1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
4 ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
5 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
6 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
7 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
8 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
9 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
10 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
11 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
12 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
13 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
14 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
15 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
16 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
17 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; This file is part of GNU Guix.
21 ;;; GNU Guix is free software; you can redistribute it and/or modify it
22 ;;; under the terms of the GNU General Public License as published by
23 ;;; the Free Software Foundation; either version 3 of the License, or (at
24 ;;; your option) any later version.
26 ;;; GNU Guix is distributed in the hope that it will be useful, but
27 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
28 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
29 ;;; GNU General Public License for more details.
31 ;;; You should have received a copy of the GNU General Public License
32 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
34 (define-module (gnu packages cran)
35 #:use-module ((guix licenses) #:prefix license:)
36 #:use-module (guix packages)
37 #:use-module (guix download)
38 #:use-module (guix git-download)
39 #:use-module (guix utils)
40 #:use-module (guix build-system r)
41 #:use-module (gnu packages algebra)
42 #:use-module (gnu packages base)
43 #:use-module (gnu packages bioinformatics)
44 #:use-module (gnu packages c)
45 #:use-module (gnu packages compression)
46 #:use-module (gnu packages curl)
47 #:use-module (gnu packages databases)
48 #:use-module (gnu packages fontutils)
49 #:use-module (gnu packages gcc)
50 #:use-module (gnu packages geo)
51 #:use-module (gnu packages ghostscript)
52 #:use-module (gnu packages gl)
53 #:use-module (gnu packages gnome)
54 #:use-module (gnu packages graph)
55 #:use-module (gnu packages gtk)
56 #:use-module (gnu packages haskell)
57 #:use-module (gnu packages icu4c)
58 #:use-module (gnu packages image)
59 #:use-module (gnu packages imagemagick)
60 #:use-module (gnu packages java)
61 #:use-module (gnu packages javascript)
62 #:use-module (gnu packages lisp)
63 #:use-module (gnu packages machine-learning)
64 #:use-module (gnu packages maths)
65 #:use-module (gnu packages mpi)
66 #:use-module (gnu packages multiprecision)
67 #:use-module (gnu packages networking)
68 #:use-module (gnu packages pcre)
69 #:use-module (gnu packages perl)
70 #:use-module (gnu packages pkg-config)
71 #:use-module (gnu packages python)
72 #:use-module (gnu packages python-xyz)
73 #:use-module (gnu packages statistics)
74 #:use-module (gnu packages tls)
75 #:use-module (gnu packages web)
76 #:use-module (gnu packages xorg))
78 (define-public r-clipr
85 (uri (cran-uri "clipr" version))
88 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
89 (build-system r-build-system)
90 (home-page "https://github.com/mdlincoln/clipr")
91 (synopsis "Read and write from the system clipboard")
93 "This package provides simple utility functions to read from and write to
94 the system clipboards.")
95 (license license:gpl3)))
97 (define-public r-ellipsis
104 (uri (cran-uri "ellipsis" version))
107 "0hx9l043433bwm1np9sypph77c7y9dddpz0wrhbkcv01x32jhr8f"))))
108 (build-system r-build-system)
110 `(("r-rlang" ,r-rlang)))
111 (home-page "https://github.com/hadley/ellipsis")
112 (synopsis "Tools for working with additional arguments")
114 "In S3 generics, it's useful to take @code{...} so that methods can have
115 additional arguments. But this flexibility comes at a cost: misspelled
116 arguments will be silently ignored. The @code{ellipsis} package is an
117 experiment that allows a generic to warn if any arguments passed in @code{...}
119 (license license:gpl3)))
128 (uri (cran-uri "grr" version))
131 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
132 (build-system r-build-system)
133 (home-page "https://cran.r-project.org/web/packages/grr")
134 (synopsis "Alternative implementations of base R functions")
136 "This package provides alternative implementations of some base R
137 functions, including @code{sort}, @code{order}, and @code{match}. The
138 functions are simplified but can be faster or have other advantages.")
139 (license license:gpl3)))
141 (define-public r-matrix-utils
143 (name "r-matrix-utils")
148 (uri (cran-uri "Matrix.utils" version))
151 "1x64r4aj3gy1dzjjysyrk1j9jq3qsnyrqws8i6bs7q8pf6gvr7va"))))
152 (properties `((upstream-name . "Matrix.utils")))
153 (build-system r-build-system)
156 ("r-matrix" ,r-matrix)))
157 (home-page "https://github.com/cvarrichio/Matrix.utils")
159 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
161 "This package implements data manipulation methods such as @code{cast},
162 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
164 (license license:gpl3)))
173 (uri (cran-uri "sys" version))
176 "1k5vk5q9wa5sin0n226i05nymg469s24f6lx64yyhb7yc624j698"))))
177 (build-system r-build-system)
178 (home-page "https://github.com/jeroen/sys")
179 (synopsis "Powerful and reliable tools for running system commands in R")
181 "This package provides drop-in replacements for the base @code{system2()}
182 function with fine control and consistent behavior across platforms. It
183 supports clean interruption, timeout, background tasks, and streaming STDIN /
184 STDOUT / STDERR over binary or text connections. The package also provides
185 functions for evaluating expressions inside a temporary fork. Such
186 evaluations have no side effects on the main R process, and support reliable
187 interrupts and timeouts. This provides the basis for a sandboxing
189 (license license:expat)))
191 (define-public r-askpass
198 (uri (cran-uri "askpass" version))
201 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
202 (build-system r-build-system)
203 (propagated-inputs `(("r-sys" ,r-sys)))
204 (home-page "https://github.com/jeroen/askpass")
205 (synopsis "Safe password entry for R")
207 "This package provides cross-platform utilities for prompting the user
208 for credentials or a passphrase, for example to authenticate with a server or
209 read a protected key.")
210 (license license:expat)))
212 (define-public r-vegan
219 (uri (cran-uri "vegan" version))
222 "0wb90ng02gi13854bjq0b8a2vrknyhb0s0l1v3z38c4zy9k54sw7"))))
223 (build-system r-build-system)
225 `(("gfortran" ,gfortran)))
227 `(("r-cluster" ,r-cluster)
228 ("r-knitr" ,r-knitr) ; needed for vignettes
229 ("r-lattice" ,r-lattice)
232 ("r-permute" ,r-permute)))
233 (home-page "https://cran.r-project.org/web/packages/vegan")
234 (synopsis "Functions for community ecology")
236 "The vegan package provides tools for descriptive community ecology. It
237 has most basic functions of diversity analysis, community ordination and
238 dissimilarity analysis. Most of its multivariate tools can be used for other
239 data types as well.")
240 (license license:gpl2+)))
242 (define-public r-tidyverse
249 (uri (cran-uri "tidyverse" version))
252 "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"))))
253 (build-system r-build-system)
255 `(("r-broom" ,r-broom)
257 ("r-crayon" ,r-crayon)
258 ("r-dbplyr" ,r-dbplyr)
260 ("r-forcats" ,r-forcats)
261 ("r-ggplot2" ,r-ggplot2)
265 ("r-jsonlite" ,r-jsonlite)
266 ("r-lubridate" ,r-lubridate)
267 ("r-magrittr" ,r-magrittr)
268 ("r-modelr" ,r-modelr)
271 ("r-readxl" ,r-readxl)
272 ("r-reprex" ,r-reprex)
274 ("r-rstudioapi" ,r-rstudioapi)
276 ("r-stringr" ,r-stringr)
277 ("r-tibble" ,r-tibble)
280 (home-page "https://tidyverse.tidyverse.org")
281 (synopsis "Install and load packages from the \"Tidyverse\"")
283 "The @code{tidyverse} is a set of packages that work in harmony because
284 they share common data representations and API design. This package is
285 designed to make it easy to install and load multiple tidyverse packages in a
287 (license license:gpl3)))
289 (define-public r-rvest
296 (uri (cran-uri "rvest" version))
299 "0ji5lk8g1gbv4d9c4jg1fg6rgsqrrwkm05j1id7drdw9kqdifgj1"))))
300 (build-system r-build-system)
303 ("r-magrittr" ,r-magrittr)
304 ("r-selectr" ,r-selectr)
306 (home-page "https://github.com/hadley/rvest")
307 (synopsis "Simple web scraping for R")
309 "@code{r-rvest} helps you scrape information from web pages. It is
310 designed to work with @code{magrittr} to make it easy to express common web
311 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
312 (license license:gpl3)))
314 (define-public r-selectr
321 (uri (cran-uri "selectr" version))
324 "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b"))))
325 (build-system r-build-system)
327 `(("r-stringr" ,r-stringr)
329 (home-page "https://sjp.co.nz/projects/selectr/")
330 (synopsis "Translate CSS selectors to XPath expressions")
332 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
333 expression. This allows you to use CSS selectors when working with the XML
334 package as it can only evaluate XPath expressions. Also provided are
335 convenience functions useful for using CSS selectors on XML nodes. This
336 package is a port of the Python package @code{cssselect}.")
337 (license license:bsd-3)))
339 (define-public r-reprex
346 (uri (cran-uri "reprex" version))
349 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
350 (build-system r-build-system)
352 `(("r-callr" ,r-callr)
356 ("r-rmarkdown" ,r-rmarkdown)
357 ("r-whisker" ,r-whisker)
358 ("r-withr" ,r-withr)))
359 (home-page "https://github.com/tidyverse/reprex")
360 (synopsis "Prepare reproducible R code examples for sharing")
362 "This package provides a convenience wrapper that uses the
363 @code{rmarkdown} package to render small snippets of code to target formats
364 that include both code and output. The goal is to encourage the sharing of
365 small, reproducible, and runnable examples on code-oriented websites or email.
366 @code{reprex} also extracts clean, runnable R code from various common formats,
367 such as copy/paste from an R session.")
368 (license license:expat)))
370 (define-public r-callr
377 (uri (cran-uri "callr" version))
380 "0rvrlg86fxr5nadvqa0dr1iifqjs4d1rc32v76m3ccvx6m3xlq5z"))))
381 (build-system r-build-system)
384 ("r-processx" ,r-processx)))
385 (home-page "https://github.com/r-lib/callr#readme")
386 (synopsis "Call R from R")
388 "It is sometimes useful to perform a computation in a separate R process,
389 without affecting the current R process at all. This package does exactly
391 (license license:expat)))
393 (define-public r-readxl
400 (uri (cran-uri "readxl" version))
403 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
404 (build-system r-build-system)
406 `(("r-cellranger" ,r-cellranger)
407 ("r-progress" ,r-progress)
409 ("r-tibble" ,r-tibble)))
410 (home-page "https://readxl.tidyverse.org")
411 (synopsis "Read Excel files")
413 "This package lets you import Excel files into R. It supports
414 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
415 the embedded @code{RapidXML} C++ library.")
416 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
417 ;; 'rapidxml' which is Boost.
418 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
420 (define-public r-modelr
427 (uri (cran-uri "modelr" version))
430 "0nnfhlzz75ihs8azy963cc4cwg1kx81rybk4z3wm98bbghwfxfs5"))))
431 (build-system r-build-system)
433 `(("r-broom" ,r-broom)
435 ("r-magrittr" ,r-magrittr)
438 ("r-tibble" ,r-tibble)
439 ("r-tidyr" ,r-tidyr)))
440 (home-page "https://github.com/tidyverse/modelr")
441 (synopsis "Helper functions for modelling in pipelines")
443 "Functions for modelling that help you seamlessly integrate modelling
444 into a pipeline of data manipulation and visualisation.")
445 (license license:gpl3)))
447 (define-public r-httpuv
453 (uri (cran-uri "httpuv" version))
456 "042piypg4c8sqrlcdl3dwajkafkbglsky3x7d0jpjv8s5wxnpfxm"))))
457 (build-system r-build-system)
461 ("r-promises" ,r-promises)
464 (home-page "https://github.com/rstudio/httpuv")
465 (synopsis "HTTP and WebSocket server library for R")
467 "The httpuv package provides low-level socket and protocol support for
468 handling HTTP and WebSocket requests directly from within R. It is primarily
469 intended as a building block for other packages, rather than making it
470 particularly easy to create complete web applications using httpuv alone.")
471 ;; This package includes third-party code that was originally released
472 ;; under various non-copyleft licenses. Full licensing information can be
473 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
474 (license license:gpl3+)))
476 (define-public r-jsonlite
482 (uri (cran-uri "jsonlite" version))
485 "0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
486 (build-system r-build-system)
487 (home-page "http://arxiv.org/abs/1403.2805")
488 (synopsis "Robust, high performance JSON parser and generator for R")
490 "The jsonlite package provides a fast JSON parser and generator optimized
491 for statistical data and the web. It offers flexible, robust, high
492 performance tools for working with JSON in R and is particularly powerful for
493 building pipelines and interacting with a web API. In addition to converting
494 JSON data from/to R objects, jsonlite contains functions to stream, validate,
495 and prettify JSON data. The unit tests included with the package verify that
496 all edge cases are encoded and decoded consistently for use with dynamic data
497 in systems and applications.")
498 (license license:expat)))
500 (define-public r-servr
506 (uri (cran-uri "servr" version))
509 "199k9aghwk9rf1rm8pjg60xacqww25cza259h5dfj1ixil0m6dxi"))))
510 (build-system r-build-system)
512 `(("r-httpuv" ,r-httpuv)
513 ("r-jsonlite" ,r-jsonlite)
516 (home-page "https://github.com/yihui/servr")
517 (synopsis "Simple HTTP server to serve static files or dynamic documents")
519 "Servr provides an HTTP server in R to serve static files, or dynamic
520 documents that can be converted to HTML files (e.g., R Markdown) under a given
522 (license license:expat)))
524 (define-public r-htmltools
530 (uri (cran-uri "htmltools" version))
533 "18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4"))))
534 (build-system r-build-system)
537 (modify-phases %standard-phases
538 ;; See https://github.com/rstudio/htmltools/pull/68
539 ;; The resource files are in the store and have mode 444. After
540 ;; copying the files R fails to remove them again because it doesn't
541 ;; have write access to them.
542 (add-after 'unpack 'copy-files-without-mode
544 (substitute* "R/html_dependency.R"
545 (("file.copy\\(from, to, " prefix)
546 (string-append prefix
547 "copy.mode = FALSE, ")))
550 `(("r-digest" ,r-digest)
552 (home-page "https://cran.r-project.org/web/packages/htmltools")
553 (synopsis "R tools for HTML")
555 "This package provides tools for HTML generation and output in R.")
556 (license license:expat)))
558 (define-public r-htmlwidgets
560 (name "r-htmlwidgets")
564 (uri (cran-uri "htmlwidgets" version))
567 "04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i"))))
568 (build-system r-build-system)
570 `(("r-htmltools" ,r-htmltools)
571 ("r-jsonlite" ,r-jsonlite)
573 (home-page "https://github.com/ramnathv/htmlwidgets")
574 (synopsis "HTML Widgets for R")
576 "HTML widgets is a framework for creating HTML widgets that render in
577 various contexts including the R console, R Markdown documents, and Shiny web
579 (license license:expat)))
581 (define-public r-htmltable
588 (uri (cran-uri "htmlTable" version))
591 "1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8"))))
592 (properties `((upstream-name . "htmlTable")))
593 (build-system r-build-system)
595 `(("r-checkmate" ,r-checkmate)
596 ("r-htmltools" ,r-htmltools)
597 ("r-htmlwidgets" ,r-htmlwidgets)
599 ("r-magrittr" ,r-magrittr)
600 ("r-rstudioapi" ,r-rstudioapi)
601 ("r-stringr" ,r-stringr)))
602 (home-page "http://gforge.se/packages/")
603 (synopsis "Advanced tables for Markdown/HTML")
605 "This package provides functions to build tables with advanced layout
606 elements such as row spanners, column spanners, table spanners, zebra
607 striping, and more. While allowing advanced layout, the underlying
608 CSS-structure is simple in order to maximize compatibility with word
609 processors such as LibreOffice. The package also contains a few text
610 formatting functions that help outputting text compatible with HTML or
612 (license license:gpl3+)))
614 (define-public r-curl
620 (uri (cran-uri "curl" version))
623 "0wb1j87fa2nd4a9x1w2nmc453nzvx6qiq8dviwc4jr36hsf9ra89"))))
624 (build-system r-build-system)
627 (modify-phases %standard-phases
628 ;; The environment variable CURL_CA_BUNDLE is only respected when
629 ;; running Windows, so we disable the platform checks.
630 ;; This can be removed once the libcurl has been patched.
631 (add-after 'unpack 'allow-CURL_CA_BUNDLE
633 (substitute* "R/onload.R"
634 (("if \\(!grepl\\(\"mingw\".*")
636 (substitute* "src/handle.c"
637 (("#ifdef _WIN32") "#if 1"))
643 `(("pkg-config" ,pkg-config)))
644 (home-page "https://github.com/jeroenooms/curl")
645 (synopsis "HTTP client for R")
647 "The @code{curl()} and @code{curl_download()} functions provide highly
648 configurable drop-in replacements for base @code{url()} and
649 @code{download.file()} with better performance, support for encryption, gzip
650 compression, authentication, and other @code{libcurl} goodies. The core of
651 the package implements a framework for performing fully customized requests
652 where data can be processed either in memory, on disk, or streaming via the
653 callback or connection interfaces.")
654 (license license:expat)))
656 (define-public r-hwriter
663 (uri (cran-uri "hwriter" version))
666 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
667 (build-system r-build-system)
668 (home-page "https://cran.r-project.org/web/packages/hwriter")
669 (synopsis "Output R objects in HTML format")
671 "This package provides easy-to-use and versatile functions to output R
672 objects in HTML format.")
673 (license license:lgpl2.1+)))
675 (define-public r-rjson
682 (uri (cran-uri "rjson" version))
685 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
686 (build-system r-build-system)
687 (home-page "https://cran.r-project.org/web/packages/rjson")
688 (synopsis "JSON library for R")
690 "This package provides functions to convert R objects into JSON objects
692 (license license:gpl2+)))
694 (define-public r-shiny
702 (url "https://github.com/rstudio/shiny.git")
703 (commit (string-append "v" version))))
704 (file-name (git-file-name name version))
707 "1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
708 (build-system r-build-system)
710 `(#:modules ((guix build r-build-system)
711 (guix build minify-build-system)
714 #:imported-modules (,@%r-build-system-modules
715 (guix build minify-build-system))
717 (modify-phases (@ (guix build r-build-system) %standard-phases)
718 (add-after 'unpack 'replace-bundled-minified-JavaScript
719 (lambda* (#:key inputs #:allow-other-keys)
720 (let ((replace-file (lambda (old new)
721 (format #t "replacing ~a with ~a\n" old new)
724 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
725 ;; contain just data. They are not minified code, so we don't
727 (with-directory-excursion "inst/www/shared"
728 (replace-file "bootstrap/shim/respond.min.js"
729 (string-append (assoc-ref inputs "js-respond")
730 "/share/javascript/respond.min.js"))
731 (replace-file "bootstrap/shim/html5shiv.min.js"
732 (string-append (assoc-ref inputs "js-html5shiv")
733 "/share/javascript/html5shiv.min.js"))
734 (replace-file "json2-min.js"
735 (string-append (assoc-ref inputs "js-json2")
736 "/share/javascript/json2.min.js"))
737 (replace-file "strftime/strftime-min.js"
738 (string-append (assoc-ref inputs "js-strftime")
739 "/share/javascript/strftime.min.js"))
740 (replace-file "highlight/highlight.pack.js"
741 (string-append (assoc-ref inputs "js-highlight")
742 "/share/javascript/highlight.min.js"))
743 (replace-file "datatables/js/jquery.dataTables.min.js"
744 (string-append (assoc-ref inputs "js-datatables")
745 "/share/javascript/jquery.dataTables.min.js"))
746 (replace-file "selectize/js/selectize.min.js"
747 (string-append (assoc-ref inputs "js-selectize")
748 "/share/javascript/selectize.min.js"))
749 (replace-file "selectize/js/es5-shim.min.js"
750 (string-append (assoc-ref inputs "js-es5-shim")
751 "/share/javascript/es5-shim.min.js"))
752 (for-each (match-lambda
755 (minify source #:target target)))
756 '(("jqueryui/jquery-ui.js" .
757 "jqueryui/jquery-ui.min.js")
758 ("datepicker/js/bootstrap-datepicker.js" .
759 "datepicker/js/bootstrap-datepicker.min.js")
760 ("ionrangeslider/js/ion.rangeSlider.js" .
761 "ionrangeslider/js/ion.rangeSlider.min.js")
762 ("bootstrap/js/bootstrap.js" .
763 "bootstrap/js/bootstrap.min.js")
770 `(("r-crayon" ,r-crayon)
771 ("r-httpuv" ,r-httpuv)
773 ("r-jsonlite" ,r-jsonlite)
774 ("r-xtable" ,r-xtable)
775 ("r-digest" ,r-digest)
776 ("r-htmltools" ,r-htmltools)
778 ("r-sourcetools" ,r-sourcetools)))
780 `(("js-datatables" ,js-datatables)
781 ("js-html5shiv" ,js-html5shiv)
782 ("js-json2" ,js-json2)
783 ("js-respond" ,js-respond)
784 ("js-selectize" ,js-selectize)
785 ("js-strftime" ,js-strftime)
786 ("js-highlight" ,js-highlight)
787 ("js-es5-shim" ,js-es5-shim)))
789 `(("uglify-js" ,uglify-js)))
790 (home-page "http://shiny.rstudio.com")
791 (synopsis "Easy interactive web applications with R")
793 "Makes it incredibly easy to build interactive web applications
794 with R. Automatic \"reactive\" binding between inputs and outputs and
795 extensive prebuilt widgets make it possible to build beautiful,
796 responsive, and powerful applications with minimal effort.")
797 (license license:artistic2.0)))
799 (define-public r-shinydashboard
801 (name "r-shinydashboard")
805 (uri (cran-uri "shinydashboard" version))
808 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
809 (build-system r-build-system)
810 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
811 ;; Regenerate it from the included sources.
813 `(#:modules ((guix build utils)
814 (guix build r-build-system)
817 (modify-phases %standard-phases
818 (add-after 'unpack 'generate-minified-javascript
820 (with-directory-excursion "inst/AdminLTE"
821 (delete-file "app.min.js")
822 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
823 (call-with-output-file "app.min.js"
825 (dump-port minified port))))))))))
827 `(("r-htmltools" ,r-htmltools)
828 ("r-promises" ,r-promises)
829 ("r-shiny" ,r-shiny)))
831 `(("uglify-js" ,uglify-js)))
832 (home-page "http://rstudio.github.io/shinydashboard/")
833 (synopsis "Create dashboards with shiny")
834 (description "This package provides an extension to the Shiny web
835 application framework for R, making it easy to create attractive dashboards.")
836 ;; This package includes software that was released under the Expat
837 ;; license, but the whole package is released under GPL version 2 or
839 (license license:gpl2+)))
841 (define-public r-shinyfiles
843 (name "r-shinyfiles")
848 (uri (cran-uri "shinyFiles" version))
851 "01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i"))))
852 (properties `((upstream-name . "shinyFiles")))
853 (build-system r-build-system)
856 ("r-htmltools" ,r-htmltools)
857 ("r-jsonlite" ,r-jsonlite)
859 ("r-tibble" ,r-tibble)))
860 (home-page "https://github.com/thomasp85/shinyFiles")
861 (synopsis "Server-side file system viewer for Shiny")
863 "This package provides functionality for client-side navigation of the
864 server side file system in shiny apps. In case the app is running locally
865 this gives the user direct access to the file system without the need to
866 \"download\" files to a temporary location. Both file and folder selection as
867 well as file saving is available.")
868 (license license:gpl2+)))
870 ;; The package sources include minified variants of d3.js and non-minified
871 ;; source code of d3-jetpack.
879 (uri (cran-uri "d3r" version))
882 "0vcmiyhd000xyl28k6rm7ba50x5sz5b2cpllxnq36q13qhdnqw6k"))))
883 (build-system r-build-system)
885 `(#:modules ((guix build utils)
886 (guix build r-build-system)
890 (modify-phases %standard-phases
891 (add-after 'unpack 'process-javascript
892 (lambda* (#:key inputs #:allow-other-keys)
893 (with-directory-excursion "inst/www/d3/"
897 `((,(assoc-ref inputs "d3.v3.js")
899 (,(assoc-ref inputs "d3.v4.js")
901 (,(assoc-ref inputs "d3.v5.js")
902 "v5/dist/d3.min.js"))))
903 (lambda (sources targets)
904 (for-each (lambda (source target)
905 (format #t "Processing ~a --> ~a~%"
908 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
909 (call-with-output-file target
911 (dump-port minified port)))))
915 `(("r-dplyr" ,r-dplyr)
916 ("r-htmltools" ,r-htmltools)
917 ("r-tidyr" ,r-tidyr)))
919 `(("uglify-js" ,uglify-js)
923 (uri "https://d3js.org/d3.v3.js")
926 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
930 (uri "https://d3js.org/d3.v4.js")
933 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
937 (uri "https://d3js.org/d3.v5.js")
940 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
941 (home-page "https://github.com/timelyportfolio/d3r")
942 (synopsis "d3.js utilities for R")
944 "This package provides a suite of functions to help ease the use of the
945 d3.js visualization library in R. These helpers include
946 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
947 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
948 R objects into the JSON format that the d3.js library expects.")
949 (license license:bsd-3)))
951 ;; We use the latest commit here because the last release was in 2016 while
952 ;; the latest commit was in 2018.
953 (define-public r-sankeyd3
954 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
958 (version (git-version "0.3.2" revision commit))
963 (url "https://github.com/fbreitwieser/sankeyD3.git")
965 (file-name (git-file-name name version))
968 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
969 (build-system r-build-system)
972 ("r-htmlwidgets" ,r-htmlwidgets)
974 ("r-magrittr" ,r-magrittr)))
975 (home-page "https://github.com/fbreitwieser/sankeyD3")
976 (synopsis "Sankey network graphs from R")
978 "This package provides an R library to generate Sankey network graphs
979 in R and Shiny via the D3 visualization library.")
980 ;; The R code is licensed under GPLv3+. It includes the non-minified
981 ;; JavaScript source code of d3-sankey, which is released under the
982 ;; 3-clause BSD license.
983 (license (list license:gpl3+ license:bsd-3)))))
985 (define-public r-crosstalk
992 (uri (cran-uri "crosstalk" version))
995 "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
996 (build-system r-build-system)
998 `(("r-ggplot2" ,r-ggplot2)
999 ("r-htmltools" ,r-htmltools)
1000 ("r-jsonlite" ,r-jsonlite)
1001 ("r-lazyeval" ,r-lazyeval)
1003 ("r-shiny" ,r-shiny)))
1004 (home-page "https://rstudio.github.io/crosstalk/")
1005 (synopsis "Inter-widget interactivity for HTML widgets")
1007 "This package provides building blocks for allowing HTML widgets to
1008 communicate with each other, with Shiny or without (i.e. static @code{.html}
1009 files). It currently supports linked brushing and filtering.")
1010 (license license:expat)))
1012 (define-public r-rook
1019 (uri (cran-uri "Rook" version))
1022 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1023 (properties `((upstream-name . "Rook")))
1024 (build-system r-build-system)
1025 (propagated-inputs `(("r-brew" ,r-brew)))
1026 (home-page "https://cran.r-project.org/web/packages/Rook")
1027 (synopsis "Web server interface for R")
1029 "This package contains the Rook specification and convenience software
1030 for building and running Rook applications. A Rook application is an R
1031 reference class object that implements a @code{call} method or an R closure
1032 that takes exactly one argument, an environment, and returns a list with three
1033 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1034 (license license:gpl2)))
1036 (define-public r-miniui
1043 (uri (cran-uri "miniUI" version))
1046 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1047 (properties `((upstream-name . "miniUI")))
1048 (build-system r-build-system)
1050 `(("r-htmltools" ,r-htmltools)
1051 ("r-shiny" ,r-shiny)))
1052 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1053 (synopsis "Shiny UI widgets for small screens")
1055 "This package provides UI widget and layout functions for writing Shiny apps that
1056 work well on small screens.")
1057 (license license:gpl3)))
1059 (define-public r-feather
1066 (uri (cran-uri "feather" version))
1069 "0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa"))))
1070 (build-system r-build-system)
1074 ("r-tibble" ,r-tibble)))
1075 (home-page "https://github.com/wesm/feather")
1076 (synopsis "R Bindings to the Feather API")
1077 (description "Read and write feather files, a lightweight binary columnar
1078 data store designed for maximum speed.")
1079 (license license:asl2.0)))
1081 (define-public r-maps
1088 (uri (cran-uri "maps" version))
1091 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1092 (build-system r-build-system)
1093 (home-page "https://cran.r-project.org/web/packages/maps")
1094 (synopsis "Draw geographical maps")
1095 (description "This package provides an R module for display of maps.
1096 Projection code and larger maps are in separate packages (@code{mapproj} and
1098 (license license:gpl2)))
1100 (define-public r-mapproj
1107 (uri (cran-uri "mapproj" version))
1110 "1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
1111 (build-system r-build-system)
1112 (propagated-inputs `(("r-maps" ,r-maps)))
1113 (home-page "https://cran.r-project.org/web/packages/mapproj")
1114 (synopsis "Map projection in R")
1115 (description "This package converts latitude/longitude into projected
1117 (license (list license:gpl2 ; The R interface
1118 (license:non-copyleft ; The C code
1119 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1120 "Lucent Public License Version 1.02")))))
1122 (define-public r-rgooglemaps
1124 (name "r-rgooglemaps")
1129 (uri (cran-uri "RgoogleMaps" version))
1132 "06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
1133 (properties `((upstream-name . "RgoogleMaps")))
1134 (build-system r-build-system)
1135 (propagated-inputs `(("r-png" ,r-png)))
1136 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1137 (synopsis "Use Google Maps in R")
1138 (description "This package serves two purposes:
1140 @item Provide a comfortable R interface to query the Google server for static
1142 @item Use the map as a background image to overlay plots within R. This
1143 requires proper coordinate scaling.
1145 (license license:gpl2+)))
1147 (define-public r-geosphere
1149 (name "r-geosphere")
1154 (uri (cran-uri "geosphere" version))
1157 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1158 (build-system r-build-system)
1159 (propagated-inputs `(("r-sp" ,r-sp)))
1160 (home-page "https://cran.r-project.org/web/packages/geosphere")
1161 (synopsis "Spherical trigonometry")
1162 (description "This package computes spherical trigonometry for geographic
1163 applications. That is, compute distances and related measures for angular
1164 (longitude/latitude) locations.")
1165 (license license:gpl3+)))
1167 (define-public r-ggmap
1174 (uri (cran-uri "ggmap" version))
1177 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1178 (build-system r-build-system)
1180 `(("r-bitops" ,r-bitops)
1181 ("r-digest" ,r-digest)
1182 ("r-dplyr" ,r-dplyr)
1183 ("r-ggplot2" ,r-ggplot2)
1187 ("r-magrittr" ,r-magrittr)
1190 ("r-purrr" ,r-purrr)
1191 ("r-rgooglemaps" ,r-rgooglemaps)
1192 ("r-rjson" ,r-rjson)
1193 ("r-scales" ,r-scales)
1194 ("r-stringr" ,r-stringr)
1195 ("r-tibble" ,r-tibble)
1196 ("r-tidyr" ,r-tidyr)))
1197 (home-page "https://github.com/dkahle/ggmap")
1198 (synopsis "Spatial visualization with ggplot2")
1199 (description "This package provides a collection of functions to visualize
1200 spatial data and models on top of static maps from various online sources (e.g
1201 Google Maps and Stamen Maps). It includes tools common to those tasks,
1202 including functions for geolocation and routing.")
1203 (license license:gpl2)))
1205 (define-public r-haven
1212 (uri (cran-uri "haven" version))
1215 "12h64r2v2451igyl7v4w2kg0hzw9rnanph0m7smffq29ybkv9g4h"))))
1216 (build-system r-build-system)
1220 `(("r-forcats" ,r-forcats)
1223 ("r-readr" ,r-readr)
1224 ("r-tibble" ,r-tibble)))
1225 (home-page "https://haven.tidyverse.org")
1226 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1228 "This package lets you mport foreign statistical formats into R via the
1229 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1230 (license license:expat)))
1232 (define-public r-amap
1238 (uri (cran-uri "amap" version))
1241 "1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
1242 (build-system r-build-system)
1244 `(("gfortran" ,gfortran)))
1245 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1246 (synopsis "Another multidimensional analysis package")
1247 (description "This package provides tools for clustering and principal
1248 component analysis (with robust methods, and parallelized functions).")
1249 (license license:gpl2+)))
1251 (define-public r-ape
1258 (uri (cran-uri "ape" version))
1261 "08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
1262 (build-system r-build-system)
1264 `(("r-lattice" ,r-lattice)
1266 ("r-rcpp" ,r-rcpp)))
1267 (home-page "http://ape-package.ird.fr/")
1268 (synopsis "Analyses of phylogenetics and evolution")
1270 "This package provides functions for reading, writing, plotting, and
1271 manipulating phylogenetic trees, analyses of comparative data in a
1272 phylogenetic framework, ancestral character analyses, analyses of
1273 diversification and macroevolution, computing distances from DNA sequences,
1274 and several other tools.")
1275 (license license:gpl2+)))
1277 (define-public r-abbyyr
1284 (uri (cran-uri "abbyyR" version))
1287 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1288 (properties `((upstream-name . "abbyyR")))
1289 (build-system r-build-system)
1291 `(("r-curl" ,r-curl)
1294 ("r-progress" ,r-progress)
1295 ("r-readr" ,r-readr)
1297 (home-page "https://github.com/soodoku/abbyyR")
1298 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1300 "This package provides tools to get text from images of text using Abbyy
1301 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1302 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1303 passports and get the results in a variety of formats including plain text and
1304 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1305 (license license:expat)))
1307 (define-public r-colorspace
1309 (name "r-colorspace")
1314 (uri (cran-uri "colorspace" version))
1316 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1317 (build-system r-build-system)
1318 (home-page "https://cran.r-project.org/web/packages/colorspace")
1319 (synopsis "Color space manipulation")
1321 "This package carries out a mapping between assorted color spaces
1322 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1323 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1324 colors are provided.")
1325 (license license:bsd-3)))
1327 (define-public r-glue
1334 (uri (cran-uri "glue" version))
1337 "1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
1338 (build-system r-build-system)
1339 (home-page "https://github.com/tidyverse/glue")
1340 (synopsis "Interpreted string literals")
1342 "This package provides an implementation of interpreted string literals,
1343 inspired by Python's Literal String Interpolation (PEP-0498) and
1344 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1345 (license license:expat)))
1347 (define-public r-pastecs
1353 (uri (cran-uri "pastecs" version))
1356 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1357 (build-system r-build-system)
1359 `(("r-boot" ,r-boot)))
1360 (home-page "http://www.sciviews.org/pastecs")
1361 (synopsis "Analysis of space-time ecological series")
1363 "This package provides functions for regulation, decomposition and analysis
1364 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1365 initiative to bring PASSTEC 2000 functionalities to R.")
1366 (license license:gpl2+)))
1368 (define-public r-plogr
1375 (uri (cran-uri "plogr" version))
1378 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1379 (build-system r-build-system)
1380 (home-page "https://github.com/krlmlr/plogr")
1381 (synopsis "R bindings for the plog C++ logging library")
1383 "This package provides the header files for a stripped-down version of
1384 the plog header-only C++ logging library, and a method to log to R's standard
1386 (license license:expat)))
1388 (define-public r-pls
1395 (uri (cran-uri "pls" version))
1398 "0jw3zl5z06023zxr74phnvwax8m3i4a4i6lsqiq6j15aq9zq3zgq"))))
1399 (build-system r-build-system)
1400 (home-page "http://mevik.net/work/software/pls.html")
1401 (synopsis "Partial Least Squares and Principal Component Regression")
1403 "The pls package implements multivariate regression methods: Partial Least
1404 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1405 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1408 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1409 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1410 @item multi-response models (or @dfn{PLS2})
1411 @item flexible cross-validation
1412 @item Jackknife variance estimates of regression coefficients
1413 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1414 (R)MSEP, R², and correlation loadings
1415 @item formula interface, modelled after @code{lm()}, with methods for predict,
1416 print, summary, plot, update, etc.
1417 @item extraction functions for coefficients, scores, and loadings
1418 @item MSEP, RMSEP, and R² estimates
1419 @item multiplicative scatter correction (@dfn{MSC})
1421 (license license:gpl2)))
1430 (uri (cran-uri "ps" version))
1432 (base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
1433 (build-system r-build-system)
1434 (home-page "http://ps.r-lib.org")
1435 (synopsis "List, query, and manipulate system processes")
1437 "The ps package implements an API to list, query, and manipulate system
1438 processes. Most of its code is based on the @code{psutil} Python package.")
1439 (license license:bsd-3)))
1441 (define-public r-pkgbuild
1448 (uri (cran-uri "pkgbuild" version))
1451 "0prvx91dha5pvd0k4jca2arkngvi6vnfs2indmiy3kwwzyjyyd19"))))
1452 (build-system r-build-system)
1454 `(("r-callr" ,r-callr)
1456 ("r-crayon" ,r-crayon)
1458 ("r-prettyunits" ,r-prettyunits)
1460 ("r-rprojroot" ,r-rprojroot)
1461 ("r-withr" ,r-withr)))
1462 (home-page "https://github.com/r-pkgs/pkgbuild")
1463 (synopsis "Find tools needed to build R packages")
1465 "This package provides functions used to build R packages. It locates
1466 compilers needed to build R packages on various platforms and ensures the PATH
1467 is configured appropriately so R can use them.")
1468 (license license:gpl3)))
1470 (define-public r-pkgload
1477 (uri (cran-uri "pkgload" version))
1480 "0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
1481 (build-system r-build-system)
1483 `(("r-desc" ,r-desc)
1484 ("r-pkgbuild" ,r-pkgbuild)
1485 ("r-rlang" ,r-rlang)
1486 ("r-rprojroot" ,r-rprojroot)
1487 ("r-rstudioapi" ,r-rstudioapi)
1488 ("r-withr" ,r-withr)))
1489 (home-page "https://github.com/r-lib/pkgload")
1490 (synopsis "Simulate package installation and attach")
1492 "This package simulates the process of installing a package and then
1493 attaching it. This is a key part of the @code{devtools} package as it allows
1494 you to rapidly iterate while developing a package.")
1495 (license license:gpl3)))
1497 (define-public r-rcpp
1504 (uri (cran-uri "Rcpp" version))
1506 (base32 "170jlmjrs92z5qdv58badhxycjvfjpqwwpic7rm13pc9zkb3i4xd"))))
1507 (build-system r-build-system)
1509 `(("r-knitr" ,r-knitr))) ; for vignettes
1510 (home-page "http://www.rcpp.org")
1511 (synopsis "Seamless R and C++ integration")
1513 "The Rcpp package provides R functions as well as C++ classes which offer
1514 a seamless integration of R and C++. Many R data types and objects can be
1515 mapped back and forth to C++ equivalents which facilitates both writing of new
1516 code as well as easier integration of third-party libraries. Documentation
1517 about Rcpp is provided by several vignettes included in this package, via the
1518 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
1519 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
1520 @code{citation(\"Rcpp\")} for details on these last two.")
1521 (license license:gpl2+)))
1523 (define-public r-bindr
1530 (uri (cran-uri "bindr" version))
1533 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
1534 (build-system r-build-system)
1535 (home-page "https://github.com/krlmlr/bindr")
1536 (synopsis "Parametrized active bindings")
1538 "This package provides a simple interface for creating active bindings
1539 where the bound function accepts additional arguments.")
1540 (license license:expat)))
1542 (define-public r-bindrcpp
1549 (uri (cran-uri "bindrcpp" version))
1552 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
1553 (build-system r-build-system)
1555 `(("r-bindr" ,r-bindr)
1556 ("r-plogr" ,r-plogr)
1557 ("r-rcpp" ,r-rcpp)))
1558 (home-page "https://github.com/krlmlr/bindrcpp")
1559 (synopsis "Rcpp interface to active bindings")
1561 "This package provides an easy way to fill an environment with active
1562 bindings that call a C++ function.")
1563 (license license:expat)))
1565 (define-public r-auc
1572 (uri (cran-uri "AUC" version))
1575 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
1576 (properties `((upstream-name . "AUC")))
1577 (build-system r-build-system)
1578 (home-page "https://cran.r-project.org/web/packages/AUC")
1579 (synopsis "Compute the area under the curve of selected measures")
1581 "This package includes functions to compute the area under the curve of
1582 selected measures: the area under the sensitivity curve (AUSEC), the area
1583 under the specificity curve (AUSPC), the area under the accuracy
1584 curve (AUACC), and the area under the receiver operating characteristic
1585 curve (AUROC). The curves can also be visualized. Support for partial areas
1587 (license license:gpl2+)))
1589 (define-public r-calibrate
1591 (name "r-calibrate")
1596 (uri (cran-uri "calibrate" version))
1599 "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
1600 (build-system r-build-system)
1602 `(("r-mass" ,r-mass)))
1603 (home-page "https://cran.r-project.org/web/packages/calibrate")
1604 (synopsis "Calibration of scatterplot and biplot axes")
1606 "This is a package for drawing calibrated scales with tick marks
1607 on (non-orthogonal) variable vectors in scatterplots and biplots.")
1608 (license license:gpl2)))
1610 (define-public r-shape
1617 (uri (cran-uri "shape" version))
1620 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
1621 (build-system r-build-system)
1622 (home-page "https://cran.r-project.org/web/packages/shape")
1623 (synopsis "Functions for plotting graphical shapes")
1625 "This package provides functions for plotting graphical shapes such as
1626 ellipses, circles, cylinders, arrows, ...")
1627 (license license:gpl3+)))
1629 (define-public r-globaloptions
1631 (name "r-globaloptions")
1636 (uri (cran-uri "GlobalOptions" version))
1639 "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn"))))
1640 (properties `((upstream-name . "GlobalOptions")))
1641 (build-system r-build-system)
1642 (home-page "https://github.com/jokergoo/GlobalOptions")
1643 (synopsis "Generate functions to get or set global options")
1645 "This package provides more controls on the option values such as
1646 validation and filtering on the values, making options invisible or private.")
1647 (license license:gpl2+)))
1649 (define-public r-circlize
1656 (uri (cran-uri "circlize" version))
1659 "1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f"))))
1660 (build-system r-build-system)
1662 `(("r-colorspace" ,r-colorspace)
1663 ("r-globaloptions" ,r-globaloptions)
1664 ("r-shape" ,r-shape)))
1665 (home-page "https://github.com/jokergoo/circlize")
1666 (synopsis "Circular visualization")
1668 "Circular layout is an efficient way to visualise huge amounts of
1669 information. This package provides an implementation of circular layout
1670 generation in R as well as an enhancement of available software. Its
1671 flexibility is based on the usage of low-level graphics functions such that
1672 self-defined high-level graphics can be easily implemented by users for
1673 specific purposes. Together with the seamless connection between the powerful
1674 computational and visual environment in R, it gives users more convenience and
1675 freedom to design figures for better understanding complex patterns behind
1676 multi-dimensional data.")
1677 (license license:gpl2+)))
1679 (define-public r-powerlaw
1686 (uri (cran-uri "poweRlaw" version))
1689 "1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
1690 (properties `((upstream-name . "poweRlaw")))
1691 (build-system r-build-system)
1693 `(("r-vgam" ,r-vgam)))
1694 (home-page "https://github.com/csgillespie/poweRlaw")
1695 (synopsis "Tools for the analysis of heavy tailed distributions")
1697 "This package provides an implementation of maximum likelihood estimators
1698 for a variety of heavy tailed distributions, including both the discrete and
1699 continuous power law distributions. Additionally, a goodness-of-fit based
1700 approach is used to estimate the lower cut-off for the scaling region.")
1701 ;; Any of these GPL versions.
1702 (license (list license:gpl2 license:gpl3))))
1704 (define-public r-compare
1711 (uri (cran-uri "compare" version))
1714 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
1715 (build-system r-build-system)
1716 (home-page "https://cran.r-project.org/web/packages/compare")
1717 (synopsis "Comparing objects for differences")
1719 "This package provides functions to compare a model object to a
1720 comparison object. If the objects are not identical, the functions can be
1721 instructed to explore various modifications of the objects (e.g., sorting
1722 rows, dropping names) to see if the modified versions are identical.")
1723 (license license:gpl2+)))
1725 (define-public r-dendextend
1727 (name "r-dendextend")
1732 (uri (cran-uri "dendextend" version))
1735 "0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl"))))
1736 (build-system r-build-system)
1738 `(("r-ggplot2" ,r-ggplot2)
1739 ("r-magrittr" ,r-magrittr)
1740 ("r-viridis" ,r-viridis)))
1741 (home-page "https://cran.r-project.org/web/packages/dendextend")
1742 (synopsis "Extending 'dendrogram' functionality in R")
1744 "This package offers a set of functions for extending @code{dendrogram}
1745 objects in R, letting you visualize and compare trees of hierarchical
1746 clusterings. You can adjust a tree's graphical parameters (the color, size,
1747 type, etc of its branches, nodes and labels) and visually and statistically
1748 compare different dendrograms to one another.")
1749 ;; Any of these versions
1750 (license (list license:gpl2 license:gpl3))))
1752 (define-public r-getoptlong
1754 (name "r-getoptlong")
1759 (uri (cran-uri "GetoptLong" version))
1762 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
1763 (properties `((upstream-name . "GetoptLong")))
1764 (build-system r-build-system)
1768 `(("r-globaloptions" ,r-globaloptions)
1769 ("r-rjson" ,r-rjson)))
1770 (home-page "https://github.com/jokergoo/GetoptLong")
1771 (synopsis "Parsing command-line arguments and variable interpolation")
1773 "This is yet another command-line argument parser which wraps the
1774 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
1775 use in R. It also provides a simple way for variable interpolation in R.")
1776 (license license:gpl2+)))
1778 (define-public r-fastmatch
1780 (name "r-fastmatch")
1785 (uri (cran-uri "fastmatch" version))
1788 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
1789 (build-system r-build-system)
1790 (home-page "http://www.rforge.net/fastmatch")
1791 (synopsis "Fast match function")
1793 "This package provides a fast @code{match} replacement for cases that
1794 require repeated look-ups. It is slightly faster that R's built-in
1795 @code{match} function on first match against a table, but extremely fast on
1796 any subsequent lookup as it keeps the hash table in memory.")
1797 (license license:gpl2)))
1806 (uri (cran-uri "ff" version))
1809 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
1810 (build-system r-build-system)
1811 (propagated-inputs `(("r-bit" ,r-bit)))
1812 (home-page "http://ff.r-forge.r-project.org/")
1813 (synopsis "Memory-efficient storage of large data on disk and access functions")
1815 "This package provides data structures that are stored on disk but
1816 behave (almost) as if they were in RAM by transparently mapping only a section
1818 ;; error Architecture not supported.
1819 (supported-systems (delete "aarch64-linux" %supported-systems))
1820 (license license:gpl2)))
1822 (define-public r-ffbase
1829 (uri (cran-uri "ffbase" version))
1832 "04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
1833 (build-system r-build-system)
1836 ("r-fastmatch" ,r-fastmatch)
1838 (home-page "http://github.com/edwindj/ffbase")
1839 (synopsis "Basic statistical functions for package 'ff'")
1841 "This package extends the out of memory vectors of @code{ff} with
1842 statistical functions and other utilities to ease their usage.")
1843 (license license:gpl3)))
1845 (define-public r-prettyunits
1847 (name "r-prettyunits")
1852 (uri (cran-uri "prettyunits" version))
1855 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
1856 (build-system r-build-system)
1858 `(("r-assertthat" ,r-assertthat)
1859 ("r-magrittr" ,r-magrittr)))
1860 (home-page "https://github.com/gaborcsardi/prettyunits")
1861 (synopsis "Pretty, human readable formatting of quantities")
1863 "This package provides tools for pretty, human readable formatting of
1865 (license license:expat)))
1867 (define-public r-reshape
1874 (uri (cran-uri "reshape" version))
1877 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
1878 (build-system r-build-system)
1880 `(("r-plyr" ,r-plyr)
1881 ("r-rcpp" ,r-rcpp)))
1882 (home-page "http://had.co.nz/reshape")
1883 (synopsis "Flexibly reshape data")
1885 "Flexibly restructure and aggregate data using just two functions:
1886 @code{melt} and @code{cast}. This package provides them.")
1887 (license license:expat)))
1889 (define-public r-progress
1896 (uri (cran-uri "progress" version))
1899 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
1900 (build-system r-build-system)
1902 `(("r-crayon" ,r-crayon)
1904 ("r-prettyunits" ,r-prettyunits)
1906 (home-page "https://github.com/gaborcsardi/progress")
1907 (synopsis "Terminal progress bars")
1909 "This package provides configurable progress bars. They may include
1910 percentage, elapsed time, and/or the estimated completion time. They work in
1911 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
1912 package also provides a C++ API, that works with or without Rcpp.")
1913 (license license:expat)))
1915 (define-public r-ggally
1922 (uri (cran-uri "GGally" version))
1925 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
1926 (properties `((upstream-name . "GGally")))
1927 (build-system r-build-system)
1929 `(("libressl" ,libressl)))
1931 `(("r-ggplot2" ,r-ggplot2)
1932 ("r-gtable" ,r-gtable)
1934 ("r-progress" ,r-progress)
1935 ("r-rcolorbrewer" ,r-rcolorbrewer)
1936 ("r-reshape" ,r-reshape)
1937 ("r-rlang" ,r-rlang)))
1938 (home-page "https://ggobi.github.io/ggally")
1939 (synopsis "Extension to ggplot2")
1941 "The R package ggplot2 is a plotting system based on the grammar of
1942 graphics. GGally extends ggplot2 by adding several functions to reduce the
1943 complexity of combining geometric objects with transformed data. Some of
1944 these functions include a pairwise plot matrix, a two group pairwise plot
1945 matrix, a parallel coordinates plot, a survival plot, and several functions to
1947 (license license:gpl2+)))
1949 (define-public r-proxy
1956 (uri (cran-uri "proxy" version))
1959 "17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
1960 (build-system r-build-system)
1961 (home-page "https://cran.r-project.org/web/packages/proxy")
1962 (synopsis "Distance and similarity measures")
1964 "This package provides an extensible framework for the efficient
1965 calculation of auto- and cross-proximities, along with implementations of the
1966 most popular ones.")
