-scales" ,r-scales)
4827 ("r-shiny" ,r-shiny)
4828 ("r-shinyfiles" ,r-shinyfiles)
4829 ("r-shinyace" ,r-shinyace)
4830 ("r-stringi" ,r-stringi)
4831 ("r-tibble" ,r-tibble)
4832 ("r-tidyr" ,r-tidyr)
4833 ("r-writexl" ,r-writexl)))
4834 (home-page "https://github.com/radiant-rstats/radiant.data")
4835 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4837 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4838 visualizing, summarizing, transforming, and combining data. It also contains
4839 functionality to generate reproducible reports of the analyses conducted in
4841 (license license:agpl3)))
4843 (define-public r-algdesign
4845 (name "r-algdesign")
4850 (uri (cran-uri "AlgDesign" version))
4853 "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
4854 (properties `((upstream-name . "AlgDesign")))
4855 (build-system r-build-system)
4856 (home-page "https://github.com/jvbraun/AlgDesign")
4857 (synopsis "Algorithmic experimental design")
4859 "This package provides tools to calculate exact and approximate theory
4860 experimental designs for D, A, and I criteria. Very large designs may be
4861 created. Experimental designs may be blocked or blocked designs created from
4862 a candidate list, using several criteria. The blocking can be done when whole
4863 and within plot factors interact.")
4864 (license license:gpl2+)))
4866 (define-public r-signal
4873 (uri (cran-uri "signal" version))
4876 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
4877 (build-system r-build-system)
4878 (propagated-inputs `(("r-mass" ,r-mass)))
4879 (native-inputs `(("gfortran" ,gfortran)))
4880 (home-page "https://cran.r-project.org/web/packages/signal/")
4881 (synopsis "Signal processing")
4883 "This package provides a set of signal processing functions originally
4884 written for Matlab and GNU Octave. It includes filter generation utilities,
4885 filtering functions, resampling routines, and visualization of filter models.
4886 It also includes interpolation functions.")
4887 (license license:gpl2)))
4889 (define-public r-gsubfn
4896 (uri (cran-uri "gsubfn" version))
4899 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
4900 (build-system r-build-system)
4901 (propagated-inputs `(("r-proto" ,r-proto)))
4902 (home-page "http://gsubfn.googlecode.com")
4903 (synopsis "Utilities for strings and function arguments.")
4905 "This package provides @code{gsubfn} which is like @code{gsub} but can
4906 take a replacement function or certain other objects instead of the
4907 replacement string. Matches and back references are input to the replacement
4908 function and replaced by the function output. @code{gsubfn} can be used to
4909 split strings based on content rather than delimiters and for quasi-perl-style
4910 string interpolation. The package also has facilities for translating
4911 formulas to functions and allowing such formulas in function calls instead of
4913 (license license:gpl2+)))
4915 (define-public r-sqldf
4922 (uri (cran-uri "sqldf" version))
4925 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
4926 (build-system r-build-system)
4928 `(("r-chron" ,r-chron)
4930 ("r-gsubfn" ,r-gsubfn)
4931 ("r-proto" ,r-proto)
4932 ("r-rsqlite" ,r-rsqlite)))
4933 (home-page "https://github.com/ggrothendieck/sqldf")
4934 (synopsis "Manipulate R data frames using SQL")
4936 "The @code{sqldf} function is typically passed a single argument which is
4937 an SQL select statement where the table names are ordinary R data frame names.
4938 @code{sqldf} transparently sets up a database, imports the data frames into
4939 that database, performs the SQL statement and returns the result using a
4940 heuristic to determine which class to assign to each column of the returned
4941 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
4942 used to read filtered files into R even if the original files are larger than
4943 R itself can handle.")
4944 (license license:gpl2)))
4946 (define-public r-abind
4953 (uri (cran-uri "abind" version))
4956 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
4957 (build-system r-build-system)
4958 (home-page "https://cran.r-project.org/web/packages/abind/")
4959 (synopsis "Combine multidimensional arrays")
4961 "This package provides tools to combine multidimensional arrays into a
4962 single array. This is a generalization of @code{cbind} and @code{rbind}. It
4963 works with vectors, matrices, and higher-dimensional arrays. It also provides
4964 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
4965 extracting and replacing data in arrays.")
4966 (license license:lgpl2.0+)))
4968 (define-public r-prroc
4975 (uri (cran-uri "PRROC" version))
4978 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
4979 (properties `((upstream-name . "PRROC")))
4980 (build-system r-build-system)
4981 (home-page "https://cran.r-project.org/web/packages/PRROC/")
4982 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
4984 "This package computes the areas under the @dfn{precision-recall} (PR)
4985 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
4986 contrast to other implementations, the interpolation between points of the PR
4987 curve is done by a non-linear piecewise function. In addition to the areas
4988 under the curves, the curves themselves can also be computed and plotted by a
4989 specific S3-method.")
4990 (license license:gpl3)))
4992 (define-public r-vim
4999 (uri (cran-uri "VIM" version))
5002 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
5003 (properties `((upstream-name . "VIM")))
5004 (build-system r-build-system)
5007 ("r-colorspace" ,r-colorspace)
5008 ("r-data-table" ,r-data-table)
5009 ("r-e1071" ,r-e1071)
5010 ("r-laeken" ,r-laeken)
5013 ("r-ranger" ,r-ranger)
5015 ("r-robustbase" ,r-robustbase)
5018 (home-page "https://github.com/alexkowa/VIM")
5019 (synopsis "Visualization and imputation of missing values")
5021 "This package provides tools for the visualization of missing and/or
5022 imputed values are introduced, which can be used for exploring the data and
5023 the structure of the missing and/or imputed values. Depending on this
5024 structure of the missing values, the corresponding methods may help to
5025 identify the mechanism generating the missing values and allows to explore the
5026 data including missing values. In addition, the quality of imputation can be
5027 visually explored using various univariate, bivariate, multiple and
5028 multivariate plot methods.")
5029 (license license:gpl2+)))
5031 (define-public r-fnn
5038 (uri (cran-uri "FNN" version))
5041 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5042 (properties `((upstream-name . "FNN")))
5043 (build-system r-build-system)
5044 (home-page "https://cran.r-project.org/web/packages/FNN")
5045 (synopsis "Fast nearest neighbor search algorithms and applications")
5047 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5048 search algorithms. Related applications including KNN classification,
5049 regression and information measures are implemented.")
5050 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5051 ;; later can be used.
5052 (license license:gpl2+)))
5054 (define-public r-smoother
5061 (uri (cran-uri "smoother" version))
5064 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5065 (build-system r-build-system)
5067 `(("r-ttr" ,r-ttr)))
5068 (home-page "http://cran.r-project.org/web/packages/smoother")
5069 (synopsis "Functions relating to the smoothing of numerical data")
5071 "This package provides a collection of methods for smoothing numerical
5072 data, commencing with a port of the Matlab gaussian window smoothing function.
5073 In addition, several functions typically used in smoothing of financial data
5075 (license license:gpl2)))
5077 (define-public r-riverplot
5079 (name "r-riverplot")
5084 (uri (cran-uri "riverplot" version))
5087 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5088 (build-system r-build-system)
5089 (home-page "https://logfc.wordpress.com")
5090 (synopsis "Sankey or ribbon plots")
5092 "Sankey plots are a type of diagram that is convenient to illustrate how
5093 flow of information, resources etc. separates and joins, much like observing
5094 how rivers split and merge. For example, they can be used to compare
5095 different clusterings. This package provides an implementation of Sankey
5097 (license license:gpl2+)))
5099 (define-public r-dyn
5106 (uri (cran-uri "dyn" version))
5109 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5110 (build-system r-build-system)
5112 `(("r-zoo" ,r-zoo)))
5113 (home-page "https://cran.r-project.org/web/packages/dyn")
5114 (synopsis "Time series regression")
5116 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5117 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5118 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5119 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5120 @code{randomForest::randomForest()} and other regression functions, allowing
5121 those functions to be used with time series including specifications that may
5122 contain lags, diffs and missing values.")
5124 (license license:gpl2+)))
5126 (define-public r-catdap
5133 (uri (cran-uri "catdap" version))
5136 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5137 (build-system r-build-system)
5139 `(("gfortran" ,gfortran)))
5140 (home-page "https://cran.r-project.org/web/packages/catdap/")
5141 (synopsis "Tools for categorical data analysis")
5143 "This package provides functions for analyzing multivariate data.
5144 Dependencies of the distribution of the specified variable (response
5145 variable) to other variables (explanatory variables) are derived and
5146 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5147 (license license:gpl2+)))
5149 (define-public r-arules
5156 (uri (cran-uri "arules" version))
5159 "003c5cd3xzq39h7c19px077ygm0n1v7k83icy5zzrnkagyds2p8n"))))
5160 (build-system r-build-system)
5162 `(("r-matrix" ,r-matrix)))
5163 (home-page "https://github.com/mhahsler/arules")
5164 (synopsis "Mining association rules and frequent itemsets")
5166 "This package provides an infrastructure for representing, manipulating
5167 and analyzing transaction data and patterns (frequent itemsets and association rules).
5168 It also provides C implementations of the association mining algorithms Apriori
5170 (license license:gpl3)))
5172 (define-public r-parsedate
5174 (name "r-parsedate")
5179 (uri (cran-uri "parsedate" version))
5182 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5183 (build-system r-build-system)
5185 `(("r-rematch2" ,r-rematch2)))
5186 (home-page "https://github.com/gaborcsardi/parsedate")
5188 "Recognize and parse dates in various formats")
5190 "This package provides three functions for dealing with dates:
5191 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5192 time formats, @code{parse_date} parses dates in unspecified formats,
5193 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5194 (license license:gpl2)))
5196 (define-public r-abc-data
5203 (uri (cran-uri "abc.data" version))
5206 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5207 (properties `((upstream-name . "abc.data")))
5208 (build-system r-build-system)
5209 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5210 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5212 "This package contains data which are used by functions of the abc
5213 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5214 algorithms for performing parameter estimation, model selection, and
5216 (license license:gpl3+)))
5218 (define-public r-abc
5225 (uri (cran-uri "abc" version))
5228 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5229 (build-system r-build-system)
5231 `(("r-abc-data" ,r-abc-data)
5232 ("r-locfit" ,r-locfit)
5235 ("r-quantreg" ,r-quantreg)))
5236 (home-page "https://cran.r-project.org/web/packages/abc/")
5237 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5239 "This package implements several @dfn{Approximate Bayesian
5240 Computation} (ABC) algorithms for performing parameter estimation, model
5241 selection, and goodness-of-fit. Cross-validation tools are also available for
5242 measuring the accuracy of ABC estimates, and to calculate the
5243 misclassification probabilities of different models.")
5244 (license license:gpl3+)))
5246 (define-public r-zip
5253 (uri (cran-uri "zip" version))
5256 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5257 (build-system r-build-system)
5258 (home-page "https://github.com/gaborcsardi/zip")
5259 (synopsis "Cross-platform Zip compression")
5261 "This package provides a cross-platform Zip compression library for R.
5262 It is a replacement for the @code{zip} function, that does not require any
5263 additional external tools on any platform.")
5264 (license license:cc0)))
5266 (define-public r-openxlsx
5273 (uri (cran-uri "openxlsx" version))
5276 "1lflygpi1z4rlb1c6g6wsmi334maiiy7jhpg6ph4sw8lpvg12w4b"))))
5277 (build-system r-build-system)
5279 `(("r-rcpp" ,r-rcpp)
5281 (home-page "https://github.com/awalker89/openxlsx")
5282 (synopsis "Read, write and edit XLSX files")
5284 "This package simplifies the creation of Excel @code{.xlsx} files by
5285 providing a high level interface to writing, styling and editing worksheets.
5286 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5287 and @code{XLConnect} packages with the added benefit of removing the
5288 dependency on Java.")
5289 (license license:gpl3)))
5291 (define-public r-rio
5298 (uri (cran-uri "rio" version))
5301 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5302 (build-system r-build-system)
5304 `(("r-curl" ,r-curl)
5305 ("r-data-table" ,r-data-table)
5306 ("r-foreign" ,r-foreign)
5307 ("r-haven" ,r-haven)
5308 ("r-openxlsx" ,r-openxlsx)
5309 ("r-readxl" ,r-readxl)
5310 ("r-tibble" ,r-tibble)))
5311 (home-page "https://github.com/leeper/rio")
5312 (synopsis "Swiss-army knife for data I/O")
5314 "This package provides streamlined data import and export infrastructure
5315 by making assumptions that the user is probably willing to make: @code{import}
5316 and @code{export} determine the data structure from the file extension,
5317 reasonable defaults are used for data import and export (e.g.,
5318 @code{stringsAsFactors=FALSE}), web-based import is natively
5319 supported (including from SSL/HTTPS), compressed files can be read directly
5320 without explicit decompression, and fast import packages are used where
5321 appropriate. An additional convenience function, @code{convert}, provides a
5322 simple method for converting between file types.")
5323 (license license:gpl2)))
5325 (define-public r-maptools
5332 (uri (cran-uri "maptools" version))
5335 "1ix3cg74w0w6cj8nwi0r9n3y5q9ljc21hm8xq6yqqngs57prvn2x"))))
5336 (build-system r-build-system)
5338 `(("r-foreign" ,r-foreign)
5339 ("r-lattice" ,r-lattice)
5341 (home-page "http://r-forge.r-project.org/projects/maptools/")
5342 (synopsis "Tools for reading and handling spatial objects")
5344 "This package provides a set of tools for manipulating and reading
5345 geographic data, in particular ESRI Shapefiles. It includes binary access to
5346 GSHHG shoreline files. The package also provides interface wrappers for
5347 exchanging spatial objects with other R packages.")
5348 ;; The C source files from shapelib are released under the Expat license.
5349 ;; The R code is released under GPL version 2 or later.
5350 (license (list license:gpl2+
5353 (define-public r-later
5360 (uri (cran-uri "later" version))
5363 "11xjavj7siz0xv2ffq1ld4bwl35jyrcfpvvs4p3ilpifxx49hyr7"))))
5364 (build-system r-build-system)
5368 ("r-rlang" ,r-rlang)))
5369 (home-page "https://github.com/r-lib/later")
5370 (synopsis "Utilities for delaying function execution")
5372 "This package provides tools to execute arbitrary R or C functions some
5373 time after the current time, after the R execution stack has emptied.")
5374 (license license:gpl2+)))
5376 (define-public r-promises
5383 (uri (cran-uri "promises" version))
5386 "01l0ydjvvy6afcg5d6pzvk1ikd3djq8n2flv8c831ksn68z0zsn8"))))
5387 (build-system r-build-system)
5389 `(("r-later" ,r-later)
5390 ("r-magrittr" ,r-magrittr)
5393 ("r-rlang" ,r-rlang)))
5394 (home-page "https://rstudio.github.io/promises")
5395 (synopsis "Abstractions for promise-based asynchronous programming")
5397 "This package provides fundamental abstractions for doing asynchronous
5398 programming in R using promises. Asynchronous programming is useful for
5399 allowing a single R process to orchestrate multiple tasks in the background
5400 while also attending to something else. Semantics are similar to JavaScript
5401 promises, but with a syntax that is idiomatic R.")
5402 (license license:expat)))
5404 (define-public r-dosnow
5411 (uri (cran-uri "doSNOW" version))
5414 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5415 (properties `((upstream-name . "doSNOW")))
5416 (build-system r-build-system)
5418 `(("r-foreach" ,r-foreach)
5419 ("r-iterators" ,r-iterators)
5420 ("r-snow" ,r-snow)))
5421 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5422 (synopsis "Foreach parallel adaptor for the snow package")
5424 "This package provides a parallel backend for the @code{%dopar%} function
5425 using the @code{snow} package.")
5426 (license license:gpl2)))
5428 (define-public r-snowfall
5431 (version "1.84-6.1")
5434 (uri (cran-uri "snowfall" version))
5436 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5437 (build-system r-build-system)
5439 `(("r-snow" ,r-snow)))
5440 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5441 (synopsis "Easier cluster computing")
5442 (description "This package is a usability wrapper around snow for easier
5443 development of parallel R programs. This package offers e.g. extended error
5444 checks, and additional functions. All functions work in sequential mode, too,
5445 if no cluster is present or wished. The package is also designed as connector
5446 to the cluster management tool @code{sfCluster}, but can also used without
5448 (license license:gpl2+)))
5450 (define-public r-rappdirs
5457 (uri (cran-uri "rappdirs" version))
5460 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5461 (build-system r-build-system)
5462 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5463 (synopsis "Determine where to save data, caches, and logs")
5465 "This package provides an easy way to determine which directories on the
5466 user's computer should be used to save data, caches and logs. It is a port of
5467 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5468 (license license:expat)))
5470 (define-public r-learnr
5477 (uri (cran-uri "learnr" version))
5480 "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5"))))
5481 (build-system r-build-system)
5483 `(("r-evaluate" ,r-evaluate)
5484 ("r-htmltools" ,r-htmltools)
5485 ("r-htmlwidgets" ,r-htmlwidgets)
5486 ("r-jsonlite" ,r-jsonlite)
5487 ("r-knitr" ,r-knitr)
5488 ("r-markdown" ,r-markdown)
5489 ("r-rappdirs" ,r-rappdirs)
5490 ("r-rmarkdown" ,r-rmarkdown)
5491 ("r-rprojroot" ,r-rprojroot)
5492 ("r-shiny" ,r-shiny)
5493 ("r-withr" ,r-withr)))
5494 (home-page "https://rstudio.github.io/learnr/")
5495 (synopsis "Interactive tutorials for R")
5497 "This package provides tools to create interactive tutorials using R
5498 Markdown. Use a combination of narrative, figures, videos, exercises, and
5499 quizzes to create self-paced tutorials for learning about R and R packages.")
5500 (license license:asl2.0)))
5502 (define-public r-analytics
5504 (name "r-analytics")
5509 (uri (cran-uri "analytics" version))
5512 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5513 (build-system r-build-system)
5516 ("r-cluster" ,r-cluster)
5517 ("r-fractal" ,r-fractal)
5518 ("r-lmtest" ,r-lmtest)
5521 ("r-powerplus" ,r-powerplus)
5522 ("r-robust" ,r-robust)
5523 ("r-trend" ,r-trend)
5527 (home-page "https://cran.r-project.org/web/packages/analytics/")
5528 (synopsis "Collection of data analysis tools")
5530 "This package is a collection of data analysis tools. It includes tools
5531 for regression outlier detection in a fitted linear model, stationary
5532 bootstrap using a truncated geometric distribution, a comprehensive test for
5533 weak stationarity, column means by group, weighted biplots, and a heuristic to
5534 obtain a better initial configuration in non-metric MDS.")
5535 (license license:gpl2)))
5537 (define-public r-reticulate
5539 (name "r-reticulate")
5544 (uri (cran-uri "reticulate" version))
5547 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
5548 (build-system r-build-system)
5549 (inputs `(("python" ,python)))
5551 `(("r-jsonlite" ,r-jsonlite)
5552 ("r-matrix" ,r-matrix)
5553 ("r-rcpp" ,r-rcpp)))
5554 (home-page "https://github.com/rstudio/reticulate")
5555 (synopsis "R interface to Python")
5557 "This package provides an interface from R to Python modules, classes,
5558 and functions. When calling into Python, R data types are automatically
5559 converted to their equivalent Python types. When values are returned from
5560 Python to R they are converted back to R types.")
5561 (license license:asl2.0)))
5563 (define-public r-bibtex
5570 (uri (cran-uri "bibtex" version))
5573 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5574 (build-system r-build-system)
5575 (propagated-inputs `(("r-stringr" ,r-stringr)))
5576 (home-page "https://github.com/romainfrancois/bibtex")
5577 (synopsis "Bibtex parser")
5578 (description "This package provides a utility for R to parse a bibtex
5580 (license license:gpl2+)))
5582 (define-public r-ggseqlogo
5584 (name "r-ggseqlogo")
5589 (uri (cran-uri "ggseqlogo" version))
5592 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5593 (build-system r-build-system)
5594 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5595 (home-page "https://github.com/omarwagih/ggseqlogo")
5596 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5598 "The range of functions provided by this package makes it possible to
5599 draw highly versatile genomic sequence logos. Features include, but are not
5600 limited to, modifying colour schemes and fonts used to draw the logo,
5601 generating multiple logo plots, and aiding the visualisation with annotations.
5602 Sequence logos can easily be combined with other ggplot2 plots.")
5603 ;; Unspecified version of the LGPL.
5604 (license license:lgpl3+)))
5606 (define-public r-ggsci
5613 (uri (cran-uri "ggsci" version))
5616 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5617 (build-system r-build-system)
5619 `(("r-ggplot2" ,r-ggplot2)
5620 ("r-scales" ,r-scales)))
5621 (home-page "https://nanx.me/ggsci/")
5622 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5624 "This package provides a collection of ggplot2 color palettes inspired by
5625 plots in scientific journals, data visualization libraries, science fiction
5626 movies, and TV shows.")
5627 (license license:gpl3)))
5629 (define-public r-ggsignif
5636 (uri (cran-uri "ggsignif" version))
5639 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5640 (build-system r-build-system)
5642 `(("r-ggplot2" ,r-ggplot2)))
5643 (home-page "https://github.com/const-ae/ggsignif")
5644 (synopsis "Significance brackets for ggplot2")
5646 "Enrich your ggplots with group-wise comparisons. This package provides
5647 an easy way to indicate if two groups are significantly different. Commonly
5648 this is shown by a bracket on top connecting the groups of interest which
5649 itself is annotated with the level of significance. The package provides a
5650 single layer that takes the groups for comparison and the test as arguments
5651 and adds the annotation to the plot.")
5652 (license license:gpl3)))
5654 (define-public r-ggpubr
5661 (uri (cran-uri "ggpubr" version))
5664 "0i81mmz4qn9yzcgfa6dhkcrx4ddlflkm2c3b40isc8all43rm8rn"))))
5665 (build-system r-build-system)
5667 `(("r-cowplot" ,r-cowplot)
5668 ("r-dplyr" ,r-dplyr)
5669 ("r-ggplot2" ,r-ggplot2)
5670 ("r-ggrepel" ,r-ggrepel)
5671 ("r-ggsci" ,r-ggsci)
5672 ("r-ggsignif" ,r-ggsignif)
5674 ("r-gridextra" ,r-gridextra)
5675 ("r-magrittr" ,r-magrittr)
5676 ("r-polynom" ,r-polynom)
5677 ("r-purrr" ,r-purrr)
5678 ("r-rlang" ,r-rlang)
5679 ("r-scales" ,r-scales)
5680 ("r-tidyr" ,r-tidyr)))
5681 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5682 (synopsis "ggplot2-based publication-ready plots")
5684 "The ggplot2 package is an excellent and flexible package for elegant
5685 data visualization in R. However the default generated plots require some
5686 formatting before we can send them for publication. The ggpubr package
5687 provides some easy-to-use functions for creating and customizing ggplot2-based
5688 publication-ready plots.")
5689 (license license:gpl2)))
5691 (define-public r-ellipse
5698 (uri (cran-uri "ellipse" version))
5701 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5702 (build-system r-build-system)
5703 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5704 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5706 "This package contains various routines for drawing ellipses and
5707 ellipse-like confidence regions, implementing the plots described in Murdoch
5708 and Chow (1996), A graphical display of large correlation matrices, The
5709 American Statistician 50, 178-180. There are also routines implementing the
5710 profile plots described in Bates and Watts (1988), Nonlinear Regression
5711 Analysis and its Applications.")
5712 (license license:gpl2+)))
5714 (define-public r-flashclust
5716 (name "r-flashclust")
5721 (uri (cran-uri "flashClust" version))
5724 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5725 (properties `((upstream-name . "flashClust")))
5726 (build-system r-build-system)
5727 (native-inputs `(("gfortran" ,gfortran)))
5728 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5729 (synopsis "Implementation of optimal hierarchical clustering")
5731 "This package provides a fast implementation of hierarchical
5733 (license license:gpl2+)))
5735 (define-public r-factominer
5737 (name "r-factominer")
5742 (uri (cran-uri "FactoMineR" version))
5745 "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
5746 (properties `((upstream-name . "FactoMineR")))
5747 (build-system r-build-system)
5750 ("r-cluster" ,r-cluster)
5751 ("r-ellipse" ,r-ellipse)
5752 ("r-flashclust" ,r-flashclust)
5753 ("r-lattice" ,r-lattice)
5754 ("r-leaps" ,r-leaps)
5756 ("r-scatterplot3d" ,r-scatterplot3d)))
5757 (home-page "http://factominer.free.fr")
5758 (synopsis "Multivariate exploratory data analysis and data mining")
5760 "This package provides exploratory data analysis methods to summarize,
5761 visualize and describe datasets. The main principal component methods are
5762 available, those with the largest potential in terms of applications:
5763 principal component analysis (PCA) when variables are quantitative,
5764 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5765 variables are categorical, Multiple Factor Analysis when variables are
5766 structured in groups, etc. and hierarchical cluster analysis.")
5767 (license license:gpl2+)))
5769 (define-public r-factoextra
5771 (name "r-factoextra")
5776 (uri (cran-uri "factoextra" version))
5779 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
5780 (build-system r-build-system)
5782 `(("r-abind" ,r-abind)
5783 ("r-cluster" ,r-cluster)
5784 ("r-dendextend" ,r-dendextend)
5785 ("r-factominer" ,r-factominer)
5786 ("r-ggplot2" ,r-ggplot2)
5787 ("r-ggpubr" ,r-ggpubr)
5788 ("r-ggrepel" ,r-ggrepel)
5789 ("r-reshape2" ,r-reshape2)
5790 ("r-tidyr" ,r-tidyr)))
5791 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5792 (synopsis "Extract and visualize the results of multivariate data analyses")
5794 "This package provides some easy-to-use functions to extract and
5795 visualize the output of multivariate data analyses, including
5796 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5797 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5798 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5799 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5800 packages. It contains also functions for simplifying some clustering analysis
5801 steps and provides ggplot2-based elegant data visualization.")
5802 (license license:gpl2)))
5804 (define-public r-fansi
5811 (uri (cran-uri "fansi" version))
5814 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
5815 (build-system r-build-system)
5817 `(("r-knitr" ,r-knitr))) ; for vignettes
5818 (home-page "https://github.com/brodieG/fansi")
5819 (synopsis "ANSI control sequence aware string functions")
5821 "This package provides counterparts to R string manipulation functions
5822 that account for the effects of ANSI text formatting control sequences.")
5823 (license license:gpl2+)))
5825 (define-public r-nbclust
5832 (uri (cran-uri "NbClust" version))
5835 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
5836 (properties `((upstream-name . "NbClust")))
5837 (build-system r-build-system)
5838 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
5839 (synopsis "Determine the best number of clusters in a data set")
5841 "NbClust provides 30 indexes for determining the optimal number of
5842 clusters in a data set and offers the best clustering scheme from different
5843 results to the user.")
5844 (license license:gpl2)))
5846 (define-public r-hdf5r
5853 (uri (cran-uri "hdf5r" version))
5856 "1pq12vkfqxvcaznwaxvjdg3acimk5a20m8h18sixvxc34vnqxw8f"))))
5857 (build-system r-build-system)
5862 `(("r-bit64" ,r-bit64)
5864 (home-page "https://hhoeflin.github.io/hdf5r")
5865 (synopsis "Interface to the HDF5 binary data format")
5867 "HDF5 is a data model, library and file format for storing and managing
5868 large amounts of data. This package provides a nearly feature complete,
5869 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
5870 functionality is added so that HDF5 objects behave very similar to their
5871 corresponding R counterparts.")
5872 (license license:asl2.0)))
5874 (define-public r-itertools
5876 (name "r-itertools")
5881 (uri (cran-uri "itertools" version))
5884 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
5885 (build-system r-build-system)
5887 `(("r-iterators" ,r-iterators)))
5888 (home-page "https://cran.r-project.org/web/packages/itertools/")
5889 (synopsis "Iterator tools")
5891 "This package provides various tools for creating iterators, many
5892 patterned after functions in the Python @code{itertools} module, and others
5893 patterned after functions in the snow package.")
5894 (license license:gpl2)))
5896 (define-public r-polynom
5903 (uri (cran-uri "polynom" version))
5906 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
5907 (build-system r-build-system)
5908 (home-page "https://cran.r-project.org/web/packages/polynom/")
5909 (synopsis "Functions for univariate polynomial manipulations")
5911 "This package provides a collection of functions to implement a class for
5912 univariate polynomial manipulations.")
5913 (license license:gpl2)))
5915 (define-public r-gbrd
5922 (uri (cran-uri "gbRd" version))
5925 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
5926 (properties `((upstream-name . "gbRd")))
5927 (build-system r-build-system)
5928 (home-page "https://cran.r-project.org/web/packages/gbRd/")
5929 (synopsis "Utilities for processing Rd objects and files")
5931 "This package provides utilities for processing Rd objects and files.
5932 Extract argument descriptions and other parts of the help pages of
5934 (license license:gpl2+)))
5936 (define-public r-rjags
5943 (uri (cran-uri "rjags" version))
5946 "1vrmxxfnia2mkmfkp5yaq5qrlh4xg3ggab6fnj14mrp1231wb91a"))))
5947 (build-system r-build-system)
5949 `(("r-coda" ,r-coda)))
5953 `(("pkg-config" ,pkg-config)))
5954 (home-page "http://mcmc-jags.sourceforge.net")
5955 (synopsis "Bayesian graphical models using MCMC")
5957 "This package provides an R interface to the JAGS MCMC library. JAGS is
5958 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
5959 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
5960 (license license:gpl2)))
5962 (define-public r-rdpack
5969 (uri (cran-uri "Rdpack" version))
5972 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
5973 (properties `((upstream-name . "Rdpack")))
5974 (build-system r-build-system)
5976 `(("r-bibtex" ,r-bibtex)
5977 ("r-gbrd" ,r-gbrd)))
5978 (home-page "https://github.com/GeoBosh/Rdpack")
5979 (synopsis "Update and manipulate Rd documentation objects")
5981 "This package provides functions for manipulation of R documentation
5982 objects, including functions @code{reprompt()} and @code{ereprompt()} for
5983 updating Rd documentation for functions, methods and classes; it also includes
5984 Rd macros for citations and import of references from bibtex files for use in
5985 Rd files and roxygen2 comments, as well as many functions for manipulation of
5986 references and Rd files.")
5987 (license license:gpl2+)))
5989 (define-public r-officer
5996 (uri (cran-uri "officer" version))
5999 "005kaxjhr40shpav2pg7s7gj8f49579r7rbgwlncbwv16nn0rbbg"))))
6000 (build-system r-build-system)
6002 `(("r-base64enc" ,r-base64enc)
6003 ("r-digest" ,r-digest)
6004 ("r-htmltools" ,r-htmltools)
6005 ("r-magrittr" ,r-magrittr)
6008 ("r-rlang" ,r-rlang)
6012 (home-page "https://davidgohel.github.io/officer")
6013 (synopsis "Manipulation of Word and PowerPoint documents")
6015 "This package provides tools to access and manipulate Word and PowerPoint
6016 documents from R. The package focuses on tabular and graphical reporting from
6017 R; it also provides two functions that let users get document content into
6018 data objects. A set of functions lets add and remove images, tables and
6019 paragraphs of text in new or existing documents. When working with PowerPoint
6020 presentations, slides can be added or removed; shapes inside slides can also
6021 be added or removed. When working with Word documents, a cursor can be used
6022 to help insert or delete content at a specific location in the document.")
6023 (license license:gpl3)))
6025 (define-public r-abn
6032 (uri (cran-uri "abn" version))
6035 "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b"))))
6036 (build-system r-build-system)
6040 `(("r-lme4" ,r-lme4)
6044 ("r-rcpparmadillo" ,r-rcpparmadillo)
6045 ("r-rjags" ,r-rjags)))
6046 (home-page "http://www.r-bayesian-networks.org")
6047 (synopsis "Modelling multivariate data with additive bayesian networks")
6049 "Bayesian network analysis is a form of probabilistic graphical models
6050 which derives from empirical data a directed acyclic graph, DAG, describing
6051 the dependency structure between random variables. An additive Bayesian
6052 network model consists of a form of a DAG where each node comprises a
6053 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6054 equivalent to Bayesian multivariate regression using graphical modelling, they
6055 generalises the usual multivariable regression, GLM, to multiple dependent
6056 variables. This package provides routines to help determine optimal Bayesian
6057 network models for a given data set, where these models are used to identify
6058 statistical dependencies in messy, complex data.")
6059 (license license:gpl2+)))
6061 (define-public r-acd
6068 (uri (cran-uri "ACD" version))
6071 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6072 (properties `((upstream-name . "ACD")))
6073 (build-system r-build-system)
6074 (home-page "https://cran.r-project.org/web/packages/ACD/")
6075 (synopsis "Categorical data analysis with complete or missing responses")
6077 "This package provides tools for categorical data analysis with complete
6078 or missing responses.")
6079 (license license:gpl2+)))
6081 (define-public r-acdm
6088 (uri (cran-uri "ACDm" version))
6091 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6092 (properties `((upstream-name . "ACDm")))
6093 (build-system r-build-system)
6095 `(("r-dplyr" ,r-dplyr)
6096 ("r-ggplot2" ,r-ggplot2)
6098 ("r-rsolnp" ,r-rsolnp)
6100 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6101 (synopsis "Tools for Autoregressive Conditional Duration Models")
6103 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6104 and Russell, 1998) models. It creates trade, price or volume durations from
6105 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6107 (license license:gpl2+)))
6109 (define-public r-overlap
6116 (uri (cran-uri "overlap" version))
6119 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6120 (build-system r-build-system)
6121 (home-page "https://cran.r-project.org/web/packages/overlap/")
6122 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6124 "This package provides functions to fit kernel density functions to data
6125 on temporal activity patterns of animals; estimate coefficients of overlapping
6126 of densities for two species; and calculate bootstrap estimates of confidence
6128 (license license:gpl3+)))
6130 (define-public r-snakecase
6132 (name "r-snakecase")
6137 (uri (cran-uri "snakecase" version))
6140 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6141 (build-system r-build-system)
6143 `(("r-stringi" ,r-stringi)
6144 ("r-stringr" ,r-stringr)))
6145 (home-page "https://github.com/Tazinho/snakecase")
6146 (synopsis "Convert strings into any case")
6148 "This package provides a consistent, flexible and easy to use tool to
6149 parse and convert strings into cases like snake or camel among others.")
6150 (license license:gpl3)))
6152 (define-public r-prediction
6154 (name "r-prediction")
6159 (uri (cran-uri "prediction" version))
6162 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6163 (build-system r-build-system)
6165 `(("r-data-table" ,r-data-table)))
6166 (home-page "https://github.com/leeper/prediction")
6167 (synopsis "Tidy, type-safe prediction methods")
6169 "This package provides the @code{prediction()} function, a type-safe
6170 alternative to @code{predict()} that always returns a data frame. The package
6171 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6172 from the @code{stats} package, as well as numerous other model classes from
6173 other add-on packages.")
6174 (license license:expat)))
6176 (define-public r-insight
6183 (uri (cran-uri "insight" version))
6186 "1izqh4j0gzyk25cga67gs0i6rl0j471h5y2c3y1maz79r32fs7fd"))))
6187 (build-system r-build-system)
6188 (home-page "https://easystats.github.io/insight/")
6189 (synopsis "Easy access to model information for various model objects")
6191 "This package provides a tool to provide an easy, intuitive and
6192 consistent access to information contained in various R models, like model
6193 formulas, model terms, information about random effects, data that was used to
6194 fit the model or data from response variables. The package mainly revolves
6195 around two types of functions: Functions that find (the names of) information,
6196 starting with @code{find_}, and functions that get the underlying data,
6197 starting with @code{get_}. The package has a consistent syntax and works with
6198 many different model objects, where otherwise functions to access these
6199 information are missing.")
