1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
5 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
6 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
8 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
9 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
10 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
11 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
12 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
13 ;;; Copyright © 2018, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
14 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
15 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
16 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
17 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
18 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
19 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
20 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
21 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
22 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
23 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
25 ;;; This file is part of GNU Guix.
27 ;;; GNU Guix is free software; you can redistribute it and/or modify it
28 ;;; under the terms of the GNU General Public License as published by
29 ;;; the Free Software Foundation; either version 3 of the License, or (at
30 ;;; your option) any later version.
32 ;;; GNU Guix is distributed in the hope that it will be useful, but
33 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
34 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
35 ;;; GNU General Public License for more details.
37 ;;; You should have received a copy of the GNU General Public License
38 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
40 (define-module (gnu packages cran)
41 #:use-module ((guix licenses) #:prefix license:)
42 #:use-module (guix packages)
43 #:use-module (guix download)
44 #:use-module (guix git-download)
45 #:use-module (guix utils)
46 #:use-module (guix build-system r)
47 #:use-module (gnu packages algebra)
48 #:use-module (gnu packages autotools)
49 #:use-module (gnu packages base)
50 #:use-module (gnu packages bioinformatics)
51 #:use-module (gnu packages c)
52 #:use-module (gnu packages compression)
53 #:use-module (gnu packages curl)
54 #:use-module (gnu packages databases)
55 #:use-module (gnu packages fontutils)
56 #:use-module (gnu packages gcc)
57 #:use-module (gnu packages geo)
58 #:use-module (gnu packages ghostscript)
59 #:use-module (gnu packages gl)
60 #:use-module (gnu packages gnome)
61 #:use-module (gnu packages graph)
62 #:use-module (gnu packages gtk)
63 #:use-module (gnu packages haskell-xyz)
64 #:use-module (gnu packages icu4c)
65 #:use-module (gnu packages image)
66 #:use-module (gnu packages imagemagick)
67 #:use-module (gnu packages java)
68 #:use-module (gnu packages javascript)
69 #:use-module (gnu packages lisp-xyz)
70 #:use-module (gnu packages machine-learning)
71 #:use-module (gnu packages maths)
72 #:use-module (gnu packages mpi)
73 #:use-module (gnu packages multiprecision)
74 #:use-module (gnu packages networking)
75 #:use-module (gnu packages node)
76 #:use-module (gnu packages pcre)
77 #:use-module (gnu packages perl)
78 #:use-module (gnu packages pkg-config)
79 #:use-module (gnu packages pulseaudio) ;libsndfile
80 #:use-module (gnu packages python)
81 #:use-module (gnu packages python-xyz)
82 #:use-module (gnu packages statistics)
83 #:use-module (gnu packages tcl)
84 #:use-module (gnu packages tls)
85 #:use-module (gnu packages web)
86 #:use-module (gnu packages xorg))
88 (define-public r-bezier
94 (uri (cran-uri "bezier" version))
97 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
98 (build-system r-build-system)
99 (home-page "https://cran.r-project.org/web/packages/bezier/")
100 (synopsis "Bezier curve and spline toolkit")
102 "This package is a toolkit for working with Bezier curves and splines.
103 The package provides functions for point generation, arc length estimation,
104 degree elevation and curve fitting.")
105 (license license:gpl2+)))
114 (uri (cran-uri "V8" version))
117 "0z0dwa538lkggawiwrlplz698xznzlgv9fwhdslm7g7gdxyf0xgm"))))
118 (properties `((upstream-name . "V8")))
119 (build-system r-build-system)
122 (modify-phases %standard-phases
123 (add-after 'unpack 'find-v8
124 (lambda* (#:key inputs #:allow-other-keys)
125 (substitute* "configure"
127 (string-append "PKG_LIBS="
128 (assoc-ref inputs "node")
129 "/lib/libnode.so.64\n")))
130 (setenv "INCLUDE_DIR"
132 (assoc-ref inputs "node")
136 (assoc-ref inputs "node") "/lib"))
139 `(("node" ,libnode)))
142 ("r-jsonlite" ,r-jsonlite)
145 `(("r-knitr" ,r-knitr)))
146 (home-page "https://jeroen.cran.dev/V8")
147 (synopsis "Embedded JavaScript and WebAssembly engine for R")
149 "This package provides an R interface to V8: Google's JavaScript and
150 WebAssembly engine.")
151 (license license:expat)))
160 (uri (cran-uri "DOT" version))
163 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
164 (properties `((upstream-name . "DOT")))
165 (build-system r-build-system)
168 (home-page "http://haghish.com/dot")
169 (synopsis "Render and Export DOT Graphs in R")
171 "This package provides tools to render DOT diagram markup language in R
172 and also provides the possibility to export the graphs in PostScript and
173 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
174 programming packages such as @code{knitr} and @code{rmarkdown}.")
175 (license license:expat)))
177 (define-public r-clipr
184 (uri (cran-uri "clipr" version))
187 "1qn2p13d0c1bpqss6mv9hk60980rzhznfqpyaf5x0fy65svy9903"))))
188 (build-system r-build-system)
189 (home-page "https://github.com/mdlincoln/clipr")
190 (synopsis "Read and write from the system clipboard")
192 "This package provides simple utility functions to read from and write to
193 the system clipboards.")
194 (license license:gpl3)))
202 (uri (cran-uri "zoo" version))
205 "1rrw431jwaxd9xljp73f15rhcxvwc0xlyrmr0ghi5fj7a03c932f"))))
206 (build-system r-build-system)
208 `(("r-lattice" ,r-lattice)))
209 (home-page "http://zoo.R-Forge.R-project.org/")
210 (synopsis "S3 infrastructure for regular and irregular time series")
211 (description "This package contains an S3 class with methods for totally
212 ordered indexed observations. It is particularly aimed at irregular time
213 series of numeric vectors/matrices and factors.")
214 (license license:gpl2+)))
216 (define-public r-ggpmisc
222 (uri (cran-uri "ggpmisc" version))
225 "0ma2d3a3v8n85sghxr9anl6vgbs8gi82i1dllw99n81gsm59wgin"))))
226 (build-system r-build-system)
228 `(("r-broom" ,r-broom)
230 ("r-ggplot2" ,r-ggplot2)
231 ("r-gridextra" ,r-gridextra)
232 ("r-lubridate" ,r-lubridate)
233 ("r-magrittr" ,r-magrittr)
236 ("r-polynom" ,r-polynom)
238 ("r-scales" ,r-scales)
239 ("r-splus2r" ,r-splus2r)
240 ("r-stringr" ,r-stringr)
241 ("r-tibble" ,r-tibble)
245 `(("r-knitr" ,r-knitr)))
246 (home-page "https://www.r4photobiology.info/")
247 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
248 (description "This package provides extensions to @code{ggplot2},
249 respecting the grammar of its graphics paradigm.")
250 (license license:gpl2+)))
252 (define-public r-gprofiler
259 (uri (cran-uri "gProfileR" version))
262 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
263 (properties `((upstream-name . "gProfileR")))
264 (build-system r-build-system)
267 ("r-rcurl" ,r-rcurl)))
268 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
269 (synopsis "Interface to the g:Profiler toolkit")
271 "This package provides tools for functional enrichment analysis,
272 gene identifier conversion and mapping homologous genes across related
273 organisms via the @code{g:Profiler} toolkit.")
274 (license license:gpl2+)))
276 (define-public r-gprofiler2
278 (name "r-gprofiler2")
283 (uri (cran-uri "gprofiler2" version))
286 "112hmmvdwg8xz90w1bsbzc55y4xi9jj4dqy0q4bsgp49x58r92rb"))))
287 (properties `((upstream-name . "gprofiler2")))
288 (build-system r-build-system)
290 `(("r-crosstalk" ,r-crosstalk)
292 ("r-ggplot2" ,r-ggplot2)
293 ("r-gridextra" ,r-gridextra)
294 ("r-jsonlite" ,r-jsonlite)
295 ("r-plotly" ,r-plotly)
298 ("r-viridislite" ,r-viridislite)))
299 (native-inputs `(("r-knitr" ,r-knitr)))
300 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
301 (synopsis "Interface to the g:Profiler toolset")
303 "This package provides a toolset for functional enrichment analysis and
304 visualization, gene/protein/SNP identifier conversion and mapping orthologous
305 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
309 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
311 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
313 @item @code{g:Orth}, orthology search across species;
314 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
315 genes and variant effects.
318 This package is an R interface corresponding to the 2019 update of
319 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
321 (license license:gpl2+)))
323 (define-public r-oenb
330 (uri (cran-uri "oenb" version))
333 "1x1jlqp6r27c4gb7wafzpmh5rq6yq61a2d395r5lsmv2g5jb4biz"))))
334 (properties `((upstream-name . "oenb")))
335 (build-system r-build-system)
337 `(("r-dplyr" ,r-dplyr)
339 (native-inputs `(("r-knitr" ,r-knitr)))
340 (home-page "https://github.com/franzmohr/oenb")
341 (synopsis "Tools for the OeNB Data Web Service")
343 "Tools to access data from the data web service of the
344 @acronym{OeNB, Oesterreichische Nationalbank},
345 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
346 (license license:gpl2+)))
348 (define-public r-scales
355 (uri (cran-uri "scales" version))
357 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
358 (build-system r-build-system)
360 `(("r-farver" ,r-farver)
361 ("r-labeling" ,r-labeling)
362 ("r-lifecycle" ,r-lifecycle)
363 ("r-munsell" ,r-munsell)
364 ("r-rcolorbrewer" ,r-rcolorbrewer)
366 ("r-viridislite" ,r-viridislite)))
367 (home-page "https://github.com/hadley/scales")
368 (synopsis "Scale functions for visualization")
370 "This package provides graphical scales that map data to aesthetics, and
371 provides methods for automatically determining breaks and labels for axes and
373 (license license:expat)))
375 (define-public r-pheatmap
382 (uri (cran-uri "pheatmap" version))
385 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
386 (build-system r-build-system)
388 `(("r-gtable" ,r-gtable)
389 ("r-rcolorbrewer" ,r-rcolorbrewer)
390 ("r-scales" ,r-scales)))
391 (home-page "https://cran.r-project.org/web/packages/pheatmap")
392 (synopsis "Pretty heatmaps")
394 "This package provides an implementation of heatmaps that offers more
395 control over dimensions and appearance.")
396 (license license:gpl2+)))
404 (uri (cran-uri "ecp" version))
407 "11f9p869xr0zg779i46gmflxlq4xclk9wxbab0nj2fan26pn4sfy"))))
408 (build-system r-build-system)
410 `(("r-rcpp" ,r-rcpp)))
411 (home-page "https://cran.r-project.org/web/packages/ecp/")
412 (synopsis "Multiple change-point analysis of multivariate data")
414 "This package implements various procedures for finding multiple
415 change-points. Two methods make use of dynamic programming and pruning, with
416 no distributional assumptions other than the existence of certain absolute
417 moments in one method. Hierarchical and exact search methods are included.
418 All methods return the set of estimated change-points as well as other summary
420 (license license:gpl2+)))
422 (define-public r-ellipsis
429 (uri (cran-uri "ellipsis" version))
432 "1nvmkcca57d9067rcggw1gby80ibx5hplk2myz0cs9zwilaib2jg"))))
433 (build-system r-build-system)
435 `(("r-rlang" ,r-rlang)))
436 (home-page "https://github.com/hadley/ellipsis")
437 (synopsis "Tools for working with additional arguments")
439 "In S3 generics, it's useful to take @code{...} so that methods can have
440 additional arguments. But this flexibility comes at a cost: misspelled
441 arguments will be silently ignored. The @code{ellipsis} package is an
442 experiment that allows a generic to warn if any arguments passed in @code{...}
444 (license license:gpl3)))
453 (uri (cran-uri "grr" version))
456 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
457 (build-system r-build-system)
458 (home-page "https://cran.r-project.org/web/packages/grr")
459 (synopsis "Alternative implementations of base R functions")
461 "This package provides alternative implementations of some base R
462 functions, including @code{sort}, @code{order}, and @code{match}. The
463 functions are simplified but can be faster or have other advantages.")
464 (license license:gpl3)))
466 (define-public r-matrix-utils
468 (name "r-matrix-utils")
473 (uri (cran-uri "Matrix.utils" version))
476 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
477 (properties `((upstream-name . "Matrix.utils")))
478 (build-system r-build-system)
481 ("r-matrix" ,r-matrix)))
482 (home-page "https://github.com/cvarrichio/Matrix.utils")
484 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
486 "This package implements data manipulation methods such as @code{cast},
487 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
489 (license license:gpl3)))
498 (uri (cran-uri "sys" version))
501 "14wvy46i2iz9jn7lj3cvifmps932s3395wq681hniva0f8m7q8d6"))))
502 (build-system r-build-system)
503 (home-page "https://github.com/jeroen/sys")
504 (synopsis "Powerful and reliable tools for running system commands in R")
506 "This package provides drop-in replacements for the base @code{system2()}
507 function with fine control and consistent behavior across platforms. It
508 supports clean interruption, timeout, background tasks, and streaming STDIN /
509 STDOUT / STDERR over binary or text connections. The package also provides
510 functions for evaluating expressions inside a temporary fork. Such
511 evaluations have no side effects on the main R process, and support reliable
512 interrupts and timeouts. This provides the basis for a sandboxing
514 (license license:expat)))
516 (define-public r-askpass
523 (uri (cran-uri "askpass" version))
526 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
527 (build-system r-build-system)
528 (propagated-inputs `(("r-sys" ,r-sys)))
529 (home-page "https://github.com/jeroen/askpass")
530 (synopsis "Safe password entry for R")
532 "This package provides cross-platform utilities for prompting the user
533 for credentials or a passphrase, for example to authenticate with a server or
534 read a protected key.")
535 (license license:expat)))
537 (define-public r-vegan
544 (uri (cran-uri "vegan" version))
547 "0g60rgn1i7wqf9pf5m1yki1m45gcp7i5hmjic0ci0f6vng70mh5k"))))
548 (build-system r-build-system)
550 `(("gfortran" ,gfortran)))
552 `(("r-cluster" ,r-cluster)
553 ("r-knitr" ,r-knitr) ; needed for vignettes
554 ("r-lattice" ,r-lattice)
557 ("r-permute" ,r-permute)))
558 (home-page "https://cran.r-project.org/web/packages/vegan")
559 (synopsis "Functions for community ecology")
561 "The vegan package provides tools for descriptive community ecology. It
562 has most basic functions of diversity analysis, community ordination and
563 dissimilarity analysis. Most of its multivariate tools can be used for other
564 data types as well.")
565 (license license:gpl2+)))
567 (define-public r-tidyverse
574 (uri (cran-uri "tidyverse" version))
577 "02gyys08qv2v4cl2d66gml4d31ipxay0iyfwwksvxyclx60wp2kd"))))
578 (build-system r-build-system)
580 `(("r-broom" ,r-broom)
582 ("r-crayon" ,r-crayon)
583 ("r-dbplyr" ,r-dbplyr)
585 ("r-forcats" ,r-forcats)
586 ("r-ggplot2" ,r-ggplot2)
590 ("r-jsonlite" ,r-jsonlite)
591 ("r-lubridate" ,r-lubridate)
592 ("r-magrittr" ,r-magrittr)
593 ("r-modelr" ,r-modelr)
594 ("r-pillar" ,r-pillar)
597 ("r-readxl" ,r-readxl)
598 ("r-reprex" ,r-reprex)
600 ("r-rstudioapi" ,r-rstudioapi)
602 ("r-stringr" ,r-stringr)
603 ("r-tibble" ,r-tibble)
606 (home-page "https://tidyverse.tidyverse.org")
607 (synopsis "Install and load packages from the \"Tidyverse\"")
609 "The @code{tidyverse} is a set of packages that work in harmony because
610 they share common data representations and API design. This package is
611 designed to make it easy to install and load multiple tidyverse packages in a
613 (license license:gpl3)))
615 (define-public r-rvest
622 (uri (cran-uri "rvest" version))
624 (base32 "0r0a5jic09xw5pk0x42pr99r3zab5m9s4x85ymx1sl769jz42zqf"))))
625 (build-system r-build-system)
628 ("r-magrittr" ,r-magrittr)
629 ("r-selectr" ,r-selectr)
631 (home-page "https://github.com/hadley/rvest")
632 (synopsis "Simple web scraping for R")
634 "@code{r-rvest} helps you scrape information from web pages. It is
635 designed to work with @code{magrittr} to make it easy to express common web
636 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
637 (license license:gpl3)))
639 (define-public r-selectr
646 (uri (cran-uri "selectr" version))
648 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
649 (build-system r-build-system)
651 `(("r-stringr" ,r-stringr)
653 (home-page "https://sjp.co.nz/projects/selectr/")
654 (synopsis "Translate CSS selectors to XPath expressions")
656 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
657 expression. This allows you to use CSS selectors when working with the XML
658 package as it can only evaluate XPath expressions. Also provided are
659 convenience functions useful for using CSS selectors on XML nodes. This
660 package is a port of the Python package @code{cssselect}.")
661 (license license:bsd-3)))
663 (define-public r-reprex
670 (uri (cran-uri "reprex" version))
673 "0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
674 (build-system r-build-system)
676 `(("r-callr" ,r-callr)
680 ("r-rmarkdown" ,r-rmarkdown)
681 ("r-whisker" ,r-whisker)
682 ("r-withr" ,r-withr)))
683 (home-page "https://github.com/tidyverse/reprex")
684 (synopsis "Prepare reproducible R code examples for sharing")
686 "This package provides a convenience wrapper that uses the
687 @code{rmarkdown} package to render small snippets of code to target formats
688 that include both code and output. The goal is to encourage the sharing of
689 small, reproducible, and runnable examples on code-oriented websites or email.
690 @code{reprex} also extracts clean, runnable R code from various common formats,
691 such as copy/paste from an R session.")
692 (license license:expat)))
694 (define-public r-reordercluster
696 (name "r-reordercluster")
700 (uri (cran-uri "ReorderCluster" version))
703 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
704 (build-system r-build-system)
706 `(("r-gplots" ,r-gplots)
708 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
709 (synopsis "Reordering the dendrogram according to the class labels")
710 (description "This package provides tools for performing the leaf reordering
711 for the dendrogram that preserves the hierarchical clustering result and at the
712 same time tries to group instances from the same class together.")
713 (license license:gpl3+)))
715 (define-public r-callr
722 (uri (cran-uri "callr" version))
725 "1dc20gdawy9mhnc452qlshv2p4krs6c2gymvpv365mn141zjgdq1"))))
726 (build-system r-build-system)
729 ("r-processx" ,r-processx)))
730 (home-page "https://github.com/r-lib/callr#readme")
731 (synopsis "Call R from R")
733 "It is sometimes useful to perform a computation in a separate R process,
734 without affecting the current R process at all. This package does exactly
736 (license license:expat)))
738 (define-public r-readxl
745 (uri (cran-uri "readxl" version))
748 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
749 (build-system r-build-system)
751 `(("r-cellranger" ,r-cellranger)
752 ("r-progress" ,r-progress)
754 ("r-tibble" ,r-tibble)))
755 (home-page "https://readxl.tidyverse.org")
756 (synopsis "Read Excel files")
758 "This package lets you import Excel files into R. It supports
759 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
760 the embedded @code{RapidXML} C++ library.")
761 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
762 ;; 'rapidxml' which is Boost.
763 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
765 (define-public r-modelr
772 (uri (cran-uri "modelr" version))
775 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
776 (build-system r-build-system)
778 `(("r-broom" ,r-broom)
779 ("r-magrittr" ,r-magrittr)
782 ("r-tibble" ,r-tibble)
784 ("r-tidyselect" ,r-tidyselect)
785 ("r-vctrs" ,r-vctrs)))
786 (home-page "https://github.com/tidyverse/modelr")
787 (synopsis "Helper functions for modelling in pipelines")
789 "Functions for modelling that help you seamlessly integrate modelling
790 into a pipeline of data manipulation and visualisation.")
791 (license license:gpl3)))
793 (define-public r-httpuv
799 (uri (cran-uri "httpuv" version))
802 "066rprqvz9qln6xd85x1yh1wbbmzd157xjl8zq1zbgr8l6347inm"))))
803 (build-system r-build-system)
807 ("r-promises" ,r-promises)
810 (home-page "https://github.com/rstudio/httpuv")
811 (synopsis "HTTP and WebSocket server library for R")
813 "The httpuv package provides low-level socket and protocol support for
814 handling HTTP and WebSocket requests directly from within R. It is primarily
815 intended as a building block for other packages, rather than making it
816 particularly easy to create complete web applications using httpuv alone.")
817 ;; This package includes third-party code that was originally released
818 ;; under various non-copyleft licenses. Full licensing information can be
819 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
820 (license license:gpl3+)))
822 (define-public r-jsonlite
828 (uri (cran-uri "jsonlite" version))
831 "0xrki07wc17bkmhz0h7jay784j1sls2i9bf1mfpj6yl59791v4kl"))))
832 (build-system r-build-system)
833 (home-page "https://arxiv.org/abs/1403.2805")
834 (synopsis "Robust, high performance JSON parser and generator for R")
836 "The jsonlite package provides a fast JSON parser and generator optimized
837 for statistical data and the web. It offers flexible, robust, high
838 performance tools for working with JSON in R and is particularly powerful for
839 building pipelines and interacting with a web API. In addition to converting
840 JSON data from/to R objects, jsonlite contains functions to stream, validate,
841 and prettify JSON data. The unit tests included with the package verify that
842 all edge cases are encoded and decoded consistently for use with dynamic data
843 in systems and applications.")
844 (license license:expat)))
846 (define-public r-servr
852 (uri (cran-uri "servr" version))
855 "0lxkjr7mwdk96cdpx66j92nn4w2vkgn2j2bbg7kd4238jsk9srs7"))))
856 (build-system r-build-system)
858 `(("r-httpuv" ,r-httpuv)
859 ("r-jsonlite" ,r-jsonlite)
862 (home-page "https://github.com/yihui/servr")
863 (synopsis "Simple HTTP server to serve static files or dynamic documents")
865 "Servr provides an HTTP server in R to serve static files, or dynamic
866 documents that can be converted to HTML files (e.g., R Markdown) under a given
868 (license license:expat)))
870 (define-public r-htmltools
876 (uri (cran-uri "htmltools" version))
879 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
880 (build-system r-build-system)
882 `(("r-base64enc" ,r-base64enc)
883 ("r-digest" ,r-digest)
884 ("r-rlang" ,r-rlang)))
885 (home-page "https://cran.r-project.org/web/packages/htmltools")
886 (synopsis "R tools for HTML")
888 "This package provides tools for HTML generation and output in R.")