1967 (license license:gpl2)))
1976 (uri (cran-uri "sp" version))
1979 "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p"))))
1980 (build-system r-build-system)
1982 `(("r-lattice" ,r-lattice)))
1983 (home-page "https://cran.r-project.org/web/packages/sp")
1984 (synopsis "Classes and methods for spatial data")
1986 "This package provides classes and methods for spatial data; the classes
1987 document where the spatial location information resides, for 2D or 3D data.
1988 Utility functions are provided, e.g. for plotting data as maps, spatial
1989 selection, as well as methods for retrieving coordinates, for subsetting,
1990 print, summary, etc.")
1991 (license license:gpl2+)))
1993 (define-public r-rmtstat
2000 (uri (cran-uri "RMTstat" version))
2003 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2004 (properties `((upstream-name . "RMTstat")))
2005 (build-system r-build-system)
2006 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2007 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2009 "This package provides functions for working with the Tracy-Widom laws
2010 and other distributions related to the eigenvalues of large Wishart
2012 (license license:bsd-3)))
2014 (define-public r-rmpi
2020 (uri (cran-uri "Rmpi" version))
2023 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2024 (properties `((upstream-name . "Rmpi")))
2025 (build-system r-build-system)
2027 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2028 #:phases (modify-phases %standard-phases
2029 (add-before 'install 'mpi-setup
2032 `(("openmpi" ,openmpi)))
2034 `(("pkg-config" ,pkg-config)))
2035 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2036 (synopsis "R interface to message-passing interface (MPI)")
2038 "This package provides an interface (wrapper) to MPI APIs. It also
2039 provides an interactive R manager and worker environment.")
2040 (license license:gpl2+)))
2042 (define-public r-lmoments
2049 (uri (cran-uri "Lmoments" version))
2052 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2053 (properties `((upstream-name . "Lmoments")))
2054 (build-system r-build-system)
2056 `(("r-rcpp" ,r-rcpp)
2057 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2058 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2059 (synopsis "L-moments and quantile mixtures")
2061 "This package contains functions to estimate L-moments and trimmed
2062 L-moments from the data. It also contains functions to estimate the
2063 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2064 quantile mixture from L-moments and trimmed L-moments.")
2065 (license license:gpl2)))
2067 (define-public r-distillery
2069 (name "r-distillery")
2074 (uri (cran-uri "distillery" version))
2077 "1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
2078 (build-system r-build-system)
2079 (home-page "http://www.ral.ucar.edu/staff/ericg")
2080 (synopsis "Functions for confidence intervals and object information")
2082 "This package provides some very simple method functions for confidence
2083 interval calculation and to distill pertinent information from a potentially
2084 complex object; primarily used in common with the packages extRemes and
2086 (license license:gpl2+)))
2088 (define-public r-extremes
2095 (uri (cran-uri "extRemes" version))
2098 "08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic"))))
2099 (properties `((upstream-name . "extRemes")))
2100 (build-system r-build-system)
2102 `(("r-distillery" ,r-distillery)
2103 ("r-lmoments" ,r-lmoments)))
2104 (home-page "http://www.assessment.ucar.edu/toolkit/")
2105 (synopsis "Extreme value analysis")
2107 "ExtRemes is a suite of functions for carrying out analyses on the
2108 extreme values of a process of interest; be they block maxima over long blocks
2109 or excesses over a high threshold.")
2110 (license license:gpl2+)))
2112 (define-public r-lmtest
2119 (uri (cran-uri "lmtest" version))
2122 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2123 (build-system r-build-system)
2125 `(("r-zoo" ,r-zoo)))
2127 `(("gfortran" ,gfortran)))
2128 (home-page "https://cran.r-project.org/web/packages/lmtest")
2129 (synopsis "Testing linear regression models")
2131 "This package provides a collection of tests, data sets, and examples for
2132 diagnostic checking in linear regression models. Furthermore, some generic
2133 tools for inference in parametric models are provided.")
2134 ;; Either version is okay
2135 (license (list license:gpl2 license:gpl3))))
2137 (define-public r-idr
2143 (uri (cran-uri "idr" version))
2146 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2147 (build-system r-build-system)
2148 (home-page "https://cran.r-project.org/web/packages/idr/")
2149 (synopsis "Irreproducible discovery rate")
2151 "This is a package for estimating the copula mixture model and plotting
2152 correspondence curves in \"Measuring reproducibility of high-throughput
2153 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2154 by Li, Brown, Huang, and Bickel")
2155 (license license:gpl2+)))
2157 (define-public r-inline
2163 (uri (cran-uri "inline" version))
2166 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2167 (build-system r-build-system)
2168 (home-page "https://cran.r-project.org/web/packages/inline")
2169 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2171 "This package provides functionality to dynamically define R functions
2172 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2173 @code{.Call} calling conventions.")
2174 ;; Any version of the LGPL.
2175 (license license:lgpl3+)))
2177 (define-public r-bbmle
2184 (uri (cran-uri "bbmle" version))
2187 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
2188 (build-system r-build-system)
2190 `(("r-lattice" ,r-lattice)
2192 ("r-numderiv" ,r-numderiv)))
2193 (home-page "https://cran.r-project.org/web/packages/bbmle")
2194 (synopsis "Tools for General Maximum Likelihood Estimation")
2196 "This package provides methods and functions for fitting maximum
2197 likelihood models in R. This package modifies and extends the @code{mle}
2198 classes in the @code{stats4} package.")
2199 ;; Any version of the GPL
2200 (license license:gpl2+)))
2202 (define-public r-emdbook
2209 (uri (cran-uri "emdbook" version))
2212 "0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
2213 (build-system r-build-system)
2215 `(("r-bbmle" ,r-bbmle)
2217 ("r-lattice" ,r-lattice)
2220 ("r-rcpp" ,r-rcpp)))
2221 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2222 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2224 "This package provides auxiliary functions and data sets for \"Ecological
2225 Models and Data\", a book presenting maximum likelihood estimation and related
2226 topics for ecologists (ISBN 978-0-691-12522-0).")
2228 (license (list license:gpl2 license:gpl3))))
2230 (define-public r-lpsolve
2233 (version "5.6.13.3")
2237 (uri (cran-uri "lpSolve" version))
2240 "1xazby8amb47vw5n12k13awv7x3bjci3q8vdd3vk1ms0ii16ahg6"))))
2241 (properties `((upstream-name . "lpSolve")))
2242 (build-system r-build-system)
2243 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2244 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2246 "Lp_solve is software for solving linear, integer and mixed integer
2247 programs. This implementation supplies a \"wrapper\" function in C and some R
2248 functions that solve general linear/integer problems, assignment problems, and
2249 transportation problems.")
2250 (license license:lgpl2.0)))
2252 (define-public r-limsolve
2259 (uri (cran-uri "limSolve" version))
2262 "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
2263 (properties `((upstream-name . "limSolve")))
2264 (build-system r-build-system)
2266 `(("r-lpsolve" ,r-lpsolve)
2268 ("r-quadprog" ,r-quadprog)))
2269 (native-inputs `(("gfortran" ,gfortran)))
2270 (home-page "https://cran.r-project.org/web/packages/limSolve")
2271 (synopsis "Solving linear inverse models")
2273 "This package provides functions that:
2276 @item find the minimum/maximum of a linear or quadratic function,
2277 @item sample an underdetermined or overdetermined system,
2278 @item solve a linear system Ax=B for the unknown x.
2281 It includes banded and tridiagonal linear systems. The package calls Fortran
2282 functions from LINPACK.")
2284 (license (list license:gpl2+ license:gpl3+))))
2286 (define-public r-fitdistrplus
2288 (name "r-fitdistrplus")
2293 (uri (cran-uri "fitdistrplus" version))
2296 "10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
2297 (build-system r-build-system)
2299 `(("r-mass" ,r-mass)
2300 ("r-npsurv" ,r-npsurv)
2301 ("r-survival" ,r-survival)))
2302 (home-page "http://riskassessment.r-forge.r-project.org")
2303 (synopsis "Fitting a parametric distribution from data")
2305 "This package extends the @code{fitdistr} function of the MASS package
2306 with several functions to help the fit of a parametric distribution to
2307 non-censored or censored data. Censored data may contain left-censored,
2308 right-censored and interval-censored values, with several lower and upper
2309 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2310 provides moment matching (MME), quantile matching (QME) and maximum
2311 goodness-of-fit estimation (MGE) methods (available only for non-censored
2312 data). Weighted versions of MLE, MME and QME are available.")
2313 (license license:gpl2+)))
2315 (define-public r-energy
2322 (uri (cran-uri "energy" version))
2325 "16m8bxfgr9sdisjy2qrv6fv5xxwcc9q890l0hpbwq6qzisrdn3lh"))))
2326 (build-system r-build-system)
2328 `(("r-boot" ,r-boot)
2329 ("r-rcpp" ,r-rcpp)))
2330 (home-page "https://cran.r-project.org/web/packages/energy")
2331 (synopsis "Multivariate inference via the energy of data")
2333 "This package provides e-statistics (energy) tests and statistics for
2334 multivariate and univariate inference, including distance correlation,
2335 one-sample, two-sample, and multi-sample tests for comparing multivariate
2336 distributions, are implemented. Measuring and testing multivariate
2337 independence based on distance correlation, partial distance correlation,
2338 multivariate goodness-of-fit tests, clustering based on energy distance,
2339 testing for multivariate normality, distance components (disco) for
2340 non-parametric analysis of structured data, and other energy
2341 statistics/methods are implemented.")
2342 (license license:gpl2+)))
2344 (define-public r-suppdists
2346 (name "r-suppdists")
2351 (uri (cran-uri "SuppDists" version))
2354 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
2355 (properties `((upstream-name . "SuppDists")))
2356 (build-system r-build-system)
2357 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2358 (synopsis "Supplementary distributions")
2360 "This package provides ten distributions supplementing those built into
2361 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2362 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2363 coefficient, Johnson distributions, normal scores and generalized
2364 hypergeometric distributions. In addition two random number generators of
2365 George Marsaglia are included.")
2366 (license license:gpl2+)))
2368 (define-public r-ksamples
2375 (uri (cran-uri "kSamples" version))
2378 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2379 (properties `((upstream-name . "kSamples")))
2380 (build-system r-build-system)
2382 `(("r-suppdists" ,r-suppdists)))
2383 (home-page "https://cran.r-project.org/web/packages/kSamples")
2384 (synopsis "K-Sample rank tests and their combinations")
2386 "This package provides tools to compares k samples using the
2387 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2388 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2389 test. It computes asymptotic, simulated or (limited) exact P-values, all
2390 valid under randomization, with or without ties, or conditionally under random
2391 sampling from populations, given the observed tie pattern. Except for Steel's
2392 test and the JT test it also combines these tests across several blocks of
2394 (license license:gpl2+)))
2396 (define-public r-cvst
2403 (uri (cran-uri "CVST" version))
2406 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2407 (properties `((upstream-name . "CVST")))
2408 (build-system r-build-system)
2410 `(("r-kernlab" ,r-kernlab)
2411 ("r-matrix" ,r-matrix)))
2412 (home-page "https://cran.r-project.org/web/packages/CVST")
2413 (synopsis "Fast cross-validation via sequential testing")
2415 "This package implements the fast cross-validation via sequential
2416 testing (CVST) procedure. CVST is an improved cross-validation procedure
2417 which uses non-parametric testing coupled with sequential analysis to
2418 determine the best parameter set on linearly increasing subsets of the data.
2419 Additionally to the CVST the package contains an implementation of the
2420 ordinary k-fold cross-validation with a flexible and powerful set of helper
2421 objects and methods to handle the overall model selection process. The
2422 implementations of the Cochran's Q test with permutations and the sequential
2423 testing framework of Wald are generic and can therefore also be used in other
2425 (license license:gpl2+)))
2427 (define-public r-squarem
2430 (version "2017.10-1")
2434 (uri (cran-uri "SQUAREM" version))
2437 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
2438 (properties `((upstream-name . "SQUAREM")))
2439 (build-system r-build-system)
2440 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
2441 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2443 "This package provides algorithms for accelerating the convergence of
2444 slow, monotone sequences from smooth, contraction mapping such as the EM
2445 algorithm. It can be used to accelerate any smooth, linearly convergent
2446 acceleration scheme. A tutorial style introduction to this package is
2447 available in a vignette.")
2448 (license license:gpl2+)))
2450 (define-public r-lava
2457 (uri (cran-uri "lava" version))
2460 "0nfab5fgnmxh8cplg8rd8cp34fny5j0k5wn4baj51r6ck7fq9g3s"))))
2461 (build-system r-build-system)
2463 `(("r-numderiv" ,r-numderiv)
2464 ("r-squarem" ,r-squarem)
2465 ("r-survival" ,r-survival)))
2466 (home-page "https://github.com/kkholst/lava")
2467 (synopsis "Latent variable models")
2469 "This package provides tools for the estimation and simulation of latent
2471 (license license:gpl3)))
2473 (define-public r-drr
2480 (uri (cran-uri "DRR" version))
2483 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
2484 (properties `((upstream-name . "DRR")))
2485 (build-system r-build-system)
2487 `(("r-cvst" ,r-cvst)
2488 ("r-kernlab" ,r-kernlab)
2489 ("r-matrix" ,r-matrix)))
2490 (home-page "https://cran.r-project.org/web/packages/DRR")
2491 (synopsis "Dimensionality reduction via regression")
2493 "This package provides an implementation of dimensionality reduction via
2494 regression using Kernel Ridge Regression.")
2495 (license license:gpl3)))
2497 (define-public r-prodlim
2500 (version "2018.04.18")
2504 (uri (cran-uri "prodlim" version))
2507 "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb"))))
2508 (build-system r-build-system)
2510 `(("r-kernsmooth" ,r-kernsmooth)
2513 ("r-survival" ,r-survival)))
2514 (home-page "https://cran.r-project.org/web/packages/prodlim")
2515 (synopsis "Product-limit estimation for censored event history analysis")
2517 "This package provides a fast and user-friendly implementation of
2518 nonparametric estimators for censored event history (survival) analysis with
2519 the Kaplan-Meier and Aalen-Johansen methods.")
2520 (license license:gpl2+)))
2522 (define-public r-dimred
2529 (uri (cran-uri "dimRed" version))
2532 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
2533 (properties `((upstream-name . "dimRed")))
2534 (build-system r-build-system)
2537 ("r-magrittr" ,r-magrittr)))
2538 (home-page "https://github.com/gdkrmr/dimRed")
2539 (synopsis "Framework for dimensionality reduction")
2541 "This package provides a collection of dimensionality reduction
2542 techniques from R packages and provides a common interface for calling the
2544 (license license:gpl3)))
2546 (define-public r-timedate
2549 (version "3043.102")
2553 (uri (cran-uri "timeDate" version))
2556 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
2557 (properties `((upstream-name . "timeDate")))
2558 (build-system r-build-system)
2559 (home-page "https://www.rmetrics.org")
2560 (synopsis "Chronological and calendar objects")
2562 "This package provides an environment for teaching \"Financial
2563 Engineering and Computational Finance\" and for managing chronological and
2565 (license license:gpl2+)))
2567 (define-public r-magic
2574 (uri (cran-uri "magic" version))
2577 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
2578 (build-system r-build-system)
2580 `(("r-abind" ,r-abind)))
2581 (home-page "https://github.com/RobinHankin/magic.git")
2582 (synopsis "Create and investigate magic squares")
2584 "This package provides a collection of efficient, vectorized algorithms
2585 for the creation and investigation of magic squares and hypercubes, including
2586 a variety of functions for the manipulation and analysis of arbitrarily
2587 dimensioned arrays.")
2588 (license license:gpl2)))
2590 (define-public r-rmysql
2597 (uri (cran-uri "RMySQL" version))
2600 "1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
2601 (properties `((upstream-name . "RMySQL")))
2602 (build-system r-build-system)
2604 `(("mariadb" ,mariadb)
2607 `(("r-dbi" ,r-dbi)))
2608 (home-page "https://github.com/r-dbi/RMySQL")
2609 (synopsis "Database interface and MySQL driver for R")
2611 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
2612 package contains an old implementation based on legacy code from S-PLUS which
2613 is being phased out. A modern MySQL client based on Rcpp is available from
2614 the RMariaDB package.")
2615 (license license:gpl2)))
2617 (define-public r-rpostgresql
2619 (name "r-rpostgresql")
2624 (uri (cran-uri "RPostgreSQL" version))
2627 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
2628 (properties `((upstream-name . "RPostgreSQL")))
2629 (build-system r-build-system)
2631 `(("postgresql" ,postgresql)))
2633 `(("r-dbi" ,r-dbi)))
2634 (home-page "https://github.com/tomoakin/RPostgreSQL")
2635 (synopsis "R interface to the PostgreSQL database system")
2637 "This package provides a Database Interface (DBI) compliant driver for R
2638 to access PostgreSQL database systems.")
2639 ;; The whole package is released under GPL version 2. It includes code
2640 ;; under the PostgreSQL license.
2641 (license license:gpl2)))
2643 (define-public r-linprog
2650 (uri (cran-uri "linprog" version))
2653 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
2654 (build-system r-build-system)
2655 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
2656 (home-page "http://linprog.r-forge.r-project.org/")
2657 (synopsis "Linear programming and optimization")
2659 "This package can be used to solve Linear Programming / Linear
2660 Optimization problems by using the simplex algorithm.")
2661 (license license:gpl2+)))
2663 (define-public r-geometry
2670 (uri (cran-uri "geometry" version))
2673 "0vq334115qi039vy198ggv1dsp6n1s6jwcm9ivipf5r8lbm287zz"))))
2674 (build-system r-build-system)
2676 `(("r-magic" ,r-magic)
2677 ("r-linprog" ,r-linprog)
2678 ("r-lpsolve" ,r-lpsolve)
2680 ("r-rcppprogress" ,r-rcppprogress)))
2681 (home-page "http://geometry.r-forge.r-project.org/")
2682 (synopsis "Mesh generation and surface tesselation")
2684 "This package makes the qhull library available in R, in a similar manner
2685 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
2686 intersections about a point, Voronoi diagrams, furthest-site Delaunay
2687 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
2688 and higher dimensions. It implements the Quickhull algorithm for computing
2689 the convex hull. Qhull does not support constrained Delaunay triangulations,
2690 or mesh generation of non-convex objects, but the package does include some R
2691 functions that allow for this. Currently the package only gives access to
2692 Delaunay triangulation and convex hull computation.")
2693 ;; The Qhull sources are included and are distributed under a custom
2694 ;; non-copyleft license. The R sources are released under GPL version 2.
2695 (license (list license:gpl2
2696 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
2698 (define-public r-ddalpha
2705 (uri (cran-uri "ddalpha" version))
2708 "1vzs0cvl6xw3h9i00rg3hs02xwgxcnh8326y10kxmhs3qq4m7nb2"))))
2709 (build-system r-build-system)
2712 ("r-class" ,r-class)
2713 ("r-geometry" ,r-geometry)
2716 ("r-robustbase" ,r-robustbase)
2717 ("r-sfsmisc" ,r-sfsmisc)))
2719 `(("gfortran" ,gfortran)))
2720 (home-page "https://cran.r-project.org/web/packages/ddalpha")
2721 (synopsis "Depth-Based classification and calculation of data depth")
2723 "This package contains procedures for depth-based supervised learning,
2724 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
2725 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
2726 statistical depth function to a compact low-dimensional space, where the final
2727 classification is done. It also offers an extension to functional data and
2728 routines for calculating certain notions of statistical depth functions. 50
2729 multivariate and 5 functional classification problems are included.")
2730 (license license:gpl2)))
2732 (define-public r-gower
2739 (uri (cran-uri "gower" version))
2742 "007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
2743 (build-system r-build-system)
2744 (home-page "https://github.com/markvanderloo/gower")
2745 (synopsis "Gower's distance")
2747 "This package provides tools to compute Gower's distance (or similarity)
2748 coefficient between records, and to compute the top-n matches between records.
2749 Core algorithms are executed in parallel on systems supporting OpenMP.")
2750 (license license:gpl3)))
2752 (define-public r-rcpproll
2759 (uri (cran-uri "RcppRoll" version))
2762 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
2763 (properties `((upstream-name . "RcppRoll")))
2764 (build-system r-build-system)
2766 `(("r-rcpp" ,r-rcpp)))
2767 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
2768 (synopsis "Efficient rolling and windowed operations")
2770 "This package provides fast and efficient routines for common rolling /
2771 windowed operations. Routines for the efficient computation of windowed mean,
2772 median, sum, product, minimum, maximum, standard deviation and variance are
2774 (license license:gpl2+)))
2776 (define-public r-ipred
2783 (uri (cran-uri "ipred" version))
2786 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
2787 (build-system r-build-system)
2789 `(("r-class" ,r-class)
2792 ("r-prodlim" ,r-prodlim)
2793 ("r-rpart" ,r-rpart)
2794 ("r-survival" ,r-survival)))
2795 (home-page "https://cran.r-project.org/web/packages/ipred")
2796 (synopsis "Improved predictors")
2798 "This package provides improved predictive models by indirect
2799 classification and bagging for classification, regression and survival
2800 problems as well as resampling based estimators of prediction error.")
2801 (license license:gpl2+)))
2803 (define-public r-psych
2810 (uri (cran-uri "psych" version))
2813 "0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
2814 (build-system r-build-system)
2816 `(("r-foreign" ,r-foreign)
2817 ("r-lattice" ,r-lattice)
2818 ("r-mnormt" ,r-mnormt)
2819 ("r-nlme" ,r-nlme)))
2820 (home-page "https://cran.r-project.org/web/packages/psych/")
2821 (synopsis "Procedures for psychological, psychometric, and personality research")
2823 "This package provides a general purpose toolbox for personality,
2824 psychometric theory and experimental psychology. Functions are primarily for
2825 multivariate analysis and scale construction using factor analysis, principal
2826 component analysis, cluster analysis and reliability analysis, although others
2827 provide basic descriptive statistics. Item Response Theory is done using
2828 factor analysis of tetrachoric and polychoric correlations. Functions for
2829 analyzing data at multiple levels include within and between group statistics,
2830 including correlations and factor analysis. Functions for simulating and
2831 testing particular item and test structures are included. Several functions
2832 serve as a useful front end for structural equation modeling. Graphical
2833 displays of path diagrams, factor analysis and structural equation models are
2834 created using basic graphics.")
2835 (license license:gpl2+)))
2837 (define-public r-generics
2844 (uri (cran-uri "generics" version))
2847 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
2848 (build-system r-build-system)
2849 (home-page "https://github.com/r-lib/generics")
2850 (synopsis "Common S3 generics not provided by base R methods")
2852 "In order to reduce potential package dependencies and conflicts,
2853 generics provides a number of commonly used S3 generics that are not provided
2854 by base R methods related to model fitting.")
2855 (license license:gpl2)))
2857 (define-public r-broom
2864 (uri (cran-uri "broom" version))
2867 "0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
2868 (build-system r-build-system)
2870 `(("r-backports" ,r-backports)
2871 ("r-dplyr" ,r-dplyr)
2872 ("r-generics" ,r-generics)
2874 ("r-purrr" ,r-purrr)
2875 ("r-reshape2" ,r-reshape2)
2876 ("r-stringr" ,r-stringr)
2877 ("r-tibble" ,r-tibble)
2878 ("r-tidyr" ,r-tidyr)))
2879 (home-page "https://github.com/tidyverse/broom")
2880 (synopsis "Convert statistical analysis objects into tidy data frames")
2882 "This package provides tools to convert statistical analysis objects from
2883 R into tidy data frames, so that they can more easily be combined, reshaped
2884 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
2885 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
2886 summarizes a model's statistical findings such as coefficients of a
2887 regression; @code{augment}, which adds columns to the original data such as
2888 predictions, residuals and cluster assignments; and @code{glance}, which
2889 provides a one-row summary of model-level statistics.")
2890 (license license:expat)))
2892 (define-public r-recipes
2899 (uri (cran-uri "recipes" version))
2902 "1ndz9h0zvdj141r63l8047wbhaj0x8fwzzyq7b8mh78pvrrdpq2i"))))
2903 (build-system r-build-system)
2905 `(("r-dplyr" ,r-dplyr)
2906 ("r-generics" ,r-generics)
2908 ("r-gower" ,r-gower)
2909 ("r-ipred" ,r-ipred)
2910 ("r-lubridate" ,r-lubridate)
2911 ("r-magrittr" ,r-magrittr)
2912 ("r-matrix" ,r-matrix)
2913 ("r-purrr" ,r-purrr)
2914 ("r-rlang" ,r-rlang)
2915 ("r-tibble" ,r-tibble)
2916 ("r-tidyr" ,r-tidyr)
2917 ("r-tidyselect" ,r-tidyselect)
2918 ("r-timedate" ,r-timedate)
2919 ("r-withr" ,r-withr)))
2920 (home-page "https://github.com/topepo/recipes")
2921 (synopsis "Preprocessing tools to create design matrices")
2923 "Recipes is an extensible framework to create and preprocess design
2924 matrices. Recipes consist of one or more data manipulation and analysis
2925 \"steps\". Statistical parameters for the steps can be estimated from an
2926 initial data set and then applied to other data sets. The resulting design
2927 matrices can then be used as inputs into statistical or machine learning
2929 (license license:gpl2)))
2931 (define-public r-pdist
2938 (uri (cran-uri "pdist" version))
2941 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
2942 (build-system r-build-system)
2943 (home-page "https://github.com/jeffwong/pdist")
2944 (synopsis "Partitioned distance function")
2946 "Pdist computes the euclidean distance between rows of a matrix X and
2947 rows of another matrix Y. Previously, this could be done by binding the two
2948 matrices together and calling @code{dist}, but this creates unnecessary
2949 computation by computing the distances between a row of X and another row of
2950 X, and likewise for Y. Pdist strictly computes distances across the two
2951 matrices, not within the same matrix, making computations significantly faster
2952 for certain use cases.")
2953 (license license:gpl3+)))
2955 (define-public r-ggrepel
2962 (uri (cran-uri "ggrepel" version))
2965 "10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
2966 (build-system r-build-system)
2968 `(("r-ggplot2" ,r-ggplot2)
2970 ("r-scales" ,r-scales)))
2971 (home-page "http://github.com/slowkow/ggrepel")
2972 (synopsis "Repulsive text and label geometries for ggplot2")
2974 "This package provides text and label geometries for ggplot2 that help to
2975 avoid overlapping text labels. Labels repel away from each other and away
2976 from the data points.")
2977 (license license:gpl3)))
2979 (define-public r-corrplot
2986 (uri (cran-uri "corrplot" version))
2989 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
2990 (build-system r-build-system)
2991 (home-page "https://github.com/taiyun/corrplot")
2992 (synopsis "Visualization of a correlation matrix")
2994 "This package provides a graphical display of a correlation matrix or
2995 general matrix. It also contains some algorithms to do matrix reordering. In
2996 addition, corrplot is good at details, including choosing color, text labels,
2997 color labels, layout, etc.")
2998 ;; Any version of the GPL
2999 (license license:gpl2+)))
3001 (define-public r-stringdist
3003 (name "r-stringdist")
3008 (uri (cran-uri "stringdist" version))
3011 "0nw8c317qkfq63pr0prl0hx522ddfq4cbgixb5r4pq3fxk9z303l"))))
3012 (build-system r-build-system)
3013 (home-page "https://github.com/markvanderloo/stringdist")
3014 (synopsis "Approximate string matching and string distance functions")
3016 "This package implements an approximate string matching version of R's
3017 native @code{match} function. It can calculate various string distances based
3018 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3019 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3020 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3021 can be computed between character vectors while taking proper care of encoding
3022 or between integer vectors representing generic sequences.")
3023 (license license:gpl3+)))
3025 (define-public r-ucminf
3032 (uri (cran-uri "ucminf" version))
3035 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3036 (build-system r-build-system)
3037 (native-inputs `(("gfortran" ,gfortran)))
3038 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3039 (synopsis "General-purpose unconstrained non-linear optimization")
3041 "This package provides an implementation of an algorithm for
3042 general-purpose unconstrained non-linear optimization. The algorithm is of
3043 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3044 search with a trust region type monitoring of the input to the line search
3045 algorithm. The interface of @code{ucminf} is designed for easy interchange
3046 with the package @code{optim}.")
3047 (license license:gpl2+)))
3049 (define-public r-ordinal
3052 (version "2019.4-25")
3056 (uri (cran-uri "ordinal" version))
3059 "1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
3060 (build-system r-build-system)
3062 `(("r-mass" ,r-mass)
3063 ("r-matrix" ,r-matrix)
3064 ("r-numderiv" ,r-numderiv)
3065 ("r-ucminf" ,r-ucminf)))
3066 (home-page "https://github.com/runehaubo/ordinal")
3067 (synopsis "Regression models for ordinal data")
3069 "This package provides an implementation of cumulative link (mixed)
3070 models also known as ordered regression models, proportional odds models,
3071 proportional hazards models for grouped survival times and ordered models.
3072 Estimation is via maximum likelihood and mixed models are fitted with the
3073 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3074 (license license:gpl2+)))
3076 (define-public r-jomo
3083 (uri (cran-uri "jomo" version))
3086 "16ychdhhv8cii8zrdfdf5gzgnvmfaq573bmi00xqdf323q3lf3xr"))))
3087 (build-system r-build-system)
3089 `(("r-lme4" ,r-lme4)
3091 ("r-ordinal" ,r-ordinal)
3092 ("r-survival" ,r-survival)))
3093 (home-page "https://cran.r-project.org/web/packages/jomo/")
3094 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3096 "Similarly to Schafer's package pan, jomo is a package for multilevel
3097 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3098 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3099 possibility of handling binary and categorical data through latent normal
3100 variables, the option to use cluster-specific covariance matrices and to
3101 impute compatibly with the substantive model.")
3102 (license license:gpl2)))
3104 (define-public r-pan
3111 (uri (cran-uri "pan" version))
3114 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3115 (build-system r-build-system)
3116 (native-inputs `(("gfortran" ,gfortran)))
3117 (home-page "https://cran.r-project.org/web/packages/pan/")
3118 (synopsis "Multiple imputation for multivariate panel or clustered data")
3120 "This package implements multiple imputation for multivariate panel or
3122 (license license:gpl3)))
3124 (define-public r-mitml
3131 (uri (cran-uri "mitml" version))
3134 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3135 (build-system r-build-system)
3137 `(("r-haven" ,r-haven)
3140 (home-page "https://cran.r-project.org/web/packages/mitml/")
3141 (synopsis "Tools for multiple imputation in multilevel modeling")
3143 "This package provides tools for multiple imputation of missing data in
3144 multilevel modeling. It includes a user-friendly interface to the packages
3145 pan and jomo, and several functions for visualization, data management and the
3146 analysis of multiply imputed data sets.")
3147 (license license:gpl2+)))
3149 (define-public r-mice
3156 (uri (cran-uri "mice" version))
3159 "0pgcxdmp77604h6f4x8hhs6j4xdjgf5b9zvnixyzdj8vcgdjpivv"))))
3160 (build-system r-build-system)
3162 `(("r-broom" ,r-broom)
3163 ("r-dplyr" ,r-dplyr)
3164 ("r-lattice" ,r-lattice)
3166 ("r-mitml" ,r-mitml)
3169 ("r-rlang" ,r-rlang)
3170 ("r-rpart" ,r-rpart)
3171 ("r-survival" ,r-survival)))
3172 (home-page "https://cran.r-project.org/web/packages/mice/")
3173 (synopsis "Multivariate imputation by chained equations")
3175 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3176 implemented by the MICE algorithm as described in @url{Van Buuren and
3177 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3178 variable has its own imputation model. Built-in imputation models are
3179 provided for continuous data (predictive mean matching, normal), binary
3180 data (logistic regression), unordered categorical data (polytomous logistic
3181 regression) and ordered categorical data (proportional odds). MICE can also
3182 impute continuous two-level data (normal model, pan, second-level variables).
3183 Passive imputation can be used to maintain consistency between variables.
3184 Various diagnostic plots are available to inspect the quality of the
3186 ;; Any of these two versions.
3187 (license (list license:gpl2 license:gpl3))))
3189 (define-public r-truncnorm
3191 (name "r-truncnorm")
3196 (uri (cran-uri "truncnorm" version))
3199 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3200 (build-system r-build-system)
3201 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3202 (synopsis "Truncated normal distribution")
3203 (description "This package provides functions for the truncated normal
3204 distribution with mean equal to @code{mean} and standard deviation equal to
3205 @code{sd}. It includes density, distribution, quantile, and expected value
3206 functions, as well as a random generation function.")
3207 (license license:gpl2)))
3209 (define-public r-rsolnp
3216 (uri (cran-uri "Rsolnp" version))
3219 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3220 (properties `((upstream-name . "Rsolnp")))
3221 (build-system r-build-system)
3223 `(("r-truncnorm" ,r-truncnorm)))
3224 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3225 (synopsis "General non-linear optimization")
3226 (description "The Rsolnp package implements a general non-linear augmented
3227 Lagrange multiplier method solver, a @dfn{sequential quadratic
3228 programming} (SQP) based solver).")
3229 ;; Any version of the GPL.
3230 (license license:gpl2+)))
3232 (define-public r-hardyweinberg
3234 (name "r-hardyweinberg")
3239 (uri (cran-uri "HardyWeinberg" version))
3242 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3243 (properties `((upstream-name . "HardyWeinberg")))
3244 (build-system r-build-system)
3246 `(("r-mice" ,r-mice)
3248 ("r-rsolnp" ,r-rsolnp)))
3249 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3250 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3252 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3253 diallelic genetic marker data. All classical tests (chi-square, exact,
3254 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3255 included in the package, as well as functions for power computation and for
3256 the simulation of marker data under equilibrium and disequilibrium. Routines
3257 for dealing with markers on the X-chromosome are included. Functions for
3258 testing equilibrium in the presence of missing data by using multiple
3259 imputation are also provided. Implements several graphics for exploring the
3260 equilibrium status of a large set of diallelic markers: ternary plots with
3261 acceptance regions, log-ratio plots and Q-Q plots.")
3262 (license license:gpl2+)))
3271 (uri (cran-uri "sm" version))
3274 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3275 (build-system r-build-system)
3276 (native-inputs `(("gfortran" ,gfortran)))
3277 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3278 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3280 "This is software accompanying the book 'Applied Smoothing Techniques for
3281 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3282 University Press. It provides smoothing methods for nonparametric regression
3283 and density estimation")
3284 (license license:gpl2+)))
3286 (define-public r-venndiagram
3288 (name "r-venndiagram")
3292 (uri (cran-uri "VennDiagram" version))
3295 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3296 (properties `((upstream-name . "VennDiagram")))
3297 (build-system r-build-system)
3299 `(("r-futile-logger" ,r-futile-logger)))
3300 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3301 (synopsis "Generate High-Resolution Venn and Euler Plots")
3303 "This package provides a set of functions to generate high-resolution
3304 Venn and Euler plots. It includes handling for several special cases,
3305 including two-case scaling, and extensive customization of plot shape and
3307 (license license:gpl2+)))
3309 (define-public r-vioplot
3316 (uri (cran-uri "vioplot" version))
3319 "13kfjp747bnzksai8j39y2hyl3ljc6n53c2cfhaw78q3d63x0lbv"))))
3320 (build-system r-build-system)
3324 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3325 (synopsis "Violin plot")
3327 "This package provides a violin plot, which is a combination of a box
3328 plot and a kernel density plot.")
3329 (license license:bsd-3)))
3331 (define-public r-rsofia
3337 ;; This package has been removed from CRAN, so we can
3338 ;; only fetch it from the archives.
3339 (uri (string-append "https://cran.r-project.org/src/"
3340 "contrib/Archive/RSofia/RSofia_"
3344 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3345 (properties `((upstream-name . "RSofia")))
3346 (build-system r-build-system)
3348 `(("r-rcpp" ,r-rcpp)))
3349 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3350 (synopsis "Port of sofia-ml to R")
3351 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3352 suite of fast incremental algorithms for machine learning that can be used for
3353 training models for classification or ranking.")
3354 (license license:asl2.0)))
3356 (define-public r-xts
3363 (uri (cran-uri "xts" version))
3366 "1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
3367 (build-system r-build-system)
3368 (propagated-inputs `(("r-zoo" ,r-zoo)))
3369 (home-page "https://github.com/joshuaulrich/xts")
3370 (synopsis "Extensible time series")
3372 "This package provides for uniform handling of R's different time-based
3373 data classes by extending @code{zoo}, maximizing native format information
3374 preservation and allowing for user-level customization and extension, while
3375 simplifying cross-class interoperability.")
3376 (license license:gpl2+)))
3378 (define-public r-performanceanalytics
3380 (name "r-performanceanalytics")
3385 (uri (cran-uri "PerformanceAnalytics" version))
3388 "0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
3390 `((upstream-name . "PerformanceAnalytics")))
3391 (build-system r-build-system)
3393 `(("r-quadprog" ,r-quadprog)
3396 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3397 (synopsis "Econometric tools for performance and risk analysis")
3398 (description "This is a collection of econometric functions for
3399 performance and risk analysis. This package aims to aid practitioners and
3400 researchers in utilizing the latest research in analysis of non-normal return
3401 streams. In general, it is most tested on return (rather than price) data on
3402 a regular scale, but most functions will work with irregular return data as
3403 well, and increasing numbers of functions will work with P&L or price data
3405 ;; Either version may be picked.
3406 (license (list license:gpl2 license:gpl3))))
3408 (define-public r-laeken
3415 (uri (cran-uri "laeken" version))
3418 "1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
3419 (build-system r-build-system)
3421 `(("r-boot" ,r-boot)
3422 ("r-mass" ,r-mass)))
3423 (home-page "https://cran.r-project.org/web/packages/laeken/")
3424 (synopsis "Estimation of indicators on social exclusion and poverty")
3425 (description "This package provides tools for the estimation of indicators
3426 on social exclusion and poverty, as well as an implementation of Pareto tail
3427 modeling for empirical income distributions.")
3428 (license license:gpl2+)))
3430 (define-public r-vcd
3437 (uri (cran-uri "vcd" version))
3440 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
3441 (build-system r-build-system)
3443 `(("r-colorspace" ,r-colorspace)
3444 ("r-lmtest" ,r-lmtest)
3445 ("r-mass" ,r-mass)))
3446 (home-page "https://cran.r-project.org/web/packages/vcd/")
3447 (synopsis "Visualizing categorical data")
3448 (description "This package provides visualization techniques, data sets,
3449 summary and inference procedures aimed particularly at categorical data.
3450 Special emphasis is given to highly extensible grid graphics. The package was
3451 originally inspired by the book \"Visualizing Categorical Data\" by Michael
3452 Friendly and is now the main support package for a new book, \"Discrete Data
3453 Analysis with R\" by Michael Friendly and David Meyer (2015).")
3454 (license license:gpl2)))
3456 (define-public r-ica
3463 (uri (cran-uri "ica" version))
3466 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
3467 (build-system r-build-system)
3468 (home-page "https://cran.r-project.org/web/packages/ica/")
3469 (synopsis "Independent component analysis")
3470 (description "This package provides tools for @dfn{Independent Component
3471 Analysis} (ICA) using various algorithms: FastICA,
3472 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
3473 of Eigenmatrices} (JADE).")
3474 (license license:gpl2+)))
3476 (define-public r-dtw
3483 (uri (cran-uri "dtw" version))
3486 "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
3487 (build-system r-build-system)
3488 (propagated-inputs `(("r-proxy" ,r-proxy)))
3489 (home-page "http://dtw.r-forge.r-project.org/")
3490 (synopsis "Dynamic Time Warping Algorithms")
3491 (description "This package provides a comprehensive implementation of
3492 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
3493 optimal (least cumulative distance) alignment between points of two time
3494 series. Common DTW variants covered include local (slope) and global (window)
3495 constraints, subsequence matches, arbitrary distance definitions,
3496 normalizations, minimum variance matching, and so on.")
3497 (license license:gpl2+)))
3499 (define-public r-sdmtools
3502 (version "1.1-221.1")
3506 (uri (cran-uri "SDMTools" version))
3509 "1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q"))))
3510 (properties `((upstream-name . "SDMTools")))
3511 (build-system r-build-system)
3512 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
3513 (home-page "http://www.rforge.net/SDMTools/")
3514 (synopsis "Species distribution modelling tools")
3515 (description "This package provides a set of tools for post processing
3516 the outcomes of species distribution modeling exercises. It includes novel
3517 methods for comparing models and tracking changes in distributions through
3518 time. It further includes methods for visualizing outcomes, selecting
3519 thresholds, calculating measures of accuracy and landscape fragmentation
3521 (license license:gpl3+)))
3523 (define-public r-scatterplot3d
3525 (name "r-scatterplot3d")
3530 (uri (cran-uri "scatterplot3d" version))
3533 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
3534 (build-system r-build-system)
3535 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
3536 (synopsis "3D scatter plot")
3537 (description "This package provides an implementation of scatter plots for
3538 plotting. a three dimensional point cloud.")
3539 (license license:gpl2)))
3541 (define-public r-ggridges
3548 (uri (cran-uri "ggridges" version))
3551 "0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
3552 (build-system r-build-system)
3554 `(("r-ggplot2" ,r-ggplot2)
3556 ("r-scales" ,r-scales)
3557 ("r-withr" ,r-withr)))
3558 (home-page "https://github.com/clauswilke/ggridges")
3559 (synopsis "Ridgeline plots in ggplot2")
3561 "Ridgeline plots provide a convenient way of visualizing changes in
3562 distributions over time or space. This package enables the creation of such
3563 plots in @code{ggplot2}.")
3564 (license license:gpl2)))
3566 (define-public r-ggjoy
3573 (uri (cran-uri "ggjoy" version))
3576 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
3577 (build-system r-build-system)
3579 `(("r-ggplot2" ,r-ggplot2)
3580 ("r-ggridges" ,r-ggridges)))
3581 (home-page "https://github.com/clauswilke/ggjoy")
3582 (synopsis "Joyplots in ggplot2")
3583 (description "Joyplots provide a convenient way of visualizing changes in
3584 distributions over time or space. This package enables the creation of such
3585 plots in @code{ggplot2}.")
3586 (license license:gpl2)))
3588 (define-public r-cli
3595 (uri (cran-uri "cli" version))
3598 "02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g"))))
3599 (build-system r-build-system)
3601 `(("r-assertthat" ,r-assertthat)
3602 ("r-crayon" ,r-crayon)))
3603 (home-page "https://github.com/r-lib/cli#readme")
3604 (synopsis "Helpers for developing command line interfaces")
3605 (description "This package provides a suite of tools designed to build
3606 attractive command line interfaces (CLIs). It includes tools for drawing
3607 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
3608 (license license:expat)))
3610 (define-public r-argparser
3612 (name "r-argparser")
3617 (uri (cran-uri "argparser" version))
3620 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
3621 (build-system r-build-system)
3622 (home-page "https://bitbucket.org/djhshih/argparser")
3623 (synopsis "Command-line argument parser")
3625 "This package provides a cross-platform command-line argument parser
3626 written purely in R with no external dependencies. It is useful with the
3627 Rscript front-end and facilitates turning an R script into an executable
3629 (license license:gpl3+)))
3631 (define-public r-debugme
3638 (uri (cran-uri "debugme" version))
3641 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
3642 (build-system r-build-system)
3643 (propagated-inputs `(("r-crayon" ,r-crayon)))
3644 (home-page "https://github.com/r-lib/debugme#readme")
3645 (synopsis "Debug R packages")
3647 "This package allows the user to specify debug messages as special string
3648 constants, and control debugging of packages via environment variables.")
3649 (license license:expat)))
3651 (define-public r-processx
3658 (uri (cran-uri "processx" version))
3661 "1g6ipcaxg9y94lyrnbp7kkbqfkcdh1fyrqjjclbjp3x7iysdvazi"))))
3662 (build-system r-build-system)
3666 (home-page "https://github.com/r-lib/processx3")
3667 (synopsis "Execute and control system processes")
3669 "This package provides portable tools to run system processes in the
3670 background. It can check if a background process is running; wait on a
3671 background process to finish; get the exit status of finished processes; kill
3672 background processes and their children; restart processes. It can read the
3673 standard output and error of the processes, using non-blocking connections.
3674 @code{processx} can poll a process for standard output or error, with a
3675 timeout. It can also poll several processes at once.")
3676 (license license:expat)))
3678 (define-public r-tsp
3685 (uri (cran-uri "TSP" version))
3688 "0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
3689 (properties `((upstream-name . "TSP")))
3690 (build-system r-build-system)
3691 (propagated-inputs `(("r-foreach" ,r-foreach)))
3692 (home-page "https://cran.r-project.org/web/packages/TSP/")
3693 (synopsis "Traveling salesperson problem (TSP)")
3694 (description "This package provides basic infrastructure and some
3695 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
3696 traveling salesman problem).")
3697 (license license:gpl3)))
3699 (define-public r-qap
3706 (uri (cran-uri "qap" version))
3709 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
3710 (build-system r-build-system)
3711 (native-inputs `(("gfortran" ,gfortran)))
3712 (home-page "https://cran.r-project.org/web/packages/qap/")
3713 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
3714 (description "This package implements heuristics for the @dfn{quadratic
3715 assignment problem} (QAP). Currently only a simulated annealing heuristic is
3717 (license license:gpl3)))
3719 (define-public r-gclus
3726 (uri (cran-uri "gclus" version))
3729 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
3730 (build-system r-build-system)
3731 (propagated-inputs `(("r-cluster" ,r-cluster)))
3732 (home-page "https://cran.r-project.org/web/packages/gclus/")
3733 (synopsis "Clustering graphics")
3734 (description "This package orders panels in scatterplot matrices and
3735 parallel coordinate displays by some merit index. It contains various indices
3736 of merit, ordering functions, and enhanced versions of @code{pairs} and
3737 @code{parcoord} which color panels according to their merit level.")
3738 (license license:gpl2+)))
3740 (define-public r-webshot
3747 (uri (cran-uri "webshot" version))
3750 "08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr"))))
3751 (build-system r-build-system)
3753 `(("r-callr" ,r-callr)
3754 ("r-jsonlite" ,r-jsonlite)
3755 ("r-magrittr" ,r-magrittr)))
3756 (home-page "https://github.com/wch/webshot/")
3757 (synopsis "Take screenshots of web pages")
3759 "Webshot makes it easy to take screenshots of web pages from within R.
3760 It can also run Shiny applications locally and take screenshots of the
3761 application; and it can render and screenshot static as well as interactive R
3762 Markdown documents.")
3763 (license license:gpl2)))
3765 (define-public r-seriation
3767 (name "r-seriation")
3772 (uri (cran-uri "seriation" version))
3775 "0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6"))))
3776 (build-system r-build-system)
3778 `(("r-cluster" ,r-cluster)
3779 ("r-colorspace" ,r-colorspace)
3780 ("r-dendextend" ,r-dendextend)
3781 ("r-gclus" ,r-gclus)
3782 ("r-gplots" ,r-gplots)
3785 ("r-registry" ,r-registry)
3787 (native-inputs `(("gfortran" ,gfortran)))
3788 (home-page "http://s2.smu.edu/IDA/seriation/")
3789 (synopsis "Infrastructure for ordering objects using seriation")
3791 "This package provides infrastructure for seriation with an
3792 implementation of several seriation/sequencing techniques to reorder matrices,
3793 dissimilarity matrices, and dendrograms. It also provides (optimally)
3794 reordered heatmaps, color images and clustering visualizations like
3795 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
3797 (license license:gpl3)))
3799 (define-public r-xfun
3806 (uri (cran-uri "xfun" version))
3809 "05jlbi5byqpw0fkhmmxqglnaxh9gwbcigx77kcpw1pkxnpwfry62"))))
3810 (build-system r-build-system)
3811 (home-page "https://github.com/yihui/xfun")
3812 (synopsis "Miscellaneous functions")
3814 "This package provides miscellaneous functions commonly used in other
3815 packages maintained by Yihui Xie.")
3816 (license license:expat)))
3818 (define-public r-utf8
3825 (uri (cran-uri "utf8" version))
3828 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
3829 (build-system r-build-system)
3830 (home-page "https://github.com/patperry/r-utf8")
3831 (synopsis "Unicode text processing")
3833 "This package provides tools to process and print UTF-8 encoded
3834 international text (Unicode). Input, validate, normalize, encode, format, and
3836 (license license:asl2.0)))
3838 (define-public r-zeallot
3845 (uri (cran-uri "zeallot" version))
3848 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
3849 (build-system r-build-system)
3850 (home-page "https://github.com/nteetor/zeallot")
3851 (synopsis "Multiple, unpacking, and destructuring assignment")
3853 "This package provides a @code{%<-%} operator to perform multiple,
3854 unpacking, and destructuring assignment in R. The operator unpacks the
3855 right-hand side of an assignment into multiple values and assigns these values
3856 to variables on the left-hand side of the assignment.")
3857 (license license:expat)))
3859 (define-public r-vctrs
3866 (uri (cran-uri "vctrs" version))
3869 "05h0y8qzwc899qj84gkhg4jwzscd065as00d4d8smv42h4i8zkjv"))))
3870 (build-system r-build-system)
3872 `(("r-backports" ,r-backports)
3873 ("r-digest" ,r-digest)
3874 ("r-ellipsis" ,r-ellipsis)
3876 ("r-rlang" ,r-rlang)
3877 ("r-zeallot" ,r-zeallot)))
3878 (home-page "https://github.com/r-lib/vctrs")
3879 (synopsis "Vector helpers")
3881 "There are three main goals to the @code{vctrs} package:
3884 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
3885 @code{length()} and @code{class()}. These definitions are paired with a
3886 framework for type-coercion and size-recycling.