6200 (license license:gpl3)))
6202 (define-public r-sjlabelled
6204 (name "r-sjlabelled")
6209 (uri (cran-uri "sjlabelled" version))
6212 "0c9wy0gsr2sbkrv2638xbi7qm0gl6jyr6sfricavhkm7l4hljjkz"))))
6213 (build-system r-build-system)
6215 `(("r-haven" ,r-haven)
6216 ("r-insight" ,r-insight)
6217 ("r-magrittr" ,r-magrittr)
6218 ("r-purrr" ,r-purrr)
6219 ("r-rlang" ,r-rlang)
6220 ("r-tidyselect" ,r-tidyselect)))
6221 (home-page "https://github.com/strengejacke/sjlabelled")
6222 (synopsis "Labelled data utility functions")
6224 "This package provides a collection of functions dealing with labelled
6225 data, like reading and writing data between R and other statistical software
6226 packages. This includes easy ways to get, set or change value and variable
6227 label attributes, to convert labelled vectors into factors or numeric (and
6228 vice versa), or to deal with multiple declared missing values.")
6229 (license license:gpl3)))
6231 (define-public r-sjmisc
6238 (uri (cran-uri "sjmisc" version))
6241 "0rl0bmk91wc4dxdgy008fl0dwkx3ffvys30vgpnr78lb4pk45nb2"))))
6242 (build-system r-build-system)
6244 `(("r-dplyr" ,r-dplyr)
6245 ("r-insight" ,r-insight)
6246 ("r-magrittr" ,r-magrittr)
6247 ("r-purrr" ,r-purrr)
6248 ("r-rlang" ,r-rlang)
6249 ("r-sjlabelled" ,r-sjlabelled)
6250 ("r-tidyselect" ,r-tidyselect)))
6251 (home-page "https://github.com/strengejacke/sjmisc")
6252 (synopsis "Data and variable transformation functions")
6254 "This package is a collection of miscellaneous utility functions,
6255 supporting data transformation tasks like recoding, dichotomizing or grouping
6256 variables, setting and replacing missing values. The data transformation
6257 functions also support labelled data, and all integrate seamlessly into a
6258 tidyverse workflow.")
6259 (license license:gpl3)))
6261 (define-public r-nortest
6268 (uri (cran-uri "nortest" version))
6271 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6272 (build-system r-build-system)
6273 (home-page "https://cran.r-project.org/web/packages/nortest/")
6274 (synopsis "Tests for normality")
6276 "This package provides five omnibus tests for testing the composite
6277 hypothesis of normality.")
6278 (license license:gpl2+)))
6280 (define-public r-moonbook
6287 (uri (cran-uri "moonBook" version))
6290 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6291 (properties `((upstream-name . "moonBook")))
6292 (build-system r-build-system)
6294 `(("r-magrittr" ,r-magrittr)
6295 ("r-nortest" ,r-nortest)
6296 ("r-purrr" ,r-purrr)
6297 ("r-sjmisc" ,r-sjmisc)
6298 ("r-stringr" ,r-stringr)
6299 ("r-survival" ,r-survival)))
6300 (home-page "https://github.com/cardiomoon/moonBook")
6301 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6303 "This package provides several analysis-related functions for the book
6304 entitled \"R statistics and graph for medical articles\" (written in Korean),
6305 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6307 (license license:gpl2)))
6309 (define-public r-flextable
6311 (name "r-flextable")
6316 (uri (cran-uri "flextable" version))
6319 "1q6x9mfk5gikqjbbra1dn8hs1rq5ws99jdjav3m113gx9f2j5yxh"))))
6320 (build-system r-build-system)
6322 `(("r-base64enc" ,r-base64enc)
6323 ("r-data-table" ,r-data-table)
6324 ("r-gdtools" ,r-gdtools)
6325 ("r-htmltools" ,r-htmltools)
6326 ("r-knitr" ,r-knitr)
6327 ("r-officer" ,r-officer)
6328 ("r-rlang" ,r-rlang)
6329 ("r-rmarkdown" ,r-rmarkdown)
6330 ("r-xml2" ,r-xml2)))
6331 (home-page "https://davidgohel.github.io/flextable")
6332 (synopsis "Functions for tabular reporting")
6334 "This package provides tools to create pretty tables for HTML documents
6335 and other formats. Functions are provided to let users create tables, modify
6336 and format their content. It extends the @code{officer} package and can be
6337 used within R markdown documents when rendering to HTML and to Word
6339 (license license:gpl3)))
6341 (define-public r-writexl
6348 (uri (cran-uri "writexl" version))
6351 "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"))))
6352 (build-system r-build-system)
6353 (inputs `(("zlib" ,zlib)))
6354 (home-page "https://github.com/ropensci/writexl")
6355 (synopsis "Export data frames to xlsx format")
6357 "This package provides a data frame to xlsx exporter based on
6359 (license license:bsd-2)))
6361 (define-public r-biasedurn
6363 (name "r-biasedurn")
6368 (uri (cran-uri "BiasedUrn" version))
6371 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6372 (properties `((upstream-name . "BiasedUrn")))
6373 (build-system r-build-system)
6374 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6375 (synopsis "Biased Urn model distributions")
6377 "This package provides statistical models of biased sampling in the form
6378 of univariate and multivariate noncentral hypergeometric distributions,
6379 including Wallenius' noncentral hypergeometric distribution and Fisher's
6380 noncentral hypergeometric distribution (also called extended hypergeometric
6382 (license license:gpl3)))
6384 (define-public r-goplot
6391 (uri (cran-uri "GOplot" version))
6394 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6395 (properties `((upstream-name . "GOplot")))
6396 (build-system r-build-system)
6398 `(("r-ggdendro" ,r-ggdendro)
6399 ("r-ggplot2" ,r-ggplot2)
6400 ("r-gridextra" ,r-gridextra)
6401 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6402 (home-page "https://github.com/wencke/wencke.github.io")
6403 (synopsis "Visualization of functional analysis data")
6405 "This package provides an implementation of multilayered visualizations
6406 for enhanced graphical representation of functional analysis data. It
6407 combines and integrates omics data derived from expression and functional
6408 annotation enrichment analyses. Its plotting functions have been developed
6409 with an hierarchical structure in mind: starting from a general overview to
6410 identify the most enriched categories (modified bar plot, bubble plot) to a
6411 more detailed one displaying different types of relevant information for the
6412 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6413 Venn diagram, heatmap).")
6414 (license license:gpl2)))
6416 (define-public r-getopt
6423 (uri (cran-uri "getopt" version))
6426 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6427 (build-system r-build-system)
6428 (home-page "https://github.com/trevorld/getopt")
6429 (synopsis "Command-line option processor for R")
6431 "This package is designed to be used with Rscript to write shebang
6432 scripts that accept short and long options. Many users will prefer to
6433 use the packages @code{optparse} or @code{argparse} which add extra
6434 features like automatically generated help options and usage texts,
6435 support for default values, positional argument support, etc.")
6436 (license license:gpl2+)))
6438 (define-public r-findpython
6440 (name "r-findpython")
6445 (uri (cran-uri "findpython" version))
6448 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6449 (build-system r-build-system)
6450 (home-page "https://github.com/trevorld/findpython")
6451 (synopsis "Functions to find an acceptable Python binary")
6453 "This package was designed to find an acceptable Python binary that
6454 matches version and feature constraints.")
6455 (license license:expat)))
6457 ;; This in not the same as "r-argparser"
6458 (define-public r-argparse
6465 (uri (cran-uri "argparse" version))
6468 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6469 (build-system r-build-system)
6470 (inputs `(("python" ,python)))
6472 `(("r-findpython" ,r-findpython)
6473 ("r-jsonlite" ,r-jsonlite)
6475 (home-page "https://github.com/trevorld/argparse")
6476 (synopsis "Command line optional and positional argument parser")
6478 "This package provides a command line parser to be used with Rscript to
6479 write shebang scripts that gracefully accept positional and optional arguments
6480 and automatically generate usage notices.")
6481 (license license:gpl2+)))
6483 (define-public r-hash
6490 (uri (cran-uri "hash" version))
6493 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6494 (build-system r-build-system)
6495 (home-page "https://cran.r-project.org/web/packages/hash/")
6496 (synopsis "Implementation of hash/associated arrays/dictionaries")
6498 "This package implements a data structure similar to hashes in Perl and
6499 dictionaries in Python but with a purposefully R flavor. For objects of
6500 appreciable size, access using hashes outperforms native named lists and
6502 (license license:gpl2+)))
6504 (define-public r-orddom
6511 (uri (cran-uri "orddom" version))
6514 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6515 (build-system r-build-system)
6516 (propagated-inputs `(("r-psych" ,r-psych)))
6517 (home-page "https://cran.r-project.org/web/packages/orddom/")
6518 (synopsis "Ordinal dominance statistics")
6520 "This package provides tools to compute ordinal, statistics and effect
6521 sizes as an alternative to mean comparison: Cliff's delta or success rate
6522 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6523 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6524 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6525 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6526 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6527 Group (Non-)Overlap considerations.")
6528 (license license:gpl2)))
6530 (define-public r-doby
6537 (uri (cran-uri "doBy" version))
6540 "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb"))))
6541 (properties `((upstream-name . "doBy")))
6542 (build-system r-build-system)
6544 `(("r-dplyr" ,r-dplyr)
6545 ("r-magrittr" ,r-magrittr)
6547 ("r-matrix" ,r-matrix)
6548 ("r-plyr" ,r-plyr)))
6549 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6550 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6552 "This package contains:
6555 @item facilities for working with grouped data: @code{do}
6556 something to data stratified @code{by} some variables.
6557 @item implementations of least-squares means, general linear contrasts, and
6558 @item miscellaneous other utilities.
6560 (license license:gpl2+)))
6562 (define-public r-refgenome
6564 (name "r-refgenome")
6569 (uri (cran-uri "refGenome" version))
6572 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6573 (properties `((upstream-name . "refGenome")))
6574 (build-system r-build-system)
6578 ("r-rsqlite" ,r-rsqlite)))
6579 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6581 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6583 "This package contains functionality for importing and managing of
6584 downloaded genome annotation data from the Ensembl genome browser (European
6585 Bioinformatics Institute) and from the UCSC genome browser (University of
6586 California, Santa Cruz) and annotation routines for genomic positions and
6587 splice site positions.")
6588 (license license:gpl2)))
6590 (define-public r-basix
6597 (uri (cran-uri "BASIX" version))
6600 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6601 (properties `((upstream-name . "BASIX")))
6602 (build-system r-build-system)
6603 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6604 (synopsis "Efficient C/C++ toolset for R")
6606 "BASIX provides some efficient C/C++ implementations of native R
6607 procedures to speed up calculations in R.")
6608 (license license:gpl2)))
6610 (define-public r-blockfest
6612 (name "r-blockfest")
6617 (uri (cran-uri "BlockFeST" version))
6620 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6621 (properties `((upstream-name . "BlockFeST")))
6622 (build-system r-build-system)
6623 (propagated-inputs `(("r-basix" ,r-basix)))
6624 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6625 (synopsis "Bayesian calculation of region-specific fixation index")
6627 "This package provides an R implementation of an extension of the
6628 BayeScan software for codominant markers, adding the option to group
6629 individual SNPs into pre-defined blocks. A typical application of this new
6630 approach is the identification of genomic regions, genes, or gene sets
6631 containing one or more SNPs that evolved under directional selection.")
6632 (license license:gpl2)))
6634 (define-public r-proc
6641 (uri (cran-uri "pROC" version))
6644 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6645 (properties `((upstream-name . "pROC")))
6646 (build-system r-build-system)
6648 `(("r-plyr" ,r-plyr)
6649 ("r-rcpp" ,r-rcpp)))
6650 (home-page "http://expasy.org/tools/pROC/")
6651 (synopsis "Display and analyze ROC curves")
6653 "This package provides tools for visualizing, smoothing and comparing
6654 receiver operating characteristic (ROC curves). The area under the
6655 curve (AUC) can be compared with statistical tests based on U-statistics or
6656 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6657 (license license:gpl3+)))
6659 (define-public r-rootsolve
6661 (name "r-rootsolve")
6666 (uri (cran-uri "rootSolve" version))
6669 "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8"))))
6670 (properties `((upstream-name . "rootSolve")))
6671 (build-system r-build-system)
6672 (native-inputs `(("gfortran" ,gfortran)))
6673 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6674 (synopsis "Tools for the analysis of ordinary differential equations")
6676 "This package provides routines to find the root of nonlinear functions,
6677 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6678 differential equations} (ODE). It includes routines that:
6681 @item generate gradient and jacobian matrices (full and banded),
6682 @item find roots of non-linear equations by the Newton-Raphson method,
6683 @item estimate steady-state conditions of a system of (differential) equations
6684 in full, banded or sparse form, using the Newton-Raphson method, or by
6685 dynamically running,
6686 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6687 and 3-D partial differential equations, that have been converted to ordinary
6688 differential equations by numerical differencing (using the method-of-lines
6691 (license license:gpl2+)))
6693 (define-public r-abcanalysis
6695 (name "r-abcanalysis")
6700 (uri (cran-uri "ABCanalysis" version))
6702 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6703 (properties `((upstream-name . "ABCanalysis")))
6704 (build-system r-build-system)
6705 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6706 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6707 (synopsis "Computed ABC Analysis")
6709 "Multivariate data sets often differ in several factors or derived statistical
6710 parameters, which have to be selected for a valid interpretation. Basing this
6711 selection on traditional statistical limits leads occasionally to the perception
6712 of losing information from a data set. This package provides tools to calculate
6713 these limits on the basis of the mathematical properties of the distribution of
6714 the analyzed items.")
6715 (license license:gpl3)))
6717 (define-public r-slam
6724 (uri (cran-uri "slam" version))
6726 (base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4"))))
6727 (build-system r-build-system)
6728 (home-page "https://cran.r-project.org/web/packages/slam/")
6729 (synopsis "Sparse lightweight arrays and matrices")
6731 "This package contains data structures and algorithms for sparse arrays and matrices,
6732 based on index arrays and simple triplet representations, respectively.")
6733 (license license:gpl2)))
6735 (define-public r-manipulatewidget
6737 (name "r-manipulatewidget")
6742 (uri (cran-uri "manipulateWidget" version))
6744 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6746 `((upstream-name . "manipulateWidget")))
6747 (build-system r-build-system)
6749 `(("r-base64enc" ,r-base64enc)
6750 ("r-codetools" ,r-codetools)
6751 ("r-htmltools" ,r-htmltools)
6752 ("r-htmlwidgets" ,r-htmlwidgets)
6753 ("r-knitr" ,r-knitr)
6754 ("r-miniui" ,r-miniui)
6755 ("r-shiny" ,r-shiny)
6756 ("r-webshot" ,r-webshot)))
6757 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6758 (synopsis "Add even more interactivity to interactive charts")
6760 "This package lets you create in just a few lines of R code a nice user interface to
6761 modify the data or the graphical parameters of one or multiple interactive
6762 charts. It is useful to quickly explore visually some data or for package
6763 developers to generate user interfaces easy to maintain.")
6764 (license license:gpl2+)))
6773 (uri (cran-uri "A3" version))
6775 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6776 (properties `((upstream-name . "A3")))
6777 (build-system r-build-system)
6779 `(("r-pbapply" ,r-pbapply)
6780 ("r-xtable" ,r-xtable)))
6781 (home-page "https://cran.r-project.org/web/packages/A3/")
6782 (synopsis "Error metrics for predictive models")
6784 "This package supplies tools for tabulating and analyzing the results of predictive
6785 models. The methods employed are applicable to virtually any predictive model
6786 and make comparisons between different methodologies straightforward.")
6787 (license license:gpl2+)))
6789 (define-public r-infotheo
6796 (uri (cran-uri "infotheo" version))
6799 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
6800 (build-system r-build-system)
6801 (home-page "http://homepage.meyerp.com/software")
6802 (synopsis "Information-theoretic measures")
6804 "This package implements various measures of information theory based on
6805 several entropy estimators.")
6806 (license license:gpl3+)))
6808 (define-public r-abcoptim
6815 (uri (cran-uri "ABCoptim" version))
6817 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
6818 (properties `((upstream-name . "ABCoptim")))
6819 (build-system r-build-system)
6820 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
6821 (home-page "https://github.com/gvegayon/ABCoptim/")
6822 (synopsis "Optimization of Artificial Bee Colony algorithm")
6824 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
6825 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
6826 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
6827 algorithms, and uses only common control parameters such as colony size and
6828 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
6829 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
6830 This version is a work-in-progress and is written in R code.")
6831 (license license:expat)))
6833 (define-public r-abcp2
6840 (uri (cran-uri "ABCp2" version))
6842 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
6843 (properties `((upstream-name . "ABCp2")))
6844 (build-system r-build-system)
6845 (propagated-inputs `(("r-mass" ,r-mass)))
6846 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
6847 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
6849 "This package tests the goodness of fit of a distribution of offspring to the Normal,
6850 Poisson, and Gamma distribution and estimates the proportional paternity of the
6851 second male (P2) based on the best fit distribution.")
6852 (license license:gpl2)))
6854 (define-public r-abcrf
6861 (uri (cran-uri "abcrf" version))
6863 (base32 "0r31ki89z8zzcffm0yvd2zw3q96rk6g6fnwwkql902mgajbrha1f"))))
6864 (build-system r-build-system)
6866 `(("r-doparallel" ,r-doparallel)
6867 ("r-foreach" ,r-foreach)
6869 ("r-matrixstats" ,r-matrixstats)
6870 ("r-ranger" ,r-ranger)
6872 ("r-rcpparmadillo" ,r-rcpparmadillo)
6873 ("r-readr" ,r-readr)
6874 ("r-stringr" ,r-stringr)))
6875 (home-page "https://cran.r-project.org/web/packages/abcrf/")
6876 (synopsis "Approximate bayesian computation via random forests")
6878 "This package performs approximate bayesian computation (ABC) model choice and
6879 parameter inference via random forests. This machine learning tool named random
6880 forests (RF) can conduct selection among the highly complex models covered by
6882 (license license:gpl2+)))
6884 (define-public r-abctools
6891 (uri (cran-uri "abctools" version))
6893 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
6894 (build-system r-build-system)
6897 ("r-abind" ,r-abind)
6898 ("r-hmisc" ,r-hmisc)
6899 ("r-plyr" ,r-plyr)))
6900 (home-page "https://github.com/dennisprangle/abctools/")
6901 (synopsis "Tools for ABC analyses")
6903 "This @code{r-abctools} package provides tools for approximate Bayesian computation
6904 including summary statistic selection and assessing coverage. This includes
6905 recent dimension reduction algorithms to tune the choice of summary statistics,
6906 and coverage methods to tune the choice of threshold.")
6907 (license license:gpl2+)))
6909 (define-public r-ggstance
6916 (uri (cran-uri "ggstance" version))
6918 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
6919 (build-system r-build-system)
6921 `(("r-ggplot2" ,r-ggplot2)
6923 ("r-rlang" ,r-rlang)
6924 ("r-withr" ,r-withr)))
6925 (home-page "https://cran.r-project.org/web/packages/ggstance/")
6926 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
6928 "This package is a @code{r-ggplot2} extension that provides flipped components:
6930 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
6931 @item vertical versions of @code{r-ggplot2} positions.
6933 (license license:gpl3)))
6935 (define-public r-mosaiccore
6937 (name "r-mosaiccore")
6942 (uri (cran-uri "mosaicCore" version))
6944 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
6945 (properties `((upstream-name . "mosaicCore")))
6946 (build-system r-build-system)
6948 `(("r-dplyr" ,r-dplyr)
6949 ("r-lazyeval" ,r-lazyeval)
6951 ("r-rlang" ,r-rlang)
6952 ("r-tidyr" ,r-tidyr)))
6953 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
6954 (synopsis "Common utilities for mosaic family packages")
6956 "Common utilities used in other Mosaic family packages are collected here.")
6957 (license license:gpl2+)))
6959 (define-public r-ggformula
6961 (name "r-ggformula")
6966 (uri (cran-uri "ggformula" version))
6968 (base32 "16ycabhnp78fsiv1dc63ccgh9gmpsy2683vbmq0fdzl6w3pd87sr"))))
6969 (build-system r-build-system)
6971 `(("r-ggplot2" ,r-ggplot2)
6972 ("r-ggstance" ,r-ggstance)
6973 ("r-magrittr" ,r-magrittr)
6974 ("r-mosaiccore" ,r-mosaiccore)
6975 ("r-rlang" ,r-rlang)
6976 ("r-stringr" ,r-stringr)
6977 ("r-tibble" ,r-tibble)
6978 ("r-tidyr" ,r-tidyr)))
6979 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
6980 (synopsis "Formula interface for the @code{r-ggplot2}")
6982 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
6983 gf_density(), and so on, bring the formula interface to ggplot(). This captures
6984 and extends the excellent simplicity of the lattice-graphics formula interface,
6985 while providing the intuitive capabilities of @code{r-ggplot2}.")
6986 (license license:expat)))
6988 (define-public r-mosaicdata
6990 (name "r-mosaicdata")
6995 (uri (cran-uri "mosaicData" version))
6997 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
6998 (properties `((upstream-name . "mosaicData")))
6999 (build-system r-build-system)
7000 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7001 (synopsis "Data sets for project Mosaic")
7003 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7004 used to teach mathematics, statistics, computation and modeling.")
7005 (license license:gpl2+)))
7007 (define-public r-raster
7014 (uri (cran-uri "raster" version))
7017 "0faxv71hlxkblvbi3ps1vfzm3wwi0brwzmpsr5114bddcqyiqkvn"))))
7018 (build-system r-build-system)
7020 `(("r-rcpp" ,r-rcpp)
7022 (home-page "https://www.rspatial.org/")
7023 (synopsis "Geographic data analysis and modeling")
7025 "The package implements basic and high-level functions for reading,
7026 writing, manipulating, analyzing and modeling of gridded spatial data.
7027 Processing of very large files is supported.")
7028 (license license:gpl3+)))
7030 (define-public r-mosaic
7037 (uri (cran-uri "mosaic" version))
7039 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7040 (build-system r-build-system)
7042 `(("r-broom" ,r-broom)
7043 ("r-dplyr" ,r-dplyr)
7044 ("r-ggdendro" ,r-ggdendro)
7045 ("r-ggformula" ,r-ggformula)
7046 ("r-ggplot2" ,r-ggplot2)
7047 ("r-ggrepel" ,r-ggrepel)
7049 ("r-gridextra" ,r-gridextra)
7050 ("r-lattice" ,r-lattice)
7051 ("r-latticeextra" ,r-latticeextra)
7052 ("r-lazyeval" ,r-lazyeval)
7054 ("r-matrix" ,r-matrix)
7055 ("r-mosaiccore" ,r-mosaiccore)
7056 ("r-mosaicdata" ,r-mosaicdata)
7057 ("r-readr" ,r-readr)
7058 ("r-tidyr" ,r-tidyr)))
7059 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7060 (synopsis "Mathematics, statistics, and computation teaching utilities")
7062 "This package contain data sets and utilities from
7063 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7064 statistics, computation and modeling. Project MOSAIC is a community of
7065 educators working to tie together aspects of quantitative work that students
7066 in science, technology, engineering and mathematics will need in their
7067 professional lives, but which are usually taught in isolation, if at all.")
7068 (license license:gpl2+)))
7070 (define-public r-abd
7077 (uri (cran-uri "abd" version))
7079 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7080 (build-system r-build-system)
7082 `(("r-lattice" ,r-lattice)
7083 ("r-mosaic" ,r-mosaic)
7084 ("r-nlme" ,r-nlme)))
7085 (home-page "https://cran.r-project.org/web/packages/abd/")
7086 (synopsis "Analysis of biological data")
7088 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7089 biological data by Michael Whitlock and Dolph Schluter.")
7090 (license license:gpl2)))
7092 (define-public r-svgui
7099 (uri (cran-uri "svGUI" version))
7101 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7102 (properties `((upstream-name . "svGUI")))
7103 (build-system r-build-system)
7104 (home-page "https://github.com/SciViews/svGUI/")
7105 (synopsis "Functions for managing GUI clients in R")
7107 "The SciViews @code{svGUI} package eases the management of Graphical User
7108 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7109 centralizes info about GUI elements currently used, and it dispatches GUI
7110 calls to the particular toolkits in use in function of the context.")
7111 (license license:gpl2)))
7113 (define-public r-svdialogs
7115 (name "r-svdialogs")
7120 (uri (cran-uri "svDialogs" version))
7122 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7123 (properties `((upstream-name . "svDialogs")))
7124 (build-system r-build-system)
7127 ("zenity" ,zenity)))
7129 `(("r-rstudioapi" ,r-rstudioapi)
7130 ("r-svgui" ,r-svgui)))
7131 (home-page "https://github.com/SciViews/svDialogs/")
7132 (synopsis "Portable dialog boxes")
7134 "This package helps to construct standard dialog boxes for your GUI, including
7135 message boxes, input boxes, list, file or directory selection, and others. In
7136 case R cannot display GUI dialog boxes, a simpler command line version of these
7137 interactive elements is also provided as a fallback solution.")
7138 (license license:gpl2)))
7140 (define-public r-abe
7147 (uri (cran-uri "abe" version))
7150 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7151 (build-system r-build-system)
7152 (home-page "https://cran.r-project.org/web/packages/abe/")
7153 (synopsis "Augmented backward elimination")
7155 "This package performs augmented backward elimination and checks the
7156 stability of the obtained model. Augmented backward elimination combines
7157 significance or information based criteria with the change in estimate to
7158 either select the optimal model for prediction purposes or to serve as a tool
7159 to obtain a practically sound, highly interpretable model.")
7160 (license license:gpl2+)))
7162 (define-public r-abf2
7169 (uri (cran-uri "abf2" version))
7171 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7172 (build-system r-build-system)
7173 (home-page "https://cran.r-project.org/web/packages/abf2/")
7174 (synopsis "Load gap-free axon @code{r-abf2} files")
7176 "This package loads electrophysiology data from ABF2 files, as created by
7177 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7178 mode are currently supported.")
7179 (license license:artistic2.0)))
7181 (define-public r-abhgenotyper
7183 (name "r-abhgenotyper")
7188 (uri (cran-uri "ABHgenotypeR" version))
7190 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7191 (properties `((upstream-name . "ABHgenotypeR")))
7192 (build-system r-build-system)
7194 `(("r-ggplot2" ,r-ggplot2)
7195 ("r-reshape2" ,r-reshape2)))
7196 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7197 (synopsis "Visualize and manipulate ABH genotypes")
7199 "The @code{r-abhgenotyper} package provides simple imputation,
7200 error-correction and plotting capacities for genotype data. The package is
7201 supposed to serve as an intermediate but independent analysis tool between the
7202 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7203 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7204 genotypes as \"graphical genotypes\".")
7205 (license license:gpl3)))
7207 (define-public r-furrr
7214 (uri (cran-uri "furrr" version))
7217 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7218 (build-system r-build-system)
7220 `(("r-future" ,r-future)
7221 ("r-globals" ,r-globals)
7222 ("r-purrr" ,r-purrr)
7223 ("r-rlang" ,r-rlang)))
7224 (home-page "https://github.com/DavisVaughan/furrr")
7225 (synopsis "Apply mapping functions in parallel using futures")
7227 "This package provides implementations of the family of @code{map()}
7228 functions from the @code{purrr} package that can be resolved using any
7229 @code{future}-supported backend, e.g. parallel on the local machine or
7230 distributed on a compute cluster.")
7231 (license license:lgpl2.1+)))
7233 (define-public r-abjutils
7240 (uri (cran-uri "abjutils" version))
7242 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7243 (build-system r-build-system)
7245 `(("r-devtools" ,r-devtools)
7246 ("r-dplyr" ,r-dplyr)
7247 ("r-furrr" ,r-furrr)
7248 ("r-future" ,r-future)
7251 ("r-magrittr" ,r-magrittr)
7252 ("r-progress" ,r-progress)
7253 ("r-purrr" ,r-purrr)
7254 ("r-readr" ,r-readr)
7255 ("r-rlang" ,r-rlang)
7256 ("r-rstudioapi" ,r-rstudioapi)
7257 ("r-scales" ,r-scales)
7258 ("r-stringi" ,r-stringi)
7259 ("r-stringr" ,r-stringr)
7260 ("r-tibble" ,r-tibble)
7261 ("r-tidyr" ,r-tidyr)))
7262 (home-page "https://github.com/abjur/abjutils/")
7263 (synopsis "Collection of tools for jurimetrical analysis")
7265 "This package implements general purpose tools, such as functions for
7266 sampling and basic manipulation of Brazilian lawsuits identification number.
7267 It also implements functions for text cleaning, such as accentuation
7269 (license license:expat)))
7271 (define-public r-abnormality
7273 (name "r-abnormality")
7278 (uri (cran-uri "abnormality" version))
7280 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7281 (build-system r-build-system)
7283 `(("r-mass" ,r-mass)
7284 ("r-matrix" ,r-matrix)))
7285 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7286 (synopsis "Measure a subject's abnormality with respect to a reference population")
7288 "This package contains functions to implement the methodology and
7289 considerations laid out by Marks et al. in the article \"Measuring abnormality
7290 in high dimensional spaces: applications in biomechanical gait analysis\".
7291 Using high-dimensional datasets to measure a subject's overall level of
7292 abnormality as compared to a reference population is often needed in outcomes
7294 (license license:expat)))
7296 (define-public r-abodoutlier
7298 (name "r-abodoutlier")
7303 (uri (cran-uri "abodOutlier" version))
7305 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7306 (properties `((upstream-name . "abodOutlier")))
7307 (build-system r-build-system)
7309 `(("r-cluster" ,r-cluster)))
7310 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7311 (synopsis "Angle-based outlier detection")
7313 "This package performs angle-based outlier detection on a given data
7314 frame. It offers three methods to process data:
7316 @item full but slow implementation using all the data that has cubic
7318 @item a fully randomized method;
7319 @item a method using k-nearest neighbours.
7321 These algorithms are well suited for high dimensional data outlier
7323 (license license:expat)))
7325 (define-public r-abps
7332 (uri (cran-uri "ABPS" version))
7334 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7335 (properties `((upstream-name . "ABPS")))
7336 (build-system r-build-system)
7337 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7338 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7339 (synopsis "Abnormal blood profile score to detect blood doping")
7341 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7342 The ABPS is a part of the Athlete biological passport program of the World
7343 anti-doping agency, which combines several blood parameters into a single
7344 score in order to detect blood doping. The package also contains functions to
7345 calculate other scores used in anti-doping programs, such as the ratio of
7346 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7347 (license license:gpl2+)))
7349 (define-public r-parmigene
7351 (name "r-parmigene")
7356 (uri (cran-uri "parmigene" version))
7359 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7360 (build-system r-build-system)
7361 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7362 (synopsis "Mutual information estimation for gene network reconstruction")
7364 "This package provides a parallel estimation of the mutual information
7365 based on entropy estimates from k-nearest neighbors distances and algorithms
7366 for the reconstruction of gene regulatory networks.")
7367 (license license:agpl3+)))
7369 (define-public r-pscl
7376 (uri (cran-uri "pscl" version))
7378 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7379 (build-system r-build-system)
7381 `(("r-mass" ,r-mass)))
7382 (home-page "https://github.com/atahk/pscl/")
7383 (synopsis "Political science computational laboratory")
7385 "The @code{pscl} is an R package providing classes and methods for:
7387 @item Bayesian analysis of roll call data (item-response models);
7388 @item elementary Bayesian statistics;
7389 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7391 @item utility functions.
7393 (license license:gpl2)))
7395 (define-public r-accelmissing
7397 (name "r-accelmissing")
7402 (uri (cran-uri "accelmissing" version))
7404 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7405 (build-system r-build-system)
7407 `(("r-mice" ,r-mice)
7408 ("r-pscl" ,r-pscl)))
7409 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7410 (synopsis "Missing value imputation for accelerometer data")
7412 "This package provides a statistical method to impute the missing values in
7413 accelerometer data. The methodology includes both parametric and
7414 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7415 model. It also provides multiple functions to preprocess the accelerometer data
7416 previous to the missing data imputation. These include detecting the wearing
7417 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7418 (license license:gpl2+)))
7420 (define-public r-mhsmm
7427 (uri (cran-uri "mhsmm" version))
7429 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7430 (build-system r-build-system)
7431 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7432 (home-page "https://github.com/jaredo/mhsmm/")
7433 (synopsis "Inference for hidden Markov and semi-Markov models")
7435 "The @code{r-mhsmm} package implements estimation and prediction methods for
7436 hidden Markov and semi-Markov models for multiple observation sequences. Such
7437 techniques are of interest when observed data is thought to be dependent on some
7438 unobserved (or hidden) state. Also, this package is suitable for equidistant
7439 time series data, with multivariate and/or missing data. Allows user defined
7440 emission distributions.")
7441 (license license:gpl2+)))
7443 (define-public r-nleqslv
7450 (uri (cran-uri "nleqslv" version))
7452 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7453 (build-system r-build-system)
7454 (native-inputs `(("gfortran" ,gfortran)))
7455 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7456 (synopsis "Solve systems of nonlinear equations")
7458 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7459 Broyden or a Newton method with a choice of global strategies such as line
7460 search and trust region. There are options for using a numerical or user
7461 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7462 singular or ill-conditioned Jacobian.")
7463 (license license:gpl2+)))
7465 (define-public r-physicalactivity
7467 (name "r-physicalactivity")
7472 (uri (cran-uri "PhysicalActivity" version))
7474 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7476 `((upstream-name . "PhysicalActivity")))
7477 (build-system r-build-system)
7478 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7479 (synopsis "Procesing accelerometer data for physical activity measurement")
7481 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7482 for classification of monitor wear and nonwear time intervals in accelerometer
7483 data collected to assess physical activity. The package also contains functions
7484 for making plots of accelerometer data and obtaining the summary of various
7485 information including daily monitor wear time and the mean monitor wear time
7486 during valid days. The revised package version 0.2-1 improved the functions
7487 regarding speed, robustness and add better support for time zones and daylight
7488 saving. In addition, several functions were added:
7490 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7491 @item the @code{markPAI} can categorize physical activity intensity level based
7492 on user-defined cut-points of accelerometer counts.
7494 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7495 @code{queryActigraph} functions.")
7496 (license license:gpl3+)))
7498 (define-public r-acc
7505 (uri (cran-uri "acc" version))
7507 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7508 (build-system r-build-system)
7510 `(("r-circlize" ,r-circlize)
7512 ("r-ggplot2" ,r-ggplot2)
7513 ("r-iterators" ,r-iterators)
7514 ("r-mhsmm" ,r-mhsmm)
7515 ("r-nleqslv" ,r-nleqslv)
7516 ("r-physicalactivity" ,r-physicalactivity)
7518 ("r-r-utils" ,r-r-utils)
7520 ("r-rcpparmadillo" ,r-rcpparmadillo)
7521 ("r-rsqlite" ,r-rsqlite)
7523 (home-page "https://cran.r-project.org/web/packages/acc/")
7524 (synopsis "Exploring accelerometer data")
7526 "This package processes accelerometer data from uni-axial and tri-axial devices
7527 and generates data summaries. Also, includes functions to plot, analyze, and
7528 simulate accelerometer data.")