889 (license license:expat)))
891 (define-public r-htmlwidgets
893 (name "r-htmlwidgets")
897 (uri (cran-uri "htmlwidgets" version))
900 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
901 (build-system r-build-system)
903 `(("r-htmltools" ,r-htmltools)
904 ("r-jsonlite" ,r-jsonlite)
906 (home-page "https://github.com/ramnathv/htmlwidgets")
907 (synopsis "HTML Widgets for R")
909 "HTML widgets is a framework for creating HTML widgets that render in
910 various contexts including the R console, R Markdown documents, and Shiny web
912 (license license:expat)))
914 (define-public r-htmltable
921 (uri (cran-uri "htmlTable" version))
924 "1a1al4kld7lrapc2i086crr78kbgrskahs221iy9v77x0nhin2q3"))))
925 (properties `((upstream-name . "htmlTable")))
926 (build-system r-build-system)
928 `(("r-checkmate" ,r-checkmate)
929 ("r-htmltools" ,r-htmltools)
930 ("r-htmlwidgets" ,r-htmlwidgets)
932 ("r-magrittr" ,r-magrittr)
933 ("r-rstudioapi" ,r-rstudioapi)
934 ("r-stringr" ,r-stringr)))
936 `(("r-knitr" ,r-knitr)))
937 (home-page "http://gforge.se/packages/")
938 (synopsis "Advanced tables for Markdown/HTML")
940 "This package provides functions to build tables with advanced layout
941 elements such as row spanners, column spanners, table spanners, zebra
942 striping, and more. While allowing advanced layout, the underlying
943 CSS-structure is simple in order to maximize compatibility with word
944 processors such as LibreOffice. The package also contains a few text
945 formatting functions that help outputting text compatible with HTML or
947 (license license:gpl3+)))
949 (define-public r-curl
955 (uri (cran-uri "curl" version))
958 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
959 (build-system r-build-system)
962 (modify-phases %standard-phases
963 ;; The environment variable CURL_CA_BUNDLE is only respected when
964 ;; running Windows, so we disable the platform checks.
965 ;; This can be removed once the libcurl has been patched.
966 (add-after 'unpack 'allow-CURL_CA_BUNDLE
968 (substitute* "R/onload.R"
969 (("if \\(!grepl\\(\"mingw\".*")
971 (substitute* "src/handle.c"
974 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
975 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
982 `(("pkg-config" ,pkg-config)))
983 (home-page "https://github.com/jeroenooms/curl")
984 (synopsis "HTTP client for R")
986 "The @code{curl()} and @code{curl_download()} functions provide highly
987 configurable drop-in replacements for base @code{url()} and
988 @code{download.file()} with better performance, support for encryption, gzip
989 compression, authentication, and other @code{libcurl} goodies. The core of
990 the package implements a framework for performing fully customized requests
991 where data can be processed either in memory, on disk, or streaming via the
992 callback or connection interfaces.")
993 (license license:expat)))
995 (define-public r-hwriter
1002 (uri (cran-uri "hwriter" version))
1005 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1006 (build-system r-build-system)
1007 (home-page "https://cran.r-project.org/web/packages/hwriter")
1008 (synopsis "Output R objects in HTML format")
1010 "This package provides easy-to-use and versatile functions to output R
1011 objects in HTML format.")
1012 (license license:lgpl2.1+)))
1014 (define-public r-rjson
1021 (uri (cran-uri "rjson" version))
1024 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1025 (build-system r-build-system)
1026 (home-page "https://cran.r-project.org/web/packages/rjson")
1027 (synopsis "JSON library for R")
1029 "This package provides functions to convert R objects into JSON objects
1031 (license license:gpl2+)))
1033 (define-public r-fastmap
1040 (uri (cran-uri "fastmap" version))
1043 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1044 (properties `((upstream-name . "fastmap")))
1045 (build-system r-build-system)
1046 (home-page "https://r-lib.github.io/fastmap/")
1047 (synopsis "Fast implementation of a key-value store")
1049 "This package provides a fast implementation of a key-value store.
1050 Environments are commonly used as key-value stores, but every time a new key
1051 is used, it is added to R's global symbol table, causing a small amount of
1052 memory leakage. This can be problematic in cases where many different keys
1053 are used. Fastmap avoids this memory leak issue by implementing the map using
1054 data structures in C++.")
1055 (license license:expat)))
1057 (define-public r-shiny
1065 (url "https://github.com/rstudio/shiny.git")
1066 (commit (string-append "v" version))))
1067 (file-name (git-file-name name version))
1070 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1071 (build-system r-build-system)
1073 `(#:modules ((guix build r-build-system)
1074 (guix build minify-build-system)
1077 #:imported-modules (,@%r-build-system-modules
1078 (guix build minify-build-system))
1080 (modify-phases (@ (guix build r-build-system) %standard-phases)
1081 (add-after 'unpack 'replace-bundled-minified-JavaScript
1082 (lambda* (#:key inputs #:allow-other-keys)
1083 (let ((replace-file (lambda (old new)
1084 (format #t "replacing ~a with ~a\n" old new)
1086 (symlink new old))))
1087 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1088 ;; contain just data. They are not minified code, so we don't
1090 (with-directory-excursion "inst/www/shared"
1091 (replace-file "bootstrap/shim/respond.min.js"
1092 (string-append (assoc-ref inputs "js-respond")
1093 "/share/javascript/respond.min.js"))
1094 (replace-file "bootstrap/shim/html5shiv.min.js"
1095 (string-append (assoc-ref inputs "js-html5shiv")
1096 "/share/javascript/html5shiv.min.js"))
1097 (replace-file "json2-min.js"
1098 (string-append (assoc-ref inputs "js-json2")
1099 "/share/javascript/json2-min.js"))
1100 (replace-file "strftime/strftime-min.js"
1101 (string-append (assoc-ref inputs "js-strftime")
1102 "/share/javascript/strftime.min.js"))
1103 (replace-file "highlight/highlight.pack.js"
1104 (string-append (assoc-ref inputs "js-highlight")
1105 "/share/javascript/highlight.min.js"))
1106 (replace-file "datatables/js/jquery.dataTables.min.js"
1107 (string-append (assoc-ref inputs "js-datatables")
1108 "/share/javascript/jquery.dataTables.min.js"))
1109 (replace-file "selectize/js/selectize.min.js"
1110 (string-append (assoc-ref inputs "js-selectize")
1111 "/share/javascript/selectize.min.js"))
1112 (replace-file "selectize/js/es5-shim.min.js"
1113 (string-append (assoc-ref inputs "js-es5-shim")
1114 "/share/javascript/es5-shim.min.js"))
1115 (for-each (match-lambda
1117 (delete-file target)
1118 (minify source #:target target)))
1119 '(("jqueryui/jquery-ui.js" .
1120 "jqueryui/jquery-ui.min.js")
1121 ("datepicker/js/bootstrap-datepicker.js" .
1122 "datepicker/js/bootstrap-datepicker.min.js")
1123 ("ionrangeslider/js/ion.rangeSlider.js" .
1124 "ionrangeslider/js/ion.rangeSlider.min.js")
1125 ("bootstrap/js/bootstrap.js" .
1126 "bootstrap/js/bootstrap.min.js")
1131 ("legacy/jquery.js" .
1132 "legacy/jquery.min.js")
1133 ("showdown/src/showdown.js" .
1134 "showdown/compressed/showdown.js")))))
1137 `(("r-crayon" ,r-crayon)
1138 ("r-digest" ,r-digest)
1139 ("r-fastmap" ,r-fastmap)
1140 ("r-htmltools" ,r-htmltools)
1141 ("r-httpuv" ,r-httpuv)
1142 ("r-jsonlite" ,r-jsonlite)
1143 ("r-later" ,r-later)
1145 ("r-promises" ,r-promises)
1147 ("r-rlang" ,r-rlang)
1148 ("r-sourcetools" ,r-sourcetools)
1149 ("r-withr" ,r-withr)
1150 ("r-xtable" ,r-xtable)))
1152 `(("js-datatables" ,js-datatables)
1153 ("js-html5shiv" ,js-html5shiv)
1154 ("js-json2" ,js-json2)
1155 ("js-respond" ,js-respond)
1156 ("js-selectize" ,js-selectize)
1157 ("js-strftime" ,js-strftime)
1158 ("js-highlight" ,js-highlight)
1159 ("js-es5-shim" ,js-es5-shim)))
1161 `(("uglify-js" ,uglify-js)
1162 ("gfortran" ,gfortran)))
1163 (home-page "http://shiny.rstudio.com")
1164 (synopsis "Easy interactive web applications with R")
1166 "Makes it incredibly easy to build interactive web applications
1167 with R. Automatic \"reactive\" binding between inputs and outputs and
1168 extensive prebuilt widgets make it possible to build beautiful,
1169 responsive, and powerful applications with minimal effort.")
1170 (license license:artistic2.0)))
1172 ;; This package includes minified JavaScript files. When upgrading please
1173 ;; check that there are no new minified JavaScript files.
1174 (define-public r-shinytree
1176 (name "r-shinytree")
1181 (uri (cran-uri "shinyTree" version))
1184 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1185 (modules '((guix build utils)))
1188 ;; Delete minified JavaScript
1189 (for-each delete-file
1190 '("inst/www/jsTree-3.3.7/libs/require.js"
1191 "inst/www/jsTree-3.3.7/libs/jquery.js"
1192 "inst/www/jsTree-3.3.7/jstree.min.js"))
1194 (properties `((upstream-name . "shinyTree")))
1195 (build-system r-build-system)
1197 `(#:modules ((guix build utils)
1198 (guix build r-build-system)
1202 (modify-phases %standard-phases
1203 (add-after 'unpack 'replace-minified-javascript
1204 (lambda* (#:key inputs #:allow-other-keys)
1205 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1206 (symlink (string-append (assoc-ref inputs "js-requirejs")
1207 "/share/javascript/require.min.js")
1212 `((,(assoc-ref inputs "js-jquery")
1216 (lambda (sources targets)
1217 (for-each (lambda (source target)
1218 (format #t "Processing ~a --> ~a~%"
1220 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1221 (call-with-output-file target
1223 (dump-port minified port)))))
1227 `(("r-htmlwidgets" ,r-htmlwidgets)
1228 ("r-jsonlite" ,r-jsonlite)
1229 ("r-promises" ,r-promises)
1230 ("r-shiny" ,r-shiny)
1231 ("r-stringr" ,r-stringr)))
1233 `(("js-requirejs" ,js-requirejs)))
1235 `(("uglify-js" ,uglify-js)
1239 (uri "https://code.jquery.com/jquery-3.3.1.js")
1242 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1243 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1244 (synopsis "jsTree bindings for Shiny")
1246 "This package exposes R bindings to jsTree, a JavaScript library that
1247 supports interactive trees, to enable rich, editable trees in Shiny.")
1248 (license license:expat)))
1250 (define-public r-shinydashboard
1252 (name "r-shinydashboard")
1256 (uri (cran-uri "shinydashboard" version))
1259 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1260 (build-system r-build-system)
1261 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1262 ;; Regenerate it from the included sources.
1264 `(#:modules ((guix build utils)
1265 (guix build r-build-system)
1268 (modify-phases %standard-phases
1269 (add-after 'unpack 'generate-minified-javascript
1271 (with-directory-excursion "inst/AdminLTE"
1272 (delete-file "app.min.js")
1273 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1274 (call-with-output-file "app.min.js"
1276 (dump-port minified port))))))))))
1278 `(("r-htmltools" ,r-htmltools)
1279 ("r-promises" ,r-promises)
1280 ("r-shiny" ,r-shiny)))
1282 `(("uglify-js" ,uglify-js)))
1283 (home-page "https://rstudio.github.io/shinydashboard/")
1284 (synopsis "Create dashboards with shiny")
1285 (description "This package provides an extension to the Shiny web
1286 application framework for R, making it easy to create attractive dashboards.")
1287 ;; This package includes software that was released under the Expat
1288 ;; license, but the whole package is released under GPL version 2 or
1290 (license license:gpl2+)))
1292 (define-public r-shinyfiles
1294 (name "r-shinyfiles")
1299 (uri (cran-uri "shinyFiles" version))
1301 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1302 (properties `((upstream-name . "shinyFiles")))
1303 (build-system r-build-system)
1306 ("r-htmltools" ,r-htmltools)
1307 ("r-jsonlite" ,r-jsonlite)
1308 ("r-shiny" ,r-shiny)
1309 ("r-tibble" ,r-tibble)))
1310 (home-page "https://github.com/thomasp85/shinyFiles")
1311 (synopsis "Server-side file system viewer for Shiny")
1313 "This package provides functionality for client-side navigation of the
1314 server side file system in shiny apps. In case the app is running locally
1315 this gives the user direct access to the file system without the need to
1316 \"download\" files to a temporary location. Both file and folder selection as
1317 well as file saving is available.")
1318 (license license:gpl2+)))
1320 (define-public r-shinythemes
1322 (name "r-shinythemes")
1327 (uri (cran-uri "shinythemes" version))
1330 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1331 (properties `((upstream-name . "shinythemes")))
1332 (build-system r-build-system)
1333 (propagated-inputs `(("r-shiny" ,r-shiny)))
1334 (home-page "https://rstudio.github.io/shinythemes/")
1335 (synopsis "Themes for Shiny")
1337 "This package provides themes for use with Shiny. It includes several
1338 Bootstrap themes, which are packaged for use with Shiny applications.")
1339 ;; The package is released under version 3 of the GPL, but it includes
1340 ;; source files that are covered by the Expat license. It also includes
1341 ;; fonts under SIL or the ASL.
1342 (license (list license:gpl3 license:expat
1343 license:silofl1.1 license:asl2.0))))
1345 ;; The package sources include minified variants of d3.js and non-minified
1346 ;; source code of d3-jetpack.
1347 (define-public r-d3r
1354 (uri (cran-uri "d3r" version))
1357 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1358 (build-system r-build-system)
1360 `(#:modules ((guix build utils)
1361 (guix build r-build-system)
1365 (modify-phases %standard-phases
1366 (add-after 'unpack 'process-javascript
1367 (lambda* (#:key inputs #:allow-other-keys)
1368 (with-directory-excursion "inst/www/d3/"
1372 `((,(assoc-ref inputs "d3.v3.js")
1373 "v3/dist/d3.min.js")
1374 (,(assoc-ref inputs "d3.v4.js")
1375 "v4/dist/d3.min.js")
1376 (,(assoc-ref inputs "d3.v5.js")
1377 "v5/dist/d3.min.js"))))
1378 (lambda (sources targets)
1379 (for-each (lambda (source target)
1380 (format #t "Processing ~a --> ~a~%"
1382 (delete-file target)
1383 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1384 (call-with-output-file target
1386 (dump-port minified port)))))
1390 `(("r-dplyr" ,r-dplyr)
1391 ("r-htmltools" ,r-htmltools)
1392 ("r-rlang" ,r-rlang)
1393 ("r-tidyr" ,r-tidyr)))
1395 `(("uglify-js" ,uglify-js)
1399 (uri "https://d3js.org/d3.v3.js")
1402 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1406 (uri "https://d3js.org/d3.v4.js")
1409 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1413 (uri "https://d3js.org/d3.v5.js")
1416 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1417 (home-page "https://github.com/timelyportfolio/d3r")
1418 (synopsis "d3.js utilities for R")
1420 "This package provides a suite of functions to help ease the use of the
1421 d3.js visualization library in R. These helpers include
1422 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1423 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1424 R objects into the JSON format that the d3.js library expects.")
1425 (license license:bsd-3)))
1427 ;; We use the latest commit here because the last release was in 2016 while
1428 ;; the latest commit was in 2018.
1429 (define-public r-sankeyd3
1430 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1434 (version (git-version "0.3.2" revision commit))
1439 (url "https://github.com/fbreitwieser/sankeyD3.git")
1441 (file-name (git-file-name name version))
1444 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1445 (build-system r-build-system)
1448 ("r-htmlwidgets" ,r-htmlwidgets)
1449 ("r-shiny" ,r-shiny)
1450 ("r-magrittr" ,r-magrittr)))
1451 (home-page "https://github.com/fbreitwieser/sankeyD3")
1452 (synopsis "Sankey network graphs from R")
1454 "This package provides an R library to generate Sankey network graphs
1455 in R and Shiny via the D3 visualization library.")
1456 ;; The R code is licensed under GPLv3+. It includes the non-minified
1457 ;; JavaScript source code of d3-sankey, which is released under the
1458 ;; 3-clause BSD license.
1459 (license (list license:gpl3+ license:bsd-3)))))
1461 (define-public r-crosstalk
1463 (name "r-crosstalk")
1468 (uri (cran-uri "crosstalk" version))
1471 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1472 (build-system r-build-system)
1474 `(("r-htmltools" ,r-htmltools)
1475 ("r-jsonlite" ,r-jsonlite)
1476 ("r-lazyeval" ,r-lazyeval)
1478 (home-page "https://rstudio.github.io/crosstalk/")
1479 (synopsis "Inter-widget interactivity for HTML widgets")
1481 "This package provides building blocks for allowing HTML widgets to
1482 communicate with each other, with Shiny or without (i.e. static @code{.html}
1483 files). It currently supports linked brushing and filtering.")
1484 (license license:expat)))
1486 (define-public r-rook
1493 (uri (cran-uri "Rook" version))
1496 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1497 (properties `((upstream-name . "Rook")))
1498 (build-system r-build-system)
1499 (propagated-inputs `(("r-brew" ,r-brew)))
1500 (home-page "https://cran.r-project.org/web/packages/Rook")
1501 (synopsis "Web server interface for R")
1503 "This package contains the Rook specification and convenience software
1504 for building and running Rook applications. A Rook application is an R
1505 reference class object that implements a @code{call} method or an R closure
1506 that takes exactly one argument, an environment, and returns a list with three
1507 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1508 (license license:gpl2)))
1510 (define-public r-miniui
1517 (uri (cran-uri "miniUI" version))
1520 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1521 (properties `((upstream-name . "miniUI")))
1522 (build-system r-build-system)
1524 `(("r-htmltools" ,r-htmltools)
1525 ("r-shiny" ,r-shiny)))
1526 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1527 (synopsis "Shiny UI widgets for small screens")
1529 "This package provides UI widget and layout functions for writing Shiny apps that
1530 work well on small screens.")
1531 (license license:gpl3)))
1533 (define-public r-feather
1540 (uri (cran-uri "feather" version))
1543 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1544 (build-system r-build-system)
1548 ("r-tibble" ,r-tibble)))
1549 (home-page "https://github.com/wesm/feather")
1550 (synopsis "R Bindings to the Feather API")
1551 (description "Read and write feather files, a lightweight binary columnar
1552 data store designed for maximum speed.")
1553 (license license:asl2.0)))
1555 (define-public r-maps
1562 (uri (cran-uri "maps" version))
1565 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1566 (build-system r-build-system)
1567 (home-page "https://cran.r-project.org/web/packages/maps")
1568 (synopsis "Draw geographical maps")
1569 (description "This package provides an R module for display of maps.
1570 Projection code and larger maps are in separate packages (@code{mapproj} and
1572 (license license:gpl2)))
1574 (define-public r-mapproj
1581 (uri (cran-uri "mapproj" version))
1584 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1585 (build-system r-build-system)
1586 (propagated-inputs `(("r-maps" ,r-maps)))
1587 (home-page "https://cran.r-project.org/web/packages/mapproj")
1588 (synopsis "Map projection in R")
1589 (description "This package converts latitude/longitude into projected
1591 (license (list license:gpl2 ; The R interface
1592 (license:non-copyleft ; The C code
1593 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1594 "Lucent Public License Version 1.02")))))
1596 (define-public r-rgooglemaps
1598 (name "r-rgooglemaps")
1603 (uri (cran-uri "RgoogleMaps" version))
1606 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1607 (properties `((upstream-name . "RgoogleMaps")))
1608 (build-system r-build-system)
1612 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1613 (synopsis "Use Google Maps in R")
1614 (description "This package serves two purposes:
1616 @item Provide a comfortable R interface to query the Google server for static
1618 @item Use the map as a background image to overlay plots within R. This
1619 requires proper coordinate scaling.
1621 (license license:gpl2+)))
1623 (define-public r-geosphere
1625 (name "r-geosphere")
1630 (uri (cran-uri "geosphere" version))
1633 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1634 (build-system r-build-system)
1635 (propagated-inputs `(("r-sp" ,r-sp)))
1636 (home-page "https://cran.r-project.org/web/packages/geosphere")
1637 (synopsis "Spherical trigonometry")
1638 (description "This package computes spherical trigonometry for geographic
1639 applications. That is, compute distances and related measures for angular
1640 (longitude/latitude) locations.")
1641 (license license:gpl3+)))
1643 (define-public r-jpeg
1650 (uri (cran-uri "jpeg" version))
1653 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1654 (build-system r-build-system)
1655 (inputs `(("libjpeg" ,libjpeg-turbo)))
1656 (home-page "https://www.rforge.net/jpeg/")
1657 (synopsis "Read and write JPEG images with R")
1658 (description "This package provides a way to read, write and display
1659 bitmap images stored in the JPEG format with R. It can read and write both
1660 files and in-memory raw vectors.")
1661 (license license:gpl2+)))
1663 (define-public r-ggmap
1670 (uri (cran-uri "ggmap" version))
1673 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1674 (build-system r-build-system)
1676 `(("r-bitops" ,r-bitops)
1677 ("r-digest" ,r-digest)
1678 ("r-dplyr" ,r-dplyr)
1679 ("r-ggplot2" ,r-ggplot2)
1683 ("r-magrittr" ,r-magrittr)
1686 ("r-purrr" ,r-purrr)
1687 ("r-rgooglemaps" ,r-rgooglemaps)
1688 ("r-rjson" ,r-rjson)
1689 ("r-scales" ,r-scales)
1690 ("r-stringr" ,r-stringr)
1691 ("r-tibble" ,r-tibble)
1692 ("r-tidyr" ,r-tidyr)))
1693 (home-page "https://github.com/dkahle/ggmap")
1694 (synopsis "Spatial visualization with ggplot2")
1695 (description "This package provides a collection of functions to visualize
1696 spatial data and models on top of static maps from various online sources (e.g
1697 Google Maps and Stamen Maps). It includes tools common to those tasks,
1698 including functions for geolocation and routing.")