3887 @item To define type- and size-stability as desirable function properties, use
3888 them to analyse existing base function, and to propose better alternatives.
3889 This work has been particularly motivated by thinking about the ideal
3890 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
3891 @item To provide a new @code{vctr} base class that makes it easy to create new
3892 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
3893 a few new @code{vctrs} generics, making implementation considerably simpler
3896 (license license:gpl3)))
3898 (define-public r-pillar
3905 (uri (cran-uri "pillar" version))
3908 "0988047mf0xdhdkqqmavzx4ifjhndjnxniyrrhrdq1nvnrvbpfms"))))
3909 (build-system r-build-system)
3912 ("r-crayon" ,r-crayon)
3913 ("r-fansi" ,r-fansi)
3914 ("r-rlang" ,r-rlang)
3916 ("r-vctrs" ,r-vctrs)))
3917 (home-page "https://github.com/r-lib/pillar")
3918 (synopsis "Coloured formatting for columns")
3920 "This package provides a @code{pillar} generic designed for formatting
3921 columns of data using the full range of colours provided by modern
3923 (license license:gpl3)))
3925 (define-public r-uuid
3932 (uri (cran-uri "uuid" version))
3935 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
3936 (build-system r-build-system)
3937 (home-page "http://www.rforge.net/uuid")
3938 (synopsis "Tools for generating and handling of UUIDs")
3940 "This package provides tools for generating and handling of
3941 @dfn{Universally Unique Identifiers} (UUIDs).")
3942 (license license:expat)))
3944 (define-public r-tinytex
3951 (uri (cran-uri "tinytex" version))
3954 "145dmgq7h55mmqqlnnj153j484x2a9s1fbvjbjkdyqzpnz9qh2ax"))))
3955 (build-system r-build-system)
3957 `(("r-xfun" ,r-xfun)))
3958 (home-page "https://github.com/yihui/tinytex")
3959 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
3961 "This package provides helper functions to install and maintain the LaTeX
3962 distribution named TinyTeX, a lightweight, cross-platform, portable, and
3963 easy-to-maintain version of TeX Live. This package also contains helper
3964 functions to compile LaTeX documents, and install missing LaTeX packages
3966 (license license:expat)))
3968 (define-public r-metap
3975 (uri (cran-uri "metap" version))
3978 "10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0"))))
3979 (build-system r-build-system)
3981 `(("r-lattice" ,r-lattice)
3982 ("r-rdpack" ,r-rdpack)))
3983 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
3984 (synopsis "Meta-analysis of significance values")
3986 "The canonical way to perform meta-analysis involves using effect sizes.
3987 When they are not available this package provides a number of methods for
3988 meta-analysis of significance values including the methods of Edgington,
3989 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
3990 published results; and a routine for graphical display.")
3991 (license license:gpl2)))
3993 (define-public r-network
4000 (uri (cran-uri "network" version))
4003 "1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
4004 (build-system r-build-system)
4006 `(("r-magrittr" ,r-magrittr)
4007 ("r-tibble" ,r-tibble)))
4008 (home-page "https://statnet.org/")
4009 (synopsis "Classes for relational data")
4011 "This package provides tools to create and modify network objects. The
4012 @code{network} class can represent a range of relational data types, and
4013 supports arbitrary vertex/edge/graph attributes.")
4014 (license license:gpl2+)))
4016 (define-public r-statnet-common
4018 (name "r-statnet-common")
4023 (uri (cran-uri "statnet.common" version))
4026 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4028 `((upstream-name . "statnet.common")))
4029 (build-system r-build-system)
4031 `(("r-coda" ,r-coda)))
4032 (home-page "https://statnet.org")
4033 (synopsis "R scripts and utilities used by the Statnet software")
4034 (description "This package provides non-statistical utilities used by the
4035 software developed by the Statnet Project.")
4036 (license license:gpl3)))
4038 (define-public r-sna
4045 (uri (cran-uri "sna" version))
4048 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
4049 (build-system r-build-system)
4051 `(("r-network" ,r-network)
4052 ("r-statnet-common" ,r-statnet-common)))
4053 (home-page "https://statnet.org")
4054 (synopsis "Tools for social network analysis")
4056 "This package provides a range of tools for social network analysis,
4057 including node and graph-level indices, structural distance and covariance
4058 methods, structural equivalence detection, network regression, random graph
4059 generation, and 2D/3D network visualization.")
4060 (license license:gpl2+)))
4062 (define-public r-ttr
4069 (uri (cran-uri "TTR" version))
4072 "18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb"))))
4073 (properties `((upstream-name . "TTR")))
4074 (build-system r-build-system)
4076 `(("r-curl" ,r-curl)
4079 (native-inputs `(("gfortran" ,gfortran)))
4080 (home-page "https://github.com/joshuaulrich/TTR")
4081 (synopsis "Technical trading rules")
4083 "This package provides functions and data to construct technical trading
4085 (license license:gpl2)))
4087 (define-public r-leaps
4094 (uri (cran-uri "leaps" version))
4097 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
4098 (build-system r-build-system)
4099 (native-inputs `(("gfortran" ,gfortran)))
4100 (home-page "https://cran.r-project.org/web/packages/leaps/")
4101 (synopsis "Regression subset selection")
4103 "This package provides tools for regression subset selection, including
4104 exhaustive search.")
4105 (license license:gpl2+)))
4107 (define-public r-splus2r
4114 (uri (cran-uri "splus2R" version))
4117 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4118 (properties `((upstream-name . "splus2R")))
4119 (build-system r-build-system)
4120 (native-inputs `(("gfortran" ,gfortran)))
4121 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4122 (synopsis "Supplemental S-PLUS functionality in R")
4124 "Currently there are many functions in S-PLUS that are missing in R. To
4125 facilitate the conversion of S-PLUS packages to R packages, this package
4126 provides some missing S-PLUS functionality in R.")
4127 (license license:gpl2)))
4129 (define-public r-ifultools
4131 (name "r-ifultools")
4136 (uri (cran-uri "ifultools" version))
4139 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4140 (build-system r-build-system)
4142 `(("r-mass" ,r-mass)
4143 ("r-splus2r" ,r-splus2r)))
4144 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4145 (synopsis "Insightful research tools")
4146 (description "This package provides C code used by the wmtsa, fractal, and
4148 (license license:gpl2)))
4150 (define-public r-sapa
4157 (uri (cran-uri "sapa" version))
4160 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4161 (build-system r-build-system)
4163 `(("r-ifultools" ,r-ifultools)
4164 ("r-splus2r" ,r-splus2r)))
4165 (home-page "https://cran.r-project.org/web/packages/sapa/")
4166 (synopsis "Spectral analysis for physical applications")
4167 (description "This package provides software for the book Spectral
4168 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4169 Cambridge University Press, 1993.")
4170 (license license:gpl2)))
4172 (define-public r-aggregation
4174 (name "r-aggregation")
4179 (uri (cran-uri "aggregation" version))
4182 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4183 (build-system r-build-system)
4184 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4185 (synopsis "Methods for p-value aggregation")
4187 "This package contains functionality for performing the following methods
4188 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4189 Fisher's method), and Sidak correction.")
4190 (license license:gpl3)))
4192 (define-public r-quantmod
4199 (uri (cran-uri "quantmod" version))
4202 "0lyzaf5ypk93v6zj9gdghy05cc7cxgn9yasv1apx5r6qsjcfgwky"))))
4203 (build-system r-build-system)
4205 `(("r-curl" ,r-curl)
4209 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4210 (synopsis "Quantitative financial modelling framework")
4211 (description "This package provides a quantitative financial modelling
4212 framework to allow users to specify, build, trade, and analyse quantitative
4213 financial trading strategies.")
4214 (license license:gpl3)))
4216 (define-public r-tseries
4223 (uri (cran-uri "tseries" version))
4226 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4227 (build-system r-build-system)
4229 `(("r-quadprog" ,r-quadprog)
4230 ("r-quantmod" ,r-quantmod)
4233 `(("gfortran" ,gfortran)))
4234 (home-page "https://cran.r-project.org/web/packages/tseries/")
4235 (synopsis "Time series analysis and computational finance")
4237 "This package provides functions relating to time series analysis and
4238 computational finance.")
4239 (license license:gpl2)))
4241 (define-public r-wmtsa
4248 (uri (cran-uri "wmtsa" version))
4251 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4252 (build-system r-build-system)
4254 `(("r-ifultools" ,r-ifultools)
4256 ("r-splus2r" ,r-splus2r)))
4257 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4258 (synopsis "Wavelet methods for time series analysis")
4260 "This package provides software to accompany the book \"Wavelet Methods
4261 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4262 University Press, 2000.")
4263 (license license:gpl2)))
4265 (define-public r-tsa
4272 (uri (cran-uri "TSA" version))
4275 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4276 (properties `((upstream-name . "TSA")))
4277 (build-system r-build-system)
4279 `(("r-leaps" ,r-leaps)
4280 ("r-locfit" ,r-locfit)
4281 ("r-mgcv" ,r-mgcv)))
4282 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
4283 (synopsis "Time series analysis")
4285 "This package contains R functions and datasets detailed in the book
4286 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4287 Cryer and Kung-Sik Chan.")
4288 (license license:gpl2+)))
4290 (define-public r-extradistr
4292 (name "r-extradistr")
4297 (uri (cran-uri "extraDistr" version))
4300 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4301 (properties `((upstream-name . "extraDistr")))
4302 (build-system r-build-system)
4304 `(("r-rcpp" ,r-rcpp)))
4305 (home-page "https://github.com/twolodzko/extraDistr")
4306 (synopsis "Additional univariate and multivariate distributions")
4308 "This package implements density, distribution functions, quantile
4309 functions and random generation functions for a large number of univariate and
4310 multivariate distributions.")
4311 (license license:gpl2)))
4313 (define-public r-fractal
4320 (uri (cran-uri "fractal" version))
4323 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4324 (build-system r-build-system)
4326 `(("r-ifultools" ,r-ifultools)
4329 ("r-scatterplot3d" ,r-scatterplot3d)
4330 ("r-splus2r" ,r-splus2r)
4331 ("r-wmtsa" ,r-wmtsa)))
4332 (home-page "https://cran.r-project.org/web/packages/fractal/")
4333 (synopsis "Fractal time series modeling and analysis")
4335 "This package provides tools for stochastic fractal and deterministic
4336 chaotic time series analysis.")
4337 (license license:gpl2)))
4339 (define-public r-urca
4346 (uri (cran-uri "urca" version))
4349 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4350 (build-system r-build-system)
4351 (propagated-inputs `(("r-nlme" ,r-nlme)))
4352 (native-inputs `(("gfortran" ,gfortran)))
4353 (home-page "https://cran.r-project.org/web/packages/urca/")
4354 (synopsis "Unit root and cointegration tests for time series data")
4356 "This package provides unit root and cointegration tests encountered in
4357 applied econometric analysis.")
4358 (license license:gpl2+)))
4360 (define-public r-cubature
4367 (uri (cran-uri "cubature" version))
4370 "0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"))))
4371 (build-system r-build-system)
4373 `(("r-rcpp" ,r-rcpp)))
4374 (home-page "https://github.com/bnaras/cubature")
4375 (synopsis "Adaptive multivariate integration over hypercubes")
4377 "This package is an R wrapper around the cubature C library for adaptive
4378 multivariate integration over hypercubes. This version provides both
4379 @code{hcubature} and @code{pcubature} routines in addition to a vector
4381 ;; The included cubature C library is released under GPLv2+, but the
4382 ;; wrapper declares the license to be GPLv3+.
4383 (license (list license:gpl2+ license:gpl3+))))
4385 (define-public r-trend
4392 (uri (cran-uri "trend" version))
4395 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
4396 (build-system r-build-system)
4398 `(("r-extradistr" ,r-extradistr)))
4400 `(("gfortran" ,gfortran)))
4401 (home-page "https://cran.r-project.org/web/packages/trend/")
4402 (synopsis "Non-parametric trend tests and change-point detection")
4404 "The analysis of environmental data often requires the detection of
4405 trends and change-points. This package includes tests for trend
4406 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4407 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4408 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4409 correlation trend test), change-point detection (Lanzante's test procedures,
4410 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4411 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4412 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
4413 sample Robust Rank-Order Distributional Test.")
4414 (license license:gpl3)))
4416 (define-public r-expm
4423 (uri (cran-uri "expm" version))
4426 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
4427 (build-system r-build-system)
4428 (propagated-inputs `(("r-matrix" ,r-matrix)))
4429 (native-inputs `(("gfortran" ,gfortran)))
4430 (home-page "https://r-forge.r-project.org/projects/expm/")
4431 (synopsis "Tools for matrix exponentials and related quantities")
4433 "This package provides tools for the computation of the matrix
4434 exponential, logarithm, square root, and related quantities.")
4435 (license license:gpl2+)))
4437 (define-public r-complexplus
4439 (name "r-complexplus")
4444 (uri (cran-uri "complexplus" version))
4447 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
4448 (build-system r-build-system)
4450 `(("r-expm" ,r-expm)
4451 ("r-matrix" ,r-matrix)))
4452 (home-page "https://cran.r-project.org/web/packages/complexplus/")
4453 (synopsis "Functions of complex or real variables")
4455 "This package extends several functions to the complex domain, including
4456 the matrix exponential and logarithm, and the determinant.")
4457 (license license:gpl2)))
4459 (define-public r-phontools
4461 (name "r-phontools")
4466 (uri (cran-uri "phonTools" version))
4469 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
4470 (properties `((upstream-name . "phonTools")))
4471 (build-system r-build-system)
4472 (home-page "http://www.santiagobarreda.com/rscripts.html")
4473 (synopsis "Tools for phonetic and acoustic analyses")
4475 "This package contains tools for the organization, display, and analysis
4476 of the sorts of data frequently encountered in phonetics research and
4477 experimentation, including the easy creation of IPA vowel plots, and the
4478 creation and manipulation of WAVE audio files.")
4479 (license license:bsd-2)))
4488 (uri (cran-uri "np" version))
4491 "1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
4492 (build-system r-build-system)
4494 `(("r-boot" ,r-boot)
4495 ("r-cubature" ,r-cubature)
4496 ("r-quadprog" ,r-quadprog)
4497 ("r-quantreg" ,r-quantreg)))
4498 (home-page "https://github.com/JeffreyRacine/R-Package-np")
4499 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
4500 (description "This package provides non-parametric (and semi-parametric)
4501 kernel methods that seamlessly handle a mix of continuous, unordered, and
4502 ordered factor data types.")
4503 ;; Any version of the GPL.
4504 (license license:gpl3+)))
4506 (define-public r-powerplus
4508 (name "r-powerplus")
4513 (uri (cran-uri "powerplus" version))
4516 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
4517 (build-system r-build-system)
4519 `(("r-complexplus" ,r-complexplus)
4522 ("r-matrix" ,r-matrix)
4523 ("r-phontools" ,r-phontools)))
4524 (home-page "https://cran.r-project.org/web/packages/powerplus/")
4525 (synopsis "Exponentiation operations")
4527 "This package provides tools for the computation of matrix and scalar
4529 (license license:gpl2)))
4531 (define-public r-heatmaply
4533 (name "r-heatmaply")
4538 (uri (cran-uri "heatmaply" version))
4541 "1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1"))))
4542 (build-system r-build-system)
4544 `(("r-assertthat" ,r-assertthat)
4545 ("r-colorspace" ,r-colorspace)
4546 ("r-dendextend" ,r-dendextend)
4547 ("r-ggplot2" ,r-ggplot2)
4548 ("r-htmlwidgets" ,r-htmlwidgets)
4549 ("r-magrittr" ,r-magrittr)
4550 ("r-plotly" ,r-plotly)
4551 ("r-rcolorbrewer" ,r-rcolorbrewer)
4552 ("r-reshape2" ,r-reshape2)
4553 ("r-scales" ,r-scales)
4554 ("r-seriation" ,r-seriation)
4555 ("r-viridis" ,r-viridis)
4556 ("r-webshot" ,r-webshot)))
4557 (home-page "https://cran.r-project.org/package=heatmaply")
4558 (synopsis "Interactive cluster heat maps using plotly")
4560 "This package enables you to create interactive cluster heatmaps that can
4561 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
4562 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
4563 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
4564 a popular graphical method for visualizing high-dimensional data, in which a
4565 table of numbers is encoded as a grid of colored cells. The rows and columns
4566 of the matrix are ordered to highlight patterns and are often accompanied by
4568 ;; Either version of the license.
4569 (license (list license:gpl2 license:gpl3))))
4578 (uri (cran-uri "h5" version))
4581 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
4582 (build-system r-build-system)
4587 `(("which" ,which)))
4589 `(("r-rcpp" ,r-rcpp)))
4590 (home-page "https://github.com/mannau/h5")
4591 (synopsis "Interface to the HDF5 Library")
4593 "This package provides an S4 interface to the HDF5 library supporting
4594 fast storage and retrieval of R-objects like vectors, matrices and arrays to
4595 binary files in a language independent format. The HDF5 format can therefore
4596 be used as an alternative to R's save/load mechanism. Since h5 is able to
4597 access only subsets of stored data it can also handle data sets which do not
4599 (license license:bsd-2)))
4601 (define-public r-cgdsr
4608 (uri (cran-uri "cgdsr" version))
4611 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
4612 (build-system r-build-system)
4614 `(("r-httr" ,r-httr)
4615 ("r-r-methodss3" ,r-r-methodss3)
4616 ("r-r-oo" ,r-r-oo)))
4617 (home-page "https://github.com/cBioPortal/cgdsr")
4618 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
4620 "This package provides a basic set of R functions for querying the Cancer
4621 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
4622 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
4623 (license license:lgpl3)))
4625 (define-public r-import
4632 (uri (cran-uri "import" version))
4635 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
4636 (build-system r-build-system)
4637 (home-page "https://github.com/smbache/import")
4638 (synopsis "Import mechanism for R")
4640 "This is an alternative mechanism for importing objects from packages.
4641 The syntax allows for importing multiple objects from a package with a single
4642 command in an expressive way. The import package bridges some of the gap
4643 between using @code{library} (or @code{require}) and direct (single-object)
4644 imports. Furthermore the imported objects are not placed in the current
4645 environment. It is also possible to import objects from stand-alone @code{.R}
4647 (license license:expat)))
4649 (define-public r-shinyace
4656 (uri (cran-uri "shinyAce" version))
4659 "0hvih5g0pswlnz5rf3blx5yqw11ssxvm8w4klxddp1ap20ncbgl1"))))
4660 (properties `((upstream-name . "shinyAce")))
4661 (build-system r-build-system)
4663 `(("r-shiny" ,r-shiny)
4664 ("r-jsonlite" ,r-jsonlite)))
4665 (home-page "http://cran.r-project.org/web/packages/shinyAce")
4666 (synopsis "Ace editor bindings for Shiny")
4668 "This package provides Ace editor bindings to enable a rich text editing
4669 environment within Shiny.")
4670 (license license:expat)))
4672 (define-public r-base64url
4674 (name "r-base64url")
4679 (uri (cran-uri "base64url" version))
4682 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
4683 (build-system r-build-system)
4685 `(("r-backports" ,r-backports)))
4686 (home-page "https://github.com/mllg/base64url")
4687 (synopsis "Fast and URL-safe base64 encoder and decoder")
4689 "This package provides a URL-safe base64 encoder and decoder. In
4690 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
4691 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
4692 encoder does not fill the string with trailing @code{=}. The resulting
4693 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
4694 and thus are safe to use in URLs or for file names. The package also comes
4695 with a simple base32 encoder/decoder suited for case insensitive file
4697 (license license:gpl3)))
4699 (define-public r-radiant-data
4701 (name "r-radiant-data")
4706 (uri (cran-uri "radiant.data" version))
4709 "0b35jn4mcj10hqra18l8pi6s4pvj6fxipslbn6hkr4zza1z27gzw"))
4710 (modules '((guix build utils)))
4713 ;; Delete files that are under CC-NC-SA.
4714 (delete-file-recursively "inst/app/tools/help")
4716 (properties `((upstream-name . "radiant.data")))
4717 (build-system r-build-system)
4719 `(("r-base64enc" ,r-base64enc)
4720 ("r-broom" ,r-broom)
4723 ("r-dplyr" ,r-dplyr)
4726 ("r-ggplot2" ,r-ggplot2)
4727 ("r-gridextra" ,r-gridextra)
4728 ("r-import" ,r-import)
4729 ("r-jsonlite" ,r-jsonlite)
4730 ("r-knitr" ,r-knitr)
4731 ("r-lubridate" ,r-lubridate)
4732 ("r-magrittr" ,r-magrittr)
4733 ("r-markdown" ,r-markdown)
4734 ("r-plotly" ,r-plotly)
4735 ("r-psych" ,r-psych)
4736 ("r-readr" ,r-readr)
4737 ("r-readxl" ,r-readxl)
4738 ("r-rlang" ,r-rlang)
4739 ("r-rmarkdown" ,r-rmarkdown)
4740 ("r-rstudioapi" ,r-rstudioapi)
4741 ("r-scales" ,r-scales)
4742 ("r-shiny" ,r-shiny)
4743 ("r-shinyfiles" ,r-shinyfiles)
4744 ("r-shinyace" ,r-shinyace)
4745 ("r-stringi" ,r-stringi)
4746 ("r-tibble" ,r-tibble)
4747 ("r-tidyr" ,r-tidyr)
4748 ("r-writexl" ,r-writexl)))
4749 (home-page "https://github.com/radiant-rstats/radiant.data")
4750 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
4752 "The Radiant Data menu includes interfaces for loading, saving, viewing,
4753 visualizing, summarizing, transforming, and combining data. It also contains
4754 functionality to generate reproducible reports of the analyses conducted in
4756 (license license:agpl3)))
4758 (define-public r-algdesign
4760 (name "r-algdesign")
4765 (uri (cran-uri "AlgDesign" version))
4768 "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
4769 (properties `((upstream-name . "AlgDesign")))
4770 (build-system r-build-system)
4771 (home-page "https://github.com/jvbraun/AlgDesign")
4772 (synopsis "Algorithmic experimental design")
4774 "This package provides tools to calculate exact and approximate theory
4775 experimental designs for D, A, and I criteria. Very large designs may be
4776 created. Experimental designs may be blocked or blocked designs created from
4777 a candidate list, using several criteria. The blocking can be done when whole
4778 and within plot factors interact.")
4779 (license license:gpl2+)))
4781 (define-public r-signal
4788 (uri (cran-uri "signal" version))
4791 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
4792 (build-system r-build-system)
4793 (propagated-inputs `(("r-mass" ,r-mass)))
4794 (native-inputs `(("gfortran" ,gfortran)))
4795 (home-page "https://cran.r-project.org/web/packages/signal/")
4796 (synopsis "Signal processing")
4798 "This package provides a set of signal processing functions originally
4799 written for Matlab and GNU Octave. It includes filter generation utilities,
4800 filtering functions, resampling routines, and visualization of filter models.
4801 It also includes interpolation functions.")
4802 (license license:gpl2)))
4804 (define-public r-gsubfn
4811 (uri (cran-uri "gsubfn" version))
4814 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
4815 (build-system r-build-system)
4816 (propagated-inputs `(("r-proto" ,r-proto)))
4817 (home-page "http://gsubfn.googlecode.com")
4818 (synopsis "Utilities for strings and function arguments.")
4820 "This package provides @code{gsubfn} which is like @code{gsub} but can
4821 take a replacement function or certain other objects instead of the
4822 replacement string. Matches and back references are input to the replacement
4823 function and replaced by the function output. @code{gsubfn} can be used to
4824 split strings based on content rather than delimiters and for quasi-perl-style
4825 string interpolation. The package also has facilities for translating
4826 formulas to functions and allowing such formulas in function calls instead of
4828 (license license:gpl2+)))
4830 (define-public r-sqldf
4837 (uri (cran-uri "sqldf" version))
4840 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
4841 (build-system r-build-system)
4843 `(("r-chron" ,r-chron)
4845 ("r-gsubfn" ,r-gsubfn)
4846 ("r-proto" ,r-proto)
4847 ("r-rsqlite" ,r-rsqlite)))
4848 (home-page "https://github.com/ggrothendieck/sqldf")
4849 (synopsis "Manipulate R data frames using SQL")
4851 "The @code{sqldf} function is typically passed a single argument which is
4852 an SQL select statement where the table names are ordinary R data frame names.
4853 @code{sqldf} transparently sets up a database, imports the data frames into
4854 that database, performs the SQL statement and returns the result using a
4855 heuristic to determine which class to assign to each column of the returned
4856 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
4857 used to read filtered files into R even if the original files are larger than
4858 R itself can handle.")
4859 (license license:gpl2)))
4861 (define-public r-abind
4868 (uri (cran-uri "abind" version))
4871 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
4872 (build-system r-build-system)
4873 (home-page "https://cran.r-project.org/web/packages/abind/")
4874 (synopsis "Combine multidimensional arrays")
4876 "This package provides tools to combine multidimensional arrays into a
4877 single array. This is a generalization of @code{cbind} and @code{rbind}. It
4878 works with vectors, matrices, and higher-dimensional arrays. It also provides
4879 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
4880 extracting and replacing data in arrays.")
4881 (license license:lgpl2.0+)))
4883 (define-public r-prroc
4890 (uri (cran-uri "PRROC" version))
4893 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
4894 (properties `((upstream-name . "PRROC")))
4895 (build-system r-build-system)
4896 (home-page "https://cran.r-project.org/web/packages/PRROC/")
4897 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
4899 "This package computes the areas under the @dfn{precision-recall} (PR)
4900 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
4901 contrast to other implementations, the interpolation between points of the PR
4902 curve is done by a non-linear piecewise function. In addition to the areas
4903 under the curves, the curves themselves can also be computed and plotted by a
4904 specific S3-method.")
4905 (license license:gpl3)))
4907 (define-public r-vim
4914 (uri (cran-uri "VIM" version))
4917 "08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
4918 (properties `((upstream-name . "VIM")))
4919 (build-system r-build-system)
4922 ("r-colorspace" ,r-colorspace)
4923 ("r-data-table" ,r-data-table)
4924 ("r-e1071" ,r-e1071)
4925 ("r-laeken" ,r-laeken)
4928 ("r-ranger" ,r-ranger)
4930 ("r-robustbase" ,r-robustbase)
4933 (home-page "https://github.com/alexkowa/VIM")
4934 (synopsis "Visualization and imputation of missing values")
4936 "This package provides tools for the visualization of missing and/or
4937 imputed values are introduced, which can be used for exploring the data and
4938 the structure of the missing and/or imputed values. Depending on this
4939 structure of the missing values, the corresponding methods may help to
4940 identify the mechanism generating the missing values and allows to explore the
4941 data including missing values. In addition, the quality of imputation can be
4942 visually explored using various univariate, bivariate, multiple and
4943 multivariate plot methods.")
4944 (license license:gpl2+)))
4946 (define-public r-fnn
4953 (uri (cran-uri "FNN" version))
4956 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
4957 (properties `((upstream-name . "FNN")))
4958 (build-system r-build-system)
4959 (home-page "https://cran.r-project.org/web/packages/FNN")
4960 (synopsis "Fast nearest neighbor search algorithms and applications")
4962 "This package provides cover-tree and kd-tree fast k-nearest neighbor
4963 search algorithms. Related applications including KNN classification,
4964 regression and information measures are implemented.")
4965 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
4966 ;; later can be used.
4967 (license license:gpl2+)))
4969 (define-public r-smoother
4976 (uri (cran-uri "smoother" version))
4979 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
4980 (build-system r-build-system)
4982 `(("r-ttr" ,r-ttr)))
4983 (home-page "http://cran.r-project.org/web/packages/smoother")
4984 (synopsis "Functions relating to the smoothing of numerical data")
4986 "This package provides a collection of methods for smoothing numerical
4987 data, commencing with a port of the Matlab gaussian window smoothing function.
4988 In addition, several functions typically used in smoothing of financial data
4990 (license license:gpl2)))
4992 (define-public r-riverplot
4994 (name "r-riverplot")
4999 (uri (cran-uri "riverplot" version))
5002 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5003 (build-system r-build-system)
5004 (home-page "https://logfc.wordpress.com")
5005 (synopsis "Sankey or ribbon plots")
5007 "Sankey plots are a type of diagram that is convenient to illustrate how
5008 flow of information, resources etc. separates and joins, much like observing
5009 how rivers split and merge. For example, they can be used to compare
5010 different clusterings. This package provides an implementation of Sankey
5012 (license license:gpl2+)))
5014 (define-public r-dyn
5021 (uri (cran-uri "dyn" version))
5024 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5025 (build-system r-build-system)
5027 `(("r-zoo" ,r-zoo)))
5028 (home-page "https://cran.r-project.org/web/packages/dyn")
5029 (synopsis "Time series regression")
5031 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5032 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5033 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5034 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5035 @code{randomForest::randomForest()} and other regression functions, allowing
5036 those functions to be used with time series including specifications that may
5037 contain lags, diffs and missing values.")
5039 (license license:gpl2+)))
5041 (define-public r-catdap
5048 (uri (cran-uri "catdap" version))
5051 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
5052 (build-system r-build-system)
5054 `(("gfortran" ,gfortran)))
5055 (home-page "https://cran.r-project.org/web/packages/catdap/")
5056 (synopsis "Tools for categorical data analysis")
5058 "This package provides functions for analyzing multivariate data.
5059 Dependencies of the distribution of the specified variable (response
5060 variable) to other variables (explanatory variables) are derived and
5061 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5062 (license license:gpl2+)))
5064 (define-public r-arules
5071 (uri (cran-uri "arules" version))
5074 "0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y"))))
5075 (build-system r-build-system)
5077 `(("r-matrix" ,r-matrix)))
5078 (home-page "https://github.com/mhahsler/arules")
5079 (synopsis "Mining association rules and frequent itemsets")
5081 "This package provides an infrastructure for representing, manipulating
5082 and analyzing transaction data and patterns (frequent itemsets and association rules).
5083 It also provides C implementations of the association mining algorithms Apriori
5085 (license license:gpl3)))
5087 (define-public r-parsedate
5089 (name "r-parsedate")
5094 (uri (cran-uri "parsedate" version))
5097 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5098 (build-system r-build-system)
5100 `(("r-rematch2" ,r-rematch2)))
5101 (home-page "https://github.com/gaborcsardi/parsedate")
5103 "Recognize and parse dates in various formats")
5105 "This package provides three functions for dealing with dates:
5106 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5107 time formats, @code{parse_date} parses dates in unspecified formats,
5108 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5109 (license license:gpl2)))
5111 (define-public r-abc-data
5118 (uri (cran-uri "abc.data" version))
5121 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5122 (properties `((upstream-name . "abc.data")))
5123 (build-system r-build-system)
5124 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5125 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5127 "This package contains data which are used by functions of the abc
5128 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5129 algorithms for performing parameter estimation, model selection, and
5131 (license license:gpl3+)))
5133 (define-public r-abc
5140 (uri (cran-uri "abc" version))
5143 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5144 (build-system r-build-system)
5146 `(("r-abc-data" ,r-abc-data)
5147 ("r-locfit" ,r-locfit)
5150 ("r-quantreg" ,r-quantreg)))
5151 (home-page "https://cran.r-project.org/web/packages/abc/")
5152 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5154 "This package implements several @dfn{Approximate Bayesian
5155 Computation} (ABC) algorithms for performing parameter estimation, model
5156 selection, and goodness-of-fit. Cross-validation tools are also available for
5157 measuring the accuracy of ABC estimates, and to calculate the
5158 misclassification probabilities of different models.")
5159 (license license:gpl3+)))
5161 (define-public r-zip
5168 (uri (cran-uri "zip" version))
5171 "0zii05jg9v9ljd0wd67g9x4bhlmpmsy5dzd093sbnc5n3vjbi32a"))))
5172 (build-system r-build-system)
5173 (home-page "https://github.com/gaborcsardi/zip")
5174 (synopsis "Cross-platform Zip compression")
5176 "This package provides a cross-platform Zip compression library for R.
5177 It is a replacement for the @code{zip} function, that does not require any
5178 additional external tools on any platform.")
5179 (license license:cc0)))
5181 (define-public r-openxlsx
5188 (uri (cran-uri "openxlsx" version))
5191 "1lflygpi1z4rlb1c6g6wsmi334maiiy7jhpg6ph4sw8lpvg12w4b"))))
5192 (build-system r-build-system)
5194 `(("r-rcpp" ,r-rcpp)
5196 (home-page "https://github.com/awalker89/openxlsx")
5197 (synopsis "Read, write and edit XLSX files")
5199 "This package simplifies the creation of Excel @code{.xlsx} files by
5200 providing a high level interface to writing, styling and editing worksheets.
5201 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5202 and @code{XLConnect} packages with the added benefit of removing the
5203 dependency on Java.")
5204 (license license:gpl3)))
5206 (define-public r-rio
5213 (uri (cran-uri "rio" version))
5216 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5217 (build-system r-build-system)
5219 `(("r-curl" ,r-curl)
5220 ("r-data-table" ,r-data-table)
5221 ("r-foreign" ,r-foreign)
5222 ("r-haven" ,r-haven)
5223 ("r-openxlsx" ,r-openxlsx)
5224 ("r-readxl" ,r-readxl)
5225 ("r-tibble" ,r-tibble)))
5226 (home-page "https://github.com/leeper/rio")
5227 (synopsis "Swiss-army knife for data I/O")
5229 "This package provides streamlined data import and export infrastructure
5230 by making assumptions that the user is probably willing to make: @code{import}
5231 and @code{export} determine the data structure from the file extension,
5232 reasonable defaults are used for data import and export (e.g.,
5233 @code{stringsAsFactors=FALSE}), web-based import is natively
5234 supported (including from SSL/HTTPS), compressed files can be read directly
5235 without explicit decompression, and fast import packages are used where
5236 appropriate. An additional convenience function, @code{convert}, provides a
5237 simple method for converting between file types.")
5238 (license license:gpl2)))
5240 (define-public r-maptools
5247 (uri (cran-uri "maptools" version))
5250 "1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax"))))
5251 (build-system r-build-system)
5253 `(("r-foreign" ,r-foreign)
5254 ("r-lattice" ,r-lattice)
5256 (home-page "http://r-forge.r-project.org/projects/maptools/")
5257 (synopsis "Tools for reading and handling spatial objects")
5259 "This package provides a set of tools for manipulating and reading
5260 geographic data, in particular ESRI Shapefiles. It includes binary access to
5261 GSHHG shoreline files. The package also provides interface wrappers for
5262 exchanging spatial objects with other R packages.")
5263 ;; The C source files from shapelib are released under the Expat license.
5264 ;; The R code is released under GPL version 2 or later.
5265 (license (list license:gpl2+
5268 (define-public r-later
5275 (uri (cran-uri "later" version))
5278 "08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb"))))
5279 (build-system r-build-system)
5283 ("r-rlang" ,r-rlang)))
5284 (home-page "https://github.com/r-lib/later")
5285 (synopsis "Utilities for delaying function execution")
5287 "This package provides tools to execute arbitrary R or C functions some
5288 time after the current time, after the R execution stack has emptied.")
5289 (license license:gpl2+)))
5291 (define-public r-promises
5298 (uri (cran-uri "promises" version))
5301 "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
5302 (build-system r-build-system)
5304 `(("r-later" ,r-later)
5305 ("r-magrittr" ,r-magrittr)
5308 ("r-rlang" ,r-rlang)))
5309 (home-page "https://rstudio.github.io/promises")
5310 (synopsis "Abstractions for promise-based asynchronous programming")
5312 "This package provides fundamental abstractions for doing asynchronous
5313 programming in R using promises. Asynchronous programming is useful for
5314 allowing a single R process to orchestrate multiple tasks in the background
5315 while also attending to something else. Semantics are similar to JavaScript
5316 promises, but with a syntax that is idiomatic R.")
5317 (license license:expat)))
5319 (define-public r-dosnow
5326 (uri (cran-uri "doSNOW" version))
5329 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5330 (properties `((upstream-name . "doSNOW")))
5331 (build-system r-build-system)
5333 `(("r-foreach" ,r-foreach)
5334 ("r-iterators" ,r-iterators)
5335 ("r-snow" ,r-snow)))
5336 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5337 (synopsis "Foreach parallel adaptor for the snow package")
5339 "This package provides a parallel backend for the @code{%dopar%} function
5340 using the @code{snow} package.")
5341 (license license:gpl2)))
5343 (define-public r-snowfall
5346 (version "1.84-6.1")
5349 (uri (cran-uri "snowfall" version))
5351 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
5352 (build-system r-build-system)
5354 `(("r-snow" ,r-snow)))
5355 (home-page "http://cran.r-project.org/web/packages/snowfall/")
5356 (synopsis "Easier cluster computing")
5357 (description "This package is a usability wrapper around snow for easier
5358 development of parallel R programs. This package offers e.g. extended error
5359 checks, and additional functions. All functions work in sequential mode, too,
5360 if no cluster is present or wished. The package is also designed as connector
5361 to the cluster management tool @code{sfCluster}, but can also used without
5363 (license license:gpl2+)))
5365 (define-public r-rappdirs
5372 (uri (cran-uri "rappdirs" version))
5375 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
5376 (build-system r-build-system)
5377 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
5378 (synopsis "Determine where to save data, caches, and logs")
5380 "This package provides an easy way to determine which directories on the
5381 user's computer should be used to save data, caches and logs. It is a port of
5382 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
5383 (license license:expat)))
5385 (define-public r-learnr
5392 (uri (cran-uri "learnr" version))
5395 "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5"))))
5396 (build-system r-build-system)
5398 `(("r-evaluate" ,r-evaluate)
5399 ("r-htmltools" ,r-htmltools)
5400 ("r-htmlwidgets" ,r-htmlwidgets)
5401 ("r-jsonlite" ,r-jsonlite)
5402 ("r-knitr" ,r-knitr)
5403 ("r-markdown" ,r-markdown)
5404 ("r-rappdirs" ,r-rappdirs)
5405 ("r-rmarkdown" ,r-rmarkdown)
5406 ("r-rprojroot" ,r-rprojroot)
5407 ("r-shiny" ,r-shiny)
5408 ("r-withr" ,r-withr)))
5409 (home-page "https://rstudio.github.io/learnr/")
5410 (synopsis "Interactive tutorials for R")
5412 "This package provides tools to create interactive tutorials using R
5413 Markdown. Use a combination of narrative, figures, videos, exercises, and
5414 quizzes to create self-paced tutorials for learning about R and R packages.")
5415 (license license:asl2.0)))
5417 (define-public r-analytics
5419 (name "r-analytics")
5424 (uri (cran-uri "analytics" version))
5427 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
5428 (build-system r-build-system)
5431 ("r-cluster" ,r-cluster)
5432 ("r-fractal" ,r-fractal)
5433 ("r-lmtest" ,r-lmtest)
5436 ("r-powerplus" ,r-powerplus)
5437 ("r-robust" ,r-robust)
5438 ("r-trend" ,r-trend)
5442 (home-page "https://cran.r-project.org/web/packages/analytics/")
5443 (synopsis "Collection of data analysis tools")
5445 "This package is a collection of data analysis tools. It includes tools
5446 for regression outlier detection in a fitted linear model, stationary
5447 bootstrap using a truncated geometric distribution, a comprehensive test for
5448 weak stationarity, column means by group, weighted biplots, and a heuristic to
5449 obtain a better initial configuration in non-metric MDS.")
5450 (license license:gpl2)))
5452 (define-public r-reticulate
5454 (name "r-reticulate")
5459 (uri (cran-uri "reticulate" version))
5462 "1qwxh7zq9igl7dxl5g5qjbvv0mlac3w80djnkm0w8rxnaval3gmd"))))
5463 (build-system r-build-system)
5464 (inputs `(("python" ,python)))
5466 `(("r-jsonlite" ,r-jsonlite)
5467 ("r-matrix" ,r-matrix)
5468 ("r-rcpp" ,r-rcpp)))
5469 (home-page "https://github.com/rstudio/reticulate")
5470 (synopsis "R interface to Python")
5472 "This package provides an interface from R to Python modules, classes,
5473 and functions. When calling into Python, R data types are automatically
5474 converted to their equivalent Python types. When values are returned from
5475 Python to R they are converted back to R types.")
5476 (license license:asl2.0)))
5478 (define-public r-bibtex
5485 (uri (cran-uri "bibtex" version))
5488 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
5489 (build-system r-build-system)
5490 (propagated-inputs `(("r-stringr" ,r-stringr)))
5491 (home-page "https://github.com/romainfrancois/bibtex")
5492 (synopsis "Bibtex parser")
5493 (description "This package provides a utility for R to parse a bibtex
5495 (license license:gpl2+)))
5497 (define-public r-ggseqlogo
5499 (name "r-ggseqlogo")
5504 (uri (cran-uri "ggseqlogo" version))
5507 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
5508 (build-system r-build-system)
5509 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
5510 (home-page "https://github.com/omarwagih/ggseqlogo")
5511 (synopsis "ggplot2 extension for drawing genetic sequence logos")
5513 "The range of functions provided by this package makes it possible to
5514 draw highly versatile genomic sequence logos. Features include, but are not
5515 limited to, modifying colour schemes and fonts used to draw the logo,
5516 generating multiple logo plots, and aiding the visualisation with annotations.
5517 Sequence logos can easily be combined with other ggplot2 plots.")
5518 ;; Unspecified version of the LGPL.
5519 (license license:lgpl3+)))
5521 (define-public r-ggsci
5528 (uri (cran-uri "ggsci" version))
5531 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
5532 (build-system r-build-system)
5534 `(("r-ggplot2" ,r-ggplot2)
5535 ("r-scales" ,r-scales)))
5536 (home-page "https://nanx.me/ggsci/")
5537 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
5539 "This package provides a collection of ggplot2 color palettes inspired by
5540 plots in scientific journals, data visualization libraries, science fiction
5541 movies, and TV shows.")
5542 (license license:gpl3)))
5544 (define-public r-ggsignif
5551 (uri (cran-uri "ggsignif" version))
5554 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
5555 (build-system r-build-system)
5557 `(("r-ggplot2" ,r-ggplot2)))
5558 (home-page "https://github.com/const-ae/ggsignif")
5559 (synopsis "Significance brackets for ggplot2")
5561 "Enrich your ggplots with group-wise comparisons. This package provides
5562 an easy way to indicate if two groups are significantly different. Commonly
5563 this is shown by a bracket on top connecting the groups of interest which
5564 itself is annotated with the level of significance. The package provides a
5565 single layer that takes the groups for comparison and the test as arguments
5566 and adds the annotation to the plot.")
5567 (license license:gpl3)))
5569 (define-public r-ggpubr
5576 (uri (cran-uri "ggpubr" version))
5579 "0r5knv3707pmpngmj60zn761y3bh8lj89dhh1b80ss083xnxr4qw"))))
5580 (build-system r-build-system)
5582 `(("r-cowplot" ,r-cowplot)
5583 ("r-dplyr" ,r-dplyr)
5584 ("r-ggplot2" ,r-ggplot2)
5585 ("r-ggrepel" ,r-ggrepel)
5586 ("r-ggsci" ,r-ggsci)
5587 ("r-ggsignif" ,r-ggsignif)
5589 ("r-gridextra" ,r-gridextra)
5590 ("r-magrittr" ,r-magrittr)
5591 ("r-polynom" ,r-polynom)
5592 ("r-purrr" ,r-purrr)
5593 ("r-rlang" ,r-rlang)
5594 ("r-scales" ,r-scales)
5595 ("r-tidyr" ,r-tidyr)))
5596 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
5597 (synopsis "ggplot2-based publication-ready plots")
5599 "The ggplot2 package is an excellent and flexible package for elegant
5600 data visualization in R. However the default generated plots require some
5601 formatting before we can send them for publication. The ggpubr package
5602 provides some easy-to-use functions for creating and customizing ggplot2-based
5603 publication-ready plots.")
5604 (license license:gpl2)))
5606 (define-public r-ellipse
5613 (uri (cran-uri "ellipse" version))
5616 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
5617 (build-system r-build-system)
5618 (home-page "https://cran.r-project.org/web/packages/ellipse/")
5619 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
5621 "This package contains various routines for drawing ellipses and
5622 ellipse-like confidence regions, implementing the plots described in Murdoch
5623 and Chow (1996), A graphical display of large correlation matrices, The
5624 American Statistician 50, 178-180. There are also routines implementing the
5625 profile plots described in Bates and Watts (1988), Nonlinear Regression
5626 Analysis and its Applications.")
5627 (license license:gpl2+)))
5629 (define-public r-flashclust
5631 (name "r-flashclust")
5636 (uri (cran-uri "flashClust" version))
5639 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
5640 (properties `((upstream-name . "flashClust")))
5641 (build-system r-build-system)
5642 (native-inputs `(("gfortran" ,gfortran)))
5643 (home-page "https://cran.r-project.org/web/packages/flashClust/")
5644 (synopsis "Implementation of optimal hierarchical clustering")
5646 "This package provides a fast implementation of hierarchical
5648 (license license:gpl2+)))
5650 (define-public r-factominer
5652 (name "r-factominer")
5657 (uri (cran-uri "FactoMineR" version))
5660 "1yl16inb2m89l1czgaf0pgy9655dpr751hyx92yw6rqpd2ryznac"))))
5661 (properties `((upstream-name . "FactoMineR")))
5662 (build-system r-build-system)
5665 ("r-cluster" ,r-cluster)
5666 ("r-ellipse" ,r-ellipse)
5667 ("r-flashclust" ,r-flashclust)
5668 ("r-lattice" ,r-lattice)
5669 ("r-leaps" ,r-leaps)
5671 ("r-scatterplot3d" ,r-scatterplot3d)))
5672 (home-page "http://factominer.free.fr")
5673 (synopsis "Multivariate exploratory data analysis and data mining")
5675 "This package provides exploratory data analysis methods to summarize,
5676 visualize and describe datasets. The main principal component methods are
5677 available, those with the largest potential in terms of applications:
5678 principal component analysis (PCA) when variables are quantitative,
5679 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
5680 variables are categorical, Multiple Factor Analysis when variables are
5681 structured in groups, etc. and hierarchical cluster analysis.")
5682 (license license:gpl2+)))
5684 (define-public r-factoextra
5686 (name "r-factoextra")
5691 (uri (cran-uri "factoextra" version))
5694 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
5695 (build-system r-build-system)
5697 `(("r-abind" ,r-abind)
5698 ("r-cluster" ,r-cluster)
5699 ("r-dendextend" ,r-dendextend)
5700 ("r-factominer" ,r-factominer)
5701 ("r-ggplot2" ,r-ggplot2)
5702 ("r-ggpubr" ,r-ggpubr)
5703 ("r-ggrepel" ,r-ggrepel)
5704 ("r-reshape2" ,r-reshape2)
5705 ("r-tidyr" ,r-tidyr)))
5706 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
5707 (synopsis "Extract and visualize the results of multivariate data analyses")
5709 "This package provides some easy-to-use functions to extract and
5710 visualize the output of multivariate data analyses, including
5711 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
5712 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
5713 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
5714 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
5715 packages. It contains also functions for simplifying some clustering analysis
5716 steps and provides ggplot2-based elegant data visualization.")
5717 (license license:gpl2)))
5719 (define-public r-fansi
5726 (uri (cran-uri "fansi" version))
5729 "02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
5730 (build-system r-build-system)
5732 `(("r-knitr" ,r-knitr))) ; for vignettes
5733 (home-page "https://github.com/brodieG/fansi")
5734 (synopsis "ANSI control sequence aware string functions")
5736 "This package provides counterparts to R string manipulation functions
5737 that account for the effects of ANSI text formatting control sequences.")
5738 (license license:gpl2+)))
5740 (define-public r-nbclust
5747 (uri (cran-uri "NbClust" version))
5750 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
5751 (properties `((upstream-name . "NbClust")))
5752 (build-system r-build-system)
5753 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
5754 (synopsis "Determine the best number of clusters in a data set")
5756 "NbClust provides 30 indexes for determining the optimal number of
5757 clusters in a data set and offers the best clustering scheme from different
5758 results to the user.")
5759 (license license:gpl2)))
5761 (define-public r-hdf5r
5768 (uri (cran-uri "hdf5r" version))
5771 "10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq"))))
5772 (build-system r-build-system)
5777 `(("r-bit64" ,r-bit64)
5779 (home-page "https://hhoeflin.github.io/hdf5r")
5780 (synopsis "Interface to the HDF5 binary data format")
5782 "HDF5 is a data model, library and file format for storing and managing
5783 large amounts of data. This package provides a nearly feature complete,
5784 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
5785 functionality is added so that HDF5 objects behave very similar to their
5786 corresponding R counterparts.")
5787 (license license:asl2.0)))
5789 (define-public r-itertools
5791 (name "r-itertools")
5796 (uri (cran-uri "itertools" version))
5799 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
5800 (build-system r-build-system)
5802 `(("r-iterators" ,r-iterators)))
5803 (home-page "https://cran.r-project.org/web/packages/itertools/")
5804 (synopsis "Iterator tools")
5806 "This package provides various tools for creating iterators, many
5807 patterned after functions in the Python @code{itertools} module, and others
5808 patterned after functions in the snow package.")
5809 (license license:gpl2)))
5811 (define-public r-polynom
5818 (uri (cran-uri "polynom" version))
5821 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
5822 (build-system r-build-system)
5823 (home-page "https://cran.r-project.org/web/packages/polynom/")
5824 (synopsis "Functions for univariate polynomial manipulations")
5826 "This package provides a collection of functions to implement a class for
5827 univariate polynomial manipulations.")
5828 (license license:gpl2)))
5830 (define-public r-gbrd
5837 (uri (cran-uri "gbRd" version))
5840 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
5841 (properties `((upstream-name . "gbRd")))
5842 (build-system r-build-system)
5843 (home-page "https://cran.r-project.org/web/packages/gbRd/")
5844 (synopsis "Utilities for processing Rd objects and files")
5846 "This package provides utilities for processing Rd objects and files.