7529 (license license:gpl2+)))
7531 (define-public r-rbenchmark
7533 (name "r-rbenchmark")
7538 (uri (cran-uri "rbenchmark" version))
7540 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7541 (build-system r-build-system)
7542 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7543 (synopsis "Benchmarking routine for R")
7545 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7546 and is intended to facilitate benchmarking of arbitrary R code. The library
7547 consists of just one function, benchmark, which is a simple wrapper around
7548 system.time. Given a specification of the benchmarking process (counts of
7549 replications, evaluation environment) and an arbitrary number of expressions,
7550 benchmark evaluates each of the expressions in the specified environment,
7551 replicating the evaluation as many times as specified, and returning the results
7552 conveniently wrapped into a data frame.")
7553 (license license:gpl2+)))
7555 (define-public r-mitools
7562 (uri (cran-uri "mitools" version))
7565 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7566 (build-system r-build-system)
7567 (propagated-inputs `(("r-dbi" ,r-dbi)))
7568 (home-page "https://cran.r-project.org/web/packages/mitools/")
7569 (synopsis "Tools for multiple imputation of missing data")
7571 "This package provides tools to perform analyses and combine results from
7572 multiple-imputation datasets.")
7573 (license license:gpl2)))
7575 (define-public r-magick
7582 (uri (cran-uri "magick" version))
7585 "1xh5mhaks3wk1iwqs9d3lnbfv121lc1yz5fqdzk5il9ppr831l85"))))
7586 (build-system r-build-system)
7588 `(("imagemagick" ,imagemagick)
7591 `(("r-curl" ,r-curl)
7592 ("r-magrittr" ,r-magrittr)
7593 ("r-rcpp" ,r-rcpp)))
7595 `(("pkg-config" ,pkg-config)))
7596 (home-page "https://github.com/ropensci/magick")
7597 (synopsis "Advanced graphics and image-processing in R")
7599 "This package provides bindings to ImageMagick, a comprehensive image
7600 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7601 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7602 operations are vectorized via the Magick++ STL meaning they operate either on
7603 a single frame or a series of frames for working with layers, collages, or
7604 animation. In RStudio, images are automatically previewed when printed to the
7605 console, resulting in an interactive editing environment.")
7606 (license license:expat)))
7608 (define-public r-survey
7615 (uri (cran-uri "survey" version))
7618 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7619 (build-system r-build-system)
7621 `(("r-lattice" ,r-lattice)
7622 ("r-matrix" ,r-matrix)
7623 ("r-minqa" ,r-minqa)
7624 ("r-mitools" ,r-mitools)
7625 ("r-numderiv" ,r-numderiv)
7626 ("r-survival" ,r-survival)))
7627 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7628 (synopsis "Analysis of complex survey samples")
7630 "This package provides tools for the analysis of complex survey samples.
7631 The provided features include: summary statistics, two-sample tests, rank
7632 tests, generalised linear models, cumulative link models, Cox models,
7633 loglinear models, and general maximum pseudolikelihood estimation for
7634 multistage stratified, cluster-sampled, unequally weighted survey samples;
7635 variances by Taylor series linearisation or replicate weights;
7636 post-stratification, calibration, and raking; two-phase subsampling designs;
7637 graphics; PPS sampling without replacement; principal components, and factor
7639 ;; Either version of the GPL.
7640 (license (list license:gpl2 license:gpl3))))
7642 (define-public r-dvmisc
7649 (uri (cran-uri "dvmisc" version))
7651 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7652 (build-system r-build-system)
7654 `(("r-cubature" ,r-cubature)
7655 ("r-data-table" ,r-data-table)
7656 ("r-dplyr" ,r-dplyr)
7657 ("r-ggplot2" ,r-ggplot2)
7659 ("r-mvtnorm" ,r-mvtnorm)
7660 ("r-pracma" ,r-pracma)
7661 ("r-purrr" ,r-purrr)
7662 ("r-rbenchmark" ,r-rbenchmark)
7664 ("r-survey" ,r-survey)))
7665 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7666 (synopsis "Faster computation of common statistics and miscellaneous functions")
7668 "This package implements faster versions of base R functions (e.g. mean, standard
7669 deviation, covariance, weighted mean), mostly written in C++, along with
7670 miscellaneous functions for various purposes (e.g. create the histogram with
7671 fitted probability density function or probability mass function curve, create
7672 the body mass index groups, assess the linearity assumption in logistic
7674 (license license:gpl2)))
7676 (define-public r-accelerometry
7678 (name "r-accelerometry")
7683 (uri (cran-uri "accelerometry" version))
7685 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7686 (build-system r-build-system)
7688 `(("r-dvmisc" ,r-dvmisc)
7689 ("r-rcpp" ,r-rcpp)))
7690 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7691 (synopsis "Functions for processing accelerometer data")
7693 "This package provides a collection of functions that perform operations on
7694 time-series accelerometer data, such as identify the non-wear time, flag minutes
7695 that are part of an activity bout, and find the maximum 10-minute average count
7696 value. The functions are generally very flexible, allowing for a variety of
7697 algorithms to be implemented.")
7698 (license license:gpl3)))
7700 (define-public r-absim
7707 (uri (cran-uri "AbSim" version))
7709 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7710 (properties `((upstream-name . "AbSim")))
7711 (build-system r-build-system)
7714 ("r-powerlaw" ,r-powerlaw)))
7715 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7716 (synopsis "Time resolved simulations of antibody repertoires")
7718 "This package provides simulation methods for the evolution of antibody repertoires.
7719 The heavy and light chain variable region of both human and C57BL/6 mice can
7720 be simulated in a time-dependent fashion. Both single lineages using one set of
7721 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7722 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7723 Upon completion, the main loop of the algorithm begins, with each iteration
7724 representing one simulated time step. Various mutation events are possible at
7725 each time step, contributing to a diverse final repertoire.")
7726 (license license:gpl2)))
7728 (define-public r-quic
7735 (uri (cran-uri "QUIC" version))
7737 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7738 (properties `((upstream-name . "QUIC")))
7739 (build-system r-build-system)
7740 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7741 (synopsis "Regularized sparse inverse covariance matrix estimation")
7743 "This package implements the regularized Gaussian maximum likelihood
7744 estimation of the inverse of a covariance matrix. It uses Newton's method and
7745 coordinate descent to solve the regularized inverse covariance matrix
7746 estimation problem.")
7747 ;; The project home page states that the release is under GPLv3 or later.
7748 ;; The CRAN page only says GPL-3.
7749 (license license:gpl3+)))
7751 (define-public r-abundant
7758 (uri (cran-uri "abundant" version))
7760 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7761 (build-system r-build-system)
7763 `(("r-quic" ,r-quic)))
7764 (home-page "https://cran.r-project.org/web/packages/abundant/")
7765 (synopsis "Abundant regression and high-dimensional principal fitted components")
7767 "This package provides tools to fit and predict with the high-dimensional
7768 principal fitted components model. This model is described by Cook, Forzani,
7769 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7770 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7771 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7772 (license license:gpl2+)))
7774 (define-public r-ac3net
7781 (uri (cran-uri "Ac3net" version))
7783 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7784 (properties `((upstream-name . "Ac3net")))
7785 (build-system r-build-system)
7787 `(("r-data-table" ,r-data-table)))
7788 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
7789 (synopsis "Inferring directional conservative causal core gene networks")
7790 (description "This package infers directional Conservative causal core
7791 (gene) networks (C3NET). This is a version of the algorithm C3NET with
7792 directional network.")
7793 (license license:gpl3+)))
7795 (define-public r-aca
7802 (uri (cran-uri "ACA" version))
7804 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
7805 (properties `((upstream-name . "ACA")))
7806 (build-system r-build-system)
7807 (home-page "https://cran.r-project.org/web/packages/ACA/")
7808 (synopsis "Abrupt change-point or aberration detection in point series")
7810 "This package offers an interactive function for the detection of breakpoints in
7812 ;; Any version of the GPL
7813 (license (list license:gpl2+ license:gpl3+))))
7815 (define-public r-acceptancesampling
7817 (name "r-acceptancesampling")
7822 (uri (cran-uri "AcceptanceSampling" version))
7824 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
7826 `((upstream-name . "AcceptanceSampling")))
7827 (build-system r-build-system)
7828 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
7829 (synopsis "Creation and evaluation of acceptance sampling plans")
7831 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
7832 acceptance sampling plans. Acceptance sampling is a methodology commonly used
7833 in quality control and improvement. International standards of acceptance
7834 sampling provide sampling plans for specific circumstances. The aim of this
7835 package is to provide an easy-to-use interface to visualize single, double or
7836 multiple sampling plans. In addition, methods have been provided to enable the
7837 user to assess sampling plans against pre-specified levels of performance, as
7838 measured by the probability of acceptance for a given level of quality in the
7840 (license license:gpl3+)))
7842 (define-public r-acclma
7849 (uri (cran-uri "ACCLMA" version))
7851 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
7852 (properties `((upstream-name . "ACCLMA")))
7853 (build-system r-build-system)
7854 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
7855 (synopsis "ACC & LMA graph plotting")
7857 "This package contains a function that imports data from a @acronym{CSV,
7858 Comma-Separated Values} file, or uses manually entered data from the format (x,
7859 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
7860 Curve} vs @acronym{LOI, Line of Independence} graph and
7861 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
7862 function is @code{plotLMA} (source file, header) that takes a data set and plots the
7863 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
7864 string) was passed, a manual data entry window is opened. The header parameter
7865 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
7866 a header row or not. The dataset should contain only one independent variable
7867 (x) and one dependent variable (y) and can contain a weight for each
7869 (license license:gpl2)))
7871 (define-public r-aspi
7878 (uri (cran-uri "aspi" version))
7880 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
7881 (build-system r-build-system)
7883 "https://cran.r-project.org/web/packages/aspi/")
7885 "Analysis of symmetry of parasitic infections")
7887 "This package provides tools for the analysis and visualization of bilateral
7888 asymmetry in parasitic infections.")
7889 (license license:gpl3+)))
7891 (define-public r-sandwich
7898 (uri (cran-uri "sandwich" version))
7901 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
7902 (build-system r-build-system)
7904 `(("r-zoo" ,r-zoo)))
7905 (home-page "https://cran.r-project.org/web/packages/sandwich/")
7906 (synopsis "Robust Covariance Matrix Estimators")
7908 "This package provides model-robust standard error estimators for
7909 cross-sectional, time series, clustered, panel, and longitudinal data.")
7910 ;; Either version of the license.
7911 (license (list license:gpl2 license:gpl3))))
7913 (define-public r-th-data
7920 (uri (cran-uri "TH.data" version))
7923 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
7924 (properties `((upstream-name . "TH.data")))
7925 (build-system r-build-system)
7927 `(("r-mass" ,r-mass)
7928 ("r-survival" ,r-survival)))
7929 (home-page "https://cran.r-project.org/web/packages/TH.data/")
7930 (synopsis "Shared data sets")
7932 "This package contains supporting data sets that are used in other
7933 packages maintained by Torsten Hothorn.")
7934 (license license:gpl3)))
7936 (define-public r-multcomp
7943 (uri (cran-uri "multcomp" version))
7946 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
7947 (build-system r-build-system)
7949 `(("r-codetools" ,r-codetools)
7950 ("r-mvtnorm" ,r-mvtnorm)
7951 ("r-sandwich" ,r-sandwich)
7952 ("r-survival" ,r-survival)
7953 ("r-th-data" ,r-th-data)))
7954 (home-page "https://cran.r-project.org/web/packages/multcomp/")
7955 (synopsis "Simultaneous inference in general parametric models")
7957 "Simultaneous tests and confidence intervals for general linear
7958 hypotheses in parametric models, including linear, generalized linear, linear
7959 mixed effects, and survival models. The package includes demos reproducing
7960 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
7961 Hothorn, Westfall, 2010, CRC Press).")
7962 (license license:gpl2)))
7964 (define-public r-emmeans
7971 (uri (cran-uri "emmeans" version))
7974 "1fpawaxnmj67md169a9mzrnnh2d0c973xydfg6hw865933jil9lq"))))
7975 (build-system r-build-system)
7977 `(("r-estimability" ,r-estimability)
7978 ("r-mvtnorm" ,r-mvtnorm)
7979 ("r-numderiv" ,r-numderiv)
7981 ("r-xtable" ,r-xtable)))
7982 (home-page "https://github.com/rvlenth/emmeans")
7983 (synopsis "Estimated marginal means, aka least-squares means")
7985 "This package provides tools to obtain @dfn{estimated marginal
7986 means} (EMMs) for many linear, generalized linear, and mixed models. It can
7987 be used to compute contrasts or linear functions of EMMs, trends, and
7988 comparisons of slopes.")
7989 ;; Either version of the license.
7990 (license (list license:gpl2 license:gpl3))))
7992 (define-public r-pwr
7999 (uri (cran-uri "pwr" version))
8002 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
8003 (build-system r-build-system)
8005 `(("r-knitr" ,r-knitr)))
8006 (home-page "https://github.com/heliosdrm/pwr")
8007 (synopsis "Basic functions for power analysis")
8009 "This package provides power analysis functions along the lines of
8011 (license license:gpl3+)))
8013 (define-public r-libcoin
8020 (uri (cran-uri "libcoin" version))
8023 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8024 (build-system r-build-system)
8025 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8026 (home-page "https://cran.r-project.org/web/packages/libcoin")
8027 (synopsis "Linear test statistics for permutation inference")
8029 "This package provides basic infrastructure for linear test statistics
8030 and permutation inference in the framework of Strasser and Weber (1999).")
8031 (license license:gpl2)))
8033 (define-public r-coin
8040 (uri (cran-uri "coin" version))
8043 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8044 (build-system r-build-system)
8046 `(("r-libcoin" ,r-libcoin)
8047 ("r-matrixstats" ,r-matrixstats)
8048 ("r-modeltools" ,r-modeltools)
8049 ("r-multcomp" ,r-multcomp)
8050 ("r-mvtnorm" ,r-mvtnorm)
8051 ("r-survival" ,r-survival)))
8052 (home-page "http://coin.r-forge.r-project.org")
8053 (synopsis "Conditional inference procedures in a permutation test framework")
8055 "This package provides conditional inference procedures for the general
8056 independence problem including two-sample, K-sample (non-parametric ANOVA),
8057 correlation, censored, ordered and multivariate problems.")
8058 (license license:gpl2)))
8060 (define-public r-bayesplot
8062 (name "r-bayesplot")
8067 (uri (cran-uri "bayesplot" version))
8070 "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
8071 (build-system r-build-system)
8073 `(("pandoc" ,ghc-pandoc)
8074 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8076 `(("r-dplyr" ,r-dplyr)
8077 ("r-ggplot2" ,r-ggplot2)
8078 ("r-ggridges" ,r-ggridges)
8080 ("r-reshape2" ,r-reshape2)
8081 ("r-rlang" ,r-rlang)
8082 ("r-tibble" ,r-tibble)
8083 ("r-tidyselect" ,r-tidyselect)))
8084 (home-page "http://mc-stan.org/bayesplot")
8085 (synopsis "Plotting for Bayesian models")
8087 "This package provides plotting functions for posterior analysis, model
8088 checking, and MCMC diagnostics. The package is designed not only to provide
8089 convenient functionality for users, but also a common set of functions that
8090 can be easily used by developers working on a variety of R packages for
8091 Bayesian modeling.")
8092 (license license:gpl3+)))
8094 (define-public r-tmb
8101 (uri (cran-uri "TMB" version))
8104 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8105 (properties `((upstream-name . "TMB")))
8106 (build-system r-build-system)
8108 `(("r-matrix" ,r-matrix)
8109 ("r-rcppeigen" ,r-rcppeigen)))
8110 (home-page "http://tmb-project.org")
8111 (synopsis "Template model builder: a general random effect tool")
8113 "With this tool, a user should be able to quickly implement complex
8114 random effect models through simple C++ templates. The package combines
8115 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8116 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8117 from R) to obtain an efficient implementation of the applied Laplace
8118 approximation with exact derivatives. Key features are: Automatic sparseness
8119 detection, parallelism through BLAS and parallel user templates.")
8120 (license license:gpl2)))
8122 (define-public r-sjstats
8129 (uri (cran-uri "sjstats" version))
8132 "11z1wfi0d74d1rld0320l3vmv6rl41wa0v9bjc44rk06yc90wld2"))))
8133 (build-system r-build-system)
8135 `(("r-bayestestr" ,r-bayestestr)
8136 ("r-broom" ,r-broom)
8137 ("r-dplyr" ,r-dplyr)
8138 ("r-emmeans" ,r-emmeans)
8139 ("r-insight" ,r-insight)
8141 ("r-magrittr" ,r-magrittr)
8143 ("r-modelr" ,r-modelr)
8144 ("r-parameters" ,r-parameters)
8145 ("r-performance" ,r-performance)
8146 ("r-purrr" ,r-purrr)
8147 ("r-rlang" ,r-rlang)
8148 ("r-sjlabelled" ,r-sjlabelled)
8149 ("r-sjmisc" ,r-sjmisc)
8150 ("r-tidyr" ,r-tidyr)))
8151 (home-page "https://github.com/strengejacke/sjstats")
8152 (synopsis "Functions for common statistical computations")
8154 "This package provides a collection of convenient functions for common
8155 statistical computations, which are not directly provided by R's @code{base}
8156 or @code{stats} packages. This package aims at providing, first, shortcuts
8157 for statistical measures, which otherwise could only be calculated with
8158 additional effort. Second, these shortcut functions are generic, and can be
8159 applied not only to vectors, but also to other objects as well. The focus of
8160 most functions lies on summary statistics or fit measures for regression
8161 models, including generalized linear models, mixed effects models and Bayesian
8163 (license license:gpl3)))
8165 (define-public r-glmmtmb
8172 (uri (cran-uri "glmmTMB" version))
8175 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8176 (properties `((upstream-name . "glmmTMB")))
8177 (build-system r-build-system)
8179 `(("r-lme4" ,r-lme4)
8180 ("r-matrix" ,r-matrix)
8182 ("r-rcppeigen" ,r-rcppeigen)
8185 `(("r-knitr" ,r-knitr))) ; for vignettes
8186 (home-page "https://github.com/glmmTMB")
8187 (synopsis "Generalized linear mixed models")
8189 "Fit linear and generalized linear mixed models with various extensions,
8190 including zero-inflation. The models are fitted using maximum likelihood
8191 estimation via the Template Model Builder. Random effects are assumed to be
8192 Gaussian on the scale of the linear predictor and are integrated out using the
8193 Laplace approximation. Gradients are calculated using automatic
8195 (license license:agpl3+)))
8197 (define-public r-bayestestr
8199 (name "r-bayestestr")
8204 (uri (cran-uri "bayestestR" version))
8207 "0r453zb106hj9w53jjgckxqajjf7shlrgv10gjxsv8if6qybdz5b"))))
8208 (properties `((upstream-name . "bayestestR")))
8209 (build-system r-build-system)
8211 `(("r-insight" ,r-insight)))
8212 (home-page "https://github.com/easystats/bayestestR")
8213 (synopsis "Describe Bayesian models and posterior distributions")
8215 "This package provides utilities to understand and describe posterior
8216 distributions and Bayesian models. It includes point-estimates such as
8217 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8218 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8219 ROPE percentage and pd).")
8220 (license license:gpl3)))
8222 (define-public r-performance
8224 (name "r-performance")
8229 (uri (cran-uri "performance" version))
8232 "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w"))))
8233 (build-system r-build-system)
8235 `(("r-bayestestr" ,r-bayestestr)
8236 ("r-insight" ,r-insight)))
8237 (home-page "https://easystats.github.io/performance/")
8238 (synopsis "Assessment of regression models performance")
8240 "This package provides utilities for computing measures to assess model
8241 quality, which are not directly provided by R's @code{base} or @code{stats}
8242 packages. These include e.g. measures like r-squared, intraclass correlation
8243 coefficient, root mean squared error or functions to check models for
8244 overdispersion, singularity or zero-inflation and more. Functions apply to a
8245 large variety of regression models, including generalized linear models, mixed
8246 effects models and Bayesian models.")
8247 (license license:gpl3)))
8249 (define-public r-ggeffects
8251 (name "r-ggeffects")
8256 (uri (cran-uri "ggeffects" version))
8259 "0idfycjk05gyykfp9ibmhxfcjvd01ikh1dl0fb4nqw6znw3ar0xp"))))
8260 (build-system r-build-system)
8262 `(("r-dplyr" ,r-dplyr)
8263 ("r-insight" ,r-insight)
8264 ("r-magrittr" ,r-magrittr)
8266 ("r-purrr" ,r-purrr)
8267 ("r-rlang" ,r-rlang)
8268 ("r-scales" ,r-scales)
8269 ("r-sjlabelled" ,r-sjlabelled)
8270 ("r-sjmisc" ,r-sjmisc)))
8271 (home-page "https://github.com/strengejacke/ggeffects")
8272 (synopsis "Create tidy data frames of marginal effects for ggplot")
8274 "This package provides tools to compute marginal effects from statistical
8275 models and return the result as tidy data frames. These data frames are ready
8276 to use with the @code{ggplot2} package. Marginal effects can be calculated
8277 for many different models. Interaction terms, splines and polynomial terms
8278 are also supported. The two main functions are @code{ggpredict()} and
8279 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8280 results using @code{ggplot2}.")
8281 (license license:gpl3)))
8283 (define-public r-sjplot
8290 (uri (cran-uri "sjPlot" version))
8292 (base32 "1kx1qqgp4fhwwwpqn9mv8m1pnpjxfs7ww36ns7j1ja4a7ydwn2hp"))))
8293 (properties `((upstream-name . "sjPlot")))
8294 (build-system r-build-system)
8296 `(("r-bayestestr" ,r-bayestestr)
8297 ("r-broom" ,r-broom)
8298 ("r-dplyr" ,r-dplyr)
8299 ("r-forcats" ,r-forcats)
8300 ("r-ggeffects" ,r-ggeffects)
8301 ("r-ggplot2" ,r-ggplot2)
8302 ("r-ggrepel" ,r-ggrepel)
8303 ("r-glmmtmb" ,r-glmmtmb)
8304 ("r-insight" ,r-insight)
8305 ("r-knitr" ,r-knitr)
8307 ("r-magrittr" ,r-magrittr)
8309 ("r-modelr" ,r-modelr)
8311 ("r-performance" ,r-performance)
8312 ("r-psych" ,r-psych)
8313 ("r-purrr" ,r-purrr)
8314 ("r-rlang" ,r-rlang)
8315 ("r-scales" ,r-scales)
8316 ("r-sjlabelled" ,r-sjlabelled)
8317 ("r-sjmisc" ,r-sjmisc)
8318 ("r-sjstats" ,r-sjstats)
8319 ("r-tidyr" ,r-tidyr)))
8320 (home-page "https://strengejacke.github.io/sjPlot/")
8321 (synopsis "Data visualization for statistics in social science")
8323 "This package represents a collection of plotting and table output
8324 functions for data visualization. Results of various statistical
8325 analyses (that are commonly used in social sciences) can be visualized using
8326 this package, including simple and cross tabulated frequencies, histograms,
8327 box plots, (generalized) linear models, mixed effects models, principal
8328 component analysis and correlation matrices, cluster analyses, scatter plots,
8329 stacked scales, effects plots of regression models (including interaction
8330 terms) and much more. This package supports labelled data.")
8331 (license license:gpl3)))
8333 (define-public r-ini
8340 (uri (cran-uri "ini" version))
8343 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8344 (build-system r-build-system)
8345 (home-page "https://github.com/dvdscripter/ini")
8346 (synopsis "Read and write configuration files")
8348 "This package provides tools to parse simple @code{.ini} configuration
8349 files to an structured list. Users can manipulate this resulting list with
8350 @code{lapply()} functions. This same structured list can be used to write
8351 back to file after modifications.")
8352 (license license:gpl3)))
8361 (uri (cran-uri "gh" version))
8364 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8365 (build-system r-build-system)
8367 `(("r-httr" ,r-httr)
8369 ("r-jsonlite" ,r-jsonlite)))
8370 (home-page "https://github.com/r-lib/gh#readme")
8371 (synopsis "Access the GitHub API via R")
8373 "This package provides a minimal R client to access the GitHub API.")
8374 (license license:expat)))
8383 (uri (cran-uri "fs" version))
8386 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8387 (build-system r-build-system)
8389 `(("r-rcpp" ,r-rcpp)))
8391 `(("pkg-config" ,pkg-config)))
8392 (home-page "http://fs.r-lib.org")
8393 (synopsis "Cross-platform file system operations based on libuv")
8395 "This package provides a cross-platform interface to file system
8396 operations, built on top of the libuv C library.")
8397 (license license:gpl3)))
8399 (define-public r-clisymbols
8401 (name "r-clisymbols")
8406 (uri (cran-uri "clisymbols" version))
8409 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8410 (build-system r-build-system)
8411 (home-page "https://github.com/gaborcsardi/clisymbols")
8412 (synopsis "Unicode symbols at the R prompt")
8414 "This package provides a small subset of Unicode symbols, that are useful
8415 when building command line applications. They fall back to alternatives on
8416 terminals that do not support Unicode.")
8417 (license license:expat)))
8419 (define-public r-usethis
8426 (uri (cran-uri "usethis" version))
8429 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8430 (build-system r-build-system)
8432 `(("r-clipr" ,r-clipr)
8433 ("r-clisymbols" ,r-clisymbols)
8434 ("r-crayon" ,r-crayon)
8439 ("r-git2r" ,r-git2r)
8441 ("r-purrr" ,r-purrr)
8442 ("r-rlang" ,r-rlang)
8443 ("r-rprojroot" ,r-rprojroot)
8444 ("r-rstudioapi" ,r-rstudioapi)
8445 ("r-whisker" ,r-whisker)
8446 ("r-withr" ,r-withr)
8447 ("r-yaml" ,r-yaml)))
8448 (home-page "https://github.com/r-lib/usethis")
8449 (synopsis "Automate R package and project setup")
8451 "This package helps you to automate R package and project setup tasks
8452 that are otherwise performed manually. This includes setting up unit testing,
8453 test coverage, continuous integration, Git, GitHub integration, licenses,
8454 Rcpp, RStudio projects, and more.")
8455 (license license:gpl3)))
8457 (define-public r-sessioninfo
8459 (name "r-sessioninfo")
8464 (uri (cran-uri "sessioninfo" version))
8467 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8468 (build-system r-build-system)
8471 ("r-withr" ,r-withr)))
8472 (home-page "https://github.com/r-lib/sessioninfo#readme")
8473 (synopsis "R session information")
8475 "This package provides tools to query and print information about the
8476 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8477 more information about packages, and where they were installed from.")
8478 (license license:gpl2)))
8480 (define-public r-remotes
8487 (uri (cran-uri "remotes" version))
8490 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8491 (build-system r-build-system)
8492 (home-page "https://github.com/r-lib/remotes#readme")
8493 (synopsis "R package installation from remote repositories")
8495 "Download and install R packages stored in GitHub, BitBucket, or plain
8496 subversion or git repositories. This package is a lightweight replacement of
8497 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8498 the code was copied over from @code{devtools}.")
8499 (license license:gpl2+)))
8501 (define-public r-xopen
8508 (uri (cran-uri "xopen" version))
8511 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8512 (build-system r-build-system)
8514 `(("r-processx" ,r-processx)))
8515 (home-page "https://github.com/r-lib/xopen#readme")
8516 (synopsis "Open system files, URLs, anything")
8518 "This package provides a cross-platform solution to open files,
8519 directories or URLs with their associated programs.")
8520 (license license:expat)))
8522 (define-public r-rcmdcheck
8524 (name "r-rcmdcheck")
8529 (uri (cran-uri "rcmdcheck" version))
8532 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8533 (build-system r-build-system)
8535 `(("r-callr" ,r-callr)
8537 ("r-crayon" ,r-crayon)
8539 ("r-digest" ,r-digest)
8540 ("r-pkgbuild" ,r-pkgbuild)
8541 ("r-prettyunits" ,r-prettyunits)
8543 ("r-rprojroot" ,r-rprojroot)
8544 ("r-sessioninfo" ,r-sessioninfo)
8545 ("r-withr" ,r-withr)
8546 ("r-xopen" ,r-xopen)))
8547 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8548 (synopsis "Run R CMD check from R and capture results")
8550 "Run @code{R CMD check} from R programmatically, and capture the results
8551 of the individual checks.")
8552 (license license:expat)))
8554 (define-public r-rapportools
8556 (name "r-rapportools")
8561 (uri (cran-uri "rapportools" version))
8564 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8565 (build-system r-build-system)
8567 `(("r-pander" ,r-pander)
8569 ("r-reshape" ,r-reshape)))
8570 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8571 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8573 "This package provides helper functions that act as wrappers to more
8574 advanced statistical methods with the advantage of having sane defaults for
8576 (license license:agpl3+)))
8578 (define-public r-pander
8585 (uri (cran-uri "pander" version))
8588 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8589 (build-system r-build-system)
8591 `(("r-digest" ,r-digest)
8592 ("r-rcpp" ,r-rcpp)))
8593 (home-page "https://rapporter.github.io/pander")
8594 (synopsis "Render R objects into Pandoc's markdown")
8596 "The main aim of the pander R package is to provide a minimal and easy
8597 tool for rendering R objects into Pandoc's markdown. The package is also
8598 capable of exporting/converting complex Pandoc documents (reports) in various
8600 ;; This package is licensed under either the AGPLv3+ or the very rarely
8602 (license license:agpl3+)))
8604 (define-public r-summarytools
8606 (name "r-summarytools")
8611 (uri (cran-uri "summarytools" version))
8614 "1n695baz56mg4f13xjjadfq0xalw5xsn6xicil0yap5hgi8fsr3a"))))
8615 (build-system r-build-system)
8617 `(("r-checkmate" ,r-checkmate)
8618 ("r-dplyr" ,r-dplyr)
8619 ("r-htmltools" ,r-htmltools)
8620 ("r-lubridate" ,r-lubridate)
8621 ("r-magick" ,r-magick)
8622 ("r-matrixstats" ,r-matrixstats)
8623 ("r-pander" ,r-pander)
8625 ("r-rapportools" ,r-rapportools)
8626 ("r-rcurl" ,r-rcurl)
8627 ("r-tibble" ,r-tibble)
8628 ("r-tidyr" ,r-tidyr)))
8629 (home-page "https://github.com/dcomtois/summarytools")
8630 (synopsis "Tools to quickly and neatly summarize data")
8632 "This package provides tools for data frame summaries, cross-tabulations,
8633 weight-enabled frequency tables and common univariate statistics in concise
8634 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8635 good point-of-entry for exploring data, both for experienced and new R
8637 (license license:gpl2)))
8639 (define-public r-lsei
8646 (uri (cran-uri "lsei" version))
8649 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8650 (build-system r-build-system)
8652 `(("gfortran" ,gfortran)))
8653 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8654 (synopsis "Solve regression problems under equality/inequality constraints")
8656 "It contains functions that solve least squares linear regression
8657 problems under linear equality/inequality constraints. Functions for solving
8658 quadratic programming problems are also available, which transform such
8659 problems into least squares ones first.")
8660 (license license:gpl2+)))
8662 (define-public r-npsurv
8669 (uri (cran-uri "npsurv" version))
8672 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8673 (build-system r-build-system)
8675 `(("r-lsei" ,r-lsei)))
8676 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8677 (synopsis "Nonparametric survival analysis")
8679 "This package contains functions for non-parametric survival analysis of
8680 exact and interval-censored observations.")
8681 (license license:gpl2+)))
8683 (define-public r-clusteval
8685 (name "r-clusteval")
8690 (uri (cran-uri "clusteval" version))
8693 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8694 (build-system r-build-system)
8696 `(("r-mvtnorm" ,r-mvtnorm)
8697 ("r-rcpp" ,r-rcpp)))
8698 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8699 (synopsis "Evaluation of clustering algorithms")
8701 "This R package provides a suite of tools to evaluate clustering
8702 algorithms, clusterings, and individual clusters.")
8703 (license license:expat)))
8705 (define-public r-tweedie
8712 (uri (cran-uri "tweedie" version))
8715 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8716 (build-system r-build-system)
8717 (native-inputs `(("gfortran" ,gfortran)))
8718 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8719 (synopsis "Evaluation of Tweedie exponential family models")
8721 "Maximum likelihood computations for Tweedie families, including the
8722 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8723 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8724 and related methods.")
8725 (license license:gpl2+)))
8727 (define-public r-rcppgsl
8734 (uri (cran-uri "RcppGSL" version))
8736 (base32 "0cnw2k7cfqrm79r6j283aybflxig80x4n4rjkfp2317wf10mrsa5"))))
8737 (properties `((upstream-name . "RcppGSL")))
8738 (build-system r-build-system)
8740 `(("r-rcpp" ,r-rcpp)
8743 `(("r-knitr" ,r-knitr))) ; for vignettes
8744 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8745 (synopsis "Rcpp integration for GSL vectors and matrices")
8747 "The GNU Scientific Library (or GSL) is a collection of numerical
8748 routines for scientific computing. It is particularly useful for C and C++
8749 programs as it provides a standard C interface to a wide range of mathematical
8750 routines. There are over 1000 functions in total with an extensive test
8751 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8752 structures and R using concepts from Rcpp which is itself a package that eases
8753 the interfaces between R and C++.")
8754 (license license:gpl2+)))
8756 (define-public r-mvabund
8763 (uri (cran-uri "mvabund" version))
8766 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
8767 (build-system r-build-system)
8769 `(("r-mass" ,r-mass)
8771 ("r-rcppgsl" ,r-rcppgsl)
8772 ("r-statmod" ,r-statmod)
8773 ("r-tweedie" ,r-tweedie)))
8774 (home-page "https://cran.r-project.org/web/packages/mvabund/")
8775 (synopsis "Statistical methods for analysing multivariate abundance data")
8777 "This package provides a set of tools for displaying, modeling and
8778 analysing multivariate abundance data in community ecology.")
8779 (license license:lgpl2.1+)))
8781 (define-public r-afex
8788 (uri (cran-uri "afex" version))
8791 "12n020y7rjm7402940gkqxa5j901p093f381i23p66fa3fyrshkf"))))
8792 (build-system r-build-system)
8796 ("r-lmertest" ,r-lmertest)
8797 ("r-pbkrtest" ,r-pbkrtest)
8798 ("r-reshape2" ,r-reshape2)))
8799 (home-page "https://afex.singmann.science/")
8800 (synopsis "Analysis of factorial experiments")
8802 "This package provides convenience functions for analyzing factorial
8803 experiments using ANOVA or mixed models.")
8804 (license license:gpl2+)))
8806 (define-public r-lmertest
8813 (uri (cran-uri "lmerTest" version))
8816 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
8817 (properties `((upstream-name . "lmerTest")))
8818 (build-system r-build-system)
8820 `(("r-ggplot2" ,r-ggplot2)
8823 ("r-numderiv" ,r-numderiv)))
8824 (home-page "https://github.com/runehaubo/lmerTestR")
8825 (synopsis "Tests in linear mixed effects models")
8827 "This package provides p-values in type I, II or III anova and summary
8828 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
8829 method. A Kenward-Roger method is also available via the @code{pbkrtest}
8830 package. Model selection methods include step, drop1 and anova-like tables
8831 for random effects (ranova). Methods for Least-Square means (LS-means) and
8832 tests of linear contrasts of fixed effects are also available.")