1699 (license license:gpl2)))
1701 (define-public r-haven
1708 (uri (cran-uri "haven" version))
1711 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1712 (build-system r-build-system)
1716 `(("r-knitr" ,r-knitr)))
1718 `(("r-forcats" ,r-forcats)
1721 ("r-rlang" ,r-rlang)
1722 ("r-readr" ,r-readr)
1723 ("r-tibble" ,r-tibble)
1724 ("r-tidyselect" ,r-tidyselect)
1725 ("r-vctrs" ,r-vctrs)))
1726 (home-page "https://haven.tidyverse.org")
1727 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1729 "This package lets you mport foreign statistical formats into R via the
1730 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1731 (license license:expat)))
1733 (define-public r-amap
1739 (uri (cran-uri "amap" version))
1742 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1743 (build-system r-build-system)
1745 `(("gfortran" ,gfortran)))
1746 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1747 (synopsis "Another multidimensional analysis package")
1748 (description "This package provides tools for clustering and principal
1749 component analysis (with robust methods, and parallelized functions).")
1750 (license license:gpl2+)))
1752 (define-public r-ape
1759 (uri (cran-uri "ape" version))
1762 "0f74x9vx9sxpns2hlq4w2x80cd2gw42isfgncvs9pqbjf4hiyqnr"))))
1763 (build-system r-build-system)
1765 `(("r-lattice" ,r-lattice)
1767 ("r-rcpp" ,r-rcpp)))
1768 (home-page "http://ape-package.ird.fr/")
1769 (synopsis "Analyses of phylogenetics and evolution")
1771 "This package provides functions for reading, writing, plotting, and
1772 manipulating phylogenetic trees, analyses of comparative data in a
1773 phylogenetic framework, ancestral character analyses, analyses of
1774 diversification and macroevolution, computing distances from DNA sequences,
1775 and several other tools.")
1776 (license license:gpl2+)))
1778 (define-public r-abbyyr
1785 (uri (cran-uri "abbyyR" version))
1788 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1789 (properties `((upstream-name . "abbyyR")))
1790 (build-system r-build-system)
1792 `(("r-curl" ,r-curl)
1795 ("r-progress" ,r-progress)
1796 ("r-readr" ,r-readr)
1798 (home-page "https://github.com/soodoku/abbyyR")
1799 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1801 "This package provides tools to get text from images of text using Abbyy
1802 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1803 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1804 passports and get the results in a variety of formats including plain text and
1805 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1806 (license license:expat)))
1808 (define-public r-colorspace
1810 (name "r-colorspace")
1815 (uri (cran-uri "colorspace" version))
1817 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1818 (build-system r-build-system)
1819 (home-page "https://cran.r-project.org/web/packages/colorspace")
1820 (synopsis "Color space manipulation")
1822 "This package carries out a mapping between assorted color spaces
1823 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1824 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1825 colors are provided.")
1826 (license license:bsd-3)))
1828 (define-public r-glue
1835 (uri (cran-uri "glue" version))
1838 "1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq"))))
1839 (build-system r-build-system)
1840 ;; knitr depends on glue, so we can't add knitr here to build the
1844 `(("r-knitr" ,r-knitr)))
1845 (home-page "https://github.com/tidyverse/glue")
1846 (synopsis "Interpreted string literals")
1848 "This package provides an implementation of interpreted string literals,
1849 inspired by Python's Literal String Interpolation (PEP-0498) and
1850 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1851 (license license:expat)))
1853 (define-public r-pastecs
1859 (uri (cran-uri "pastecs" version))
1862 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1863 (build-system r-build-system)
1865 `(("r-boot" ,r-boot)))
1866 (home-page "http://www.sciviews.org/pastecs")
1867 (synopsis "Analysis of space-time ecological series")
1869 "This package provides functions for regulation, decomposition and analysis
1870 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1871 initiative to bring PASSTEC 2000 functionalities to R.")
1872 (license license:gpl2+)))
1874 (define-public r-plogr
1881 (uri (cran-uri "plogr" version))
1884 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1885 (build-system r-build-system)
1886 (home-page "https://github.com/krlmlr/plogr")
1887 (synopsis "R bindings for the plog C++ logging library")
1889 "This package provides the header files for a stripped-down version of
1890 the plog header-only C++ logging library, and a method to log to R's standard
1892 (license license:expat)))
1894 (define-public r-pls
1901 (uri (cran-uri "pls" version))
1903 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1904 (build-system r-build-system)
1905 (home-page "https://mevik.net/work/software/pls.html")
1906 (synopsis "Partial Least Squares and Principal Component Regression")
1908 "The pls package implements multivariate regression methods: Partial Least
1909 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1910 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1913 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1914 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1915 @item multi-response models (or @dfn{PLS2})
1916 @item flexible cross-validation
1917 @item Jackknife variance estimates of regression coefficients
1918 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1919 (R)MSEP, R², and correlation loadings
1920 @item formula interface, modelled after @code{lm()}, with methods for predict,
1921 print, summary, plot, update, etc.
1922 @item extraction functions for coefficients, scores, and loadings
1923 @item MSEP, RMSEP, and R² estimates
1924 @item multiplicative scatter correction (@dfn{MSC})
1926 (license license:gpl2)))
1935 (uri (cran-uri "ps" version))
1937 (base32 "1x10zgvq75gnkmzqhbqn6jyvp9h1y4qxgnbdds0bwmc8ad8md903"))))
1938 (build-system r-build-system)
1939 (home-page "https://ps.r-lib.org")
1940 (synopsis "List, query, and manipulate system processes")
1942 "The ps package implements an API to list, query, and manipulate system
1943 processes. Most of its code is based on the @code{psutil} Python package.")
1944 (license license:bsd-3)))
1946 (define-public r-pkgbuild
1953 (uri (cran-uri "pkgbuild" version))
1955 (base32 "188r2ba7y5j80mnfqdf210af40yd28jjgx7rbya4iwcfx7rzqjdi"))))
1956 (build-system r-build-system)
1958 `(("r-callr" ,r-callr)
1960 ("r-crayon" ,r-crayon)
1962 ("r-prettyunits" ,r-prettyunits)
1964 ("r-rprojroot" ,r-rprojroot)
1965 ("r-withr" ,r-withr)))
1966 (home-page "https://github.com/r-pkgs/pkgbuild")
1967 (synopsis "Find tools needed to build R packages")
1969 "This package provides functions used to build R packages. It locates
1970 compilers needed to build R packages on various platforms and ensures the PATH
1971 is configured appropriately so R can use them.")
1972 (license license:gpl3)))
1974 (define-public r-pkgload
1981 (uri (cran-uri "pkgload" version))
1984 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
1985 (build-system r-build-system)
1988 ("r-crayon" ,r-crayon)
1990 ("r-pkgbuild" ,r-pkgbuild)
1991 ("r-rlang" ,r-rlang)
1992 ("r-rprojroot" ,r-rprojroot)
1993 ("r-rstudioapi" ,r-rstudioapi)
1994 ("r-withr" ,r-withr)))
1995 (home-page "https://github.com/r-lib/pkgload")
1996 (synopsis "Simulate package installation and attach")
1998 "This package simulates the process of installing a package and then
1999 attaching it. This is a key part of the @code{devtools} package as it allows
2000 you to rapidly iterate while developing a package.")
2001 (license license:gpl3)))
2003 (define-public r-rcpp
2010 (uri (cran-uri "Rcpp" version))
2012 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
2013 (build-system r-build-system)
2014 (home-page "http://www.rcpp.org")
2015 (synopsis "Seamless R and C++ integration")
2017 "The Rcpp package provides R functions as well as C++ classes which offer
2018 a seamless integration of R and C++. Many R data types and objects can be
2019 mapped back and forth to C++ equivalents which facilitates both writing of new
2020 code as well as easier integration of third-party libraries. Documentation
2021 about Rcpp is provided by several vignettes included in this package, via the
2022 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2023 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2024 @code{citation(\"Rcpp\")} for details on these last two.")
2025 (license license:gpl2+)))
2027 (define-public r-bindr
2034 (uri (cran-uri "bindr" version))
2037 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2038 (build-system r-build-system)
2039 (home-page "https://github.com/krlmlr/bindr")
2040 (synopsis "Parametrized active bindings")
2042 "This package provides a simple interface for creating active bindings
2043 where the bound function accepts additional arguments.")
2044 (license license:expat)))
2046 (define-public r-bindrcpp
2053 (uri (cran-uri "bindrcpp" version))
2056 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2057 (build-system r-build-system)
2059 `(("r-bindr" ,r-bindr)
2060 ("r-plogr" ,r-plogr)
2061 ("r-rcpp" ,r-rcpp)))
2062 (home-page "https://github.com/krlmlr/bindrcpp")
2063 (synopsis "Rcpp interface to active bindings")
2065 "This package provides an easy way to fill an environment with active
2066 bindings that call a C++ function.")
2067 (license license:expat)))
2069 (define-public r-auc
2076 (uri (cran-uri "AUC" version))
2079 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2080 (properties `((upstream-name . "AUC")))
2081 (build-system r-build-system)
2082 (home-page "https://cran.r-project.org/web/packages/AUC")
2083 (synopsis "Compute the area under the curve of selected measures")
2085 "This package includes functions to compute the area under the curve of
2086 selected measures: the area under the sensitivity curve (AUSEC), the area
2087 under the specificity curve (AUSPC), the area under the accuracy
2088 curve (AUACC), and the area under the receiver operating characteristic
2089 curve (AUROC). The curves can also be visualized. Support for partial areas
2091 (license license:gpl2+)))
2093 (define-public r-calibrate
2095 (name "r-calibrate")
2100 (uri (cran-uri "calibrate" version))
2102 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2103 (build-system r-build-system)
2105 `(("r-mass" ,r-mass)))
2106 (home-page "https://cran.r-project.org/web/packages/calibrate")
2107 (synopsis "Calibration of scatterplot and biplot axes")
2109 "This is a package for drawing calibrated scales with tick marks
2110 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2111 (license license:gpl2)))
2113 (define-public r-shape
2120 (uri (cran-uri "shape" version))
2123 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2124 (build-system r-build-system)
2125 (home-page "https://cran.r-project.org/web/packages/shape")
2126 (synopsis "Functions for plotting graphical shapes")
2128 "This package provides functions for plotting graphical shapes such as
2129 ellipses, circles, cylinders, arrows, ...")
2130 (license license:gpl3+)))
2132 (define-public r-globaloptions
2134 (name "r-globaloptions")
2139 (uri (cran-uri "GlobalOptions" version))
2141 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2142 (properties `((upstream-name . "GlobalOptions")))
2143 (build-system r-build-system)
2145 `(("r-knitr" ,r-knitr)))
2146 (home-page "https://github.com/jokergoo/GlobalOptions")
2147 (synopsis "Generate functions to get or set global options")
2149 "This package provides more controls on the option values such as
2150 validation and filtering on the values, making options invisible or private.")
2151 (license license:gpl2+)))
2153 (define-public r-circlize
2160 (uri (cran-uri "circlize" version))
2163 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2164 (build-system r-build-system)
2166 `(("r-colorspace" ,r-colorspace)
2167 ("r-globaloptions" ,r-globaloptions)
2168 ("r-shape" ,r-shape)))
2170 `(("r-knitr" ,r-knitr)))
2171 (home-page "https://github.com/jokergoo/circlize")
2172 (synopsis "Circular visualization")
2174 "Circular layout is an efficient way to visualise huge amounts of
2175 information. This package provides an implementation of circular layout
2176 generation in R as well as an enhancement of available software. Its
2177 flexibility is based on the usage of low-level graphics functions such that
2178 self-defined high-level graphics can be easily implemented by users for
2179 specific purposes. Together with the seamless connection between the powerful
2180 computational and visual environment in R, it gives users more convenience and
2181 freedom to design figures for better understanding complex patterns behind
2182 multi-dimensional data.")
2183 (license license:gpl2+)))
2185 (define-public r-powerlaw
2192 (uri (cran-uri "poweRlaw" version))
2194 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2195 (properties `((upstream-name . "poweRlaw")))
2196 (build-system r-build-system)
2198 `(("r-pracma" ,r-pracma)))
2200 `(("r-knitr" ,r-knitr)))
2201 (home-page "https://github.com/csgillespie/poweRlaw")
2202 (synopsis "Tools for the analysis of heavy tailed distributions")
2204 "This package provides an implementation of maximum likelihood estimators
2205 for a variety of heavy tailed distributions, including both the discrete and
2206 continuous power law distributions. Additionally, a goodness-of-fit based
2207 approach is used to estimate the lower cut-off for the scaling region.")
2208 ;; Any of these GPL versions.
2209 (license (list license:gpl2 license:gpl3))))
2211 (define-public r-compare
2218 (uri (cran-uri "compare" version))
2221 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2222 (build-system r-build-system)
2223 (home-page "https://cran.r-project.org/web/packages/compare")
2224 (synopsis "Comparing objects for differences")
2226 "This package provides functions to compare a model object to a
2227 comparison object. If the objects are not identical, the functions can be
2228 instructed to explore various modifications of the objects (e.g., sorting
2229 rows, dropping names) to see if the modified versions are identical.")
2230 (license license:gpl2+)))
2232 (define-public r-dendextend
2234 (name "r-dendextend")
2239 (uri (cran-uri "dendextend" version))
2242 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2243 (build-system r-build-system)
2245 `(("r-ggplot2" ,r-ggplot2)
2246 ("r-magrittr" ,r-magrittr)
2247 ("r-viridis" ,r-viridis)))
2248 (home-page "https://cran.r-project.org/web/packages/dendextend")
2249 (synopsis "Extending 'dendrogram' functionality in R")
2251 "This package offers a set of functions for extending @code{dendrogram}
2252 objects in R, letting you visualize and compare trees of hierarchical
2253 clusterings. You can adjust a tree's graphical parameters (the color, size,
2254 type, etc of its branches, nodes and labels) and visually and statistically
2255 compare different dendrograms to one another.")
2256 ;; Any of these versions
2257 (license (list license:gpl2 license:gpl3))))
2259 (define-public r-getoptlong
2261 (name "r-getoptlong")
2266 (uri (cran-uri "GetoptLong" version))
2269 "1fswgy5j4xaipqs7nk7nzrl66vrchhxrk0w7hcsbyij3sxgn3z9j"))))
2270 (properties `((upstream-name . "GetoptLong")))
2271 (build-system r-build-system)
2275 `(("r-crayon" ,r-crayon)
2276 ("r-globaloptions" ,r-globaloptions)
2277 ("r-rjson" ,r-rjson)))
2279 `(("r-knitr" ,r-knitr)))
2280 (home-page "https://github.com/jokergoo/GetoptLong")
2281 (synopsis "Parsing command-line arguments and variable interpolation")
2283 "This is yet another command-line argument parser which wraps the
2284 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2285 use in R. It also provides a simple way for variable interpolation in R.")
2286 (license license:gpl2+)))
2288 (define-public r-fastmatch
2290 (name "r-fastmatch")
2295 (uri (cran-uri "fastmatch" version))
2298 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2299 (build-system r-build-system)
2300 (home-page "https://www.rforge.net/fastmatch")
2301 (synopsis "Fast match function")
2303 "This package provides a fast @code{match} replacement for cases that
2304 require repeated look-ups. It is slightly faster that R's built-in
2305 @code{match} function on first match against a table, but extremely fast on
2306 any subsequent lookup as it keeps the hash table in memory.")
2307 (license license:gpl2)))
2312 (version "2.2-14.2")
2316 (uri (cran-uri "ff" version))
2319 "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
2320 (build-system r-build-system)
2321 (propagated-inputs `(("r-bit" ,r-bit)))
2322 (home-page "http://ff.r-forge.r-project.org/")
2323 (synopsis "Memory-efficient storage of large data on disk and access functions")
2325 "This package provides data structures that are stored on disk but
2326 behave (almost) as if they were in RAM by transparently mapping only a section
2328 ;; error Architecture not supported.
2329 (supported-systems (delete "aarch64-linux" %supported-systems))
2330 (license license:gpl2)))
2332 (define-public r-ffbase
2339 (uri (cran-uri "ffbase" version))
2342 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2343 (build-system r-build-system)
2346 ("r-fastmatch" ,r-fastmatch)
2348 (home-page "http://github.com/edwindj/ffbase")
2349 (synopsis "Basic statistical functions for package 'ff'")
2351 "This package extends the out of memory vectors of @code{ff} with
2352 statistical functions and other utilities to ease their usage.")
2353 (license license:gpl3)))
2355 (define-public r-prettyunits
2357 (name "r-prettyunits")
2362 (uri (cran-uri "prettyunits" version))
2365 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2366 (build-system r-build-system)
2367 (home-page "https://github.com/gaborcsardi/prettyunits")
2368 (synopsis "Pretty, human readable formatting of quantities")
2370 "This package provides tools for pretty, human readable formatting of
2372 (license license:expat)))
2374 (define-public r-reshape
2381 (uri (cran-uri "reshape" version))
2384 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2385 (build-system r-build-system)
2387 `(("r-plyr" ,r-plyr)
2388 ("r-rcpp" ,r-rcpp)))
2389 (home-page "http://had.co.nz/reshape")
2390 (synopsis "Flexibly reshape data")
2392 "Flexibly restructure and aggregate data using just two functions:
2393 @code{melt} and @code{cast}. This package provides them.")
2394 (license license:expat)))
2396 (define-public r-progress
2403 (uri (cran-uri "progress" version))
2406 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2407 (build-system r-build-system)
2409 `(("r-crayon" ,r-crayon)
2411 ("r-prettyunits" ,r-prettyunits)
2413 (home-page "https://github.com/gaborcsardi/progress")
2414 (synopsis "Terminal progress bars")
2416 "This package provides configurable progress bars. They may include
2417 percentage, elapsed time, and/or the estimated completion time. They work in
2418 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2419 package also provides a C++ API, that works with or without Rcpp.")
2420 (license license:expat)))
2422 (define-public r-ggally
2429 (uri (cran-uri "GGally" version))
2432 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2433 (properties `((upstream-name . "GGally")))
2434 (build-system r-build-system)
2436 `(("libressl" ,libressl)))
2438 `(("r-ggplot2" ,r-ggplot2)
2439 ("r-gtable" ,r-gtable)
2440 ("r-lifecycle" ,r-lifecycle)
2442 ("r-progress" ,r-progress)
2443 ("r-rcolorbrewer" ,r-rcolorbrewer)
2444 ("r-reshape" ,r-reshape)
2445 ("r-rlang" ,r-rlang)
2446 ("r-scales" ,r-scales)))
2447 (home-page "https://ggobi.github.io/ggally")
2448 (synopsis "Extension to ggplot2")
2450 "The R package ggplot2 is a plotting system based on the grammar of
2451 graphics. GGally extends ggplot2 by adding several functions to reduce the
2452 complexity of combining geometric objects with transformed data. Some of
2453 these functions include a pairwise plot matrix, a two group pairwise plot
2454 matrix, a parallel coordinates plot, a survival plot, and several functions to
2456 (license license:gpl2+)))
2458 (define-public r-proxy
2465 (uri (cran-uri "proxy" version))
2468 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2469 (build-system r-build-system)
2470 (home-page "https://cran.r-project.org/web/packages/proxy")
2471 (synopsis "Distance and similarity measures")
2473 "This package provides an extensible framework for the efficient
2474 calculation of auto- and cross-proximities, along with implementations of the
2475 most popular ones.")
2476 (license license:gpl2)))
2485 (uri (cran-uri "sp" version))
2487 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2488 (build-system r-build-system)
2490 `(("r-lattice" ,r-lattice)))
2491 (home-page "https://cran.r-project.org/web/packages/sp")
2492 (synopsis "Classes and methods for spatial data")
2494 "This package provides classes and methods for spatial data; the classes
2495 document where the spatial location information resides, for 2D or 3D data.
2496 Utility functions are provided, e.g. for plotting data as maps, spatial
2497 selection, as well as methods for retrieving coordinates, for subsetting,
2498 print, summary, etc.")
2499 (license license:gpl2+)))
2501 (define-public r-rmtstat
2508 (uri (cran-uri "RMTstat" version))
2511 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2512 (properties `((upstream-name . "RMTstat")))
2513 (build-system r-build-system)
2514 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2515 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2517 "This package provides functions for working with the Tracy-Widom laws
2518 and other distributions related to the eigenvalues of large Wishart
2520 (license license:bsd-3)))
2522 (define-public r-rmpi
2528 (uri (cran-uri "Rmpi" version))
2531 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2532 (properties `((upstream-name . "Rmpi")))
2533 (build-system r-build-system)
2535 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2536 #:phases (modify-phases %standard-phases
2537 (add-before 'install 'mpi-setup
2540 `(("openmpi" ,openmpi)))
2542 `(("pkg-config" ,pkg-config)))
2543 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2544 (synopsis "R interface to message-passing interface (MPI)")
2546 "This package provides an interface (wrapper) to MPI APIs. It also
2547 provides an interactive R manager and worker environment.")
2548 (license license:gpl2+)))
2550 (define-public r-lmoments
2557 (uri (cran-uri "Lmoments" version))
2560 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2561 (properties `((upstream-name . "Lmoments")))
2562 (build-system r-build-system)
2564 `(("r-rcpp" ,r-rcpp)
2565 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2566 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2567 (synopsis "L-moments and quantile mixtures")
2569 "This package contains functions to estimate L-moments and trimmed
2570 L-moments from the data. It also contains functions to estimate the
2571 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2572 quantile mixture from L-moments and trimmed L-moments.")
2573 (license license:gpl2)))
2575 (define-public r-distillery
2577 (name "r-distillery")
2582 (uri (cran-uri "distillery" version))
2585 "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
2586 (build-system r-build-system)
2587 (home-page "https://ral.ucar.edu/staff/ericg/")
2588 (synopsis "Functions for confidence intervals and object information")
2590 "This package provides some very simple method functions for confidence
2591 interval calculation and to distill pertinent information from a potentially
2592 complex object; primarily used in common with the packages extRemes and
2594 (license license:gpl2+)))
2596 (define-public r-extremes
2603 (uri (cran-uri "extRemes" version))
2606 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2607 (properties `((upstream-name . "extRemes")))
2608 (build-system r-build-system)
2610 `(("r-distillery" ,r-distillery)
2611 ("r-lmoments" ,r-lmoments)))
2612 (home-page "https://www.assessment.ucar.edu/toolkit/")
2613 (synopsis "Extreme value analysis")
2615 "ExtRemes is a suite of functions for carrying out analyses on the
2616 extreme values of a process of interest; be they block maxima over long blocks
2617 or excesses over a high threshold.")