5847 Extract argument descriptions and other parts of the help pages of
5849 (license license:gpl2+)))
5851 (define-public r-rjags
5858 (uri (cran-uri "rjags" version))
5861 "1vrmxxfnia2mkmfkp5yaq5qrlh4xg3ggab6fnj14mrp1231wb91a"))))
5862 (build-system r-build-system)
5864 `(("r-coda" ,r-coda)))
5868 `(("pkg-config" ,pkg-config)))
5869 (home-page "http://mcmc-jags.sourceforge.net")
5870 (synopsis "Bayesian graphical models using MCMC")
5872 "This package provides an R interface to the JAGS MCMC library. JAGS is
5873 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
5874 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
5875 (license license:gpl2)))
5877 (define-public r-rdpack
5884 (uri (cran-uri "Rdpack" version))
5887 "11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
5888 (properties `((upstream-name . "Rdpack")))
5889 (build-system r-build-system)
5891 `(("r-bibtex" ,r-bibtex)
5892 ("r-gbrd" ,r-gbrd)))
5893 (home-page "https://github.com/GeoBosh/Rdpack")
5894 (synopsis "Update and manipulate Rd documentation objects")
5896 "This package provides functions for manipulation of R documentation
5897 objects, including functions @code{reprompt()} and @code{ereprompt()} for
5898 updating Rd documentation for functions, methods and classes; it also includes
5899 Rd macros for citations and import of references from bibtex files for use in
5900 Rd files and roxygen2 comments, as well as many functions for manipulation of
5901 references and Rd files.")
5902 (license license:gpl2+)))
5904 (define-public r-officer
5911 (uri (cran-uri "officer" version))
5914 "005kaxjhr40shpav2pg7s7gj8f49579r7rbgwlncbwv16nn0rbbg"))))
5915 (build-system r-build-system)
5917 `(("r-base64enc" ,r-base64enc)
5918 ("r-digest" ,r-digest)
5919 ("r-htmltools" ,r-htmltools)
5920 ("r-magrittr" ,r-magrittr)
5923 ("r-rlang" ,r-rlang)
5927 (home-page "https://davidgohel.github.io/officer")
5928 (synopsis "Manipulation of Word and PowerPoint documents")
5930 "This package provides tools to access and manipulate Word and PowerPoint
5931 documents from R. The package focuses on tabular and graphical reporting from
5932 R; it also provides two functions that let users get document content into
5933 data objects. A set of functions lets add and remove images, tables and
5934 paragraphs of text in new or existing documents. When working with PowerPoint
5935 presentations, slides can be added or removed; shapes inside slides can also
5936 be added or removed. When working with Word documents, a cursor can be used
5937 to help insert or delete content at a specific location in the document.")
5938 (license license:gpl3)))
5940 (define-public r-abn
5947 (uri (cran-uri "abn" version))
5950 "08jlvb6i5f7ry2dwm0jgrnn2w95vr0l67dpx13n9878lz9ld131b"))))
5951 (build-system r-build-system)
5955 `(("r-lme4" ,r-lme4)
5959 ("r-rcpparmadillo" ,r-rcpparmadillo)
5960 ("r-rjags" ,r-rjags)))
5961 (home-page "http://www.r-bayesian-networks.org")
5962 (synopsis "Modelling multivariate data with additive bayesian networks")
5964 "Bayesian network analysis is a form of probabilistic graphical models
5965 which derives from empirical data a directed acyclic graph, DAG, describing
5966 the dependency structure between random variables. An additive Bayesian
5967 network model consists of a form of a DAG where each node comprises a
5968 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
5969 equivalent to Bayesian multivariate regression using graphical modelling, they
5970 generalises the usual multivariable regression, GLM, to multiple dependent
5971 variables. This package provides routines to help determine optimal Bayesian
5972 network models for a given data set, where these models are used to identify
5973 statistical dependencies in messy, complex data.")
5974 (license license:gpl2+)))
5976 (define-public r-acd
5983 (uri (cran-uri "ACD" version))
5986 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
5987 (properties `((upstream-name . "ACD")))
5988 (build-system r-build-system)
5989 (home-page "https://cran.r-project.org/web/packages/ACD/")
5990 (synopsis "Categorical data analysis with complete or missing responses")
5992 "This package provides tools for categorical data analysis with complete
5993 or missing responses.")
5994 (license license:gpl2+)))
5996 (define-public r-acdm
6003 (uri (cran-uri "ACDm" version))
6006 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6007 (properties `((upstream-name . "ACDm")))
6008 (build-system r-build-system)
6010 `(("r-dplyr" ,r-dplyr)
6011 ("r-ggplot2" ,r-ggplot2)
6013 ("r-rsolnp" ,r-rsolnp)
6015 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6016 (synopsis "Tools for Autoregressive Conditional Duration Models")
6018 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6019 and Russell, 1998) models. It creates trade, price or volume durations from
6020 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6022 (license license:gpl2+)))
6024 (define-public r-overlap
6031 (uri (cran-uri "overlap" version))
6034 "1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
6035 (build-system r-build-system)
6036 (home-page "https://cran.r-project.org/web/packages/overlap/")
6037 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6039 "This package provides functions to fit kernel density functions to data
6040 on temporal activity patterns of animals; estimate coefficients of overlapping
6041 of densities for two species; and calculate bootstrap estimates of confidence
6043 (license license:gpl3+)))
6045 (define-public r-snakecase
6047 (name "r-snakecase")
6052 (uri (cran-uri "snakecase" version))
6055 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6056 (build-system r-build-system)
6058 `(("r-stringi" ,r-stringi)
6059 ("r-stringr" ,r-stringr)))
6060 (home-page "https://github.com/Tazinho/snakecase")
6061 (synopsis "Convert strings into any case")
6063 "This package provides a consistent, flexible and easy to use tool to
6064 parse and convert strings into cases like snake or camel among others.")
6065 (license license:gpl3)))
6067 (define-public r-prediction
6069 (name "r-prediction")
6074 (uri (cran-uri "prediction" version))
6077 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6078 (build-system r-build-system)
6080 `(("r-data-table" ,r-data-table)))
6081 (home-page "https://github.com/leeper/prediction")
6082 (synopsis "Tidy, type-safe prediction methods")
6084 "This package provides the @code{prediction()} function, a type-safe
6085 alternative to @code{predict()} that always returns a data frame. The package
6086 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6087 from the @code{stats} package, as well as numerous other model classes from
6088 other add-on packages.")
6089 (license license:expat)))
6091 (define-public r-insight
6098 (uri (cran-uri "insight" version))
6101 "1lw1r3mb97z5p9z25jfzlhs0sbnwp6v8kzysf0am01x4m7l3iz82"))))
6102 (build-system r-build-system)
6103 (home-page "https://easystats.github.io/insight/")
6104 (synopsis "Easy access to model information for various model objects")
6106 "This package provides a tool to provide an easy, intuitive and
6107 consistent access to information contained in various R models, like model
6108 formulas, model terms, information about random effects, data that was used to
6109 fit the model or data from response variables. The package mainly revolves
6110 around two types of functions: Functions that find (the names of) information,
6111 starting with @code{find_}, and functions that get the underlying data,
6112 starting with @code{get_}. The package has a consistent syntax and works with
6113 many different model objects, where otherwise functions to access these
6114 information are missing.")
6115 (license license:gpl3)))
6117 (define-public r-sjlabelled
6119 (name "r-sjlabelled")
6124 (uri (cran-uri "sjlabelled" version))
6127 "0rnmlwpp41h04dzfjd5ncvzjzs43slaimb4v2in1axznv3haafyc"))))
6128 (build-system r-build-system)
6130 `(("r-haven" ,r-haven)
6131 ("r-insight" ,r-insight)
6132 ("r-magrittr" ,r-magrittr)
6133 ("r-purrr" ,r-purrr)
6134 ("r-rlang" ,r-rlang)
6135 ("r-tidyselect" ,r-tidyselect)))
6136 (home-page "https://github.com/strengejacke/sjlabelled")
6137 (synopsis "Labelled data utility functions")
6139 "This package provides a collection of functions dealing with labelled
6140 data, like reading and writing data between R and other statistical software
6141 packages. This includes easy ways to get, set or change value and variable
6142 label attributes, to convert labelled vectors into factors or numeric (and
6143 vice versa), or to deal with multiple declared missing values.")
6144 (license license:gpl3)))
6146 (define-public r-sjmisc
6153 (uri (cran-uri "sjmisc" version))
6156 "1a30n3cyd9h9ilaiai9ywy53f03nikafc47rvpws2c2vghc8mbn7"))))
6157 (build-system r-build-system)
6159 `(("r-dplyr" ,r-dplyr)
6160 ("r-insight" ,r-insight)
6161 ("r-magrittr" ,r-magrittr)
6162 ("r-purrr" ,r-purrr)
6163 ("r-rlang" ,r-rlang)
6164 ("r-sjlabelled" ,r-sjlabelled)))
6165 (home-page "https://github.com/strengejacke/sjmisc")
6166 (synopsis "Data and variable transformation functions")
6168 "This package is a collection of miscellaneous utility functions,
6169 supporting data transformation tasks like recoding, dichotomizing or grouping
6170 variables, setting and replacing missing values. The data transformation
6171 functions also support labelled data, and all integrate seamlessly into a
6172 tidyverse workflow.")
6173 (license license:gpl3)))
6175 (define-public r-nortest
6182 (uri (cran-uri "nortest" version))
6185 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6186 (build-system r-build-system)
6187 (home-page "https://cran.r-project.org/web/packages/nortest/")
6188 (synopsis "Tests for normality")
6190 "This package provides five omnibus tests for testing the composite
6191 hypothesis of normality.")
6192 (license license:gpl2+)))
6194 (define-public r-moonbook
6201 (uri (cran-uri "moonBook" version))
6204 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
6205 (properties `((upstream-name . "moonBook")))
6206 (build-system r-build-system)
6208 `(("r-magrittr" ,r-magrittr)
6209 ("r-nortest" ,r-nortest)
6210 ("r-purrr" ,r-purrr)
6211 ("r-sjmisc" ,r-sjmisc)
6212 ("r-stringr" ,r-stringr)
6213 ("r-survival" ,r-survival)))
6214 (home-page "https://github.com/cardiomoon/moonBook")
6215 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
6217 "This package provides several analysis-related functions for the book
6218 entitled \"R statistics and graph for medical articles\" (written in Korean),
6219 version 1, by Keon-Woong Moon with Korean demographic data with several plot
6221 (license license:gpl2)))
6223 (define-public r-flextable
6225 (name "r-flextable")
6230 (uri (cran-uri "flextable" version))
6233 "1q6x9mfk5gikqjbbra1dn8hs1rq5ws99jdjav3m113gx9f2j5yxh"))))
6234 (build-system r-build-system)
6236 `(("r-base64enc" ,r-base64enc)
6237 ("r-data-table" ,r-data-table)
6238 ("r-gdtools" ,r-gdtools)
6239 ("r-htmltools" ,r-htmltools)
6240 ("r-knitr" ,r-knitr)
6241 ("r-officer" ,r-officer)
6242 ("r-rlang" ,r-rlang)
6243 ("r-rmarkdown" ,r-rmarkdown)
6244 ("r-xml2" ,r-xml2)))
6245 (home-page "https://davidgohel.github.io/flextable")
6246 (synopsis "Functions for tabular reporting")
6248 "This package provides tools to create pretty tables for HTML documents
6249 and other formats. Functions are provided to let users create tables, modify
6250 and format their content. It extends the @code{officer} package and can be
6251 used within R markdown documents when rendering to HTML and to Word
6253 (license license:gpl3)))
6255 (define-public r-writexl
6262 (uri (cran-uri "writexl" version))
6265 "0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"))))
6266 (build-system r-build-system)
6267 (inputs `(("zlib" ,zlib)))
6268 (home-page "https://github.com/ropensci/writexl")
6269 (synopsis "Export data frames to xlsx format")
6271 "This package provides a data frame to xlsx exporter based on
6273 (license license:bsd-2)))
6275 (define-public r-biasedurn
6277 (name "r-biasedurn")
6282 (uri (cran-uri "BiasedUrn" version))
6285 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
6286 (properties `((upstream-name . "BiasedUrn")))
6287 (build-system r-build-system)
6288 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
6289 (synopsis "Biased Urn model distributions")
6291 "This package provides statistical models of biased sampling in the form
6292 of univariate and multivariate noncentral hypergeometric distributions,
6293 including Wallenius' noncentral hypergeometric distribution and Fisher's
6294 noncentral hypergeometric distribution (also called extended hypergeometric
6296 (license license:gpl3)))
6298 (define-public r-goplot
6305 (uri (cran-uri "GOplot" version))
6308 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
6309 (properties `((upstream-name . "GOplot")))
6310 (build-system r-build-system)
6312 `(("r-ggdendro" ,r-ggdendro)
6313 ("r-ggplot2" ,r-ggplot2)
6314 ("r-gridextra" ,r-gridextra)
6315 ("r-rcolorbrewer" ,r-rcolorbrewer)))
6316 (home-page "https://github.com/wencke/wencke.github.io")
6317 (synopsis "Visualization of functional analysis data")
6319 "This package provides an implementation of multilayered visualizations
6320 for enhanced graphical representation of functional analysis data. It
6321 combines and integrates omics data derived from expression and functional
6322 annotation enrichment analyses. Its plotting functions have been developed
6323 with an hierarchical structure in mind: starting from a general overview to
6324 identify the most enriched categories (modified bar plot, bubble plot) to a
6325 more detailed one displaying different types of relevant information for the
6326 molecules in a given set of categories (circle plot, chord plot, cluster plot,
6327 Venn diagram, heatmap).")
6328 (license license:gpl2)))
6330 (define-public r-getopt
6337 (uri (cran-uri "getopt" version))
6340 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
6341 (build-system r-build-system)
6342 (home-page "https://github.com/trevorld/getopt")
6343 (synopsis "Command-line option processor for R")
6345 "This package is designed to be used with Rscript to write shebang
6346 scripts that accept short and long options. Many users will prefer to
6347 use the packages @code{optparse} or @code{argparse} which add extra
6348 features like automatically generated help options and usage texts,
6349 support for default values, positional argument support, etc.")
6350 (license license:gpl2+)))
6352 (define-public r-findpython
6354 (name "r-findpython")
6359 (uri (cran-uri "findpython" version))
6362 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
6363 (build-system r-build-system)
6364 (home-page "https://github.com/trevorld/findpython")
6365 (synopsis "Functions to find an acceptable Python binary")
6367 "This package was designed to find an acceptable Python binary that
6368 matches version and feature constraints.")
6369 (license license:expat)))
6371 ;; This in not the same as "r-argparser"
6372 (define-public r-argparse
6379 (uri (cran-uri "argparse" version))
6382 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
6383 (build-system r-build-system)
6384 (inputs `(("python" ,python)))
6386 `(("r-findpython" ,r-findpython)
6387 ("r-jsonlite" ,r-jsonlite)
6389 (home-page "https://github.com/trevorld/argparse")
6390 (synopsis "Command line optional and positional argument parser")
6392 "This package provides a command line parser to be used with Rscript to
6393 write shebang scripts that gracefully accept positional and optional arguments
6394 and automatically generate usage notices.")
6395 (license license:gpl2+)))
6397 (define-public r-hash
6404 (uri (cran-uri "hash" version))
6407 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
6408 (build-system r-build-system)
6409 (home-page "https://cran.r-project.org/web/packages/hash/")
6410 (synopsis "Implementation of hash/associated arrays/dictionaries")
6412 "This package implements a data structure similar to hashes in Perl and
6413 dictionaries in Python but with a purposefully R flavor. For objects of
6414 appreciable size, access using hashes outperforms native named lists and
6416 (license license:gpl2+)))
6418 (define-public r-orddom
6425 (uri (cran-uri "orddom" version))
6428 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
6429 (build-system r-build-system)
6430 (propagated-inputs `(("r-psych" ,r-psych)))
6431 (home-page "https://cran.r-project.org/web/packages/orddom/")
6432 (synopsis "Ordinal dominance statistics")
6434 "This package provides tools to compute ordinal, statistics and effect
6435 sizes as an alternative to mean comparison: Cliff's delta or success rate
6436 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
6437 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
6438 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
6439 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
6440 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
6441 Group (Non-)Overlap considerations.")
6442 (license license:gpl2)))
6444 (define-public r-doby
6451 (uri (cran-uri "doBy" version))
6454 "02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb"))))
6455 (properties `((upstream-name . "doBy")))
6456 (build-system r-build-system)
6458 `(("r-dplyr" ,r-dplyr)
6459 ("r-magrittr" ,r-magrittr)
6461 ("r-matrix" ,r-matrix)
6462 ("r-plyr" ,r-plyr)))
6463 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
6464 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
6466 "This package contains:
6469 @item facilities for working with grouped data: @code{do}
6470 something to data stratified @code{by} some variables.
6471 @item implementations of least-squares means, general linear contrasts, and
6472 @item miscellaneous other utilities.
6474 (license license:gpl2+)))
6476 (define-public r-refgenome
6478 (name "r-refgenome")
6483 (uri (cran-uri "refGenome" version))
6486 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
6487 (properties `((upstream-name . "refGenome")))
6488 (build-system r-build-system)
6492 ("r-rsqlite" ,r-rsqlite)))
6493 (home-page "https://cran.r-project.org/web/packages/refGenome/")
6495 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
6497 "This package contains functionality for importing and managing of
6498 downloaded genome annotation data from the Ensembl genome browser (European
6499 Bioinformatics Institute) and from the UCSC genome browser (University of
6500 California, Santa Cruz) and annotation routines for genomic positions and
6501 splice site positions.")
6502 (license license:gpl2)))
6504 (define-public r-basix
6511 (uri (cran-uri "BASIX" version))
6514 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
6515 (properties `((upstream-name . "BASIX")))
6516 (build-system r-build-system)
6517 (home-page "https://cran.r-project.org/web/packages/BASIX/")
6518 (synopsis "Efficient C/C++ toolset for R")
6520 "BASIX provides some efficient C/C++ implementations of native R
6521 procedures to speed up calculations in R.")
6522 (license license:gpl2)))
6524 (define-public r-blockfest
6526 (name "r-blockfest")
6531 (uri (cran-uri "BlockFeST" version))
6534 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
6535 (properties `((upstream-name . "BlockFeST")))
6536 (build-system r-build-system)
6537 (propagated-inputs `(("r-basix" ,r-basix)))
6538 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
6539 (synopsis "Bayesian calculation of region-specific fixation index")
6541 "This package provides an R implementation of an extension of the
6542 BayeScan software for codominant markers, adding the option to group
6543 individual SNPs into pre-defined blocks. A typical application of this new
6544 approach is the identification of genomic regions, genes, or gene sets
6545 containing one or more SNPs that evolved under directional selection.")
6546 (license license:gpl2)))
6548 (define-public r-proc
6555 (uri (cran-uri "pROC" version))
6558 "1jx8af9p6sxbypqvj1cci7q9sbyaw310inbjxibjcr3acj59h45h"))))
6559 (properties `((upstream-name . "pROC")))
6560 (build-system r-build-system)
6562 `(("r-plyr" ,r-plyr)
6563 ("r-rcpp" ,r-rcpp)))
6564 (home-page "http://expasy.org/tools/pROC/")
6565 (synopsis "Display and analyze ROC curves")
6567 "This package provides tools for visualizing, smoothing and comparing
6568 receiver operating characteristic (ROC curves). The area under the
6569 curve (AUC) can be compared with statistical tests based on U-statistics or
6570 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
6571 (license license:gpl3+)))
6573 (define-public r-rootsolve
6575 (name "r-rootsolve")
6580 (uri (cran-uri "rootSolve" version))
6583 "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8"))))
6584 (properties `((upstream-name . "rootSolve")))
6585 (build-system r-build-system)
6586 (native-inputs `(("gfortran" ,gfortran)))
6587 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
6588 (synopsis "Tools for the analysis of ordinary differential equations")
6590 "This package provides routines to find the root of nonlinear functions,
6591 and to perform steady-state and equilibrium analysis of @dfn{ordinary
6592 differential equations} (ODE). It includes routines that:
6595 @item generate gradient and jacobian matrices (full and banded),
6596 @item find roots of non-linear equations by the Newton-Raphson method,
6597 @item estimate steady-state conditions of a system of (differential) equations
6598 in full, banded or sparse form, using the Newton-Raphson method, or by
6599 dynamically running,
6600 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
6601 and 3-D partial differential equations, that have been converted to ordinary
6602 differential equations by numerical differencing (using the method-of-lines
6605 (license license:gpl2+)))
6607 (define-public r-abcanalysis
6609 (name "r-abcanalysis")
6614 (uri (cran-uri "ABCanalysis" version))
6616 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
6617 (properties `((upstream-name . "ABCanalysis")))
6618 (build-system r-build-system)
6619 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
6620 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
6621 (synopsis "Computed ABC Analysis")
6623 "Multivariate data sets often differ in several factors or derived statistical
6624 parameters, which have to be selected for a valid interpretation. Basing this
6625 selection on traditional statistical limits leads occasionally to the perception
6626 of losing information from a data set. This package provides tools to calculate
6627 these limits on the basis of the mathematical properties of the distribution of
6628 the analyzed items.")
6629 (license license:gpl3)))
6631 (define-public r-slam
6638 (uri (cran-uri "slam" version))
6640 (base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4"))))
6641 (build-system r-build-system)
6642 (home-page "https://cran.r-project.org/web/packages/slam/")
6643 (synopsis "Sparse lightweight arrays and matrices")
6645 "This package contains data structures and algorithms for sparse arrays and matrices,
6646 based on index arrays and simple triplet representations, respectively.")
6647 (license license:gpl2)))
6649 (define-public r-manipulatewidget
6651 (name "r-manipulatewidget")
6656 (uri (cran-uri "manipulateWidget" version))
6658 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
6660 `((upstream-name . "manipulateWidget")))
6661 (build-system r-build-system)
6663 `(("r-base64enc" ,r-base64enc)
6664 ("r-codetools" ,r-codetools)
6665 ("r-htmltools" ,r-htmltools)
6666 ("r-htmlwidgets" ,r-htmlwidgets)
6667 ("r-knitr" ,r-knitr)
6668 ("r-miniui" ,r-miniui)
6669 ("r-shiny" ,r-shiny)
6670 ("r-webshot" ,r-webshot)))
6671 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
6672 (synopsis "Add even more interactivity to interactive charts")
6674 "This package lets you create in just a few lines of R code a nice user interface to
6675 modify the data or the graphical parameters of one or multiple interactive
6676 charts. It is useful to quickly explore visually some data or for package
6677 developers to generate user interfaces easy to maintain.")
6678 (license license:gpl2+)))
6687 (uri (cran-uri "A3" version))
6689 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
6690 (properties `((upstream-name . "A3")))
6691 (build-system r-build-system)
6693 `(("r-pbapply" ,r-pbapply)
6694 ("r-xtable" ,r-xtable)))
6695 (home-page "https://cran.r-project.org/web/packages/A3/")
6696 (synopsis "Error metrics for predictive models")
6698 "This package supplies tools for tabulating and analyzing the results of predictive
6699 models. The methods employed are applicable to virtually any predictive model
6700 and make comparisons between different methodologies straightforward.")
6701 (license license:gpl2+)))
6703 (define-public r-infotheo
6710 (uri (cran-uri "infotheo" version))
6713 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
6714 (build-system r-build-system)
6715 (home-page "http://homepage.meyerp.com/software")
6716 (synopsis "Information-theoretic measures")
6718 "This package implements various measures of information theory based on
6719 several entropy estimators.")
6720 (license license:gpl3+)))
6722 (define-public r-abcoptim
6729 (uri (cran-uri "ABCoptim" version))
6731 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
6732 (properties `((upstream-name . "ABCoptim")))
6733 (build-system r-build-system)
6734 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
6735 (home-page "https://github.com/gvegayon/ABCoptim/")
6736 (synopsis "Optimization of Artificial Bee Colony algorithm")
6738 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
6739 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
6740 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
6741 algorithms, and uses only common control parameters such as colony size and
6742 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
6743 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
6744 This version is a work-in-progress and is written in R code.")
6745 (license license:expat)))
6747 (define-public r-abcp2
6754 (uri (cran-uri "ABCp2" version))
6756 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
6757 (properties `((upstream-name . "ABCp2")))
6758 (build-system r-build-system)
6759 (propagated-inputs `(("r-mass" ,r-mass)))
6760 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
6761 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
6763 "This package tests the goodness of fit of a distribution of offspring to the Normal,
6764 Poisson, and Gamma distribution and estimates the proportional paternity of the
6765 second male (P2) based on the best fit distribution.")
6766 (license license:gpl2)))
6768 (define-public r-abcrf
6775 (uri (cran-uri "abcrf" version))
6777 (base32 "0r31ki89z8zzcffm0yvd2zw3q96rk6g6fnwwkql902mgajbrha1f"))))
6778 (build-system r-build-system)
6780 `(("r-doparallel" ,r-doparallel)
6781 ("r-foreach" ,r-foreach)
6783 ("r-matrixstats" ,r-matrixstats)
6784 ("r-ranger" ,r-ranger)
6786 ("r-rcpparmadillo" ,r-rcpparmadillo)
6787 ("r-readr" ,r-readr)
6788 ("r-stringr" ,r-stringr)))
6789 (home-page "https://cran.r-project.org/web/packages/abcrf/")
6790 (synopsis "Approximate bayesian computation via random forests")
6792 "This package performs approximate bayesian computation (ABC) model choice and
6793 parameter inference via random forests. This machine learning tool named random
6794 forests (RF) can conduct selection among the highly complex models covered by
6796 (license license:gpl2+)))
6798 (define-public r-abctools
6805 (uri (cran-uri "abctools" version))
6807 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
6808 (build-system r-build-system)
6811 ("r-abind" ,r-abind)
6812 ("r-hmisc" ,r-hmisc)
6813 ("r-plyr" ,r-plyr)))
6814 (home-page "https://github.com/dennisprangle/abctools/")
6815 (synopsis "Tools for ABC analyses")
6817 "This @code{r-abctools} package provides tools for approximate Bayesian computation
6818 including summary statistic selection and assessing coverage. This includes
6819 recent dimension reduction algorithms to tune the choice of summary statistics,
6820 and coverage methods to tune the choice of threshold.")
6821 (license license:gpl2+)))
6823 (define-public r-ggstance
6830 (uri (cran-uri "ggstance" version))
6832 (base32 "0kdksay61hyb6612b07r84chh7a9aibjyclk3qcypvr9aang8hkh"))))
6833 (build-system r-build-system)
6835 `(("r-ggplot2" ,r-ggplot2)
6837 ("r-rlang" ,r-rlang)
6838 ("r-withr" ,r-withr)))
6839 (home-page "https://cran.r-project.org/web/packages/ggstance/")
6840 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
6842 "This package is a @code{r-ggplot2} extension that provides flipped components:
6844 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
6845 @item vertical versions of @code{r-ggplot2} positions.
6847 (license license:gpl3)))
6849 (define-public r-mosaiccore
6851 (name "r-mosaiccore")
6856 (uri (cran-uri "mosaicCore" version))
6858 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
6859 (properties `((upstream-name . "mosaicCore")))
6860 (build-system r-build-system)
6862 `(("r-dplyr" ,r-dplyr)
6863 ("r-lazyeval" ,r-lazyeval)
6865 ("r-rlang" ,r-rlang)
6866 ("r-tidyr" ,r-tidyr)))
6867 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
6868 (synopsis "Common utilities for mosaic family packages")
6870 "Common utilities used in other Mosaic family packages are collected here.")
6871 (license license:gpl2+)))
6873 (define-public r-ggformula
6875 (name "r-ggformula")
6880 (uri (cran-uri "ggformula" version))
6882 (base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx"))))
6883 (build-system r-build-system)
6885 `(("r-ggplot2" ,r-ggplot2)
6886 ("r-ggstance" ,r-ggstance)
6887 ("r-magrittr" ,r-magrittr)
6888 ("r-mosaiccore" ,r-mosaiccore)
6889 ("r-rlang" ,r-rlang)
6890 ("r-stringr" ,r-stringr)
6891 ("r-tibble" ,r-tibble)
6892 ("r-tidyr" ,r-tidyr)))
6893 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
6894 (synopsis "Formula interface for the @code{r-ggplot2}")
6896 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
6897 gf_density(), and so on, bring the formula interface to ggplot(). This captures
6898 and extends the excellent simplicity of the lattice-graphics formula interface,
6899 while providing the intuitive capabilities of @code{r-ggplot2}.")
6900 (license license:expat)))
6902 (define-public r-mosaicdata
6904 (name "r-mosaicdata")
6909 (uri (cran-uri "mosaicData" version))
6911 (base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
6912 (properties `((upstream-name . "mosaicData")))
6913 (build-system r-build-system)
6914 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
6915 (synopsis "Data sets for project Mosaic")
6917 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
6918 used to teach mathematics, statistics, computation and modeling.")
6919 (license license:gpl2+)))
6921 (define-public r-raster
6928 (uri (cran-uri "raster" version))
6931 "1brqigic8ygr223bp2hgk5qjz3q03r4sfglrv4an0ghy7fgfralh"))))
6932 (build-system r-build-system)
6934 `(("r-rcpp" ,r-rcpp)
6936 (home-page "https://www.rspatial.org/")
6937 (synopsis "Geographic data analysis and modeling")
6939 "The package implements basic and high-level functions for reading,
6940 writing, manipulating, analyzing and modeling of gridded spatial data.
6941 Processing of very large files is supported.")
6942 (license license:gpl3+)))
6944 (define-public r-mosaic
6951 (uri (cran-uri "mosaic" version))
6953 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
6954 (build-system r-build-system)
6956 `(("r-broom" ,r-broom)
6957 ("r-dplyr" ,r-dplyr)
6958 ("r-ggdendro" ,r-ggdendro)
6959 ("r-ggformula" ,r-ggformula)
6960 ("r-ggplot2" ,r-ggplot2)
6961 ("r-ggrepel" ,r-ggrepel)
6963 ("r-gridextra" ,r-gridextra)
6964 ("r-lattice" ,r-lattice)
6965 ("r-latticeextra" ,r-latticeextra)
6966 ("r-lazyeval" ,r-lazyeval)
6968 ("r-matrix" ,r-matrix)
6969 ("r-mosaiccore" ,r-mosaiccore)
6970 ("r-mosaicdata" ,r-mosaicdata)
6971 ("r-readr" ,r-readr)
6972 ("r-tidyr" ,r-tidyr)))
6973 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
6974 (synopsis "Mathematics, statistics, and computation teaching utilities")
6976 "This package contain data sets and utilities from
6977 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
6978 statistics, computation and modeling. Project MOSAIC is a community of
6979 educators working to tie together aspects of quantitative work that students
6980 in science, technology, engineering and mathematics will need in their
6981 professional lives, but which are usually taught in isolation, if at all.")
6982 (license license:gpl2+)))
6984 (define-public r-abd
6991 (uri (cran-uri "abd" version))
6993 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
6994 (build-system r-build-system)
6996 `(("r-lattice" ,r-lattice)
6997 ("r-mosaic" ,r-mosaic)
6998 ("r-nlme" ,r-nlme)))
6999 (home-page "https://cran.r-project.org/web/packages/abd/")
7000 (synopsis "Analysis of biological data")
7002 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7003 biological data by Michael Whitlock and Dolph Schluter.")
7004 (license license:gpl2)))
7006 (define-public r-svgui
7013 (uri (cran-uri "svGUI" version))
7015 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7016 (properties `((upstream-name . "svGUI")))
7017 (build-system r-build-system)
7018 (home-page "https://github.com/SciViews/svGUI/")
7019 (synopsis "Functions for managing GUI clients in R")
7021 "The SciViews @code{svGUI} package eases the management of Graphical User
7022 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7023 centralizes info about GUI elements currently used, and it dispatches GUI
7024 calls to the particular toolkits in use in function of the context.")
7025 (license license:gpl2)))
7027 (define-public r-svdialogs
7029 (name "r-svdialogs")
7034 (uri (cran-uri "svDialogs" version))
7036 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7037 (properties `((upstream-name . "svDialogs")))
7038 (build-system r-build-system)
7041 ("zenity" ,zenity)))
7043 `(("r-rstudioapi" ,r-rstudioapi)
7044 ("r-svgui" ,r-svgui)))
7045 (home-page "https://github.com/SciViews/svDialogs/")
7046 (synopsis "Portable dialog boxes")
7048 "This package helps to construct standard dialog boxes for your GUI, including
7049 message boxes, input boxes, list, file or directory selection, and others. In
7050 case R cannot display GUI dialog boxes, a simpler command line version of these
7051 interactive elements is also provided as a fallback solution.")
7052 (license license:gpl2)))
7054 (define-public r-abe
7061 (uri (cran-uri "abe" version))
7064 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7065 (build-system r-build-system)
7066 (home-page "https://cran.r-project.org/web/packages/abe/")
7067 (synopsis "Augmented backward elimination")
7069 "This package performs augmented backward elimination and checks the
7070 stability of the obtained model. Augmented backward elimination combines
7071 significance or information based criteria with the change in estimate to
7072 either select the optimal model for prediction purposes or to serve as a tool
7073 to obtain a practically sound, highly interpretable model.")
7074 (license license:gpl2+)))
7076 (define-public r-abf2
7083 (uri (cran-uri "abf2" version))
7085 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7086 (build-system r-build-system)
7087 (home-page "https://cran.r-project.org/web/packages/abf2/")
7088 (synopsis "Load gap-free axon @code{r-abf2} files")
7090 "This package loads electrophysiology data from ABF2 files, as created by
7091 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7092 mode are currently supported.")
7093 (license license:artistic2.0)))
7095 (define-public r-abhgenotyper
7097 (name "r-abhgenotyper")
7102 (uri (cran-uri "ABHgenotypeR" version))
7104 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7105 (properties `((upstream-name . "ABHgenotypeR")))
7106 (build-system r-build-system)
7108 `(("r-ggplot2" ,r-ggplot2)
7109 ("r-reshape2" ,r-reshape2)))
7110 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7111 (synopsis "Visualize and manipulate ABH genotypes")
7113 "The @code{r-abhgenotyper} package provides simple imputation,
7114 error-correction and plotting capacities for genotype data. The package is
7115 supposed to serve as an intermediate but independent analysis tool between the
7116 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7117 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7118 genotypes as \"graphical genotypes\".")
7119 (license license:gpl3)))
7121 (define-public r-furrr
7128 (uri (cran-uri "furrr" version))
7131 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7132 (build-system r-build-system)
7134 `(("r-future" ,r-future)
7135 ("r-globals" ,r-globals)
7136 ("r-purrr" ,r-purrr)
7137 ("r-rlang" ,r-rlang)))
7138 (home-page "https://github.com/DavisVaughan/furrr")
7139 (synopsis "Apply mapping functions in parallel using futures")
7141 "This package provides implementations of the family of @code{map()}
7142 functions from the @code{purrr} package that can be resolved using any
7143 @code{future}-supported backend, e.g. parallel on the local machine or
7144 distributed on a compute cluster.")
7145 (license license:lgpl2.1+)))
7147 (define-public r-abjutils
7154 (uri (cran-uri "abjutils" version))
7156 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7157 (build-system r-build-system)
7159 `(("r-devtools" ,r-devtools)
7160 ("r-dplyr" ,r-dplyr)
7161 ("r-furrr" ,r-furrr)
7162 ("r-future" ,r-future)
7165 ("r-magrittr" ,r-magrittr)
7166 ("r-progress" ,r-progress)
7167 ("r-purrr" ,r-purrr)
7168 ("r-readr" ,r-readr)
7169 ("r-rlang" ,r-rlang)
7170 ("r-rstudioapi" ,r-rstudioapi)
7171 ("r-scales" ,r-scales)
7172 ("r-stringi" ,r-stringi)
7173 ("r-stringr" ,r-stringr)
7174 ("r-tibble" ,r-tibble)
7175 ("r-tidyr" ,r-tidyr)))
7176 (home-page "https://github.com/abjur/abjutils/")
7177 (synopsis "Collection of tools for jurimetrical analysis")
7179 "This package implements general purpose tools, such as functions for
7180 sampling and basic manipulation of Brazilian lawsuits identification number.
7181 It also implements functions for text cleaning, such as accentuation
7183 (license license:expat)))
7185 (define-public r-abnormality
7187 (name "r-abnormality")
7192 (uri (cran-uri "abnormality" version))
7194 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
7195 (build-system r-build-system)
7197 `(("r-mass" ,r-mass)
7198 ("r-matrix" ,r-matrix)))
7199 (home-page "https://cran.r-project.org/web/packages/abnormality/")
7200 (synopsis "Measure a subject's abnormality with respect to a reference population")
7202 "This package contains functions to implement the methodology and
7203 considerations laid out by Marks et al. in the article \"Measuring abnormality
7204 in high dimensional spaces: applications in biomechanical gait analysis\".
7205 Using high-dimensional datasets to measure a subject's overall level of
7206 abnormality as compared to a reference population is often needed in outcomes
7208 (license license:expat)))
7210 (define-public r-abodoutlier
7212 (name "r-abodoutlier")
7217 (uri (cran-uri "abodOutlier" version))
7219 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
7220 (properties `((upstream-name . "abodOutlier")))
7221 (build-system r-build-system)
7223 `(("r-cluster" ,r-cluster)))
7224 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
7225 (synopsis "Angle-based outlier detection")
7227 "This package performs angle-based outlier detection on a given data
7228 frame. It offers three methods to process data:
7230 @item full but slow implementation using all the data that has cubic
7232 @item a fully randomized method;
7233 @item a method using k-nearest neighbours.
7235 These algorithms are well suited for high dimensional data outlier
7237 (license license:expat)))
7239 (define-public r-abps
7246 (uri (cran-uri "ABPS" version))
7248 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
7249 (properties `((upstream-name . "ABPS")))
7250 (build-system r-build-system)
7251 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
7252 (home-page "https://cran.r-project.org/web/packages/ABPS/")
7253 (synopsis "Abnormal blood profile score to detect blood doping")
7255 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
7256 The ABPS is a part of the Athlete biological passport program of the World
7257 anti-doping agency, which combines several blood parameters into a single
7258 score in order to detect blood doping. The package also contains functions to
7259 calculate other scores used in anti-doping programs, such as the ratio of
7260 hemoglobin to reticulocytes (OFF-score), as well as example data.")
7261 (license license:gpl2+)))
7263 (define-public r-parmigene
7265 (name "r-parmigene")
7270 (uri (cran-uri "parmigene" version))
7273 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
7274 (build-system r-build-system)
7275 (home-page "https://cran.r-project.org/web/packages/parmigene/")
7276 (synopsis "Mutual information estimation for gene network reconstruction")
7278 "This package provides a parallel estimation of the mutual information
7279 based on entropy estimates from k-nearest neighbors distances and algorithms
7280 for the reconstruction of gene regulatory networks.")
7281 (license license:agpl3+)))
7283 (define-public r-pscl
7290 (uri (cran-uri "pscl" version))
7292 (base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
7293 (build-system r-build-system)
7295 `(("r-mass" ,r-mass)))
7296 (home-page "https://github.com/atahk/pscl/")
7297 (synopsis "Political science computational laboratory")
7299 "The @code{pscl} is an R package providing classes and methods for:
7301 @item Bayesian analysis of roll call data (item-response models);
7302 @item elementary Bayesian statistics;
7303 @item maximum likelihood estimation of zero-inflated and hurdle models for count
7305 @item utility functions.
7307 (license license:gpl2)))
7309 (define-public r-accelmissing
7311 (name "r-accelmissing")
7316 (uri (cran-uri "accelmissing" version))
7318 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
7319 (build-system r-build-system)
7321 `(("r-mice" ,r-mice)
7322 ("r-pscl" ,r-pscl)))
7323 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
7324 (synopsis "Missing value imputation for accelerometer data")
7326 "This package provides a statistical method to impute the missing values in
7327 accelerometer data. The methodology includes both parametric and
7328 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
7329 model. It also provides multiple functions to preprocess the accelerometer data
7330 previous to the missing data imputation. These include detecting the wearing
7331 and the non-wearing time, selecting valid days and subjects, and creating plots.")
7332 (license license:gpl2+)))
7334 (define-public r-mhsmm
7341 (uri (cran-uri "mhsmm" version))
7343 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
7344 (build-system r-build-system)
7345 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7346 (home-page "https://github.com/jaredo/mhsmm/")
7347 (synopsis "Inference for hidden Markov and semi-Markov models")
7349 "The @code{r-mhsmm} package implements estimation and prediction methods for
7350 hidden Markov and semi-Markov models for multiple observation sequences. Such
7351 techniques are of interest when observed data is thought to be dependent on some
7352 unobserved (or hidden) state. Also, this package is suitable for equidistant
7353 time series data, with multivariate and/or missing data. Allows user defined
7354 emission distributions.")
7355 (license license:gpl2+)))
7357 (define-public r-nleqslv
7364 (uri (cran-uri "nleqslv" version))
7366 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
7367 (build-system r-build-system)
7368 (native-inputs `(("gfortran" ,gfortran)))
7369 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
7370 (synopsis "Solve systems of nonlinear equations")
7372 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
7373 Broyden or a Newton method with a choice of global strategies such as line
7374 search and trust region. There are options for using a numerical or user
7375 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
7376 singular or ill-conditioned Jacobian.")
7377 (license license:gpl2+)))
7379 (define-public r-physicalactivity
7381 (name "r-physicalactivity")
7386 (uri (cran-uri "PhysicalActivity" version))
7388 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
7390 `((upstream-name . "PhysicalActivity")))
7391 (build-system r-build-system)
7392 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
7393 (synopsis "Procesing accelerometer data for physical activity measurement")
7395 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
7396 for classification of monitor wear and nonwear time intervals in accelerometer
7397 data collected to assess physical activity. The package also contains functions
7398 for making plots of accelerometer data and obtaining the summary of various
7399 information including daily monitor wear time and the mean monitor wear time
7400 during valid days. The revised package version 0.2-1 improved the functions
7401 regarding speed, robustness and add better support for time zones and daylight
7402 saving. In addition, several functions were added:
7404 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
7405 @item the @code{markPAI} can categorize physical activity intensity level based
7406 on user-defined cut-points of accelerometer counts.
7408 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
7409 @code{queryActigraph} functions.")
7410 (license license:gpl3+)))
7412 (define-public r-acc
7419 (uri (cran-uri "acc" version))
7421 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
7422 (build-system r-build-system)
7424 `(("r-circlize" ,r-circlize)
7426 ("r-ggplot2" ,r-ggplot2)
7427 ("r-iterators" ,r-iterators)
7428 ("r-mhsmm" ,r-mhsmm)
7429 ("r-nleqslv" ,r-nleqslv)
7430 ("r-physicalactivity" ,r-physicalactivity)
7432 ("r-r-utils" ,r-r-utils)
7434 ("r-rcpparmadillo" ,r-rcpparmadillo)
7435 ("r-rsqlite" ,r-rsqlite)
7437 (home-page "https://cran.r-project.org/web/packages/acc/")
7438 (synopsis "Exploring accelerometer data")
7440 "This package processes accelerometer data from uni-axial and tri-axial devices
7441 and generates data summaries. Also, includes functions to plot, analyze, and
7442 simulate accelerometer data.")
7443 (license license:gpl2+)))
7445 (define-public r-rbenchmark
7447 (name "r-rbenchmark")
7452 (uri (cran-uri "rbenchmark" version))
7454 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
7455 (build-system r-build-system)
7456 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
7457 (synopsis "Benchmarking routine for R")
7459 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
7460 and is intended to facilitate benchmarking of arbitrary R code. The library
7461 consists of just one function, benchmark, which is a simple wrapper around
7462 system.time. Given a specification of the benchmarking process (counts of
7463 replications, evaluation environment) and an arbitrary number of expressions,
7464 benchmark evaluates each of the expressions in the specified environment,
7465 replicating the evaluation as many times as specified, and returning the results
7466 conveniently wrapped into a data frame.")
7467 (license license:gpl2+)))
7469 (define-public r-mitools
7476 (uri (cran-uri "mitools" version))
7479 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
7480 (build-system r-build-system)
7481 (propagated-inputs `(("r-dbi" ,r-dbi)))
7482 (home-page "https://cran.r-project.org/web/packages/mitools/")
7483 (synopsis "Tools for multiple imputation of missing data")
7485 "This package provides tools to perform analyses and combine results from
7486 multiple-imputation datasets.")
7487 (license license:gpl2)))
7489 (define-public r-magick
7496 (uri (cran-uri "magick" version))
7499 "1pz71maz05gx4ds1wfw0alggc8nn2w75lj12dg1zr72s3kybhkzg"))))
7500 (build-system r-build-system)
7502 `(("imagemagick" ,imagemagick)
7505 `(("r-curl" ,r-curl)
7506 ("r-magrittr" ,r-magrittr)
7507 ("r-rcpp" ,r-rcpp)))
7509 `(("pkg-config" ,pkg-config)))
7510 (home-page "https://github.com/ropensci/magick")
7511 (synopsis "Advanced graphics and image-processing in R")
7513 "This package provides bindings to ImageMagick, a comprehensive image
7514 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
7515 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
7516 operations are vectorized via the Magick++ STL meaning they operate either on
7517 a single frame or a series of frames for working with layers, collages, or
7518 animation. In RStudio, images are automatically previewed when printed to the
7519 console, resulting in an interactive editing environment.")
7520 (license license:expat)))
7522 (define-public r-survey
7529 (uri (cran-uri "survey" version))
7532 "0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
7533 (build-system r-build-system)
7535 `(("r-lattice" ,r-lattice)
7536 ("r-matrix" ,r-matrix)
7537 ("r-minqa" ,r-minqa)
7538 ("r-mitools" ,r-mitools)
7539 ("r-numderiv" ,r-numderiv)
7540 ("r-survival" ,r-survival)))
7541 (home-page "http://r-survey.r-forge.r-project.org/survey/")
7542 (synopsis "Analysis of complex survey samples")
7544 "This package provides tools for the analysis of complex survey samples.
7545 The provided features include: summary statistics, two-sample tests, rank
7546 tests, generalised linear models, cumulative link models, Cox models,
7547 loglinear models, and general maximum pseudolikelihood estimation for
7548 multistage stratified, cluster-sampled, unequally weighted survey samples;
7549 variances by Taylor series linearisation or replicate weights;
7550 post-stratification, calibration, and raking; two-phase subsampling designs;
7551 graphics; PPS sampling without replacement; principal components, and factor
7553 ;; Either version of the GPL.
7554 (license (list license:gpl2 license:gpl3))))
7556 (define-public r-dvmisc
7563 (uri (cran-uri "dvmisc" version))
7565 (base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
7566 (build-system r-build-system)
7568 `(("r-cubature" ,r-cubature)
7569 ("r-data-table" ,r-data-table)
7570 ("r-dplyr" ,r-dplyr)
7571 ("r-ggplot2" ,r-ggplot2)
7573 ("r-mvtnorm" ,r-mvtnorm)
7574 ("r-pracma" ,r-pracma)
7575 ("r-purrr" ,r-purrr)
7576 ("r-rbenchmark" ,r-rbenchmark)
7578 ("r-survey" ,r-survey)))
7579 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
7580 (synopsis "Faster computation of common statistics and miscellaneous functions")
7582 "This package implements faster versions of base R functions (e.g. mean, standard
7583 deviation, covariance, weighted mean), mostly written in C++, along with
7584 miscellaneous functions for various purposes (e.g. create the histogram with
7585 fitted probability density function or probability mass function curve, create
7586 the body mass index groups, assess the linearity assumption in logistic
7588 (license license:gpl2)))
7590 (define-public r-accelerometry
7592 (name "r-accelerometry")
7597 (uri (cran-uri "accelerometry" version))
7599 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
7600 (build-system r-build-system)
7602 `(("r-dvmisc" ,r-dvmisc)
7603 ("r-rcpp" ,r-rcpp)))
7604 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
7605 (synopsis "Functions for processing accelerometer data")
7607 "This package provides a collection of functions that perform operations on
7608 time-series accelerometer data, such as identify the non-wear time, flag minutes
7609 that are part of an activity bout, and find the maximum 10-minute average count
7610 value. The functions are generally very flexible, allowing for a variety of
7611 algorithms to be implemented.")
7612 (license license:gpl3)))
7614 (define-public r-absim
7621 (uri (cran-uri "AbSim" version))
7623 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
7624 (properties `((upstream-name . "AbSim")))
7625 (build-system r-build-system)
7628 ("r-powerlaw" ,r-powerlaw)))
7629 (home-page "https://cran.r-project.org/web/packages/AbSim/")
7630 (synopsis "Time resolved simulations of antibody repertoires")
7632 "This package provides simulation methods for the evolution of antibody repertoires.
7633 The heavy and light chain variable region of both human and C57BL/6 mice can
7634 be simulated in a time-dependent fashion. Both single lineages using one set of
7635 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
7636 with an initial V-D-J recombination event, starting the first phylogenetic tree.
7637 Upon completion, the main loop of the algorithm begins, with each iteration
7638 representing one simulated time step. Various mutation events are possible at
7639 each time step, contributing to a diverse final repertoire.")
7640 (license license:gpl2)))
7642 (define-public r-quic
7649 (uri (cran-uri "QUIC" version))
7651 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
7652 (properties `((upstream-name . "QUIC")))
7653 (build-system r-build-system)
7654 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
7655 (synopsis "Regularized sparse inverse covariance matrix estimation")
7657 "This package implements the regularized Gaussian maximum likelihood
7658 estimation of the inverse of a covariance matrix. It uses Newton's method and
7659 coordinate descent to solve the regularized inverse covariance matrix
7660 estimation problem.")
7661 ;; The project home page states that the release is under GPLv3 or later.
7662 ;; The CRAN page only says GPL-3.