8833 (license license:gpl2+)))
8835 (define-public r-r2glmm
8842 (uri (cran-uri "r2glmm" version))
8845 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
8846 (build-system r-build-system)
8848 `(("r-afex" ,r-afex)
8849 ("r-data-table" ,r-data-table)
8850 ("r-dplyr" ,r-dplyr)
8851 ("r-ggplot2" ,r-ggplot2)
8852 ("r-gridextra" ,r-gridextra)
8853 ("r-lmertest" ,r-lmertest)
8855 ("r-matrix" ,r-matrix)
8857 ("r-pbkrtest" ,r-pbkrtest)))
8858 (home-page "https://github.com/bcjaeger/r2glmm")
8859 (synopsis "Compute R squared for mixed (multilevel) models")
8861 "This package computes model and semi partial R squared with confidence
8862 limits for the linear and generalized linear mixed model (LMM and GLMM). The
8863 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
8864 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
8866 (license license:gpl2)))
8868 (define-public r-weights
8875 (uri (cran-uri "weights" version))
8878 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
8879 (build-system r-build-system)
8881 `(("r-gdata" ,r-gdata)
8882 ("r-hmisc" ,r-hmisc)
8883 ("r-mice" ,r-mice)))
8885 "https://cran.r-project.org/web/packages/weights/")
8886 (synopsis "Weighting and weighted statistics")
8887 (description "This package Provides a variety of functions for producing
8888 simple weighted statistics, such as weighted Pearson's correlations, partial
8889 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
8890 includes some software for quickly recoding survey data and plotting point
8891 estimates from interaction terms in regressions (and multiply imputed
8892 regressions). NOTE: Weighted partial correlation calculations pulled to
8894 (license license:gpl2+)))
8896 (define-public r-rcppannoy
8898 (name "r-rcppannoy")
8903 (uri (cran-uri "RcppAnnoy" version))
8906 "1jibp9b07c5ka1kif0nl7f168hxfvysj32wnmnxg85l663hmvm8j"))))
8907 (properties `((upstream-name . "RcppAnnoy")))
8908 (build-system r-build-system)
8910 `(("r-rcpp" ,r-rcpp)))
8912 `(("r-knitr" ,r-knitr))) ; for vignettes
8913 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
8914 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
8916 "Annoy is a small C++ library for Approximate Nearest Neighbors written
8917 for efficient memory usage as well an ability to load from and save to disk.
8918 This package provides an R interface.")
8919 ;; Annoy is released under ASL 2.0, but this wrapper is released under
8921 (license (list license:gpl2+ license:asl2.0))))
8923 (define-public r-rcpphnsw
8930 (uri (cran-uri "RcppHNSW" version))
8933 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
8934 (properties `((upstream-name . "RcppHNSW")))
8935 (build-system r-build-system)
8936 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8937 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
8938 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
8940 "Hnswlib is a C++ library for approximate nearest neighbors. This
8941 package provides a minimal R interface by relying on the Rcpp package.")
8942 ;; hnswlib is released under Version 2.0 of the Apache License.
8943 (license (list license:gpl3 license:asl2.0))))
8945 (define-public r-rcppparallel
8947 (name "r-rcppparallel")
8952 (uri (cran-uri "RcppParallel" version))
8955 "0p13f2mywjr7gmskf8ri4y8p5yr1bvr4xrpw2w11vdvafwz1vcia"))))
8956 (properties `((upstream-name . "RcppParallel")))
8957 (build-system r-build-system)
8958 (home-page "http://rcppcore.github.io/RcppParallel")
8959 (synopsis "Parallel programming tools for Rcpp")
8961 "This package provides high level functions for parallel programming with
8962 Rcpp. For example, the @code{parallelFor()} function can be used to convert
8963 the work of a standard serial @code{for} loop into a parallel one and the
8964 @code{parallelReduce()} function can be used for accumulating aggregates or
8966 (license license:gpl2)))
8968 (define-public r-ncdf4
8975 (uri (cran-uri "ncdf4" version))
8978 "083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd"))))
8979 (build-system r-build-system)
8981 `(("netcdf" ,netcdf)
8983 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
8984 (synopsis "R interface to Unidata netCDF format data files")
8986 "This package provides a high-level R interface to data files written
8987 using Unidata's netCDF library (version 4 or earlier), which are binary data
8988 files that are portable across platforms and include metadata information in
8989 addition to the data sets. Using this package, netCDF files can be opened and
8990 data sets read in easily. It is also easy to create new netCDF dimensions,
8991 variables, and files, in either version 3 or 4 format, and manipulate existing
8993 (license license:gpl3+)))
8995 (define-public r-biocmanager
8997 (name "r-biocmanager")
9002 (uri (cran-uri "BiocManager" version))
9005 "0pqgb7j4aqpcp3bapl313rmyxxj3j96s9csip4f65444gjy5r2x2"))))
9006 (properties `((upstream-name . "BiocManager")))
9007 (build-system r-build-system)
9008 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9009 (synopsis "Access the Bioconductor project package repository")
9011 "This package provides a convenient tool to install and update
9012 Bioconductor packages.")
9013 (license license:artistic2.0)))
9015 (define-public r-rgl
9018 (version "0.100.30")
9022 (uri (cran-uri "rgl" version))
9025 "0rzqzskcwf2ah4yr62x5rjwf7yh90d43h39gk7jmfc5lc08zaxc5"))))
9026 (build-system r-build-system)
9028 `(("pkg-config" ,pkg-config)))
9030 `(("freetype" ,freetype)
9034 ("ghc-pandoc" ,ghc-pandoc)
9037 `(("r-crosstalk" ,r-crosstalk)
9038 ("r-htmltools" ,r-htmltools)
9039 ("r-htmlwidgets" ,r-htmlwidgets)
9040 ("r-jsonlite" ,r-jsonlite)
9041 ("r-knitr" ,r-knitr)
9042 ("r-magrittr" ,r-magrittr)
9043 ("r-manipulatewidget" ,r-manipulatewidget)
9044 ("r-shiny" ,r-shiny)))
9045 (home-page "https://r-forge.r-project.org/projects/rgl/")
9046 (synopsis "3D visualization using OpenGL")
9048 "This package provides medium to high level functions for 3D interactive graphics,
9049 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9050 as functions for constructing representations of geometric
9051 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9052 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9053 image formats, including PNG, Postscript, SVG, PGF.")
9054 ;; Any version of the GPL.
9055 (license (list license:gpl2+ license:gpl3+))))
9057 (define-public r-multicool
9059 (name "r-multicool")
9064 (uri (cran-uri "multicool" version))
9067 "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
9068 (build-system r-build-system)
9069 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9070 (home-page "https://cran.r-project.org/web/packages/multicool/")
9071 (synopsis "Permutations of multisets in cool-lex order")
9073 "This package provides a set of tools to permute multisets without loops
9074 or hash tables and to generate integer partitions. Cool-lex order is similar
9075 to colexicographical order.")
9076 (license license:gpl2)))
9078 (define-public r-misc3d
9085 (uri (cran-uri "misc3d" version))
9088 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9089 (build-system r-build-system)
9090 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9091 (synopsis "Miscellaneous 3D Plots")
9093 "This package provides a collection of miscellaneous 3d plots, including
9095 ;; Any version of the GPL.
9096 (license (list license:gpl2+ license:gpl3+))))
9105 (uri (cran-uri "ks" version))
9108 "06ymx244yknmpl6935l4pafqbm4gcbpnhqg7rinql6rrfr9mcrag"))))
9109 (build-system r-build-system)
9112 ("r-kernlab" ,r-kernlab)
9113 ("r-kernsmooth" ,r-kernsmooth)
9114 ("r-matrix" ,r-matrix)
9115 ("r-mclust" ,r-mclust)
9117 ("r-multicool" ,r-multicool)
9118 ("r-mvtnorm" ,r-mvtnorm)))
9119 (home-page "http://www.mvstat.net/tduong/")
9120 (synopsis "Kernel smoothing")
9122 "This package provides kernel smoothers for univariate and multivariate
9123 data, including density functions, density derivatives, cumulative
9124 distributions, modal clustering, discriminant analysis, and two-sample
9125 hypothesis testing.")
9126 ;; Either version of the GPL.
9127 (license (list license:gpl2 license:gpl3))))
9129 (define-public r-feature
9136 (uri (cran-uri "feature" version))
9139 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9140 (build-system r-build-system)
9143 ("r-misc3d" ,r-misc3d)
9145 (home-page "http://www.mvstat.net/tduong/")
9146 (synopsis "Inferential feature significance for kernel density estimation")
9148 "The feature package contains functions to display and compute kernel
9149 density estimates, significant gradient and significant curvature regions.
9150 Significant gradient and/or curvature regions often correspond to significant
9151 features (e.g. local modes).")
9152 ;; Either version of the GPL.
9153 (license (list license:gpl2 license:gpl3))))
9155 (define-public r-arm
9162 (uri (cran-uri "arm" version))
9165 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9166 (build-system r-build-system)
9168 `(("r-abind" ,r-abind)
9172 ("r-matrix" ,r-matrix)
9173 ("r-nlme" ,r-nlme)))
9174 (home-page "https://cran.r-project.org/web/packages/arm/")
9175 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9177 "This package provides functions to accompany A. Gelman and J. Hill,
9178 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9179 University Press, 2007.")
9180 (license license:gpl3+)))
9182 (define-public r-circular
9189 (uri (cran-uri "circular" version))
9192 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9193 (build-system r-build-system)
9195 `(("r-boot" ,r-boot)
9196 ("r-mvtnorm" ,r-mvtnorm)))
9198 `(("gfortran" ,gfortran)))
9199 (home-page "https://cran.r-project.org/web/packages/circular/")
9200 (synopsis "Circular statistics")
9202 "This package provides tools for circular statistics, from \"Topics in
9203 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9205 (license license:gpl2+)))
9207 (define-public r-activity
9214 (uri (cran-uri "activity" version))
9217 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
9218 (build-system r-build-system)
9220 `(("r-circular" ,r-circular)
9221 ("r-insol" ,r-insol)
9222 ("r-pbapply" ,r-pbapply)))
9223 (home-page "https://cran.r-project.org/web/packages/activity/")
9224 (synopsis "Animal activity statistics")
9226 "This package provides functions to fit kernel density functions to
9227 animal activity time data; plot activity distributions; quantify overall
9228 levels of activity; statistically compare activity metrics through
9229 bootstrapping; and evaluate variation in linear variables with time (or other
9230 circular variables).")
9231 (license license:gpl3)))
9233 (define-public r-ouch
9240 (uri (cran-uri "ouch" version))
9243 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9244 (build-system r-build-system)
9245 (propagated-inputs `(("r-subplex" ,r-subplex)))
9246 (home-page "http://kingaa.github.io/ouch/")
9247 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9249 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9250 for evolution along a phylogenetic tree.")
9251 (license license:gpl2+)))
9253 (define-public r-fmsb
9260 (uri (cran-uri "fmsb" version))
9263 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
9264 (build-system r-build-system)
9265 (home-page "http://minato.sip21c.org/msb/")
9266 (synopsis "Functions for medical statistics book with demographic data")
9268 "This package provides several utility functions for the book entitled
9269 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9270 Japan, 2007) with Japanese demographic data and some demographic analysis
9271 related functions.")
9272 (license license:gpl2+)))
9274 (define-public r-stabledist
9276 (name "r-stabledist")
9281 (uri (cran-uri "stabledist" version))
9284 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9285 (build-system r-build-system)
9286 (home-page "http://www.rmetrics.org")
9287 (synopsis "Stable distribution functions")
9289 "This package provides density, probability and quantile functions, and
9290 random number generation for (skew) stable distributions, using the
9291 parametrizations of Nolan.")
9292 (license license:gpl2+)))
9294 (define-public r-gsl
9301 (uri (cran-uri "gsl" version))
9304 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9305 (build-system r-build-system)
9308 (home-page "https://cran.r-project.org/web/packages/gsl")
9309 (synopsis "Wrapper for the GNU Scientific Library")
9311 "This package provides an R wrapper for the special functions and quasi
9312 random number generators of the GNU Scientific Library.")
9313 (license license:gpl2+)))
9315 (define-public r-adgoftest
9317 (name "r-adgoftest")
9322 (uri (cran-uri "ADGofTest" version))
9325 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9326 (properties `((upstream-name . "ADGofTest")))
9327 (build-system r-build-system)
9328 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9329 (synopsis "Anderson-Darling GoF test")
9331 "This package provides an implementation of the Anderson-Darling GoF test
9332 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9333 Anderson-Darling Distribution\".")
9334 ;; Any version of the GPL.
9335 (license license:gpl3+)))
9337 (define-public r-softimpute
9339 (name "r-softimpute")
9344 (uri (cran-uri "softImpute" version))
9347 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9348 (properties `((upstream-name . "softImpute")))
9349 (build-system r-build-system)
9351 `(("r-matrix" ,r-matrix)))
9353 `(("gfortran" ,gfortran)))
9354 (home-page "https://cran.r-project.org/web/packages/softImpute")
9355 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9357 "This package provides iterative methods for matrix completion that use
9358 nuclear-norm regularization. The package includes procedures for centering
9359 and scaling rows, columns or both, and for computing low-rank @dfn{single
9360 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9362 (license license:gpl2)))
9364 (define-public r-fftwtools
9366 (name "r-fftwtools")
9371 (uri (cran-uri "fftwtools" version))
9374 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9375 (build-system r-build-system)
9376 (inputs `(("fftw" ,fftw)))
9377 (home-page "https://github.com/krahim/fftwtools")
9378 (synopsis "Wrapper for FFTW3")
9380 "This package provides a wrapper for several FFTW functions. It provides
9381 access to the two-dimensional FFT, the multivariate FFT, and the
9382 one-dimensional real to complex FFT using the FFTW3 library. The package
9383 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9384 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9385 The FFT functions have a parameter that allows them to not return the
9386 redundant complex conjugate when the input is real data.")
9387 (license license:gpl2+)))
9389 (define-public r-tiff
9396 (uri (cran-uri "tiff" version))
9399 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9400 (build-system r-build-system)
9402 `(("libtiff" ,libtiff)
9403 ("libjpeg" ,libjpeg)
9405 (home-page "http://www.rforge.net/tiff/")
9406 (synopsis "Read and write TIFF images")
9408 "This package provides an easy and simple way to read, write and display
9409 bitmap images stored in the TIFF format. It can read and write both files and
9410 in-memory raw vectors.")
9411 ;; Either of these two license versions.
9412 (license (list license:gpl2 license:gpl3))))
9414 (define-public r-nlp
9421 (uri (cran-uri "NLP" version))
9424 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
9425 (properties `((upstream-name . "NLP")))
9426 (build-system r-build-system)
9427 (home-page "https://cran.r-project.org/web/packages/NLP/")
9428 (synopsis "Natural language processing infrastructure")
9430 "This package provides basic classes and methods for Natural Language
9432 (license license:gpl3)))
9441 (uri (cran-uri "tm" version))
9444 "0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"))))
9445 (properties `((upstream-name . "tm")))
9446 (build-system r-build-system)
9452 ("r-xml2" ,r-xml2)))
9453 (home-page "http://tm.r-forge.r-project.org/")
9454 (synopsis "Text mining package")
9456 "This package provides a framework for text mining applications within R.")
9457 (license license:gpl3)))
9459 (define-public r-waveslim
9466 (uri (cran-uri "waveslim" version))
9469 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9470 (build-system r-build-system)
9472 `(("gfortran" ,gfortran)))
9473 (home-page "http://waveslim.blogspot.com")
9474 (synopsis "Basic wavelet routines for signal processing")
9476 "This package provides basic wavelet routines for time series (1D),
9477 image (2D) and array (3D) analysis. The code provided here is based on
9478 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9479 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9480 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9481 pairs (Selesnick 2001, 2002).")
9482 (license license:bsd-3)))
9484 (define-public r-wordcloud
9486 (name "r-wordcloud")
9491 (uri (cran-uri "wordcloud" version))
9494 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9495 (build-system r-build-system)
9497 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9499 ;; The "tm" package is only "suggested" according to CRAN, but the
9500 ;; wordcloud package cannot be loaded without it.
9502 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9503 (synopsis "Word clouds")
9505 "This package provides functionality to create pretty word clouds,
9506 visualize differences and similarity between documents, and avoid
9507 over-plotting in scatter plots with text.")
9508 (license license:lgpl2.1)))
9510 (define-public r-colorramps
9512 (name "r-colorramps")
9517 (uri (cran-uri "colorRamps" version))
9520 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9521 (properties `((upstream-name . "colorRamps")))
9522 (build-system r-build-system)
9523 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9524 (synopsis "Build color tables")
9525 (description "This package provides features to build gradient color
9527 ;; Any version of the GPL
9528 (license license:gpl3+)))
9530 (define-public r-tidytree
9537 (uri (cran-uri "tidytree" version))
9540 "1hkddl8kj1g01dy7xiracx81f6b405b3ga2qp4wlrl552b9xxpby"))))
9541 (build-system r-build-system)
9544 ("r-dplyr" ,r-dplyr)
9545 ("r-lazyeval" ,r-lazyeval)
9546 ("r-magrittr" ,r-magrittr)
9547 ("r-rlang" ,r-rlang)
9548 ("r-tibble" ,r-tibble)))
9549 (home-page "https://github.com/GuangchuangYu/tidytree")
9550 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9552 "Phylogenetic trees generally contain multiple components including nodes,
9553 edges, branches and associated data. This package provides an approach to
9554 convert tree objects to tidy data frames. It also provides tidy interfaces to
9555 manipulate tree data.")
9556 (license license:artistic2.0)))
9558 (define-public r-rvcheck
9565 (uri (cran-uri "rvcheck" version))
9567 (base32 "15222q3sglq0mad5q806p99fhrb96qizmpqw35fa1rb148f95paf"))))
9568 (build-system r-build-system)
9570 `(("r-biocmanager" ,r-biocmanager)
9571 ("r-rlang" ,r-rlang)))
9572 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9573 (synopsis "R package version check")
9575 "This package provides tools to check the latest release version of R and
9576 R packages (on CRAN, Bioconductor or Github).")
9577 (license license:artistic2.0)))
9579 (define-public r-docopt
9586 (uri (cran-uri "docopt" version))
9589 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9590 (build-system r-build-system)
9591 (home-page "https://github.com/docopt/docopt.R")
9592 (synopsis "Command-line interface specification language")
9594 "This package enables you to define a command-line interface by just
9595 giving it a description in the specific format.")
9596 (license license:expat)))
9598 (define-public r-sparsesvd
9600 (name "r-sparsesvd")
9605 (uri (cran-uri "sparsesvd" version))
9608 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9609 (build-system r-build-system)
9610 (propagated-inputs `(("r-matrix" ,r-matrix)))
9611 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9612 (synopsis "Sparse truncated singular value decomposition")
9614 "This package provides a Wrapper around the SVDLIBC library
9615 for (truncated) singular value decomposition of a sparse matrix. Currently,
9616 only sparse real matrices in Matrix package format are supported.")
9617 ;; SVDLIBC is released under BSD-2. The R interface is released under
9619 (license (list license:bsd-3 license:bsd-2))))
9621 (define-public r-speedglm
9628 (uri (cran-uri "speedglm" version))
9631 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9632 (build-system r-build-system)
9634 `(("r-mass" ,r-mass)
9635 ("r-matrix" ,r-matrix)))
9636 (home-page "https://cran.r-project.org/web/packages/speedglm")
9637 (synopsis "Fit linear and generalized linear models to large data sets")
9639 "This package provides tools for fitting linear models and generalized
9640 linear models to large data sets by updating algorithms.")
9641 ;; Any version of the GPL
9642 (license license:gpl2+)))
9644 (define-public r-densityclust
9646 (name "r-densityclust")
9651 (uri (cran-uri "densityClust" version))
9654 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9655 (properties `((upstream-name . "densityClust")))
9656 (build-system r-build-system)
9659 ("r-ggplot2" ,r-ggplot2)
9660 ("r-ggrepel" ,r-ggrepel)
9661 ("r-gridextra" ,r-gridextra)
9662 ("r-rcolorbrewer" ,r-rcolorbrewer)
9664 ("r-rtsne" ,r-rtsne)))
9665 (home-page "https://cran.r-project.org/web/packages/densityClust")
9666 (synopsis "Clustering by fast search and find of density peaks")
9668 "This package provides an improved implementation (based on k-nearest
9669 neighbors) of the density peak clustering algorithm, originally described by
9670 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9671 large datasets (> 100,000 samples) very efficiently.")
9672 (license license:gpl2+)))
9674 (define-public r-combinat
9681 (uri (cran-uri "combinat" version))
9684 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9685 (build-system r-build-system)
9686 (home-page "https://cran.r-project.org/web/packages/combinat")
9687 (synopsis "Combinatorics utilities")
9688 (description "This package provides assorted routines for combinatorics.")
9689 (license license:gpl2)))
9691 (define-public r-qlcmatrix
9693 (name "r-qlcmatrix")
9698 (uri (cran-uri "qlcMatrix" version))
9701 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9702 (properties `((upstream-name . "qlcMatrix")))
9703 (build-system r-build-system)
9705 `(("r-docopt" ,r-docopt)
9706 ("r-matrix" ,r-matrix)
9708 ("r-sparsesvd" ,r-sparsesvd)))
9709 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9710 (synopsis "Sparse matrix functions for quantitative language comparison")
9712 "This package provides an extension of the functionality of the Matrix
9713 package for using sparse matrices. Some of the functions are very general,
9714 while other are highly specific for the special data format used for
9715 @dfn{quantitative language comparison} (QLC).")
9716 (license license:gpl3)))
9718 (define-public r-ddrtree
9725 (uri (cran-uri "DDRTree" version))
9728 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9729 (properties `((upstream-name . "DDRTree")))
9730 (build-system r-build-system)
9733 ("r-irlba" ,r-irlba)
9735 ("r-rcppeigen" ,r-rcppeigen)))
9736 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9737 (synopsis "Learning principal graphs with DDRTree")
9739 "This package provides an implementation of the framework of
9740 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9741 dimensional space while constructs a principal tree which passes through the
9742 middle of the data simultaneously. DDRTree shows superiority to
9743 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9744 intrinsic structure of single cell genomics data. In general, it could be
9745 used to reconstruct the temporal progression as well as the bifurcation
9746 structure of any data type.")
9747 (license license:asl2.0)))
9749 (define-public r-corpcor
9756 (uri (cran-uri "corpcor" version))
9759 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9760 (build-system r-build-system)
9761 (home-page "http://strimmerlab.org/software/corpcor/")
9762 (synopsis "Efficient estimation of covariance and (partial) correlation")
9764 "This package implements a James-Stein-type shrinkage estimator for the
9765 covariance matrix, with separate shrinkage for variances and correlations.
9766 Furthermore, functions are available for fast singular value decomposition,
9767 for computing the pseudoinverse, and for checking the rank and positive
9768 definiteness of a matrix.")
9769 (license license:gpl3+)))
9771 (define-public r-rspectra
9778 (uri (cran-uri "RSpectra" version))
9781 "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s"))))
9782 (properties `((upstream-name . "RSpectra")))
9783 (build-system r-build-system)
9785 `(("r-matrix" ,r-matrix)
9787 ("r-rcppeigen" ,r-rcppeigen)))
9788 (home-page "https://github.com/yixuan/RSpectra")
9789 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
9791 "This package provides an R interface to the Spectra library for
9792 large-scale eigenvalue and SVD problems. It is typically used to compute a
9793 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
9794 which is usually more efficient than @code{eigen()} if k << n.")
9796 (license license:mpl2.0)))
9798 (define-public r-vbsr
9805 (uri (cran-uri "vbsr" version))
9808 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
9809 (build-system r-build-system)
9810 (home-page "https://cran.r-project.org/web/packages/vbsr")
9811 (synopsis "Variational Bayes spike regression regularized linear models")
9813 "This package provides an efficient algorithm for solving ultra-sparse
9814 regularized regression models using a variational Bayes algorithm with a spike
9815 prior. The algorithm is solved on a path, with coordinate updates, and is
9816 capable of generating very sparse models. Very general model
9817 diagnostics for controlling type-1 errors are also provided.")
9818 (license license:gpl2)))
9820 (define-public r-flare
9827 (uri (cran-uri "flare" version))
9830 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
9831 (build-system r-build-system)
9833 `(("r-igraph" ,r-igraph)
9834 ("r-lattice" ,r-lattice)
9836 ("r-matrix" ,r-matrix)))
9837 (home-page "https://cran.r-project.org/web/packages/flare")
9838 (synopsis "Family of Lasso regression implementations")
9840 "This package provides implementations of a family of Lasso variants
9841 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
9842 high dimensional sparse linear models.")
9843 (license license:gpl2)))
9845 (define-public r-lassopv
9852 (uri (cran-uri "lassopv" version))
9855 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
9856 (build-system r-build-system)
9857 (propagated-inputs `(("r-lars" ,r-lars)))
9858 (home-page "https://github.com/lingfeiwang/lassopv")
9859 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
9861 "This package enables you to estimate the p-values for predictors x
9862 against target variable y in Lasso regression, using the regularization
9863 strength when each predictor enters the active set of regularization path for
9864 the first time as the statistic.")
9865 (license license:gpl3)))
9867 (define-public r-splitstackshape
9869 (name "r-splitstackshape")
9874 (uri (cran-uri "splitstackshape" version))
9877 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
9878 (build-system r-build-system)
9880 `(("r-data-table" ,r-data-table)))
9881 (home-page "https://github.com/mrdwab/splitstackshape")
9882 (synopsis "Stack and reshape datasets after splitting concatenated values")
9884 "Online data collection tools like Google Forms often export
9885 multiple-response questions with data concatenated in cells. The
9886 @code{concat.split} (cSplit) family of functions provided by this package
9887 splits such data into separate cells. This package also includes functions to
9888 stack groups of columns and to reshape wide data, even when the data are
9889 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
9890 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
9892 (license license:gpl3)))
9894 (define-public r-tfmpvalue
9896 (name "r-tfmpvalue")
9901 (uri (cran-uri "TFMPvalue" version))
9904 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
9905 (properties `((upstream-name . "TFMPvalue")))
9906 (build-system r-build-system)
9907 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9908 (home-page "https://github.com/ge11232002/TFMPvalue")
9909 (synopsis "P-value computation for position weight matrices")
9911 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
9912 identification from sequence/alignments, we are interested in the significance
9913 of certain match scores. TFMPvalue provides the accurate calculation of a
9914 p-value with a score threshold for position weight matrices, or the score with
9915 a given p-value. It is an interface to code originally made available by
9916 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
9917 Touzet and Varre (2007).")
9918 (license license:gpl2)))
9920 (define-public r-rnifti
9927 (uri (cran-uri "RNifti" version))
9930 "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg"))))
9931 (properties `((upstream-name . "RNifti")))
9932 (build-system r-build-system)
9933 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9934 (home-page "https://github.com/jonclayden/RNifti")
9935 (synopsis "Fast R and C++ access to NIfTI images")
9937 "This package provides very fast read and write access to images stored
9938 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
9939 compiled C and interpreted R code. It also provides a C/C++ API that can be
9940 used by other packages.")
9941 (license license:gpl2)))
9943 (define-public r-shades
9950 (uri (cran-uri "shades" version))
9953 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
9954 (build-system r-build-system)
9955 (home-page "https://github.com/jonclayden/shades")
9956 (synopsis "Simple color manipulation")
9958 "This package provides functions for easily manipulating colors,
9959 creating color scales and calculating color distances.")
9960 (license license:bsd-3)))
9962 (define-public r-ore
9969 (uri (cran-uri "ore" version))
9972 "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m"))))
9973 (build-system r-build-system)
9974 (home-page "https://github.com/jonclayden/ore")
9975 (synopsis "R interface to the Onigmo regular expression library")
9977 "This package provides an alternative to R's built-in functionality for
9978 handling regular expressions, based on the Onigmo library. It offers
9979 first-class compiled regex objects, partial matching and function-based
9980 substitutions, amongst other features.")
9981 (license license:bsd-3)))
9983 (define-public r-reportr
9990 (uri (cran-uri "reportr" version))
9993 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
9994 (build-system r-build-system)
9995 (propagated-inputs `(("r-ore" ,r-ore)))
9996 (home-page "https://github.com/jonclayden/reportr")
9997 (synopsis "General message and error reporting system")
9999 "This package provides a system for reporting messages, which offers
10000 certain useful features over the standard R system, such as the incorporation
10001 of output consolidation, message filtering, assertions, expression
10002 substitution, automatic generation of stack traces for debugging, and
10003 conditional reporting based on the current \"output level\".")
10004 (license license:gpl2)))
10006 (define-public r-tractor-base
10008 (name "r-tractor-base")
10013 (uri (cran-uri "tractor.base" version))
10016 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10017 (properties `((upstream-name . "tractor.base")))
10018 (build-system r-build-system)
10021 ("r-reportr" ,r-reportr)
10022 ("r-rnifti" ,r-rnifti)
10023 ("r-shades" ,r-shades)))
10024 (home-page "http://www.tractor-mri.org.uk")
10025 (synopsis "Read, manipulate and visualize magnetic resonance images")
10027 "This package provides functions for working with magnetic resonance
10028 images. It supports reading and writing of popular file formats (DICOM,
10029 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10030 visualization; flexible image manipulation; metadata and sparse image
10032 (license license:gpl2)))
10034 (define-public r-grimport
10036 (name "r-grimport")
10041 (uri (cran-uri "grImport" version))
10044 "0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16"))))
10045 (properties `((upstream-name . "grImport")))
10046 (build-system r-build-system)
10048 `(("ghostscript" ,ghostscript)))
10050 `(("r-xml" ,r-xml)))
10051 (home-page "https://cran.r-project.org/web/packages/grImport")
10052 (synopsis "Convert, import, and draw PostScript pictures")
10054 "This package provides functions for converting, importing, and drawing
10055 PostScript pictures in R plots.")
10056 (license license:gpl2+)))
10058 (define-public r-grimport2
10060 (name "r-grimport2")
10065 (uri (cran-uri "grImport2" version))
10068 "0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls"))))
10069 (properties `((upstream-name . "grImport2")))
10070 (build-system r-build-system)
10072 `(("r-base64enc" ,r-base64enc)
10076 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10077 (synopsis "Import SVG graphics")
10079 "This package provides functions for importing external vector images and
10080 drawing them as part of R plots. This package is different from the
10081 @code{grImport} package because, where that package imports PostScript format
10082 images, this package imports SVG format images. Furthermore, this package
10083 imports a specific subset of SVG, so external images must be preprocessed
10084 using a package like @code{rsvg} to produce SVG that this package can import.
10085 SVG features that are not supported by R graphics, such as gradient fills, can
10086 be imported and then exported via the @code{gridSVG} package.")
10087 (license license:gpl2+)))
10089 (define-public r-kohonen
10096 (uri (cran-uri "kohonen" version))
10099 "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"))))
10100 (build-system r-build-system)
10102 `(("r-mass" ,r-mass)
10103 ("r-rcpp" ,r-rcpp)))
10104 (home-page "https://cran.r-project.org/web/packages/kohonen")
10105 (synopsis "Supervised and unsupervised self-organising maps")
10107 "This package provides functions to train @dfn{self-organising
10108 maps} (SOMs). Also interrogation of the maps and prediction using trained
10109 maps are supported. The name of the package refers to Teuvo Kohonen, the
10110 inventor of the SOM.")
10111 (license license:gpl2+)))
10113 (define-public r-nnls
10120 (uri (cran-uri "nnls" version))
10123 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10124 (build-system r-build-system)
10125 (native-inputs `(("gfortran" ,gfortran)))
10126 (home-page "https://cran.r-project.org/web/packages/nnls")
10127 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10129 "This package provides an R interface to the Lawson-Hanson implementation
10130 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10131 the combination of non-negative and non-positive constraints.")
10132 (license license:gpl2+)))
10134 (define-public r-iso
10141 (uri (cran-uri "Iso" version))
10144 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10145 (properties `((upstream-name . "Iso")))
10146 (build-system r-build-system)
10147 (native-inputs `(("gfortran" ,gfortran)))
10148 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10149 (synopsis "Functions to perform isotonic regression")
10151 "This package provides support for linear order and unimodal
10152 order (univariate) isotonic regression and bivariate isotonic regression with
10153 linear order on both variables.")
10154 (license license:gpl2+)))
10156 (define-public r-chemometricswithr
10158 (name "r-chemometricswithr")
10163 (uri (cran-uri "ChemometricsWithR" version))
10166 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10168 `((upstream-name . "ChemometricsWithR")))
10169 (build-system r-build-system)
10171 `(("r-devtools" ,r-devtools)
10172 ("r-kohonen" ,r-kohonen)
10175 (home-page "https://github.com/rwehrens/CWR")
10176 (synopsis "Chemometrics with R")
10178 "This package provides functions and scripts used in the book
10179 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10180 Life Sciences\" by Ron Wehrens, Springer (2011).")
10181 (license license:gpl2+)))
10183 (define-public r-als
10190 (uri (cran-uri "ALS" version))
10193 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10194 (properties `((upstream-name . "ALS")))
10195 (build-system r-build-system)
10198 ("r-nnls" ,r-nnls)))
10199 (home-page "https://cran.r-project.org/web/packages/ALS")
10200 (synopsis "Multivariate curve resolution alternating least squares")
10202 "Alternating least squares is often used to resolve components
10203 contributing to data with a bilinear structure; the basic technique may be
10204 extended to alternating constrained least squares. This package provides an
10205 implementation of @dfn{multivariate curve resolution alternating least
10206 squares} (MCR-ALS).
10208 Commonly applied constraints include unimodality, non-negativity, and
10209 normalization of components. Several data matrices may be decomposed
10210 simultaneously by assuming that one of the two matrices in the bilinear
10211 decomposition is shared between datasets.")
10212 (license license:gpl2+)))
10214 (define-public r-strucchange
10216 (name "r-strucchange")
10221 (uri (cran-uri "strucchange" version))
10224 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
10225 (build-system r-build-system)
10227 `(("r-sandwich" ,r-sandwich)
10229 (home-page "https://cran.r-project.org/web/packages/strucchange")
10230 (synopsis "Testing, monitoring, and dating structural changes")
10232 "This package provides tools for testing, monitoring and dating
10233 structural changes in (linear) regression models. It features tests/methods
10234 from the generalized fluctuation test framework as well as from the F
10235 test (Chow test) framework. This includes methods to fit, plot and test
10236 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10237 statistics, respectively. It is possible to monitor incoming data online
10238 using fluctuation processes. Finally, the breakpoints in regression models
10239 with structural changes can be estimated together with confidence intervals.
10240 Emphasis is always given to methods for visualizing the data.")
10241 ;; Either of these two GPL versions
10242 (license (list license:gpl2 license:gpl3))))
10244 (define-public r-pixmap
10251 (uri (cran-uri "pixmap" version))
10254 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10255 (build-system r-build-system)
10256 (home-page "https://cran.r-project.org/web/packages/pixmap")
10257 (synopsis "Tools for bitmap images")
10259 "This package provides functions for importing, exporting, plotting and
10260 other manipulations of bitmapped images.")
10261 (license license:gpl2)))
10263 (define-public r-rapidjsonr
10265 (name "r-rapidjsonr")
10270 (uri (cran-uri "rapidjsonr" version))
10273 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10274 (build-system r-build-system)
10275 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10276 (synopsis "JSON parser")
10278 "This package provides JSON parsing capability through the Rapidjson
10280 (license license:expat)))
10282 (define-public r-ontologyindex
10284 (name "r-ontologyindex")
10289 (uri (cran-uri "ontologyIndex" version))
10292 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10293 (properties `((upstream-name . "ontologyIndex")))
10294 (build-system r-build-system)
10295 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10296 (synopsis "Functions for processing ontologies in R")
10298 "This package provides functions for reading ontologies into R as lists
10299 and manipulating sets of ontological terms.")