2618 (license license:gpl2+)))
2620 (define-public r-lmtest
2627 (uri (cran-uri "lmtest" version))
2630 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2631 (build-system r-build-system)
2633 `(("r-zoo" ,r-zoo)))
2635 `(("gfortran" ,gfortran)))
2636 (home-page "https://cran.r-project.org/web/packages/lmtest")
2637 (synopsis "Testing linear regression models")
2639 "This package provides a collection of tests, data sets, and examples for
2640 diagnostic checking in linear regression models. Furthermore, some generic
2641 tools for inference in parametric models are provided.")
2642 ;; Either version is okay
2643 (license (list license:gpl2 license:gpl3))))
2645 (define-public r-idr
2651 (uri (cran-uri "idr" version))
2654 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2655 (build-system r-build-system)
2656 (home-page "https://cran.r-project.org/web/packages/idr/")
2657 (synopsis "Irreproducible discovery rate")
2659 "This is a package for estimating the copula mixture model and plotting
2660 correspondence curves in \"Measuring reproducibility of high-throughput
2661 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2662 by Li, Brown, Huang, and Bickel")
2663 (license license:gpl2+)))
2665 (define-public r-inline
2671 (uri (cran-uri "inline" version))
2674 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2675 (build-system r-build-system)
2676 (home-page "https://cran.r-project.org/web/packages/inline")
2677 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2679 "This package provides functionality to dynamically define R functions
2680 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2681 @code{.Call} calling conventions.")
2682 ;; Any version of the LGPL.
2683 (license license:lgpl3+)))
2685 (define-public r-inum
2691 (uri (cran-uri "inum" version))
2694 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2695 (build-system r-build-system)
2697 `(("r-libcoin" ,r-libcoin)))
2698 (home-page "https://cran.r-project.org/web/packages/inum/")
2699 (synopsis "Interval and enum-type representation of vectors")
2701 "This package provides an enum-type representation of vectors and
2702 representation of intervals, including a method of coercing variables
2704 (license license:gpl2)))
2706 (define-public r-bdsmatrix
2708 (name "r-bdsmatrix")
2713 (uri (cran-uri "bdsmatrix" version))
2716 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2717 (properties `((upstream-name . "bdsmatrix")))
2718 (build-system r-build-system)
2719 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2720 (synopsis "Routines for block diagonal symmetric matrices")
2722 "This package provides procedures to work with block diagonal symmetric
2723 matrices, a special case of sparse matrices.")
2724 (license license:lgpl2.0)))
2726 (define-public r-bbmle
2729 (version "1.0.23.1")
2733 (uri (cran-uri "bbmle" version))
2736 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2737 (build-system r-build-system)
2739 `(("r-bdsmatrix" ,r-bdsmatrix)
2740 ("r-lattice" ,r-lattice)
2742 ("r-matrix" ,r-matrix)
2743 ("r-mvtnorm" ,r-mvtnorm)
2744 ("r-numderiv" ,r-numderiv)))
2745 (home-page "https://cran.r-project.org/web/packages/bbmle")
2746 (synopsis "Tools for General Maximum Likelihood Estimation")
2748 "This package provides methods and functions for fitting maximum
2749 likelihood models in R. This package modifies and extends the @code{mle}
2750 classes in the @code{stats4} package.")
2751 ;; Any version of the GPL
2752 (license license:gpl2+)))
2754 (define-public r-emdbook
2761 (uri (cran-uri "emdbook" version))
2764 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2765 (build-system r-build-system)
2767 `(("r-bbmle" ,r-bbmle)
2769 ("r-lattice" ,r-lattice)
2771 ("r-plyr" ,r-plyr)))
2772 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2773 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2775 "This package provides auxiliary functions and data sets for \"Ecological
2776 Models and Data\", a book presenting maximum likelihood estimation and related
2777 topics for ecologists (ISBN 978-0-691-12522-0).")
2779 (license (list license:gpl2 license:gpl3))))
2781 (define-public r-lpsolve
2788 (uri (cran-uri "lpSolve" version))
2791 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2792 (properties `((upstream-name . "lpSolve")))
2793 (build-system r-build-system)
2794 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2795 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2797 "Lp_solve is software for solving linear, integer and mixed integer
2798 programs. This implementation supplies a \"wrapper\" function in C and some R
2799 functions that solve general linear/integer problems, assignment problems, and
2800 transportation problems.")
2801 (license license:lgpl2.0)))
2803 (define-public r-limsolve
2810 (uri (cran-uri "limSolve" version))
2813 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2814 (properties `((upstream-name . "limSolve")))
2815 (build-system r-build-system)
2817 `(("r-lpsolve" ,r-lpsolve)
2819 ("r-quadprog" ,r-quadprog)))
2820 (native-inputs `(("gfortran" ,gfortran)))
2821 (home-page "https://cran.r-project.org/web/packages/limSolve")
2822 (synopsis "Solving linear inverse models")
2824 "This package provides functions that:
2827 @item find the minimum/maximum of a linear or quadratic function,
2828 @item sample an underdetermined or overdetermined system,
2829 @item solve a linear system Ax=B for the unknown x.
2832 It includes banded and tridiagonal linear systems. The package calls Fortran
2833 functions from LINPACK.")
2835 (license (list license:gpl2+ license:gpl3+))))
2837 (define-public r-fitdistrplus
2839 (name "r-fitdistrplus")
2844 (uri (cran-uri "fitdistrplus" version))
2847 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
2848 (build-system r-build-system)
2850 `(("r-mass" ,r-mass)
2851 ("r-survival" ,r-survival)))
2853 `(("r-knitr" ,r-knitr)))
2854 (home-page "http://riskassessment.r-forge.r-project.org")
2855 (synopsis "Fitting a parametric distribution from data")
2857 "This package extends the @code{fitdistr} function of the MASS package
2858 with several functions to help the fit of a parametric distribution to
2859 non-censored or censored data. Censored data may contain left-censored,
2860 right-censored and interval-censored values, with several lower and upper
2861 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2862 provides moment matching (MME), quantile matching (QME) and maximum
2863 goodness-of-fit estimation (MGE) methods (available only for non-censored
2864 data). Weighted versions of MLE, MME and QME are available.")
2865 (license license:gpl2+)))
2867 (define-public r-energy
2874 (uri (cran-uri "energy" version))
2877 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2878 (build-system r-build-system)
2880 `(("r-boot" ,r-boot)
2881 ("r-rcpp" ,r-rcpp)))
2882 (home-page "https://cran.r-project.org/web/packages/energy")
2883 (synopsis "Multivariate inference via the energy of data")
2885 "This package provides e-statistics (energy) tests and statistics for
2886 multivariate and univariate inference, including distance correlation,
2887 one-sample, two-sample, and multi-sample tests for comparing multivariate
2888 distributions, are implemented. Measuring and testing multivariate
2889 independence based on distance correlation, partial distance correlation,
2890 multivariate goodness-of-fit tests, clustering based on energy distance,
2891 testing for multivariate normality, distance components (disco) for
2892 non-parametric analysis of structured data, and other energy
2893 statistics/methods are implemented.")
2894 (license license:gpl2+)))
2896 (define-public r-suppdists
2898 (name "r-suppdists")
2903 (uri (cran-uri "SuppDists" version))
2906 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2907 (properties `((upstream-name . "SuppDists")))
2908 (build-system r-build-system)
2909 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2910 (synopsis "Supplementary distributions")
2912 "This package provides ten distributions supplementing those built into
2913 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2914 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2915 coefficient, Johnson distributions, normal scores and generalized
2916 hypergeometric distributions. In addition two random number generators of
2917 George Marsaglia are included.")
2918 (license license:gpl2+)))
2920 (define-public r-ksamples
2927 (uri (cran-uri "kSamples" version))
2930 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2931 (properties `((upstream-name . "kSamples")))
2932 (build-system r-build-system)
2934 `(("r-suppdists" ,r-suppdists)))
2935 (home-page "https://cran.r-project.org/web/packages/kSamples")
2936 (synopsis "K-Sample rank tests and their combinations")
2938 "This package provides tools to compares k samples using the
2939 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2940 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2941 test. It computes asymptotic, simulated or (limited) exact P-values, all
2942 valid under randomization, with or without ties, or conditionally under random
2943 sampling from populations, given the observed tie pattern. Except for Steel's
2944 test and the JT test it also combines these tests across several blocks of
2946 (license license:gpl2+)))
2948 (define-public r-cvst
2955 (uri (cran-uri "CVST" version))
2958 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2959 (properties `((upstream-name . "CVST")))
2960 (build-system r-build-system)
2962 `(("r-kernlab" ,r-kernlab)
2963 ("r-matrix" ,r-matrix)))
2964 (home-page "https://cran.r-project.org/web/packages/CVST")
2965 (synopsis "Fast cross-validation via sequential testing")
2967 "This package implements the fast cross-validation via sequential
2968 testing (CVST) procedure. CVST is an improved cross-validation procedure
2969 which uses non-parametric testing coupled with sequential analysis to
2970 determine the best parameter set on linearly increasing subsets of the data.
2971 Additionally to the CVST the package contains an implementation of the
2972 ordinary k-fold cross-validation with a flexible and powerful set of helper
2973 objects and methods to handle the overall model selection process. The
2974 implementations of the Cochran's Q test with permutations and the sequential
2975 testing framework of Wald are generic and can therefore also be used in other
2977 (license license:gpl2+)))
2979 (define-public r-squarem
2986 (uri (cran-uri "SQUAREM" version))
2989 "17l05i87vwvcsk79fbg52zrx04zdlwiiyl3ga8qafs7mqx0j976q"))))
2990 (properties `((upstream-name . "SQUAREM")))
2991 (build-system r-build-system)
2992 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2993 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2995 "This package provides algorithms for accelerating the convergence of
2996 slow, monotone sequences from smooth, contraction mapping such as the EM
2997 algorithm. It can be used to accelerate any smooth, linearly convergent
2998 acceleration scheme. A tutorial style introduction to this package is
2999 available in a vignette.")
3000 (license license:gpl2+)))
3002 (define-public r-lava
3009 (uri (cran-uri "lava" version))
3012 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3013 (build-system r-build-system)
3015 `(("r-numderiv" ,r-numderiv)
3016 ("r-squarem" ,r-squarem)
3017 ("r-survival" ,r-survival)))
3018 (home-page "https://github.com/kkholst/lava")
3019 (synopsis "Latent variable models")
3021 "This package provides tools for the estimation and simulation of latent
3023 (license license:gpl3)))
3025 (define-public r-drr
3032 (uri (cran-uri "DRR" version))
3035 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3036 (properties `((upstream-name . "DRR")))
3037 (build-system r-build-system)
3039 `(("r-cvst" ,r-cvst)
3040 ("r-kernlab" ,r-kernlab)
3041 ("r-matrix" ,r-matrix)))
3042 (home-page "https://cran.r-project.org/web/packages/DRR")
3043 (synopsis "Dimensionality reduction via regression")
3045 "This package provides an implementation of dimensionality reduction via
3046 regression using Kernel Ridge Regression.")
3047 (license license:gpl3)))
3049 (define-public r-prodlim
3052 (version "2019.11.13")
3056 (uri (cran-uri "prodlim" version))
3059 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3060 (build-system r-build-system)
3062 `(("r-kernsmooth" ,r-kernsmooth)
3065 ("r-survival" ,r-survival)))
3066 (home-page "https://cran.r-project.org/web/packages/prodlim")
3067 (synopsis "Product-limit estimation for censored event history analysis")
3069 "This package provides a fast and user-friendly implementation of
3070 nonparametric estimators for censored event history (survival) analysis with
3071 the Kaplan-Meier and Aalen-Johansen methods.")
3072 (license license:gpl2+)))
3074 (define-public r-dimred
3081 (uri (cran-uri "dimRed" version))
3084 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3085 (properties `((upstream-name . "dimRed")))
3086 (build-system r-build-system)
3089 ("r-magrittr" ,r-magrittr)))
3090 (home-page "https://github.com/gdkrmr/dimRed")
3091 (synopsis "Framework for dimensionality reduction")
3093 "This package provides a collection of dimensionality reduction
3094 techniques from R packages and provides a common interface for calling the
3096 (license license:gpl3)))
3098 (define-public r-timedate
3101 (version "3043.102")
3105 (uri (cran-uri "timeDate" version))
3108 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3109 (properties `((upstream-name . "timeDate")))
3110 (build-system r-build-system)
3111 (home-page "https://www.rmetrics.org")
3112 (synopsis "Chronological and calendar objects")
3114 "This package provides an environment for teaching \"Financial
3115 Engineering and Computational Finance\" and for managing chronological and
3117 (license license:gpl2+)))
3119 (define-public r-magic
3126 (uri (cran-uri "magic" version))
3129 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3130 (build-system r-build-system)
3132 `(("r-abind" ,r-abind)))
3133 (home-page "https://github.com/RobinHankin/magic.git")
3134 (synopsis "Create and investigate magic squares")
3136 "This package provides a collection of efficient, vectorized algorithms
3137 for the creation and investigation of magic squares and hypercubes, including
3138 a variety of functions for the manipulation and analysis of arbitrarily
3139 dimensioned arrays.")
3140 (license license:gpl2)))
3142 (define-public r-rmysql
3149 (uri (cran-uri "RMySQL" version))
3152 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3153 (properties `((upstream-name . "RMySQL")))
3154 (build-system r-build-system)
3156 `(("mariadb" ,mariadb "lib")
3157 ("mariadb-dev" ,mariadb "dev")
3160 `(("r-dbi" ,r-dbi)))
3161 (home-page "https://github.com/r-dbi/RMySQL")
3162 (synopsis "Database interface and MySQL driver for R")
3164 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3165 package contains an old implementation based on legacy code from S-PLUS which
3166 is being phased out. A modern MySQL client based on Rcpp is available from
3167 the RMariaDB package.")
3168 (license license:gpl2)))
3170 (define-public r-rpostgresql
3172 (name "r-rpostgresql")
3177 (uri (cran-uri "RPostgreSQL" version))
3180 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3181 (properties `((upstream-name . "RPostgreSQL")))
3182 (build-system r-build-system)
3184 `(("postgresql" ,postgresql)))
3186 `(("r-dbi" ,r-dbi)))
3187 (home-page "https://github.com/tomoakin/RPostgreSQL")
3188 (synopsis "R interface to the PostgreSQL database system")
3190 "This package provides a Database Interface (DBI) compliant driver for R
3191 to access PostgreSQL database systems.")
3192 ;; The whole package is released under GPL version 2. It includes code
3193 ;; under the PostgreSQL license.
3194 (license license:gpl2)))
3196 (define-public r-linprog
3203 (uri (cran-uri "linprog" version))
3206 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3207 (build-system r-build-system)
3208 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3209 (home-page "http://linprog.r-forge.r-project.org/")
3210 (synopsis "Linear programming and optimization")
3212 "This package can be used to solve Linear Programming / Linear
3213 Optimization problems by using the simplex algorithm.")
3214 (license license:gpl2+)))
3216 (define-public r-geometry
3223 (uri (cran-uri "geometry" version))
3226 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3227 (build-system r-build-system)
3229 `(("r-magic" ,r-magic)
3230 ("r-linprog" ,r-linprog)
3231 ("r-lpsolve" ,r-lpsolve)
3233 ("r-rcppprogress" ,r-rcppprogress)))
3234 (home-page "http://geometry.r-forge.r-project.org/")
3235 (synopsis "Mesh generation and surface tesselation")
3237 "This package makes the qhull library available in R, in a similar manner
3238 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3239 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3240 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3241 and higher dimensions. It implements the Quickhull algorithm for computing
3242 the convex hull. Qhull does not support constrained Delaunay triangulations,
3243 or mesh generation of non-convex objects, but the package does include some R
3244 functions that allow for this. Currently the package only gives access to
3245 Delaunay triangulation and convex hull computation.")
3246 ;; The Qhull sources are included and are distributed under a custom
3247 ;; non-copyleft license. The R sources are released under GPL version 2.
3248 (license (list license:gpl2
3249 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3251 (define-public r-ddalpha
3258 (uri (cran-uri "ddalpha" version))
3261 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3262 (build-system r-build-system)
3265 ("r-class" ,r-class)
3266 ("r-geometry" ,r-geometry)
3269 ("r-robustbase" ,r-robustbase)
3270 ("r-sfsmisc" ,r-sfsmisc)))
3272 `(("gfortran" ,gfortran)))
3273 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3274 (synopsis "Depth-Based classification and calculation of data depth")
3276 "This package contains procedures for depth-based supervised learning,
3277 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3278 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3279 statistical depth function to a compact low-dimensional space, where the final
3280 classification is done. It also offers an extension to functional data and
3281 routines for calculating certain notions of statistical depth functions. 50
3282 multivariate and 5 functional classification problems are included.")
3283 (license license:gpl2)))
3285 (define-public r-gower
3292 (uri (cran-uri "gower" version))
3295 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3296 (build-system r-build-system)
3297 (home-page "https://github.com/markvanderloo/gower")
3298 (synopsis "Gower's distance")
3300 "This package provides tools to compute Gower's distance (or similarity)
3301 coefficient between records, and to compute the top-n matches between records.
3302 Core algorithms are executed in parallel on systems supporting OpenMP.")
3303 (license license:gpl3)))
3305 (define-public r-rcpproll
3312 (uri (cran-uri "RcppRoll" version))
3315 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3316 (properties `((upstream-name . "RcppRoll")))
3317 (build-system r-build-system)
3319 `(("r-rcpp" ,r-rcpp)))
3320 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3321 (synopsis "Efficient rolling and windowed operations")
3323 "This package provides fast and efficient routines for common rolling /
3324 windowed operations. Routines for the efficient computation of windowed mean,
3325 median, sum, product, minimum, maximum, standard deviation and variance are
3327 (license license:gpl2+)))
3329 (define-public r-ipred
3336 (uri (cran-uri "ipred" version))
3339 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3340 (build-system r-build-system)
3342 `(("r-class" ,r-class)
3345 ("r-prodlim" ,r-prodlim)
3346 ("r-rpart" ,r-rpart)
3347 ("r-survival" ,r-survival)))
3348 (home-page "https://cran.r-project.org/web/packages/ipred")
3349 (synopsis "Improved predictors")
3351 "This package provides improved predictive models by indirect
3352 classification and bagging for classification, regression and survival
3353 problems as well as resampling based estimators of prediction error.")
3354 (license license:gpl2+)))
3356 (define-public r-psych
3359 (version "1.9.12.31")
3363 (uri (cran-uri "psych" version))
3366 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3367 (build-system r-build-system)
3369 `(("r-lattice" ,r-lattice)
3370 ("r-mnormt" ,r-mnormt)
3371 ("r-nlme" ,r-nlme)))
3372 (home-page "https://cran.r-project.org/web/packages/psych/")
3373 (synopsis "Procedures for psychological, psychometric, and personality research")
3375 "This package provides a general purpose toolbox for personality,
3376 psychometric theory and experimental psychology. Functions are primarily for
3377 multivariate analysis and scale construction using factor analysis, principal
3378 component analysis, cluster analysis and reliability analysis, although others
3379 provide basic descriptive statistics. Item Response Theory is done using
3380 factor analysis of tetrachoric and polychoric correlations. Functions for
3381 analyzing data at multiple levels include within and between group statistics,
3382 including correlations and factor analysis. Functions for simulating and
3383 testing particular item and test structures are included. Several functions
3384 serve as a useful front end for structural equation modeling. Graphical
3385 displays of path diagrams, factor analysis and structural equation models are
3386 created using basic graphics.")
3387 (license license:gpl2+)))
3389 (define-public r-generics
3396 (uri (cran-uri "generics" version))
3399 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3400 (build-system r-build-system)
3401 (home-page "https://github.com/r-lib/generics")
3402 (synopsis "Common S3 generics not provided by base R methods")
3404 "In order to reduce potential package dependencies and conflicts,
3405 generics provides a number of commonly used S3 generics that are not provided
3406 by base R methods related to model fitting.")
3407 (license license:gpl2)))
3409 (define-public r-broom
3416 (uri (cran-uri "broom" version))
3419 "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
3420 (build-system r-build-system)
3422 `(("r-backports" ,r-backports)
3423 ("r-dplyr" ,r-dplyr)
3424 ("r-generics" ,r-generics)
3426 ("r-purrr" ,r-purrr)
3427 ("r-reshape2" ,r-reshape2)
3428 ("r-stringr" ,r-stringr)
3429 ("r-tibble" ,r-tibble)
3430 ("r-tidyr" ,r-tidyr)))
3432 `(("r-knitr" ,r-knitr)))
3433 (home-page "https://github.com/tidyverse/broom")
3434 (synopsis "Convert statistical analysis objects into tidy data frames")
3436 "This package provides tools to convert statistical analysis objects from
3437 R into tidy data frames, so that they can more easily be combined, reshaped
3438 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3439 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3440 summarizes a model's statistical findings such as coefficients of a
3441 regression; @code{augment}, which adds columns to the original data such as
3442 predictions, residuals and cluster assignments; and @code{glance}, which
3443 provides a one-row summary of model-level statistics.")
3444 (license license:expat)))
3446 (define-public r-recipes
3453 (uri (cran-uri "recipes" version))
3456 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3457 (build-system r-build-system)
3459 `(("r-dplyr" ,r-dplyr)
3460 ("r-generics" ,r-generics)
3462 ("r-gower" ,r-gower)
3463 ("r-ipred" ,r-ipred)
3464 ("r-lifecycle" ,r-lifecycle)
3465 ("r-lubridate" ,r-lubridate)
3466 ("r-magrittr" ,r-magrittr)
3467 ("r-matrix" ,r-matrix)
3468 ("r-purrr" ,r-purrr)
3469 ("r-rlang" ,r-rlang)
3470 ("r-tibble" ,r-tibble)
3471 ("r-tidyr" ,r-tidyr)
3472 ("r-tidyselect" ,r-tidyselect)
3473 ("r-timedate" ,r-timedate)
3474 ("r-withr" ,r-withr)))
3476 `(("r-knitr" ,r-knitr)))
3477 (home-page "https://github.com/topepo/recipes")
3478 (synopsis "Preprocessing tools to create design matrices")
3480 "Recipes is an extensible framework to create and preprocess design
3481 matrices. Recipes consist of one or more data manipulation and analysis
3482 \"steps\". Statistical parameters for the steps can be estimated from an
3483 initial data set and then applied to other data sets. The resulting design
3484 matrices can then be used as inputs into statistical or machine learning
3486 (license license:gpl2)))
3488 (define-public r-pdist
3495 (uri (cran-uri "pdist" version))
3498 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3499 (build-system r-build-system)
3500 (home-page "https://github.com/jeffwong/pdist")
3501 (synopsis "Partitioned distance function")
3503 "Pdist computes the euclidean distance between rows of a matrix X and
3504 rows of another matrix Y. Previously, this could be done by binding the two
3505 matrices together and calling @code{dist}, but this creates unnecessary
3506 computation by computing the distances between a row of X and another row of
3507 X, and likewise for Y. Pdist strictly computes distances across the two
3508 matrices, not within the same matrix, making computations significantly faster
3509 for certain use cases.")