7663 (license license:gpl3+)))
7665 (define-public r-abundant
7672 (uri (cran-uri "abundant" version))
7674 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
7675 (build-system r-build-system)
7677 `(("r-quic" ,r-quic)))
7678 (home-page "https://cran.r-project.org/web/packages/abundant/")
7679 (synopsis "Abundant regression and high-dimensional principal fitted components")
7681 "This package provides tools to fit and predict with the high-dimensional
7682 principal fitted components model. This model is described by Cook, Forzani,
7683 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
7684 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
7685 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
7686 (license license:gpl2+)))
7688 (define-public r-ac3net
7695 (uri (cran-uri "Ac3net" version))
7697 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
7698 (properties `((upstream-name . "Ac3net")))
7699 (build-system r-build-system)
7701 `(("r-data-table" ,r-data-table)))
7702 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
7703 (synopsis "Inferring directional conservative causal core gene networks")
7704 (description "This package infers directional Conservative causal core
7705 (gene) networks (C3NET). This is a version of the algorithm C3NET with
7706 directional network.")
7707 (license license:gpl3+)))
7709 (define-public r-aca
7716 (uri (cran-uri "ACA" version))
7718 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
7719 (properties `((upstream-name . "ACA")))
7720 (build-system r-build-system)
7721 (home-page "https://cran.r-project.org/web/packages/ACA/")
7722 (synopsis "Abrupt change-point or aberration detection in point series")
7724 "This package offers an interactive function for the detection of breakpoints in
7726 ;; Any version of the GPL
7727 (license (list license:gpl2+ license:gpl3+))))
7729 (define-public r-acceptancesampling
7731 (name "r-acceptancesampling")
7736 (uri (cran-uri "AcceptanceSampling" version))
7738 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
7740 `((upstream-name . "AcceptanceSampling")))
7741 (build-system r-build-system)
7742 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
7743 (synopsis "Creation and evaluation of acceptance sampling plans")
7745 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
7746 acceptance sampling plans. Acceptance sampling is a methodology commonly used
7747 in quality control and improvement. International standards of acceptance
7748 sampling provide sampling plans for specific circumstances. The aim of this
7749 package is to provide an easy-to-use interface to visualize single, double or
7750 multiple sampling plans. In addition, methods have been provided to enable the
7751 user to assess sampling plans against pre-specified levels of performance, as
7752 measured by the probability of acceptance for a given level of quality in the
7754 (license license:gpl3+)))
7756 (define-public r-acclma
7763 (uri (cran-uri "ACCLMA" version))
7765 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
7766 (properties `((upstream-name . "ACCLMA")))
7767 (build-system r-build-system)
7768 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
7769 (synopsis "ACC & LMA graph plotting")
7771 "This package contains a function that imports data from a @acronym{CSV,
7772 Comma-Separated Values} file, or uses manually entered data from the format (x,
7773 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
7774 Curve} vs @acronym{LOI, Line of Independence} graph and
7775 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
7776 function is @code{plotLMA} (source file, header) that takes a data set and plots the
7777 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
7778 string) was passed, a manual data entry window is opened. The header parameter
7779 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
7780 a header row or not. The dataset should contain only one independent variable
7781 (x) and one dependent variable (y) and can contain a weight for each
7783 (license license:gpl2)))
7785 (define-public r-aspi
7792 (uri (cran-uri "aspi" version))
7794 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
7795 (build-system r-build-system)
7797 "https://cran.r-project.org/web/packages/aspi/")
7799 "Analysis of symmetry of parasitic infections")
7801 "This package provides tools for the analysis and visualization of bilateral
7802 asymmetry in parasitic infections.")
7803 (license license:gpl3+)))
7805 (define-public r-sandwich
7812 (uri (cran-uri "sandwich" version))
7815 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
7816 (build-system r-build-system)
7818 `(("r-zoo" ,r-zoo)))
7819 (home-page "https://cran.r-project.org/web/packages/sandwich/")
7820 (synopsis "Robust Covariance Matrix Estimators")
7822 "This package provides model-robust standard error estimators for
7823 cross-sectional, time series, clustered, panel, and longitudinal data.")
7824 ;; Either version of the license.
7825 (license (list license:gpl2 license:gpl3))))
7827 (define-public r-th-data
7834 (uri (cran-uri "TH.data" version))
7837 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
7838 (properties `((upstream-name . "TH.data")))
7839 (build-system r-build-system)
7841 `(("r-mass" ,r-mass)
7842 ("r-survival" ,r-survival)))
7843 (home-page "https://cran.r-project.org/web/packages/TH.data/")
7844 (synopsis "Shared data sets")
7846 "This package contains supporting data sets that are used in other
7847 packages maintained by Torsten Hothorn.")
7848 (license license:gpl3)))
7850 (define-public r-multcomp
7857 (uri (cran-uri "multcomp" version))
7860 "1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
7861 (build-system r-build-system)
7863 `(("r-codetools" ,r-codetools)
7864 ("r-mvtnorm" ,r-mvtnorm)
7865 ("r-sandwich" ,r-sandwich)
7866 ("r-survival" ,r-survival)
7867 ("r-th-data" ,r-th-data)))
7868 (home-page "https://cran.r-project.org/web/packages/multcomp/")
7869 (synopsis "Simultaneous inference in general parametric models")
7871 "Simultaneous tests and confidence intervals for general linear
7872 hypotheses in parametric models, including linear, generalized linear, linear
7873 mixed effects, and survival models. The package includes demos reproducing
7874 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
7875 Hothorn, Westfall, 2010, CRC Press).")
7876 (license license:gpl2)))
7878 (define-public r-emmeans
7885 (uri (cran-uri "emmeans" version))
7888 "1ynf9hhbch83k63lwps69ijfch30fk5v0sc418ck264c5vih26dh"))))
7889 (build-system r-build-system)
7891 `(("r-estimability" ,r-estimability)
7892 ("r-mvtnorm" ,r-mvtnorm)
7893 ("r-numderiv" ,r-numderiv)
7895 ("r-xtable" ,r-xtable)))
7896 (home-page "https://github.com/rvlenth/emmeans")
7897 (synopsis "Estimated marginal means, aka least-squares means")
7899 "This package provides tools to obtain @dfn{estimated marginal
7900 means} (EMMs) for many linear, generalized linear, and mixed models. It can
7901 be used to compute contrasts or linear functions of EMMs, trends, and
7902 comparisons of slopes.")
7903 ;; Either version of the license.
7904 (license (list license:gpl2 license:gpl3))))
7906 (define-public r-pwr
7913 (uri (cran-uri "pwr" version))
7916 "0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
7917 (build-system r-build-system)
7919 `(("r-knitr" ,r-knitr)))
7920 (home-page "https://github.com/heliosdrm/pwr")
7921 (synopsis "Basic functions for power analysis")
7923 "This package provides power analysis functions along the lines of
7925 (license license:gpl3+)))
7927 (define-public r-libcoin
7934 (uri (cran-uri "libcoin" version))
7937 "1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i"))))
7938 (build-system r-build-system)
7939 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
7940 (home-page "https://cran.r-project.org/web/packages/libcoin")
7941 (synopsis "Linear test statistics for permutation inference")
7943 "This package provides basic infrastructure for linear test statistics
7944 and permutation inference in the framework of Strasser and Weber (1999).")
7945 (license license:gpl2)))
7947 (define-public r-coin
7954 (uri (cran-uri "coin" version))
7957 "1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd"))))
7958 (build-system r-build-system)
7960 `(("r-libcoin" ,r-libcoin)
7961 ("r-matrixstats" ,r-matrixstats)
7962 ("r-modeltools" ,r-modeltools)
7963 ("r-multcomp" ,r-multcomp)
7964 ("r-mvtnorm" ,r-mvtnorm)
7965 ("r-survival" ,r-survival)))
7966 (home-page "http://coin.r-forge.r-project.org")
7967 (synopsis "Conditional inference procedures in a permutation test framework")
7969 "This package provides conditional inference procedures for the general
7970 independence problem including two-sample, K-sample (non-parametric ANOVA),
7971 correlation, censored, ordered and multivariate problems.")
7972 (license license:gpl2)))
7974 (define-public r-bayesplot
7976 (name "r-bayesplot")
7981 (uri (cran-uri "bayesplot" version))
7984 "0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
7985 (build-system r-build-system)
7987 `(("pandoc" ,ghc-pandoc)
7988 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
7990 `(("r-dplyr" ,r-dplyr)
7991 ("r-ggplot2" ,r-ggplot2)
7992 ("r-ggridges" ,r-ggridges)
7994 ("r-reshape2" ,r-reshape2)
7995 ("r-rlang" ,r-rlang)
7996 ("r-tibble" ,r-tibble)
7997 ("r-tidyselect" ,r-tidyselect)))
7998 (home-page "http://mc-stan.org/bayesplot")
7999 (synopsis "Plotting for Bayesian models")
8001 "This package provides plotting functions for posterior analysis, model
8002 checking, and MCMC diagnostics. The package is designed not only to provide
8003 convenient functionality for users, but also a common set of functions that
8004 can be easily used by developers working on a variety of R packages for
8005 Bayesian modeling.")
8006 (license license:gpl3+)))
8008 (define-public r-tmb
8015 (uri (cran-uri "TMB" version))
8018 "1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
8019 (properties `((upstream-name . "TMB")))
8020 (build-system r-build-system)
8022 `(("r-matrix" ,r-matrix)
8023 ("r-rcppeigen" ,r-rcppeigen)))
8024 (home-page "http://tmb-project.org")
8025 (synopsis "Template model builder: a general random effect tool")
8027 "With this tool, a user should be able to quickly implement complex
8028 random effect models through simple C++ templates. The package combines
8029 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8030 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8031 from R) to obtain an efficient implementation of the applied Laplace
8032 approximation with exact derivatives. Key features are: Automatic sparseness
8033 detection, parallelism through BLAS and parallel user templates.")
8034 (license license:gpl2)))
8036 (define-public r-sjstats
8043 (uri (cran-uri "sjstats" version))
8046 "1x9ybvz84vgaabmqp4z6crbv5q6kqjg6msk1spbr11zx9dbj06ca"))))
8047 (build-system r-build-system)
8049 `(("r-bayestestr" ,r-bayestestr)
8050 ("r-broom" ,r-broom)
8051 ("r-dplyr" ,r-dplyr)
8052 ("r-emmeans" ,r-emmeans)
8053 ("r-insight" ,r-insight)
8055 ("r-magrittr" ,r-magrittr)
8057 ("r-modelr" ,r-modelr)
8058 ("r-performance" ,r-performance)
8059 ("r-purrr" ,r-purrr)
8060 ("r-rlang" ,r-rlang)
8061 ("r-sjlabelled" ,r-sjlabelled)
8062 ("r-sjmisc" ,r-sjmisc)
8063 ("r-tidyr" ,r-tidyr)))
8064 (home-page "https://github.com/strengejacke/sjstats")
8065 (synopsis "Functions for common statistical computations")
8067 "This package provides a collection of convenient functions for common
8068 statistical computations, which are not directly provided by R's @code{base}
8069 or @code{stats} packages. This package aims at providing, first, shortcuts
8070 for statistical measures, which otherwise could only be calculated with
8071 additional effort. Second, these shortcut functions are generic, and can be
8072 applied not only to vectors, but also to other objects as well. The focus of
8073 most functions lies on summary statistics or fit measures for regression
8074 models, including generalized linear models, mixed effects models and Bayesian
8076 (license license:gpl3)))
8078 (define-public r-glmmtmb
8085 (uri (cran-uri "glmmTMB" version))
8088 "035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
8089 (properties `((upstream-name . "glmmTMB")))
8090 (build-system r-build-system)
8092 `(("r-lme4" ,r-lme4)
8093 ("r-matrix" ,r-matrix)
8095 ("r-rcppeigen" ,r-rcppeigen)
8098 `(("r-knitr" ,r-knitr))) ; for vignettes
8099 (home-page "https://github.com/glmmTMB")
8100 (synopsis "Generalized linear mixed models")
8102 "Fit linear and generalized linear mixed models with various extensions,
8103 including zero-inflation. The models are fitted using maximum likelihood
8104 estimation via the Template Model Builder. Random effects are assumed to be
8105 Gaussian on the scale of the linear predictor and are integrated out using the
8106 Laplace approximation. Gradients are calculated using automatic
8108 (license license:agpl3+)))
8110 (define-public r-bayestestr
8112 (name "r-bayestestr")
8117 (uri (cran-uri "bayestestR" version))
8120 "08d3bsb6li59n17bx1zrqnlnvniyb3vls9kl856km4chx3b2ff82"))))
8121 (properties `((upstream-name . "bayestestR")))
8122 (build-system r-build-system)
8124 `(("r-insight" ,r-insight)))
8125 (home-page "https://github.com/easystats/bayestestR")
8126 (synopsis "Describe Bayesian models and posterior distributions")
8128 "This package provides utilities to understand and describe posterior
8129 distributions and Bayesian models. It includes point-estimates such as
8130 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
8131 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
8132 ROPE percentage and pd).")
8133 (license license:gpl3)))
8135 (define-public r-performance
8137 (name "r-performance")
8142 (uri (cran-uri "performance" version))
8145 "13j74ffhx950kacs86ixx84nviq9qlwzr7hjnhkmzw2hspjxq99w"))))
8146 (build-system r-build-system)
8148 `(("r-bayestestr" ,r-bayestestr)
8149 ("r-insight" ,r-insight)))
8150 (home-page "https://easystats.github.io/performance/")
8151 (synopsis "Assessment of regression models performance")
8153 "This package provides utilities for computing measures to assess model
8154 quality, which are not directly provided by R's @code{base} or @code{stats}
8155 packages. These include e.g. measures like r-squared, intraclass correlation
8156 coefficient, root mean squared error or functions to check models for
8157 overdispersion, singularity or zero-inflation and more. Functions apply to a
8158 large variety of regression models, including generalized linear models, mixed
8159 effects models and Bayesian models.")
8160 (license license:gpl3)))
8162 (define-public r-ggeffects
8164 (name "r-ggeffects")
8169 (uri (cran-uri "ggeffects" version))
8172 "1b0lxa8bljdh6h4lk7pql1lrhjlvh7p5c8qlgb8ac6ay8hb79vmi"))))
8173 (build-system r-build-system)
8175 `(("r-dplyr" ,r-dplyr)
8176 ("r-insight" ,r-insight)
8177 ("r-magrittr" ,r-magrittr)
8179 ("r-purrr" ,r-purrr)
8180 ("r-rlang" ,r-rlang)
8181 ("r-scales" ,r-scales)
8182 ("r-sjlabelled" ,r-sjlabelled)
8183 ("r-sjmisc" ,r-sjmisc)))
8184 (home-page "https://github.com/strengejacke/ggeffects")
8185 (synopsis "Create tidy data frames of marginal effects for ggplot")
8187 "This package provides tools to compute marginal effects from statistical
8188 models and return the result as tidy data frames. These data frames are ready
8189 to use with the @code{ggplot2} package. Marginal effects can be calculated
8190 for many different models. Interaction terms, splines and polynomial terms
8191 are also supported. The two main functions are @code{ggpredict()} and
8192 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
8193 results using @code{ggplot2}.")
8194 (license license:gpl3)))
8196 (define-public r-sjplot
8203 (uri (cran-uri "sjPlot" version))
8206 "1m0gy991fmxvqry91kkzdkdapyalhrwql25d0hg2a2naxgfw4zpk"))))
8207 (properties `((upstream-name . "sjPlot")))
8208 (build-system r-build-system)
8210 `(("r-bayestestr" ,r-bayestestr)
8211 ("r-broom" ,r-broom)
8212 ("r-dplyr" ,r-dplyr)
8213 ("r-forcats" ,r-forcats)
8214 ("r-ggeffects" ,r-ggeffects)
8215 ("r-ggplot2" ,r-ggplot2)
8216 ("r-ggrepel" ,r-ggrepel)
8217 ("r-glmmtmb" ,r-glmmtmb)
8218 ("r-insight" ,r-insight)
8219 ("r-knitr" ,r-knitr)
8221 ("r-magrittr" ,r-magrittr)
8223 ("r-modelr" ,r-modelr)
8225 ("r-performance" ,r-performance)
8226 ("r-psych" ,r-psych)
8227 ("r-purrr" ,r-purrr)
8228 ("r-rlang" ,r-rlang)
8229 ("r-scales" ,r-scales)
8230 ("r-sjlabelled" ,r-sjlabelled)
8231 ("r-sjmisc" ,r-sjmisc)
8232 ("r-sjstats" ,r-sjstats)
8233 ("r-tidyr" ,r-tidyr)))
8234 (home-page "https://strengejacke.github.io/sjPlot/")
8235 (synopsis "Data visualization for statistics in social science")
8237 "This package represents a collection of plotting and table output
8238 functions for data visualization. Results of various statistical
8239 analyses (that are commonly used in social sciences) can be visualized using
8240 this package, including simple and cross tabulated frequencies, histograms,
8241 box plots, (generalized) linear models, mixed effects models, principal
8242 component analysis and correlation matrices, cluster analyses, scatter plots,
8243 stacked scales, effects plots of regression models (including interaction
8244 terms) and much more. This package supports labelled data.")
8245 (license license:gpl3)))
8247 (define-public r-ini
8254 (uri (cran-uri "ini" version))
8257 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
8258 (build-system r-build-system)
8259 (home-page "https://github.com/dvdscripter/ini")
8260 (synopsis "Read and write configuration files")
8262 "This package provides tools to parse simple @code{.ini} configuration
8263 files to an structured list. Users can manipulate this resulting list with
8264 @code{lapply()} functions. This same structured list can be used to write
8265 back to file after modifications.")
8266 (license license:gpl3)))
8275 (uri (cran-uri "gh" version))
8278 "1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
8279 (build-system r-build-system)
8281 `(("r-httr" ,r-httr)
8283 ("r-jsonlite" ,r-jsonlite)))
8284 (home-page "https://github.com/r-lib/gh#readme")
8285 (synopsis "Access the GitHub API via R")
8287 "This package provides a minimal R client to access the GitHub API.")
8288 (license license:expat)))
8297 (uri (cran-uri "fs" version))
8300 "1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
8301 (build-system r-build-system)
8303 `(("r-rcpp" ,r-rcpp)))
8305 `(("pkg-config" ,pkg-config)))
8306 (home-page "http://fs.r-lib.org")
8307 (synopsis "Cross-platform file system operations based on libuv")
8309 "This package provides a cross-platform interface to file system
8310 operations, built on top of the libuv C library.")
8311 (license license:gpl3)))
8313 (define-public r-clisymbols
8315 (name "r-clisymbols")
8320 (uri (cran-uri "clisymbols" version))
8323 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
8324 (build-system r-build-system)
8325 (home-page "https://github.com/gaborcsardi/clisymbols")
8326 (synopsis "Unicode symbols at the R prompt")
8328 "This package provides a small subset of Unicode symbols, that are useful
8329 when building command line applications. They fall back to alternatives on
8330 terminals that do not support Unicode.")
8331 (license license:expat)))
8333 (define-public r-usethis
8340 (uri (cran-uri "usethis" version))
8343 "07an5wbikilg7cb3q6x5aykw8dfqnjrc3wpfb7gjmy0d9fh20fcy"))))
8344 (build-system r-build-system)
8346 `(("r-clipr" ,r-clipr)
8347 ("r-clisymbols" ,r-clisymbols)
8348 ("r-crayon" ,r-crayon)
8353 ("r-git2r" ,r-git2r)
8355 ("r-purrr" ,r-purrr)
8356 ("r-rlang" ,r-rlang)
8357 ("r-rprojroot" ,r-rprojroot)
8358 ("r-rstudioapi" ,r-rstudioapi)
8359 ("r-whisker" ,r-whisker)
8360 ("r-withr" ,r-withr)
8361 ("r-yaml" ,r-yaml)))
8362 (home-page "https://github.com/r-lib/usethis")
8363 (synopsis "Automate R package and project setup")
8365 "This package helps you to automate R package and project setup tasks
8366 that are otherwise performed manually. This includes setting up unit testing,
8367 test coverage, continuous integration, Git, GitHub integration, licenses,
8368 Rcpp, RStudio projects, and more.")
8369 (license license:gpl3)))
8371 (define-public r-sessioninfo
8373 (name "r-sessioninfo")
8378 (uri (cran-uri "sessioninfo" version))
8381 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
8382 (build-system r-build-system)
8385 ("r-withr" ,r-withr)))
8386 (home-page "https://github.com/r-lib/sessioninfo#readme")
8387 (synopsis "R session information")
8389 "This package provides tools to query and print information about the
8390 current R session. It is similar to @code{utils::sessionInfo()}, but includes
8391 more information about packages, and where they were installed from.")
8392 (license license:gpl2)))
8394 (define-public r-remotes
8401 (uri (cran-uri "remotes" version))
8404 "19v8dmnk9l4i9m64p7zgmj7y1vhnnwhi5kyn0k5d034zzkvchi49"))))
8405 (build-system r-build-system)
8406 (home-page "https://github.com/r-lib/remotes#readme")
8407 (synopsis "R package installation from remote repositories")
8409 "Download and install R packages stored in GitHub, BitBucket, or plain
8410 subversion or git repositories. This package is a lightweight replacement of
8411 the @code{install_*} functions in the @code{devtools} package. Indeed most of
8412 the code was copied over from @code{devtools}.")
8413 (license license:gpl2+)))
8415 (define-public r-xopen
8422 (uri (cran-uri "xopen" version))
8425 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
8426 (build-system r-build-system)
8428 `(("r-processx" ,r-processx)))
8429 (home-page "https://github.com/r-lib/xopen#readme")
8430 (synopsis "Open system files, URLs, anything")
8432 "This package provides a cross-platform solution to open files,
8433 directories or URLs with their associated programs.")
8434 (license license:expat)))
8436 (define-public r-rcmdcheck
8438 (name "r-rcmdcheck")
8443 (uri (cran-uri "rcmdcheck" version))
8446 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
8447 (build-system r-build-system)
8449 `(("r-callr" ,r-callr)
8451 ("r-crayon" ,r-crayon)
8453 ("r-digest" ,r-digest)
8454 ("r-pkgbuild" ,r-pkgbuild)
8455 ("r-prettyunits" ,r-prettyunits)
8457 ("r-rprojroot" ,r-rprojroot)
8458 ("r-sessioninfo" ,r-sessioninfo)
8459 ("r-withr" ,r-withr)
8460 ("r-xopen" ,r-xopen)))
8461 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
8462 (synopsis "Run R CMD check from R and capture results")
8464 "Run @code{R CMD check} from R programmatically, and capture the results
8465 of the individual checks.")
8466 (license license:expat)))
8468 (define-public r-rapportools
8470 (name "r-rapportools")
8475 (uri (cran-uri "rapportools" version))
8478 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
8479 (build-system r-build-system)
8481 `(("r-pander" ,r-pander)
8483 ("r-reshape" ,r-reshape)))
8484 (home-page "https://cran.r-project.org/web/packages/rapportools/")
8485 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
8487 "This package provides helper functions that act as wrappers to more
8488 advanced statistical methods with the advantage of having sane defaults for
8490 (license license:agpl3+)))
8492 (define-public r-pander
8499 (uri (cran-uri "pander" version))
8502 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
8503 (build-system r-build-system)
8505 `(("r-digest" ,r-digest)
8506 ("r-rcpp" ,r-rcpp)))
8507 (home-page "https://rapporter.github.io/pander")
8508 (synopsis "Render R objects into Pandoc's markdown")
8510 "The main aim of the pander R package is to provide a minimal and easy
8511 tool for rendering R objects into Pandoc's markdown. The package is also
8512 capable of exporting/converting complex Pandoc documents (reports) in various
8514 ;; This package is licensed under either the AGPLv3+ or the very rarely
8516 (license license:agpl3+)))
8518 (define-public r-summarytools
8520 (name "r-summarytools")
8525 (uri (cran-uri "summarytools" version))
8528 "1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f"))))
8529 (build-system r-build-system)
8531 `(("r-checkmate" ,r-checkmate)
8532 ("r-dplyr" ,r-dplyr)
8533 ("r-htmltools" ,r-htmltools)
8534 ("r-lubridate" ,r-lubridate)
8535 ("r-magick" ,r-magick)
8536 ("r-matrixstats" ,r-matrixstats)
8537 ("r-pander" ,r-pander)
8539 ("r-rapportools" ,r-rapportools)
8540 ("r-rcurl" ,r-rcurl)
8541 ("r-tibble" ,r-tibble)
8542 ("r-tidyr" ,r-tidyr)))
8543 (home-page "https://github.com/dcomtois/summarytools")
8544 (synopsis "Tools to quickly and neatly summarize data")
8546 "This package provides tools for data frame summaries, cross-tabulations,
8547 weight-enabled frequency tables and common univariate statistics in concise
8548 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
8549 good point-of-entry for exploring data, both for experienced and new R
8551 (license license:gpl2)))
8553 (define-public r-lsei
8560 (uri (cran-uri "lsei" version))
8563 "1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
8564 (build-system r-build-system)
8566 `(("gfortran" ,gfortran)))
8567 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8568 (synopsis "Solve regression problems under equality/inequality constraints")
8570 "It contains functions that solve least squares linear regression
8571 problems under linear equality/inequality constraints. Functions for solving
8572 quadratic programming problems are also available, which transform such
8573 problems into least squares ones first.")
8574 (license license:gpl2+)))
8576 (define-public r-npsurv
8583 (uri (cran-uri "npsurv" version))
8586 "1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
8587 (build-system r-build-system)
8589 `(("r-lsei" ,r-lsei)))
8590 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
8591 (synopsis "Nonparametric survival analysis")
8593 "This package contains functions for non-parametric survival analysis of
8594 exact and interval-censored observations.")
8595 (license license:gpl2+)))
8597 (define-public r-clusteval
8599 (name "r-clusteval")
8604 (uri (cran-uri "clusteval" version))
8607 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
8608 (build-system r-build-system)
8610 `(("r-mvtnorm" ,r-mvtnorm)
8611 ("r-rcpp" ,r-rcpp)))
8612 (home-page "https://cran.r-project.org/web/packages/clusteval/")
8613 (synopsis "Evaluation of clustering algorithms")
8615 "This R package provides a suite of tools to evaluate clustering
8616 algorithms, clusterings, and individual clusters.")
8617 (license license:expat)))
8619 (define-public r-tweedie
8626 (uri (cran-uri "tweedie" version))
8629 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
8630 (build-system r-build-system)
8631 (native-inputs `(("gfortran" ,gfortran)))
8632 (home-page "https://cran.r-project.org/web/packages/tweedie/")
8633 (synopsis "Evaluation of Tweedie exponential family models")
8635 "Maximum likelihood computations for Tweedie families, including the
8636 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
8637 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
8638 and related methods.")
8639 (license license:gpl2+)))
8641 (define-public r-rcppgsl
8648 (uri (cran-uri "RcppGSL" version))
8651 "16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m"))))
8652 (properties `((upstream-name . "RcppGSL")))
8653 (build-system r-build-system)
8655 `(("r-rcpp" ,r-rcpp)
8658 `(("r-knitr" ,r-knitr))) ; for vignettes
8659 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
8660 (synopsis "Rcpp integration for GSL vectors and matrices")
8662 "The GNU Scientific Library (or GSL) is a collection of numerical
8663 routines for scientific computing. It is particularly useful for C and C++
8664 programs as it provides a standard C interface to a wide range of mathematical
8665 routines. There are over 1000 functions in total with an extensive test
8666 suite. The RcppGSL package provides an easy-to-use interface between GSL data
8667 structures and R using concepts from Rcpp which is itself a package that eases
8668 the interfaces between R and C++.")
8669 (license license:gpl2+)))
8671 (define-public r-mvabund
8678 (uri (cran-uri "mvabund" version))
8681 "0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
8682 (build-system r-build-system)
8684 `(("r-mass" ,r-mass)
8686 ("r-rcppgsl" ,r-rcppgsl)
8687 ("r-statmod" ,r-statmod)
8688 ("r-tweedie" ,r-tweedie)))
8689 (home-page "https://cran.r-project.org/web/packages/mvabund/")
8690 (synopsis "Statistical methods for analysing multivariate abundance data")
8692 "This package provides a set of tools for displaying, modeling and
8693 analysing multivariate abundance data in community ecology.")
8694 (license license:lgpl2.1+)))
8696 (define-public r-afex
8703 (uri (cran-uri "afex" version))
8706 "14w7kcwr5hxmjcjmdm5ia9ka3bw1nl18pxlm1vpw62nmvicn3455"))))
8707 (build-system r-build-system)
8711 ("r-lmertest" ,r-lmertest)
8712 ("r-pbkrtest" ,r-pbkrtest)
8713 ("r-reshape2" ,r-reshape2)))
8714 (home-page "https://afex.singmann.science/")
8715 (synopsis "Analysis of factorial experiments")
8717 "This package provides convenience functions for analyzing factorial
8718 experiments using ANOVA or mixed models.")
8719 (license license:gpl2+)))
8721 (define-public r-lmertest
8728 (uri (cran-uri "lmerTest" version))
8731 "1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
8732 (properties `((upstream-name . "lmerTest")))
8733 (build-system r-build-system)
8735 `(("r-ggplot2" ,r-ggplot2)
8738 ("r-numderiv" ,r-numderiv)))
8739 (home-page "https://github.com/runehaubo/lmerTestR")
8740 (synopsis "Tests in linear mixed effects models")
8742 "This package provides p-values in type I, II or III anova and summary
8743 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
8744 method. A Kenward-Roger method is also available via the @code{pbkrtest}
8745 package. Model selection methods include step, drop1 and anova-like tables
8746 for random effects (ranova). Methods for Least-Square means (LS-means) and
8747 tests of linear contrasts of fixed effects are also available.")
8748 (license license:gpl2+)))
8750 (define-public r-r2glmm
8757 (uri (cran-uri "r2glmm" version))
8760 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
8761 (build-system r-build-system)
8763 `(("r-afex" ,r-afex)
8764 ("r-data-table" ,r-data-table)
8765 ("r-dplyr" ,r-dplyr)
8766 ("r-ggplot2" ,r-ggplot2)
8767 ("r-gridextra" ,r-gridextra)
8768 ("r-lmertest" ,r-lmertest)
8770 ("r-matrix" ,r-matrix)
8772 ("r-pbkrtest" ,r-pbkrtest)))
8773 (home-page "https://github.com/bcjaeger/r2glmm")
8774 (synopsis "Compute R squared for mixed (multilevel) models")
8776 "This package computes model and semi partial R squared with confidence
8777 limits for the linear and generalized linear mixed model (LMM and GLMM). The
8778 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
8779 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
8781 (license license:gpl2)))
8783 (define-public r-weights
8790 (uri (cran-uri "weights" version))
8793 "0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
8794 (build-system r-build-system)
8796 `(("r-gdata" ,r-gdata)
8797 ("r-hmisc" ,r-hmisc)
8798 ("r-mice" ,r-mice)))
8800 "https://cran.r-project.org/web/packages/weights/")
8801 (synopsis "Weighting and weighted statistics")
8802 (description "This package Provides a variety of functions for producing
8803 simple weighted statistics, such as weighted Pearson's correlations, partial
8804 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
8805 includes some software for quickly recoding survey data and plotting point
8806 estimates from interaction terms in regressions (and multiply imputed
8807 regressions). NOTE: Weighted partial correlation calculations pulled to
8809 (license license:gpl2+)))
8811 (define-public r-rcppannoy
8813 (name "r-rcppannoy")
8818 (uri (cran-uri "RcppAnnoy" version))
8821 "1b0fmip9c4i0my1yjrvqy8jxfiiqcggq2kms135q0b53njxnqwwg"))))
8822 (properties `((upstream-name . "RcppAnnoy")))
8823 (build-system r-build-system)
8825 `(("r-rcpp" ,r-rcpp)))
8827 `(("r-knitr" ,r-knitr))) ; for vignettes
8828 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
8829 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
8831 "Annoy is a small C++ library for Approximate Nearest Neighbors written
8832 for efficient memory usage as well an ability to load from and save to disk.
8833 This package provides an R interface.")
8834 ;; Annoy is released under ASL 2.0, but this wrapper is released under
8836 (license (list license:gpl2+ license:asl2.0))))
8838 (define-public r-rcpphnsw
8845 (uri (cran-uri "RcppHNSW" version))
8848 "158a069n42pbnjrlmvqsr6bm2cfp9hxpnk3nhp3dwi9qjlq4r9bm"))))
8849 (properties `((upstream-name . "RcppHNSW")))
8850 (build-system r-build-system)
8851 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8852 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
8853 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
8855 "Hnswlib is a C++ library for approximate nearest neighbors. This
8856 package provides a minimal R interface by relying on the Rcpp package.")
8857 ;; hnswlib is released under Version 2.0 of the Apache License.
8858 (license (list license:gpl3 license:asl2.0))))
8860 (define-public r-rcppparallel
8862 (name "r-rcppparallel")
8867 (uri (cran-uri "RcppParallel" version))
8870 "1ym0bzs9g6bsg2lz24fisxxa3gypr6xcvrczn304czmrrag9413s"))))
8871 (properties `((upstream-name . "RcppParallel")))
8872 (build-system r-build-system)
8873 (home-page "http://rcppcore.github.io/RcppParallel")
8874 (synopsis "Parallel programming tools for Rcpp")
8876 "This package provides high level functions for parallel programming with
8877 Rcpp. For example, the @code{parallelFor()} function can be used to convert
8878 the work of a standard serial @code{for} loop into a parallel one and the
8879 @code{parallelReduce()} function can be used for accumulating aggregates or
8881 (license license:gpl2)))
8883 (define-public r-ncdf4
8890 (uri (cran-uri "ncdf4" version))
8893 "083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd"))))
8894 (build-system r-build-system)
8896 `(("netcdf" ,netcdf)
8898 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
8899 (synopsis "R interface to Unidata netCDF format data files")
8901 "This package provides a high-level R interface to data files written
8902 using Unidata's netCDF library (version 4 or earlier), which are binary data
8903 files that are portable across platforms and include metadata information in
8904 addition to the data sets. Using this package, netCDF files can be opened and
8905 data sets read in easily. It is also easy to create new netCDF dimensions,
8906 variables, and files, in either version 3 or 4 format, and manipulate existing
8908 (license license:gpl3+)))
8910 (define-public r-biocmanager
8912 (name "r-biocmanager")
8917 (uri (cran-uri "BiocManager" version))
8920 "0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah"))))
8921 (properties `((upstream-name . "BiocManager")))
8922 (build-system r-build-system)
8923 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
8924 (synopsis "Access the Bioconductor project package repository")
8926 "This package provides a convenient tool to install and update
8927 Bioconductor packages.")
8928 (license license:artistic2.0)))
8930 (define-public r-rgl
8933 (version "0.100.26")
8937 (uri (cran-uri "rgl" version))
8940 "0h77akviwjd86j2qyx326xynbmwhypd6ydprzlwqnidd4ckrr271"))))
8941 (build-system r-build-system)
8943 `(("pkg-config" ,pkg-config)))
8945 `(("freetype" ,freetype)
8949 ("ghc-pandoc" ,ghc-pandoc)
8952 `(("r-crosstalk" ,r-crosstalk)
8953 ("r-htmltools" ,r-htmltools)
8954 ("r-htmlwidgets" ,r-htmlwidgets)
8955 ("r-jsonlite" ,r-jsonlite)
8956 ("r-knitr" ,r-knitr)
8957 ("r-magrittr" ,r-magrittr)
8958 ("r-manipulatewidget" ,r-manipulatewidget)
8959 ("r-shiny" ,r-shiny)))
8960 (home-page "https://r-forge.r-project.org/projects/rgl/")
8961 (synopsis "3D visualization using OpenGL")
8963 "This package provides medium to high level functions for 3D interactive graphics,
8964 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
8965 as functions for constructing representations of geometric
8966 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
8967 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
8968 image formats, including PNG, Postscript, SVG, PGF.")
8969 ;; Any version of the GPL.
8970 (license (list license:gpl2+ license:gpl3+))))
8972 (define-public r-multicool
8974 (name "r-multicool")
8979 (uri (cran-uri "multicool" version))
8982 "1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
8983 (build-system r-build-system)
8984 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
8985 (home-page "https://cran.r-project.org/web/packages/multicool/")
8986 (synopsis "Permutations of multisets in cool-lex order")
8988 "This package provides a set of tools to permute multisets without loops
8989 or hash tables and to generate integer partitions. Cool-lex order is similar
8990 to colexicographical order.")
8991 (license license:gpl2)))
8993 (define-public r-misc3d
9000 (uri (cran-uri "misc3d" version))
9003 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9004 (build-system r-build-system)
9005 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9006 (synopsis "Miscellaneous 3D Plots")
9008 "This package provides a collection of miscellaneous 3d plots, including
9010 ;; Any version of the GPL.
9011 (license (list license:gpl2+ license:gpl3+))))
9020 (uri (cran-uri "ks" version))
9023 "06ymx244yknmpl6935l4pafqbm4gcbpnhqg7rinql6rrfr9mcrag"))))
9024 (build-system r-build-system)
9027 ("r-kernlab" ,r-kernlab)
9028 ("r-kernsmooth" ,r-kernsmooth)
9029 ("r-matrix" ,r-matrix)
9030 ("r-mclust" ,r-mclust)
9032 ("r-multicool" ,r-multicool)
9033 ("r-mvtnorm" ,r-mvtnorm)))
9034 (home-page "http://www.mvstat.net/tduong/")
9035 (synopsis "Kernel smoothing")
9037 "This package provides kernel smoothers for univariate and multivariate
9038 data, including density functions, density derivatives, cumulative
9039 distributions, modal clustering, discriminant analysis, and two-sample
9040 hypothesis testing.")
9041 ;; Either version of the GPL.
9042 (license (list license:gpl2 license:gpl3))))
9044 (define-public r-feature
9051 (uri (cran-uri "feature" version))
9054 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9055 (build-system r-build-system)
9058 ("r-misc3d" ,r-misc3d)
9060 (home-page "http://www.mvstat.net/tduong/")
9061 (synopsis "Inferential feature significance for kernel density estimation")
9063 "The feature package contains functions to display and compute kernel
9064 density estimates, significant gradient and significant curvature regions.
9065 Significant gradient and/or curvature regions often correspond to significant
9066 features (e.g. local modes).")
9067 ;; Either version of the GPL.
9068 (license (list license:gpl2 license:gpl3))))
9070 (define-public r-arm
9077 (uri (cran-uri "arm" version))
9080 "0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
9081 (build-system r-build-system)
9083 `(("r-abind" ,r-abind)
9087 ("r-matrix" ,r-matrix)
9088 ("r-nlme" ,r-nlme)))
9089 (home-page "https://cran.r-project.org/web/packages/arm/")
9090 (synopsis "Data analysis using regression and multilevel/hierarchical models")
9092 "This package provides functions to accompany A. Gelman and J. Hill,
9093 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
9094 University Press, 2007.")
9095 (license license:gpl3+)))
9097 (define-public r-circular
9104 (uri (cran-uri "circular" version))
9107 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
9108 (build-system r-build-system)
9110 `(("r-boot" ,r-boot)
9111 ("r-mvtnorm" ,r-mvtnorm)))
9113 `(("gfortran" ,gfortran)))
9114 (home-page "https://cran.r-project.org/web/packages/circular/")
9115 (synopsis "Circular statistics")
9117 "This package provides tools for circular statistics, from \"Topics in
9118 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
9120 (license license:gpl2+)))
9122 (define-public r-activity
9129 (uri (cran-uri "activity" version))
9132 "11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs"))))
9133 (build-system r-build-system)
9135 `(("r-circular" ,r-circular)
9136 ("r-pbapply" ,r-pbapply)))
9137 (home-page "https://cran.r-project.org/web/packages/activity/")
9138 (synopsis "Animal activity statistics")
9140 "This package provides functions to fit kernel density functions to
9141 animal activity time data; plot activity distributions; quantify overall
9142 levels of activity; statistically compare activity metrics through
9143 bootstrapping; and evaluate variation in linear variables with time (or other
9144 circular variables).")
9145 (license license:gpl3)))
9147 (define-public r-ouch
9154 (uri (cran-uri "ouch" version))
9157 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
9158 (build-system r-build-system)
9159 (propagated-inputs `(("r-subplex" ,r-subplex)))
9160 (home-page "http://kingaa.github.io/ouch/")
9161 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
9163 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
9164 for evolution along a phylogenetic tree.")
9165 (license license:gpl2+)))
9167 (define-public r-fmsb
9174 (uri (cran-uri "fmsb" version))
9177 "1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
9178 (build-system r-build-system)
9179 (home-page "http://minato.sip21c.org/msb/")
9180 (synopsis "Functions for medical statistics book with demographic data")
9182 "This package provides several utility functions for the book entitled
9183 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
9184 Japan, 2007) with Japanese demographic data and some demographic analysis
9185 related functions.")
9186 (license license:gpl2+)))
9188 (define-public r-stabledist
9190 (name "r-stabledist")
9195 (uri (cran-uri "stabledist" version))
9198 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
9199 (build-system r-build-system)
9200 (home-page "http://www.rmetrics.org")
9201 (synopsis "Stable distribution functions")
9203 "This package provides density, probability and quantile functions, and
9204 random number generation for (skew) stable distributions, using the
9205 parametrizations of Nolan.")
9206 (license license:gpl2+)))
9208 (define-public r-gsl
9215 (uri (cran-uri "gsl" version))
9218 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
9219 (build-system r-build-system)
9222 (home-page "https://cran.r-project.org/web/packages/gsl")
9223 (synopsis "Wrapper for the GNU Scientific Library")
9225 "This package provides an R wrapper for the special functions and quasi
9226 random number generators of the GNU Scientific Library.")
9227 (license license:gpl2+)))
9229 (define-public r-adgoftest
9231 (name "r-adgoftest")
9236 (uri (cran-uri "ADGofTest" version))
9239 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
9240 (properties `((upstream-name . "ADGofTest")))
9241 (build-system r-build-system)
9242 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
9243 (synopsis "Anderson-Darling GoF test")
9245 "This package provides an implementation of the Anderson-Darling GoF test
9246 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
9247 Anderson-Darling Distribution\".")
9248 ;; Any version of the GPL.
9249 (license license:gpl3+)))
9251 (define-public r-softimpute
9253 (name "r-softimpute")
9258 (uri (cran-uri "softImpute" version))
9261 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
9262 (properties `((upstream-name . "softImpute")))
9263 (build-system r-build-system)
9265 `(("r-matrix" ,r-matrix)))
9267 `(("gfortran" ,gfortran)))
9268 (home-page "https://cran.r-project.org/web/packages/softImpute")
9269 (synopsis "Matrix completion via iterative soft-thresholded SVD")
9271 "This package provides iterative methods for matrix completion that use
9272 nuclear-norm regularization. The package includes procedures for centering
9273 and scaling rows, columns or both, and for computing low-rank @dfn{single
9274 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
9276 (license license:gpl2)))
9278 (define-public r-fftwtools
9280 (name "r-fftwtools")
9285 (uri (cran-uri "fftwtools" version))
9288 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
9289 (build-system r-build-system)
9290 (inputs `(("fftw" ,fftw)))
9291 (home-page "https://github.com/krahim/fftwtools")
9292 (synopsis "Wrapper for FFTW3")
9294 "This package provides a wrapper for several FFTW functions. It provides
9295 access to the two-dimensional FFT, the multivariate FFT, and the
9296 one-dimensional real to complex FFT using the FFTW3 library. The package
9297 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
9298 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
9299 The FFT functions have a parameter that allows them to not return the
9300 redundant complex conjugate when the input is real data.")
9301 (license license:gpl2+)))
9303 (define-public r-tiff
9310 (uri (cran-uri "tiff" version))
9313 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
9314 (build-system r-build-system)
9316 `(("libtiff" ,libtiff)
9317 ("libjpeg" ,libjpeg)
9319 (home-page "http://www.rforge.net/tiff/")
9320 (synopsis "Read and write TIFF images")
9322 "This package provides an easy and simple way to read, write and display
9323 bitmap images stored in the TIFF format. It can read and write both files and
9324 in-memory raw vectors.")
9325 ;; Either of these two license versions.
9326 (license (list license:gpl2 license:gpl3))))
9328 (define-public r-waveslim
9335 (uri (cran-uri "waveslim" version))
9338 "0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
9339 (build-system r-build-system)
9341 `(("gfortran" ,gfortran)))
9342 (home-page "http://waveslim.blogspot.com")
9343 (synopsis "Basic wavelet routines for signal processing")
9345 "This package provides basic wavelet routines for time series (1D),
9346 image (2D) and array (3D) analysis. The code provided here is based on
9347 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
9348 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
9349 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
9350 pairs (Selesnick 2001, 2002).")
9351 (license license:bsd-3)))
9353 (define-public r-wordcloud
9355 (name "r-wordcloud")
9360 (uri (cran-uri "wordcloud" version))
9363 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
9364 (build-system r-build-system)
9366 `(("r-rcolorbrewer" ,r-rcolorbrewer)
9367 ("r-rcpp" ,r-rcpp)))
9368 (home-page "https://cran.r-project.org/web/packages/wordcloud")
9369 (synopsis "Word clouds")
9371 "This package provides functionality to create pretty word clouds,
9372 visualize differences and similarity between documents, and avoid
9373 over-plotting in scatter plots with text.")
9374 (license license:lgpl2.1)))
9376 (define-public r-colorramps
9378 (name "r-colorramps")
9383 (uri (cran-uri "colorRamps" version))
9386 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
9387 (properties `((upstream-name . "colorRamps")))
9388 (build-system r-build-system)
9389 (home-page "https://cran.r-project.org/web/packages/colorRamps")
9390 (synopsis "Build color tables")
9391 (description "This package provides features to build gradient color
9393 ;; Any version of the GPL
9394 (license license:gpl3+)))
9396 (define-public r-tidytree
9403 (uri (cran-uri "tidytree" version))
9406 "13mhizbsawmfqjpnzb73yw6kn1f1wlz0vhyzj3g0rj6ry880rw89"))))
9407 (build-system r-build-system)
9410 ("r-dplyr" ,r-dplyr)
9411 ("r-lazyeval" ,r-lazyeval)
9412 ("r-magrittr" ,r-magrittr)
9413 ("r-rlang" ,r-rlang)
9414 ("r-tibble" ,r-tibble)))
9415 (home-page "https://github.com/GuangchuangYu/tidytree")
9416 (synopsis "Tidy tool for phylogenetic tree data manipulation")
9418 "Phylogenetic trees generally contain multiple components including nodes,
9419 edges, branches and associated data. This package provides an approach to
9420 convert tree objects to tidy data frames. It also provides tidy interfaces to
9421 manipulate tree data.")
9422 (license license:artistic2.0)))
9424 (define-public r-rvcheck
9431 (uri (cran-uri "rvcheck" version))
9434 "1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b"))))
9435 (build-system r-build-system)
9437 `(("r-rlang" ,r-rlang)))
9438 (home-page "https://cran.r-project.org/web/packages/rvcheck")
9439 (synopsis "R package version check")
9441 "This package provides tools to check the latest release version of R and
9442 R packages (on CRAN, Bioconductor or Github).")
9443 (license license:artistic2.0)))
9445 (define-public r-docopt
9452 (uri (cran-uri "docopt" version))
9455 "06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
9456 (build-system r-build-system)
9457 (home-page "https://github.com/docopt/docopt.R")
9458 (synopsis "Command-line interface specification language")
9460 "This package enables you to define a command-line interface by just
9461 giving it a description in the specific format.")
9462 (license license:expat)))
9464 (define-public r-sparsesvd
9466 (name "r-sparsesvd")
9471 (uri (cran-uri "sparsesvd" version))
9474 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
9475 (build-system r-build-system)
9476 (propagated-inputs `(("r-matrix" ,r-matrix)))
9477 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
9478 (synopsis "Sparse truncated singular value decomposition")
9480 "This package provides a Wrapper around the SVDLIBC library
9481 for (truncated) singular value decomposition of a sparse matrix. Currently,
9482 only sparse real matrices in Matrix package format are supported.")
9483 ;; SVDLIBC is released under BSD-2. The R interface is released under
9485 (license (list license:bsd-3 license:bsd-2))))
9487 (define-public r-speedglm
9494 (uri (cran-uri "speedglm" version))
9497 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
9498 (build-system r-build-system)
9500 `(("r-mass" ,r-mass)
9501 ("r-matrix" ,r-matrix)))
9502 (home-page "https://cran.r-project.org/web/packages/speedglm")
9503 (synopsis "Fit linear and generalized linear models to large data sets")
9505 "This package provides tools for fitting linear models and generalized
9506 linear models to large data sets by updating algorithms.")
9507 ;; Any version of the GPL
9508 (license license:gpl2+)))
9510 (define-public r-densityclust
9512 (name "r-densityclust")
9517 (uri (cran-uri "densityClust" version))
9520 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
9521 (properties `((upstream-name . "densityClust")))
9522 (build-system r-build-system)
9525 ("r-ggplot2" ,r-ggplot2)
9526 ("r-ggrepel" ,r-ggrepel)
9527 ("r-gridextra" ,r-gridextra)
9528 ("r-rcolorbrewer" ,r-rcolorbrewer)
9530 ("r-rtsne" ,r-rtsne)))
9531 (home-page "https://cran.r-project.org/web/packages/densityClust")
9532 (synopsis "Clustering by fast search and find of density peaks")
9534 "This package provides an improved implementation (based on k-nearest
9535 neighbors) of the density peak clustering algorithm, originally described by
9536 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
9537 large datasets (> 100,000 samples) very efficiently.")
9538 (license license:gpl2+)))
9540 (define-public r-combinat
9547 (uri (cran-uri "combinat" version))
9550 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
9551 (build-system r-build-system)
9552 (home-page "https://cran.r-project.org/web/packages/combinat")
9553 (synopsis "Combinatorics utilities")
9554 (description "This package provides assorted routines for combinatorics.")