10300 (license license:gpl2+)))
10302 (define-public r-gargle
10309 (uri (cran-uri "gargle" version))
10312 "08zhfk2sl342w35i5n2c93ayypg3z0kbl0020l3y9adqka1vazgx"))))
10313 (build-system r-build-system)
10318 ("r-jsonlite" ,r-jsonlite)
10319 ("r-rlang" ,r-rlang)
10320 ("r-withr" ,r-withr)))
10321 (home-page "https://gargle.r-lib.org")
10322 (synopsis "Utilities for working with Google APIs")
10324 "This package provides utilities for working with Google APIs. This
10325 includes functions and classes for handling common credential types and for
10326 preparing, executing, and processing HTTP requests.")
10327 (license license:expat)))
10329 (define-public r-bigrquery
10331 (name "r-bigrquery")
10336 (uri (cran-uri "bigrquery" version))
10339 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10340 (build-system r-build-system)
10342 `(("r-assertthat" ,r-assertthat)
10343 ("r-bit64" ,r-bit64)
10346 ("r-gargle" ,r-gargle)
10349 ("r-jsonlite" ,r-jsonlite)
10350 ("r-prettyunits" ,r-prettyunits)
10351 ("r-progress" ,r-progress)
10352 ("r-rapidjsonr" ,r-rapidjsonr)
10354 ("r-rlang" ,r-rlang)
10355 ("r-tibble" ,r-tibble)))
10356 (home-page "https://github.com/rstats-db/bigrquery")
10357 (synopsis "R interface to Google's BigQuery API")
10359 "This package provides an R interface to Google's BigQuery database.")
10360 (license license:gpl3)))
10362 (define-public r-gmp
10365 (version "0.5-13.5")
10369 (uri (cran-uri "gmp" version))
10372 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10373 (build-system r-build-system)
10376 (modify-phases %standard-phases
10377 (add-after 'unpack 'set-CC
10378 (lambda _ (setenv "CC" "gcc") #t)))))
10379 (inputs `(("gmp" ,gmp)))
10380 (home-page "https://cran.r-project.org/web/packages/gmp")
10381 (synopsis "Multiple precision arithmetic")
10383 "This package supports multiple precision arithmetic (big integers and
10384 rationals, prime number tests, matrix computation), \"arithmetic without
10385 limitations\" using the GNU Multiple Precision library.")
10386 ;; Any version of the GPL.
10387 (license license:gpl3+)))
10389 (define-public r-rmpfr
10396 (uri (cran-uri "Rmpfr" version))
10399 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10400 (properties `((upstream-name . "Rmpfr")))
10401 (build-system r-build-system)
10405 `(("r-gmp" ,r-gmp)))
10406 (home-page "http://rmpfr.r-forge.r-project.org/")
10407 (synopsis "R bindings to the MPFR library")
10409 "This package supports arithmetic (via S4 classes and methods) for
10410 arbitrary precision floating point numbers, including transcendental
10411 functions. To this end, the package interfaces with the @dfn{Multiple
10412 Precision Floating-Point Reliable} (MPFR) library.")
10413 (license license:gpl2+)))
10415 (define-public r-assertive-base
10417 (name "r-assertive-base")
10422 (uri (cran-uri "assertive.base" version))
10425 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10427 `((upstream-name . "assertive.base")))
10428 (build-system r-build-system)
10429 (home-page "https://bitbucket.org/richierocks/assertive.base")
10430 (synopsis "Core of the assertive package")
10432 "This package provides a minimal set of predicates and assertions used by
10433 the assertive package. This is mainly for use by other package developers who
10434 want to include run-time testing features in their own packages.")
10435 (license license:gpl3+)))
10437 (define-public r-assertive-properties
10439 (name "r-assertive-properties")
10444 (uri (cran-uri "assertive.properties" version))
10447 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10449 `((upstream-name . "assertive.properties")))
10450 (build-system r-build-system)
10452 `(("r-assertive-base" ,r-assertive-base)))
10453 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10454 (synopsis "Assertions to check properties of variables")
10456 "This package provides a set of predicates and assertions for checking
10457 the properties of variables, such as length, names and attributes. This is
10458 mainly for use by other package developers who want to include run-time
10459 testing features in their own packages.")
10460 (license license:gpl3+)))
10462 (define-public r-assertive-numbers
10464 (name "r-assertive-numbers")
10469 (uri (cran-uri "assertive.numbers" version))
10472 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10474 `((upstream-name . "assertive.numbers")))
10475 (build-system r-build-system)
10477 `(("r-assertive-base" ,r-assertive-base)))
10478 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10479 (synopsis "Assertions to check properties of numbers")
10481 "This package provides a set of predicates and assertions for checking
10482 the properties of numbers. This is mainly for use by other package developers
10483 who want to include run-time testing features in their own packages.")
10484 (license license:gpl3+)))
10486 (define-public r-assertive-sets
10488 (name "r-assertive-sets")
10493 (uri (cran-uri "assertive.sets" version))
10496 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10498 `((upstream-name . "assertive.sets")))
10499 (build-system r-build-system)
10501 `(("r-assertive-base" ,r-assertive-base)))
10502 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10503 (synopsis "Assertions to check properties of sets")
10505 "This package provides a set of predicates and assertions for checking
10506 the properties of sets. This is mainly for use by other package developers
10507 who want to include run-time testing features in their own packages.")
10508 (license license:gpl3+)))
10510 (define-public r-assertive-matrices
10512 (name "r-assertive-matrices")
10517 (uri (cran-uri "assertive.matrices" version))
10520 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10522 `((upstream-name . "assertive.matrices")))
10523 (build-system r-build-system)
10525 `(("r-assertive-base" ,r-assertive-base)))
10526 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10527 (synopsis "Assertions to check properties of matrices")
10529 "This package provides a set of predicates and assertions for checking
10530 the properties of matrices. This is mainly for use by other package
10531 developers who want to include run-time testing features in their own
10533 (license license:gpl3+)))
10535 (define-public r-assertive-models
10537 (name "r-assertive-models")
10542 (uri (cran-uri "assertive.models" version))
10545 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10547 `((upstream-name . "assertive.models")))
10548 (build-system r-build-system)
10550 `(("r-assertive-base" ,r-assertive-base)))
10551 (home-page "https://bitbucket.org/richierocks/assertive.models")
10552 (synopsis "Assertions to check properties of models")
10554 "This package provides a set of predicates and assertions for checking
10555 the properties of models. This is mainly for use by other package developers
10556 who want to include run-time testing features in their own packages.")
10557 (license license:gpl3+)))
10559 (define-public r-assertive-reflection
10561 (name "r-assertive-reflection")
10566 (uri (cran-uri "assertive.reflection" version))
10569 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10571 `((upstream-name . "assertive.reflection")))
10572 (build-system r-build-system)
10574 `(("r-assertive-base" ,r-assertive-base)))
10575 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10576 (synopsis "Assertions for checking the state of R")
10578 "This package provides a set of predicates and assertions for checking
10579 the state and capabilities of R, the operating system it is running on, and
10580 the IDE being used. This is mainly for use by other package developers who
10581 want to include run-time testing features in their own packages.")
10582 (license license:gpl3+)))
10584 (define-public r-assertive-types
10586 (name "r-assertive-types")
10591 (uri (cran-uri "assertive.types" version))
10594 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10596 `((upstream-name . "assertive.types")))
10597 (build-system r-build-system)
10599 `(("r-assertive-base" ,r-assertive-base)
10600 ("r-assertive-properties" ,r-assertive-properties)
10601 ("r-codetools" ,r-codetools)))
10602 (home-page "https://bitbucket.org/richierocks/assertive.types")
10603 (synopsis "Assertions to check types of variables")
10605 "This package provides a set of predicates and assertions for checking
10606 the types of variables. This is mainly for use by other package developers
10607 who want to include run-time testing features in their own packages.")
10608 (license license:gpl3+)))
10610 (define-public r-assertive-files
10612 (name "r-assertive-files")
10617 (uri (cran-uri "assertive.files" version))
10620 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10622 `((upstream-name . "assertive.files")))
10623 (build-system r-build-system)
10625 `(("r-assertive-base" ,r-assertive-base)
10626 ("r-assertive-numbers" ,r-assertive-numbers)))
10627 (home-page "https://bitbucket.org/richierocks/assertive.files")
10628 (synopsis "Assertions to check properties of files")
10630 "This package provides a set of predicates and assertions for checking
10631 the properties of files and connections. This is mainly for use by other
10632 package developers who want to include run-time testing features in their own
10634 (license license:gpl3+)))
10636 (define-public r-assertive-code
10638 (name "r-assertive-code")
10643 (uri (cran-uri "assertive.code" version))
10646 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10648 `((upstream-name . "assertive.code")))
10649 (build-system r-build-system)
10651 `(("r-assertive-base" ,r-assertive-base)
10652 ("r-assertive-properties" ,r-assertive-properties)
10653 ("r-assertive-types" ,r-assertive-types)))
10654 (home-page "https://bitbucket.org/richierocks/assertive.code")
10655 (synopsis "Assertions to check properties of code")
10657 "This package provides a set of predicates and assertions for checking
10658 the properties of code. This is mainly for use by other package developers
10659 who want to include run-time testing features in their own packages.")
10660 (license license:gpl3+)))
10662 (define-public r-assertive-datetimes
10664 (name "r-assertive-datetimes")
10669 (uri (cran-uri "assertive.datetimes" version))
10672 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10674 `((upstream-name . "assertive.datetimes")))
10675 (build-system r-build-system)
10677 `(("r-assertive-base" ,r-assertive-base)
10678 ("r-assertive-types" ,r-assertive-types)))
10679 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10680 (synopsis "Assertions to check properties of dates and times")
10682 "This package provides a set of predicates and assertions for checking
10683 the properties of dates and times. This is mainly for use by other package
10684 developers who want to include run-time testing features in their own
10686 (license license:gpl3+)))
10688 (define-public r-assertive-strings
10690 (name "r-assertive-strings")
10695 (uri (cran-uri "assertive.strings" version))
10698 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10700 `((upstream-name . "assertive.strings")))
10701 (build-system r-build-system)
10703 `(("r-assertive-base" ,r-assertive-base)
10704 ("r-assertive-types" ,r-assertive-types)
10705 ("r-stringi" ,r-stringi)))
10706 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10707 (synopsis "Assertions to check properties of strings")
10709 "This package provides a set of predicates and assertions for checking
10710 the properties of strings. This is mainly for use by other package developers
10711 who want to include run-time testing features in their own packages.")
10712 (license license:gpl3+)))
10714 (define-public r-assertive-data-us
10716 (name "r-assertive-data-us")
10721 (uri (cran-uri "assertive.data.us" version))
10724 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10726 `((upstream-name . "assertive.data.us")))
10727 (build-system r-build-system)
10729 `(("r-assertive-base" ,r-assertive-base)
10730 ("r-assertive-strings" ,r-assertive-strings)))
10731 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10732 (synopsis "Assertions to check properties of strings")
10734 "This package provides a set of predicates and assertions for checking
10735 the properties of US-specific complex data types. This is mainly for use by
10736 other package developers who want to include run-time testing features in
10737 their own packages.")
10738 (license license:gpl3+)))
10740 (define-public r-assertive-data-uk
10742 (name "r-assertive-data-uk")
10747 (uri (cran-uri "assertive.data.uk" version))
10750 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10752 `((upstream-name . "assertive.data.uk")))
10753 (build-system r-build-system)
10755 `(("r-assertive-base" ,r-assertive-base)
10756 ("r-assertive-strings" ,r-assertive-strings)))
10757 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10758 (synopsis "Assertions to check properties of strings")
10760 "This package provides a set of predicates and assertions for checking
10761 the properties of UK-specific complex data types. This is mainly for use by
10762 other package developers who want to include run-time testing features in
10763 their own packages.")
10764 (license license:gpl3+)))
10766 (define-public r-assertive-data
10768 (name "r-assertive-data")
10773 (uri (cran-uri "assertive.data" version))
10776 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
10778 `((upstream-name . "assertive.data")))
10779 (build-system r-build-system)
10781 `(("r-assertive-base" ,r-assertive-base)
10782 ("r-assertive-strings" ,r-assertive-strings)))
10783 (home-page "https://bitbucket.org/richierocks/assertive.data")
10784 (synopsis "Assertions to check properties of data")
10786 "This package provides a set of predicates and assertions for checking
10787 the properties of (country independent) complex data types. This is mainly
10788 for use by other package developers who want to include run-time testing
10789 features in their own packages.")
10790 (license license:gpl3+)))
10792 (define-public r-assertive
10794 (name "r-assertive")
10799 (uri (cran-uri "assertive" version))
10802 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
10803 (build-system r-build-system)
10805 `(("r-assertive-base" ,r-assertive-base)
10806 ("r-assertive-code" ,r-assertive-code)
10807 ("r-assertive-data" ,r-assertive-data)
10808 ("r-assertive-data-uk" ,r-assertive-data-uk)
10809 ("r-assertive-data-us" ,r-assertive-data-us)
10810 ("r-assertive-datetimes" ,r-assertive-datetimes)
10811 ("r-assertive-files" ,r-assertive-files)
10812 ("r-assertive-matrices" ,r-assertive-matrices)
10813 ("r-assertive-models" ,r-assertive-models)
10814 ("r-assertive-numbers" ,r-assertive-numbers)
10815 ("r-assertive-properties" ,r-assertive-properties)
10816 ("r-assertive-reflection" ,r-assertive-reflection)
10817 ("r-assertive-sets" ,r-assertive-sets)
10818 ("r-assertive-strings" ,r-assertive-strings)
10819 ("r-assertive-types" ,r-assertive-types)
10820 ("r-knitr" ,r-knitr)))
10821 (home-page "https://bitbucket.org/richierocks/assertive")
10822 (synopsis "Readable check functions to ensure code integrity")
10824 "This package provides lots of predicates (@code{is_*} functions) to
10825 check the state of your variables, and assertions (@code{assert_*} functions)
10826 to throw errors if they aren't in the right form.")
10827 (license license:gpl3+)))
10829 (define-public r-dotcall64
10831 (name "r-dotcall64")
10836 (uri (cran-uri "dotCall64" version))
10839 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
10840 (properties `((upstream-name . "dotCall64")))
10841 (build-system r-build-system)
10842 (native-inputs `(("gfortran" ,gfortran)))
10843 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
10844 (synopsis "Enhanced foreign function interface supporting long vectors")
10846 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
10847 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
10848 supports long vectors, arguments of type 64-bit integer, and provides a
10849 mechanism to avoid unnecessary copies of read-only and write-only arguments.
10850 This makes it a convenient and fast interface to C/C++ and Fortran code.")
10851 (license license:gpl2+)))
10853 (define-public r-spam
10860 (uri (cran-uri "spam" version))
10863 "194n5mgvyms9ckjqixl3h33apii8h9kqspqg2si9k741k578qb3w"))))
10864 (build-system r-build-system)
10866 `(("r-dotcall64" ,r-dotcall64)))
10867 (native-inputs `(("gfortran" ,gfortran)))
10868 (home-page "https://www.math.uzh.ch/pages/spam/")
10869 (synopsis "Sparse matrix algebra")
10871 "This package provides a set of functions for sparse matrix algebra.
10872 Differences with other sparse matrix packages are:
10875 @item it only supports (essentially) one sparse matrix format;
10876 @item it is based on transparent and simple structure(s);
10877 @item it is tailored for MCMC calculations within G(M)RF;
10878 @item and it is fast and scalable (with the extension package @code{spam64}).
10880 ;; Either of these licenses
10881 (license (list license:bsd-3 license:lgpl2.0))))
10883 (define-public r-fields
10890 (uri (cran-uri "fields" version))
10892 (base32 "1qbqdqq76xgnlbc9z643zn4s8k493h1jmav2f465hfvp63306br6"))))
10893 (build-system r-build-system)
10895 `(("r-maps" ,r-maps)
10896 ("r-spam" ,r-spam)))
10898 `(("gfortran" ,gfortran)))
10899 (home-page "https://www.image.ucar.edu/fields")
10900 (synopsis "Tools for spatial data")
10902 "This is a package for curve, surface and function fitting with an
10903 emphasis on splines, spatial data and spatial statistics. The major methods
10904 include cubic, and thin plate splines, Kriging, and compactly supported
10905 covariance functions for large data sets.")
10906 (license license:gpl2+)))
10908 (define-public r-spatialextremes
10910 (name "r-spatialextremes")
10911 (version "2.0-7.2")
10915 (uri (cran-uri "SpatialExtremes" version))
10918 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
10920 `((upstream-name . "SpatialExtremes")))
10921 (build-system r-build-system)
10923 `(("r-fields" ,r-fields)
10924 ("r-maps" ,r-maps)))
10925 (home-page "http://spatialextremes.r-forge.r-project.org/")
10926 (synopsis "Modelling spatial extremes")
10928 "This package provides tools for the statistical modelling of spatial
10929 extremes using max-stable processes, copula or Bayesian hierarchical models.
10930 More precisely, this package allows (conditional) simulations from various
10931 parametric max-stable models, analysis of the extremal spatial dependence, the
10932 fitting of such processes using composite likelihoods or least square (simple
10933 max-stable processes only), model checking and selection and prediction.")
10934 (license license:gpl2+)))
10936 (define-public r-drc
10943 (uri (cran-uri "drc" version))
10946 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
10947 (build-system r-build-system)
10950 ("r-gtools" ,r-gtools)
10952 ("r-multcomp" ,r-multcomp)
10953 ("r-plotrix" ,r-plotrix)
10954 ("r-scales" ,r-scales)))
10955 (home-page "https://cran.r-project.org/web/packages/drc")
10956 (synopsis "Analysis of dose-response curves")
10958 "This package provides a suite of flexible and versatile model fitting
10959 and after-fitting functions for the analysis of dose-response data.")
10960 (license license:gpl2+)))
10962 (define-public r-rmeta
10969 (uri (cran-uri "rmeta" version))
10972 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
10973 (build-system r-build-system)
10974 (home-page "https://cran.r-project.org/web/packages/rmeta")
10975 (synopsis "Tools for meta-analysis")
10977 "This package provides functions for simple fixed and random effects
10978 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
10979 draws standard summary plots, funnel plots, and computes summaries and tests
10980 for association and heterogeneity.")
10981 (license license:gpl2)))
10983 (define-public r-bootstrap
10985 (name "r-bootstrap")
10990 (uri (cran-uri "bootstrap" version))
10993 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
10994 (build-system r-build-system)
10995 (native-inputs `(("gfortran" ,gfortran)))
10996 (home-page "https://cran.r-project.org/web/packages/bootstrap")
10997 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
10999 "This package provides software and data for the book \"An Introduction
11000 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11001 This package is primarily provided for projects already based on it, and for
11002 support of the book. New projects should preferentially use the recommended
11003 package \"boot\".")
11004 (license license:bsd-3)))
11006 (define-public r-survivalroc
11008 (name "r-survivalroc")
11013 (uri (cran-uri "survivalROC" version))
11016 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11017 (properties `((upstream-name . "survivalROC")))
11018 (build-system r-build-system)
11019 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11020 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11022 "Compute time-dependent ROC curve from censored survival data using
11023 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11024 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11025 (license license:gpl2+)))
11027 (define-public r-longitudinal
11029 (name "r-longitudinal")
11034 (uri (cran-uri "longitudinal" version))
11037 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11038 (build-system r-build-system)
11039 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11040 (home-page "http://strimmerlab.org/software/longitudinal/")
11041 (synopsis "Analysis of multiple time course data")
11043 "This package contains general data structures and functions for
11044 longitudinal data with multiple variables, repeated measurements, and
11045 irregularly spaced time points. It also implements a shrinkage estimator of
11046 dynamical correlation and dynamical covariance.")
11047 (license license:gpl3+)))
11049 (define-public r-genenet
11056 (uri (cran-uri "GeneNet" version))
11059 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
11060 (properties `((upstream-name . "GeneNet")))
11061 (build-system r-build-system)
11063 `(("r-corpcor" ,r-corpcor)
11064 ("r-fdrtool" ,r-fdrtool)
11065 ("r-longitudinal" ,r-longitudinal)))
11066 (home-page "http://strimmerlab.org/software/genenet/")
11067 (synopsis "Modeling and inferring gene networks")
11069 "This package analyzes gene expression (time series) data with focus on
11070 the inference of gene networks. In particular, GeneNet implements the methods
11071 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11072 for learning large-scale gene association networks (including assignment of
11073 putative directions).")
11074 (license license:gpl3+)))
11076 (define-public r-rbamtools
11078 (name "r-rbamtools")
11079 (version "2.16.11.2")
11083 (uri (cran-uri "rbamtools" version))
11086 "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj"))))
11087 (build-system r-build-system)
11088 (inputs `(("zlib" ,zlib)))
11090 `(("r-refgenome" ,r-refgenome)))
11091 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11092 (synopsis "Read and write BAM (binary alignment) files")
11094 "This package provides an R interface to functions of the SAMtools
11096 (license license:artistic2.0)))
11098 (define-public r-protviz
11105 (uri (cran-uri "protViz" version))
11108 "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1"))))
11109 (properties `((upstream-name . "protViz")))
11110 (build-system r-build-system)
11113 ("python-2" ,python-2)))
11114 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11115 (home-page "https://github.com/protViz/protViz/")
11116 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11118 "This package helps with quality checks, visualizations and analysis of
11119 mass spectrometry data, coming from proteomics experiments. The package is
11120 developed, tested and used at the Functional Genomics Center Zurich, where it
11121 is used mainly for prototyping, teaching, and having fun with proteomics data.
11122 But it can also be used to do data analysis for small scale data sets.")
11123 (license license:gpl3)))
11125 (define-public r-cmprsk
11132 (uri (cran-uri "cmprsk" version))
11134 (base32 "0xhgfg5b4i9skkaxp7gzkafgg5bqs5q1rp4hpw2jjmykg2nifn99"))))
11135 (build-system r-build-system)
11137 `(("r-survival" ,r-survival)))
11139 `(("gfortran" ,gfortran)))
11140 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11141 (synopsis "Subdistribution analysis of competing risks")
11143 "This package provides tool for estimation, testing and regression
11144 modeling of subdistribution functions in competing risks, as described in
11145 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11146 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11147 A proportional hazards model for the subdistribution of a competing risk,
11148 JASA, 94:496-509.")
11149 (license license:gpl2+)))
11151 (define-public r-etm
11158 (uri (cran-uri "etm" version))
11161 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11162 (build-system r-build-system)
11164 `(("r-data-table" ,r-data-table)
11165 ("r-lattice" ,r-lattice)
11167 ("r-rcpparmadillo" ,r-rcpparmadillo)
11168 ("r-survival" ,r-survival)))
11169 (home-page "https://cran.r-project.org/web/packages/etm")
11170 (synopsis "Empirical transition matrix")
11172 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11173 the matrix of transition probabilities for any time-inhomogeneous multistate
11174 model with finite state space using the Aalen-Johansen estimator.")
11175 (license license:expat)))
11177 (define-public r-epi
11184 (uri (cran-uri "Epi" version))
11187 "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd"))))
11188 (properties `((upstream-name . "Epi")))
11189 (build-system r-build-system)
11191 `(("r-cmprsk" ,r-cmprsk)
11192 ("r-data-table" ,r-data-table)
11195 ("r-matrix" ,r-matrix)
11197 ("r-numderiv" ,r-numderiv)
11199 ("r-survival" ,r-survival)
11201 (home-page "http://BendixCarstensen.com/Epi/")
11202 (synopsis "Statistical analysis in epidemiology")
11204 "This package provides functions for demographic and epidemiological
11205 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11206 particular representation, manipulation and simulation of multistate data -
11207 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11208 @code{etm} and @code{cmprsk} packages. It also contains functions for
11209 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11210 data and some useful functions for tabulation and plotting, as well as a
11211 number of epidemiological data sets.")
11212 (license license:gpl2)))
11214 (define-public r-ppls
11217 (version "1.6-1.1")
11221 (uri (cran-uri "ppls" version))
11224 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11225 (build-system r-build-system)
11226 (propagated-inputs `(("r-mass" ,r-mass)))
11227 (home-page "https://cran.r-project.org/web/packages/ppls")
11228 (synopsis "Penalized partial least squares")
11230 "This package contains linear and nonlinear regression methods based on
11231 partial least squares and penalization techniques. Model parameters are
11232 selected via cross-validation, and confidence intervals ans tests for the
11233 regression coefficients can be conducted via jackknifing.")
11234 (license license:gpl2+)))
11236 (define-public r-huge
11243 (uri (cran-uri "huge" version))
11246 "18f8w4hdp9fdi2k5ip6fnrn5z47w4ybgxs2m6a7jdvd2v4wfdr69"))))
11247 (build-system r-build-system)
11249 `(("r-igraph" ,r-igraph)
11251 ("r-matrix" ,r-matrix)
11253 ("r-rcppeigen" ,r-rcppeigen)))
11254 (home-page "https://cran.r-project.org/web/packages/huge")
11255 (synopsis "High-dimensional undirected graph estimation")
11257 "This package provides a general framework for high-dimensional
11258 undirected graph estimation. It integrates data preprocessing, neighborhood
11259 screening, graph estimation, and model selection techniques into a pipeline.")
11260 (license license:gpl2)))
11262 (define-public r-parcor
11269 (uri (cran-uri "parcor" version))
11272 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11273 (build-system r-build-system)
11276 ("r-genenet" ,r-genenet)
11277 ("r-glmnet" ,r-glmnet)
11279 ("r-ppls" ,r-ppls)))
11280 (home-page "https://cran.r-project.org/web/packages/parcor")
11281 (synopsis "Regularized estimation of partial correlation matrices")
11283 "This package estimates the matrix of partial correlations based on
11284 different regularized regression methods: lasso, adaptive lasso, PLS, and
11285 Ridge Regression. In addition, the package provides model selection for
11286 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11287 (license license:gpl2+)))
11289 (define-public r-mcmc
11296 (uri (cran-uri "mcmc" version))
11299 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11300 (build-system r-build-system)
11301 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11302 (synopsis "Markov chain Monte Carlo")
11304 "This package simulates continuous distributions of random vectors using
11305 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11306 function that evaluates the log unnormalized density. Algorithms are random
11307 walk Metropolis algorithm (function @code{metrop}), simulated
11308 tempering (function @code{temper}), and morphometric random walk
11309 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11310 by change of variable.")
11311 (license license:expat)))
11313 (define-public r-listenv
11320 (uri (cran-uri "listenv" version))
11323 "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1"))))
11324 (build-system r-build-system)
11326 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11327 (home-page "https://github.com/HenrikBengtsson/listenv")
11328 (synopsis "Environments behaving (almost) as lists")
11330 "This package implements list environments. List environments are
11331 environments that have list-like properties. For instance, the elements of a
11332 list environment are ordered and can be accessed and iterated over using index
11334 (license license:lgpl2.1+)))
11336 (define-public r-globals
11343 (uri (cran-uri "globals" version))
11346 "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br"))))
11347 (build-system r-build-system)
11349 `(("r-codetools" ,r-codetools)))
11350 (home-page "https://github.com/HenrikBengtsson/globals")
11351 (synopsis "Identify global objects in R expressions")
11353 "This package provides tools to identify global (\"unknown\" or \"free\")
11354 objects in R expressions by code inspection using various strategies, e.g.
11355 conservative or liberal. The objective of this package is to make it as
11356 simple as possible to identify global objects for the purpose of exporting
11357 them in distributed compute environments.")
11358 (license license:lgpl2.1+)))
11360 (define-public r-future
11367 (uri (cran-uri "future" version))
11370 "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa"))))
11371 (build-system r-build-system)
11373 `(("r-digest" ,r-digest)
11374 ("r-globals" ,r-globals)
11375 ("r-listenv" ,r-listenv)))
11377 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11378 (home-page "https://github.com/HenrikBengtsson/future")
11379 (synopsis "Unified parallel and distributed processing in R")
11381 "The purpose of this package is to provide a lightweight and unified
11382 Future API for sequential and parallel processing of R expression via futures.
11383 This package implements sequential, multicore, multisession, and cluster
11384 futures. With these, R expressions can be evaluated on the local machine, in
11385 parallel a set of local machines, or distributed on a mix of local and remote
11386 machines. Extensions to this package implement additional backends for
11387 processing futures via compute cluster schedulers etc. Because of its unified
11388 API, there is no need to modify any code in order to switch from sequential on
11389 the local machine to, say, distributed processing on a remote compute cluster.")
11390 (license license:lgpl2.1+)))
11392 (define-public r-future-apply
11394 (name "r-future-apply")
11399 (uri (cran-uri "future.apply" version))
11402 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11403 (properties `((upstream-name . "future.apply")))
11404 (build-system r-build-system)
11406 `(("r-future" ,r-future)
11407 ("r-globals" ,r-globals)))
11409 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11410 (home-page "https://github.com/HenrikBengtsson/future.apply")
11411 (synopsis "Apply function to elements in parallel using futures")
11413 "This package provides implementations of @code{apply()},
11414 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11415 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11416 can be resolved using any future-supported backend, e.g. parallel on the local
11417 machine or distributed on a compute cluster.")
11418 (license license:gpl2+)))
11420 (define-public r-rsvd
11427 (uri (cran-uri "rsvd" version))
11430 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11431 (build-system r-build-system)
11433 `(("r-matrix" ,r-matrix)))
11434 (home-page "https://github.com/erichson/rSVD")
11435 (synopsis "Randomized singular value decomposition")
11437 "Low-rank matrix decompositions are fundamental tools and widely used for
11438 data analysis, dimension reduction, and data compression. Classically, highly
11439 accurate deterministic matrix algorithms are used for this task. However, the
11440 emergence of large-scale data has severely challenged our computational
11441 ability to analyze big data. The concept of randomness has been demonstrated
11442 as an effective strategy to quickly produce approximate answers to familiar
11443 problems such as the @dfn{singular value decomposition} (SVD). This package
11444 provides several randomized matrix algorithms such as the randomized singular
11445 value decomposition (@code{rsvd}), randomized principal component
11446 analysis (@code{rpca}), randomized robust principal component
11447 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11448 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11449 functions are provided.")
11450 (license license:gpl3+)))
11452 (define-public r-sloop
11459 (uri (cran-uri "sloop" version))
11462 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11463 (build-system r-build-system)
11465 `(("r-codetools" ,r-codetools)
11466 ("r-crayon" ,r-crayon)
11467 ("r-purrr" ,r-purrr)
11468 ("r-rlang" ,r-rlang)
11469 ("r-tibble" ,r-tibble)))
11470 (home-page "https://github.com/r-lib/sloop")
11471 (synopsis "Helpers for object-oriented programming in R")
11473 "This package provides a collection of helper functions designed to
11474 help you to better understand object oriented programming in R, particularly
11476 (license license:gpl3)))
11478 (define-public r-capushe
11485 (uri (cran-uri "capushe" version))
11488 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11489 (build-system r-build-system)
11490 (propagated-inputs `(("r-mass" ,r-mass)))
11491 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11492 (synopsis "Calibrating penalties using slope heuristics")
11494 "This package provides tools for the calibration of penalized criteria
11495 for model selection. The calibration methods available are based on the slope
11497 (license license:gpl2+)))
11499 (define-public r-dorng
11506 (uri (cran-uri "doRNG" version))
11509 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11510 (properties `((upstream-name . "doRNG")))
11511 (build-system r-build-system)
11513 `(("r-foreach" ,r-foreach)
11514 ("r-iterators" ,r-iterators)
11515 ("r-pkgmaker" ,r-pkgmaker)
11516 ("r-rngtools" ,r-rngtools)))
11517 (home-page "https://renozao.github.io/doRNG/")
11518 (synopsis "Generic reproducible parallel backend for foreach loops")
11520 "This package provides functions to perform reproducible parallel
11521 @code{foreach} loops, using independent random streams as generated by
11522 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11523 convert standard @code{%dopar%} loops into fully reproducible loops,
11524 independently of the number of workers, the task scheduling strategy, or the
11525 chosen parallel environment and associated foreach backend.")
11526 (license license:gpl2+)))
11528 (define-public r-blockmodeling
11530 (name "r-blockmodeling")
11535 (uri (cran-uri "blockmodeling" version))
11538 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11539 (build-system r-build-system)
11541 `(("r-doparallel" ,r-doparallel)
11542 ("r-dorng" ,r-dorng)
11543 ("r-foreach" ,r-foreach)
11544 ("r-matrix" ,r-matrix)))
11545 (native-inputs `(("gfortran" ,gfortran)))
11546 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11547 (synopsis "Generalized and classical blockmodeling of valued networks")
11549 "This package is primarily meant as an implementation of generalized
11550 blockmodeling for valued networks. In addition, measures of similarity or
11551 dissimilarity based on structural equivalence and regular equivalence (REGE
11552 algorithms) can be computed and partitioned matrices can be plotted.")
11553 (license license:gpl2+)))
11555 (define-public r-upsetr
11562 (uri (cran-uri "UpSetR" version))
11565 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11566 (properties `((upstream-name . "UpSetR")))
11567 (build-system r-build-system)
11569 `(("r-ggplot2" ,r-ggplot2)
11570 ("r-gridextra" ,r-gridextra)
11572 ("r-scales" ,r-scales)))
11573 (home-page "https://github.com/hms-dbmi/UpSetR")
11574 (synopsis "Visualize intersecting sets")
11576 "This package provides a more scalable alternative to Venn and Euler
11577 diagrams for visualizing intersecting sets. Create visualizations of
11578 intersecting sets using a novel matrix design, along with visualizations of
11579 several common set, element and attribute related tasks.")
11580 (license license:expat)))
11582 ;; This package includes a JavaScript file, which is not minified. When
11583 ;; upgrading please check that there are no new minified JavaScript files.
11584 (define-public r-shinybs
11591 (uri (cran-uri "shinyBS" version))
11594 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11595 (properties `((upstream-name . "shinyBS")))
11596 (build-system r-build-system)
11597 ;; The tests spawn Shiny browser apps. They cannot be run
11598 ;; non-interactively.
11599 (arguments '(#:tests? #f))
11601 `(("r-htmltools" ,r-htmltools)
11602 ("r-shiny" ,r-shiny)))
11603 (home-page "https://ebailey78.github.io/shinyBS/")
11604 (synopsis "Twitter Bootstrap components for Shiny")
11606 "This package adds additional Twitter Bootstrap components to Shiny.")
11607 (license license:gpl3)))
11609 (define-public r-outliers
11611 (name "r-outliers")
11616 (uri (cran-uri "outliers" version))
11619 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11620 (build-system r-build-system)
11621 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11622 (synopsis "Tests for outliers")
11624 "This package provides a collection of some tests commonly used for
11625 identifying outliers.")
11626 (license license:gpl2+)))
11628 (define-public r-bayesm
11635 (uri (cran-uri "bayesm" version))
11637 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
11638 (build-system r-build-system)
11640 `(("r-rcpp" ,r-rcpp)
11641 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11642 (home-page "http://www.perossi.org/home/bsm-1")
11643 (synopsis "Bayesian inference for marketing/micro-econometrics")
11645 "This package covers many important models used in marketing and
11646 micro-econometrics applications, including Bayes Regression (univariate or
11647 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11648 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11649 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11650 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11651 Estimation with normal base, Hierarchical Linear Models with normal prior and
11652 covariates, Hierarchical Linear Models with a mixture of normals prior and
11653 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11654 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11655 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11656 analysis of choice-based conjoint data, Bayesian treatment of linear
11657 instrumental variables models, Analysis of Multivariate Ordinal survey data
11658 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11659 Coefficient Logit Models.")