3510 (license license:gpl3+)))
3512 (define-public r-ggrepel
3519 (uri (cran-uri "ggrepel" version))
3522 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3523 (build-system r-build-system)
3525 `(("r-ggplot2" ,r-ggplot2)
3527 ("r-scales" ,r-scales)))
3529 `(("r-knitr" ,r-knitr))) ; for vignettes
3530 (home-page "http://github.com/slowkow/ggrepel")
3531 (synopsis "Repulsive text and label geometries for ggplot2")
3533 "This package provides text and label geometries for ggplot2 that help to
3534 avoid overlapping text labels. Labels repel away from each other and away
3535 from the data points.")
3536 (license license:gpl3)))
3538 (define-public r-corrplot
3545 (uri (cran-uri "corrplot" version))
3548 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3549 (build-system r-build-system)
3550 (home-page "https://github.com/taiyun/corrplot")
3551 (synopsis "Visualization of a correlation matrix")
3553 "This package provides a graphical display of a correlation matrix or
3554 general matrix. It also contains some algorithms to do matrix reordering. In
3555 addition, corrplot is good at details, including choosing color, text labels,
3556 color labels, layout, etc.")
3557 ;; Any version of the GPL
3558 (license license:gpl2+)))
3560 (define-public r-stringdist
3562 (name "r-stringdist")
3567 (uri (cran-uri "stringdist" version))
3569 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3570 (build-system r-build-system)
3571 (home-page "https://github.com/markvanderloo/stringdist")
3572 (synopsis "Approximate string matching and string distance functions")
3574 "This package implements an approximate string matching version of R's
3575 native @code{match} function. It can calculate various string distances based
3576 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3577 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3578 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3579 can be computed between character vectors while taking proper care of encoding
3580 or between integer vectors representing generic sequences.")
3581 (license license:gpl3+)))
3583 (define-public r-ucminf
3590 (uri (cran-uri "ucminf" version))
3593 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3594 (build-system r-build-system)
3595 (native-inputs `(("gfortran" ,gfortran)))
3596 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3597 (synopsis "General-purpose unconstrained non-linear optimization")
3599 "This package provides an implementation of an algorithm for
3600 general-purpose unconstrained non-linear optimization. The algorithm is of
3601 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3602 search with a trust region type monitoring of the input to the line search
3603 algorithm. The interface of @code{ucminf} is designed for easy interchange
3604 with the package @code{optim}.")
3605 (license license:gpl2+)))
3607 (define-public r-ordinal
3610 (version "2019.12-10")
3614 (uri (cran-uri "ordinal" version))
3617 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3618 (build-system r-build-system)
3620 `(("r-mass" ,r-mass)
3621 ("r-matrix" ,r-matrix)
3622 ("r-numderiv" ,r-numderiv)
3623 ("r-ucminf" ,r-ucminf)))
3624 (home-page "https://github.com/runehaubo/ordinal")
3625 (synopsis "Regression models for ordinal data")
3627 "This package provides an implementation of cumulative link (mixed)
3628 models also known as ordered regression models, proportional odds models,
3629 proportional hazards models for grouped survival times and ordered models.
3630 Estimation is via maximum likelihood and mixed models are fitted with the
3631 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3632 (license license:gpl2+)))
3634 (define-public r-jomo
3641 (uri (cran-uri "jomo" version))
3644 "0cdy9m4ylarkk9d0v1s61k2d877l4bbxly8a4jwhfy43fdvskz1w"))))
3645 (build-system r-build-system)
3647 `(("r-lme4" ,r-lme4)
3649 ("r-ordinal" ,r-ordinal)
3650 ("r-survival" ,r-survival)))
3651 (home-page "https://cran.r-project.org/web/packages/jomo/")
3652 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3654 "Similarly to Schafer's package pan, jomo is a package for multilevel
3655 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3656 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3657 possibility of handling binary and categorical data through latent normal
3658 variables, the option to use cluster-specific covariance matrices and to
3659 impute compatibly with the substantive model.")
3660 (license license:gpl2)))
3662 (define-public r-pan
3669 (uri (cran-uri "pan" version))
3672 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3673 (build-system r-build-system)
3674 (native-inputs `(("gfortran" ,gfortran)))
3675 (home-page "https://cran.r-project.org/web/packages/pan/")
3676 (synopsis "Multiple imputation for multivariate panel or clustered data")
3678 "This package implements multiple imputation for multivariate panel or
3680 (license license:gpl3)))
3682 (define-public r-mitml
3689 (uri (cran-uri "mitml" version))
3692 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3693 (build-system r-build-system)
3695 `(("r-haven" ,r-haven)
3698 (home-page "https://cran.r-project.org/web/packages/mitml/")
3699 (synopsis "Tools for multiple imputation in multilevel modeling")
3701 "This package provides tools for multiple imputation of missing data in
3702 multilevel modeling. It includes a user-friendly interface to the packages
3703 pan and jomo, and several functions for visualization, data management and the
3704 analysis of multiply imputed data sets.")
3705 (license license:gpl2+)))
3707 (define-public r-mice
3714 (uri (cran-uri "mice" version))
3717 "1wycbc2iqp68gfzvqx1gsn5n1k1h4bg79dy8m5msqf226hy83ncn"))))
3718 (build-system r-build-system)
3720 `(("r-broom" ,r-broom)
3721 ("r-dplyr" ,r-dplyr)
3722 ("r-lattice" ,r-lattice)
3724 ("r-tidyr" ,r-tidyr)))
3725 (home-page "https://cran.r-project.org/web/packages/mice/")
3726 (synopsis "Multivariate imputation by chained equations")
3728 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3729 implemented by the MICE algorithm as described in @url{Van Buuren and
3730 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3731 variable has its own imputation model. Built-in imputation models are
3732 provided for continuous data (predictive mean matching, normal), binary
3733 data (logistic regression), unordered categorical data (polytomous logistic
3734 regression) and ordered categorical data (proportional odds). MICE can also
3735 impute continuous two-level data (normal model, pan, second-level variables).
3736 Passive imputation can be used to maintain consistency between variables.
3737 Various diagnostic plots are available to inspect the quality of the
3739 ;; Any of these two versions.
3740 (license (list license:gpl2 license:gpl3))))
3742 (define-public r-truncnorm
3744 (name "r-truncnorm")
3749 (uri (cran-uri "truncnorm" version))
3752 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3753 (build-system r-build-system)
3754 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3755 (synopsis "Truncated normal distribution")
3756 (description "This package provides functions for the truncated normal
3757 distribution with mean equal to @code{mean} and standard deviation equal to
3758 @code{sd}. It includes density, distribution, quantile, and expected value
3759 functions, as well as a random generation function.")
3760 (license license:gpl2)))
3762 (define-public r-rsolnp
3769 (uri (cran-uri "Rsolnp" version))
3772 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3773 (properties `((upstream-name . "Rsolnp")))
3774 (build-system r-build-system)
3776 `(("r-truncnorm" ,r-truncnorm)))
3777 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3778 (synopsis "General non-linear optimization")
3779 (description "The Rsolnp package implements a general non-linear augmented
3780 Lagrange multiplier method solver, a @dfn{sequential quadratic
3781 programming} (SQP) based solver).")
3782 ;; Any version of the GPL.
3783 (license license:gpl2+)))
3785 (define-public r-hardyweinberg
3787 (name "r-hardyweinberg")
3792 (uri (cran-uri "HardyWeinberg" version))
3795 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3796 (properties `((upstream-name . "HardyWeinberg")))
3797 (build-system r-build-system)
3799 `(("r-mice" ,r-mice)
3801 ("r-rsolnp" ,r-rsolnp)))
3802 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3803 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3805 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3806 diallelic genetic marker data. All classical tests (chi-square, exact,
3807 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3808 included in the package, as well as functions for power computation and for
3809 the simulation of marker data under equilibrium and disequilibrium. Routines
3810 for dealing with markers on the X-chromosome are included. Functions for
3811 testing equilibrium in the presence of missing data by using multiple
3812 imputation are also provided. Implements several graphics for exploring the
3813 equilibrium status of a large set of diallelic markers: ternary plots with
3814 acceptance regions, log-ratio plots and Q-Q plots.")
3815 (license license:gpl2+)))
3824 (uri (cran-uri "sm" version))
3827 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3828 (build-system r-build-system)
3829 (native-inputs `(("gfortran" ,gfortran)))
3830 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3831 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3833 "This is software accompanying the book 'Applied Smoothing Techniques for
3834 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3835 University Press. It provides smoothing methods for nonparametric regression
3836 and density estimation")
3837 (license license:gpl2+)))
3839 (define-public r-venndiagram
3841 (name "r-venndiagram")
3845 (uri (cran-uri "VennDiagram" version))
3848 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3849 (properties `((upstream-name . "VennDiagram")))
3850 (build-system r-build-system)
3852 `(("r-futile-logger" ,r-futile-logger)))
3853 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3854 (synopsis "Generate High-Resolution Venn and Euler Plots")
3856 "This package provides a set of functions to generate high-resolution
3857 Venn and Euler plots. It includes handling for several special cases,
3858 including two-case scaling, and extensive customization of plot shape and
3860 (license license:gpl2+)))
3862 (define-public r-vioplot
3869 (uri (cran-uri "vioplot" version))
3872 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
3873 (build-system r-build-system)
3878 `(("r-knitr" ,r-knitr)))
3879 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3880 (synopsis "Violin plot")
3882 "This package provides a violin plot, which is a combination of a box
3883 plot and a kernel density plot.")
3884 (license license:bsd-3)))
3886 (define-public r-rsofia
3892 ;; This package has been removed from CRAN, so we can
3893 ;; only fetch it from the archives.
3894 (uri (string-append "https://cran.r-project.org/src/"
3895 "contrib/Archive/RSofia/RSofia_"
3899 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3900 (properties `((upstream-name . "RSofia")))
3901 (build-system r-build-system)
3903 `(("r-rcpp" ,r-rcpp)))
3904 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3905 (synopsis "Port of sofia-ml to R")
3906 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3907 suite of fast incremental algorithms for machine learning that can be used for
3908 training models for classification or ranking.")
3909 (license license:asl2.0)))
3911 (define-public r-xts
3918 (uri (cran-uri "xts" version))
3921 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3922 (build-system r-build-system)
3923 (propagated-inputs `(("r-zoo" ,r-zoo)))
3924 (home-page "https://github.com/joshuaulrich/xts")
3925 (synopsis "Extensible time series")
3927 "This package provides for uniform handling of R's different time-based
3928 data classes by extending @code{zoo}, maximizing native format information
3929 preservation and allowing for user-level customization and extension, while
3930 simplifying cross-class interoperability.")
3931 (license license:gpl2+)))
3933 (define-public r-performanceanalytics
3935 (name "r-performanceanalytics")
3940 (uri (cran-uri "PerformanceAnalytics" version))
3943 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3945 `((upstream-name . "PerformanceAnalytics")))
3946 (build-system r-build-system)
3948 `(("r-quadprog" ,r-quadprog)
3951 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3952 (synopsis "Econometric tools for performance and risk analysis")
3953 (description "This is a collection of econometric functions for
3954 performance and risk analysis. This package aims to aid practitioners and
3955 researchers in utilizing the latest research in analysis of non-normal return
3956 streams. In general, it is most tested on return (rather than price) data on
3957 a regular scale, but most functions will work with irregular return data as
3958 well, and increasing numbers of functions will work with P&L or price data
3960 ;; Either version may be picked.
3961 (license (list license:gpl2 license:gpl3))))
3963 (define-public r-laeken
3970 (uri (cran-uri "laeken" version))
3973 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3974 (build-system r-build-system)
3976 `(("r-boot" ,r-boot)
3977 ("r-mass" ,r-mass)))
3978 (home-page "https://cran.r-project.org/web/packages/laeken/")
3979 (synopsis "Estimation of indicators on social exclusion and poverty")
3980 (description "This package provides tools for the estimation of indicators
3981 on social exclusion and poverty, as well as an implementation of Pareto tail
3982 modeling for empirical income distributions.")
3983 (license license:gpl2+)))
3985 (define-public r-vcd
3992 (uri (cran-uri "vcd" version))
3995 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3996 (build-system r-build-system)
3998 `(("r-colorspace" ,r-colorspace)
3999 ("r-lmtest" ,r-lmtest)
4000 ("r-mass" ,r-mass)))
4001 (home-page "https://cran.r-project.org/web/packages/vcd/")
4002 (synopsis "Visualizing categorical data")
4003 (description "This package provides visualization techniques, data sets,
4004 summary and inference procedures aimed particularly at categorical data.
4005 Special emphasis is given to highly extensible grid graphics. The package was
4006 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4007 Friendly and is now the main support package for a new book, \"Discrete Data
4008 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4009 (license license:gpl2)))
4011 (define-public r-ica
4018 (uri (cran-uri "ica" version))
4021 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4022 (build-system r-build-system)
4023 (home-page "https://cran.r-project.org/web/packages/ica/")
4024 (synopsis "Independent component analysis")
4025 (description "This package provides tools for @dfn{Independent Component
4026 Analysis} (ICA) using various algorithms: FastICA,
4027 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4028 of Eigenmatrices} (JADE).")
4029 (license license:gpl2+)))
4031 (define-public r-dtw
4038 (uri (cran-uri "dtw" version))
4041 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4042 (build-system r-build-system)
4043 (propagated-inputs `(("r-proxy" ,r-proxy)))
4044 (home-page "http://dtw.r-forge.r-project.org/")
4045 (synopsis "Dynamic Time Warping Algorithms")
4046 (description "This package provides a comprehensive implementation of
4047 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4048 optimal (least cumulative distance) alignment between points of two time
4049 series. Common DTW variants covered include local (slope) and global (window)
4050 constraints, subsequence matches, arbitrary distance definitions,
4051 normalizations, minimum variance matching, and so on.")
4052 (license license:gpl2+)))
4054 (define-public r-sdmtools
4057 (version "1.1-221.2")
4061 (uri (cran-uri "SDMTools" version))
4064 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4065 (properties `((upstream-name . "SDMTools")))
4066 (build-system r-build-system)
4067 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4068 (home-page "https://www.rforge.net/SDMTools/")
4069 (synopsis "Species distribution modelling tools")
4070 (description "This package provides a set of tools for post processing
4071 the outcomes of species distribution modeling exercises. It includes novel
4072 methods for comparing models and tracking changes in distributions through
4073 time. It further includes methods for visualizing outcomes, selecting
4074 thresholds, calculating measures of accuracy and landscape fragmentation
4076 (license license:gpl3+)))
4078 (define-public r-scatterplot3d
4080 (name "r-scatterplot3d")
4085 (uri (cran-uri "scatterplot3d" version))
4088 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4089 (build-system r-build-system)
4090 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4091 (synopsis "3D scatter plot")
4092 (description "This package provides an implementation of scatter plots for
4093 plotting. a three dimensional point cloud.")
4094 (license license:gpl2)))
4096 (define-public r-ggridges
4103 (uri (cran-uri "ggridges" version))
4106 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4107 (build-system r-build-system)
4109 `(("r-ggplot2" ,r-ggplot2)
4111 ("r-scales" ,r-scales)
4112 ("r-withr" ,r-withr)))
4113 (home-page "https://github.com/clauswilke/ggridges")
4114 (synopsis "Ridgeline plots in ggplot2")
4116 "Ridgeline plots provide a convenient way of visualizing changes in
4117 distributions over time or space. This package enables the creation of such
4118 plots in @code{ggplot2}.")
4119 (license license:gpl2)))
4121 (define-public r-ggjoy
4128 (uri (cran-uri "ggjoy" version))
4131 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4132 (build-system r-build-system)
4134 `(("r-ggplot2" ,r-ggplot2)
4135 ("r-ggridges" ,r-ggridges)))
4136 (home-page "https://github.com/clauswilke/ggjoy")
4137 (synopsis "Joyplots in ggplot2")
4138 (description "Joyplots provide a convenient way of visualizing changes in
4139 distributions over time or space. This package enables the creation of such
4140 plots in @code{ggplot2}.")
4141 (license license:gpl2)))
4143 (define-public r-cli
4150 (uri (cran-uri "cli" version))
4153 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4154 (build-system r-build-system)
4156 `(("r-assertthat" ,r-assertthat)
4157 ("r-crayon" ,r-crayon)
4158 ("r-fansi" ,r-fansi)
4159 ("r-glue" ,r-glue)))
4160 (home-page "https://github.com/r-lib/cli#readme")
4161 (synopsis "Helpers for developing command line interfaces")
4162 (description "This package provides a suite of tools designed to build
4163 attractive command line interfaces (CLIs). It includes tools for drawing
4164 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4165 (license license:expat)))
4167 (define-public r-argparser
4169 (name "r-argparser")
4174 (uri (cran-uri "argparser" version))
4177 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4178 (build-system r-build-system)
4179 (home-page "https://bitbucket.org/djhshih/argparser")
4180 (synopsis "Command-line argument parser")
4182 "This package provides a cross-platform command-line argument parser
4183 written purely in R with no external dependencies. It is useful with the
4184 Rscript front-end and facilitates turning an R script into an executable
4186 (license license:gpl3+)))
4188 (define-public r-debugme
4195 (uri (cran-uri "debugme" version))
4198 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4199 (build-system r-build-system)
4200 (propagated-inputs `(("r-crayon" ,r-crayon)))
4201 (home-page "https://github.com/r-lib/debugme#readme")
4202 (synopsis "Debug R packages")
4204 "This package allows the user to specify debug messages as special string
4205 constants, and control debugging of packages via environment variables.")
4206 (license license:expat)))
4208 (define-public r-processx
4215 (uri (cran-uri "processx" version))
4218 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
4219 (build-system r-build-system)
4223 (home-page "https://github.com/r-lib/processx3")
4224 (synopsis "Execute and control system processes")
4226 "This package provides portable tools to run system processes in the
4227 background. It can check if a background process is running; wait on a
4228 background process to finish; get the exit status of finished processes; kill
4229 background processes and their children; restart processes. It can read the
4230 standard output and error of the processes, using non-blocking connections.
4231 @code{processx} can poll a process for standard output or error, with a
4232 timeout. It can also poll several processes at once.")
4233 (license license:expat)))
4235 (define-public r-tsp
4242 (uri (cran-uri "TSP" version))
4245 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4246 (properties `((upstream-name . "TSP")))
4247 (build-system r-build-system)
4248 (propagated-inputs `(("r-foreach" ,r-foreach)))
4249 (home-page "https://cran.r-project.org/web/packages/TSP/")
4250 (synopsis "Traveling salesperson problem (TSP)")
4251 (description "This package provides basic infrastructure and some
4252 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4253 traveling salesman problem).")
4254 (license license:gpl3)))
4256 (define-public r-qap
4263 (uri (cran-uri "qap" version))
4266 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4267 (build-system r-build-system)
4268 (native-inputs `(("gfortran" ,gfortran)))
4269 (home-page "https://cran.r-project.org/web/packages/qap/")
4270 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4271 (description "This package implements heuristics for the @dfn{quadratic
4272 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4274 (license license:gpl3)))
4276 (define-public r-gclus
4283 (uri (cran-uri "gclus" version))
4286 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4287 (build-system r-build-system)
4288 (propagated-inputs `(("r-cluster" ,r-cluster)))
4289 (home-page "https://cran.r-project.org/web/packages/gclus/")
4290 (synopsis "Clustering graphics")
4291 (description "This package orders panels in scatterplot matrices and
4292 parallel coordinate displays by some merit index. It contains various indices
4293 of merit, ordering functions, and enhanced versions of @code{pairs} and
4294 @code{parcoord} which color panels according to their merit level.")
4295 (license license:gpl2+)))
4297 (define-public r-webshot
4304 (uri (cran-uri "webshot" version))
4307 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4308 (build-system r-build-system)
4310 `(("r-callr" ,r-callr)
4311 ("r-jsonlite" ,r-jsonlite)
4312 ("r-magrittr" ,r-magrittr)))
4313 (home-page "https://github.com/wch/webshot/")
4314 (synopsis "Take screenshots of web pages")
4316 "Webshot makes it easy to take screenshots of web pages from within R.
4317 It can also run Shiny applications locally and take screenshots of the
4318 application; and it can render and screenshot static as well as interactive R
4319 Markdown documents.")
4320 (license license:gpl2)))
4322 (define-public r-seriation
4324 (name "r-seriation")
4329 (uri (cran-uri "seriation" version))
4332 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4333 (build-system r-build-system)
4335 `(("r-cluster" ,r-cluster)
4336 ("r-colorspace" ,r-colorspace)
4337 ("r-dendextend" ,r-dendextend)
4338 ("r-gclus" ,r-gclus)
4339 ("r-gplots" ,r-gplots)
4342 ("r-registry" ,r-registry)
4344 (native-inputs `(("gfortran" ,gfortran)))
4345 (home-page "https://s2.smu.edu/IDA/seriation/")
4346 (synopsis "Infrastructure for ordering objects using seriation")
4348 "This package provides infrastructure for seriation with an
4349 implementation of several seriation/sequencing techniques to reorder matrices,
4350 dissimilarity matrices, and dendrograms. It also provides (optimally)
4351 reordered heatmaps, color images and clustering visualizations like
4352 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4354 (license license:gpl3)))
4356 (define-public r-xfun
4363 (uri (cran-uri "xfun" version))
4365 (base32 "1fdipwrl45bznb17da4169ria5jax0f2649yj5accw6qr6wsc8bj"))))
4366 (build-system r-build-system)
4367 ;; knitr itself depends on xfun
4370 `(("r-knitr" ,r-knitr)))
4371 (home-page "https://github.com/yihui/xfun")
4372 (synopsis "Miscellaneous functions")
4374 "This package provides miscellaneous functions commonly used in other
4375 packages maintained by Yihui Xie.")