9555 (license license:gpl2)))
9557 (define-public r-qlcmatrix
9559 (name "r-qlcmatrix")
9564 (uri (cran-uri "qlcMatrix" version))
9567 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
9568 (properties `((upstream-name . "qlcMatrix")))
9569 (build-system r-build-system)
9571 `(("r-docopt" ,r-docopt)
9572 ("r-matrix" ,r-matrix)
9574 ("r-sparsesvd" ,r-sparsesvd)))
9575 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
9576 (synopsis "Sparse matrix functions for quantitative language comparison")
9578 "This package provides an extension of the functionality of the Matrix
9579 package for using sparse matrices. Some of the functions are very general,
9580 while other are highly specific for the special data format used for
9581 @dfn{quantitative language comparison} (QLC).")
9582 (license license:gpl3)))
9584 (define-public r-ddrtree
9591 (uri (cran-uri "DDRTree" version))
9594 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
9595 (properties `((upstream-name . "DDRTree")))
9596 (build-system r-build-system)
9599 ("r-irlba" ,r-irlba)
9601 ("r-rcppeigen" ,r-rcppeigen)))
9602 (home-page "https://cran.r-project.org/web/packages/DDRTree")
9603 (synopsis "Learning principal graphs with DDRTree")
9605 "This package provides an implementation of the framework of
9606 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
9607 dimensional space while constructs a principal tree which passes through the
9608 middle of the data simultaneously. DDRTree shows superiority to
9609 alternatives (Wishbone, DPT) for inferring the ordering as well as the
9610 intrinsic structure of single cell genomics data. In general, it could be
9611 used to reconstruct the temporal progression as well as the bifurcation
9612 structure of any data type.")
9613 (license license:asl2.0)))
9615 (define-public r-corpcor
9622 (uri (cran-uri "corpcor" version))
9625 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
9626 (build-system r-build-system)
9627 (home-page "http://strimmerlab.org/software/corpcor/")
9628 (synopsis "Efficient estimation of covariance and (partial) correlation")
9630 "This package implements a James-Stein-type shrinkage estimator for the
9631 covariance matrix, with separate shrinkage for variances and correlations.
9632 Furthermore, functions are available for fast singular value decomposition,
9633 for computing the pseudoinverse, and for checking the rank and positive
9634 definiteness of a matrix.")
9635 (license license:gpl3+)))
9637 (define-public r-rspectra
9644 (uri (cran-uri "RSpectra" version))
9647 "1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s"))))
9648 (properties `((upstream-name . "RSpectra")))
9649 (build-system r-build-system)
9651 `(("r-matrix" ,r-matrix)
9653 ("r-rcppeigen" ,r-rcppeigen)))
9654 (home-page "https://github.com/yixuan/RSpectra")
9655 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
9657 "This package provides an R interface to the Spectra library for
9658 large-scale eigenvalue and SVD problems. It is typically used to compute a
9659 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
9660 which is usually more efficient than @code{eigen()} if k << n.")
9662 (license license:mpl2.0)))
9664 (define-public r-vbsr
9671 (uri (cran-uri "vbsr" version))
9674 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
9675 (build-system r-build-system)
9676 (home-page "https://cran.r-project.org/web/packages/vbsr")
9677 (synopsis "Variational Bayes spike regression regularized linear models")
9679 "This package provides an efficient algorithm for solving ultra-sparse
9680 regularized regression models using a variational Bayes algorithm with a spike
9681 prior. The algorithm is solved on a path, with coordinate updates, and is
9682 capable of generating very sparse models. Very general model
9683 diagnostics for controlling type-1 errors are also provided.")
9684 (license license:gpl2)))
9686 (define-public r-flare
9693 (uri (cran-uri "flare" version))
9696 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
9697 (build-system r-build-system)
9699 `(("r-igraph" ,r-igraph)
9700 ("r-lattice" ,r-lattice)
9702 ("r-matrix" ,r-matrix)))
9703 (home-page "https://cran.r-project.org/web/packages/flare")
9704 (synopsis "Family of Lasso regression implementations")
9706 "This package provides implementations of a family of Lasso variants
9707 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
9708 high dimensional sparse linear models.")
9709 (license license:gpl2)))
9711 (define-public r-lassopv
9718 (uri (cran-uri "lassopv" version))
9721 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
9722 (build-system r-build-system)
9723 (propagated-inputs `(("r-lars" ,r-lars)))
9724 (home-page "https://github.com/lingfeiwang/lassopv")
9725 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
9727 "This package enables you to estimate the p-values for predictors x
9728 against target variable y in Lasso regression, using the regularization
9729 strength when each predictor enters the active set of regularization path for
9730 the first time as the statistic.")
9731 (license license:gpl3)))
9733 (define-public r-splitstackshape
9735 (name "r-splitstackshape")
9740 (uri (cran-uri "splitstackshape" version))
9743 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
9744 (build-system r-build-system)
9746 `(("r-data-table" ,r-data-table)))
9747 (home-page "https://github.com/mrdwab/splitstackshape")
9748 (synopsis "Stack and reshape datasets after splitting concatenated values")
9750 "Online data collection tools like Google Forms often export
9751 multiple-response questions with data concatenated in cells. The
9752 @code{concat.split} (cSplit) family of functions provided by this package
9753 splits such data into separate cells. This package also includes functions to
9754 stack groups of columns and to reshape wide data, even when the data are
9755 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
9756 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
9758 (license license:gpl3)))
9760 (define-public r-tfmpvalue
9762 (name "r-tfmpvalue")
9767 (uri (cran-uri "TFMPvalue" version))
9770 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
9771 (properties `((upstream-name . "TFMPvalue")))
9772 (build-system r-build-system)
9773 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9774 (home-page "https://github.com/ge11232002/TFMPvalue")
9775 (synopsis "P-value computation for position weight matrices")
9777 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
9778 identification from sequence/alignments, we are interested in the significance
9779 of certain match scores. TFMPvalue provides the accurate calculation of a
9780 p-value with a score threshold for position weight matrices, or the score with
9781 a given p-value. It is an interface to code originally made available by
9782 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
9783 Touzet and Varre (2007).")
9784 (license license:gpl2)))
9786 (define-public r-rnifti
9793 (uri (cran-uri "RNifti" version))
9796 "0jcgdg5k2swmi57aqj347kfi1fc4nvag7pxdfz61kc0vqqamm0wg"))))
9797 (properties `((upstream-name . "RNifti")))
9798 (build-system r-build-system)
9799 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9800 (home-page "https://github.com/jonclayden/RNifti")
9801 (synopsis "Fast R and C++ access to NIfTI images")
9803 "This package provides very fast read and write access to images stored
9804 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
9805 compiled C and interpreted R code. It also provides a C/C++ API that can be
9806 used by other packages.")
9807 (license license:gpl2)))
9809 (define-public r-shades
9816 (uri (cran-uri "shades" version))
9819 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
9820 (build-system r-build-system)
9821 (home-page "https://github.com/jonclayden/shades")
9822 (synopsis "Simple color manipulation")
9824 "This package provides functions for easily manipulating colors,
9825 creating color scales and calculating color distances.")
9826 (license license:bsd-3)))
9828 (define-public r-ore
9835 (uri (cran-uri "ore" version))
9838 "1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m"))))
9839 (build-system r-build-system)
9840 (home-page "https://github.com/jonclayden/ore")
9841 (synopsis "R interface to the Onigmo regular expression library")
9843 "This package provides an alternative to R's built-in functionality for
9844 handling regular expressions, based on the Onigmo library. It offers
9845 first-class compiled regex objects, partial matching and function-based
9846 substitutions, amongst other features.")
9847 (license license:bsd-3)))
9849 (define-public r-reportr
9856 (uri (cran-uri "reportr" version))
9859 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
9860 (build-system r-build-system)
9861 (propagated-inputs `(("r-ore" ,r-ore)))
9862 (home-page "https://github.com/jonclayden/reportr")
9863 (synopsis "General message and error reporting system")
9865 "This package provides a system for reporting messages, which offers
9866 certain useful features over the standard R system, such as the incorporation
9867 of output consolidation, message filtering, assertions, expression
9868 substitution, automatic generation of stack traces for debugging, and
9869 conditional reporting based on the current \"output level\".")
9870 (license license:gpl2)))
9872 (define-public r-tractor-base
9874 (name "r-tractor-base")
9879 (uri (cran-uri "tractor.base" version))
9882 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
9883 (properties `((upstream-name . "tractor.base")))
9884 (build-system r-build-system)
9887 ("r-reportr" ,r-reportr)
9888 ("r-rnifti" ,r-rnifti)
9889 ("r-shades" ,r-shades)))
9890 (home-page "http://www.tractor-mri.org.uk")
9891 (synopsis "Read, manipulate and visualize magnetic resonance images")
9893 "This package provides functions for working with magnetic resonance
9894 images. It supports reading and writing of popular file formats (DICOM,
9895 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
9896 visualization; flexible image manipulation; metadata and sparse image
9898 (license license:gpl2)))
9900 (define-public r-grimport
9907 (uri (cran-uri "grImport" version))
9910 "0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16"))))
9911 (properties `((upstream-name . "grImport")))
9912 (build-system r-build-system)
9914 `(("ghostscript" ,ghostscript)))
9916 `(("r-xml" ,r-xml)))
9917 (home-page "https://cran.r-project.org/web/packages/grImport")
9918 (synopsis "Convert, import, and draw PostScript pictures")
9920 "This package provides functions for converting, importing, and drawing
9921 PostScript pictures in R plots.")
9922 (license license:gpl2+)))
9924 (define-public r-grimport2
9926 (name "r-grimport2")
9931 (uri (cran-uri "grImport2" version))
9934 "0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls"))))
9935 (properties `((upstream-name . "grImport2")))
9936 (build-system r-build-system)
9938 `(("r-base64enc" ,r-base64enc)
9942 (home-page "https://cran.r-project.org/web/packages/grImport2/")
9943 (synopsis "Import SVG graphics")
9945 "This package provides functions for importing external vector images and
9946 drawing them as part of R plots. This package is different from the
9947 @code{grImport} package because, where that package imports PostScript format
9948 images, this package imports SVG format images. Furthermore, this package
9949 imports a specific subset of SVG, so external images must be preprocessed
9950 using a package like @code{rsvg} to produce SVG that this package can import.
9951 SVG features that are not supported by R graphics, such as gradient fills, can
9952 be imported and then exported via the @code{gridSVG} package.")
9953 (license license:gpl2+)))
9955 (define-public r-kohonen
9962 (uri (cran-uri "kohonen" version))
9965 "1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"))))
9966 (build-system r-build-system)
9968 `(("r-mass" ,r-mass)
9969 ("r-rcpp" ,r-rcpp)))
9970 (home-page "https://cran.r-project.org/web/packages/kohonen")
9971 (synopsis "Supervised and unsupervised self-organising maps")
9973 "This package provides functions to train @dfn{self-organising
9974 maps} (SOMs). Also interrogation of the maps and prediction using trained
9975 maps are supported. The name of the package refers to Teuvo Kohonen, the
9976 inventor of the SOM.")
9977 (license license:gpl2+)))
9979 (define-public r-nnls
9986 (uri (cran-uri "nnls" version))
9989 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
9990 (build-system r-build-system)
9991 (native-inputs `(("gfortran" ,gfortran)))
9992 (home-page "https://cran.r-project.org/web/packages/nnls")
9993 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
9995 "This package provides an R interface to the Lawson-Hanson implementation
9996 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
9997 the combination of non-negative and non-positive constraints.")
9998 (license license:gpl2+)))
10000 (define-public r-iso
10007 (uri (cran-uri "Iso" version))
10010 "014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
10011 (properties `((upstream-name . "Iso")))
10012 (build-system r-build-system)
10013 (native-inputs `(("gfortran" ,gfortran)))
10014 (home-page "http://www.stat.auckland.ac.nz/~rolf/")
10015 (synopsis "Functions to perform isotonic regression")
10017 "This package provides support for linear order and unimodal
10018 order (univariate) isotonic regression and bivariate isotonic regression with
10019 linear order on both variables.")
10020 (license license:gpl2+)))
10022 (define-public r-chemometricswithr
10024 (name "r-chemometricswithr")
10029 (uri (cran-uri "ChemometricsWithR" version))
10032 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10034 `((upstream-name . "ChemometricsWithR")))
10035 (build-system r-build-system)
10037 `(("r-devtools" ,r-devtools)
10038 ("r-kohonen" ,r-kohonen)
10041 (home-page "https://github.com/rwehrens/CWR")
10042 (synopsis "Chemometrics with R")
10044 "This package provides functions and scripts used in the book
10045 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
10046 Life Sciences\" by Ron Wehrens, Springer (2011).")
10047 (license license:gpl2+)))
10049 (define-public r-als
10056 (uri (cran-uri "ALS" version))
10059 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
10060 (properties `((upstream-name . "ALS")))
10061 (build-system r-build-system)
10064 ("r-nnls" ,r-nnls)))
10065 (home-page "https://cran.r-project.org/web/packages/ALS")
10066 (synopsis "Multivariate curve resolution alternating least squares")
10068 "Alternating least squares is often used to resolve components
10069 contributing to data with a bilinear structure; the basic technique may be
10070 extended to alternating constrained least squares. This package provides an
10071 implementation of @dfn{multivariate curve resolution alternating least
10072 squares} (MCR-ALS).
10074 Commonly applied constraints include unimodality, non-negativity, and
10075 normalization of components. Several data matrices may be decomposed
10076 simultaneously by assuming that one of the two matrices in the bilinear
10077 decomposition is shared between datasets.")
10078 (license license:gpl2+)))
10080 (define-public r-strucchange
10082 (name "r-strucchange")
10087 (uri (cran-uri "strucchange" version))
10090 "0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl"))))
10091 (build-system r-build-system)
10093 `(("r-sandwich" ,r-sandwich)
10095 (home-page "https://cran.r-project.org/web/packages/strucchange")
10096 (synopsis "Testing, monitoring, and dating structural changes")
10098 "This package provides tools for testing, monitoring and dating
10099 structural changes in (linear) regression models. It features tests/methods
10100 from the generalized fluctuation test framework as well as from the F
10101 test (Chow test) framework. This includes methods to fit, plot and test
10102 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
10103 statistics, respectively. It is possible to monitor incoming data online
10104 using fluctuation processes. Finally, the breakpoints in regression models
10105 with structural changes can be estimated together with confidence intervals.
10106 Emphasis is always given to methods for visualizing the data.")
10107 ;; Either of these two GPL versions
10108 (license (list license:gpl2 license:gpl3))))
10110 (define-public r-pixmap
10117 (uri (cran-uri "pixmap" version))
10120 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
10121 (build-system r-build-system)
10122 (home-page "https://cran.r-project.org/web/packages/pixmap")
10123 (synopsis "Tools for bitmap images")
10125 "This package provides functions for importing, exporting, plotting and
10126 other manipulations of bitmapped images.")
10127 (license license:gpl2)))
10129 (define-public r-rapidjsonr
10131 (name "r-rapidjsonr")
10136 (uri (cran-uri "rapidjsonr" version))
10139 "0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
10140 (build-system r-build-system)
10141 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
10142 (synopsis "JSON parser")
10144 "This package provides JSON parsing capability through the Rapidjson
10146 (license license:expat)))
10148 (define-public r-ontologyindex
10150 (name "r-ontologyindex")
10155 (uri (cran-uri "ontologyIndex" version))
10158 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
10159 (properties `((upstream-name . "ontologyIndex")))
10160 (build-system r-build-system)
10161 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
10162 (synopsis "Functions for processing ontologies in R")
10164 "This package provides functions for reading ontologies into R as lists
10165 and manipulating sets of ontological terms.")
10166 (license license:gpl2+)))
10168 (define-public r-gargle
10175 (uri (cran-uri "gargle" version))
10178 "0vqgp4w03sdyj0q96gxkybqflzzbaw84zifsbi7pxk5y08fimj2v"))))
10179 (build-system r-build-system)
10184 ("r-jsonlite" ,r-jsonlite)
10185 ("r-rlang" ,r-rlang)
10186 ("r-withr" ,r-withr)))
10187 (home-page "https://gargle.r-lib.org")
10188 (synopsis "Utilities for working with Google APIs")
10190 "This package provides utilities for working with Google APIs. This
10191 includes functions and classes for handling common credential types and for
10192 preparing, executing, and processing HTTP requests.")
10193 (license license:expat)))
10195 (define-public r-bigrquery
10197 (name "r-bigrquery")
10202 (uri (cran-uri "bigrquery" version))
10205 "1ggh2gngr5x0g6y7d55y6kvn94anf7qi1bkc28cjmw61hxjq38fb"))))
10206 (build-system r-build-system)
10208 `(("r-assertthat" ,r-assertthat)
10209 ("r-bit64" ,r-bit64)
10212 ("r-gargle" ,r-gargle)
10215 ("r-jsonlite" ,r-jsonlite)
10216 ("r-prettyunits" ,r-prettyunits)
10217 ("r-progress" ,r-progress)
10218 ("r-rapidjsonr" ,r-rapidjsonr)
10220 ("r-rlang" ,r-rlang)
10221 ("r-tibble" ,r-tibble)))
10222 (home-page "https://github.com/rstats-db/bigrquery")
10223 (synopsis "R interface to Google's BigQuery API")
10225 "This package provides an R interface to Google's BigQuery database.")
10226 (license license:gpl3)))
10228 (define-public r-gmp
10231 (version "0.5-13.5")
10235 (uri (cran-uri "gmp" version))
10238 "042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
10239 (build-system r-build-system)
10242 (modify-phases %standard-phases
10243 (add-after 'unpack 'set-CC
10244 (lambda _ (setenv "CC" "gcc") #t)))))
10245 (inputs `(("gmp" ,gmp)))
10246 (home-page "https://cran.r-project.org/web/packages/gmp")
10247 (synopsis "Multiple precision arithmetic")
10249 "This package supports multiple precision arithmetic (big integers and
10250 rationals, prime number tests, matrix computation), \"arithmetic without
10251 limitations\" using the GNU Multiple Precision library.")
10252 ;; Any version of the GPL.
10253 (license license:gpl3+)))
10255 (define-public r-rmpfr
10262 (uri (cran-uri "Rmpfr" version))
10265 "1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
10266 (properties `((upstream-name . "Rmpfr")))
10267 (build-system r-build-system)
10271 `(("r-gmp" ,r-gmp)))
10272 (home-page "http://rmpfr.r-forge.r-project.org/")
10273 (synopsis "R bindings to the MPFR library")
10275 "This package supports arithmetic (via S4 classes and methods) for
10276 arbitrary precision floating point numbers, including transcendental
10277 functions. To this end, the package interfaces with the @dfn{Multiple
10278 Precision Floating-Point Reliable} (MPFR) library.")
10279 (license license:gpl2+)))
10281 (define-public r-assertive-base
10283 (name "r-assertive-base")
10288 (uri (cran-uri "assertive.base" version))
10291 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
10293 `((upstream-name . "assertive.base")))
10294 (build-system r-build-system)
10295 (home-page "https://bitbucket.org/richierocks/assertive.base")
10296 (synopsis "Core of the assertive package")
10298 "This package provides a minimal set of predicates and assertions used by
10299 the assertive package. This is mainly for use by other package developers who
10300 want to include run-time testing features in their own packages.")
10301 (license license:gpl3+)))
10303 (define-public r-assertive-properties
10305 (name "r-assertive-properties")
10310 (uri (cran-uri "assertive.properties" version))
10313 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
10315 `((upstream-name . "assertive.properties")))
10316 (build-system r-build-system)
10318 `(("r-assertive-base" ,r-assertive-base)))
10319 (home-page "https://bitbucket.org/richierocks/assertive.properties")
10320 (synopsis "Assertions to check properties of variables")
10322 "This package provides a set of predicates and assertions for checking
10323 the properties of variables, such as length, names and attributes. This is
10324 mainly for use by other package developers who want to include run-time
10325 testing features in their own packages.")
10326 (license license:gpl3+)))
10328 (define-public r-assertive-numbers
10330 (name "r-assertive-numbers")
10335 (uri (cran-uri "assertive.numbers" version))
10338 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
10340 `((upstream-name . "assertive.numbers")))
10341 (build-system r-build-system)
10343 `(("r-assertive-base" ,r-assertive-base)))
10344 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
10345 (synopsis "Assertions to check properties of numbers")
10347 "This package provides a set of predicates and assertions for checking
10348 the properties of numbers. This is mainly for use by other package developers
10349 who want to include run-time testing features in their own packages.")
10350 (license license:gpl3+)))
10352 (define-public r-assertive-sets
10354 (name "r-assertive-sets")
10359 (uri (cran-uri "assertive.sets" version))
10362 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
10364 `((upstream-name . "assertive.sets")))
10365 (build-system r-build-system)
10367 `(("r-assertive-base" ,r-assertive-base)))
10368 (home-page "https://bitbucket.org/richierocks/assertive.sets")
10369 (synopsis "Assertions to check properties of sets")
10371 "This package provides a set of predicates and assertions for checking
10372 the properties of sets. This is mainly for use by other package developers
10373 who want to include run-time testing features in their own packages.")
10374 (license license:gpl3+)))
10376 (define-public r-assertive-matrices
10378 (name "r-assertive-matrices")
10383 (uri (cran-uri "assertive.matrices" version))
10386 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
10388 `((upstream-name . "assertive.matrices")))
10389 (build-system r-build-system)
10391 `(("r-assertive-base" ,r-assertive-base)))
10392 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
10393 (synopsis "Assertions to check properties of matrices")
10395 "This package provides a set of predicates and assertions for checking
10396 the properties of matrices. This is mainly for use by other package
10397 developers who want to include run-time testing features in their own
10399 (license license:gpl3+)))
10401 (define-public r-assertive-models
10403 (name "r-assertive-models")
10408 (uri (cran-uri "assertive.models" version))
10411 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
10413 `((upstream-name . "assertive.models")))
10414 (build-system r-build-system)
10416 `(("r-assertive-base" ,r-assertive-base)))
10417 (home-page "https://bitbucket.org/richierocks/assertive.models")
10418 (synopsis "Assertions to check properties of models")
10420 "This package provides a set of predicates and assertions for checking
10421 the properties of models. This is mainly for use by other package developers
10422 who want to include run-time testing features in their own packages.")
10423 (license license:gpl3+)))
10425 (define-public r-assertive-reflection
10427 (name "r-assertive-reflection")
10432 (uri (cran-uri "assertive.reflection" version))
10435 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
10437 `((upstream-name . "assertive.reflection")))
10438 (build-system r-build-system)
10440 `(("r-assertive-base" ,r-assertive-base)))
10441 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
10442 (synopsis "Assertions for checking the state of R")
10444 "This package provides a set of predicates and assertions for checking
10445 the state and capabilities of R, the operating system it is running on, and
10446 the IDE being used. This is mainly for use by other package developers who
10447 want to include run-time testing features in their own packages.")
10448 (license license:gpl3+)))
10450 (define-public r-assertive-types
10452 (name "r-assertive-types")
10457 (uri (cran-uri "assertive.types" version))
10460 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
10462 `((upstream-name . "assertive.types")))
10463 (build-system r-build-system)
10465 `(("r-assertive-base" ,r-assertive-base)
10466 ("r-assertive-properties" ,r-assertive-properties)
10467 ("r-codetools" ,r-codetools)))
10468 (home-page "https://bitbucket.org/richierocks/assertive.types")
10469 (synopsis "Assertions to check types of variables")
10471 "This package provides a set of predicates and assertions for checking
10472 the types of variables. This is mainly for use by other package developers
10473 who want to include run-time testing features in their own packages.")
10474 (license license:gpl3+)))
10476 (define-public r-assertive-files
10478 (name "r-assertive-files")
10483 (uri (cran-uri "assertive.files" version))
10486 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
10488 `((upstream-name . "assertive.files")))
10489 (build-system r-build-system)
10491 `(("r-assertive-base" ,r-assertive-base)
10492 ("r-assertive-numbers" ,r-assertive-numbers)))
10493 (home-page "https://bitbucket.org/richierocks/assertive.files")
10494 (synopsis "Assertions to check properties of files")
10496 "This package provides a set of predicates and assertions for checking
10497 the properties of files and connections. This is mainly for use by other
10498 package developers who want to include run-time testing features in their own
10500 (license license:gpl3+)))
10502 (define-public r-assertive-code
10504 (name "r-assertive-code")
10509 (uri (cran-uri "assertive.code" version))
10512 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
10514 `((upstream-name . "assertive.code")))
10515 (build-system r-build-system)
10517 `(("r-assertive-base" ,r-assertive-base)
10518 ("r-assertive-properties" ,r-assertive-properties)
10519 ("r-assertive-types" ,r-assertive-types)))
10520 (home-page "https://bitbucket.org/richierocks/assertive.code")
10521 (synopsis "Assertions to check properties of code")
10523 "This package provides a set of predicates and assertions for checking
10524 the properties of code. This is mainly for use by other package developers
10525 who want to include run-time testing features in their own packages.")
10526 (license license:gpl3+)))
10528 (define-public r-assertive-datetimes
10530 (name "r-assertive-datetimes")
10535 (uri (cran-uri "assertive.datetimes" version))
10538 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
10540 `((upstream-name . "assertive.datetimes")))
10541 (build-system r-build-system)
10543 `(("r-assertive-base" ,r-assertive-base)
10544 ("r-assertive-types" ,r-assertive-types)))
10545 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
10546 (synopsis "Assertions to check properties of dates and times")
10548 "This package provides a set of predicates and assertions for checking
10549 the properties of dates and times. This is mainly for use by other package
10550 developers who want to include run-time testing features in their own
10552 (license license:gpl3+)))
10554 (define-public r-assertive-strings
10556 (name "r-assertive-strings")
10561 (uri (cran-uri "assertive.strings" version))
10564 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
10566 `((upstream-name . "assertive.strings")))
10567 (build-system r-build-system)
10569 `(("r-assertive-base" ,r-assertive-base)
10570 ("r-assertive-types" ,r-assertive-types)
10571 ("r-stringi" ,r-stringi)))
10572 (home-page "https://bitbucket.org/richierocks/assertive.strings")
10573 (synopsis "Assertions to check properties of strings")
10575 "This package provides a set of predicates and assertions for checking
10576 the properties of strings. This is mainly for use by other package developers
10577 who want to include run-time testing features in their own packages.")
10578 (license license:gpl3+)))
10580 (define-public r-assertive-data-us
10582 (name "r-assertive-data-us")
10587 (uri (cran-uri "assertive.data.us" version))
10590 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
10592 `((upstream-name . "assertive.data.us")))
10593 (build-system r-build-system)
10595 `(("r-assertive-base" ,r-assertive-base)
10596 ("r-assertive-strings" ,r-assertive-strings)))
10597 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
10598 (synopsis "Assertions to check properties of strings")
10600 "This package provides a set of predicates and assertions for checking
10601 the properties of US-specific complex data types. This is mainly for use by
10602 other package developers who want to include run-time testing features in
10603 their own packages.")
10604 (license license:gpl3+)))
10606 (define-public r-assertive-data-uk
10608 (name "r-assertive-data-uk")
10613 (uri (cran-uri "assertive.data.uk" version))
10616 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
10618 `((upstream-name . "assertive.data.uk")))
10619 (build-system r-build-system)
10621 `(("r-assertive-base" ,r-assertive-base)
10622 ("r-assertive-strings" ,r-assertive-strings)))
10623 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
10624 (synopsis "Assertions to check properties of strings")
10626 "This package provides a set of predicates and assertions for checking
10627 the properties of UK-specific complex data types. This is mainly for use by
10628 other package developers who want to include run-time testing features in
10629 their own packages.")
10630 (license license:gpl3+)))
10632 (define-public r-assertive-data
10634 (name "r-assertive-data")
10639 (uri (cran-uri "assertive.data" version))
10642 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
10644 `((upstream-name . "assertive.data")))
10645 (build-system r-build-system)
10647 `(("r-assertive-base" ,r-assertive-base)
10648 ("r-assertive-strings" ,r-assertive-strings)))
10649 (home-page "https://bitbucket.org/richierocks/assertive.data")
10650 (synopsis "Assertions to check properties of data")
10652 "This package provides a set of predicates and assertions for checking
10653 the properties of (country independent) complex data types. This is mainly
10654 for use by other package developers who want to include run-time testing
10655 features in their own packages.")
10656 (license license:gpl3+)))
10658 (define-public r-assertive
10660 (name "r-assertive")
10665 (uri (cran-uri "assertive" version))
10668 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
10669 (build-system r-build-system)
10671 `(("r-assertive-base" ,r-assertive-base)
10672 ("r-assertive-code" ,r-assertive-code)
10673 ("r-assertive-data" ,r-assertive-data)
10674 ("r-assertive-data-uk" ,r-assertive-data-uk)
10675 ("r-assertive-data-us" ,r-assertive-data-us)
10676 ("r-assertive-datetimes" ,r-assertive-datetimes)
10677 ("r-assertive-files" ,r-assertive-files)
10678 ("r-assertive-matrices" ,r-assertive-matrices)
10679 ("r-assertive-models" ,r-assertive-models)
10680 ("r-assertive-numbers" ,r-assertive-numbers)
10681 ("r-assertive-properties" ,r-assertive-properties)
10682 ("r-assertive-reflection" ,r-assertive-reflection)
10683 ("r-assertive-sets" ,r-assertive-sets)
10684 ("r-assertive-strings" ,r-assertive-strings)
10685 ("r-assertive-types" ,r-assertive-types)
10686 ("r-knitr" ,r-knitr)))
10687 (home-page "https://bitbucket.org/richierocks/assertive")
10688 (synopsis "Readable check functions to ensure code integrity")
10690 "This package provides lots of predicates (@code{is_*} functions) to
10691 check the state of your variables, and assertions (@code{assert_*} functions)
10692 to throw errors if they aren't in the right form.")
10693 (license license:gpl3+)))
10695 (define-public r-dotcall64
10697 (name "r-dotcall64")
10702 (uri (cran-uri "dotCall64" version))
10705 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
10706 (properties `((upstream-name . "dotCall64")))
10707 (build-system r-build-system)
10708 (native-inputs `(("gfortran" ,gfortran)))
10709 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
10710 (synopsis "Enhanced foreign function interface supporting long vectors")
10712 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
10713 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
10714 supports long vectors, arguments of type 64-bit integer, and provides a
10715 mechanism to avoid unnecessary copies of read-only and write-only arguments.
10716 This makes it a convenient and fast interface to C/C++ and Fortran code.")
10717 (license license:gpl2+)))
10719 (define-public r-spam
10726 (uri (cran-uri "spam" version))
10729 "024dgfnjfxvsiymbzrhadinamj6qy509f4sbd1zxql8ymkyxn7vi"))))
10730 (build-system r-build-system)
10732 `(("r-dotcall64" ,r-dotcall64)))
10733 (native-inputs `(("gfortran" ,gfortran)))
10734 (home-page "https://www.math.uzh.ch/pages/spam/")
10735 (synopsis "Sparse matrix algebra")
10737 "This package provides a set of functions for sparse matrix algebra.
10738 Differences with other sparse matrix packages are:
10741 @item it only supports (essentially) one sparse matrix format;
10742 @item it is based on transparent and simple structure(s);
10743 @item it is tailored for MCMC calculations within G(M)RF;
10744 @item and it is fast and scalable (with the extension package @code{spam64}).
10746 ;; Either of these licenses
10747 (license (list license:bsd-3 license:lgpl2.0))))
10749 (define-public r-fields
10756 (uri (cran-uri "fields" version))
10759 "1q9x68dczjym56v7x90x4x5br59vj3dww6w8v42zd3yl17h7c1h1"))))
10760 (build-system r-build-system)
10762 `(("r-maps" ,r-maps)
10763 ("r-spam" ,r-spam)))
10765 `(("gfortran" ,gfortran)))
10766 (home-page "http://www.image.ucar.edu/fields")
10767 (synopsis "Tools for spatial data")
10769 "This is a package for curve, surface and function fitting with an
10770 emphasis on splines, spatial data and spatial statistics. The major methods
10771 include cubic, and thin plate splines, Kriging, and compactly supported
10772 covariance functions for large data sets.")
10773 (license license:gpl2+)))
10775 (define-public r-spatialextremes
10777 (name "r-spatialextremes")
10778 (version "2.0-7.2")
10782 (uri (cran-uri "SpatialExtremes" version))
10785 "0aqq9ryxi4xsdqjhc1lhb7ai8szs7m2vys6nn0ygps1w3pm4xwj8"))))
10787 `((upstream-name . "SpatialExtremes")))
10788 (build-system r-build-system)
10790 `(("r-fields" ,r-fields)
10791 ("r-maps" ,r-maps)))
10792 (home-page "http://spatialextremes.r-forge.r-project.org/")
10793 (synopsis "Modelling spatial extremes")
10795 "This package provides tools for the statistical modelling of spatial
10796 extremes using max-stable processes, copula or Bayesian hierarchical models.
10797 More precisely, this package allows (conditional) simulations from various
10798 parametric max-stable models, analysis of the extremal spatial dependence, the
10799 fitting of such processes using composite likelihoods or least square (simple
10800 max-stable processes only), model checking and selection and prediction.")
10801 (license license:gpl2+)))
10803 (define-public r-drc
10810 (uri (cran-uri "drc" version))
10813 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
10814 (build-system r-build-system)
10817 ("r-gtools" ,r-gtools)
10819 ("r-multcomp" ,r-multcomp)
10820 ("r-plotrix" ,r-plotrix)
10821 ("r-scales" ,r-scales)))
10822 (home-page "https://cran.r-project.org/web/packages/drc")
10823 (synopsis "Analysis of dose-response curves")
10825 "This package provides a suite of flexible and versatile model fitting
10826 and after-fitting functions for the analysis of dose-response data.")
10827 (license license:gpl2+)))
10829 (define-public r-rmeta
10836 (uri (cran-uri "rmeta" version))
10839 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
10840 (build-system r-build-system)
10841 (home-page "https://cran.r-project.org/web/packages/rmeta")
10842 (synopsis "Tools for meta-analysis")
10844 "This package provides functions for simple fixed and random effects
10845 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
10846 draws standard summary plots, funnel plots, and computes summaries and tests
10847 for association and heterogeneity.")
10848 (license license:gpl2)))
10850 (define-public r-bootstrap
10852 (name "r-bootstrap")
10857 (uri (cran-uri "bootstrap" version))
10860 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
10861 (build-system r-build-system)
10862 (native-inputs `(("gfortran" ,gfortran)))
10863 (home-page "https://cran.r-project.org/web/packages/bootstrap")
10864 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
10866 "This package provides software and data for the book \"An Introduction
10867 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
10868 This package is primarily provided for projects already based on it, and for
10869 support of the book. New projects should preferentially use the recommended
10870 package \"boot\".")
10871 (license license:bsd-3)))
10873 (define-public r-survivalroc
10875 (name "r-survivalroc")
10880 (uri (cran-uri "survivalROC" version))
10883 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
10884 (properties `((upstream-name . "survivalROC")))
10885 (build-system r-build-system)
10886 (home-page "https://cran.r-project.org/web/packages/survivalROC")
10887 (synopsis "Time-dependent ROC curve estimation from censored survival data")
10889 "Compute time-dependent ROC curve from censored survival data using
10890 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
10891 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
10892 (license license:gpl2+)))
10894 (define-public r-longitudinal
10896 (name "r-longitudinal")
10901 (uri (cran-uri "longitudinal" version))
10904 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
10905 (build-system r-build-system)
10906 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
10907 (home-page "http://strimmerlab.org/software/longitudinal/")
10908 (synopsis "Analysis of multiple time course data")
10910 "This package contains general data structures and functions for
10911 longitudinal data with multiple variables, repeated measurements, and
10912 irregularly spaced time points. It also implements a shrinkage estimator of
10913 dynamical correlation and dynamical covariance.")
10914 (license license:gpl3+)))
10916 (define-public r-genenet
10923 (uri (cran-uri "GeneNet" version))
10926 "0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
10927 (properties `((upstream-name . "GeneNet")))
10928 (build-system r-build-system)
10930 `(("r-corpcor" ,r-corpcor)
10931 ("r-fdrtool" ,r-fdrtool)
10932 ("r-longitudinal" ,r-longitudinal)))
10933 (home-page "http://strimmerlab.org/software/genenet/")
10934 (synopsis "Modeling and inferring gene networks")
10936 "This package analyzes gene expression (time series) data with focus on
10937 the inference of gene networks. In particular, GeneNet implements the methods
10938 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
10939 for learning large-scale gene association networks (including assignment of
10940 putative directions).")
10941 (license license:gpl3+)))
10943 (define-public r-rbamtools
10945 (name "r-rbamtools")
10946 (version "2.16.11.2")
10950 (uri (cran-uri "rbamtools" version))
10953 "0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj"))))
10954 (build-system r-build-system)
10955 (inputs `(("zlib" ,zlib)))
10957 `(("r-refgenome" ,r-refgenome)))
10958 (home-page "https://cran.r-project.org/web/packages/rbamtools")
10959 (synopsis "Read and write BAM (binary alignment) files")
10961 "This package provides an R interface to functions of the SAMtools
10963 (license license:artistic2.0)))
10965 (define-public r-protviz
10972 (uri (cran-uri "protViz" version))
10975 "150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1"))))
10976 (properties `((upstream-name . "protViz")))
10977 (build-system r-build-system)
10980 ("python-2" ,python-2)))
10981 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10982 (home-page "https://github.com/protViz/protViz/")
10983 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
10985 "This package helps with quality checks, visualizations and analysis of
10986 mass spectrometry data, coming from proteomics experiments. The package is
10987 developed, tested and used at the Functional Genomics Center Zurich, where it
10988 is used mainly for prototyping, teaching, and having fun with proteomics data.
10989 But it can also be used to do data analysis for small scale data sets.")
10990 (license license:gpl3)))
10992 (define-public r-cmprsk
10999 (uri (cran-uri "cmprsk" version))
11002 "1nacbzx950ygaqgnj0949skhwpzar5i3xlscd44jsimk2gsppx6z"))))
11003 (build-system r-build-system)
11005 `(("r-survival" ,r-survival)))
11007 `(("gfortran" ,gfortran)))
11008 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11009 (synopsis "Subdistribution analysis of competing risks")
11011 "This package provides tool for estimation, testing and regression
11012 modeling of subdistribution functions in competing risks, as described in
11013 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11014 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11015 A proportional hazards model for the subdistribution of a competing risk,
11016 JASA, 94:496-509.")
11017 (license license:gpl2+)))
11019 (define-public r-etm
11026 (uri (cran-uri "etm" version))
11029 "1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
11030 (build-system r-build-system)
11032 `(("r-data-table" ,r-data-table)
11033 ("r-lattice" ,r-lattice)
11035 ("r-rcpparmadillo" ,r-rcpparmadillo)
11036 ("r-survival" ,r-survival)))
11037 (home-page "https://cran.r-project.org/web/packages/etm")
11038 (synopsis "Empirical transition matrix")
11040 "The @dfn{empirical transition matrix} (etm) package permits to estimate
11041 the matrix of transition probabilities for any time-inhomogeneous multistate
11042 model with finite state space using the Aalen-Johansen estimator.")
11043 (license license:expat)))
11045 (define-public r-epi
11052 (uri (cran-uri "Epi" version))
11055 "0ald9fjynrlyah8nzwfs49a08j4myd3c5bm56zn61gg5pyyhi8hd"))))
11056 (properties `((upstream-name . "Epi")))
11057 (build-system r-build-system)
11059 `(("r-cmprsk" ,r-cmprsk)
11060 ("r-data-table" ,r-data-table)
11063 ("r-matrix" ,r-matrix)
11065 ("r-numderiv" ,r-numderiv)
11067 ("r-survival" ,r-survival)
11069 (home-page "http://BendixCarstensen.com/Epi/")
11070 (synopsis "Statistical analysis in epidemiology")
11072 "This package provides functions for demographic and epidemiological
11073 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
11074 particular representation, manipulation and simulation of multistate data -
11075 the Lexis suite of functions, which includes interfaces to the @code{mstate},
11076 @code{etm} and @code{cmprsk} packages. It also contains functions for
11077 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
11078 data and some useful functions for tabulation and plotting, as well as a
11079 number of epidemiological data sets.")
11080 (license license:gpl2)))
11082 (define-public r-ppls
11085 (version "1.6-1.1")
11089 (uri (cran-uri "ppls" version))
11092 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
11093 (build-system r-build-system)
11094 (propagated-inputs `(("r-mass" ,r-mass)))
11095 (home-page "https://cran.r-project.org/web/packages/ppls")
11096 (synopsis "Penalized partial least squares")
11098 "This package contains linear and nonlinear regression methods based on
11099 partial least squares and penalization techniques. Model parameters are
11100 selected via cross-validation, and confidence intervals ans tests for the
11101 regression coefficients can be conducted via jackknifing.")
11102 (license license:gpl2+)))
11104 (define-public r-huge
11111 (uri (cran-uri "huge" version))
11114 "1j93gvi1jyq3ld9jhdqhrpm2is54rk3ilmf3yw7fx6gva0y6hjqd"))))
11115 (build-system r-build-system)
11117 `(("r-igraph" ,r-igraph)
11119 ("r-matrix" ,r-matrix)
11121 ("r-rcppeigen" ,r-rcppeigen)))
11122 (home-page "https://cran.r-project.org/web/packages/huge")
11123 (synopsis "High-dimensional undirected graph estimation")
11125 "This package provides a general framework for high-dimensional
11126 undirected graph estimation. It integrates data preprocessing, neighborhood
11127 screening, graph estimation, and model selection techniques into a pipeline.")
11128 (license license:gpl2)))
11130 (define-public r-parcor
11137 (uri (cran-uri "parcor" version))
11140 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
11141 (build-system r-build-system)
11144 ("r-genenet" ,r-genenet)
11145 ("r-glmnet" ,r-glmnet)
11147 ("r-ppls" ,r-ppls)))
11148 (home-page "https://cran.r-project.org/web/packages/parcor")
11149 (synopsis "Regularized estimation of partial correlation matrices")
11151 "This package estimates the matrix of partial correlations based on
11152 different regularized regression methods: lasso, adaptive lasso, PLS, and
11153 Ridge Regression. In addition, the package provides model selection for
11154 lasso, adaptive lasso and Ridge regression based on cross-validation.")
11155 (license license:gpl2+)))
11157 (define-public r-mcmc
11164 (uri (cran-uri "mcmc" version))
11167 "1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
11168 (build-system r-build-system)
11169 (home-page "http://www.stat.umn.edu/geyer/mcmc/")
11170 (synopsis "Markov chain Monte Carlo")
11172 "This package simulates continuous distributions of random vectors using
11173 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
11174 function that evaluates the log unnormalized density. Algorithms are random
11175 walk Metropolis algorithm (function @code{metrop}), simulated
11176 tempering (function @code{temper}), and morphometric random walk
11177 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
11178 by change of variable.")
11179 (license license:expat)))
11181 (define-public r-listenv
11188 (uri (cran-uri "listenv" version))
11191 "0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1"))))
11192 (build-system r-build-system)
11194 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11195 (home-page "https://github.com/HenrikBengtsson/listenv")
11196 (synopsis "Environments behaving (almost) as lists")
11198 "This package implements list environments. List environments are
11199 environments that have list-like properties. For instance, the elements of a
11200 list environment are ordered and can be accessed and iterated over using index
11202 (license license:lgpl2.1+)))
11204 (define-public r-globals
11211 (uri (cran-uri "globals" version))
11214 "0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br"))))
11215 (build-system r-build-system)
11217 `(("r-codetools" ,r-codetools)))
11218 (home-page "https://github.com/HenrikBengtsson/globals")
11219 (synopsis "Identify global objects in R expressions")
11221 "This package provides tools to identify global (\"unknown\" or \"free\")
11222 objects in R expressions by code inspection using various strategies, e.g.
11223 conservative or liberal. The objective of this package is to make it as
11224 simple as possible to identify global objects for the purpose of exporting
11225 them in distributed compute environments.")
11226 (license license:lgpl2.1+)))
11228 (define-public r-future
11235 (uri (cran-uri "future" version))
11238 "1jyv2wlmpfqbk3hw269h4xg36na3wh1kd1lxmwdb40bsv4850lqa"))))
11239 (build-system r-build-system)
11241 `(("r-digest" ,r-digest)
11242 ("r-globals" ,r-globals)
11243 ("r-listenv" ,r-listenv)))
11245 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11246 (home-page "https://github.com/HenrikBengtsson/future")
11247 (synopsis "Unified parallel and distributed processing in R")
11249 "The purpose of this package is to provide a lightweight and unified
11250 Future API for sequential and parallel processing of R expression via futures.
11251 This package implements sequential, multicore, multisession, and cluster
11252 futures. With these, R expressions can be evaluated on the local machine, in
11253 parallel a set of local machines, or distributed on a mix of local and remote
11254 machines. Extensions to this package implement additional backends for
11255 processing futures via compute cluster schedulers etc. Because of its unified
11256 API, there is no need to modify any code in order to switch from sequential on
11257 the local machine to, say, distributed processing on a remote compute cluster.")
11258 (license license:lgpl2.1+)))
11260 (define-public r-future-apply
11262 (name "r-future-apply")
11267 (uri (cran-uri "future.apply" version))
11270 "0wd3bh114zkvrqlpn8gqz4ix1igr9hr8x72h2g00a7mqkfjfqx33"))))
11271 (properties `((upstream-name . "future.apply")))
11272 (build-system r-build-system)
11274 `(("r-future" ,r-future)
11275 ("r-globals" ,r-globals)))
11277 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
11278 (home-page "https://github.com/HenrikBengtsson/future.apply")
11279 (synopsis "Apply function to elements in parallel using futures")
11281 "This package provides implementations of @code{apply()},
11282 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
11283 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
11284 can be resolved using any future-supported backend, e.g. parallel on the local
11285 machine or distributed on a compute cluster.")
11286 (license license:gpl2+)))
11288 (define-public r-rsvd
11295 (uri (cran-uri "rsvd" version))
11298 "0fia77y5fxnhwkcxlgp98ygb8fdfraky75x80hkf7kvvpwc5rzn8"))))
11299 (build-system r-build-system)
11301 `(("r-matrix" ,r-matrix)))
11302 (home-page "https://github.com/erichson/rSVD")
11303 (synopsis "Randomized singular value decomposition")
11305 "Low-rank matrix decompositions are fundamental tools and widely used for
11306 data analysis, dimension reduction, and data compression. Classically, highly
11307 accurate deterministic matrix algorithms are used for this task. However, the
11308 emergence of large-scale data has severely challenged our computational
11309 ability to analyze big data. The concept of randomness has been demonstrated
11310 as an effective strategy to quickly produce approximate answers to familiar
11311 problems such as the @dfn{singular value decomposition} (SVD). This package
11312 provides several randomized matrix algorithms such as the randomized singular
11313 value decomposition (@code{rsvd}), randomized principal component
11314 analysis (@code{rpca}), randomized robust principal component
11315 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
11316 and the randomized CUR decomposition (@code{rcur}). In addition several plot
11317 functions are provided.")
11318 (license license:gpl3+)))
11320 (define-public r-sloop
11327 (uri (cran-uri "sloop" version))
11330 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
11331 (build-system r-build-system)
11333 `(("r-codetools" ,r-codetools)
11334 ("r-crayon" ,r-crayon)
11335 ("r-purrr" ,r-purrr)
11336 ("r-rlang" ,r-rlang)
11337 ("r-tibble" ,r-tibble)))
11338 (home-page "https://github.com/r-lib/sloop")
11339 (synopsis "Helpers for object-oriented programming in R")
11341 "This package provides a collection of helper functions designed to
11342 help you to better understand object oriented programming in R, particularly
11344 (license license:gpl3)))
11346 (define-public r-capushe
11353 (uri (cran-uri "capushe" version))
11356 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
11357 (build-system r-build-system)
11358 (propagated-inputs `(("r-mass" ,r-mass)))
11359 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
11360 (synopsis "Calibrating penalties using slope heuristics")
11362 "This package provides tools for the calibration of penalized criteria
11363 for model selection. The calibration methods available are based on the slope
11365 (license license:gpl2+)))
11367 (define-public r-dorng
11374 (uri (cran-uri "doRNG" version))
11377 "1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
11378 (properties `((upstream-name . "doRNG")))
11379 (build-system r-build-system)
11381 `(("r-foreach" ,r-foreach)
11382 ("r-iterators" ,r-iterators)
11383 ("r-pkgmaker" ,r-pkgmaker)
11384 ("r-rngtools" ,r-rngtools)))
11385 (home-page "https://renozao.github.io/doRNG/")
11386 (synopsis "Generic reproducible parallel backend for foreach loops")
11388 "This package provides functions to perform reproducible parallel
11389 @code{foreach} loops, using independent random streams as generated by
11390 L'Ecuyer's combined multiple-recursive generator. It enables to easily
11391 convert standard @code{%dopar%} loops into fully reproducible loops,
11392 independently of the number of workers, the task scheduling strategy, or the
11393 chosen parallel environment and associated foreach backend.")
11394 (license license:gpl2+)))
11396 (define-public r-blockmodeling
11398 (name "r-blockmodeling")
11403 (uri (cran-uri "blockmodeling" version))
11406 "11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
11407 (build-system r-build-system)
11409 `(("r-doparallel" ,r-doparallel)
11410 ("r-dorng" ,r-dorng)
11411 ("r-foreach" ,r-foreach)
11412 ("r-matrix" ,r-matrix)))
11413 (native-inputs `(("gfortran" ,gfortran)))
11414 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
11415 (synopsis "Generalized and classical blockmodeling of valued networks")
11417 "This package is primarily meant as an implementation of generalized
11418 blockmodeling for valued networks. In addition, measures of similarity or
11419 dissimilarity based on structural equivalence and regular equivalence (REGE
11420 algorithms) can be computed and partitioned matrices can be plotted.")
11421 (license license:gpl2+)))
11423 (define-public r-upsetr
11430 (uri (cran-uri "UpSetR" version))
11433 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
11434 (properties `((upstream-name . "UpSetR")))
11435 (build-system r-build-system)
11437 `(("r-ggplot2" ,r-ggplot2)
11438 ("r-gridextra" ,r-gridextra)
11440 ("r-scales" ,r-scales)))
11441 (home-page "https://github.com/hms-dbmi/UpSetR")
11442 (synopsis "Visualize intersecting sets")
11444 "This package provides a more scalable alternative to Venn and Euler
11445 diagrams for visualizing intersecting sets. Create visualizations of
11446 intersecting sets using a novel matrix design, along with visualizations of
11447 several common set, element and attribute related tasks.")