11660 (license license:gpl2+)))
11662 (define-public r-tensora
11669 (uri (cran-uri "tensorA" version))
11672 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11673 (properties `((upstream-name . "tensorA")))
11674 (build-system r-build-system)
11675 (home-page "http://www.stat.boogaart.de/tensorA")
11676 (synopsis "Advanced tensor arithmetic with named indices")
11678 "This package provides convenience functions for advanced linear algebra
11679 with tensors and computation with datasets of tensors on a higher level
11680 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11681 co- and contravariate indices, and parallel computations on sequences of
11683 (license license:gpl2+)))
11685 (define-public r-rarpack
11692 (uri (cran-uri "rARPACK" version))
11695 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11696 (properties `((upstream-name . "rARPACK")))
11697 (build-system r-build-system)
11698 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11699 (home-page "https://github.com/yixuan/rARPACK")
11700 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11702 "This package was previously an R wrapper of the ARPACK library, and now
11703 a shell of the R package RSpectra, an R interface to the Spectra library for
11704 solving large scale eigenvalue/vector problems. The current version of
11705 rARPACK simply imports and exports the functions provided by RSpectra. New
11706 users of rARPACK are advised to switch to the RSpectra package.")
11707 (license license:bsd-3)))
11709 (define-public r-compositions
11711 (name "r-compositions")
11716 (uri (cran-uri "compositions" version))
11719 "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i"))))
11720 (build-system r-build-system)
11722 `(("r-bayesm" ,r-bayesm)
11723 ("r-energy" ,r-energy)
11724 ("r-robustbase" ,r-robustbase)
11725 ("r-tensora" ,r-tensora)))
11726 (home-page "http://www.stat.boogaart.de/compositions")
11727 (synopsis "Compositional data analysis")
11729 "This package provides functions for the consistent analysis of
11730 compositional data (e.g. portions of substances) and positive
11731 numbers (e.g. concentrations).")
11732 (license license:gpl2+)))
11734 (define-public r-cobs
11741 (uri (cran-uri "cobs" version))
11744 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11745 (build-system r-build-system)
11747 `(("r-quantreg" ,r-quantreg)
11748 ("r-sparsem" ,r-sparsem)))
11749 (home-page "https://cran.r-project.org/web/packages/cobs")
11750 (synopsis "Constrained B-Splines (sparse matrix based)")
11752 "This package provides qualitatively constrained (regression) smoothing
11753 splines via linear programming and sparse matrices.")
11754 (license license:gpl2+)))
11756 (define-public r-drimpute
11758 (name "r-drimpute")
11763 (uri (cran-uri "DrImpute" version))
11766 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11767 (properties `((upstream-name . "DrImpute")))
11768 (build-system r-build-system)
11770 `(("r-rcpp" ,r-rcpp)
11771 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11772 (home-page "https://github.com/ikwak2/DrImpute")
11773 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11775 "This is an R package for imputing dropout events. Many statistical
11776 methods in cell type identification, visualization and lineage reconstruction
11777 do not account for dropout events. DrImpute can improve the performance of
11778 such software by imputing dropout events.")
11779 (license license:gpl3)))
11781 (define-public r-gamlss-dist
11783 (name "r-gamlss-dist")
11788 (uri (cran-uri "gamlss.dist" version))
11790 (base32 "1rl7hzdg5xpvaq3yyzwxhsaqzzs0qidi3ibv454fisijgv8l4vqw"))))
11791 (properties `((upstream-name . "gamlss.dist")))
11792 (build-system r-build-system)
11793 (propagated-inputs `(("r-mass" ,r-mass)))
11794 (home-page "http://www.gamlss.org/")
11795 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
11797 "This package provides a set of distributions which can be used for
11798 modelling the response variables in Generalized Additive Models for Location
11799 Scale and Shape. The distributions can be continuous, discrete or mixed
11800 distributions. Extra distributions can be created, by transforming, any
11801 continuous distribution defined on the real line, to a distribution defined on
11802 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
11803 transformation, respectively.")
11804 ;; Either version of the GPL.
11805 (license (list license:gpl2 license:gpl3))))
11807 ;; This package includes JavaScript files, which are not minified. When
11808 ;; upgrading please check that there are no new minified JavaScript files.
11809 (define-public r-shinyjs
11816 (uri (cran-uri "shinyjs" version))
11819 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
11820 (build-system r-build-system)
11822 `(("r-digest" ,r-digest)
11823 ("r-htmltools" ,r-htmltools)
11824 ("r-jsonlite" ,r-jsonlite)
11825 ("r-shiny" ,r-shiny)))
11826 (home-page "https://deanattali.com/shinyjs")
11827 (synopsis "Improve the user experience of your Shiny apps")
11829 "Perform common useful JavaScript operations in Shiny apps that will
11830 greatly improve your apps without having to know any JavaScript. Examples
11831 include: hiding an element, disabling an input, resetting an input back to its
11832 original value, delaying code execution by a few seconds, and many more useful
11833 functions for both the end user and the developer. Shinyjs can also be used
11834 to easily call your own custom JavaScript functions from R.")
11835 (license license:agpl3+)))
11837 ;; This package includes minified JavaScript files. When upgrading please
11838 ;; check that there are no new minified JavaScript files.
11839 (define-public r-colourpicker
11841 (name "r-colourpicker")
11846 (uri (cran-uri "colourpicker" version))
11849 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
11850 (build-system r-build-system)
11852 `(#:modules ((guix build utils)
11853 (guix build r-build-system)
11857 (modify-phases %standard-phases
11858 (add-after 'unpack 'process-javascript
11859 (lambda* (#:key inputs #:allow-other-keys)
11860 (with-directory-excursion "inst"
11864 `((,(assoc-ref inputs "js-salvattore")
11865 "examples/colourInput/www/salvattore.min.js")
11866 (,(assoc-ref inputs "js-jquery")
11867 "htmlwidgets/lib/jquery/jquery.min.js")
11868 ("www/shared/colourpicker/js/colourpicker.js"
11869 "www/shared/colourpicker/js/colourpicker.min.js"))))
11870 (lambda (sources targets)
11871 (for-each (lambda (source target)
11872 (format #t "Processing ~a --> ~a~%"
11874 (delete-file target)
11875 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
11876 (call-with-output-file target
11878 (dump-port minified port)))))
11879 sources targets))))
11882 `(("r-ggplot2" ,r-ggplot2)
11883 ("r-htmltools" ,r-htmltools)
11884 ("r-htmlwidgets" ,r-htmlwidgets)
11885 ("r-jsonlite" ,r-jsonlite)
11886 ("r-miniui" ,r-miniui)
11887 ("r-shiny" ,r-shiny)
11888 ("r-shinyjs" ,r-shinyjs)))
11890 `(("uglify-js" ,uglify-js)
11894 (uri "https://code.jquery.com/jquery-3.3.1.js")
11897 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
11901 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
11904 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
11905 (home-page "https://github.com/daattali/colourpicker")
11906 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
11908 "This package provides a color picker that can be used as an input in
11909 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
11910 custom color palettes, and many more options. A plot color helper tool is
11911 available as an RStudio Addin, which helps you pick colors to use in your
11912 plots. A more generic color picker RStudio Addin is also provided to let you
11913 select colors to use in your R code.")
11914 (license license:expat)))
11916 (define-public r-ggextra
11923 (uri (cran-uri "ggExtra" version))
11926 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
11927 (properties `((upstream-name . "ggExtra")))
11928 (build-system r-build-system)
11930 `(("r-colourpicker" ,r-colourpicker)
11931 ("r-ggplot2" ,r-ggplot2)
11932 ("r-gtable" ,r-gtable)
11933 ("r-miniui" ,r-miniui)
11935 ("r-scales" ,r-scales)
11936 ("r-shiny" ,r-shiny)
11937 ("r-shinyjs" ,r-shinyjs)))
11938 (home-page "https://github.com/daattali/ggExtra")
11939 (synopsis "Marginal histograms for ggplot2 and other enhancements")
11941 "This package is a collection of functions and layers to enhance ggplot2.
11942 The flagship function is @code{ggMarginal()}, which can be used to add
11943 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
11944 (license license:expat)))
11946 (define-public r-minpack-lm
11948 (name "r-minpack-lm")
11953 (uri (cran-uri "minpack.lm" version))
11956 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
11957 (properties `((upstream-name . "minpack.lm")))
11958 (build-system r-build-system)
11959 (native-inputs `(("gfortran" ,gfortran)))
11960 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
11961 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
11963 "The @code{nls.lm} function provides an R interface to @code{lmder} and
11964 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
11965 problems by a modification of the Levenberg-Marquardt algorithm, with support
11966 for lower and upper parameter bounds. The implementation can be used via
11967 @code{nls}-like calls using the @code{nlsLM} function.")
11968 (license license:gpl3)))
11970 (define-public r-moments
11977 (uri (cran-uri "moments" version))
11980 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
11981 (build-system r-build-system)
11982 (home-page "https://cran.r-project.org/web/packages/moments")
11983 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
11985 "This package provides functions to calculate: moments, Pearson's
11986 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
11987 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
11988 (license license:gpl2+)))
11990 (define-public r-msir
11997 (uri (cran-uri "msir" version))
12000 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12001 (build-system r-build-system)
12003 `(("r-mclust" ,r-mclust)))
12004 (home-page "https://cran.r-project.org/web/packages/msir")
12005 (synopsis "Model-based sliced inverse regression")
12007 "This is an R package for dimension reduction based on finite Gaussian
12008 mixture modeling of inverse regression.")
12009 (license license:gpl2+)))
12011 (define-public r-pbivnorm
12013 (name "r-pbivnorm")
12018 (uri (cran-uri "pbivnorm" version))
12021 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12022 (build-system r-build-system)
12023 (native-inputs `(("gfortran" ,gfortran)))
12024 (home-page "https://github.com/brentonk/pbivnorm")
12025 (synopsis "Vectorized bivariate normal CDF")
12027 "This package provides a vectorized R function for calculating
12028 probabilities from a standard bivariate normal CDF.")
12029 (license license:gpl2+)))
12031 (define-public r-lavaan
12038 (uri (cran-uri "lavaan" version))
12041 "04kvsh2m6mnzlhv83phr3hjzy4sx1ck6f7dgsm7xb8cs84dnxszy"))))
12042 (build-system r-build-system)
12044 `(("r-mass" ,r-mass)
12045 ("r-mnormt" ,r-mnormt)
12046 ("r-numderiv" ,r-numderiv)
12047 ("r-pbivnorm" ,r-pbivnorm)))
12048 (home-page "http://lavaan.ugent.be")
12049 (synopsis "Latent variable analysis")
12051 "This package provides tools to fit a variety of latent variable models,
12052 including confirmatory factor analysis, structural equation modeling and
12053 latent growth curve models.")
12054 (license license:gpl2+)))
12056 (define-public r-nonnest2
12058 (name "r-nonnest2")
12063 (uri (cran-uri "nonnest2" version))
12066 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
12067 (build-system r-build-system)
12069 `(("r-compquadform" ,r-compquadform)
12070 ("r-lavaan" ,r-lavaan)
12071 ("r-mvtnorm" ,r-mvtnorm)
12072 ("r-sandwich" ,r-sandwich)))
12073 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12074 (synopsis "Tests of non-nested models")
12076 "This package allows for testing of non-nested models. It includes tests
12077 of model distinguishability and of model fit that can be applied to both
12078 nested and non-nested models. The package also includes functionality to
12079 obtain confidence intervals associated with AIC and BIC.")
12080 ;; Either version of the GPL.
12081 (license (list license:gpl2 license:gpl3))))
12083 (define-public r-penalized
12085 (name "r-penalized")
12090 (uri (cran-uri "penalized" version))
12093 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12094 (build-system r-build-system)
12096 `(("r-rcpp" ,r-rcpp)
12097 ("r-rcpparmadillo" ,r-rcpparmadillo)
12098 ("r-survival" ,r-survival)))
12099 (home-page "https://cran.r-project.org/web/packages/penalized/")
12100 (synopsis "Penalized estimation in GLMs and in the Cox model")
12102 "This package provides tools for fitting possibly high dimensional
12103 penalized regression models. The penalty structure can be any combination of
12104 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12105 constraint on the regression coefficients. The supported regression models
12106 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12107 model. Cross-validation routines allow optimization of the tuning
12109 (license license:gpl2+)))
12111 (define-public r-zim
12118 (uri (cran-uri "ZIM" version))
12121 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12122 (properties `((upstream-name . "ZIM")))
12123 (build-system r-build-system)
12124 (propagated-inputs `(("r-mass" ,r-mass)))
12125 (home-page "https://github.com/biostatstudio/ZIM")
12126 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12128 "Analyze count time series with excess zeros. Two types of statistical
12129 models are supported: Markov regression and state-space models. They are also
12130 known as observation-driven and parameter-driven models respectively in the
12131 time series literature. The functions used for Markov regression or
12132 observation-driven models can also be used to fit ordinary regression models
12133 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12134 negative binomial (ZINB) assumption. The package also contains miscellaneous
12135 functions to compute density, distribution, quantile, and generate random
12136 numbers from ZIP and ZINB distributions.")
12137 (license license:gpl3)))
12139 (define-public r-nor1mix
12146 (uri (cran-uri "nor1mix" version))
12149 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12150 (build-system r-build-system)
12151 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12152 (synopsis "Normal (1-d) mixture models")
12154 "This package provides S3 classes and methods for one-dimensional normal
12155 mixture models, for, e.g., density estimation or clustering algorithms
12156 research and teaching; it provides the widely used Marron-Wand densities. It
12157 also provides tools for efficient random number generation and graphics.")
12158 (license license:gpl2+)))
12160 (define-public r-beanplot
12162 (name "r-beanplot")
12167 (uri (cran-uri "beanplot" version))
12170 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12171 (build-system r-build-system)
12172 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12173 (synopsis "Visualization via beanplots")
12175 "This package provides beanplots, an alternative to
12176 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12178 (license license:gpl2)))
12180 (define-public r-pbdzmq
12187 (uri (cran-uri "pbdZMQ" version))
12190 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12191 (properties `((upstream-name . "pbdZMQ")))
12192 (build-system r-build-system)
12194 `(("zeromq" ,zeromq)
12197 `(("pkg-config" ,pkg-config)))
12198 (home-page "https://pbdr.org/")
12199 (synopsis "R interface to ZeroMQ")
12201 "ZeroMQ is a well-known library for high-performance asynchronous
12202 messaging in scalable, distributed applications. This package provides high
12203 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12204 interactive client/server programming frameworks. A few wrapper functions
12205 compatible with @code{rzmq} are also provided.")
12206 (license license:gpl3)))
12208 (define-public r-repr
12215 (uri (cran-uri "repr" version))
12218 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
12219 (build-system r-build-system)
12221 `(("r-base64enc" ,r-base64enc)
12222 ("r-htmltools" ,r-htmltools)
12223 ("r-jsonlite" ,r-jsonlite)
12224 ("r-pillar" ,r-pillar)))
12225 (home-page "https://cran.r-project.org/web/packages/repr/")
12226 (synopsis "Serializable representations")
12228 "This package provides string and binary representations of objects for
12229 several formats and MIME types.")
12230 (license license:gpl3)))
12232 (define-public r-irdisplay
12234 (name "r-irdisplay")
12239 (uri (cran-uri "IRdisplay" version))
12242 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12243 (properties `((upstream-name . "IRdisplay")))
12244 (build-system r-build-system)
12246 `(("r-repr" ,r-repr)))
12247 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12248 (synopsis "Jupyter display machinery")
12250 "This package provides an interface to the rich display capabilities of
12251 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12252 running IRkernel session.")
12253 (license license:expat)))
12255 (define-public r-irkernel
12257 (name "r-irkernel")
12262 (uri (cran-uri "IRkernel" version))
12265 "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
12266 (properties `((upstream-name . "IRkernel")))
12267 (build-system r-build-system)
12270 (modify-phases %standard-phases
12271 (add-after 'install 'install-kernelspec
12272 (lambda* (#:key outputs #:allow-other-keys)
12273 (let ((out (assoc-ref outputs "out")))
12274 (setenv "HOME" "/tmp")
12275 (invoke "jupyter" "kernelspec" "install"
12278 (string-append out "/site-library/IRkernel/kernelspec"))
12281 `(("jupyter" ,jupyter)))
12283 `(("r-crayon" ,r-crayon)
12284 ("r-digest" ,r-digest)
12285 ("r-evaluate" ,r-evaluate)
12286 ("r-irdisplay" ,r-irdisplay)
12287 ("r-jsonlite" ,r-jsonlite)
12288 ("r-pbdzmq" ,r-pbdzmq)
12290 ("r-uuid" ,r-uuid)))
12291 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12292 (synopsis "Native R kernel for Jupyter")
12294 "The R kernel for the Jupyter environment executes R code which the
12295 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12297 (license license:expat)))
12299 (define-public r-gmodels
12306 (uri (cran-uri "gmodels" version))
12309 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12310 (build-system r-build-system)
12312 `(("r-gdata" ,r-gdata)
12313 ("r-mass" ,r-mass)))
12314 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12315 (synopsis "Various R programming tools for model fitting")
12317 "This package provides various R programming tools for model fitting.")
12318 (license license:gpl2)))
12320 (define-public r-apcluster
12322 (name "r-apcluster")
12327 (uri (cran-uri "apcluster" version))
12330 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
12331 (build-system r-build-system)
12333 `(("r-matrix" ,r-matrix)
12334 ("r-rcpp" ,r-rcpp)))
12335 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12336 (synopsis "Affinity propagation clustering")
12338 "This package implements affinity propagation clustering introduced by
12339 Frey and Dueck (2007). The package further provides leveraged affinity
12340 propagation and an algorithm for exemplar-based agglomerative clustering that
12341 can also be used to join clusters obtained from affinity propagation. Various
12342 plotting functions are available for analyzing clustering results.")
12343 (license license:gpl2+)))
12345 (define-public r-valr
12352 (uri (cran-uri "valr" version))
12355 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12356 (build-system r-build-system)
12358 `(("r-broom" ,r-broom)
12359 ("r-dplyr" ,r-dplyr)
12360 ("r-ggplot2" ,r-ggplot2)
12362 ("r-readr" ,r-readr)
12363 ("r-rlang" ,r-rlang)
12364 ("r-stringr" ,r-stringr)
12365 ("r-tibble" ,r-tibble)))
12366 (home-page "http://github.com/rnabioco/valr")
12367 (synopsis "Genome interval arithmetic in R")
12369 "This package enables you to read and manipulate genome intervals and
12370 signals. It provides functionality similar to command-line tool suites within
12371 R, enabling interactive analysis and visualization of genome-scale data.")
12372 (license license:expat)))
12374 (define-public r-rematch2
12376 (name "r-rematch2")
12381 (uri (cran-uri "rematch2" version))
12384 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12385 (build-system r-build-system)
12387 `(("r-tibble" ,r-tibble)))
12388 (home-page "https://github.com/r-lib/rematch2")
12389 (synopsis "Tidy output from regular expression matching")
12391 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12392 return the match results in tidy data frames.")
12393 (license license:expat)))
12395 (define-public r-picante
12402 (uri (cran-uri "picante" version))
12405 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12406 (build-system r-build-system)
12410 ("r-vegan" ,r-vegan)))
12411 (home-page "https://cran.r-project.org/web/packages/picante/")
12412 (synopsis "Integrating phylogenies and ecology")
12414 "This package provides functions for phylocom integration, community
12415 analyses, null-models, traits and evolution. It implements numerous
12416 ecophylogenetic approaches including measures of community phylogenetic and
12417 trait diversity, phylogenetic signal, estimation of trait values for
12418 unobserved taxa, null models for community and phylogeny randomizations, and
12419 utility functions for data input/output and phylogeny plotting. A full
12420 description of package functionality and methods are provided by Kembel et
12422 (license license:gpl2)))
12424 (define-public r-reinforcelearn
12426 (name "r-reinforcelearn")
12431 (uri (cran-uri "reinforcelearn" version))
12434 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12435 (build-system r-build-system)
12437 `(("r-checkmate" ,r-checkmate)
12439 ("r-purrr" ,r-purrr)
12441 (home-page "https://markusdumke.github.io/reinforcelearn")
12442 (synopsis "Reinforcement learning")
12444 "This package implements reinforcement learning environments and
12445 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12446 can be used with function approximation, eligibility traces (Singh & Sutton,
12447 1996) and experience replay (Mnih et al., 2013).")
12448 (license license:expat)))
12450 (define-public r-lemon
12457 (uri (cran-uri "lemon" version))
12460 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12461 (build-system r-build-system)
12463 `(("r-ggplot2" ,r-ggplot2)
12464 ("r-gridextra" ,r-gridextra)
12465 ("r-gtable" ,r-gtable)
12466 ("r-knitr" ,r-knitr)
12467 ("r-lattice" ,r-lattice)
12469 ("r-scales" ,r-scales)))
12470 (home-page "https://github.com/stefanedwards/lemon")
12471 (synopsis "Freshen up your ggplot2 plots")
12473 "This package provides functions for working with legends and axis lines
12474 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12476 (license license:gpl3)))
12478 (define-public r-wgaim
12485 (uri (cran-uri "wgaim" version))
12487 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
12488 (build-system r-build-system)
12490 `(("r-ggplot2" ,r-ggplot2)
12492 (home-page "https://cran.r-project.org/web/packages/wgaim")
12493 (synopsis "Whole genome average interval mapping for QTL detection")
12495 "This package integrates sophisticated mixed modelling methods with a
12496 whole genome approach to detecting significant QTL in linkage maps.")
12497 (license license:gpl2+)))
12499 (define-public r-bedr
12506 (uri (cran-uri "bedr" version))
12509 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12510 (build-system r-build-system)
12512 `(("r-data-table" ,r-data-table)
12513 ("r-r-utils" ,r-r-utils)
12514 ("r-testthat" ,r-testthat)
12515 ("r-venndiagram" ,r-venndiagram)
12518 ("bedtools" ,bedtools)
12519 ("htslib" ,htslib))) ; for tabix
12521 `(("r-knitr" ,r-knitr))) ; for vignettes
12522 (home-page "https://cran.r-project.org/web/packages/bedr")
12523 (synopsis "Genomic region processing")
12525 "This package is for genomic regions processing using command line tools
12526 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12527 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12528 The bedr package's API enhances access to these tools as well as offers
12529 additional utilities for genomic regions processing.")
12530 (license license:gpl2)))
12532 (define-public r-partitions
12534 (name "r-partitions")
12539 (uri (cran-uri "partitions" version))
12542 "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx"))))
12543 (build-system r-build-system)
12546 ("r-polynom" ,r-polynom)))
12547 (home-page "https://cran.r-project.org/web/packages/partitions")
12548 (synopsis "Additive partitions of integers")
12550 "This package provides tools to enumerates the partitions, unequal
12551 partitions, and restricted partitions of an integer; the three corresponding
12552 partition functions are also given.")
12553 ;; Any version of the GPL
12554 (license license:gpl2+)))
12556 (define-public r-brobdingnag
12558 (name "r-brobdingnag")
12563 (uri (cran-uri "Brobdingnag" version))
12566 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12567 (properties `((upstream-name . "Brobdingnag")))
12568 (build-system r-build-system)
12569 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12570 (synopsis "Very large numbers in R")
12572 "This package handles very large numbers in R. Real numbers are held
12573 using their natural logarithms, plus a logical flag indicating sign. The
12574 package includes a vignette that gives a step-by-step introduction to using S4
12576 ;; Any version of the GPL
12577 (license license:gpl2+)))
12579 (define-public r-untb
12586 (uri (cran-uri "untb" version))
12589 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12590 (build-system r-build-system)
12592 `(("r-brobdingnag" ,r-brobdingnag)
12593 ("r-partitions" ,r-partitions)
12594 ("r-polynom" ,r-polynom)))
12595 (home-page "https://github.com/RobinHankin/untb.git")
12596 (synopsis "Ecological drift under the UNTB")
12598 "This package provides numerical simulations, and visualizations, of
12599 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12600 (license license:gpl2+)))
12602 (define-public r-stepwise
12604 (name "r-stepwise")
12609 (uri (cran-uri "stepwise" version))
12612 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12613 (build-system r-build-system)
12614 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12615 (synopsis "Stepwise detection of recombination breakpoints")
12617 "This package provides a stepwise approach to identifying recombination
12618 breakpoints in a genomic sequence alignment.")
12619 (license license:gpl2+)))
12621 (define-public r-snpmaxsel
12623 (name "r-snpmaxsel")
12628 (uri (cran-uri "SNPmaxsel" version))
12631 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12632 (properties `((upstream-name . "SNPmaxsel")))
12633 (build-system r-build-system)
12635 `(("r-combinat" ,r-combinat)
12636 ("r-mvtnorm" ,r-mvtnorm)))
12637 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12638 (synopsis "Maximally selected statistics for SNP data")
12640 "This package implements asymptotic methods related to maximally selected
12641 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12643 (license license:gpl2+)))
12645 (define-public r-acsnminer
12647 (name "r-acsnminer")
12648 (version "0.16.8.25")
12651 (uri (cran-uri "ACSNMineR" version))
12654 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12655 (properties `((upstream-name . "ACSNMineR")))
12656 (build-system r-build-system)
12658 `(("r-ggplot2" ,r-ggplot2)
12659 ("r-gridextra" ,r-gridextra)))
12660 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12661 (synopsis "Gene enrichment analysis")
12663 "This package provides tools to compute and represent gene set enrichment
12664 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12665 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12666 enrichment can be run with hypergeometric test or Fisher exact test, and can
12667 use multiple corrections. Visualization of data can be done either by
12668 barplots or heatmaps.")
12669 (license license:gpl2+)))
12671 (define-public r-seqinr
12678 (uri (cran-uri "seqinr" version))
12681 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
12682 (build-system r-build-system)
12684 `(("r-ade4" ,r-ade4)
12685 ("r-segmented" ,r-segmented)))
12688 (home-page "http://seqinr.r-forge.r-project.org/")
12689 (synopsis "Biological sequences retrieval and analysis")
12691 "This package provides tools for exploratory data analysis and data
12692 visualization of biological sequence (DNA and protein) data. It also includes
12693 utilities for sequence data management under the ACNUC system.")
12694 (license license:gpl2+)))
12696 (define-public r-units
12703 (uri (cran-uri "units" version))
12706 "02nls8m0r1r7kljs4x35naz3szq62hyqyd5vracf1xwi1kz5kdsh"))))
12707 (build-system r-build-system)
12709 `(("udunits" ,udunits)))
12711 `(("r-rcpp" ,r-rcpp)))
12712 (home-page "https://github.com/r-quantities/units/")
12713 (synopsis "Measurement Units for R Vectors")
12715 "This package provides support for measurement units in R vectors,
12716 matrices and arrays: automatic propagation, conversion, derivation and
12717 simplification of units; raising errors in case of unit incompatibility. It
12718 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12720 (license license:gpl2)))
12722 (define-public r-classint
12724 (name "r-classint")
12729 (uri (cran-uri "classInt" version))
12732 "0w980hrw8sgfdfyd5dsimalq7gwhvqm7507abk7k363pvgks23dv"))))
12733 (properties `((upstream-name . "classInt")))
12734 (build-system r-build-system)
12736 `(("r-class" ,r-class)
12737 ("r-e1071" ,r-e1071)
12738 ("r-kernsmooth" ,r-kernsmooth)))
12739 (native-inputs `(("gfortran" ,gfortran)))
12740 (home-page "https://github.com/r-spatial/classInt/")
12741 (synopsis "Choose univariate class intervals")
12743 "This package provides selected commonly used methods for choosing
12744 univariate class intervals for mapping or other graphics purposes.")
12745 (license license:gpl2+)))
12747 (define-public r-spdata
12754 (uri (cran-uri "spData" version))
12757 "190msrrpn226x27pcnck4ac34f9k4xcn26cyz2apdri2nzkr6zbw"))))
12758 (properties `((upstream-name . "spData")))
12759 (build-system r-build-system)
12760 (home-page "https://github.com/Nowosad/spData")
12761 (synopsis "Datasets for spatial analysis")
12763 "This a package containing diverse spatial datasets for demonstrating,
12764 benchmarking and teaching spatial data analysis. It includes R data of class
12765 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
12766 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
12767 of the datasets are designed to illustrate specific analysis techniques.
12768 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
12769 illustrate point pattern analysis techniques.")
12770 (license license:cc0)))
12772 (define-public r-learnbayes
12774 (name "r-learnbayes")
12779 (uri (cran-uri "LearnBayes" version))
12782 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
12783 (properties `((upstream-name . "LearnBayes")))
12784 (build-system r-build-system)
12785 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
12786 (synopsis "Functions for learning Bayesian inference")
12788 "This package provides a collection of functions helpful in learning the
12789 basic tenets of Bayesian statistical inference. It contains functions for
12790 summarizing basic one and two parameter posterior distributions and predictive
12791 distributions. It contains MCMC algorithms for summarizing posterior
12792 distributions defined by the user. It also contains functions for regression
12793 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
12795 (license license:gpl2+)))
12797 (define-public r-deldir
12804 (uri (cran-uri "deldir" version))
12807 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
12808 (build-system r-build-system)
12809 (native-inputs `(("gfortran" ,gfortran)))
12810 (home-page "https://cran.r-project.org/web/packages/deldir")
12811 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
12813 "This package provides tools for calculating the Delaunay triangulation
12814 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
12815 of a planar point set. It plots triangulations and tessellations in various
12816 ways, clips tessellations to sub-windows, calculates perimeters of
12817 tessellations, and summarizes information about the tiles of the
12819 (license license:gpl2+)))
12821 (define-public r-sf
12828 (uri (cran-uri "sf" version))
12831 "05dyq0vcz2f1fl03hk3v1a4nz4s84yyqw4rc9w9cwfq71gvm9qwf"))))
12832 (build-system r-build-system)
12839 `(("r-classint" ,r-classint)
12841 ("r-magrittr" ,r-magrittr)
12843 ("r-units" ,r-units)))
12844 (native-inputs `(("pkg-config" ,pkg-config)))
12845 (home-page "https://github.com/r-spatial/sf/")
12846 (synopsis "Simple features for R")
12848 "This package provides support for simple features, a standardized way to
12849 encode spatial vector data. It binds to GDAL for reading and writing data, to
12850 GEOS for geometrical operations, and to PROJ for projection conversions and
12851 datum transformations.")
12852 ;; Either of these licenses
12853 (license (list license:gpl2 license:expat))))
12855 (define-public r-spdep
12862 (uri (cran-uri "spdep" version))
12865 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
12866 (build-system r-build-system)
12868 `(("r-boot" ,r-boot)
12870 ("r-deldir" ,r-deldir)
12872 ("r-gmodels" ,r-gmodels)
12873 ("r-learnbayes" ,r-learnbayes)
12875 ("r-matrix" ,r-matrix)
12879 ("r-spdata" ,r-spdata)))
12880 (home-page "https://github.com/r-spatial/spdep/")
12881 (synopsis "Spatial dependence: weighting schemes, statistics and models")
12883 "This package provides a collection of functions to create spatial
12884 weights matrix objects from polygon contiguities, from point patterns by
12885 distance and tessellations, for summarizing these objects, and for permitting
12886 their use in spatial data analysis, including regional aggregation by minimum
12888 (license license:gpl2+)))
12890 (define-public r-adegenet
12892 (name "r-adegenet")
12897 (uri (cran-uri "adegenet" version))
12900 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
12901 (build-system r-build-system)
12903 `(("r-ade4" ,r-ade4)
12906 ("r-dplyr" ,r-dplyr)
12907 ("r-ggplot2" ,r-ggplot2)
12908 ("r-igraph" ,r-igraph)
12910 ("r-reshape2" ,r-reshape2)
12911 ("r-seqinr" ,r-seqinr)
12912 ("r-shiny" ,r-shiny)
12913 ("r-spdep" ,r-spdep)
12914 ("r-vegan" ,r-vegan)))
12915 (home-page "https://github.com/thibautjombart/adegenet")
12916 (synopsis "Exploratory analysis of genetic and genomic data")
12918 "This package provides a toolset for the exploration of genetic and
12919 genomic data. Adegenet provides formal (S4) classes for storing and handling
12920 various genetic data, including genetic markers with varying ploidy and
12921 hierarchical population structure (@code{genind} class), alleles counts by
12922 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
12923 also implements original multivariate methods (DAPC, sPCA), graphics,
12924 statistical tests, simulation tools, distance and similarity measures, and
12925 several spatial methods. A range of both empirical and simulated datasets is
12926 also provided to illustrate various methods.")
12927 (license license:gpl2+)))
12929 (define-public r-pegas
12936 (uri (cran-uri "pegas" version))
12938 (base32 "0sb8cmz4d238mcb56hv9fa0cagm00k82r7aj4cj4lxa1flxlpy8p"))))
12939 (build-system r-build-system)
12941 `(("r-adegenet" ,r-adegenet)
12943 (home-page "http://ape-package.ird.fr/pegas.html")
12944 (synopsis "Population and evolutionary genetics analysis system")
12946 "This package provides functions for reading, writing, plotting,
12947 analysing, and manipulating allelic and haplotypic data, including from VCF
12948 files, and for the analysis of population nucleotide sequences and
12949 micro-satellites including coalescent analyses, linkage disequilibrium,
12950 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
12951 minimum spanning tree and network, and median-joining networks.")
12952 (license license:gpl2+)))
12954 (define-public r-rmetasim
12956 (name "r-rmetasim")
12961 (uri (cran-uri "rmetasim" version))
12964 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
12965 (build-system r-build-system)
12967 `(("r-ade4" ,r-ade4)
12968 ("r-adegenet" ,r-adegenet)
12969 ("r-gtools" ,r-gtools)
12970 ("r-pegas" ,r-pegas)))
12971 (home-page "https://cran.r-project.org/web/packages/rmetasim")
12972 (synopsis "Individual-based population genetic simulation environment")
12974 "This package provides an interface between R and the metasim simulation
12975 engine. The simulation environment is documented in: Strand, A.(2002),
12976 Metasim 1.0: an individual-based environment for simulating population
12977 genetics of complex population dynamics.")
12979 (license license:gpl2+)))
12981 (define-public r-genetics
12983 (name "r-genetics")
12984 (version "1.3.8.1.2")
12988 (uri (cran-uri "genetics" version))
12991 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
12992 (build-system r-build-system)
12994 `(("r-combinat" ,r-combinat)
12995 ("r-gdata" ,r-gdata)
12996 ("r-gtools" ,r-gtools)
12998 ("r-mvtnorm" ,r-mvtnorm)))
12999 (home-page "https://cran.r-project.org/web/packages/genetics/")
13000 (synopsis "Population genetics")
13002 "This package provides classes and methods for handling genetic data.
13003 It includes classes to represent genotypes and haplotypes at single markers up
13004 to multiple markers on multiple chromosomes. Function include allele
13005 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13006 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13007 and testing for linkage disequilibrium, ...")
13008 ;; Any GPL version.