4376 (license license:expat)))
4378 (define-public r-utf8
4385 (uri (cran-uri "utf8" version))
4388 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4389 (build-system r-build-system)
4390 (home-page "https://github.com/patperry/r-utf8")
4391 (synopsis "Unicode text processing")
4393 "This package provides tools to process and print UTF-8 encoded
4394 international text (Unicode). Input, validate, normalize, encode, format, and
4396 (license license:asl2.0)))
4398 (define-public r-zeallot
4405 (uri (cran-uri "zeallot" version))
4408 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4409 (build-system r-build-system)
4410 (home-page "https://github.com/nteetor/zeallot")
4411 (synopsis "Multiple, unpacking, and destructuring assignment")
4413 "This package provides a @code{%<-%} operator to perform multiple,
4414 unpacking, and destructuring assignment in R. The operator unpacks the
4415 right-hand side of an assignment into multiple values and assigns these values
4416 to variables on the left-hand side of the assignment.")
4417 (license license:expat)))
4419 (define-public r-vctrs
4426 (uri (cran-uri "vctrs" version))
4429 "025si8gqwsj79lna3s0hdzxmymjyzbjq3ddan7n6chah6n3kbrhp"))))
4430 (build-system r-build-system)
4432 `(("r-digest" ,r-digest)
4433 ("r-ellipsis" ,r-ellipsis)
4435 ("r-rlang" ,r-rlang)))
4437 `(("r-knitr" ,r-knitr)))
4438 (home-page "https://github.com/r-lib/vctrs")
4439 (synopsis "Vector helpers")
4441 "There are three main goals to the @code{vctrs} package:
4444 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4445 @code{length()} and @code{class()}. These definitions are paired with a
4446 framework for type-coercion and size-recycling.
4447 @item To define type- and size-stability as desirable function properties, use
4448 them to analyse existing base function, and to propose better alternatives.
4449 This work has been particularly motivated by thinking about the ideal
4450 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4451 @item To provide a new @code{vctr} base class that makes it easy to create new
4452 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4453 a few new @code{vctrs} generics, making implementation considerably simpler
4456 (license license:gpl3)))
4458 (define-public r-pillar
4465 (uri (cran-uri "pillar" version))
4468 "0viymfp1rkr7ig3m1b016r75hk8qbr9cqsjc6c20ks9pm5svmsp1"))))
4469 (build-system r-build-system)
4472 ("r-crayon" ,r-crayon)
4473 ("r-fansi" ,r-fansi)
4474 ("r-rlang" ,r-rlang)
4476 ("r-vctrs" ,r-vctrs)))
4477 (home-page "https://github.com/r-lib/pillar")
4478 (synopsis "Coloured formatting for columns")
4480 "This package provides a @code{pillar} generic designed for formatting
4481 columns of data using the full range of colours provided by modern
4483 (license license:gpl3)))
4485 (define-public r-uuid
4492 (uri (cran-uri "uuid" version))
4495 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4496 (build-system r-build-system)
4497 (home-page "https://www.rforge.net/uuid")
4498 (synopsis "Tools for generating and handling of UUIDs")
4500 "This package provides tools for generating and handling of
4501 @dfn{Universally Unique Identifiers} (UUIDs).")
4502 (license license:expat)))
4504 (define-public r-tinytex
4511 (uri (cran-uri "tinytex" version))
4514 "0mc9i7r45s5kagcfig508dbyf6jir6q4ghq9cxqvnpxp6ymh4qpr"))))
4515 (build-system r-build-system)
4517 `(("r-xfun" ,r-xfun)))
4518 (home-page "https://github.com/yihui/tinytex")
4519 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4521 "This package provides helper functions to install and maintain the LaTeX
4522 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4523 easy-to-maintain version of TeX Live. This package also contains helper
4524 functions to compile LaTeX documents, and install missing LaTeX packages
4526 (license license:expat)))
4528 (define-public r-network
4535 (uri (cran-uri "network" version))
4538 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4539 (build-system r-build-system)
4541 `(("r-magrittr" ,r-magrittr)
4542 ("r-tibble" ,r-tibble)))
4543 (home-page "https://statnet.org/")
4544 (synopsis "Classes for relational data")
4546 "This package provides tools to create and modify network objects. The
4547 @code{network} class can represent a range of relational data types, and
4548 supports arbitrary vertex/edge/graph attributes.")
4549 (license license:gpl2+)))
4551 (define-public r-statnet-common
4553 (name "r-statnet-common")
4558 (uri (cran-uri "statnet.common" version))
4561 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4563 `((upstream-name . "statnet.common")))
4564 (build-system r-build-system)
4566 `(("r-coda" ,r-coda)))
4567 (home-page "https://statnet.org")
4568 (synopsis "R scripts and utilities used by the Statnet software")
4569 (description "This package provides non-statistical utilities used by the
4570 software developed by the Statnet Project.")
4571 (license license:gpl3)))
4573 (define-public r-statcheck
4575 (name "r-statcheck")
4580 (uri (cran-uri "statcheck" version))
4583 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4584 (build-system r-build-system)
4586 `(("r-ggplot2" ,r-ggplot2)
4588 ("r-rmarkdown" ,r-rmarkdown)))
4589 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4590 (synopsis "Extract statistics from articles and recompute p-values")
4591 (description "This package can automatically extract statistical
4592 null-hypothesis significant testing (NHST) results from articles and recompute
4593 the p-values based on the reported test statistic and degrees of freedom to
4594 detect possible inconsistencies.")
4595 (license license:gpl2)))
4597 (define-public r-sna
4604 (uri (cran-uri "sna" version))
4607 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4608 (build-system r-build-system)
4610 `(("r-network" ,r-network)
4611 ("r-statnet-common" ,r-statnet-common)))
4612 (home-page "https://statnet.org")
4613 (synopsis "Tools for social network analysis")
4615 "This package provides a range of tools for social network analysis,
4616 including node and graph-level indices, structural distance and covariance
4617 methods, structural equivalence detection, network regression, random graph
4618 generation, and 2D/3D network visualization.")
4619 (license license:gpl2+)))
4621 (define-public r-tfisher
4628 (uri (cran-uri "TFisher" version))
4631 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4632 (properties `((upstream-name . "TFisher")))
4633 (build-system r-build-system)
4635 `(("r-matrix" ,r-matrix)
4636 ("r-mvtnorm" ,r-mvtnorm)
4638 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4639 (synopsis "Optimal thresholding Fisher's p-value combination method")
4641 "This package provides the @dfn{cumulative distribution function} (CDF),
4642 quantile, and statistical power calculator for a collection of thresholding
4643 Fisher's p-value combination methods, including Fisher's p-value combination
4644 method, truncated product method and, in particular, soft-thresholding
4645 Fisher's p-value combination method which is proven to be optimal in some
4646 context of signal detection. The p-value calculator for the omnibus version
4647 of these tests are also included.")
4648 (license license:gpl2)))
4650 (define-public r-ttr
4657 (uri (cran-uri "TTR" version))
4660 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4661 (properties `((upstream-name . "TTR")))
4662 (build-system r-build-system)
4664 `(("r-curl" ,r-curl)
4667 (home-page "https://github.com/joshuaulrich/TTR")
4668 (synopsis "Technical trading rules")
4670 "This package provides functions and data to construct technical trading
4672 (license license:gpl2)))
4674 (define-public r-leaps
4681 (uri (cran-uri "leaps" version))
4684 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4685 (build-system r-build-system)
4686 (native-inputs `(("gfortran" ,gfortran)))
4687 (home-page "https://cran.r-project.org/web/packages/leaps/")
4688 (synopsis "Regression subset selection")
4690 "This package provides tools for regression subset selection, including
4691 exhaustive search.")
4692 (license license:gpl2+)))
4694 (define-public r-splus2r
4701 (uri (cran-uri "splus2R" version))
4704 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4705 (properties `((upstream-name . "splus2R")))
4706 (build-system r-build-system)
4707 (native-inputs `(("gfortran" ,gfortran)))
4708 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4709 (synopsis "Supplemental S-PLUS functionality in R")
4711 "Currently there are many functions in S-PLUS that are missing in R. To
4712 facilitate the conversion of S-PLUS packages to R packages, this package
4713 provides some missing S-PLUS functionality in R.")
4714 (license license:gpl2)))
4716 (define-public r-ifultools
4718 (name "r-ifultools")
4723 (uri (cran-uri "ifultools" version))
4726 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4727 (build-system r-build-system)
4729 `(("r-mass" ,r-mass)
4730 ("r-splus2r" ,r-splus2r)))
4731 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4732 (synopsis "Insightful research tools")
4733 (description "This package provides C code used by the wmtsa, fractal, and
4735 (license license:gpl2)))
4737 (define-public r-sapa
4744 (uri (cran-uri "sapa" version))
4747 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4748 (build-system r-build-system)
4750 `(("r-ifultools" ,r-ifultools)
4751 ("r-splus2r" ,r-splus2r)))
4752 (home-page "https://cran.r-project.org/web/packages/sapa/")
4753 (synopsis "Spectral analysis for physical applications")
4754 (description "This package provides software for the book Spectral
4755 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4756 Cambridge University Press, 1993.")
4757 (license license:gpl2)))
4759 (define-public r-aggregation
4761 (name "r-aggregation")
4766 (uri (cran-uri "aggregation" version))
4769 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4770 (build-system r-build-system)
4771 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4772 (synopsis "Methods for p-value aggregation")
4774 "This package contains functionality for performing the following methods
4775 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4776 Fisher's method), and Sidak correction.")
4777 (license license:gpl3)))
4779 (define-public r-quantmod
4786 (uri (cran-uri "quantmod" version))
4789 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4790 (build-system r-build-system)
4792 `(("r-curl" ,r-curl)
4796 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4797 (synopsis "Quantitative financial modelling framework")
4798 (description "This package provides a quantitative financial modelling
4799 framework to allow users to specify, build, trade, and analyse quantitative
4800 financial trading strategies.")
4801 (license license:gpl3)))
4803 (define-public r-tseries
4810 (uri (cran-uri "tseries" version))
4813 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4814 (build-system r-build-system)
4816 `(("r-quadprog" ,r-quadprog)
4817 ("r-quantmod" ,r-quantmod)
4820 `(("gfortran" ,gfortran)))
4821 (home-page "https://cran.r-project.org/web/packages/tseries/")
4822 (synopsis "Time series analysis and computational finance")
4824 "This package provides functions relating to time series analysis and
4825 computational finance.")
4826 (license license:gpl2)))
4828 (define-public r-wmtsa
4835 (uri (cran-uri "wmtsa" version))
4838 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4839 (build-system r-build-system)
4841 `(("r-ifultools" ,r-ifultools)
4843 ("r-splus2r" ,r-splus2r)))
4844 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4845 (synopsis "Wavelet methods for time series analysis")
4847 "This package provides software to accompany the book \"Wavelet Methods
4848 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4849 University Press, 2000.")
4850 (license license:gpl2)))
4852 (define-public r-tsa
4859 (uri (cran-uri "TSA" version))
4862 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4863 (properties `((upstream-name . "TSA")))
4864 (build-system r-build-system)
4866 `(("r-leaps" ,r-leaps)
4867 ("r-locfit" ,r-locfit)
4868 ("r-mgcv" ,r-mgcv)))
4869 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4870 (synopsis "Time series analysis")
4872 "This package contains R functions and datasets detailed in the book
4873 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4874 Cryer and Kung-Sik Chan.")
4875 (license license:gpl2+)))
4877 (define-public r-extradistr
4879 (name "r-extradistr")
4884 (uri (cran-uri "extraDistr" version))
4887 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4888 (properties `((upstream-name . "extraDistr")))
4889 (build-system r-build-system)
4891 `(("r-rcpp" ,r-rcpp)))
4892 (home-page "https://github.com/twolodzko/extraDistr")
4893 (synopsis "Additional univariate and multivariate distributions")
4895 "This package implements density, distribution functions, quantile
4896 functions and random generation functions for a large number of univariate and
4897 multivariate distributions.")
4898 (license license:gpl2)))
4900 (define-public r-fractal
4907 (uri (cran-uri "fractal" version))
4910 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4911 (build-system r-build-system)
4913 `(("r-ifultools" ,r-ifultools)
4916 ("r-scatterplot3d" ,r-scatterplot3d)
4917 ("r-splus2r" ,r-splus2r)
4918 ("r-wmtsa" ,r-wmtsa)))
4919 (home-page "https://cran.r-project.org/web/packages/fractal/")
4920 (synopsis "Fractal time series modeling and analysis")
4922 "This package provides tools for stochastic fractal and deterministic
4923 chaotic time series analysis.")
4924 (license license:gpl2)))
4926 (define-public r-urca
4933 (uri (cran-uri "urca" version))
4936 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4937 (build-system r-build-system)
4938 (propagated-inputs `(("r-nlme" ,r-nlme)))
4939 (native-inputs `(("gfortran" ,gfortran)))
4940 (home-page "https://cran.r-project.org/web/packages/urca/")
4941 (synopsis "Unit root and cointegration tests for time series data")
4943 "This package provides unit root and cointegration tests encountered in
4944 applied econometric analysis.")
4945 (license license:gpl2+)))
4947 (define-public r-cubature
4954 (uri (cran-uri "cubature" version))
4957 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4958 (build-system r-build-system)
4960 `(("r-rcpp" ,r-rcpp)))
4961 (home-page "https://github.com/bnaras/cubature")
4962 (synopsis "Adaptive multivariate integration over hypercubes")
4964 "This package is an R wrapper around the cubature C library for adaptive
4965 multivariate integration over hypercubes. This version provides both
4966 @code{hcubature} and @code{pcubature} routines in addition to a vector
4968 ;; The included cubature C library is released under GPLv2+, but the
4969 ;; wrapper declares the license to be GPLv3+.
4970 (license (list license:gpl2+ license:gpl3+))))
4972 (define-public r-trend
4979 (uri (cran-uri "trend" version))
4982 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4983 (build-system r-build-system)
4985 `(("r-extradistr" ,r-extradistr)))
4987 `(("gfortran" ,gfortran)))
4988 (home-page "https://cran.r-project.org/web/packages/trend/")
4989 (synopsis "Non-parametric trend tests and change-point detection")
4991 "The analysis of environmental data often requires the detection of
4992 trends and change-points. This package includes tests for trend
4993 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4994 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4995 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4996 correlation trend test), change-point detection (Lanzante's test procedures,
4997 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
4998 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
4999 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5000 sample Robust Rank-Order Distributional Test.")
5001 (license license:gpl3)))
5003 (define-public r-expm
5010 (uri (cran-uri "expm" version))
5013 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
5014 (build-system r-build-system)
5015 (propagated-inputs `(("r-matrix" ,r-matrix)))
5016 (native-inputs `(("gfortran" ,gfortran)))
5017 (home-page "https://r-forge.r-project.org/projects/expm/")
5018 (synopsis "Tools for matrix exponentials and related quantities")
5020 "This package provides tools for the computation of the matrix
5021 exponential, logarithm, square root, and related quantities.")
5022 (license license:gpl2+)))
5024 (define-public r-complexplus
5026 (name "r-complexplus")
5031 (uri (cran-uri "complexplus" version))
5034 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5035 (build-system r-build-system)
5037 `(("r-expm" ,r-expm)
5038 ("r-matrix" ,r-matrix)))
5039 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5040 (synopsis "Functions of complex or real variables")
5042 "This package extends several functions to the complex domain, including
5043 the matrix exponential and logarithm, and the determinant.")
5044 (license license:gpl2)))
5046 (define-public r-phontools
5048 (name "r-phontools")
5053 (uri (cran-uri "phonTools" version))
5056 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5057 (properties `((upstream-name . "phonTools")))
5058 (build-system r-build-system)
5059 (home-page "http://www.santiagobarreda.com/rscripts.html")
5060 (synopsis "Tools for phonetic and acoustic analyses")
5062 "This package contains tools for the organization, display, and analysis
5063 of the sorts of data frequently encountered in phonetics research and
5064 experimentation, including the easy creation of IPA vowel plots, and the
5065 creation and manipulation of WAVE audio files.")
5066 (license license:bsd-2)))
5075 (uri (cran-uri "np" version))
5078 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5079 (build-system r-build-system)
5081 `(("r-boot" ,r-boot)
5082 ("r-cubature" ,r-cubature)
5083 ("r-quadprog" ,r-quadprog)
5084 ("r-quantreg" ,r-quantreg)))
5085 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5086 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5087 (description "This package provides non-parametric (and semi-parametric)
5088 kernel methods that seamlessly handle a mix of continuous, unordered, and
5089 ordered factor data types.")
5090 ;; Any version of the GPL.
5091 (license license:gpl3+)))
5093 (define-public r-powerplus
5095 (name "r-powerplus")
5100 (uri (cran-uri "powerplus" version))
5103 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5104 (build-system r-build-system)
5106 `(("r-complexplus" ,r-complexplus)
5109 ("r-matrix" ,r-matrix)
5110 ("r-phontools" ,r-phontools)))
5111 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5112 (synopsis "Exponentiation operations")
5114 "This package provides tools for the computation of matrix and scalar
5116 (license license:gpl2)))
5118 (define-public r-egg
5125 (uri (cran-uri "egg" version))
5128 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5129 (properties `((upstream-name . "egg")))
5130 (build-system r-build-system)
5132 `(("r-ggplot2" ,r-ggplot2)
5133 ("r-gridextra" ,r-gridextra)
5134 ("r-gtable" ,r-gtable)))
5135 (home-page "https://cran.r-project.org/web/packages/egg")
5136 (synopsis "Extensions for ggplot2")
5138 "This package provides miscellaneous functions to help customize ggplot2
5139 objects. High-level functions are provided to post-process ggplot2 layouts
5140 and allow alignment between plot panels, as well as setting panel sizes to
5141 fixed values. Other functions include a custom @code{geom}, and helper
5142 functions to enforce symmetric scales or add tags to facetted plots.")
5143 (license license:gpl3)))
5145 (define-public r-heatmaply
5147 (name "r-heatmaply")
5152 (uri (cran-uri "heatmaply" version))
5155 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
5156 (build-system r-build-system)
5158 `(("r-assertthat" ,r-assertthat)
5159 ("r-colorspace" ,r-colorspace)
5160 ("r-dendextend" ,r-dendextend)
5162 ("r-ggplot2" ,r-ggplot2)
5163 ("r-htmlwidgets" ,r-htmlwidgets)
5164 ("r-magrittr" ,r-magrittr)
5165 ("r-plotly" ,r-plotly)
5166 ("r-rcolorbrewer" ,r-rcolorbrewer)
5167 ("r-reshape2" ,r-reshape2)
5168 ("r-scales" ,r-scales)
5169 ("r-seriation" ,r-seriation)
5170 ("r-viridis" ,r-viridis)
5171 ("r-webshot" ,r-webshot)))
5173 `(("r-knitr" ,r-knitr)))
5174 (home-page "https://cran.r-project.org/package=heatmaply")
5175 (synopsis "Interactive cluster heat maps using plotly")
5177 "This package enables you to create interactive cluster heatmaps that can
5178 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5179 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5180 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5181 a popular graphical method for visualizing high-dimensional data, in which a
5182 table of numbers is encoded as a grid of colored cells. The rows and columns
5183 of the matrix are ordered to highlight patterns and are often accompanied by
5185 ;; Either version of the license.
5186 (license (list license:gpl2 license:gpl3))))
5195 (uri (cran-uri "h5" version))
5198 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5199 (build-system r-build-system)
5204 `(("which" ,which)))
5206 `(("r-rcpp" ,r-rcpp)))
5207 (home-page "https://github.com/mannau/h5")
5208 (synopsis "Interface to the HDF5 Library")
5210 "This package provides an S4 interface to the HDF5 library supporting
5211 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5212 binary files in a language independent format. The HDF5 format can therefore
5213 be used as an alternative to R's save/load mechanism. Since h5 is able to
5214 access only subsets of stored data it can also handle data sets which do not
5216 (license license:bsd-2)))
5218 (define-public r-cgdsr
5225 (uri (cran-uri "cgdsr" version))
5228 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5229 (build-system r-build-system)
5231 `(("r-httr" ,r-httr)
5232 ("r-r-methodss3" ,r-r-methodss3)
5233 ("r-r-oo" ,r-r-oo)))
5234 (home-page "https://github.com/cBioPortal/cgdsr")
5235 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5237 "This package provides a basic set of R functions for querying the Cancer
5238 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5239 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5240 (license license:lgpl3)))
5242 (define-public r-import
5249 (uri (cran-uri "import" version))
5252 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5253 (build-system r-build-system)
5254 (home-page "https://github.com/smbache/import")
5255 (synopsis "Import mechanism for R")
5257 "This is an alternative mechanism for importing objects from packages.
5258 The syntax allows for importing multiple objects from a package with a single
5259 command in an expressive way. The import package bridges some of the gap
5260 between using @code{library} (or @code{require}) and direct (single-object)
5261 imports. Furthermore the imported objects are not placed in the current
5262 environment. It is also possible to import objects from stand-alone @code{.R}
5264 (license license:expat)))
5266 (define-public r-shinyace
5273 (uri (cran-uri "shinyAce" version))
5276 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5277 (properties `((upstream-name . "shinyAce")))
5278 (build-system r-build-system)
5280 `(("r-shiny" ,r-shiny)
5281 ("r-jsonlite" ,r-jsonlite)))
5282 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5283 (synopsis "Ace editor bindings for Shiny")
5285 "This package provides Ace editor bindings to enable a rich text editing
5286 environment within Shiny.")
5287 (license license:expat)))
5289 (define-public r-randomizr
5291 (name "r-randomizr")
5296 (uri (cran-uri "randomizr" version))
5299 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5300 (properties `((upstream-name . "randomizr")))
5301 (build-system r-build-system)
5303 `(("r-knitr" ,r-knitr)))
5304 (home-page "https://declaredesign.org/r/randomizr/")
5305 (synopsis "Tools for common forms of random assignment and sampling")
5307 "This package provides tools for generating random assignments for common
5308 experimental designs and random samples for common sampling designs.")
5309 (license license:expat)))
5311 (define-public r-base64url
5313 (name "r-base64url")
5318 (uri (cran-uri "base64url" version))
5321 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5322 (build-system r-build-system)
5324 `(("r-backports" ,r-backports)))
5325 (home-page "https://github.com/mllg/base64url")
5326 (synopsis "Fast and URL-safe base64 encoder and decoder")
5328 "This package provides a URL-safe base64 encoder and decoder. In
5329 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5330 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5331 encoder does not fill the string with trailing @code{=}. The resulting
5332 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5333 and thus are safe to use in URLs or for file names. The package also comes
5334 with a simple base32 encoder/decoder suited for case insensitive file
5336 (license license:gpl3)))
5338 (define-public r-radiant-data
5340 (name "r-radiant-data")
5345 (uri (cran-uri "radiant.data" version))
5348 "19gbc7k1hsi6hg6ka8i70wlw8j9fs9wkpn36761lzbcyam6vgqn0"))
5349 (modules '((guix build utils)))
5352 ;; Delete files that are under CC-NC-SA.