11448 (license license:expat)))
11450 ;; This package includes a JavaScript file, which is not minified. When
11451 ;; upgrading please check that there are no new minified JavaScript files.
11452 (define-public r-shinybs
11459 (uri (cran-uri "shinyBS" version))
11462 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
11463 (properties `((upstream-name . "shinyBS")))
11464 (build-system r-build-system)
11465 ;; The tests spawn Shiny browser apps. They cannot be run
11466 ;; non-interactively.
11467 (arguments '(#:tests? #f))
11469 `(("r-htmltools" ,r-htmltools)
11470 ("r-shiny" ,r-shiny)))
11471 (home-page "https://ebailey78.github.io/shinyBS/")
11472 (synopsis "Twitter Bootstrap components for Shiny")
11474 "This package adds additional Twitter Bootstrap components to Shiny.")
11475 (license license:gpl3)))
11477 (define-public r-outliers
11479 (name "r-outliers")
11484 (uri (cran-uri "outliers" version))
11487 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
11488 (build-system r-build-system)
11489 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
11490 (synopsis "Tests for outliers")
11492 "This package provides a collection of some tests commonly used for
11493 identifying outliers.")
11494 (license license:gpl2+)))
11496 (define-public r-bayesm
11503 (uri (cran-uri "bayesm" version))
11506 "041ach2f2vrqzd5kz17v7wmkjz6z8cjjihpk4qvczm4cr9z85r2i"))))
11507 (build-system r-build-system)
11509 `(("r-rcpp" ,r-rcpp)
11510 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11511 (home-page "http://www.perossi.org/home/bsm-1")
11512 (synopsis "Bayesian inference for marketing/micro-econometrics")
11514 "This package covers many important models used in marketing and
11515 micro-econometrics applications, including Bayes Regression (univariate or
11516 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
11517 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
11518 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
11519 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
11520 Estimation with normal base, Hierarchical Linear Models with normal prior and
11521 covariates, Hierarchical Linear Models with a mixture of normals prior and
11522 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
11523 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
11524 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
11525 analysis of choice-based conjoint data, Bayesian treatment of linear
11526 instrumental variables models, Analysis of Multivariate Ordinal survey data
11527 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
11528 Coefficient Logit Models.")
11529 (license license:gpl2+)))
11531 (define-public r-tensora
11538 (uri (cran-uri "tensorA" version))
11541 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
11542 (properties `((upstream-name . "tensorA")))
11543 (build-system r-build-system)
11544 (home-page "http://www.stat.boogaart.de/tensorA")
11545 (synopsis "Advanced tensor arithmetic with named indices")
11547 "This package provides convenience functions for advanced linear algebra
11548 with tensors and computation with datasets of tensors on a higher level
11549 abstraction. It includes Einstein and Riemann summing conventions, dragging,
11550 co- and contravariate indices, and parallel computations on sequences of
11552 (license license:gpl2+)))
11554 (define-public r-rarpack
11561 (uri (cran-uri "rARPACK" version))
11564 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
11565 (properties `((upstream-name . "rARPACK")))
11566 (build-system r-build-system)
11567 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
11568 (home-page "https://github.com/yixuan/rARPACK")
11569 (synopsis "Solvers for large scale eigenvalue and SVD problems")
11571 "This package was previously an R wrapper of the ARPACK library, and now
11572 a shell of the R package RSpectra, an R interface to the Spectra library for
11573 solving large scale eigenvalue/vector problems. The current version of
11574 rARPACK simply imports and exports the functions provided by RSpectra. New
11575 users of rARPACK are advised to switch to the RSpectra package.")
11576 (license license:bsd-3)))
11578 (define-public r-compositions
11580 (name "r-compositions")
11585 (uri (cran-uri "compositions" version))
11588 "12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i"))))
11589 (build-system r-build-system)
11591 `(("r-bayesm" ,r-bayesm)
11592 ("r-energy" ,r-energy)
11593 ("r-robustbase" ,r-robustbase)
11594 ("r-tensora" ,r-tensora)))
11595 (home-page "http://www.stat.boogaart.de/compositions")
11596 (synopsis "Compositional data analysis")
11598 "This package provides functions for the consistent analysis of
11599 compositional data (e.g. portions of substances) and positive
11600 numbers (e.g. concentrations).")
11601 (license license:gpl2+)))
11603 (define-public r-cobs
11610 (uri (cran-uri "cobs" version))
11613 "1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
11614 (build-system r-build-system)
11616 `(("r-quantreg" ,r-quantreg)
11617 ("r-sparsem" ,r-sparsem)))
11618 (home-page "https://cran.r-project.org/web/packages/cobs")
11619 (synopsis "Constrained B-Splines (sparse matrix based)")
11621 "This package provides qualitatively constrained (regression) smoothing
11622 splines via linear programming and sparse matrices.")
11623 (license license:gpl2+)))
11625 (define-public r-drimpute
11627 (name "r-drimpute")
11632 (uri (cran-uri "DrImpute" version))
11635 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
11636 (properties `((upstream-name . "DrImpute")))
11637 (build-system r-build-system)
11639 `(("r-rcpp" ,r-rcpp)
11640 ("r-rcpparmadillo" ,r-rcpparmadillo)))
11641 (home-page "https://github.com/ikwak2/DrImpute")
11642 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
11644 "This is an R package for imputing dropout events. Many statistical
11645 methods in cell type identification, visualization and lineage reconstruction
11646 do not account for dropout events. DrImpute can improve the performance of
11647 such software by imputing dropout events.")
11648 (license license:gpl3)))
11650 (define-public r-gamlss-dist
11652 (name "r-gamlss-dist")
11657 (uri (cran-uri "gamlss.dist" version))
11660 "0zi87lgigr83l35zqq1y1g4cdq6ssjamripzz7yis74aznh6qg1l"))))
11661 (properties `((upstream-name . "gamlss.dist")))
11662 (build-system r-build-system)
11663 (propagated-inputs `(("r-mass" ,r-mass)))
11664 (home-page "http://www.gamlss.org/")
11665 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
11667 "This package provides a set of distributions which can be used for
11668 modelling the response variables in Generalized Additive Models for Location
11669 Scale and Shape. The distributions can be continuous, discrete or mixed
11670 distributions. Extra distributions can be created, by transforming, any
11671 continuous distribution defined on the real line, to a distribution defined on
11672 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
11673 transformation, respectively.")
11674 ;; Either version of the GPL.
11675 (license (list license:gpl2 license:gpl3))))
11677 ;; This package includes JavaScript files, which are not minified. When
11678 ;; upgrading please check that there are no new minified JavaScript files.
11679 (define-public r-shinyjs
11686 (uri (cran-uri "shinyjs" version))
11689 "113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
11690 (build-system r-build-system)
11692 `(("r-digest" ,r-digest)
11693 ("r-htmltools" ,r-htmltools)
11694 ("r-jsonlite" ,r-jsonlite)
11695 ("r-shiny" ,r-shiny)))
11696 (home-page "https://deanattali.com/shinyjs")
11697 (synopsis "Improve the user experience of your Shiny apps")
11699 "Perform common useful JavaScript operations in Shiny apps that will
11700 greatly improve your apps without having to know any JavaScript. Examples
11701 include: hiding an element, disabling an input, resetting an input back to its
11702 original value, delaying code execution by a few seconds, and many more useful
11703 functions for both the end user and the developer. Shinyjs can also be used
11704 to easily call your own custom JavaScript functions from R.")
11705 (license license:agpl3+)))
11707 ;; This package includes minified JavaScript files. When upgrading please
11708 ;; check that there are no new minified JavaScript files.
11709 (define-public r-colourpicker
11711 (name "r-colourpicker")
11716 (uri (cran-uri "colourpicker" version))
11719 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
11720 (build-system r-build-system)
11722 `(#:modules ((guix build utils)
11723 (guix build r-build-system)
11727 (modify-phases %standard-phases
11728 (add-after 'unpack 'process-javascript
11729 (lambda* (#:key inputs #:allow-other-keys)
11730 (with-directory-excursion "inst"
11734 `((,(assoc-ref inputs "js-salvattore")
11735 "examples/colourInput/www/salvattore.min.js")
11736 (,(assoc-ref inputs "js-jquery")
11737 "htmlwidgets/lib/jquery/jquery.min.js")
11738 ("www/shared/colourpicker/js/colourpicker.js"
11739 "www/shared/colourpicker/js/colourpicker.min.js"))))
11740 (lambda (sources targets)
11741 (for-each (lambda (source target)
11742 (format #t "Processing ~a --> ~a~%"
11744 (delete-file target)
11745 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
11746 (call-with-output-file target
11748 (dump-port minified port)))))
11749 sources targets))))
11752 `(("r-ggplot2" ,r-ggplot2)
11753 ("r-htmltools" ,r-htmltools)
11754 ("r-htmlwidgets" ,r-htmlwidgets)
11755 ("r-jsonlite" ,r-jsonlite)
11756 ("r-miniui" ,r-miniui)
11757 ("r-shiny" ,r-shiny)
11758 ("r-shinyjs" ,r-shinyjs)))
11760 `(("uglify-js" ,uglify-js)
11764 (uri "https://code.jquery.com/jquery-3.3.1.js")
11767 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
11771 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
11774 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
11775 (home-page "https://github.com/daattali/colourpicker")
11776 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
11778 "This package provides a color picker that can be used as an input in
11779 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
11780 custom color palettes, and many more options. A plot color helper tool is
11781 available as an RStudio Addin, which helps you pick colors to use in your
11782 plots. A more generic color picker RStudio Addin is also provided to let you
11783 select colors to use in your R code.")
11784 (license license:expat)))
11786 (define-public r-ggextra
11793 (uri (cran-uri "ggExtra" version))
11796 "1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
11797 (properties `((upstream-name . "ggExtra")))
11798 (build-system r-build-system)
11800 `(("r-colourpicker" ,r-colourpicker)
11801 ("r-ggplot2" ,r-ggplot2)
11802 ("r-gtable" ,r-gtable)
11803 ("r-miniui" ,r-miniui)
11804 ("r-scales" ,r-scales)
11805 ("r-shiny" ,r-shiny)
11806 ("r-shinyjs" ,r-shinyjs)))
11807 (home-page "https://github.com/daattali/ggExtra")
11808 (synopsis "Marginal histograms for ggplot2 and other enhancements")
11810 "This package is a collection of functions and layers to enhance ggplot2.
11811 The flagship function is @code{ggMarginal()}, which can be used to add
11812 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
11813 (license license:expat)))
11815 (define-public r-minpack-lm
11817 (name "r-minpack-lm")
11822 (uri (cran-uri "minpack.lm" version))
11825 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
11826 (properties `((upstream-name . "minpack.lm")))
11827 (build-system r-build-system)
11828 (native-inputs `(("gfortran" ,gfortran)))
11829 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
11830 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
11832 "The @code{nls.lm} function provides an R interface to @code{lmder} and
11833 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
11834 problems by a modification of the Levenberg-Marquardt algorithm, with support
11835 for lower and upper parameter bounds. The implementation can be used via
11836 @code{nls}-like calls using the @code{nlsLM} function.")
11837 (license license:gpl3)))
11839 (define-public r-moments
11846 (uri (cran-uri "moments" version))
11849 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
11850 (build-system r-build-system)
11851 (home-page "https://cran.r-project.org/web/packages/moments")
11852 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
11854 "This package provides functions to calculate: moments, Pearson's
11855 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
11856 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
11857 (license license:gpl2+)))
11859 (define-public r-msir
11866 (uri (cran-uri "msir" version))
11869 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
11870 (build-system r-build-system)
11872 `(("r-mclust" ,r-mclust)))
11873 (home-page "https://cran.r-project.org/web/packages/msir")
11874 (synopsis "Model-based sliced inverse regression")
11876 "This is an R package for dimension reduction based on finite Gaussian
11877 mixture modeling of inverse regression.")
11878 (license license:gpl2+)))
11880 (define-public r-pbivnorm
11882 (name "r-pbivnorm")
11887 (uri (cran-uri "pbivnorm" version))
11890 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
11891 (build-system r-build-system)
11892 (native-inputs `(("gfortran" ,gfortran)))
11893 (home-page "https://github.com/brentonk/pbivnorm")
11894 (synopsis "Vectorized bivariate normal CDF")
11896 "This package provides a vectorized R function for calculating
11897 probabilities from a standard bivariate normal CDF.")
11898 (license license:gpl2+)))
11900 (define-public r-lavaan
11907 (uri (cran-uri "lavaan" version))
11910 "1zf0sxpms35rhq2syb7r3sshhc8kjvc3pv97dk9x0gf4xl7pck4g"))))
11911 (build-system r-build-system)
11913 `(("r-mass" ,r-mass)
11914 ("r-mnormt" ,r-mnormt)
11915 ("r-numderiv" ,r-numderiv)
11916 ("r-pbivnorm" ,r-pbivnorm)))
11917 (home-page "http://lavaan.ugent.be")
11918 (synopsis "Latent variable analysis")
11920 "This package provides tools to fit a variety of latent variable models,
11921 including confirmatory factor analysis, structural equation modeling and
11922 latent growth curve models.")
11923 (license license:gpl2+)))
11925 (define-public r-nonnest2
11927 (name "r-nonnest2")
11932 (uri (cran-uri "nonnest2" version))
11935 "1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
11936 (build-system r-build-system)
11938 `(("r-compquadform" ,r-compquadform)
11939 ("r-lavaan" ,r-lavaan)
11940 ("r-mvtnorm" ,r-mvtnorm)
11941 ("r-sandwich" ,r-sandwich)))
11942 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
11943 (synopsis "Tests of non-nested models")
11945 "This package allows for testing of non-nested models. It includes tests
11946 of model distinguishability and of model fit that can be applied to both
11947 nested and non-nested models. The package also includes functionality to
11948 obtain confidence intervals associated with AIC and BIC.")
11949 ;; Either version of the GPL.
11950 (license (list license:gpl2 license:gpl3))))
11952 (define-public r-penalized
11954 (name "r-penalized")
11959 (uri (cran-uri "penalized" version))
11962 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
11963 (build-system r-build-system)
11965 `(("r-rcpp" ,r-rcpp)
11966 ("r-rcpparmadillo" ,r-rcpparmadillo)
11967 ("r-survival" ,r-survival)))
11968 (home-page "https://cran.r-project.org/web/packages/penalized/")
11969 (synopsis "Penalized estimation in GLMs and in the Cox model")
11971 "This package provides tools for fitting possibly high dimensional
11972 penalized regression models. The penalty structure can be any combination of
11973 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
11974 constraint on the regression coefficients. The supported regression models
11975 are linear, logistic and Poisson regression and the Cox Proportional Hazards
11976 model. Cross-validation routines allow optimization of the tuning
11978 (license license:gpl2+)))
11980 (define-public r-zim
11987 (uri (cran-uri "ZIM" version))
11990 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
11991 (properties `((upstream-name . "ZIM")))
11992 (build-system r-build-system)
11993 (propagated-inputs `(("r-mass" ,r-mass)))
11994 (home-page "https://github.com/biostatstudio/ZIM")
11995 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
11997 "Analyze count time series with excess zeros. Two types of statistical
11998 models are supported: Markov regression and state-space models. They are also
11999 known as observation-driven and parameter-driven models respectively in the
12000 time series literature. The functions used for Markov regression or
12001 observation-driven models can also be used to fit ordinary regression models
12002 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12003 negative binomial (ZINB) assumption. The package also contains miscellaneous
12004 functions to compute density, distribution, quantile, and generate random
12005 numbers from ZIP and ZINB distributions.")
12006 (license license:gpl3)))
12008 (define-public r-nor1mix
12015 (uri (cran-uri "nor1mix" version))
12018 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12019 (build-system r-build-system)
12020 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12021 (synopsis "Normal (1-d) mixture models")
12023 "This package provides S3 classes and methods for one-dimensional normal
12024 mixture models, for, e.g., density estimation or clustering algorithms
12025 research and teaching; it provides the widely used Marron-Wand densities. It
12026 also provides tools for efficient random number generation and graphics.")
12027 (license license:gpl2+)))
12029 (define-public r-beanplot
12031 (name "r-beanplot")
12036 (uri (cran-uri "beanplot" version))
12039 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12040 (build-system r-build-system)
12041 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12042 (synopsis "Visualization via beanplots")
12044 "This package provides beanplots, an alternative to
12045 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
12047 (license license:gpl2)))
12049 (define-public r-pbdzmq
12056 (uri (cran-uri "pbdZMQ" version))
12059 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
12060 (properties `((upstream-name . "pbdZMQ")))
12061 (build-system r-build-system)
12063 `(("zeromq" ,zeromq)
12066 `(("pkg-config" ,pkg-config)))
12067 (home-page "https://pbdr.org/")
12068 (synopsis "R interface to ZeroMQ")
12070 "ZeroMQ is a well-known library for high-performance asynchronous
12071 messaging in scalable, distributed applications. This package provides high
12072 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
12073 interactive client/server programming frameworks. A few wrapper functions
12074 compatible with @code{rzmq} are also provided.")
12075 (license license:gpl3)))
12077 (define-public r-repr
12084 (uri (cran-uri "repr" version))
12087 "0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
12088 (build-system r-build-system)
12090 `(("r-base64enc" ,r-base64enc)
12091 ("r-htmltools" ,r-htmltools)
12092 ("r-jsonlite" ,r-jsonlite)
12093 ("r-pillar" ,r-pillar)))
12094 (home-page "https://cran.r-project.org/web/packages/repr/")
12095 (synopsis "Serializable representations")
12097 "This package provides string and binary representations of objects for
12098 several formats and MIME types.")
12099 (license license:gpl3)))
12101 (define-public r-irdisplay
12103 (name "r-irdisplay")
12108 (uri (cran-uri "IRdisplay" version))
12111 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
12112 (properties `((upstream-name . "IRdisplay")))
12113 (build-system r-build-system)
12115 `(("r-repr" ,r-repr)))
12116 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
12117 (synopsis "Jupyter display machinery")
12119 "This package provides an interface to the rich display capabilities of
12120 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
12121 running IRkernel session.")
12122 (license license:expat)))
12124 (define-public r-irkernel
12126 (name "r-irkernel")
12131 (uri (cran-uri "IRkernel" version))
12134 "040qig675zaxsf81ranmvk293amrswi5098k69wyq0vgqyin6vwp"))))
12135 (properties `((upstream-name . "IRkernel")))
12136 (build-system r-build-system)
12139 (modify-phases %standard-phases
12140 (add-after 'install 'install-kernelspec
12141 (lambda* (#:key outputs #:allow-other-keys)
12142 (let ((out (assoc-ref outputs "out")))
12143 (setenv "HOME" "/tmp")
12144 (invoke "jupyter" "kernelspec" "install"
12147 (string-append out "/site-library/IRkernel/kernelspec"))
12150 `(("jupyter" ,jupyter)))
12152 `(("r-crayon" ,r-crayon)
12153 ("r-digest" ,r-digest)
12154 ("r-evaluate" ,r-evaluate)
12155 ("r-irdisplay" ,r-irdisplay)
12156 ("r-jsonlite" ,r-jsonlite)
12157 ("r-pbdzmq" ,r-pbdzmq)
12159 ("r-uuid" ,r-uuid)))
12160 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
12161 (synopsis "Native R kernel for Jupyter")
12163 "The R kernel for the Jupyter environment executes R code which the
12164 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
12166 (license license:expat)))
12168 (define-public r-gmodels
12175 (uri (cran-uri "gmodels" version))
12178 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
12179 (build-system r-build-system)
12181 `(("r-gdata" ,r-gdata)
12182 ("r-mass" ,r-mass)))
12183 (home-page "https://cran.r-project.org/web/packages/gmodels/")
12184 (synopsis "Various R programming tools for model fitting")
12186 "This package provides various R programming tools for model fitting.")
12187 (license license:gpl2)))
12189 (define-public r-apcluster
12191 (name "r-apcluster")
12196 (uri (cran-uri "apcluster" version))
12199 "188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
12200 (build-system r-build-system)
12202 `(("r-matrix" ,r-matrix)
12203 ("r-rcpp" ,r-rcpp)))
12204 (home-page "https://cran.r-project.org/web/packages/apcluster/")
12205 (synopsis "Affinity propagation clustering")
12207 "This package implements affinity propagation clustering introduced by
12208 Frey and Dueck (2007). The package further provides leveraged affinity
12209 propagation and an algorithm for exemplar-based agglomerative clustering that
12210 can also be used to join clusters obtained from affinity propagation. Various
12211 plotting functions are available for analyzing clustering results.")
12212 (license license:gpl2+)))
12214 (define-public r-valr
12221 (uri (cran-uri "valr" version))
12224 "14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
12225 (build-system r-build-system)
12227 `(("r-broom" ,r-broom)
12228 ("r-dplyr" ,r-dplyr)
12229 ("r-ggplot2" ,r-ggplot2)
12231 ("r-readr" ,r-readr)
12232 ("r-rlang" ,r-rlang)
12233 ("r-stringr" ,r-stringr)
12234 ("r-tibble" ,r-tibble)))
12235 (home-page "http://github.com/rnabioco/valr")
12236 (synopsis "Genome interval arithmetic in R")
12238 "This package enables you to read and manipulate genome intervals and
12239 signals. It provides functionality similar to command-line tool suites within
12240 R, enabling interactive analysis and visualization of genome-scale data.")
12241 (license license:expat)))
12243 (define-public r-rematch2
12245 (name "r-rematch2")
12250 (uri (cran-uri "rematch2" version))
12253 "00cznm6rk33b53w7zybkz7549bnydc66znpi5mb0xd24pmqp0rvq"))))
12254 (build-system r-build-system)
12256 `(("r-tibble" ,r-tibble)))
12257 (home-page "https://github.com/r-lib/rematch2")
12258 (synopsis "Tidy output from regular expression matching")
12260 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
12261 return the match results in tidy data frames.")
12262 (license license:expat)))
12264 (define-public r-picante
12271 (uri (cran-uri "picante" version))
12274 "1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
12275 (build-system r-build-system)
12279 ("r-vegan" ,r-vegan)))
12280 (home-page "https://cran.r-project.org/web/packages/picante/")
12281 (synopsis "Integrating phylogenies and ecology")
12283 "This package provides functions for phylocom integration, community
12284 analyses, null-models, traits and evolution. It implements numerous
12285 ecophylogenetic approaches including measures of community phylogenetic and
12286 trait diversity, phylogenetic signal, estimation of trait values for
12287 unobserved taxa, null models for community and phylogeny randomizations, and
12288 utility functions for data input/output and phylogeny plotting. A full
12289 description of package functionality and methods are provided by Kembel et
12291 (license license:gpl2)))
12293 (define-public r-reinforcelearn
12295 (name "r-reinforcelearn")
12300 (uri (cran-uri "reinforcelearn" version))
12303 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
12304 (build-system r-build-system)
12306 `(("r-checkmate" ,r-checkmate)
12308 ("r-purrr" ,r-purrr)
12310 (home-page "https://markusdumke.github.io/reinforcelearn")
12311 (synopsis "Reinforcement learning")
12313 "This package implements reinforcement learning environments and
12314 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
12315 can be used with function approximation, eligibility traces (Singh & Sutton,
12316 1996) and experience replay (Mnih et al., 2013).")
12317 (license license:expat)))
12319 (define-public r-lemon
12326 (uri (cran-uri "lemon" version))
12329 "0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
12330 (build-system r-build-system)
12332 `(("r-ggplot2" ,r-ggplot2)
12333 ("r-gridextra" ,r-gridextra)
12334 ("r-gtable" ,r-gtable)
12335 ("r-knitr" ,r-knitr)
12336 ("r-lattice" ,r-lattice)
12338 ("r-scales" ,r-scales)))
12339 (home-page "https://github.com/stefanedwards/lemon")
12340 (synopsis "Freshen up your ggplot2 plots")
12342 "This package provides functions for working with legends and axis lines
12343 of ggplot2, facets that repeat axis lines on all panels, and some knitr
12345 (license license:gpl3)))
12347 (define-public r-wgaim
12354 (uri (cran-uri "wgaim" version))
12357 "1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg"))))
12358 (build-system r-build-system)
12360 `(("r-lattice" ,r-lattice)
12362 (home-page "https://cran.r-project.org/web/packages/wgaim")
12363 (synopsis "Whole genome average interval mapping for QTL detection")
12365 "This package integrates sophisticated mixed modelling methods with a
12366 whole genome approach to detecting significant QTL in linkage maps.")
12367 (license license:gpl2+)))
12369 (define-public r-bedr
12376 (uri (cran-uri "bedr" version))
12379 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
12380 (build-system r-build-system)
12382 `(("r-data-table" ,r-data-table)
12383 ("r-r-utils" ,r-r-utils)
12384 ("r-testthat" ,r-testthat)
12385 ("r-venndiagram" ,r-venndiagram)
12388 ("bedtools" ,bedtools)
12389 ("htslib" ,htslib))) ; for tabix
12391 `(("r-knitr" ,r-knitr))) ; for vignettes
12392 (home-page "https://cran.r-project.org/web/packages/bedr")
12393 (synopsis "Genomic region processing")
12395 "This package is for genomic regions processing using command line tools
12396 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
12397 utilities to perform genome arithmetic e.g indexing, formatting and merging.
12398 The bedr package's API enhances access to these tools as well as offers
12399 additional utilities for genomic regions processing.")
12400 (license license:gpl2)))
12402 (define-public r-partitions
12404 (name "r-partitions")
12409 (uri (cran-uri "partitions" version))
12412 "1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx"))))
12413 (build-system r-build-system)
12416 ("r-polynom" ,r-polynom)))
12417 (home-page "https://cran.r-project.org/web/packages/partitions")
12418 (synopsis "Additive partitions of integers")
12420 "This package provides tools to enumerates the partitions, unequal
12421 partitions, and restricted partitions of an integer; the three corresponding
12422 partition functions are also given.")
12423 ;; Any version of the GPL
12424 (license license:gpl2+)))
12426 (define-public r-brobdingnag
12428 (name "r-brobdingnag")
12433 (uri (cran-uri "Brobdingnag" version))
12436 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
12437 (properties `((upstream-name . "Brobdingnag")))
12438 (build-system r-build-system)
12439 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
12440 (synopsis "Very large numbers in R")
12442 "This package handles very large numbers in R. Real numbers are held
12443 using their natural logarithms, plus a logical flag indicating sign. The
12444 package includes a vignette that gives a step-by-step introduction to using S4
12446 ;; Any version of the GPL
12447 (license license:gpl2+)))
12449 (define-public r-untb
12456 (uri (cran-uri "untb" version))
12459 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
12460 (build-system r-build-system)
12462 `(("r-brobdingnag" ,r-brobdingnag)
12463 ("r-partitions" ,r-partitions)
12464 ("r-polynom" ,r-polynom)))
12465 (home-page "https://github.com/RobinHankin/untb.git")
12466 (synopsis "Ecological drift under the UNTB")
12468 "This package provides numerical simulations, and visualizations, of
12469 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
12470 (license license:gpl2+)))
12472 (define-public r-stepwise
12474 (name "r-stepwise")
12479 (uri (cran-uri "stepwise" version))
12482 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
12483 (build-system r-build-system)
12484 (home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
12485 (synopsis "Stepwise detection of recombination breakpoints")
12487 "This package provides a stepwise approach to identifying recombination
12488 breakpoints in a genomic sequence alignment.")
12489 (license license:gpl2+)))
12491 (define-public r-snpmaxsel
12493 (name "r-snpmaxsel")
12498 (uri (cran-uri "SNPmaxsel" version))
12501 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
12502 (properties `((upstream-name . "SNPmaxsel")))
12503 (build-system r-build-system)
12505 `(("r-combinat" ,r-combinat)
12506 ("r-mvtnorm" ,r-mvtnorm)))
12507 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
12508 (synopsis "Maximally selected statistics for SNP data")
12510 "This package implements asymptotic methods related to maximally selected
12511 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
12513 (license license:gpl2+)))
12515 (define-public r-acsnminer
12517 (name "r-acsnminer")
12518 (version "0.16.8.25")
12521 (uri (cran-uri "ACSNMineR" version))
12524 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
12525 (properties `((upstream-name . "ACSNMineR")))
12526 (build-system r-build-system)
12528 `(("r-ggplot2" ,r-ggplot2)
12529 ("r-gridextra" ,r-gridextra)))
12530 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
12531 (synopsis "Gene enrichment analysis")
12533 "This package provides tools to compute and represent gene set enrichment
12534 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
12535 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
12536 enrichment can be run with hypergeometric test or Fisher exact test, and can
12537 use multiple corrections. Visualization of data can be done either by
12538 barplots or heatmaps.")
12539 (license license:gpl2+)))
12541 (define-public r-seqinr
12548 (uri (cran-uri "seqinr" version))
12551 "17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
12552 (build-system r-build-system)
12554 `(("r-ade4" ,r-ade4)
12555 ("r-segmented" ,r-segmented)))
12558 (home-page "http://seqinr.r-forge.r-project.org/")
12559 (synopsis "Biological sequences retrieval and analysis")
12561 "This package provides tools for exploratory data analysis and data
12562 visualization of biological sequence (DNA and protein) data. It also includes
12563 utilities for sequence data management under the ACNUC system.")
12564 (license license:gpl2+)))
12566 (define-public r-units
12573 (uri (cran-uri "units" version))
12576 "0kx640h60s3zzkdr302asap7diap6vri6d41scnx507yvkcqiph3"))))
12577 (build-system r-build-system)
12579 `(("udunits" ,udunits)))
12581 `(("r-rcpp" ,r-rcpp)))
12582 (home-page "https://github.com/r-quantities/units/")
12583 (synopsis "Measurement Units for R Vectors")
12585 "This package provides support for measurement units in R vectors,
12586 matrices and arrays: automatic propagation, conversion, derivation and
12587 simplification of units; raising errors in case of unit incompatibility. It
12588 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
12590 (license license:gpl2)))
12592 (define-public r-classint
12594 (name "r-classint")
12599 (uri (cran-uri "classInt" version))
12602 "00q1bpgblrldckn1rk166q1b0hgap2sjjyfmfcyh6ydk6y73ziir"))))
12603 (properties `((upstream-name . "classInt")))
12604 (build-system r-build-system)
12606 `(("r-class" ,r-class)
12607 ("r-e1071" ,r-e1071)
12608 ("r-kernsmooth" ,r-kernsmooth)))
12609 (native-inputs `(("gfortran" ,gfortran)))
12610 (home-page "https://github.com/r-spatial/classInt/")
12611 (synopsis "Choose univariate class intervals")
12613 "This package provides selected commonly used methods for choosing
12614 univariate class intervals for mapping or other graphics purposes.")
12615 (license license:gpl2+)))
12617 (define-public r-spdata
12624 (uri (cran-uri "spData" version))
12627 "162cqb331ki43jx4r8lpkjpn2l712figd896rnawg9j1jmjyl96y"))))
12628 (properties `((upstream-name . "spData")))
12629 (build-system r-build-system)
12630 (home-page "https://github.com/Nowosad/spData")
12631 (synopsis "Datasets for spatial analysis")
12633 "This a package containing diverse spatial datasets for demonstrating,
12634 benchmarking and teaching spatial data analysis. It includes R data of class
12635 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
12636 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
12637 of the datasets are designed to illustrate specific analysis techniques.
12638 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
12639 illustrate point pattern analysis techniques.")
12640 (license license:cc0)))
12642 (define-public r-learnbayes
12644 (name "r-learnbayes")
12649 (uri (cran-uri "LearnBayes" version))
12652 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
12653 (properties `((upstream-name . "LearnBayes")))
12654 (build-system r-build-system)
12655 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
12656 (synopsis "Functions for learning Bayesian inference")
12658 "This package provides a collection of functions helpful in learning the
12659 basic tenets of Bayesian statistical inference. It contains functions for
12660 summarizing basic one and two parameter posterior distributions and predictive
12661 distributions. It contains MCMC algorithms for summarizing posterior
12662 distributions defined by the user. It also contains functions for regression
12663 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
12665 (license license:gpl2+)))
12667 (define-public r-deldir
12674 (uri (cran-uri "deldir" version))
12677 "0790dwxb2mz1ffz8gd5vwdr0if2q76dzy3vab5rsykf9kz72n4g0"))))
12678 (build-system r-build-system)
12679 (native-inputs `(("gfortran" ,gfortran)))
12680 (home-page "https://cran.r-project.org/web/packages/deldir")
12681 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
12683 "This package provides tools for calculating the Delaunay triangulation
12684 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
12685 of a planar point set. It plots triangulations and tessellations in various
12686 ways, clips tessellations to sub-windows, calculates perimeters of
12687 tessellations, and summarizes information about the tiles of the
12689 (license license:gpl2+)))
12691 (define-public r-sf
12698 (uri (cran-uri "sf" version))
12701 "192hw52x1qlif8zyai1kff1wiyr3yl5f7jj1rk3k0nr8das0qy6i"))))
12702 (build-system r-build-system)
12709 `(("r-classint" ,r-classint)
12711 ("r-magrittr" ,r-magrittr)
12713 ("r-units" ,r-units)))
12714 (native-inputs `(("pkg-config" ,pkg-config)))
12715 (home-page "https://github.com/r-spatial/sf/")
12716 (synopsis "Simple features for R")
12718 "This package provides support for simple features, a standardized way to
12719 encode spatial vector data. It binds to GDAL for reading and writing data, to
12720 GEOS for geometrical operations, and to PROJ for projection conversions and
12721 datum transformations.")
12722 ;; Either of these licenses
12723 (license (list license:gpl2 license:expat))))
12725 (define-public r-spdep
12732 (uri (cran-uri "spdep" version))
12735 "06mk81kc1ml2wjc8wwwgr0wasjcr4mwrxpfa8vfc373bmnha635s"))))
12736 (build-system r-build-system)
12738 `(("r-boot" ,r-boot)
12740 ("r-deldir" ,r-deldir)
12742 ("r-gmodels" ,r-gmodels)
12743 ("r-learnbayes" ,r-learnbayes)
12745 ("r-matrix" ,r-matrix)
12749 ("r-spdata" ,r-spdata)))
12750 (home-page "https://github.com/r-spatial/spdep/")
12751 (synopsis "Spatial dependence: weighting schemes, statistics and models")
12753 "This package provides a collection of functions to create spatial
12754 weights matrix objects from polygon contiguities, from point patterns by
12755 distance and tessellations, for summarizing these objects, and for permitting
12756 their use in spatial data analysis, including regional aggregation by minimum
12758 (license license:gpl2+)))
12760 (define-public r-adegenet
12762 (name "r-adegenet")
12767 (uri (cran-uri "adegenet" version))
12770 "0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
12771 (build-system r-build-system)
12773 `(("r-ade4" ,r-ade4)
12776 ("r-dplyr" ,r-dplyr)
12777 ("r-ggplot2" ,r-ggplot2)
12778 ("r-igraph" ,r-igraph)
12780 ("r-reshape2" ,r-reshape2)
12781 ("r-seqinr" ,r-seqinr)
12782 ("r-shiny" ,r-shiny)
12783 ("r-spdep" ,r-spdep)
12784 ("r-vegan" ,r-vegan)))
12785 (home-page "https://github.com/thibautjombart/adegenet")
12786 (synopsis "Exploratory analysis of genetic and genomic data")
12788 "This package provides a toolset for the exploration of genetic and
12789 genomic data. Adegenet provides formal (S4) classes for storing and handling
12790 various genetic data, including genetic markers with varying ploidy and
12791 hierarchical population structure (@code{genind} class), alleles counts by
12792 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
12793 also implements original multivariate methods (DAPC, sPCA), graphics,
12794 statistical tests, simulation tools, distance and similarity measures, and
12795 several spatial methods. A range of both empirical and simulated datasets is
12796 also provided to illustrate various methods.")
12797 (license license:gpl2+)))
12799 (define-public r-pegas
12806 (uri (cran-uri "pegas" version))
12809 "0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx"))))
12810 (build-system r-build-system)
12812 `(("r-adegenet" ,r-adegenet)
12814 (home-page "http://ape-package.ird.fr/pegas.html")
12815 (synopsis "Population and evolutionary genetics analysis system")
12817 "This package provides functions for reading, writing, plotting,
12818 analysing, and manipulating allelic and haplotypic data, including from VCF
12819 files, and for the analysis of population nucleotide sequences and
12820 micro-satellites including coalescent analyses, linkage disequilibrium,
12821 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
12822 minimum spanning tree and network, and median-joining networks.")
12823 (license license:gpl2+)))
12825 (define-public r-rmetasim
12827 (name "r-rmetasim")
12832 (uri (cran-uri "rmetasim" version))
12835 "0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
12836 (build-system r-build-system)
12838 `(("r-ade4" ,r-ade4)
12839 ("r-adegenet" ,r-adegenet)
12840 ("r-gtools" ,r-gtools)
12841 ("r-pegas" ,r-pegas)))
12842 (home-page "https://cran.r-project.org/web/packages/rmetasim")
12843 (synopsis "Individual-based population genetic simulation environment")
12845 "This package provides an interface between R and the metasim simulation
12846 engine. The simulation environment is documented in: Strand, A.(2002),
12847 Metasim 1.0: an individual-based environment for simulating population
12848 genetics of complex population dynamics.")
12850 (license license:gpl2+)))
12852 (define-public r-genetics
12854 (name "r-genetics")
12855 (version "1.3.8.1.2")
12859 (uri (cran-uri "genetics" version))
12862 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
12863 (build-system r-build-system)
12865 `(("r-combinat" ,r-combinat)
12866 ("r-gdata" ,r-gdata)
12867 ("r-gtools" ,r-gtools)
12869 ("r-mvtnorm" ,r-mvtnorm)))
12870 (home-page "https://cran.r-project.org/web/packages/genetics/")
12871 (synopsis "Population genetics")
12873 "This package provides classes and methods for handling genetic data.
12874 It includes classes to represent genotypes and haplotypes at single markers up
12875 to multiple markers on multiple chromosomes. Function include allele
12876 frequencies, flagging homo/heterozygotes, flagging carriers of certain
12877 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
12878 and testing for linkage disequilibrium, ...")
12879 ;; Any GPL version.
12880 (license license:gpl2+)))
12882 (define-public r-snp-plotter
12884 (name "r-snp-plotter")
12889 (uri (cran-uri "snp.plotter" version))
12892 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
12893 (properties `((upstream-name . "snp.plotter")))
12894 (build-system r-build-system)
12895 (propagated-inputs `(("r-genetics" ,r-genetics)))
12896 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
12897 (synopsis "Plot p-values using single SNP and/or haplotype data")
12899 "This package helps you create plots of p-values using single SNP and/or
12900 haplotype data. Main features of the package include options to display a
12901 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
12902 datasets simultaneously. Plots can be created using global and/or individual
12903 haplotype p-values along with single SNP p-values. Images are created as
12904 either PDF/EPS files.")
12905 (license license:gpl2+)))
12907 (define-public r-polspline
12909 (name "r-polspline")
12914 (uri (cran-uri "polspline" version))
12917 "19zs4kpagsrzhng1byjbz1c4jxnfk58h4rgr096ml1bjwrgamnwc"))))
12918 (build-system r-build-system)
12919 (native-inputs `(("gfortran" ,gfortran)))
12920 (home-page "https://cran.r-project.org/web/packages/polspline/")
12921 (synopsis "Polynomial spline routines")
12923 "This package provides routines for the polynomial spline fitting
12924 routines hazard regression, hazard estimation with flexible tails, logspline,
12925 lspec, polyclass, and polymars.")
12926 (license license:gpl2+)))
12928 (define-public r-rms
12931 (version "5.1-3.1")
12935 (uri (cran-uri "rms" version))
12938 "0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9"))))
12939 (build-system r-build-system)
12941 `(("r-ggplot2" ,r-ggplot2)
12942 ("r-hmisc" ,r-hmisc)
12943 ("r-htmltable" ,r-htmltable)
12944 ("r-htmltools" ,r-htmltools)
12945 ("r-lattice" ,r-lattice)
12946 ("r-multcomp" ,r-multcomp)
12948 ("r-polspline" ,r-polspline)
12949 ("r-quantreg" ,r-quantreg)
12950 ("r-rpart" ,r-rpart)
12951 ("r-sparsem" ,r-sparsem)
12952 ("r-survival" ,r-survival)))
12953 (native-inputs `(("gfortran" ,gfortran)))
12954 (home-page "http://biostat.mc.vanderbilt.edu/rms")
12955 (synopsis "Regression modeling strategies")
12957 "This is a package for regression modeling, testing, estimation,
12958 validation, graphics, prediction, and typesetting by storing enhanced model
12959 design attributes in the fit. The rms package is a collection of functions
12960 that assist with and streamline modeling. It also contains functions for
12961 binary and ordinal logistic regression models, ordinal models for continuous Y
12962 with a variety of distribution families, and the Buckley-James multiple
12963 regression model for right-censored responses, and implements penalized
12964 maximum likelihood estimation for logistic and ordinary linear models. The
12965 package works with almost any regression model, but it was especially written
12966 to work with binary or ordinal regression models, Cox regression, accelerated
12967 failure time models, ordinary linear models, the Buckley-James model,
12968 generalized least squares for serially or spatially correlated observations,
12969 generalized linear models, and quantile regression.")
12970 (license license:gpl2+)))
12972 (define-public r-haplo-stats
12974 (name "r-haplo-stats")
12979 (uri (cran-uri "haplo.stats" version))
12982 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
12983 (properties `((upstream-name . "haplo.stats")))
12984 (build-system r-build-system)
12986 `(("r-rms" ,r-rms)))
12988 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
12989 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
12990 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
12992 "This package provides routines for the analysis of indirectly measured
12993 haplotypes. The statistical methods assume that all subjects are unrelated
12994 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
12995 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
12996 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
12997 examples in the vignette.")
12998 (license license:gpl2+)))
13000 (define-public r-bqtl
13007 (uri (cran-uri "bqtl" version))
13010 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
13011 (build-system r-build-system)
13012 (native-inputs `(("gfortran" ,gfortran)))
13013 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
13014 (synopsis "Bayesian QTL mapping toolkit")
13016 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
13017 lines. It includes maximum likelihood and Bayesian tools.")
13018 (license license:gpl2+)))
13020 (define-public r-ibdreg
13027 (uri (cran-uri "ibdreg" version))
13030 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
13031 (build-system r-build-system)
13032 (home-page "https://www.mayo.edu/research/labs/\
13033 statistical-genetics-genetic-epidemiology/software")
13034 (synopsis "Regression methods for IBD linkage with covariates")
13036 "This package provides a method to test genetic linkage with covariates
13037 by regression methods with response IBD sharing for relative pairs. Account
13038 for correlations of IBD statistics and covariates for relative pairs within
13039 the same pedigree.")
13040 (license license:gpl2+)))
13042 (define-public r-dlmap
13049 (uri (cran-uri "dlmap" version))
13052 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
13053 (build-system r-build-system)
13055 `(("r-ibdreg" ,r-ibdreg)
13059 ("r-wgaim" ,r-wgaim)))
13060 (home-page "https://cran.r-project.org/web/packages/dlmap/")
13061 (synopsis "Detection localization mapping for QTL")
13063 "This is package for QTL mapping in a mixed model framework with separate
13064 detection and localization stages. The first stage detects the number of QTL
13065 on each chromosome based on the genetic variation due to grouped markers on
13066 the chromosome; the second stage uses this information to determine the most
13067 likely QTL positions. The mixed model can accommodate general fixed and
13068 random effects, including spatial effects in field trials and pedigree
13069 effects. It is applicable to backcrosses, doubled haploids, recombinant
13070 inbred lines, F2 intercrosses, and association mapping populations.")
13071 (license license:gpl2)))
13073 (define-public r-ldheatmap
13075 (name "r-ldheatmap")
13080 (uri (cran-uri "LDheatmap" version))
13083 "1r0j8bihi5z1x0sgaf7dwzpsw9i0nc1vylvipvc0cia2ka1lr9dc"))))
13084 (properties `((upstream-name . "LDheatmap")))
13085 (build-system r-build-system)
13087 `(("r-genetics" ,r-genetics)
13089 ("r-snpstats" ,r-snpstats)))
13090 (home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
13091 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
13093 "This package provides tools to produce a graphical display, as a heat
13094 map, of measures of pairwise linkage disequilibria between SNPs. Users may
13095 optionally include the physical locations or genetic map distances of each SNP
13097 (license license:gpl3)))
13099 (define-public r-hwde
13106 (uri (cran-uri "hwde" version))
13109 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
13110 (build-system r-build-system)
13111 (home-page "https://cran.r-project.org/web/packages/hwde/")
13112 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
13114 "This package fits models for genotypic disequilibria, as described in
13115 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
13116 terms are available that account for first order interactions between loci.
13117 It also implements, for a single locus in a single population, a conditional
13118 exact test for Hardy-Weinberg equilibrium.")
13119 (license license:gpl2+)))
13121 (define-public r-tdthap
13128 (uri (cran-uri "tdthap" version))
13131 "0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r"))))
13132 (build-system r-build-system)
13133 (home-page "https://cran.r-project.org/web/packages/tdthap/")
13134 (synopsis "TDT tests for extended haplotypes")
13136 "Functions and examples are provided for transmission/disequilibrium
13137 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
13138 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
13139 (license license:artistic2.0)))
13141 (define-public r-sparql
13147 (uri (cran-uri "SPARQL" version))
13150 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
13151 (properties `((upstream-name . "SPARQL")))
13152 (build-system r-build-system)
13154 `(("r-rcurl" ,r-rcurl)
13156 (home-page "https://cran.r-project.org/web/packages/SPARQL")
13157 (synopsis "SPARQL client for R")
13158 (description "This package provides an interface to use SPARQL to pose
13159 SELECT or UPDATE queries to an end-point.")
13160 ;; The only license indication is found in the DESCRIPTION file,
13161 ;; which states GPL-3. So we cannot assume GPLv3+.
13162 (license license:gpl3)))
13164 (define-public r-bookdown
13166 (name "r-bookdown")
13170 (uri (cran-uri "bookdown" version))
13173 "1c2v0rpa1rrpbx8yb66sfvrf4gf57f6a8x7ydjqqbkbwhxdlrsrq"))))
13174 (build-system r-build-system)
13176 `(("r-htmltools" ,r-htmltools)
13177 ("r-knitr" ,r-knitr)
13178 ("r-rmarkdown" ,r-rmarkdown)
13179 ("r-tinytex" ,r-tinytex)
13181 ("pandoc" ,ghc-pandoc)))
13182 (home-page "https://github.com/rstudio/bookdown")
13183 (synopsis "Authoring books and technical documents with R markdown")
13184 (description "This package provides output formats and utilities for
13185 authoring books and technical documents with R Markdown.")
13186 (license license:gpl3)))
13188 (define-public r-optparse
13190 (name "r-optparse")
13195 (uri (cran-uri "optparse" version))
13198 "0zrp6jakjhawrwfri270ym83vj5a7nvjk0w6b41z41ahw2da99dm"))))
13199 (build-system r-build-system)
13201 `(("r-getopt" ,r-getopt)))
13202 (home-page "https://github.com/trevorld/optparse")
13203 (synopsis "Command line option parser")
13205 "This package provides a command line parser inspired by Python's
13206 @code{optparse} library to be used with Rscript to write shebang scripts
13207 that accept short and long options.")
13208 (license license:gpl2+)))
13210 (define-public r-wgcna
13217 (uri (cran-uri "WGCNA" version))
13220 "1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
13221 (properties `((upstream-name . "WGCNA")))
13222 (build-system r-build-system)
13224 `(("r-annotationdbi" ,r-annotationdbi)
13225 ("r-doparallel" ,r-doparallel)
13226 ("r-dynamictreecut" ,r-dynamictreecut)
13227 ("r-fastcluster" ,r-fastcluster)
13228 ("r-foreach" ,r-foreach)
13229 ("r-go-db" ,r-go-db)
13230 ("r-hmisc" ,r-hmisc)
13231 ("r-impute" ,r-impute)
13233 ("r-robust" ,r-robust)
13234 ("r-survival" ,r-survival)
13235 ("r-matrixstats" ,r-matrixstats)
13236 ("r-preprocesscore" ,r-preprocesscore)))
13238 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
13239 (synopsis "Weighted correlation network analysis")
13241 "This package provides functions necessary to perform Weighted
13242 Correlation Network Analysis on high-dimensional data. It includes functions
13243 for rudimentary data cleaning, construction and summarization of correlation
13244 networks, module identification and functions for relating both variables and
13245 modules to sample traits. It also includes a number of utility functions for
13246 data manipulation and visualization.")
13247 (license license:gpl2+)))
13249 (define-public r-kernlab
13256 (uri (cran-uri "kernlab" version))
13259 "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
13260 (build-system r-build-system)
13261 (home-page "https://cran.r-project.org/web/packages/kernlab")
13262 (synopsis "Kernel-based machine learning tools")
13264 "This package provides kernel-based machine learning methods for
13265 classification, regression, clustering, novelty detection, quantile regression
13266 and dimensionality reduction. Among other methods @code{kernlab} includes
13267 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
13269 (license license:gpl2)))
13271 (define-public r-hierfstat
13273 (name "r-hierfstat")
13274 (version "0.04-22")
13278 (uri (cran-uri "hierfstat" version))
13281 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
13282 (build-system r-build-system)
13284 `(("r-ade4" ,r-ade4)
13285 ("r-adegenet" ,r-adegenet)
13286 ("r-gtools" ,r-gtools)))
13287 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
13288 (synopsis "Estimation and tests of hierarchical F-statistics")
13290 "This package allows the estimation of hierarchical F-statistics from
13291 haploid or diploid genetic data with any numbers of levels in the hierarchy,
13292 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
13293 are also given to test via randomisations the significance of each F and
13294 variance components, using the likelihood-ratio statistics G.")