13009 (license license:gpl2+)))
13011 (define-public r-snp-plotter
13013 (name "r-snp-plotter")
13018 (uri (cran-uri "snp.plotter" version))
13021 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13022 (properties `((upstream-name . "snp.plotter")))
13023 (build-system r-build-system)
13024 (propagated-inputs `(("r-genetics" ,r-genetics)))
13025 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13026 (synopsis "Plot p-values using single SNP and/or haplotype data")
13028 "This package helps you create plots of p-values using single SNP and/or
13029 haplotype data. Main features of the package include options to display a
13030 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13031 datasets simultaneously. Plots can be created using global and/or individual
13032 haplotype p-values along with single SNP p-values. Images are created as
13033 either PDF/EPS files.")
13034 (license license:gpl2+)))
13036 (define-public r-polspline
13038 (name "r-polspline")
13043 (uri (cran-uri "polspline" version))
13045 (base32 "0d49h7if8h6d784nsnqqxakg19kvl8cmz8k53901m2h0c0amlfxa"))))
13046 (build-system r-build-system)
13047 (native-inputs `(("gfortran" ,gfortran)))
13048 (home-page "https://cran.r-project.org/web/packages/polspline/")
13049 (synopsis "Polynomial spline routines")
13051 "This package provides routines for the polynomial spline fitting
13052 routines hazard regression, hazard estimation with flexible tails, logspline,
13053 lspec, polyclass, and polymars.")
13054 (license license:gpl2+)))
13056 (define-public r-rms
13059 (version "5.1-3.1")
13063 (uri (cran-uri "rms" version))
13066 "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9"))))
13067 (build-system r-build-system)
13069 `(("r-ggplot2" ,r-ggplot2)
13070 ("r-hmisc" ,r-hmisc)
13071 ("r-htmltable" ,r-htmltable)
13072 ("r-htmltools" ,r-htmltools)
13073 ("r-lattice" ,r-lattice)
13074 ("r-multcomp" ,r-multcomp)
13076 ("r-polspline" ,r-polspline)
13077 ("r-quantreg" ,r-quantreg)
13078 ("r-rpart" ,r-rpart)
13079 ("r-sparsem" ,r-sparsem)
13080 ("r-survival" ,r-survival)))
13081 (native-inputs `(("gfortran" ,gfortran)))
13082 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13083 (synopsis "Regression modeling strategies")
13085 "This is a package for regression modeling, testing, estimation,
13086 validation, graphics, prediction, and typesetting by storing enhanced model
13087 design attributes in the fit. The rms package is a collection of functions
13088 that assist with and streamline modeling. It also contains functions for
13089 binary and ordinal logistic regression models, ordinal models for continuous Y
13090 with a variety of distribution families, and the Buckley-James multiple
13091 regression model for right-censored responses, and implements penalized
13092 maximum likelihood estimation for logistic and ordinary linear models. The
13093 package works with almost any regression model, but it was especially written
13094 to work with binary or ordinal regression models, Cox regression, accelerated
13095 failure time models, ordinary linear models, the Buckley-James model,
13096 generalized least squares for serially or spatially correlated observations,
13097 generalized linear models, and quantile regression.")
13098 (license license:gpl2+)))
13100 (define-public r-haplo-stats
13102 (name "r-haplo-stats")
13107 (uri (cran-uri "haplo.stats" version))
13110 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13111 (properties `((upstream-name . "haplo.stats")))
13112 (build-system r-build-system)
13114 `(("r-rms" ,r-rms)))
13116 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13117 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13118 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13120 "This package provides routines for the analysis of indirectly measured
13121 haplotypes. The statistical methods assume that all subjects are unrelated
13122 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13123 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13124 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13125 examples in the vignette.")
13126 (license license:gpl2+)))
13128 (define-public r-bqtl
13135 (uri (cran-uri "bqtl" version))
13138 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13139 (build-system r-build-system)
13140 (native-inputs `(("gfortran" ,gfortran)))
13141 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13142 (synopsis "Bayesian QTL mapping toolkit")
13144 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13145 lines. It includes maximum likelihood and Bayesian tools.")
13146 (license license:gpl2+)))
13148 (define-public r-ibdreg
13155 (uri (cran-uri "ibdreg" version))
13158 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13159 (build-system r-build-system)
13160 (home-page "https://www.mayo.edu/research/labs/\
13161 statistical-genetics-genetic-epidemiology/software")
13162 (synopsis "Regression methods for IBD linkage with covariates")
13164 "This package provides a method to test genetic linkage with covariates
13165 by regression methods with response IBD sharing for relative pairs. Account
13166 for correlations of IBD statistics and covariates for relative pairs within
13167 the same pedigree.")
13168 (license license:gpl2+)))
13170 (define-public r-dlmap
13177 (uri (cran-uri "dlmap" version))
13180 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13181 (build-system r-build-system)
13183 `(("r-ibdreg" ,r-ibdreg)
13187 ("r-wgaim" ,r-wgaim)))
13188 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13189 (synopsis "Detection localization mapping for QTL")
13191 "This is package for QTL mapping in a mixed model framework with separate
13192 detection and localization stages. The first stage detects the number of QTL
13193 on each chromosome based on the genetic variation due to grouped markers on
13194 the chromosome; the second stage uses this information to determine the most
13195 likely QTL positions. The mixed model can accommodate general fixed and
13196 random effects, including spatial effects in field trials and pedigree
13197 effects. It is applicable to backcrosses, doubled haploids, recombinant
13198 inbred lines, F2 intercrosses, and association mapping populations.")
13199 (license license:gpl2)))
13201 (define-public r-ldheatmap
13203 (name "r-ldheatmap")
13208 (uri (cran-uri "LDheatmap" version))
13211 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13212 (properties `((upstream-name . "LDheatmap")))
13213 (build-system r-build-system)
13215 `(("r-genetics" ,r-genetics)
13217 ("r-snpstats" ,r-snpstats)))
13218 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13219 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13221 "This package provides tools to produce a graphical display, as a heat
13222 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13223 optionally include the physical locations or genetic map distances of each SNP
13225 (license license:gpl3)))
13227 (define-public r-hwde
13234 (uri (cran-uri "hwde" version))
13237 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13238 (build-system r-build-system)
13239 (home-page "https://cran.r-project.org/web/packages/hwde/")
13240 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13242 "This package fits models for genotypic disequilibria, as described in
13243 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13244 terms are available that account for first order interactions between loci.
13245 It also implements, for a single locus in a single population, a conditional
13246 exact test for Hardy-Weinberg equilibrium.")
13247 (license license:gpl2+)))
13249 (define-public r-tdthap
13256 (uri (cran-uri "tdthap" version))
13259 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
13260 (build-system r-build-system)
13261 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13262 (synopsis "TDT tests for extended haplotypes")
13264 "Functions and examples are provided for transmission/disequilibrium
13265 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13266 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13267 (license license:artistic2.0)))
13269 (define-public r-sparql
13275 (uri (cran-uri "SPARQL" version))
13278 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13279 (properties `((upstream-name . "SPARQL")))
13280 (build-system r-build-system)
13282 `(("r-rcurl" ,r-rcurl)
13284 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13285 (synopsis "SPARQL client for R")
13286 (description "This package provides an interface to use SPARQL to pose
13287 SELECT or UPDATE queries to an end-point.")
13288 ;; The only license indication is found in the DESCRIPTION file,
13289 ;; which states GPL-3. So we cannot assume GPLv3+.
13290 (license license:gpl3)))
13292 (define-public r-bookdown
13294 (name "r-bookdown")
13298 (uri (cran-uri "bookdown" version))
13301 "1jiq2d292y0l3f4npyfzfpnmb0sqxsl212kkjfbjg5301h0na762"))))
13302 (build-system r-build-system)
13304 `(("r-htmltools" ,r-htmltools)
13305 ("r-knitr" ,r-knitr)
13306 ("r-rmarkdown" ,r-rmarkdown)
13307 ("r-tinytex" ,r-tinytex)
13309 ("pandoc" ,ghc-pandoc)))
13310 (home-page "https://github.com/rstudio/bookdown")
13311 (synopsis "Authoring books and technical documents with R markdown")
13312 (description "This package provides output formats and utilities for
13313 authoring books and technical documents with R Markdown.")
13314 (license license:gpl3)))
13316 (define-public r-optparse
13318 (name "r-optparse")
13323 (uri (cran-uri "optparse" version))
13326 "0wyrc42ja3ab5szx46zmz8lm7vzfqxkjca0m0sms8g9hqbmmay6d"))))
13327 (build-system r-build-system)
13329 `(("r-getopt" ,r-getopt)))
13330 (home-page "https://github.com/trevorld/optparse")
13331 (synopsis "Command line option parser")
13333 "This package provides a command line parser inspired by Python's
13334 @code{optparse} library to be used with Rscript to write shebang scripts
13335 that accept short and long options.")
13336 (license license:gpl2+)))
13338 (define-public r-wgcna
13345 (uri (cran-uri "WGCNA" version))
13348 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13349 (properties `((upstream-name . "WGCNA")))
13350 (build-system r-build-system)
13352 `(("r-annotationdbi" ,r-annotationdbi)
13353 ("r-doparallel" ,r-doparallel)
13354 ("r-dynamictreecut" ,r-dynamictreecut)
13355 ("r-fastcluster" ,r-fastcluster)
13356 ("r-foreach" ,r-foreach)
13357 ("r-go-db" ,r-go-db)
13358 ("r-hmisc" ,r-hmisc)
13359 ("r-impute" ,r-impute)
13361 ("r-robust" ,r-robust)
13362 ("r-survival" ,r-survival)
13363 ("r-matrixstats" ,r-matrixstats)
13364 ("r-preprocesscore" ,r-preprocesscore)))
13366 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13367 (synopsis "Weighted correlation network analysis")
13369 "This package provides functions necessary to perform Weighted
13370 Correlation Network Analysis on high-dimensional data. It includes functions
13371 for rudimentary data cleaning, construction and summarization of correlation
13372 networks, module identification and functions for relating both variables and
13373 modules to sample traits. It also includes a number of utility functions for
13374 data manipulation and visualization.")
13375 (license license:gpl2+)))
13377 (define-public r-kernlab
13384 (uri (cran-uri "kernlab" version))
13387 "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
13388 (build-system r-build-system)
13389 (home-page "https://cran.r-project.org/web/packages/kernlab")
13390 (synopsis "Kernel-based machine learning tools")
13392 "This package provides kernel-based machine learning methods for
13393 classification, regression, clustering, novelty detection, quantile regression
13394 and dimensionality reduction. Among other methods @code{kernlab} includes
13395 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13397 (license license:gpl2)))
13399 (define-public r-hierfstat
13401 (name "r-hierfstat")
13402 (version "0.04-22")
13406 (uri (cran-uri "hierfstat" version))
13409 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13410 (build-system r-build-system)
13412 `(("r-ade4" ,r-ade4)
13413 ("r-adegenet" ,r-adegenet)
13414 ("r-gtools" ,r-gtools)))
13415 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13416 (synopsis "Estimation and tests of hierarchical F-statistics")
13418 "This package allows the estimation of hierarchical F-statistics from
13419 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13420 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13421 are also given to test via randomisations the significance of each F and
13422 variance components, using the likelihood-ratio statistics G.")
13423 (license license:gpl2+)))
13425 (define-public r-hapassoc
13427 (name "r-hapassoc")
13432 (uri (cran-uri "hapassoc" version))
13435 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13436 (build-system r-build-system)
13437 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13438 (synopsis "Inference of trait associations with SNP haplotypes")
13440 "Hapassoc performs likelihood inference of trait associations with
13441 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13442 functions are developed primarily for data collected in cohort or
13443 cross-sectional studies. They can accommodate uncertain haplotype phase and
13444 handle missing genotypes at some SNPs.")
13445 (license license:gpl2)))
13447 (define-public r-sampling
13449 (name "r-sampling")
13454 (uri (cran-uri "sampling" version))
13457 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13458 (build-system r-build-system)
13460 `(("r-lpsolve" ,r-lpsolve)
13461 ("r-mass" ,r-mass)))
13462 (home-page "https://cran.r-project.org/web/packages/sampling/")
13463 (synopsis "Survey sampling")
13465 "This package provides functions for drawing and calibrating samples.")
13466 (license license:gpl2+)))
13468 (define-public r-r2html
13475 (uri (cran-uri "R2HTML" version))
13478 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13479 (properties `((upstream-name . "R2HTML")))
13480 (build-system r-build-system)
13481 (home-page "https://github.com/nalimilan/R2HTML")
13482 (synopsis "HTML export for R objects")
13484 "This package includes HTML functions and methods to write in an HTML
13485 file. Thus, making HTML reports is easy. It includes a function that allows
13486 redirection on the fly, which appears to be very useful for teaching purposes,
13487 as the student can keep a copy of the produced output to keep all that they
13488 did during the course. The package comes with a vignette describing how to
13489 write HTML reports for statistical analysis. Finally, a driver for Sweave
13490 allows to parse HTML flat files containing R code and to automatically write
13491 the corresponding outputs (tables and graphs).")
13492 (license license:gpl2+)))
13494 (define-public r-rjava
13501 (uri (cran-uri "rJava" version))
13504 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13505 (properties `((upstream-name . "rJava")))
13506 (build-system r-build-system)
13508 `(#:modules ((guix build utils)
13509 (guix build r-build-system)
13512 (modify-phases %standard-phases
13513 (add-after 'unpack 'set-JAVA_HOME
13514 (lambda* (#:key inputs #:allow-other-keys)
13515 (let ((jdk (assoc-ref inputs "jdk")))
13516 (setenv "JAVA_HOME" jdk)
13517 (setenv "JAVA" (which "java"))
13518 (setenv "JAR" (which "jar"))
13519 (setenv "JAVAC" (which "javac"))
13520 (setenv "JAVAH" (which "javah"))
13521 (setenv "JAVA_CPPFLAGS"
13522 (string-append "-I" jdk "/include "
13523 "-I" jdk "/include/linux"))
13524 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13525 ((lib) (setenv "JAVA_LIBS" lib))
13526 (_ (error "Could not find libjvm.so"))))
13530 ("jdk" ,icedtea-8 "jdk")
13533 (home-page "http://www.rforge.net/rJava/")
13534 (synopsis "Low-Level R to Java interface")
13536 "This package provides a low-level interface to the Java VM very much
13537 like .C/.Call and friends. It allows the creation of objects, calling methods
13538 and accessing fields.")
13539 (license license:gpl2)))
13541 (define-public r-svmisc
13548 (uri (cran-uri "svMisc" version))
13551 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13552 (properties `((upstream-name . "svMisc")))
13553 (build-system r-build-system)
13554 (home-page "https://github.com/SciViews/svMisc")
13555 (synopsis "Miscellaneous functions for SciViews")
13557 "This package provides miscellaneous functions for SciViews or general
13558 use, including tools to manage a temporary environment attached to the search
13559 path for temporary variables you do not want to @code{save()} or
13560 @code{load()}; test the current platform; showing progress bars, etc.")
13561 (license license:gpl2)))
13563 (define-public r-xyz
13570 (uri (cran-uri "xyz" version))
13573 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13574 (build-system r-build-system)
13576 `(("r-rcpp" ,r-rcpp)))
13577 (home-page "https://cran.r-project.org/web/packages/xyz/")
13578 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13580 "High dimensional interaction search by brute force requires a quadratic
13581 computational cost in the number of variables. The xyz algorithm provably
13582 finds strong interactions in almost linear time. For details of the algorithm
13583 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13584 interaction search in high-dimensional data.")
13585 ;; Any version of the GPL.
13586 (license license:gpl2+)))
13588 (define-public r-rttf2pt1
13590 (name "r-rttf2pt1")
13595 (uri (cran-uri "Rttf2pt1" version))
13598 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13599 (properties `((upstream-name . "Rttf2pt1")))
13600 (build-system r-build-system)
13601 (home-page "https://github.com/wch/Rttf2pt1")
13602 (synopsis "Font conversion utility")
13604 "This package contains the program @code{ttf2pt1}, for use with the
13605 @code{extrafont} package.")
13606 ;; Most of the files are covered under the Expat license. Some files are
13607 ;; covered under BSD-3. Deviations for individual files are recorded in
13608 ;; the LICENSE file.
13609 (license (list license:bsd-3 license:expat
13610 (license:non-copyleft "file://LICENSE")))))
13612 (define-public r-extrafontdb
13614 (name "r-extrafontdb")
13619 (uri (cran-uri "extrafontdb" version))
13622 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13623 (build-system r-build-system)
13624 (home-page "https://github.com/wch/extrafontdb")
13625 (synopsis "Database for the extrafont package")
13627 "This package holds the database for the @code{extrafont} package.")
13628 (license license:gpl2)))
13630 (define-public r-extrafont
13632 (name "r-extrafont")
13637 (uri (cran-uri "extrafont" version))
13640 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13641 (build-system r-build-system)
13643 `(("r-extrafontdb" ,r-extrafontdb)
13644 ("r-rttf2pt1" ,r-rttf2pt1)))
13645 (home-page "https://github.com/wch/extrafont")
13646 (synopsis "Tools for using fonts in R")
13648 "The extrafont package makes it easier to use fonts other than the basic
13649 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13650 used with PDF or PostScript output files. There are two hurdles for using
13651 fonts in PDF (or Postscript) output files:
13654 @item Making R aware of the font and the dimensions of the characters.
13655 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13656 properly on a device that doesn't have the font. This is usually needed if
13657 you want to print the PDF file or share it with others.
13660 The extrafont package makes both of these things easier.")
13661 (license license:gpl2)))
13663 (define-public r-xkcd
13670 (uri (cran-uri "xkcd" version))
13673 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13674 (build-system r-build-system)
13676 `(("r-extrafont" ,r-extrafont)
13677 ("r-ggplot2" ,r-ggplot2)
13678 ("r-hmisc" ,r-hmisc)))
13679 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13680 (synopsis "Plot ggplot2 graphics in the XKCD style")
13682 "This package provides the means to plot ggplot2 graphs in the style of
13683 the XKCD web comic.")
13684 (license license:gpl3)))
13686 (define-public r-msigdbr
13693 (uri (cran-uri "msigdbr" version))
13696 "19p8z617m3my8la7n1qgb1s2msf940r372im3q30qkbcx3qxg3sd"))))
13697 (build-system r-build-system)
13699 `(("r-dplyr" ,r-dplyr)
13700 ("r-magrittr" ,r-magrittr)
13701 ("r-rlang" ,r-rlang)
13702 ("r-tibble" ,r-tibble)))
13703 (home-page "https://github.com/igordot/msigdbr")
13704 (synopsis "MSigDB gene sets for multiple organisms")
13706 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13707 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13708 software in a standard R data frame with key-value pairs. Included are the
13709 original human gene symbols and Entrez IDs as well as the equivalents for
13710 various frequently studied model organisms such as mouse, rat, pig, fly, and
13712 ;; The package is covered under the Expat license, but the upstream MSigDB
13713 ;; files are made available under the Creative Commons Attribution 4.0
13714 ;; International license.
13715 (license (list license:expat license:cc-by4.0))))
13717 (define-public r-gridgraphics
13719 (name "r-gridgraphics")
13724 (uri (cran-uri "gridGraphics" version))
13727 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13728 (properties `((upstream-name . "gridGraphics")))
13729 (build-system r-build-system)
13730 (home-page "https://github.com/pmur002/gridgraphics")
13731 (synopsis "Redraw base graphics using @code{grid} graphics")
13733 "This package provides functions to convert a page of plots drawn with
13734 the @code{graphics} package into identical output drawn with the @code{grid}
13735 package. The result looks like the original @code{graphics}-based plot, but
13736 consists of @code{grid} grobs and viewports that can then be manipulated with
13737 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13738 (license license:gpl2+)))
13740 (define-public r-farver
13747 (uri (cran-uri "farver" version))
13750 "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0"))))
13751 (build-system r-build-system)
13752 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13753 (home-page "https://github.com/thomasp85/farver")
13754 (synopsis "Vectorized color conversion and comparison")
13756 "The encoding of color can be handled in many different ways, using
13757 different color spaces. As different color spaces have different uses,
13758 efficient conversion between these representations are important. This
13759 package provides a set of functions that gives access to very fast color space
13760 conversion and comparisons implemented in C++, and offers 100-fold speed
13761 improvements over the @code{convertColor} function in the @code{grDevices}
13763 (license license:expat)))
13765 (define-public r-ggplotify
13767 (name "r-ggplotify")
13772 (uri (cran-uri "ggplotify" version))
13775 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
13776 (build-system r-build-system)
13778 `(("r-ggplot2" ,r-ggplot2)
13779 ("r-gridgraphics" ,r-gridgraphics)
13780 ("r-rvcheck" ,r-rvcheck)))
13781 (home-page "https://github.com/GuangchuangYu/ggplotify")
13782 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
13784 "This package provides tools to convert plot function calls (using
13785 expression or formula) to @code{grob} or @code{ggplot} objects that are
13786 compatible with the @code{grid} and @code{ggplot2} environment. With this
13787 package, we are able to e.g. use @code{cowplot} to align plots produced by
13788 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
13789 converting them to @code{ggplot} objects.")
13790 (license license:artistic2.0)))
13792 (define-public r-triebeard
13794 (name "r-triebeard")
13799 (uri (cran-uri "triebeard" version))
13802 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
13803 (build-system r-build-system)
13804 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13805 (home-page "https://github.com/Ironholds/triebeard/")
13806 (synopsis "Radix trees in Rcpp")
13808 "Radix trees, or tries, are key-value data structures optimized for
13809 efficient lookups, similar in purpose to hash tables. This package provides
13810 an implementation of radix trees for use in R programming and in developing
13811 packages with Rcpp.")
13812 (license license:expat)))
13814 (define-public r-tweenr
13821 (uri (cran-uri "tweenr" version))
13824 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
13825 (build-system r-build-system)
13827 `(("r-farver" ,r-farver)
13828 ("r-magrittr" ,r-magrittr)
13830 ("r-rlang" ,r-rlang)))
13831 (home-page "https://github.com/thomasp85/tweenr")
13832 (synopsis "Interpolate data for smooth animations")
13834 "In order to create smooth animation between states of data, tweening is
13835 necessary. This package provides a range of functions for creating tweened
13836 data that can be used as basis for animation. Furthermore it adds a number of
13837 vectorized interpolaters for common R data types such as numeric, date and
13839 (license license:expat)))
13841 (define-public r-polyclip
13843 (name "r-polyclip")
13848 (uri (cran-uri "polyclip" version))
13851 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
13852 (build-system r-build-system)
13853 (native-inputs `(("pkg-config" ,pkg-config)))
13854 (home-page "http://www.angusj.com/delphi/clipper.php")
13855 (synopsis "Polygon clipping")
13857 "This package provides an R port of the library Clipper. It performs
13858 polygon clipping operations (intersection, union, set minus, set difference)
13859 for polygonal regions of arbitrary complexity, including holes. It computes
13860 offset polygons (spatial buffer zones, morphological dilations, Minkowski
13861 dilations) for polygonal regions and polygonal lines. It computes the
13862 Minkowski Sum of general polygons. There is a function for removing
13863 self-intersections from polygon data.")
13864 (license license:boost1.0)))
13866 (define-public r-urltools
13868 (name "r-urltools")
13873 (uri (cran-uri "urltools" version))
13876 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
13877 (build-system r-build-system)
13879 `(("r-rcpp" ,r-rcpp)
13880 ("r-triebeard" ,r-triebeard)))
13881 (home-page "https://github.com/Ironholds/urltools/")
13882 (synopsis "Vectorized tools for URL handling and parsing")
13884 "This package provides a toolkit for all URL-handling needs, including
13885 encoding and decoding, parsing, parameter extraction and modification. All
13886 functions are designed to be both fast and entirely vectorized. It is
13887 intended to be useful for people dealing with web-related datasets, such as
13888 server-side logs, although may be useful for other situations involving large
13890 (license license:expat)))
13892 (define-public r-ggforce
13899 (uri (cran-uri "ggforce" version))
13902 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
13903 (build-system r-build-system)
13905 `(("r-ggplot2" ,r-ggplot2)
13906 ("r-gtable" ,r-gtable)
13908 ("r-polyclip" ,r-polyclip)
13910 ("r-rcppeigen" ,r-rcppeigen)
13911 ("r-rlang" ,r-rlang)
13912 ("r-scales" ,r-scales)
13913 ("r-tidyselect" ,r-tidyselect)
13914 ("r-tweenr" ,r-tweenr)
13915 ("r-withr" ,r-withr)))
13916 (home-page "https://ggforce.data-imaginist.com")
13917 (synopsis "Accelerating ggplot2")
13919 "The aim of the ggplot2 package is to aid in visual data investigations.
13920 This focus has led to a lack of facilities for composing specialized plots.
13921 Thi package aims to be a collection of mainly new statistics and geometries
13922 that fills this gap.")
13923 (license license:expat)))
13925 (define-public r-europepmc
13927 (name "r-europepmc")
13932 (uri (cran-uri "europepmc" version))
13935 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
13936 (build-system r-build-system)
13938 `(("r-dplyr" ,r-dplyr)
13940 ("r-jsonlite" ,r-jsonlite)
13942 ("r-progress" ,r-progress)
13943 ("r-purrr" ,r-purrr)
13944 ("r-urltools" ,r-urltools)
13945 ("r-xml2" ,r-xml2)))
13946 (home-page "https://github.com/ropensci/europepmc/")
13947 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
13949 "This package provides an R Client for the
13950 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
13951 Service}. It gives access to both metadata on life science literature and
13952 open access full texts. Europe PMC indexes all PubMed content and other
13953 literature sources including Agricola, a bibliographic database of citations
13954 to the agricultural literature, or Biological Patents. In addition to
13955 bibliographic metadata, the client allows users to fetch citations and
13956 reference lists. Links between life-science literature and other EBI
13957 databases, including ENA, PDB or ChEMBL are also accessible.")
13958 (license license:gpl3)))
13960 (define-public r-ggraph
13967 (uri (cran-uri "ggraph" version))
13970 "0qj7w3af0pgmd9mil6y571jikfkln7b8csvzg6b08spwbglfy1s3"))))
13971 (build-system r-build-system)
13973 `(("r-digest" ,r-digest)
13974 ("r-dplyr" ,r-dplyr)
13975 ("r-ggforce" ,r-ggforce)
13976 ("r-ggplot2" ,r-ggplot2)
13977 ("r-ggrepel" ,r-ggrepel)
13978 ("r-graphlayouts" ,r-graphlayouts)
13979 ("r-gtable" ,r-gtable)
13980 ("r-igraph" ,r-igraph)
13983 ("r-rlang" ,r-rlang)
13984 ("r-scales" ,r-scales)
13985 ("r-tidygraph" ,r-tidygraph)
13986 ("r-viridis" ,r-viridis)))
13987 (home-page "https://cran.r-project.org/web/packages/ggraph/")
13988 (synopsis "Implementation of grammar of graphics for graphs and networks")
13990 "The grammar of graphics as implemented in ggplot2 is a poor fit for
13991 graph and network visualizations due to its reliance on tabular data input.
13992 The ggraph package is an extension of the ggplot2 API tailored to graph
13993 visualizations and provides the same flexible approach to building up plots
13995 (license license:gpl3)))
13997 (define-public r-varselrf
13999 (name "r-varselrf")
14004 (uri (cran-uri "varSelRF" version))
14007 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14008 (properties `((upstream-name . "varSelRF")))
14009 (build-system r-build-system)
14011 `(("r-randomforest" ,r-randomforest)))
14012 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
14013 (synopsis "Variable selection using random forests")
14015 "This package provides tools for the variable selection from random
14016 forests using both backwards variable elimination (for the selection of small
14017 sets of non-redundant variables) and selection based on the importance
14018 spectrum (somewhat similar to scree plots; for the selection of large,
14019 potentially highly-correlated variables). The main applications are in
14020 high-dimensional data (e.g., microarray data, and other genomics and
14021 proteomics applications).")
14022 (license license:gpl2+)))
14024 (define-public r-pamr
14031 (uri (cran-uri "pamr" version))
14034 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14035 (build-system r-build-system)
14037 `(("r-cluster" ,r-cluster)
14038 ("r-survival" ,r-survival)))
14039 (native-inputs `(("gfortran" ,gfortran)))
14040 (home-page "https://cran.r-project.org/web/packages/pamr/")
14041 (synopsis "Prediction Analysis for Microarrays")
14043 "This package provides some functions for sample classification in
14045 (license license:gpl2)))
14047 (define-public r-rda
14050 (version "1.0.2-2.1")
14054 (uri (cran-uri "rda" version))
14057 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14058 (build-system r-build-system)
14059 (home-page "https://cran.r-project.org/web/packages/rda/")
14060 (synopsis "Shrunken centroids regularized discriminant analysis")
14062 "This package provides tools for shrunken centroids regularized
14063 discriminant analysis for the purpose of classifying high dimensional data.")
14064 (license license:gpl2+)))
14066 (define-public r-ggvis
14073 (uri (cran-uri "ggvis" version))
14076 "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk"))))
14077 (build-system r-build-system)
14079 `(("r-assertthat" ,r-assertthat)
14080 ("r-dplyr" ,r-dplyr)
14081 ("r-htmltools" ,r-htmltools)
14082 ("r-jsonlite" ,r-jsonlite)
14083 ("r-lazyeval" ,r-lazyeval)
14084 ("r-magrittr" ,r-magrittr)
14085 ("r-shiny" ,r-shiny)))
14086 (home-page "https://ggvis.rstudio.com/")
14087 (synopsis "Interactive grammar of graphics")
14089 "This package is a data visualization package for R providing an
14090 implementation of an interactive grammar of graphics, taking the best parts of
14091 ggplot2, combining them with the reactive framework of Shiny and drawing web
14092 graphics using Vega.")
14093 (license license:gpl2)))
14095 (define-public r-gbm
14102 (uri (cran-uri "gbm" version))
14105 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14106 (build-system r-build-system)
14108 `(("r-gridextra" ,r-gridextra)
14109 ("r-lattice" ,r-lattice)
14110 ("r-survival" ,r-survival)))
14111 (home-page "https://github.com/gbm-developers/gbm")
14112 (synopsis "Generalized boosted regression models")
14114 "This package is an implementation of extensions to Freund and Schapire's
14115 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14116 regression methods for least squares, absolute loss, t-distribution loss,
14117 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14118 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14119 and Learning to Rank measures (LambdaMart).")
14120 (license license:gpl2+)))
14122 (define-public r-threejs
14129 (uri (cran-uri "threejs" version))
14132 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14133 (build-system r-build-system)
14135 `(#:modules ((guix build utils)
14136 (guix build r-build-system)
14140 (modify-phases %standard-phases
14141 (add-after 'unpack 'process-javascript
14142 (lambda* (#:key inputs #:allow-other-keys)
14143 (with-directory-excursion "inst"
14147 `((,(assoc-ref inputs "js-jquery")
14148 "htmlwidgets/lib/jquery/jquery.min.js")
14149 (,(assoc-ref inputs "js-threejs-85")
14150 "htmlwidgets/lib/threejs-85/three.min.js"))))
14151 (lambda (sources targets)
14152 (for-each (lambda (source target)
14153 (format #t "Processing ~a --> ~a~%"
14155 (delete-file target)
14156 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14157 (call-with-output-file target
14159 (dump-port minified port)))))
14160 sources targets))))
14163 `(("r-base64enc" ,r-base64enc)
14164 ("r-crosstalk" ,r-crosstalk)
14165 ("r-htmlwidgets" ,r-htmlwidgets)
14166 ("r-igraph" ,r-igraph)))
14168 `(("uglify-js" ,uglify-js)
14172 (uri "https://code.jquery.com/jquery-3.3.1.js")
14175 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14179 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14182 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14183 (home-page "https://bwlewis.github.io/rthreejs")
14184 (synopsis "Interactive 3D scatter plots, networks and globes")
14186 "Create interactive 3D scatter plots, network plots, and globes in R
14187 using the three.js visualization library.")
14188 (license license:expat)))
14190 (define-public r-mlbench
14197 (uri (cran-uri "mlbench" version))
14200 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14201 (build-system r-build-system)
14202 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14203 (synopsis "Machine learning benchmark problems")
14205 "This package provides a collection of artificial and real-world machine
14206 learning benchmark problems, including, e.g., several data sets from the UCI
14208 (license license:gpl2)))
14210 (define-public r-mpm
14217 (uri (cran-uri "mpm" version))
14220 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14221 (build-system r-build-system)
14223 `(("r-kernsmooth" ,r-kernsmooth)
14224 ("r-mass" ,r-mass)))
14225 (home-page "http://mpm.r-forge.r-project.org")
14226 (synopsis "Multivariate projection methods")
14228 "This is a package for exploratory graphical analysis of multivariate
14229 data, specifically gene expression data with different projection methods:
14230 principal component analysis, correspondence analysis, spectral map
14232 (license license:gpl2+)))
14234 (define-public r-png
14240 (uri (cran-uri "png" version))
14243 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14244 (build-system r-build-system)
14246 `(("libpng" ,libpng)
14248 (home-page "http://www.rforge.net/png/")
14249 (synopsis "Read and write PNG images")
14251 "This package provides an easy and simple way to read, write and display
14252 bitmap images stored in the PNG format. It can read and write both files and
14253 in-memory raw vectors.")
14254 ;; Any of these GPL versions.
14255 (license (list license:gpl2 license:gpl3))))
14257 (define-public r-ggcorrplot
14259 (name "r-ggcorrplot")
14264 (uri (cran-uri "ggcorrplot" version))
14267 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14268 (build-system r-build-system)
14270 `(("r-ggplot2" ,r-ggplot2)
14271 ("r-reshape2" ,r-reshape2)))
14272 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14273 (synopsis "Visualization of a correlation matrix using ggplot2")
14275 "The ggcorrplot package can be used to visualize easily a correlation
14276 matrix using ggplot2. It provides a solution for reordering the correlation
14277 matrix and displays the significance level on the plot. It also includes a
14278 function for computing a matrix of correlation p-values.")
14279 (license license:gpl2)))
14281 (define-public r-flexdashboard
14283 (name "r-flexdashboard")
14284 (version "0.5.1.1")
14288 (uri (cran-uri "flexdashboard" version))
14291 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14292 (build-system r-build-system)
14294 `(#:modules ((guix build utils)
14295 (guix build r-build-system)
14299 (ice-9 textual-ports))
14301 (modify-phases %standard-phases
14302 (add-after 'unpack 'process-javascript
14303 (lambda* (#:key inputs #:allow-other-keys)
14304 (with-directory-excursion "inst"
14305 ;; Concatenate all components of prism.js
14306 (let ((contents (string-join
14307 (map (lambda (name)
14308 (call-with-input-file
14309 (assoc-ref inputs name)
14313 "js-prism-line-numbers"))
14315 (call-with-output-file "prism-src.js"
14316 (cut display contents <>)))
14320 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14321 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14323 "www/sly/sly.min.js")
14325 "www/prism/prism.js")
14326 (,(assoc-ref inputs "js-raphael")
14327 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14328 (,(assoc-ref inputs "js-featherlight")
14329 "www/featherlight/featherlight.min.js"))))
14330 (lambda (sources targets)
14331 (for-each (lambda (source target)
14332 (format #t "Processing ~a --> ~a~%"
14334 (delete-file target)
14335 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14336 (call-with-output-file target
14338 (dump-port minified port)))))
14339 sources targets))))
14342 `(("r-htmltools" ,r-htmltools)
14343 ("r-htmlwidgets" ,r-htmlwidgets)
14344 ("r-jsonlite" ,r-jsonlite)
14345 ("r-knitr" ,r-knitr)
14346 ("r-rmarkdown" ,r-rmarkdown)
14347 ("r-shiny" ,r-shiny)))
14349 `(("uglify-js" ,uglify-js)
14353 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14356 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14360 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14363 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14367 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14370 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14371 ("js-prism-line-numbers"
14374 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14377 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14381 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14384 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14385 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14386 (synopsis "R Markdown format for flexible dashboards")
14388 "This package provides an R Markdown format for converting an R Markdown
14389 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14390 of its components to the containing web page.")