5353 (delete-file-recursively "inst/app/tools/help")
5355 (properties `((upstream-name . "radiant.data")))
5356 (build-system r-build-system)
5358 `(("r-base64enc" ,r-base64enc)
5359 ("r-broom" ,r-broom)
5362 ("r-dplyr" ,r-dplyr)
5365 ("r-ggplot2" ,r-ggplot2)
5366 ("r-import" ,r-import)
5367 ("r-jsonlite" ,r-jsonlite)
5368 ("r-knitr" ,r-knitr)
5369 ("r-lubridate" ,r-lubridate)
5370 ("r-magrittr" ,r-magrittr)
5371 ("r-markdown" ,r-markdown)
5373 ("r-patchwork" ,r-patchwork)
5374 ("r-plotly" ,r-plotly)
5375 ("r-psych" ,r-psych)
5376 ("r-randomizr" ,r-randomizr)
5377 ("r-readr" ,r-readr)
5378 ("r-readxl" ,r-readxl)
5379 ("r-rlang" ,r-rlang)
5380 ("r-rmarkdown" ,r-rmarkdown)
5381 ("r-rstudioapi" ,r-rstudioapi)
5382 ("r-scales" ,r-scales)
5383 ("r-shiny" ,r-shiny)
5384 ("r-shinyfiles" ,r-shinyfiles)
5385 ("r-shinyace" ,r-shinyace)
5386 ("r-stringi" ,r-stringi)
5387 ("r-tibble" ,r-tibble)
5388 ("r-tidyr" ,r-tidyr)
5389 ("r-writexl" ,r-writexl)))
5390 (home-page "https://github.com/radiant-rstats/radiant.data")
5391 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5393 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5394 visualizing, summarizing, transforming, and combining data. It also contains
5395 functionality to generate reproducible reports of the analyses conducted in
5397 (license license:agpl3)))
5399 (define-public r-algdesign
5401 (name "r-algdesign")
5406 (uri (cran-uri "AlgDesign" version))
5408 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5409 (properties `((upstream-name . "AlgDesign")))
5410 (build-system r-build-system)
5411 (home-page "https://github.com/jvbraun/AlgDesign")
5412 (synopsis "Algorithmic experimental design")
5414 "This package provides tools to calculate exact and approximate theory
5415 experimental designs for D, A, and I criteria. Very large designs may be
5416 created. Experimental designs may be blocked or blocked designs created from
5417 a candidate list, using several criteria. The blocking can be done when whole
5418 and within plot factors interact.")
5419 (license license:gpl2+)))
5421 (define-public r-signal
5428 (uri (cran-uri "signal" version))
5431 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5432 (build-system r-build-system)
5433 (propagated-inputs `(("r-mass" ,r-mass)))
5434 (native-inputs `(("gfortran" ,gfortran)))
5435 (home-page "https://cran.r-project.org/web/packages/signal/")
5436 (synopsis "Signal processing")
5438 "This package provides a set of signal processing functions originally
5439 written for Matlab and GNU Octave. It includes filter generation utilities,
5440 filtering functions, resampling routines, and visualization of filter models.
5441 It also includes interpolation functions.")
5442 (license license:gpl2)))
5444 (define-public r-gsubfn
5451 (uri (cran-uri "gsubfn" version))
5454 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5455 (build-system r-build-system)
5456 (propagated-inputs `(("r-proto" ,r-proto)))
5457 (home-page "https://code.google.com/archive/p/gsubfn/")
5458 (synopsis "Utilities for strings and function arguments.")
5460 "This package provides @code{gsubfn} which is like @code{gsub} but can
5461 take a replacement function or certain other objects instead of the
5462 replacement string. Matches and back references are input to the replacement
5463 function and replaced by the function output. @code{gsubfn} can be used to
5464 split strings based on content rather than delimiters and for quasi-perl-style
5465 string interpolation. The package also has facilities for translating
5466 formulas to functions and allowing such formulas in function calls instead of
5468 (license license:gpl2+)))
5470 (define-public r-sqldf
5477 (uri (cran-uri "sqldf" version))
5480 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5481 (build-system r-build-system)
5483 `(("r-chron" ,r-chron)
5485 ("r-gsubfn" ,r-gsubfn)
5486 ("r-proto" ,r-proto)
5487 ("r-rsqlite" ,r-rsqlite)))
5488 (home-page "https://github.com/ggrothendieck/sqldf")
5489 (synopsis "Manipulate R data frames using SQL")
5491 "The @code{sqldf} function is typically passed a single argument which is
5492 an SQL select statement where the table names are ordinary R data frame names.
5493 @code{sqldf} transparently sets up a database, imports the data frames into
5494 that database, performs the SQL statement and returns the result using a
5495 heuristic to determine which class to assign to each column of the returned
5496 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5497 used to read filtered files into R even if the original files are larger than
5498 R itself can handle.")
5499 (license license:gpl2)))
5501 (define-public r-abind
5508 (uri (cran-uri "abind" version))
5511 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5512 (build-system r-build-system)
5513 (home-page "https://cran.r-project.org/web/packages/abind/")
5514 (synopsis "Combine multidimensional arrays")
5516 "This package provides tools to combine multidimensional arrays into a
5517 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5518 works with vectors, matrices, and higher-dimensional arrays. It also provides
5519 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5520 extracting and replacing data in arrays.")
5521 (license license:lgpl2.0+)))
5523 (define-public r-prroc
5530 (uri (cran-uri "PRROC" version))
5533 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5534 (properties `((upstream-name . "PRROC")))
5535 (build-system r-build-system)
5536 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5537 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5539 "This package computes the areas under the @dfn{precision-recall} (PR)
5540 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5541 contrast to other implementations, the interpolation between points of the PR
5542 curve is done by a non-linear piecewise function. In addition to the areas
5543 under the curves, the curves themselves can also be computed and plotted by a
5544 specific S3-method.")
5545 (license license:gpl3)))
5547 (define-public r-vim
5554 (uri (cran-uri "VIM" version))
5557 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5558 (properties `((upstream-name . "VIM")))
5559 (build-system r-build-system)
5562 ("r-colorspace" ,r-colorspace)
5563 ("r-data-table" ,r-data-table)
5564 ("r-e1071" ,r-e1071)
5565 ("r-laeken" ,r-laeken)
5566 ("r-magrittr" ,r-magrittr)
5569 ("r-ranger" ,r-ranger)
5571 ("r-robustbase" ,r-robustbase)
5575 `(("r-knitr" ,r-knitr)))
5576 (home-page "https://github.com/alexkowa/VIM")
5577 (synopsis "Visualization and imputation of missing values")
5579 "This package provides tools for the visualization of missing and/or
5580 imputed values are introduced, which can be used for exploring the data and
5581 the structure of the missing and/or imputed values. Depending on this
5582 structure of the missing values, the corresponding methods may help to
5583 identify the mechanism generating the missing values and allows to explore the
5584 data including missing values. In addition, the quality of imputation can be
5585 visually explored using various univariate, bivariate, multiple and
5586 multivariate plot methods.")
5587 (license license:gpl2+)))
5589 (define-public r-fnn
5596 (uri (cran-uri "FNN" version))
5599 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5600 (properties `((upstream-name . "FNN")))
5601 (build-system r-build-system)
5602 (home-page "https://cran.r-project.org/web/packages/FNN")
5603 (synopsis "Fast nearest neighbor search algorithms and applications")
5605 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5606 search algorithms. Related applications including KNN classification,
5607 regression and information measures are implemented.")
5608 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5609 ;; later can be used.
5610 (license license:gpl2+)))
5612 (define-public r-smoother
5619 (uri (cran-uri "smoother" version))
5622 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5623 (build-system r-build-system)
5625 `(("r-ttr" ,r-ttr)))
5626 (home-page "https://cran.r-project.org/web/packages/smoother")
5627 (synopsis "Functions relating to the smoothing of numerical data")
5629 "This package provides a collection of methods for smoothing numerical
5630 data, commencing with a port of the Matlab gaussian window smoothing function.
5631 In addition, several functions typically used in smoothing of financial data
5633 (license license:gpl2)))
5635 (define-public r-riverplot
5637 (name "r-riverplot")
5642 (uri (cran-uri "riverplot" version))
5645 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5646 (build-system r-build-system)
5647 (home-page "https://logfc.wordpress.com")
5648 (synopsis "Sankey or ribbon plots")
5650 "Sankey plots are a type of diagram that is convenient to illustrate how
5651 flow of information, resources etc. separates and joins, much like observing
5652 how rivers split and merge. For example, they can be used to compare
5653 different clusterings. This package provides an implementation of Sankey
5655 (license license:gpl2+)))
5657 (define-public r-dyn
5664 (uri (cran-uri "dyn" version))
5667 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5668 (build-system r-build-system)
5670 `(("r-zoo" ,r-zoo)))
5671 (home-page "https://cran.r-project.org/web/packages/dyn")
5672 (synopsis "Time series regression")
5674 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5675 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5676 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5677 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5678 @code{randomForest::randomForest()} and other regression functions, allowing
5679 those functions to be used with time series including specifications that may
5680 contain lags, diffs and missing values.")
5682 (license license:gpl2+)))
5684 (define-public r-catdap
5691 (uri (cran-uri "catdap" version))
5694 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5695 (build-system r-build-system)
5697 `(("gfortran" ,gfortran)))
5698 (home-page "https://cran.r-project.org/web/packages/catdap/")
5699 (synopsis "Tools for categorical data analysis")
5701 "This package provides functions for analyzing multivariate data.
5702 Dependencies of the distribution of the specified variable (response
5703 variable) to other variables (explanatory variables) are derived and
5704 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5705 (license license:gpl2+)))
5707 (define-public r-arules
5714 (uri (cran-uri "arules" version))
5717 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5718 (build-system r-build-system)
5720 `(("r-matrix" ,r-matrix)))
5721 (home-page "https://github.com/mhahsler/arules")
5722 (synopsis "Mining association rules and frequent itemsets")
5724 "This package provides an infrastructure for representing, manipulating
5725 and analyzing transaction data and patterns (frequent itemsets and association rules).
5726 It also provides C implementations of the association mining algorithms Apriori
5728 (license license:gpl3)))
5730 (define-public r-parsedate
5732 (name "r-parsedate")
5737 (uri (cran-uri "parsedate" version))
5740 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5741 (build-system r-build-system)
5743 `(("r-rematch2" ,r-rematch2)))
5744 (home-page "https://github.com/gaborcsardi/parsedate")
5746 "Recognize and parse dates in various formats")
5748 "This package provides three functions for dealing with dates:
5749 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5750 time formats, @code{parse_date} parses dates in unspecified formats,
5751 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5752 (license license:gpl2)))
5754 (define-public r-abc-data
5761 (uri (cran-uri "abc.data" version))
5764 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5765 (properties `((upstream-name . "abc.data")))
5766 (build-system r-build-system)
5767 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5768 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5770 "This package contains data which are used by functions of the abc
5771 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5772 algorithms for performing parameter estimation, model selection, and
5774 (license license:gpl3+)))
5776 (define-public r-abc
5783 (uri (cran-uri "abc" version))
5786 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5787 (build-system r-build-system)
5789 `(("r-abc-data" ,r-abc-data)
5790 ("r-locfit" ,r-locfit)
5793 ("r-quantreg" ,r-quantreg)))
5794 (home-page "https://cran.r-project.org/web/packages/abc/")
5795 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5797 "This package implements several @dfn{Approximate Bayesian
5798 Computation} (ABC) algorithms for performing parameter estimation, model
5799 selection, and goodness-of-fit. Cross-validation tools are also available for
5800 measuring the accuracy of ABC estimates, and to calculate the
5801 misclassification probabilities of different models.")
5802 (license license:gpl3+)))
5804 (define-public r-zip
5811 (uri (cran-uri "zip" version))
5814 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5815 (build-system r-build-system)
5816 (home-page "https://github.com/gaborcsardi/zip")
5817 (synopsis "Cross-platform Zip compression")
5819 "This package provides a cross-platform Zip compression library for R.
5820 It is a replacement for the @code{zip} function, that does not require any
5821 additional external tools on any platform.")
5822 (license license:cc0)))
5824 (define-public r-openxlsx
5831 (uri (cran-uri "openxlsx" version))
5834 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
5835 (build-system r-build-system)
5837 `(("r-rcpp" ,r-rcpp)
5838 ("r-stringi" ,r-stringi)
5841 `(("r-knitr" ,r-knitr)))
5842 (home-page "https://github.com/awalker89/openxlsx")
5843 (synopsis "Read, write and edit XLSX files")
5845 "This package simplifies the creation of Excel @code{.xlsx} files by
5846 providing a high level interface to writing, styling and editing worksheets.
5847 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5848 and @code{XLConnect} packages with the added benefit of removing the
5849 dependency on Java.")
5850 (license license:gpl3)))
5852 (define-public r-rio
5859 (uri (cran-uri "rio" version))
5862 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5863 (build-system r-build-system)
5865 `(("r-curl" ,r-curl)
5866 ("r-data-table" ,r-data-table)
5867 ("r-foreign" ,r-foreign)
5868 ("r-haven" ,r-haven)
5869 ("r-openxlsx" ,r-openxlsx)
5870 ("r-readxl" ,r-readxl)
5871 ("r-tibble" ,r-tibble)))
5872 (home-page "https://github.com/leeper/rio")
5873 (synopsis "Swiss-army knife for data I/O")
5875 "This package provides streamlined data import and export infrastructure
5876 by making assumptions that the user is probably willing to make: @code{import}
5877 and @code{export} determine the data structure from the file extension,
5878 reasonable defaults are used for data import and export (e.g.,
5879 @code{stringsAsFactors=FALSE}), web-based import is natively
5880 supported (including from SSL/HTTPS), compressed files can be read directly
5881 without explicit decompression, and fast import packages are used where
5882 appropriate. An additional convenience function, @code{convert}, provides a
5883 simple method for converting between file types.")
5884 (license license:gpl2)))
5886 (define-public r-maptools
5893 (uri (cran-uri "maptools" version))
5896 "0fs1y3cbymcq4f76wd27h5a7ihdmxii3ca8x29x32xgxhmasni4l"))))
5897 (build-system r-build-system)
5899 `(("r-foreign" ,r-foreign)
5900 ("r-lattice" ,r-lattice)
5902 (home-page "https://r-forge.r-project.org/projects/maptools/")
5903 (synopsis "Tools for reading and handling spatial objects")
5905 "This package provides a set of tools for manipulating and reading
5906 geographic data, in particular ESRI Shapefiles. It includes binary access to
5907 GSHHG shoreline files. The package also provides interface wrappers for
5908 exchanging spatial objects with other R packages.")
5909 ;; The C source files from shapelib are released under the Expat license.
5910 ;; The R code is released under GPL version 2 or later.
5911 (license (list license:gpl2+
5914 (define-public r-later
5921 (uri (cran-uri "later" version))
5924 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
5925 (build-system r-build-system)
5929 ("r-rlang" ,r-rlang)))
5931 `(("r-knitr" ,r-knitr)))
5932 (home-page "https://github.com/r-lib/later")
5933 (synopsis "Utilities for delaying function execution")
5935 "This package provides tools to execute arbitrary R or C functions some
5936 time after the current time, after the R execution stack has emptied.")
5937 (license license:gpl2+)))
5939 (define-public r-promises
5946 (uri (cran-uri "promises" version))
5949 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
5950 (build-system r-build-system)
5952 `(("r-later" ,r-later)
5953 ("r-magrittr" ,r-magrittr)
5956 ("r-rlang" ,r-rlang)))
5958 `(("r-knitr" ,r-knitr)))
5959 (home-page "https://rstudio.github.io/promises")
5960 (synopsis "Abstractions for promise-based asynchronous programming")
5962 "This package provides fundamental abstractions for doing asynchronous
5963 programming in R using promises. Asynchronous programming is useful for
5964 allowing a single R process to orchestrate multiple tasks in the background
5965 while also attending to something else. Semantics are similar to JavaScript
5966 promises, but with a syntax that is idiomatic R.")
5967 (license license:expat)))
5969 (define-public r-dosnow
5976 (uri (cran-uri "doSNOW" version))
5979 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5980 (properties `((upstream-name . "doSNOW")))
5981 (build-system r-build-system)
5983 `(("r-foreach" ,r-foreach)
5984 ("r-iterators" ,r-iterators)
5985 ("r-snow" ,r-snow)))
5986 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5987 (synopsis "Foreach parallel adaptor for the snow package")
5989 "This package provides a parallel backend for the @code{%dopar%} function
5990 using the @code{snow} package.")
5991 (license license:gpl2)))
5993 (define-public r-snowfall
5996 (version "1.84-6.1")
5999 (uri (cran-uri "snowfall" version))
6001 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6002 (build-system r-build-system)
6004 `(("r-snow" ,r-snow)))
6005 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6006 (synopsis "Easier cluster computing")
6007 (description "This package is a usability wrapper around snow for easier
6008 development of parallel R programs. This package offers e.g. extended error
6009 checks, and additional functions. All functions work in sequential mode, too,
6010 if no cluster is present or wished. The package is also designed as connector
6011 to the cluster management tool @code{sfCluster}, but can also used without
6013 (license license:gpl2+)))
6015 (define-public r-rappdirs
6022 (uri (cran-uri "rappdirs" version))
6025 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6026 (build-system r-build-system)
6027 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6028 (synopsis "Determine where to save data, caches, and logs")
6030 "This package provides an easy way to determine which directories on the
6031 user's computer should be used to save data, caches and logs. It is a port of
6032 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6033 (license license:expat)))
6035 (define-public r-renv
6042 (uri (cran-uri "renv" version))
6045 "0yy24kq60dh9n68my132xhhkbnbs7q91z55b1yd6ymr7rxj32mif"))))
6046 (properties `((upstream-name . "renv")))
6047 (build-system r-build-system)
6049 `(("r-knitr" ,r-knitr)))
6050 (home-page "https://rstudio.github.io/renv")
6051 (synopsis "Project environments")
6053 "This package provides a dependency management toolkit for R. Using
6054 renv, you can create and manage project-local R libraries, save the state of
6055 these libraries to a lockfile, and later restore your library as required.
6056 Together, these tools can help make your projects more isolated, portable, and
6058 (license license:expat)))
6060 (define-public r-learnr
6067 (uri (cran-uri "learnr" version))
6070 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6071 (build-system r-build-system)
6073 `(("r-checkmate" ,r-checkmate)
6074 ("r-ellipsis" ,r-ellipsis)
6075 ("r-evaluate" ,r-evaluate)
6076 ("r-htmltools" ,r-htmltools)
6077 ("r-htmlwidgets" ,r-htmlwidgets)
6078 ("r-jsonlite" ,r-jsonlite)
6079 ("r-knitr" ,r-knitr)
6080 ("r-markdown" ,r-markdown)
6081 ("r-rappdirs" ,r-rappdirs)
6083 ("r-rmarkdown" ,r-rmarkdown)
6084 ("r-rprojroot" ,r-rprojroot)
6085 ("r-shiny" ,r-shiny)
6086 ("r-withr" ,r-withr)))
6087 (home-page "https://rstudio.github.io/learnr/")
6088 (synopsis "Interactive tutorials for R")
6090 "This package provides tools to create interactive tutorials using R
6091 Markdown. Use a combination of narrative, figures, videos, exercises, and
6092 quizzes to create self-paced tutorials for learning about R and R packages.")
6093 (license license:asl2.0)))
6095 (define-public r-analytics
6097 (name "r-analytics")
6102 (uri (cran-uri "analytics" version))
6105 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6106 (build-system r-build-system)
6109 ("r-cluster" ,r-cluster)
6110 ("r-fractal" ,r-fractal)
6111 ("r-lmtest" ,r-lmtest)
6114 ("r-powerplus" ,r-powerplus)
6115 ("r-robust" ,r-robust)
6116 ("r-trend" ,r-trend)
6120 (home-page "https://cran.r-project.org/web/packages/analytics/")
6121 (synopsis "Collection of data analysis tools")
6123 "This package is a collection of data analysis tools. It includes tools
6124 for regression outlier detection in a fitted linear model, stationary
6125 bootstrap using a truncated geometric distribution, a comprehensive test for
6126 weak stationarity, column means by group, weighted biplots, and a heuristic to
6127 obtain a better initial configuration in non-metric MDS.")
6128 (license license:gpl2)))
6130 (define-public r-reticulate
6132 (name "r-reticulate")
6137 (uri (cran-uri "reticulate" version))
6140 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6141 (build-system r-build-system)
6142 (inputs `(("python" ,python)))
6144 `(("r-rappdirs" ,r-rappdirs)
6145 ("r-jsonlite" ,r-jsonlite)
6146 ("r-matrix" ,r-matrix)
6147 ("r-rcpp" ,r-rcpp)))
6149 `(("r-knitr" ,r-knitr)))
6150 (home-page "https://github.com/rstudio/reticulate")
6151 (synopsis "R interface to Python")
6153 "This package provides an interface from R to Python modules, classes,
6154 and functions. When calling into Python, R data types are automatically
6155 converted to their equivalent Python types. When values are returned from
6156 Python to R they are converted back to R types.")
6157 (license license:asl2.0)))
6159 (define-public r-bibtex
6166 (uri (cran-uri "bibtex" version))
6169 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6170 (build-system r-build-system)
6171 (propagated-inputs `(("r-stringr" ,r-stringr)))
6172 (home-page "https://github.com/romainfrancois/bibtex")
6173 (synopsis "Bibtex parser")
6174 (description "This package provides a utility for R to parse a bibtex
6176 (license license:gpl2+)))
6178 (define-public r-ggseqlogo
6180 (name "r-ggseqlogo")
6185 (uri (cran-uri "ggseqlogo" version))
6188 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6189 (build-system r-build-system)
6190 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6191 (home-page "https://github.com/omarwagih/ggseqlogo")
6192 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6194 "The range of functions provided by this package makes it possible to
6195 draw highly versatile genomic sequence logos. Features include, but are not
6196 limited to, modifying colour schemes and fonts used to draw the logo,
6197 generating multiple logo plots, and aiding the visualisation with annotations.
6198 Sequence logos can easily be combined with other ggplot2 plots.")
6199 ;; Unspecified version of the LGPL.
6200 (license license:lgpl3+)))
6202 (define-public r-ggsci
6209 (uri (cran-uri "ggsci" version))
6212 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6213 (build-system r-build-system)
6215 `(("r-ggplot2" ,r-ggplot2)
6216 ("r-scales" ,r-scales)))
6217 (home-page "https://nanx.me/ggsci/")
6218 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6220 "This package provides a collection of ggplot2 color palettes inspired by
6221 plots in scientific journals, data visualization libraries, science fiction
6222 movies, and TV shows.")