13295 (license license:gpl2+)))
13297 (define-public r-hapassoc
13299 (name "r-hapassoc")
13304 (uri (cran-uri "hapassoc" version))
13307 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
13308 (build-system r-build-system)
13309 (home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
13310 (synopsis "Inference of trait associations with SNP haplotypes")
13312 "Hapassoc performs likelihood inference of trait associations with
13313 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
13314 functions are developed primarily for data collected in cohort or
13315 cross-sectional studies. They can accommodate uncertain haplotype phase and
13316 handle missing genotypes at some SNPs.")
13317 (license license:gpl2)))
13319 (define-public r-sampling
13321 (name "r-sampling")
13326 (uri (cran-uri "sampling" version))
13329 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
13330 (build-system r-build-system)
13332 `(("r-lpsolve" ,r-lpsolve)
13333 ("r-mass" ,r-mass)))
13334 (home-page "https://cran.r-project.org/web/packages/sampling/")
13335 (synopsis "Survey sampling")
13337 "This package provides functions for drawing and calibrating samples.")
13338 (license license:gpl2+)))
13340 (define-public r-r2html
13347 (uri (cran-uri "R2HTML" version))
13350 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
13351 (properties `((upstream-name . "R2HTML")))
13352 (build-system r-build-system)
13353 (home-page "https://github.com/nalimilan/R2HTML")
13354 (synopsis "HTML export for R objects")
13356 "This package includes HTML functions and methods to write in an HTML
13357 file. Thus, making HTML reports is easy. It includes a function that allows
13358 redirection on the fly, which appears to be very useful for teaching purposes,
13359 as the student can keep a copy of the produced output to keep all that they
13360 did during the course. The package comes with a vignette describing how to
13361 write HTML reports for statistical analysis. Finally, a driver for Sweave
13362 allows to parse HTML flat files containing R code and to automatically write
13363 the corresponding outputs (tables and graphs).")
13364 (license license:gpl2+)))
13366 (define-public r-rjava
13373 (uri (cran-uri "rJava" version))
13376 "0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
13377 (properties `((upstream-name . "rJava")))
13378 (build-system r-build-system)
13380 `(#:modules ((guix build utils)
13381 (guix build r-build-system)
13384 (modify-phases %standard-phases
13385 (add-after 'unpack 'set-JAVA_HOME
13386 (lambda* (#:key inputs #:allow-other-keys)
13387 (let ((jdk (assoc-ref inputs "jdk")))
13388 (setenv "JAVA_HOME" jdk)
13389 (setenv "JAVA" (which "java"))
13390 (setenv "JAR" (which "jar"))
13391 (setenv "JAVAC" (which "javac"))
13392 (setenv "JAVAH" (which "javah"))
13393 (setenv "JAVA_CPPFLAGS"
13394 (string-append "-I" jdk "/include "
13395 "-I" jdk "/include/linux"))
13396 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
13397 ((lib) (setenv "JAVA_LIBS" lib))
13398 (_ (error "Could not find libjvm.so"))))
13402 ("jdk" ,icedtea-8 "jdk")
13405 (home-page "http://www.rforge.net/rJava/")
13406 (synopsis "Low-Level R to Java interface")
13408 "This package provides a low-level interface to the Java VM very much
13409 like .C/.Call and friends. It allows the creation of objects, calling methods
13410 and accessing fields.")
13411 (license license:gpl2)))
13413 (define-public r-svmisc
13420 (uri (cran-uri "svMisc" version))
13423 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
13424 (properties `((upstream-name . "svMisc")))
13425 (build-system r-build-system)
13426 (home-page "https://github.com/SciViews/svMisc")
13427 (synopsis "Miscellaneous functions for SciViews")
13429 "This package provides miscellaneous functions for SciViews or general
13430 use, including tools to manage a temporary environment attached to the search
13431 path for temporary variables you do not want to @code{save()} or
13432 @code{load()}; test the current platform; showing progress bars, etc.")
13433 (license license:gpl2)))
13435 (define-public r-xyz
13442 (uri (cran-uri "xyz" version))
13445 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
13446 (build-system r-build-system)
13448 `(("r-rcpp" ,r-rcpp)))
13449 (home-page "https://cran.r-project.org/web/packages/xyz/")
13450 (synopsis "Algorithm for fast interaction search in high-dimensional data")
13452 "High dimensional interaction search by brute force requires a quadratic
13453 computational cost in the number of variables. The xyz algorithm provably
13454 finds strong interactions in almost linear time. For details of the algorithm
13455 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
13456 interaction search in high-dimensional data.")
13457 ;; Any version of the GPL.
13458 (license license:gpl2+)))
13460 (define-public r-rttf2pt1
13462 (name "r-rttf2pt1")
13467 (uri (cran-uri "Rttf2pt1" version))
13470 "12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
13471 (properties `((upstream-name . "Rttf2pt1")))
13472 (build-system r-build-system)
13473 (home-page "https://github.com/wch/Rttf2pt1")
13474 (synopsis "Font conversion utility")
13476 "This package contains the program @code{ttf2pt1}, for use with the
13477 @code{extrafont} package.")
13478 ;; Most of the files are covered under the Expat license. Some files are
13479 ;; covered under BSD-3. Deviations for individual files are recorded in
13480 ;; the LICENSE file.
13481 (license (list license:bsd-3 license:expat
13482 (license:non-copyleft "file://LICENSE")))))
13484 (define-public r-extrafontdb
13486 (name "r-extrafontdb")
13491 (uri (cran-uri "extrafontdb" version))
13494 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
13495 (build-system r-build-system)
13496 (home-page "https://github.com/wch/extrafontdb")
13497 (synopsis "Database for the extrafont package")
13499 "This package holds the database for the @code{extrafont} package.")
13500 (license license:gpl2)))
13502 (define-public r-extrafont
13504 (name "r-extrafont")
13509 (uri (cran-uri "extrafont" version))
13512 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
13513 (build-system r-build-system)
13515 `(("r-extrafontdb" ,r-extrafontdb)
13516 ("r-rttf2pt1" ,r-rttf2pt1)))
13517 (home-page "https://github.com/wch/extrafont")
13518 (synopsis "Tools for using fonts in R")
13520 "The extrafont package makes it easier to use fonts other than the basic
13521 PostScript fonts that R uses. Fonts that are imported into extrafont can be
13522 used with PDF or PostScript output files. There are two hurdles for using
13523 fonts in PDF (or Postscript) output files:
13526 @item Making R aware of the font and the dimensions of the characters.
13527 @item Embedding the fonts in the PDF file so that the PDF can be displayed
13528 properly on a device that doesn't have the font. This is usually needed if
13529 you want to print the PDF file or share it with others.
13532 The extrafont package makes both of these things easier.")
13533 (license license:gpl2)))
13535 (define-public r-xkcd
13542 (uri (cran-uri "xkcd" version))
13545 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
13546 (build-system r-build-system)
13548 `(("r-extrafont" ,r-extrafont)
13549 ("r-ggplot2" ,r-ggplot2)
13550 ("r-hmisc" ,r-hmisc)))
13551 (home-page "https://cran.r-project.org/web/packages/xkcd/")
13552 (synopsis "Plot ggplot2 graphics in the XKCD style")
13554 "This package provides the means to plot ggplot2 graphs in the style of
13555 the XKCD web comic.")
13556 (license license:gpl3)))
13558 (define-public r-msigdbr
13565 (uri (cran-uri "msigdbr" version))
13568 "1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg"))))
13569 (build-system r-build-system)
13571 `(("r-dplyr" ,r-dplyr)
13572 ("r-magrittr" ,r-magrittr)
13573 ("r-rlang" ,r-rlang)
13574 ("r-tibble" ,r-tibble)))
13575 (home-page "https://github.com/igordot/msigdbr")
13576 (synopsis "MSigDB gene sets for multiple organisms")
13578 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
13579 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
13580 software in a standard R data frame with key-value pairs. Included are the
13581 original human gene symbols and Entrez IDs as well as the equivalents for
13582 various frequently studied model organisms such as mouse, rat, pig, fly, and
13584 ;; The package is covered under the Expat license, but the upstream MSigDB
13585 ;; files are made available under the Creative Commons Attribution 4.0
13586 ;; International license.
13587 (license (list license:expat license:cc-by4.0))))
13589 (define-public r-gridgraphics
13591 (name "r-gridgraphics")
13596 (uri (cran-uri "gridGraphics" version))
13599 "1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
13600 (properties `((upstream-name . "gridGraphics")))
13601 (build-system r-build-system)
13602 (home-page "https://github.com/pmur002/gridgraphics")
13603 (synopsis "Redraw base graphics using @code{grid} graphics")
13605 "This package provides functions to convert a page of plots drawn with
13606 the @code{graphics} package into identical output drawn with the @code{grid}
13607 package. The result looks like the original @code{graphics}-based plot, but
13608 consists of @code{grid} grobs and viewports that can then be manipulated with
13609 @code{grid} functions (e.g., edit grobs and revisit viewports).")
13610 (license license:gpl2+)))
13612 (define-public r-farver
13619 (uri (cran-uri "farver" version))
13622 "1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0"))))
13623 (build-system r-build-system)
13624 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13625 (home-page "https://github.com/thomasp85/farver")
13626 (synopsis "Vectorized color conversion and comparison")
13628 "The encoding of color can be handled in many different ways, using
13629 different color spaces. As different color spaces have different uses,
13630 efficient conversion between these representations are important. This
13631 package provides a set of functions that gives access to very fast color space
13632 conversion and comparisons implemented in C++, and offers 100-fold speed
13633 improvements over the @code{convertColor} function in the @code{grDevices}
13635 (license license:expat)))
13637 (define-public r-ggplotify
13639 (name "r-ggplotify")
13644 (uri (cran-uri "ggplotify" version))
13647 "0nv3wdmxnc5ww9m3xlgnb0jp30j45dg33nqc6gg3y36svg8anjcg"))))
13648 (build-system r-build-system)
13650 `(("r-ggplot2" ,r-ggplot2)
13651 ("r-gridgraphics" ,r-gridgraphics)
13652 ("r-rvcheck" ,r-rvcheck)))
13653 (home-page "https://github.com/GuangchuangYu/ggplotify")
13654 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
13656 "This package provides tools to convert plot function calls (using
13657 expression or formula) to @code{grob} or @code{ggplot} objects that are
13658 compatible with the @code{grid} and @code{ggplot2} environment. With this
13659 package, we are able to e.g. use @code{cowplot} to align plots produced by
13660 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
13661 converting them to @code{ggplot} objects.")
13662 (license license:artistic2.0)))
13664 (define-public r-triebeard
13666 (name "r-triebeard")
13671 (uri (cran-uri "triebeard" version))
13674 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
13675 (build-system r-build-system)
13676 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
13677 (home-page "https://github.com/Ironholds/triebeard/")
13678 (synopsis "Radix trees in Rcpp")
13680 "Radix trees, or tries, are key-value data structures optimized for
13681 efficient lookups, similar in purpose to hash tables. This package provides
13682 an implementation of radix trees for use in R programming and in developing
13683 packages with Rcpp.")
13684 (license license:expat)))
13686 (define-public r-tweenr
13693 (uri (cran-uri "tweenr" version))
13696 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
13697 (build-system r-build-system)
13699 `(("r-farver" ,r-farver)
13700 ("r-magrittr" ,r-magrittr)
13702 ("r-rlang" ,r-rlang)))
13703 (home-page "https://github.com/thomasp85/tweenr")
13704 (synopsis "Interpolate data for smooth animations")
13706 "In order to create smooth animation between states of data, tweening is
13707 necessary. This package provides a range of functions for creating tweened
13708 data that can be used as basis for animation. Furthermore it adds a number of
13709 vectorized interpolaters for common R data types such as numeric, date and
13711 (license license:expat)))
13713 (define-public r-polyclip
13715 (name "r-polyclip")
13720 (uri (cran-uri "polyclip" version))
13723 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
13724 (build-system r-build-system)
13725 (native-inputs `(("pkg-config" ,pkg-config)))
13726 (home-page "http://www.angusj.com/delphi/clipper.php")
13727 (synopsis "Polygon clipping")
13729 "This package provides an R port of the library Clipper. It performs
13730 polygon clipping operations (intersection, union, set minus, set difference)
13731 for polygonal regions of arbitrary complexity, including holes. It computes
13732 offset polygons (spatial buffer zones, morphological dilations, Minkowski
13733 dilations) for polygonal regions and polygonal lines. It computes the
13734 Minkowski Sum of general polygons. There is a function for removing
13735 self-intersections from polygon data.")
13736 (license license:boost1.0)))
13738 (define-public r-urltools
13740 (name "r-urltools")
13745 (uri (cran-uri "urltools" version))
13748 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
13749 (build-system r-build-system)
13751 `(("r-rcpp" ,r-rcpp)
13752 ("r-triebeard" ,r-triebeard)))
13753 (home-page "https://github.com/Ironholds/urltools/")
13754 (synopsis "Vectorized tools for URL handling and parsing")
13756 "This package provides a toolkit for all URL-handling needs, including
13757 encoding and decoding, parsing, parameter extraction and modification. All
13758 functions are designed to be both fast and entirely vectorized. It is
13759 intended to be useful for people dealing with web-related datasets, such as
13760 server-side logs, although may be useful for other situations involving large
13762 (license license:expat)))
13764 (define-public r-ggforce
13771 (uri (cran-uri "ggforce" version))
13774 "118qyzy8h9kkkdpjd09667gxgw7xy1kbc8r87pswh54ixn8hymwk"))))
13775 (build-system r-build-system)
13777 `(("r-ggplot2" ,r-ggplot2)
13778 ("r-gtable" ,r-gtable)
13780 ("r-polyclip" ,r-polyclip)
13782 ("r-rcppeigen" ,r-rcppeigen)
13783 ("r-rlang" ,r-rlang)
13784 ("r-scales" ,r-scales)
13785 ("r-tidyselect" ,r-tidyselect)
13786 ("r-tweenr" ,r-tweenr)
13787 ("r-withr" ,r-withr)))
13788 (home-page "https://ggforce.data-imaginist.com")
13789 (synopsis "Accelerating ggplot2")
13791 "The aim of the ggplot2 package is to aid in visual data investigations.
13792 This focus has led to a lack of facilities for composing specialized plots.
13793 Thi package aims to be a collection of mainly new statistics and geometries
13794 that fills this gap.")
13795 (license license:expat)))
13797 (define-public r-europepmc
13799 (name "r-europepmc")
13804 (uri (cran-uri "europepmc" version))
13807 "1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
13808 (build-system r-build-system)
13810 `(("r-dplyr" ,r-dplyr)
13812 ("r-jsonlite" ,r-jsonlite)
13814 ("r-progress" ,r-progress)
13815 ("r-purrr" ,r-purrr)
13816 ("r-urltools" ,r-urltools)
13817 ("r-xml2" ,r-xml2)))
13818 (home-page "https://github.com/ropensci/europepmc/")
13819 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
13821 "This package provides an R Client for the
13822 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
13823 Service}. It gives access to both metadata on life science literature and
13824 open access full texts. Europe PMC indexes all PubMed content and other
13825 literature sources including Agricola, a bibliographic database of citations
13826 to the agricultural literature, or Biological Patents. In addition to
13827 bibliographic metadata, the client allows users to fetch citations and
13828 reference lists. Links between life-science literature and other EBI
13829 databases, including ENA, PDB or ChEMBL are also accessible.")
13830 (license license:gpl3)))
13832 (define-public r-ggraph
13839 (uri (cran-uri "ggraph" version))
13842 "0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c"))))
13843 (build-system r-build-system)
13845 `(("r-digest" ,r-digest)
13846 ("r-dplyr" ,r-dplyr)
13847 ("r-ggforce" ,r-ggforce)
13848 ("r-ggplot2" ,r-ggplot2)
13849 ("r-ggrepel" ,r-ggrepel)
13850 ("r-gtable" ,r-gtable)
13851 ("r-igraph" ,r-igraph)
13855 ("r-scales" ,r-scales)
13856 ("r-viridis" ,r-viridis)))
13857 (home-page "https://cran.r-project.org/web/packages/ggraph/")
13858 (synopsis "Implementation of grammar of graphics for graphs and networks")
13860 "The grammar of graphics as implemented in ggplot2 is a poor fit for
13861 graph and network visualizations due to its reliance on tabular data input.
13862 The ggraph package is an extension of the ggplot2 API tailored to graph
13863 visualizations and provides the same flexible approach to building up plots
13865 (license license:gpl3)))
13867 (define-public r-varselrf
13869 (name "r-varselrf")
13874 (uri (cran-uri "varSelRF" version))
13877 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
13878 (properties `((upstream-name . "varSelRF")))
13879 (build-system r-build-system)
13881 `(("r-randomforest" ,r-randomforest)))
13882 (home-page "http://ligarto.org/rdiaz/Software/Software.html")
13883 (synopsis "Variable selection using random forests")
13885 "This package provides tools for the variable selection from random
13886 forests using both backwards variable elimination (for the selection of small
13887 sets of non-redundant variables) and selection based on the importance
13888 spectrum (somewhat similar to scree plots; for the selection of large,
13889 potentially highly-correlated variables). The main applications are in
13890 high-dimensional data (e.g., microarray data, and other genomics and
13891 proteomics applications).")
13892 (license license:gpl2+)))
13894 (define-public r-pamr
13901 (uri (cran-uri "pamr" version))
13904 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
13905 (build-system r-build-system)
13907 `(("r-cluster" ,r-cluster)
13908 ("r-survival" ,r-survival)))
13909 (native-inputs `(("gfortran" ,gfortran)))
13910 (home-page "https://cran.r-project.org/web/packages/pamr/")
13911 (synopsis "Prediction Analysis for Microarrays")
13913 "This package provides some functions for sample classification in
13915 (license license:gpl2)))
13917 (define-public r-rda
13920 (version "1.0.2-2.1")
13924 (uri (cran-uri "rda" version))
13927 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
13928 (build-system r-build-system)
13929 (home-page "https://cran.r-project.org/web/packages/rda/")
13930 (synopsis "Shrunken centroids regularized discriminant analysis")
13932 "This package provides tools for shrunken centroids regularized
13933 discriminant analysis for the purpose of classifying high dimensional data.")
13934 (license license:gpl2+)))
13936 (define-public r-ggvis
13943 (uri (cran-uri "ggvis" version))
13946 "1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk"))))
13947 (build-system r-build-system)
13949 `(("r-assertthat" ,r-assertthat)
13950 ("r-dplyr" ,r-dplyr)
13951 ("r-htmltools" ,r-htmltools)
13952 ("r-jsonlite" ,r-jsonlite)
13953 ("r-lazyeval" ,r-lazyeval)
13954 ("r-magrittr" ,r-magrittr)
13955 ("r-shiny" ,r-shiny)))
13956 (home-page "https://ggvis.rstudio.com/")
13957 (synopsis "Interactive grammar of graphics")
13959 "This package is a data visualization package for R providing an
13960 implementation of an interactive grammar of graphics, taking the best parts of
13961 ggplot2, combining them with the reactive framework of Shiny and drawing web
13962 graphics using Vega.")
13963 (license license:gpl2)))
13965 (define-public r-gbm
13972 (uri (cran-uri "gbm" version))
13975 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
13976 (build-system r-build-system)
13978 `(("r-gridextra" ,r-gridextra)
13979 ("r-lattice" ,r-lattice)
13980 ("r-survival" ,r-survival)))
13981 (home-page "https://github.com/gbm-developers/gbm")
13982 (synopsis "Generalized boosted regression models")
13984 "This package is an implementation of extensions to Freund and Schapire's
13985 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
13986 regression methods for least squares, absolute loss, t-distribution loss,
13987 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
13988 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
13989 and Learning to Rank measures (LambdaMart).")
13990 (license license:gpl2+)))
13992 (define-public r-threejs
13999 (uri (cran-uri "threejs" version))
14002 "1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
14003 (build-system r-build-system)
14005 `(#:modules ((guix build utils)
14006 (guix build r-build-system)
14010 (modify-phases %standard-phases
14011 (add-after 'unpack 'process-javascript
14012 (lambda* (#:key inputs #:allow-other-keys)
14013 (with-directory-excursion "inst"
14017 `((,(assoc-ref inputs "js-jquery")
14018 "htmlwidgets/lib/jquery/jquery.min.js")
14019 (,(assoc-ref inputs "js-threejs-85")
14020 "htmlwidgets/lib/threejs-85/three.min.js"))))
14021 (lambda (sources targets)
14022 (for-each (lambda (source target)
14023 (format #t "Processing ~a --> ~a~%"
14025 (delete-file target)
14026 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14027 (call-with-output-file target
14029 (dump-port minified port)))))
14030 sources targets))))
14033 `(("r-base64enc" ,r-base64enc)
14034 ("r-crosstalk" ,r-crosstalk)
14035 ("r-htmlwidgets" ,r-htmlwidgets)
14036 ("r-igraph" ,r-igraph)))
14038 `(("uglify-js" ,uglify-js)
14042 (uri "https://code.jquery.com/jquery-3.3.1.js")
14045 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
14049 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
14052 "17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
14053 (home-page "https://bwlewis.github.io/rthreejs")
14054 (synopsis "Interactive 3D scatter plots, networks and globes")
14056 "Create interactive 3D scatter plots, network plots, and globes in R
14057 using the three.js visualization library.")
14058 (license license:expat)))
14060 (define-public r-mlbench
14067 (uri (cran-uri "mlbench" version))
14070 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
14071 (build-system r-build-system)
14072 (home-page "https://cran.r-project.org/web/packages/mlbench/")
14073 (synopsis "Machine learning benchmark problems")
14075 "This package provides a collection of artificial and real-world machine
14076 learning benchmark problems, including, e.g., several data sets from the UCI
14078 (license license:gpl2)))
14080 (define-public r-mpm
14087 (uri (cran-uri "mpm" version))
14090 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
14091 (build-system r-build-system)
14093 `(("r-kernsmooth" ,r-kernsmooth)
14094 ("r-mass" ,r-mass)))
14095 (home-page "http://mpm.r-forge.r-project.org")
14096 (synopsis "Multivariate projection methods")
14098 "This is a package for exploratory graphical analysis of multivariate
14099 data, specifically gene expression data with different projection methods:
14100 principal component analysis, correspondence analysis, spectral map
14102 (license license:gpl2+)))
14104 (define-public r-png
14110 (uri (cran-uri "png" version))
14113 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
14114 (build-system r-build-system)
14116 `(("libpng" ,libpng)
14118 (home-page "http://www.rforge.net/png/")
14119 (synopsis "Read and write PNG images")
14121 "This package provides an easy and simple way to read, write and display
14122 bitmap images stored in the PNG format. It can read and write both files and
14123 in-memory raw vectors.")
14124 ;; Any of these GPL versions.
14125 (license (list license:gpl2 license:gpl3))))
14127 (define-public r-ggcorrplot
14129 (name "r-ggcorrplot")
14134 (uri (cran-uri "ggcorrplot" version))
14137 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
14138 (build-system r-build-system)
14140 `(("r-ggplot2" ,r-ggplot2)
14141 ("r-reshape2" ,r-reshape2)))
14142 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
14143 (synopsis "Visualization of a correlation matrix using ggplot2")
14145 "The ggcorrplot package can be used to visualize easily a correlation
14146 matrix using ggplot2. It provides a solution for reordering the correlation
14147 matrix and displays the significance level on the plot. It also includes a
14148 function for computing a matrix of correlation p-values.")
14149 (license license:gpl2)))
14151 (define-public r-flexdashboard
14153 (name "r-flexdashboard")
14154 (version "0.5.1.1")
14158 (uri (cran-uri "flexdashboard" version))
14161 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
14162 (build-system r-build-system)
14164 `(#:modules ((guix build utils)
14165 (guix build r-build-system)
14169 (ice-9 textual-ports))
14171 (modify-phases %standard-phases
14172 (add-after 'unpack 'process-javascript
14173 (lambda* (#:key inputs #:allow-other-keys)
14174 (with-directory-excursion "inst"
14175 ;; Concatenate all components of prism.js
14176 (let ((contents (string-join
14177 (map (lambda (name)
14178 (call-with-input-file
14179 (assoc-ref inputs name)
14183 "js-prism-line-numbers"))
14185 (call-with-output-file "prism-src.js"
14186 (cut display contents <>)))
14190 `(("www/stickytableheaders/jquery.stickytableheaders.js"
14191 "www/stickytableheaders/jquery.stickytableheaders.min.js")
14193 "www/sly/sly.min.js")
14195 "www/prism/prism.js")
14196 (,(assoc-ref inputs "js-raphael")
14197 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
14198 (,(assoc-ref inputs "js-featherlight")
14199 "www/featherlight/featherlight.min.js"))))
14200 (lambda (sources targets)
14201 (for-each (lambda (source target)
14202 (format #t "Processing ~a --> ~a~%"
14204 (delete-file target)
14205 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
14206 (call-with-output-file target
14208 (dump-port minified port)))))
14209 sources targets))))
14212 `(("r-htmltools" ,r-htmltools)
14213 ("r-htmlwidgets" ,r-htmlwidgets)
14214 ("r-jsonlite" ,r-jsonlite)
14215 ("r-knitr" ,r-knitr)
14216 ("r-rmarkdown" ,r-rmarkdown)
14217 ("r-shiny" ,r-shiny)))
14219 `(("uglify-js" ,uglify-js)
14223 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
14226 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
14230 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
14233 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
14237 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
14240 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
14241 ("js-prism-line-numbers"
14244 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
14247 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
14251 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
14254 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
14255 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
14256 (synopsis "R Markdown format for flexible dashboards")
14258 "This package provides an R Markdown format for converting an R Markdown
14259 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
14260 of its components to the containing web page.")
14261 (license license:expat)))
14263 (define-public r-preseqr
14270 (uri (cran-uri "preseqR" version))
14273 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
14274 (properties `((upstream-name . "preseqR")))
14275 (build-system r-build-system)
14277 `(("r-polynom" ,r-polynom)))
14278 (home-page "https://cran.r-project.org/web/packages/preseqR/")
14279 (synopsis "Predicting species accumulation curves")
14281 "This package can be used to predict the r-species accumulation
14282 curve (r-SAC), which is the number of species represented at least r times as
14283 a function of the sampling effort. When r = 1, the curve is known as the
14284 species accumulation curve, or the library complexity curve in high-throughput
14285 genomic sequencing. The package includes both parametric and nonparametric
14286 methods, as described by Deng C, et al. (2018).")
14287 (license license:gpl3)))
14289 (define-public r-mapplots
14291 (name "r-mapplots")
14296 (uri (cran-uri "mapplots" version))
14299 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
14300 (build-system r-build-system)
14301 (home-page "https://cran.r-project.org/web/packages/mapplots/")
14302 (synopsis "Data visualization on maps")
14304 "This package helps you create simple maps; add sub-plots like pie plots
14305 to a map or any other plot; format, plot and export gridded data. The package
14306 was developed for displaying fisheries data but most functions can be used for
14307 more generic data visualisation.")
14308 (license license:gpl2+)))
14310 (define-public r-pmcmr
14317 (uri (cran-uri "PMCMR" version))
14320 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
14321 (properties `((upstream-name . "PMCMR")))
14322 (build-system r-build-system)
14323 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
14324 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
14326 "This is a deprecated package for calculating pairwise multiple
14327 comparisons of mean rank sums. This package is superseded by the novel
14328 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
14329 compatibility of dependent packages for some time.")
14330 (license license:gpl3+)))
14332 (define-public r-downloader
14334 (name "r-downloader")
14339 (uri (cran-uri "downloader" version))
14342 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
14343 (build-system r-build-system)
14345 `(("r-digest" ,r-digest)))
14346 (home-page "https://github.com/wch/downloader")
14347 (synopsis "Download files over HTTP and HTTPS")
14349 "This package provides a wrapper for the @code{download.file} function,
14350 making it possible to download files over HTTPS across platforms. The
14351 @code{RCurl} package provides this functionality (and much more) but has
14352 external dependencies. This package has is implemented purely in R.")
14353 (license license:gpl2)))
14355 (define-public r-rex
14362 (uri (cran-uri "rex" version))
14365 "0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
14366 (build-system r-build-system)
14368 `(("r-lazyeval" ,r-lazyeval)
14369 ("r-magrittr" ,r-magrittr)))
14370 (home-page "https://github.com/kevinushey/rex")
14371 (synopsis "Friendly regular expressions")
14373 "This package provides a friendly interface for the construction of
14374 regular expressions. Regular expressions are a very powerful feature, however
14375 they are often difficult to interpret. Rex allows you to build complex
14376 regular expressions from human readable expressions")
14377 (license license:expat)))
14379 (define-public r-sctransform
14381 (name "r-sctransform")
14386 (uri (cran-uri "sctransform" version))
14389 "1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
14390 (build-system r-build-system)
14392 `(("r-future" ,r-future)
14393 ("r-future-apply" ,r-future-apply)
14394 ("r-ggplot2" ,r-ggplot2)
14395 ("r-gridextra" ,r-gridextra)
14397 ("r-matrix" ,r-matrix)
14399 ("r-rcppeigen" ,r-rcppeigen)
14400 ("r-reshape2" ,r-reshape2)))
14401 (home-page "https://github.com/ChristophH/sctransform")
14402 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
14404 "This package provides a normalization method for single-cell UMI count
14405 data using a variance stabilizing transformation. The transformation is based
14406 on a negative binomial regression model with regularized parameters. As part
14407 of the same regression framework, this package also provides functions for
14408 batch correction, and data correction.")
14409 (license license:gpl3)))
14411 (define-public r-styler
14418 (uri (cran-uri "styler" version))
14421 "1k660lpjvd64gnf6bndcb1cq3qxsvik928kcn6271zmkhja5rgyb"))))
14422 (build-system r-build-system)
14424 `(("r-backports" ,r-backports)
14426 ("r-magrittr" ,r-magrittr)
14427 ("r-purrr" ,r-purrr)
14428 ("r-rematch2" ,r-rematch2)
14429 ("r-rlang" ,r-rlang)
14430 ("r-rprojroot" ,r-rprojroot)
14431 ("r-tibble" ,r-tibble)
14432 ("r-withr" ,r-withr)
14433 ("r-xfun" ,r-xfun)))
14434 (home-page "https://github.com/r-lib/styler")
14435 (synopsis "Non-invasive pretty printing of R code")
14437 "This is a package for pretty-printing R code without changing the user's
14438 formatting intent.")
14439 (license license:gpl3)))
14441 (define-public r-scrime
14448 (uri (cran-uri "scrime" version))
14451 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
14452 (build-system r-build-system)
14453 (home-page "https://cran.r-project.org/web/packages/scrime/")
14454 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
14456 "This package provides tools for the analysis of high-dimensional data
14457 developed/implemented at the group \"Statistical Complexity Reduction In
14458 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
14459 the functions can also be applied to other types of categorical data.")
14460 (license license:gpl2)))
14462 (define-public r-pbmcapply
14464 (name "r-pbmcapply")
14469 (uri (cran-uri "pbmcapply" version))
14472 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
14473 (build-system r-build-system)
14474 (home-page "https://github.com/kvnkuang/pbmcapply")
14475 (synopsis "Track the progress of apply procedures with a progress bar")
14477 "This light-weight package helps you track and visualize the progress of
14478 parallel versions of vectorized R functions of the @code{mc*apply} family.")
14479 (license license:expat)))
14481 (define-public r-blme
14488 (uri (cran-uri "blme" version))
14491 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
14492 (build-system r-build-system)
14493 (propagated-inputs `(("r-lme4" ,r-lme4)))
14494 (home-page "https://github.com/vdorie/blme")
14495 (synopsis "Bayesian linear mixed-effects models")
14497 "This package provides tools for maximum a posteriori estimation for
14498 linear and generalized linear mixed-effects models in a Bayesian setting. It
14499 extends the lme4 package.")
14500 (license license:gpl2+)))
14502 (define-public r-batchtools
14504 (name "r-batchtools")
14509 (uri (cran-uri "batchtools" version))
14512 "02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
14513 (build-system r-build-system)
14515 `(("r-backports" ,r-backports)
14516 ("r-base64url" ,r-base64url)
14518 ("r-checkmate" ,r-checkmate)
14519 ("r-data-table" ,r-data-table)
14520 ("r-digest" ,r-digest)
14522 ("r-progress" ,r-progress)
14524 ("r-rappdirs" ,r-rappdirs)
14525 ("r-stringi" ,r-stringi)
14526 ("r-withr" ,r-withr)))
14527 (home-page "https://github.com/mllg/batchtools")
14528 (synopsis "Tools for computation on batch systems")
14530 "As a successor of the packages BatchJobs and BatchExperiments, this
14531 package provides a parallel implementation of the Map function for high
14532 performance computing systems managed by various schedulers. A multicore and
14533 socket mode allow the parallelization on a local machines, and multiple
14534 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
14535 the package provides an abstraction mechanism to define large-scale computer
14536 experiments in a well-organized and reproducible way.")
14537 (license license:lgpl3)))
14539 (define-public r-clue
14546 (uri (cran-uri "clue" version))
14549 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
14550 (build-system r-build-system)
14551 (propagated-inputs `(("r-cluster" ,r-cluster)))
14552 (home-page "https://cran.r-project.org/web/packages/clue/")
14553 (synopsis "Tools for analyzing cluster ensembles")
14554 (description "Cluster ensembles are collections of individual solutions to
14555 a given clustering problem which are useful or necessary to consider in a wide
14556 range of applications. This R package provides an extensible computational
14557 environment for creating and analyzing cluster ensembles, with basic data
14558 structures for representing partitions and hierarchies, and facilities for
14559 computing on them, including methods for measuring proximity and obtaining
14560 consensus and secondary clusterings.")
14561 (license license:gpl2)))
14563 (define-public r-sitmo
14570 (uri (cran-uri "sitmo" version))
14573 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
14574 (build-system r-build-system)
14575 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14576 (home-page "https://github.com/coatless/sitmo/")
14577 (synopsis "Parallel pseudo random number generator header files")
14579 "This package provides two high quality and fast PPRNGs that may be used
14580 in an OpenMP parallel environment. In addition, there is a generator for one
14581 dimensional low-discrepancy sequence.")
14582 (license license:expat)))
14584 (define-public r-dqrng
14591 (uri (cran-uri "dqrng" version))
14594 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
14595 (build-system r-build-system)
14599 ("r-sitmo" ,r-sitmo)))
14600 (home-page "https://www.daqana.org/dqrng")
14601 (synopsis "Fast pseudo random number generators")
14603 "Several fast random number generators are provided as C++ header-only
14604 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
14605 Additionally, fast functions for generating random numbers according to a
14606 uniform, normal and exponential distribution are included. The latter two use
14607 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
14608 functions are exported to R and as a C++ interface and are enabled for use
14609 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
14610 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
14611 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
14612 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
14613 ;; whole is distributed under the terms of the AGPL 3.
14614 (license license:agpl3)))
14616 (define-public r-dalex
14623 (uri (cran-uri "DALEX" version))
14626 "04i17ni8g595jj8dxdfwr9vsxmdn2kkam90ab68vlwws3ywqjl6r"))))
14627 (properties `((upstream-name . "DALEX")))
14628 (build-system r-build-system)
14629 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
14630 (home-page "https://pbiecek.github.io/DALEX/")
14631 (synopsis "Descriptive machine learning explanations")
14633 "Machine Learning models are widely used and have various applications in
14634 classification or regression. Models created with boosting, bagging, stacking
14635 or similar techniques are often used due to their high performance, but such
14636 black-box models usually lack interpretability. The DALEX package contains
14637 various explainers that help to understand the link between input variables
14638 and model output.")
14639 ;; Any version of the GPL
14640 (license license:gpl3+)))
14642 (define-public r-enrichr
14649 (uri (cran-uri "enrichR" version))
14652 "056m6hksfss29fj7zvlk7pbh8g3gq84kjh3240isrsnhp9m1h9iz"))))
14653 (properties `((upstream-name . "enrichR")))
14654 (build-system r-build-system)
14656 `(("r-httr" ,r-httr)
14657 ("r-rjson" ,r-rjson)))
14658 (home-page "https://cran.r-project.org/web/packages/enrichR/")
14659 (synopsis "R Interface to Enrichr database for analyzing gene sets")
14661 "This package provides an R interface to all Enrichr databases, a
14662 web-based tool for analyzing gene sets and returns any enrichment of common
14663 annotated biological functions.")
14664 (license license:gpl2+)))
14666 (define-public r-plot3d
14673 (uri (cran-uri "plot3D" version))
14676 "0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
14677 (properties `((upstream-name . "plot3D")))
14678 (build-system r-build-system)
14679 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
14680 (home-page "https://cran.r-project.org/web/packages/plot3D")
14681 (synopsis "Plot multi-dimensional data")
14683 "This package provides functions for viewing 2D and 3D data, including
14684 perspective plots, slice plots, surface plots, scatter plots, etc. It
14685 includes data sets from oceanography.")
14686 (license license:gpl3+)))
14688 (define-public r-ggfortify
14690 (name "r-ggfortify")
14695 (uri (cran-uri "ggfortify" version))
14698 "1wk9j0xg5hj9i1vf62qjiphv8cbsgq7y6baay3pfl3wyb2dwgci0"))))
14699 (build-system r-build-system)
14701 `(("r-dplyr" ,r-dplyr)
14702 ("r-ggplot2" ,r-ggplot2)
14703 ("r-gridextra" ,r-gridextra)
14704 ("r-scales" ,r-scales)
14705 ("r-stringr" ,r-stringr)
14706 ("r-tibble" ,r-tibble)
14707 ("r-tidyr" ,r-tidyr)))
14708 (home-page "https://github.com/sinhrks/ggfortify")
14709 (synopsis "Data visualization tools for statistical analysis results")
14711 "This package provides unified plotting tools for statistics commonly
14712 used, such as GLM, time series, PCA families, clustering and survival
14713 analysis. The package offers a single plotting interface for these analysis
14714 results and plots in a unified style using the @code{ggplot2} package.")
14715 (license license:gpl2)))
14717 (define-public r-refmanager
14719 (name "r-refmanager")
14724 (uri (cran-uri "RefManageR" version))
14727 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
14728 (properties `((upstream-name . "RefManageR")))
14729 (build-system r-build-system)
14731 `(("r-bibtex" ,r-bibtex)
14733 ("r-jsonlite" ,r-jsonlite)
14734 ("r-lubridate" ,r-lubridate)
14736 ("r-stringr" ,r-stringr)
14737 ("r-xml2" ,r-xml2)))
14738 (home-page "https://github.com/ropensci/RefManageR/")
14739 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
14741 "This package provides tools for importing and working with bibliographic
14742 references. It greatly enhances the @code{bibentry} class by providing a
14743 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
14744 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
14745 by various formats for name lists (author by last names, translator by full
14746 names, etc.). Entries can be updated, combined, sorted, printed in a number
14747 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
14748 into R and converted to @code{BibEntry} objects.")
14749 ;; Any of these licenses may be picked.
14750 (license (list license:gpl2 license:gpl3 license:bsd-3))))
14752 (define-public r-citr
14759 (uri (cran-uri "citr" version))
14762 "0p2sg0fl7cppxxmr20qyqzs2469kglmgpsvykynw4qx501as57rc"))))
14763 (build-system r-build-system)
14765 `(("r-assertthat" ,r-assertthat)
14768 ("r-miniui" ,r-miniui)
14769 ("r-refmanager" ,r-refmanager)
14770 ("r-rstudioapi" ,r-rstudioapi)
14771 ("r-shiny" ,r-shiny)
14772 ("r-shinyjs" ,r-shinyjs)
14773 ("r-yaml" ,r-yaml)))
14774 (home-page "https://github.com/crsh/citr")
14775 (synopsis "RStudio add-in to insert Markdown citations")
14777 "This package provides functions and an RStudio add-in that search a
14778 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
14779 the current document.")
14780 (license license:expat)))
14782 (define-public r-xgboost
14785 (version "0.90.0.2")
14789 (uri (cran-uri "xgboost" version))
14792 "1gy9rzg43mjpfis893vf15drmbigfn0481zrzss9ajnmnk0q8194"))))
14793 (build-system r-build-system)
14795 `(("r-data-table" ,r-data-table)
14796 ("r-magrittr" ,r-magrittr)
14797 ("r-matrix" ,r-matrix)
14798 ("r-stringi" ,r-stringi)))
14799 (home-page "https://github.com/dmlc/xgboost")
14800 (synopsis "Extreme gradient boosting")
14802 "This package provides an R interface to Extreme Gradient Boosting, which
14803 is an efficient implementation of the gradient boosting framework from Chen
14804 and Guestrin (2016). The package includes efficient linear model solver and
14805 tree learning algorithms. The package can automatically do parallel
14806 computation on a single machine. It supports various objective functions,
14807 including regression, classification and ranking. The package is made to be
14808 extensible, so that users are also allowed to define their own objectives
14810 (license license:asl2.0)))
14812 (define-public r-umap
14815 (version "0.2.2.0")
14819 (uri (cran-uri "umap" version))
14822 "1s82w9gy1387h7cprjfbhp49l89zbmn3gc9s0wzqb1s73nza9n31"))))
14823 (build-system r-build-system)
14825 `(("r-rcpp" ,r-rcpp)
14826 ("r-reticulate" ,r-reticulate)
14827 ("r-rspectra" ,r-rspectra)))
14828 (home-page "https://github.com/tkonopka/umap")
14829 (synopsis "Uniform manifold approximation and projection")
14831 "Uniform manifold approximation and projection is a technique for
14832 dimension reduction. This package provides an interface to the UMAP algorithm
14833 in R, including a translation of the original algorithm into R.")
14834 (license license:expat)))
14836 (define-public r-uwot
14843 (uri (cran-uri "uwot" version))
14846 "1mq6qi8q9xslh1b99srj480s2a08pfv4bs9m2ykyijj44j9fcdj9"))))
14847 (build-system r-build-system)
14849 `(("r-dqrng" ,r-dqrng)
14851 ("r-irlba" ,r-irlba)
14852 ("r-matrix" ,r-matrix)
14854 ("r-rcppannoy" ,r-rcppannoy)
14855 ("r-rcppparallel" ,r-rcppparallel)
14856 ("r-rcppprogress" ,r-rcppprogress)
14857 ("r-rspectra" ,r-rspectra)))
14858 (home-page "https://github.com/jlmelville/uwot")
14859 (synopsis "Uniform manifold approximation and projection")
14861 "This package provides an implementation of the Uniform Manifold
14862 Approximation and Projection dimensionality reduction by McInnes et
14863 al. (2018). It also provides means to transform new data and to carry out
14864 supervised dimensionality reduction. An implementation of the related
14865 LargeVis method of Tang et al. (2016) is also provided.")
14866 (license license:gpl3)))
14868 (define-public r-kableextra
14870 (name "r-kableextra")
14875 (uri (cran-uri "kableExtra" version))
14878 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
14879 (properties `((upstream-name . "kableExtra")))
14880 (build-system r-build-system)
14882 `(("r-digest" ,r-digest)
14884 ("r-htmltools" ,r-htmltools)
14885 ("r-knitr" ,r-knitr)
14886 ("r-magrittr" ,r-magrittr)
14887 ("r-readr" ,r-readr)
14888 ("r-rmarkdown" ,r-rmarkdown)
14889 ("r-rstudioapi" ,r-rstudioapi)
14890 ("r-rvest" ,r-rvest)
14891 ("r-scales" ,r-scales)
14892 ("r-stringr" ,r-stringr)
14893 ("r-viridislite" ,r-viridislite)
14894 ("r-webshot" ,r-webshot)
14895 ("r-xml2" ,r-xml2)))
14896 (home-page "https://haozhu233.github.io/kableExtra/")
14897 (synopsis "Construct complex tables with pipe syntax")
14899 "Build complex HTML or LaTeX tables using @code{kable()} from
14900 @code{knitr} and the piping syntax from @code{magrittr}. The function
14901 @code{kable()} is a light weight table generator coming from @code{knitr}.
14902 This package simplifies the way to manipulate the HTML or LaTeX codes
14903 generated by @code{kable()} and allows users to construct complex tables and
14904 customize styles using a readable syntax.")
14905 (license license:expat)))
14907 (define-public r-glasso
14914 (uri (cran-uri "glasso" version))
14917 "0nshpx14v2yny7lr8ll6nnz71n0f02sddh2c2dglfprbk89p9yp6"))))
14918 (build-system r-build-system)
14919 (native-inputs `(("gfortran" ,gfortran)))
14920 (home-page "http://www-stat.stanford.edu/~tibs/glasso")
14921 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
14923 "This is a package for estimation of a sparse inverse covariance matrix
14924 using a lasso (L1) penalty. Facilities are provided for estimates along a
14925 path of values for the regularization parameter.")
14926 (license license:gpl2)))
14928 (define-public r-rhpcblasctl
14930 (name "r-rhpcblasctl")
14931 (version "0.18-205")
14935 (uri (cran-uri "RhpcBLASctl" version))
14938 "1ls2286fvrp1g7p8v4l6axznychh3qndranfpzqz806cm9ml1cdp"))))
14939 (properties `((upstream-name . "RhpcBLASctl")))
14940 (build-system r-build-system)
14941 (home-page "http://prs.ism.ac.jp/~nakama/Rhpc/")
14942 (synopsis "Control the number of threads on BLAS")
14944 "This package allows you to control the number of threads the BLAS
14945 library uses. It is also possible to control the number of threads in
14947 (license license:agpl3+)))
14949 (define-public r-lda
14956 (uri (cran-uri "lda" version))
14959 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
14960 (build-system r-build-system)
14961 (home-page "https://cran.r-project.org/web/packages/lda/")
14962 (synopsis "Collapsed Gibbs sampling methods for topic models")
14964 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
14965 related models. This includes (but is not limited to) sLDA, corrLDA, and the
14966 mixed-membership stochastic blockmodel. Inference for all of these models is
14967 implemented via a fast collapsed Gibbs sampler written in C. Utility
14968 functions for reading/writing data typically used in topic models, as well as
14969 tools for examining posterior distributions are also included.")
14970 ;; Any version of the LGPL
14971 (license license:lgpl3+)))
14973 (define-public r-rann-l1
14980 (uri (cran-uri "RANN.L1" version))
14983 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
14984 (properties `((upstream-name . "RANN.L1")))
14985 (build-system r-build-system)
14986 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
14987 (synopsis "Fast nearest neighbour search using L1 metric")
14989 "This package provides tools to find the k nearest neighbours for every
14990 point in a given dataset in O(N log N) time using Arya and Mount's ANN
14991 library. There is support for approximate as well as exact searches, fixed
14992 radius searches and @code{bd} as well as @code{kd} trees. The distance is
14993 computed using the L1 (Manhattan, taxicab) metric.")
14994 (license license:gpl3+)))
14996 (define-public r-patchwork
14997 ;; There has been no public release yet.
14998 (let ((commit "fd7958bae3e7a1e30237c751952e412a0a1d1242")
15001 (name "r-patchwork")
15002 (version (git-version "0.0.1" revision commit))
15006 (uri (git-reference
15007 (url "https://github.com/thomasp85/patchwork.git")
15009 (file-name (git-file-name name version))
15012 "00fq520xwy1ysg4k8x48x9b0yy9wyi8y8zj6dvxjg4bwx0yyp6s4"))))
15013 (build-system r-build-system)
15015 `(("r-ggplot2" ,r-ggplot2)
15016 ("r-gtable" ,r-gtable)))
15017 (home-page "https://github.com/thomasp85/patchwork")
15018 (synopsis "Compose ggplot2 plots")
15020 "The @code{ggplot2} package provides a strong API for sequentially
15021 building up a plot, but does not concern itself with composition of multiple
15022 plots. Patchwork is a package that expands the API to allow for arbitrarily
15023 complex composition of plots by providing mathmatical operators for combining
15025 (license license:expat))))
15027 (define-public r-liger
15034 (uri (git-reference
15035 (url "https://github.com/MacoskoLab/liger.git")
15036 (commit (string-append "v" version))))
15037 (file-name (git-file-name name version))
15040 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
15041 (modules '((guix build utils)))
15044 (delete-file "inst/java/ModularityOptimizer.jar")
15046 (build-system r-build-system)
15049 (modify-phases %standard-phases
15050 (add-after 'unpack 'build-java-part
15051 (lambda* (#:key inputs #:allow-other-keys)
15052 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
15053 (for-each (lambda (file) (invoke "javac" file))
15054 (find-files "." "\\.java$"))
15055 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
15056 (find-files "." "\\.class$"))
15059 `(("r-cowplot" ,r-cowplot)
15060 ("r-dosnow" ,r-dosnow)
15061 ("r-dplyr" ,r-dplyr)
15063 ("r-foreach" ,r-foreach)
15064 ("r-ggplot2" ,r-ggplot2)
15065 ("r-ggrepel" ,r-ggrepel)
15066 ("r-hmisc" ,r-hmisc)
15068 ("r-irlba" ,r-irlba)
15069 ("r-matrix" ,r-matrix)
15070 ("r-mclust" ,r-mclust)
15071 ("r-patchwork" ,r-patchwork)
15073 ("r-rann-l1" ,r-rann-l1)
15075 ("r-rcpparmadillo" ,r-rcpparmadillo)
15076 ("r-riverplot" ,r-riverplot)
15077 ("r-rtsne" ,r-rtsne)
15078 ("r-snow" ,r-snow)))
15080 `(("jdk" ,icedtea "jdk")
15081 ;; See https://github.com/MacoskoLab/liger/issues/96
15082 ;; The optimizer is released under the Expat license.
15086 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
15089 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
15091 ("r-knitr" ,r-knitr))) ; for vignettes
15092 (home-page "https://github.com/MacoskoLab/liger")
15093 (synopsis "Integrate and analyze multiple single-cell datasets")
15095 "LIGER is a package for integrating and analyzing multiple single-cell
15096 datasets, developed and maintained by the Macosko lab. It relies on
15097 integrative non-negative matrix factorization to identify shared and
15098 dataset-specific factors.")
15099 (license license:gpl3)))