14391 (license license:expat)))
14393 (define-public r-preseqr
14400 (uri (cran-uri "preseqR" version))
14403 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14404 (properties `((upstream-name . "preseqR")))
14405 (build-system r-build-system)
14407 `(("r-polynom" ,r-polynom)))
14408 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14409 (synopsis "Predicting species accumulation curves")
14411 "This package can be used to predict the r-species accumulation
14412 curve (r-SAC), which is the number of species represented at least r times as
14413 a function of the sampling effort. When r = 1, the curve is known as the
14414 species accumulation curve, or the library complexity curve in high-throughput
14415 genomic sequencing. The package includes both parametric and nonparametric
14416 methods, as described by Deng C, et al. (2018).")
14417 (license license:gpl3)))
14419 (define-public r-mapplots
14421 (name "r-mapplots")
14426 (uri (cran-uri "mapplots" version))
14429 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14430 (build-system r-build-system)
14431 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14432 (synopsis "Data visualization on maps")
14434 "This package helps you create simple maps; add sub-plots like pie plots
14435 to a map or any other plot; format, plot and export gridded data. The package
14436 was developed for displaying fisheries data but most functions can be used for
14437 more generic data visualisation.")
14438 (license license:gpl2+)))
14440 (define-public r-pmcmr
14447 (uri (cran-uri "PMCMR" version))
14450 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14451 (properties `((upstream-name . "PMCMR")))
14452 (build-system r-build-system)
14453 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14454 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14456 "This is a deprecated package for calculating pairwise multiple
14457 comparisons of mean rank sums. This package is superseded by the novel
14458 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14459 compatibility of dependent packages for some time.")
14460 (license license:gpl3+)))
14462 (define-public r-downloader
14464 (name "r-downloader")
14469 (uri (cran-uri "downloader" version))
14472 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14473 (build-system r-build-system)
14475 `(("r-digest" ,r-digest)))
14476 (home-page "https://github.com/wch/downloader")
14477 (synopsis "Download files over HTTP and HTTPS")
14479 "This package provides a wrapper for the @code{download.file} function,
14480 making it possible to download files over HTTPS across platforms. The
14481 @code{RCurl} package provides this functionality (and much more) but has
14482 external dependencies. This package has is implemented purely in R.")
14483 (license license:gpl2)))
14485 (define-public r-rex
14492 (uri (cran-uri "rex" version))
14495 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14496 (build-system r-build-system)
14498 `(("r-lazyeval" ,r-lazyeval)
14499 ("r-magrittr" ,r-magrittr)))
14500 (home-page "https://github.com/kevinushey/rex")
14501 (synopsis "Friendly regular expressions")
14503 "This package provides a friendly interface for the construction of
14504 regular expressions. Regular expressions are a very powerful feature, however
14505 they are often difficult to interpret. Rex allows you to build complex
14506 regular expressions from human readable expressions")
14507 (license license:expat)))
14509 (define-public r-sctransform
14511 (name "r-sctransform")
14516 (uri (cran-uri "sctransform" version))
14519 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14520 (build-system r-build-system)
14522 `(("r-future" ,r-future)
14523 ("r-future-apply" ,r-future-apply)
14524 ("r-ggplot2" ,r-ggplot2)
14525 ("r-gridextra" ,r-gridextra)
14527 ("r-matrix" ,r-matrix)
14529 ("r-rcppeigen" ,r-rcppeigen)
14530 ("r-reshape2" ,r-reshape2)))
14531 (home-page "https://github.com/ChristophH/sctransform")
14532 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14534 "This package provides a normalization method for single-cell UMI count
14535 data using a variance stabilizing transformation. The transformation is based
14536 on a negative binomial regression model with regularized parameters. As part
14537 of the same regression framework, this package also provides functions for
14538 batch correction, and data correction.")
14539 (license license:gpl3)))
14541 (define-public r-styler
14548 (uri (cran-uri "styler" version))
14551 "0rdbz60x8bymis6r6188ia1y0ip3nhf5y363i4cmakr618irjab9"))))
14552 (build-system r-build-system)
14554 `(("r-backports" ,r-backports)
14556 ("r-magrittr" ,r-magrittr)
14557 ("r-purrr" ,r-purrr)
14558 ("r-rematch2" ,r-rematch2)
14559 ("r-rlang" ,r-rlang)
14560 ("r-rprojroot" ,r-rprojroot)
14561 ("r-tibble" ,r-tibble)
14562 ("r-withr" ,r-withr)
14563 ("r-xfun" ,r-xfun)))
14564 (home-page "https://github.com/r-lib/styler")
14565 (synopsis "Non-invasive pretty printing of R code")
14567 "This is a package for pretty-printing R code without changing the user's
14568 formatting intent.")
14569 (license license:gpl3)))
14571 (define-public r-scrime
14578 (uri (cran-uri "scrime" version))
14581 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14582 (build-system r-build-system)
14583 (home-page "https://cran.r-project.org/web/packages/scrime/")
14584 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14586 "This package provides tools for the analysis of high-dimensional data
14587 developed/implemented at the group \"Statistical Complexity Reduction In
14588 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14589 the functions can also be applied to other types of categorical data.")
14590 (license license:gpl2)))
14592 (define-public r-pbmcapply
14594 (name "r-pbmcapply")
14599 (uri (cran-uri "pbmcapply" version))
14602 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14603 (build-system r-build-system)
14604 (home-page "https://github.com/kvnkuang/pbmcapply")
14605 (synopsis "Track the progress of apply procedures with a progress bar")
14607 "This light-weight package helps you track and visualize the progress of
14608 parallel versions of vectorized R functions of the @code{mc*apply} family.")
14609 (license license:expat)))
14611 (define-public r-blme
14618 (uri (cran-uri "blme" version))
14621 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14622 (build-system r-build-system)
14623 (propagated-inputs `(("r-lme4" ,r-lme4)))
14624 (home-page "https://github.com/vdorie/blme")
14625 (synopsis "Bayesian linear mixed-effects models")
14627 "This package provides tools for maximum a posteriori estimation for
14628 linear and generalized linear mixed-effects models in a Bayesian setting. It
14629 extends the lme4 package.")
14630 (license license:gpl2+)))
14632 (define-public r-batchtools
14634 (name "r-batchtools")
14639 (uri (cran-uri "batchtools" version))
14642 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14643 (build-system r-build-system)
14645 `(("r-backports" ,r-backports)
14646 ("r-base64url" ,r-base64url)
14648 ("r-checkmate" ,r-checkmate)
14649 ("r-data-table" ,r-data-table)
14650 ("r-digest" ,r-digest)
14652 ("r-progress" ,r-progress)
14654 ("r-rappdirs" ,r-rappdirs)
14655 ("r-stringi" ,r-stringi)
14656 ("r-withr" ,r-withr)))
14657 (home-page "https://github.com/mllg/batchtools")
14658 (synopsis "Tools for computation on batch systems")
14660 "As a successor of the packages BatchJobs and BatchExperiments, this
14661 package provides a parallel implementation of the Map function for high
14662 performance computing systems managed by various schedulers. A multicore and
14663 socket mode allow the parallelization on a local machines, and multiple
14664 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14665 the package provides an abstraction mechanism to define large-scale computer
14666 experiments in a well-organized and reproducible way.")
14667 (license license:lgpl3)))
14669 (define-public r-clue
14676 (uri (cran-uri "clue" version))
14679 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
14680 (build-system r-build-system)
14681 (propagated-inputs `(("r-cluster" ,r-cluster)))
14682 (home-page "https://cran.r-project.org/web/packages/clue/")
14683 (synopsis "Tools for analyzing cluster ensembles")
14684 (description "Cluster ensembles are collections of individual solutions to
14685 a given clustering problem which are useful or necessary to consider in a wide
14686 range of applications. This R package provides an extensible computational
14687 environment for creating and analyzing cluster ensembles, with basic data
14688 structures for representing partitions and hierarchies, and facilities for
14689 computing on them, including methods for measuring proximity and obtaining
14690 consensus and secondary clusterings.")
14691 (license license:gpl2)))
14693 (define-public r-sitmo
14700 (uri (cran-uri "sitmo" version))
14703 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
14704 (build-system r-build-system)
14705 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14706 (home-page "https://github.com/coatless/sitmo/")
14707 (synopsis "Parallel pseudo random number generator header files")
14709 "This package provides two high quality and fast PPRNGs that may be used
14710 in an OpenMP parallel environment. In addition, there is a generator for one
14711 dimensional low-discrepancy sequence.")
14712 (license license:expat)))
14714 (define-public r-dqrng
14721 (uri (cran-uri "dqrng" version))
14724 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
14725 (build-system r-build-system)
14729 ("r-sitmo" ,r-sitmo)))
14730 (home-page "https://www.daqana.org/dqrng")
14731 (synopsis "Fast pseudo random number generators")
14733 "Several fast random number generators are provided as C++ header-only
14734 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
14735 Additionally, fast functions for generating random numbers according to a
14736 uniform, normal and exponential distribution are included. The latter two use
14737 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
14738 functions are exported to R and as a C++ interface and are enabled for use
14739 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
14740 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
14741 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
14742 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
14743 ;; whole is distributed under the terms of the AGPL 3.
14744 (license license:agpl3)))
14746 (define-public r-dalex
14753 (uri (cran-uri "DALEX" version))
14756 "0iiwkf0pfdb90lf1xhv43qd32z3cjmkmf0ly9841n5lldkjazy3h"))))
14757 (properties `((upstream-name . "DALEX")))
14758 (build-system r-build-system)
14759 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
14760 (home-page "https://pbiecek.github.io/DALEX/")
14761 (synopsis "Descriptive machine learning explanations")
14763 "Machine Learning models are widely used and have various applications in
14764 classification or regression. Models created with boosting, bagging, stacking
14765 or similar techniques are often used due to their high performance, but such
14766 black-box models usually lack interpretability. The DALEX package contains
14767 various explainers that help to understand the link between input variables
14768 and model output.")
14769 ;; Any version of the GPL
14770 (license license:gpl3+)))
14772 (define-public r-enrichr
14779 (uri (cran-uri "enrichR" version))
14782 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
14783 (properties `((upstream-name . "enrichR")))
14784 (build-system r-build-system)
14786 `(("r-httr" ,r-httr)
14787 ("r-rjson" ,r-rjson)))
14788 (home-page "https://cran.r-project.org/web/packages/enrichR/")
14789 (synopsis "R Interface to Enrichr database for analyzing gene sets")
14791 "This package provides an R interface to all Enrichr databases, a
14792 web-based tool for analyzing gene sets and returns any enrichment of common
14793 annotated biological functions.")
14794 (license license:gpl2+)))
14796 (define-public r-plot3d
14803 (uri (cran-uri "plot3D" version))
14806 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
14807 (properties `((upstream-name . "plot3D")))
14808 (build-system r-build-system)
14809 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
14810 (home-page "https://cran.r-project.org/web/packages/plot3D")
14811 (synopsis "Plot multi-dimensional data")
14813 "This package provides functions for viewing 2D and 3D data, including
14814 perspective plots, slice plots, surface plots, scatter plots, etc. It
14815 includes data sets from oceanography.")
14816 (license license:gpl3+)))
14818 (define-public r-ggfortify
14820 (name "r-ggfortify")
14825 (uri (cran-uri "ggfortify" version))
14828 "1wk9j0xg5hj9i1vf62qjiphv8cbsgq7y6baay3pfl3wyb2dwgci0"))))
14829 (build-system r-build-system)
14831 `(("r-dplyr" ,r-dplyr)
14832 ("r-ggplot2" ,r-ggplot2)
14833 ("r-gridextra" ,r-gridextra)
14834 ("r-scales" ,r-scales)
14835 ("r-stringr" ,r-stringr)
14836 ("r-tibble" ,r-tibble)
14837 ("r-tidyr" ,r-tidyr)))
14838 (home-page "https://github.com/sinhrks/ggfortify")
14839 (synopsis "Data visualization tools for statistical analysis results")
14841 "This package provides unified plotting tools for statistics commonly
14842 used, such as GLM, time series, PCA families, clustering and survival
14843 analysis. The package offers a single plotting interface for these analysis
14844 results and plots in a unified style using the @code{ggplot2} package.")
14845 (license license:gpl2)))
14847 (define-public r-refmanager
14849 (name "r-refmanager")
14854 (uri (cran-uri "RefManageR" version))
14857 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
14858 (properties `((upstream-name . "RefManageR")))
14859 (build-system r-build-system)
14861 `(("r-bibtex" ,r-bibtex)
14863 ("r-jsonlite" ,r-jsonlite)
14864 ("r-lubridate" ,r-lubridate)
14866 ("r-stringr" ,r-stringr)
14867 ("r-xml2" ,r-xml2)))
14868 (home-page "https://github.com/ropensci/RefManageR/")
14869 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
14871 "This package provides tools for importing and working with bibliographic
14872 references. It greatly enhances the @code{bibentry} class by providing a
14873 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
14874 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
14875 by various formats for name lists (author by last names, translator by full
14876 names, etc.). Entries can be updated, combined, sorted, printed in a number
14877 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
14878 into R and converted to @code{BibEntry} objects.")
14879 ;; Any of these licenses may be picked.
14880 (license (list license:gpl2 license:gpl3 license:bsd-3))))
14882 (define-public r-citr
14889 (uri (cran-uri "citr" version))
14892 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
14893 (build-system r-build-system)
14895 `(("r-assertthat" ,r-assertthat)
14898 ("r-miniui" ,r-miniui)
14899 ("r-refmanager" ,r-refmanager)
14900 ("r-rstudioapi" ,r-rstudioapi)
14901 ("r-shiny" ,r-shiny)
14902 ("r-shinyjs" ,r-shinyjs)
14903 ("r-yaml" ,r-yaml)))
14904 (home-page "https://github.com/crsh/citr")
14905 (synopsis "RStudio add-in to insert Markdown citations")
14907 "This package provides functions and an RStudio add-in that search a
14908 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
14909 the current document.")
14910 (license license:expat)))
14912 (define-public r-xgboost
14915 (version "0.90.0.2")
14919 (uri (cran-uri "xgboost" version))
14922 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
14923 (build-system r-build-system)
14925 `(("r-data-table" ,r-data-table)
14926 ("r-magrittr" ,r-magrittr)
14927 ("r-matrix" ,r-matrix)
14928 ("r-stringi" ,r-stringi)))
14929 (home-page "https://github.com/dmlc/xgboost")
14930 (synopsis "Extreme gradient boosting")
14932 "This package provides an R interface to Extreme Gradient Boosting, which
14933 is an efficient implementation of the gradient boosting framework from Chen
14934 and Guestrin (2016). The package includes efficient linear model solver and
14935 tree learning algorithms. The package can automatically do parallel
14936 computation on a single machine. It supports various objective functions,
14937 including regression, classification and ranking. The package is made to be
14938 extensible, so that users are also allowed to define their own objectives
14940 (license license:asl2.0)))
14942 (define-public r-umap
14945 (version "0.2.3.1")
14949 (uri (cran-uri "umap" version))
14952 "0rzz1s029cn1w1bf5va2pav2lg9j1mq97ibwcln39drvm67kj76d"))))
14953 (build-system r-build-system)
14955 `(("r-openssl" ,r-openssl)
14957 ("r-reticulate" ,r-reticulate)
14958 ("r-rspectra" ,r-rspectra)))
14959 (home-page "https://github.com/tkonopka/umap")
14960 (synopsis "Uniform manifold approximation and projection")
14962 "Uniform manifold approximation and projection is a technique for
14963 dimension reduction. This package provides an interface to the UMAP algorithm
14964 in R, including a translation of the original algorithm into R.")
14965 (license license:expat)))
14967 (define-public r-uwot
14974 (uri (cran-uri "uwot" version))
14977 "1y9wpzs92d1fl2x5figfywd48lkyhwx37j542z0rf6ckrl46n89n"))))
14978 (build-system r-build-system)
14980 `(("r-dqrng" ,r-dqrng)
14982 ("r-irlba" ,r-irlba)
14983 ("r-matrix" ,r-matrix)
14985 ("r-rcppannoy" ,r-rcppannoy)
14986 ("r-rcppparallel" ,r-rcppparallel)
14987 ("r-rcppprogress" ,r-rcppprogress)
14988 ("r-rspectra" ,r-rspectra)))
14989 (home-page "https://github.com/jlmelville/uwot")
14990 (synopsis "Uniform manifold approximation and projection")
14992 "This package provides an implementation of the Uniform Manifold
14993 Approximation and Projection dimensionality reduction by McInnes et
14994 al. (2018). It also provides means to transform new data and to carry out
14995 supervised dimensionality reduction. An implementation of the related
14996 LargeVis method of Tang et al. (2016) is also provided.")
14997 (license license:gpl3)))
14999 (define-public r-kableextra
15001 (name "r-kableextra")
15006 (uri (cran-uri "kableExtra" version))
15009 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
15010 (properties `((upstream-name . "kableExtra")))
15011 (build-system r-build-system)
15013 `(("r-digest" ,r-digest)
15015 ("r-htmltools" ,r-htmltools)
15016 ("r-knitr" ,r-knitr)
15017 ("r-magrittr" ,r-magrittr)
15018 ("r-readr" ,r-readr)
15019 ("r-rmarkdown" ,r-rmarkdown)
15020 ("r-rstudioapi" ,r-rstudioapi)
15021 ("r-rvest" ,r-rvest)
15022 ("r-scales" ,r-scales)
15023 ("r-stringr" ,r-stringr)
15024 ("r-viridislite" ,r-viridislite)
15025 ("r-webshot" ,r-webshot)
15026 ("r-xml2" ,r-xml2)))
15027 (home-page "https://haozhu233.github.io/kableExtra/")
15028 (synopsis "Construct complex tables with pipe syntax")
15030 "Build complex HTML or LaTeX tables using @code{kable()} from
15031 @code{knitr} and the piping syntax from @code{magrittr}. The function
15032 @code{kable()} is a light weight table generator coming from @code{knitr}.
15033 This package simplifies the way to manipulate the HTML or LaTeX codes
15034 generated by @code{kable()} and allows users to construct complex tables and
15035 customize styles using a readable syntax.")
15036 (license license:expat)))
15038 (define-public r-glasso
15045 (uri (cran-uri "glasso" version))
15047 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
15048 (build-system r-build-system)
15049 (native-inputs `(("gfortran" ,gfortran)))
15050 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
15051 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
15053 "This is a package for estimation of a sparse inverse covariance matrix
15054 using a lasso (L1) penalty. Facilities are provided for estimates along a
15055 path of values for the regularization parameter.")
15056 (license license:gpl2)))
15058 (define-public r-rhpcblasctl
15060 (name "r-rhpcblasctl")
15061 (version "0.18-205")
15065 (uri (cran-uri "RhpcBLASctl" version))
15068 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
15069 (properties `((upstream-name . "RhpcBLASctl")))
15070 (build-system r-build-system)
15071 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
15072 (synopsis "Control the number of threads on BLAS")
15074 "This package allows you to control the number of threads the BLAS
15075 library uses. It is also possible to control the number of threads in
15077 (license license:agpl3+)))
15079 (define-public r-lda
15086 (uri (cran-uri "lda" version))
15089 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
15090 (build-system r-build-system)
15091 (home-page "https://cran.r-project.org/web/packages/lda/")
15092 (synopsis "Collapsed Gibbs sampling methods for topic models")
15094 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
15095 related models. This includes (but is not limited to) sLDA, corrLDA, and the
15096 mixed-membership stochastic blockmodel. Inference for all of these models is
15097 implemented via a fast collapsed Gibbs sampler written in C. Utility
15098 functions for reading/writing data typically used in topic models, as well as
15099 tools for examining posterior distributions are also included.")
15100 ;; Any version of the LGPL
15101 (license license:lgpl3+)))
15103 (define-public r-rann-l1
15110 (uri (cran-uri "RANN.L1" version))
15113 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
15114 (properties `((upstream-name . "RANN.L1")))
15115 (build-system r-build-system)
15116 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
15117 (synopsis "Fast nearest neighbour search using L1 metric")
15119 "This package provides tools to find the k nearest neighbours for every
15120 point in a given dataset in O(N log N) time using Arya and Mount's ANN
15121 library. There is support for approximate as well as exact searches, fixed
15122 radius searches and @code{bd} as well as @code{kd} trees. The distance is
15123 computed using the L1 (Manhattan, taxicab) metric.")
15124 (license license:gpl3+)))
15126 (define-public r-leiden
15133 (uri (cran-uri "leiden" version))
15136 "19gq27zin4gf4sh7h24gyq3f8jjir20n2l36a7pk1pbzcr4ixyhp"))))
15137 (properties `((upstream-name . "leiden")))
15138 (build-system r-build-system)
15140 `(("r-igraph" ,r-igraph)
15141 ("r-matrix" ,r-matrix)
15142 ("r-reticulate" ,r-reticulate)))
15143 (home-page "https://github.com/TomKellyGenetics/leiden")
15144 (synopsis "R implementation of Leiden clustering algorithm")
15146 "This package implements the Python @code{leidenalg} module to be called
15147 in R. It enables clustering using the Leiden algorithm for partitioning a
15148 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
15149 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
15150 (license license:gpl3)))
15152 (define-public r-patchwork
15153 ;; There has been no public release yet.
15154 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15157 (name "r-patchwork")
15158 (version (git-version "0.0.1" revision commit))
15162 (uri (git-reference
15163 (url "https://github.com/thomasp85/patchwork.git")
15165 (file-name (git-file-name name version))
15168 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15169 (build-system r-build-system)
15171 `(("r-ggplot2" ,r-ggplot2)
15172 ("r-gtable" ,r-gtable)))
15173 (home-page "https://github.com/thomasp85/patchwork")
15174 (synopsis "Compose ggplot2 plots")
15176 "The @code{ggplot2} package provides a strong API for sequentially
15177 building up a plot, but does not concern itself with composition of multiple
15178 plots. Patchwork is a package that expands the API to allow for arbitrarily
15179 complex composition of plots by providing mathmatical operators for combining
15181 (license license:expat))))
15183 (define-public r-liger
15190 (uri (git-reference
15191 (url "https://github.com/MacoskoLab/liger.git")
15192 (commit (string-append "v" version))))
15193 (file-name (git-file-name name version))
15196 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15197 (modules '((guix build utils)))
15200 (delete-file "inst/java/ModularityOptimizer.jar")
15202 (build-system r-build-system)
15205 (modify-phases %standard-phases
15206 (add-after 'unpack 'build-java-part
15207 (lambda* (#:key inputs #:allow-other-keys)
15208 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15209 (for-each (lambda (file) (invoke "javac" file))
15210 (find-files "." "\\.java$"))
15211 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15212 (find-files "." "\\.class$"))
15215 `(("r-cowplot" ,r-cowplot)
15216 ("r-dosnow" ,r-dosnow)
15217 ("r-dplyr" ,r-dplyr)
15219 ("r-foreach" ,r-foreach)
15220 ("r-ggplot2" ,r-ggplot2)
15221 ("r-ggrepel" ,r-ggrepel)
15222 ("r-hmisc" ,r-hmisc)
15224 ("r-irlba" ,r-irlba)
15225 ("r-matrix" ,r-matrix)
15226 ("r-mclust" ,r-mclust)
15227 ("r-patchwork" ,r-patchwork)
15229 ("r-rann-l1" ,r-rann-l1)
15231 ("r-rcpparmadillo" ,r-rcpparmadillo)
15232 ("r-riverplot" ,r-riverplot)
15233 ("r-rtsne" ,r-rtsne)
15234 ("r-snow" ,r-snow)))
15236 `(("jdk" ,icedtea "jdk")
15237 ;; See https://github.com/MacoskoLab/liger/issues/96
15238 ;; The optimizer is released under the Expat license.
15242 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15245 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15247 ("r-knitr" ,r-knitr))) ; for vignettes
15248 (home-page "https://github.com/MacoskoLab/liger")
15249 (synopsis "Integrate and analyze multiple single-cell datasets")
15251 "LIGER is a package for integrating and analyzing multiple single-cell
15252 datasets, developed and maintained by the Macosko lab. It relies on
15253 integrative non-negative matrix factorization to identify shared and
15254 dataset-specific factors.")
15255 (license license:gpl3)))
15257 (define-public r-harmony
15258 ;; There are no tagged commits
15259 (let ((commit "4d1653870d4dd70fff1807c182882db1fbf9af5a")
15263 (version (git-version "1.0" revision commit))
15267 (uri (git-reference
15268 (url "https://github.com/immunogenomics/harmony")
15270 (file-name (git-file-name name version))
15273 "1gasdldr4aalr9h2q9kmm3y4i7azkgnhdn4bmvsszs7lg9xacw85"))))
15274 (build-system r-build-system)
15276 `(("r-cowplot" ,r-cowplot)
15277 ("r-dplyr" ,r-dplyr)
15278 ("r-ggplot2" ,r-ggplot2)
15279 ("r-irlba" ,r-irlba)
15280 ("r-matrix" ,r-matrix)
15282 ("r-rcpparmadillo" ,r-rcpparmadillo)
15283 ("r-rcppprogress" ,r-rcppprogress)
15284 ("r-rlang" ,r-rlang)
15285 ("r-tibble" ,r-tibble)
15286 ("r-tidyr" ,r-tidyr)))
15287 (home-page "https://github.com/immunogenomics/harmony")
15288 (synopsis "Integration of single cell sequencing data")
15290 "This package provides an implementation of the Harmony algorithm for
15291 single cell integration, described in Korsunsky et al
15292 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
15293 function and interfaces to external frameworks.")
15294 (license license:gpl3))))
15296 (define-public r-covr
15303 (uri (cran-uri "covr" version))
15305 (base32 "160w0m2d06kdd8dar57lpph39rxx55xwncbpl3b21l7j9drh1s5f"))))
15306 (properties `((upstream-name . "covr")))
15307 (build-system r-build-system)
15309 `(("r-crayon" ,r-crayon)
15310 ("r-digest" ,r-digest)
15312 ("r-jsonlite" ,r-jsonlite)
15314 ("r-withr" ,r-withr)
15315 ("r-yaml" ,r-yaml)))
15316 (home-page "https://github.com/r-lib/covr")
15317 (synopsis "Test coverage for R packages")
15319 "Thisp package enables you to track and report code coverage for your
15320 package and (optionally) upload the results to a coverage service. Code
15321 coverage is a measure of the amount of code being exercised by a set of tests.
15322 It is an indirect measure of test quality and completeness. This package is
15323 compatible with any testing methodology or framework and tracks coverage of
15324 both R code and compiled C/C++/FORTRAN code.")
15325 (license license:gpl3)))
15327 (define-public r-systemfonts
15329 (name "r-systemfonts")
15334 (uri (cran-uri "systemfonts" version))
15337 "0m0ljid683xcam2f14x7k2zv1yx4npac38a3gfv11vhxfbnpgp0z"))))
15338 (properties `((upstream-name . "systemfonts")))
15339 (build-system r-build-system)
15341 `(("fontconfig" ,fontconfig)
15342 ("freetype" ,freetype)
15345 `(("pkg-config" ,pkg-config)))
15346 (home-page "https://github.com/r-lib/systemfonts")
15347 (synopsis "System native font finding")
15349 "This package provides system native access to the font catalogue. As
15350 font handling varies between systems it is difficult to correctly locate
15351 installed fonts across different operating systems. The 'systemfonts' package
15352 provides bindings to the native libraries for finding font files that can then
15353 be used further by e.g. graphic devices.")
15354 (license license:expat)))
15356 (define-public r-graphlayouts
15358 (name "r-graphlayouts")
15363 (uri (cran-uri "graphlayouts" version))
15366 "03dizbhhdhnzbj2i5zvqgs617kwcv4h2pha4f16adic0fph1rxl3"))))
15367 (properties `((upstream-name . "graphlayouts")))
15368 (build-system r-build-system)
15370 `(("r-igraph" ,r-igraph)
15372 ("r-rcpparmadillo" ,r-rcpparmadillo)))
15373 (home-page "https://github.com/schochastics/graphlayouts")
15374 (synopsis "Additional layout algorithms for network visualizations")
15376 "This package provides several layout algorithms to visualize networks
15377 which are not part of the igraph library. Most are based on the concept of
15378 stress majorization by Gansner et al. (2004)
15379 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms allow to
15380 emphasize hidden group structures in networks or focus on specific nodes.")
15381 (license license:expat)))
15383 (define-public r-tidygraph
15385 (name "r-tidygraph")
15390 (uri (cran-uri "tidygraph" version))
15393 "1zpsarm74afbc7p5dlyb0whc09670qdcddw1ckb25cfc9hfh0hjn"))))
15394 (properties `((upstream-name . "tidygraph")))
15395 (build-system r-build-system)
15397 `(("r-dplyr" ,r-dplyr)
15398 ("r-igraph" ,r-igraph)
15399 ("r-magrittr" ,r-magrittr)
15400 ("r-pillar" ,r-pillar)
15403 ("r-rlang" ,r-rlang)
15404 ("r-tibble" ,r-tibble)
15405 ("r-tidyr" ,r-tidyr)))
15406 (home-page "https://github.com/thomasp85/tidygraph")
15407 (synopsis "Tidy API for graph manipulation")
15409 "This package provides a graph implementation that can be thought of as
15410 two tidy data frames describing node and edge data respectively. It provides
15411 an approach to manipulate these two virtual data frames using the API defined
15412 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
15413 common graph algorithms.")
15414 (license license:expat)))
15416 (define-public r-soupx
15417 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
15421 (version (git-version "0.3.1" revision commit))
15425 (uri (git-reference
15426 (url "https://github.com/constantAmateur/SoupX")
15428 (file-name (git-file-name name version))
15431 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
15432 (properties `((upstream-name . "SoupX")))
15433 (build-system r-build-system)
15435 `(("r-ggplot2" ,r-ggplot2)
15436 ("r-matrix" ,r-matrix)
15437 ("r-seurat" ,r-seurat)))
15438 (home-page "https://github.com/constantAmateur/SoupX")
15439 (synopsis "Single cell mRNA Soup eXterminator")
15441 "This package provides a package for quantifying, profiling and
15442 removing cell free mRNA contamination (the \"soup\") from droplet based single
15443 cell RNA-seq experiments.")
15444 (license license:gpl2))))
15446 (define-public r-assertr
15453 (uri (cran-uri "assertr" version))
15456 "0g4ii6vhp0155a29ljhs64a09x0nzy5ybvwwchhk4mkcgsvnvfkj"))))
15457 (build-system r-build-system)
15459 `(("r-dplyr" ,r-dplyr)
15461 ("r-rlang" ,r-rlang)))
15463 `(("r-knitr" ,r-knitr))) ; needed for vignette
15464 (home-page "https://github.com/ropensci/assertr")
15465 (synopsis "Assertive programming for R analysis pipelines")
15467 "This package provides functionality to assert conditions that have to be
15468 met so that errors in data used in analysis pipelines can fail quickly. It is
15469 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
15471 (license license:expat)))
15473 (define-public r-parameters
15475 (name "r-parameters")
15480 (uri (cran-uri "parameters" version))
15483 "1mgggb3l67wgjiccq4y84wbs2dw9qk01akd553yiwbwky9rpawgh"))))
15484 (properties `((upstream-name . "parameters")))
15485 (build-system r-build-system)
15487 `(("r-bayestestr" ,r-bayestestr)
15488 ("r-insight" ,r-insight)))
15489 (home-page "https://cran.r-project.org/web/packages/parameters")
15490 (synopsis "Processing of model parameters")
15492 "This package provides utilities for processing the parameters of various
15493 statistical models. Beyond computing p values, CIs, and other indices for a
15494 wide variety of models, this package implements features like standardization
15495 or bootstrapping of parameters and models, feature reduction (feature
15496 extraction and variable selection) as well as conversion between indices of
15498 (license license:gpl3)))
15500 (define-public r-rgdal
15507 (uri (cran-uri "rgdal" version))
15509 (base32 "0lj1dax56dxxsj1hindxcvgz169p9dxd0y4wjypbyr01nja8rz4d"))))
15510 (properties `((upstream-name . "rgdal")))
15511 (build-system r-build-system)
15519 `(("pkg-config" ,pkg-config)))
15520 (home-page "http://rgdal.r-forge.r-project.org")
15521 (synopsis "Bindings for the Geospatial Data Abstraction Library")
15523 "This package provides bindings to the Geospatial Data Abstraction
15524 Library (GDAL) and access to projection/transformation operations from the
15526 (license license:gpl2+)))
15528 (define-public r-insol
15535 (uri (cran-uri "insol" version))
15538 "14ikz05375pjn9hby7kwkhcnykjilbnkdy5i8lsl7c5qdbhmqcm5"))))
15539 (properties `((upstream-name . "insol")))
15540 (build-system r-build-system)
15542 `(("r-raster" ,r-raster)
15543 ("r-rgdal" ,r-rgdal)))
15545 `(("gfortran" ,gfortran)))
15546 (home-page "https://meteoexploration.com/R/insol/index.html")
15547 (synopsis "Tools for calculating solar radiation")
15549 "This package provides functions to compute insolation on tilted
15550 surfaces, computes atmospheric transmittance and related parameters such as:
15551 Earth radius vector, declination, sunset and sunrise, daylength, equation of
15552 time, vector in the direction of the sun, vector normal to surface, and some
15553 atmospheric physics.")
15554 (license license:gpl2+)))
15556 (define-public r-lifecycle
15558 (name "r-lifecycle")
15563 (uri (cran-uri "lifecycle" version))
15566 "11rk7hkw63rfrf4aqmb4xrb88kg95xh8hajpjvjfwjym2v02h74n"))))
15567 (properties `((upstream-name . "lifecycle")))
15568 (build-system r-build-system)
15570 `(("r-glue" ,r-glue)
15571 ("r-rlang" ,r-rlang)))
15572 (home-page "https://github.com/r-lib/lifecycle")
15573 (synopsis "Manage the life cycle of your package functions")
15575 "Manage the life cycle of your exported functions with shared
15576 conventions, documentation badges, and non-invasive deprecation warnings. The
15577 lifecycle package defines four development stages (experimental, maturing,
15578 stable, and questioning) and three deprecation stages (soft-deprecated,
15579 deprecated, and defunct). It makes it easy to insert badges corresponding to
15580 these stages in your documentation. Usage of deprecated functions are
15581 signalled with increasing levels of non-invasive verbosity.")
15582 (license license:gpl3)))
15584 (define-public r-assertable
15586 (name "r-assertable")
15591 (uri (cran-uri "assertable" version))
15594 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
15595 (build-system r-build-system)
15597 `(("r-data-table" ,r-data-table)))
15598 (home-page "https://cran.r-project.org/web/packages/assertable/")
15599 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
15600 (description "This package provides simple, flexible assertions on
15601 data.frame or data.table objects with verbose output for vetting. While other
15602 assertion packages apply towards more general use-cases, @code{assertable} is
15603 tailored towards tabular data. It includes functions to check variable names
15604 and values, whether the dataset contains all combinations of a given set of
15605 unique identifiers, and whether it is a certain length. In addition,
15606 @code{assertable} includes utility functions to check the existence of target
15607 files and to efficiently import multiple tabular data files into one
15609 (license license:gpl3)))