6223 (license license:gpl3)))
6225 (define-public r-ggsignif
6232 (uri (cran-uri "ggsignif" version))
6235 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6236 (build-system r-build-system)
6238 `(("r-knitr" ,r-knitr)))
6240 `(("r-ggplot2" ,r-ggplot2)))
6241 (home-page "https://github.com/const-ae/ggsignif")
6242 (synopsis "Significance brackets for ggplot2")
6244 "Enrich your ggplots with group-wise comparisons. This package provides
6245 an easy way to indicate if two groups are significantly different. Commonly
6246 this is shown by a bracket on top connecting the groups of interest which
6247 itself is annotated with the level of significance. The package provides a
6248 single layer that takes the groups for comparison and the test as arguments
6249 and adds the annotation to the plot.")
6250 (license license:gpl3)))
6252 (define-public r-rstatix
6259 (uri (cran-uri "rstatix" version))
6262 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6263 (properties `((upstream-name . "rstatix")))
6264 (build-system r-build-system)
6266 `(("r-broom" ,r-broom)
6268 ("r-corrplot" ,r-corrplot)
6269 ("r-dplyr" ,r-dplyr)
6270 ("r-generics" ,r-generics)
6271 ("r-magrittr" ,r-magrittr)
6272 ("r-purrr" ,r-purrr)
6273 ("r-rlang" ,r-rlang)
6274 ("r-tibble" ,r-tibble)
6275 ("r-tidyr" ,r-tidyr)
6276 ("r-tidyselect" ,r-tidyselect)))
6277 (home-page "https://rpkgs.datanovia.com/rstatix/")
6278 (synopsis "Pipe-friendly framework for basic statistical tests")
6280 "This package provides a simple and intuitive pipe-friendly framework,
6281 coherent with the @code{tidyverse} design philosophy, for performing basic
6282 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6283 correlation analyses. The output of each test is automatically transformed
6284 into a tidy data frame to facilitate visualization. Additional functions are
6285 available for reshaping, reordering, manipulating and visualizing correlation
6287 (license license:gpl2)))
6289 (define-public r-ggpubr
6296 (uri (cran-uri "ggpubr" version))
6299 "1dly74cnn8iq7vsgmcz0czszdsmg5cgzm4w3s0v30k4psmmzqbxq"))))
6300 (build-system r-build-system)
6302 `(("r-cowplot" ,r-cowplot)
6303 ("r-dplyr" ,r-dplyr)
6304 ("r-ggplot2" ,r-ggplot2)
6305 ("r-ggrepel" ,r-ggrepel)
6306 ("r-ggsci" ,r-ggsci)
6307 ("r-ggsignif" ,r-ggsignif)
6309 ("r-gridextra" ,r-gridextra)
6310 ("r-magrittr" ,r-magrittr)
6311 ("r-polynom" ,r-polynom)
6312 ("r-purrr" ,r-purrr)
6313 ("r-rlang" ,r-rlang)
6314 ("r-scales" ,r-scales)
6315 ("r-rstatix" ,r-rstatix)
6316 ("r-tibble" ,r-tibble)
6317 ("r-tidyr" ,r-tidyr)))
6318 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6319 (synopsis "ggplot2-based publication-ready plots")
6321 "The ggplot2 package is an excellent and flexible package for elegant
6322 data visualization in R. However the default generated plots require some
6323 formatting before we can send them for publication. The ggpubr package
6324 provides some easy-to-use functions for creating and customizing ggplot2-based
6325 publication-ready plots.")
6326 (license license:gpl2)))
6328 (define-public r-ellipse
6335 (uri (cran-uri "ellipse" version))
6338 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6339 (build-system r-build-system)
6340 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6341 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6343 "This package contains various routines for drawing ellipses and
6344 ellipse-like confidence regions, implementing the plots described in Murdoch
6345 and Chow (1996), A graphical display of large correlation matrices, The
6346 American Statistician 50, 178-180. There are also routines implementing the
6347 profile plots described in Bates and Watts (1988), Nonlinear Regression
6348 Analysis and its Applications.")
6349 (license license:gpl2+)))
6351 (define-public r-flashclust
6353 (name "r-flashclust")
6358 (uri (cran-uri "flashClust" version))
6361 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6362 (properties `((upstream-name . "flashClust")))
6363 (build-system r-build-system)
6364 (native-inputs `(("gfortran" ,gfortran)))
6365 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6366 (synopsis "Implementation of optimal hierarchical clustering")
6368 "This package provides a fast implementation of hierarchical
6370 (license license:gpl2+)))
6372 (define-public r-factominer
6374 (name "r-factominer")
6379 (uri (cran-uri "FactoMineR" version))
6382 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6383 (properties `((upstream-name . "FactoMineR")))
6384 (build-system r-build-system)
6387 ("r-cluster" ,r-cluster)
6388 ("r-ellipse" ,r-ellipse)
6389 ("r-flashclust" ,r-flashclust)
6390 ("r-ggplot2" ,r-ggplot2)
6391 ("r-ggrepel" ,r-ggrepel)
6392 ("r-lattice" ,r-lattice)
6393 ("r-leaps" ,r-leaps)
6395 ("r-scatterplot3d" ,r-scatterplot3d)))
6396 (home-page "http://factominer.free.fr")
6397 (synopsis "Multivariate exploratory data analysis and data mining")
6399 "This package provides exploratory data analysis methods to summarize,
6400 visualize and describe datasets. The main principal component methods are
6401 available, those with the largest potential in terms of applications:
6402 principal component analysis (PCA) when variables are quantitative,
6403 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6404 variables are categorical, Multiple Factor Analysis when variables are
6405 structured in groups, etc. and hierarchical cluster analysis.")
6406 (license license:gpl2+)))
6408 (define-public r-factoextra
6410 (name "r-factoextra")
6415 (uri (cran-uri "factoextra" version))
6418 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6419 (build-system r-build-system)
6421 `(("r-abind" ,r-abind)
6422 ("r-cluster" ,r-cluster)
6423 ("r-dendextend" ,r-dendextend)
6424 ("r-factominer" ,r-factominer)
6425 ("r-ggplot2" ,r-ggplot2)
6426 ("r-ggpubr" ,r-ggpubr)
6427 ("r-ggrepel" ,r-ggrepel)
6428 ("r-reshape2" ,r-reshape2)
6429 ("r-tidyr" ,r-tidyr)))
6430 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6431 (synopsis "Extract and visualize the results of multivariate data analyses")
6433 "This package provides some easy-to-use functions to extract and
6434 visualize the output of multivariate data analyses, including
6435 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6436 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6437 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6438 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6439 packages. It contains also functions for simplifying some clustering analysis
6440 steps and provides ggplot2-based elegant data visualization.")
6441 (license license:gpl2)))
6443 (define-public r-fansi
6450 (uri (cran-uri "fansi" version))
6453 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6454 (build-system r-build-system)
6456 `(("r-knitr" ,r-knitr))) ; for vignettes
6457 (home-page "https://github.com/brodieG/fansi")
6458 (synopsis "ANSI control sequence aware string functions")
6460 "This package provides counterparts to R string manipulation functions
6461 that account for the effects of ANSI text formatting control sequences.")
6462 (license license:gpl2+)))
6464 (define-public r-nbclust
6471 (uri (cran-uri "NbClust" version))
6474 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6475 (properties `((upstream-name . "NbClust")))
6476 (build-system r-build-system)
6477 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6478 (synopsis "Determine the best number of clusters in a data set")
6480 "NbClust provides 30 indexes for determining the optimal number of
6481 clusters in a data set and offers the best clustering scheme from different
6482 results to the user.")
6483 (license license:gpl2)))
6485 (define-public r-hdf5r
6492 (uri (cran-uri "hdf5r" version))
6495 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6496 (build-system r-build-system)
6501 `(("r-bit64" ,r-bit64)
6504 `(("r-knitr" ,r-knitr)))
6505 (home-page "https://hhoeflin.github.io/hdf5r")
6506 (synopsis "Interface to the HDF5 binary data format")
6508 "HDF5 is a data model, library and file format for storing and managing
6509 large amounts of data. This package provides a nearly feature complete,
6510 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6511 functionality is added so that HDF5 objects behave very similar to their
6512 corresponding R counterparts.")
6513 (license license:asl2.0)))
6515 (define-public r-itertools
6517 (name "r-itertools")
6522 (uri (cran-uri "itertools" version))
6525 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6526 (build-system r-build-system)
6528 `(("r-iterators" ,r-iterators)))
6529 (home-page "https://cran.r-project.org/web/packages/itertools/")
6530 (synopsis "Iterator tools")
6532 "This package provides various tools for creating iterators, many
6533 patterned after functions in the Python @code{itertools} module, and others
6534 patterned after functions in the snow package.")
6535 (license license:gpl2)))
6537 (define-public r-polynom
6544 (uri (cran-uri "polynom" version))
6547 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6548 (build-system r-build-system)
6549 (home-page "https://cran.r-project.org/web/packages/polynom/")
6550 (synopsis "Functions for univariate polynomial manipulations")
6552 "This package provides a collection of functions to implement a class for
6553 univariate polynomial manipulations.")
6554 (license license:gpl2)))
6556 (define-public r-gbrd
6563 (uri (cran-uri "gbRd" version))
6566 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6567 (properties `((upstream-name . "gbRd")))
6568 (build-system r-build-system)
6569 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6570 (synopsis "Utilities for processing Rd objects and files")
6572 "This package provides utilities for processing Rd objects and files.
6573 Extract argument descriptions and other parts of the help pages of
6575 (license license:gpl2+)))
6577 (define-public r-rjags
6584 (uri (cran-uri "rjags" version))
6587 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6588 (build-system r-build-system)
6590 `(("r-coda" ,r-coda)))
6594 `(("pkg-config" ,pkg-config)))
6595 (home-page "http://mcmc-jags.sourceforge.net")
6596 (synopsis "Bayesian graphical models using MCMC")
6598 "This package provides an R interface to the JAGS MCMC library. JAGS is
6599 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6600 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6601 (license license:gpl2)))
6603 (define-public r-rdpack
6610 (uri (cran-uri "Rdpack" version))
6613 "080y15p2hl4jsq91ak2f1y2kx1iqq5c5wzyx3zyhjwp01cahy0jq"))))
6614 (properties `((upstream-name . "Rdpack")))
6615 (build-system r-build-system)
6617 `(("r-bibtex" ,r-bibtex)
6618 ("r-gbrd" ,r-gbrd)))
6619 (home-page "https://github.com/GeoBosh/Rdpack")
6620 (synopsis "Update and manipulate Rd documentation objects")
6622 "This package provides functions for manipulation of R documentation
6623 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6624 updating Rd documentation for functions, methods and classes; it also includes
6625 Rd macros for citations and import of references from bibtex files for use in
6626 Rd files and roxygen2 comments, as well as many functions for manipulation of
6627 references and Rd files.")
6628 (license license:gpl2+)))
6630 (define-public r-officer
6637 (uri (cran-uri "officer" version))
6640 "0nwasra2kb5wplcim7n57kynwhyg4vsk3fz42mbpm0hig1lzl9pp"))))
6641 (build-system r-build-system)
6643 `(("r-magrittr" ,r-magrittr)
6649 `(("r-knitr" ,r-knitr)))
6650 (home-page "https://davidgohel.github.io/officer")
6651 (synopsis "Manipulation of Word and PowerPoint documents")
6653 "This package provides tools to access and manipulate Word and PowerPoint
6654 documents from R. The package focuses on tabular and graphical reporting from
6655 R; it also provides two functions that let users get document content into
6656 data objects. A set of functions lets add and remove images, tables and
6657 paragraphs of text in new or existing documents. When working with PowerPoint
6658 presentations, slides can be added or removed; shapes inside slides can also
6659 be added or removed. When working with Word documents, a cursor can be used
6660 to help insert or delete content at a specific location in the document.")
6661 (license license:gpl3)))
6663 (define-public r-profilemodel
6665 (name "r-profilemodel")
6670 (uri (cran-uri "profileModel" version))
6673 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6674 (properties `((upstream-name . "profileModel")))
6675 (build-system r-build-system)
6676 (home-page "https://github.com/ikosmidis/profileModel")
6677 (synopsis "Profiling inference functions for various model classes")
6679 "This package provides tools that can be used to calculate, evaluate,
6680 plot and use for inference the profiles of *arbitrary* inference functions for
6681 arbitrary @code{glm}-like fitted models with linear predictors. More information
6682 on the methods that are implemented can be found in Kosmidis (2008)
6683 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6684 (license license:gpl2+)))
6686 (define-public r-brglm
6693 (uri (cran-uri "brglm" version))
6696 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6697 (properties `((upstream-name . "brglm")))
6698 (build-system r-build-system)
6700 `(("r-profilemodel" ,r-profilemodel)))
6701 (home-page "https://github.com/ikosmidis/brglm")
6702 (synopsis "Bias reduction in binomial-response generalized linear models")
6704 "Fit generalized linear models with binomial responses using either an
6705 adjusted-score approach to bias reduction or maximum penalized likelihood
6706 where penalization is by Jeffreys invariant prior. These procedures return
6707 estimates with improved frequentist properties (bias, mean squared error) that
6708 are always finite even in cases where the maximum likelihood estimates are
6709 infinite (data separation). Fitting takes place by fitting generalized linear
6710 models on iteratively updated pseudo-data. The interface is essentially the
6711 same as @code{glm}. More flexibility is provided by the fact that custom
6712 pseudo-data representations can be specified and used for model fitting.
6713 Functions are provided for the construction of confidence intervals for the
6714 reduced-bias estimates.")
6715 (license license:gpl2+)))
6717 (define-public r-entropy
6724 (uri (cran-uri "entropy" version))
6727 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6728 (properties `((upstream-name . "entropy")))
6729 (build-system r-build-system)
6730 (home-page "https://www.strimmerlab.org/software/entropy/")
6731 (synopsis "Estimation of entropy, mutual information and related quantities")
6733 "This package implements various estimators of entropy, such as the
6734 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6735 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6736 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6737 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6738 mutual information, and chi-squared statistic of independence. In addition
6739 there are functions for discretizing continuous random variables.")
6740 (license license:gpl3+)))
6742 (define-public r-abn
6749 (uri (cran-uri "abn" version))
6752 "11nbg6dwvbj0ac7qvr203vzjnw5zc1a8cibb9l6rzzr7yfg16xzc"))))
6753 (build-system r-build-system)
6757 `(("r-boot" ,r-boot)
6758 ("r-brglm" ,r-brglm)
6759 ("r-entropy" ,r-entropy)
6762 ("r-moments" ,r-moments)
6765 ("r-rcpparmadillo" ,r-rcpparmadillo)
6766 ("r-rjags" ,r-rjags)))
6767 (home-page "https://r-bayesian-networks.org/")
6768 (synopsis "Modelling multivariate data with additive bayesian networks")
6770 "Bayesian network analysis is a form of probabilistic graphical models
6771 which derives from empirical data a directed acyclic graph, DAG, describing
6772 the dependency structure between random variables. An additive Bayesian
6773 network model consists of a form of a DAG where each node comprises a
6774 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6775 equivalent to Bayesian multivariate regression using graphical modelling, they
6776 generalises the usual multivariable regression, GLM, to multiple dependent
6777 variables. This package provides routines to help determine optimal Bayesian
6778 network models for a given data set, where these models are used to identify
6779 statistical dependencies in messy, complex data.")
6780 (license license:gpl2+)))
6782 (define-public r-acd
6789 (uri (cran-uri "ACD" version))
6792 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6793 (properties `((upstream-name . "ACD")))
6794 (build-system r-build-system)
6795 (home-page "https://cran.r-project.org/web/packages/ACD/")
6796 (synopsis "Categorical data analysis with complete or missing responses")
6798 "This package provides tools for categorical data analysis with complete
6799 or missing responses.")
6800 (license license:gpl2+)))
6802 (define-public r-acdm
6809 (uri (cran-uri "ACDm" version))
6812 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6813 (properties `((upstream-name . "ACDm")))
6814 (build-system r-build-system)
6816 `(("r-dplyr" ,r-dplyr)
6817 ("r-ggplot2" ,r-ggplot2)
6819 ("r-rsolnp" ,r-rsolnp)
6821 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6822 (synopsis "Tools for Autoregressive Conditional Duration Models")
6824 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6825 and Russell, 1998) models. It creates trade, price or volume durations from
6826 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6828 (license license:gpl2+)))
6830 (define-public r-overlap
6837 (uri (cran-uri "overlap" version))
6840 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
6841 (build-system r-build-system)
6842 (home-page "https://cran.r-project.org/web/packages/overlap/")
6843 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6845 "This package provides functions to fit kernel density functions to data
6846 on temporal activity patterns of animals; estimate coefficients of overlapping
6847 of densities for two species; and calculate bootstrap estimates of confidence
6849 (license license:gpl3+)))
6851 (define-public r-snakecase
6853 (name "r-snakecase")
6858 (uri (cran-uri "snakecase" version))
6861 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6862 (build-system r-build-system)
6864 `(("r-stringi" ,r-stringi)
6865 ("r-stringr" ,r-stringr)))
6866 (home-page "https://github.com/Tazinho/snakecase")
6867 (synopsis "Convert strings into any case")
6869 "This package provides a consistent, flexible and easy to use tool to
6870 parse and convert strings into cases like snake or camel among others.")
6871 (license license:gpl3)))
6873 (define-public r-prediction
6875 (name "r-prediction")
6880 (uri (cran-uri "prediction" version))
6883 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6884 (build-system r-build-system)
6886 `(("r-data-table" ,r-data-table)))
6887 (home-page "https://github.com/leeper/prediction")
6888 (synopsis "Tidy, type-safe prediction methods")
6890 "This package provides the @code{prediction()} function, a type-safe
6891 alternative to @code{predict()} that always returns a data frame. The package
6892 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6893 from the @code{stats} package, as well as numerous other model classes from
6894 other add-on packages.")
6895 (license license:expat)))
6897 (define-public r-insight
6904 (uri (cran-uri "insight" version))
6907 "0ggczjd112kclknyxxqvjkzwzazfhjwglchafzamk4zb08ww7y7k"))))
6908 (build-system r-build-system)
6910 `(("r-knitr" ,r-knitr)))
6911 (home-page "https://easystats.github.io/insight/")
6912 (synopsis "Easy access to model information for various model objects")
6914 "This package provides a tool to provide an easy, intuitive and
6915 consistent access to information contained in various R models, like model
6916 formulas, model terms, information about random effects, data that was used to
6917 fit the model or data from response variables. The package mainly revolves
6918 around two types of functions: Functions that find (the names of) information,
6919 starting with @code{find_}, and functions that get the underlying data,
6920 starting with @code{get_}. The package has a consistent syntax and works with
6921 many different model objects, where otherwise functions to access these
6922 information are missing.")
6923 (license license:gpl3)))
6925 (define-public r-sjlabelled
6927 (name "r-sjlabelled")
6932 (uri (cran-uri "sjlabelled" version))
6935 "0grskmd7wrw31lkf85z6xz0bv246m6grvqkijvqi4q8zkl6p5vb3"))))
6936 (build-system r-build-system)
6938 `(("r-insight" ,r-insight)))
6940 `(("r-knitr" ,r-knitr)))
6941 (home-page "https://github.com/strengejacke/sjlabelled")
6942 (synopsis "Labelled data utility functions")
6944 "This package provides a collection of functions dealing with labelled
6945 data, like reading and writing data between R and other statistical software
6946 packages. This includes easy ways to get, set or change value and variable
6947 label attributes, to convert labelled vectors into factors or numeric (and
6948 vice versa), or to deal with multiple declared missing values.")
6949 (license license:gpl3)))
6951 (define-public r-sjmisc
6958 (uri (cran-uri "sjmisc" version))
6961 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
6962 (build-system r-build-system)
6964 `(("r-dplyr" ,r-dplyr)
6965 ("r-insight" ,r-insight)
6966 ("r-magrittr" ,r-magrittr)
6967 ("r-purrr" ,r-purrr)
6968 ("r-rlang" ,r-rlang)
6969 ("r-sjlabelled" ,r-sjlabelled)
6970 ("r-tidyselect" ,r-tidyselect)))
6972 `(("r-knitr" ,r-knitr)))
6973 (home-page "https://github.com/strengejacke/sjmisc")
6974 (synopsis "Data and variable transformation functions")
6976 "This package is a collection of miscellaneous utility functions,
6977 supporting data transformation tasks like recoding, dichotomizing or grouping
6978 variables, setting and replacing missing values. The data transformation
6979 functions also support labelled data, and all integrate seamlessly into a
6980 tidyverse workflow.")
6981 (license license:gpl3)))
6983 (define-public r-nortest
6990 (uri (cran-uri "nortest" version))
6993 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6994 (build-system r-build-system)
6995 (home-page "https://cran.r-project.org/web/packages/nortest/")
6996 (synopsis "Tests for normality")
6998 "This package provides five omnibus tests for testing the composite
6999 hypothesis of normality.")
7000 (license license:gpl2+)))
7002 (define-public r-moonbook
7009 (uri (cran-uri "moonBook" version))
7012 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7013 (properties `((upstream-name . "moonBook")))
7014 (build-system r-build-system)
7016 `(("r-magrittr" ,r-magrittr)
7017 ("r-nortest" ,r-nortest)
7018 ("r-purrr" ,r-purrr)
7019 ("r-sjmisc" ,r-sjmisc)
7020 ("r-stringr" ,r-stringr)
7021 ("r-survival" ,r-survival)))
7022 (home-page "https://github.com/cardiomoon/moonBook")
7023 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7025 "This package provides several analysis-related functions for the book
7026 entitled \"R statistics and graph for medical articles\" (written in Korean),
7027 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7029 (license license:gpl2)))
7031 (define-public r-flextable
7033 (name "r-flextable")
7038 (uri (cran-uri "flextable" version))
7041 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7042 (build-system r-build-system)
7044 `(("r-base64enc" ,r-base64enc)
7045 ("r-data-table" ,r-data-table)
7046 ("r-gdtools" ,r-gdtools)
7047 ("r-htmltools" ,r-htmltools)
7048 ("r-knitr" ,r-knitr)
7049 ("r-officer" ,r-officer)
7050 ("r-rlang" ,r-rlang)
7051 ("r-rmarkdown" ,r-rmarkdown)
7053 ("r-xml2" ,r-xml2)))
7054 (home-page "https://davidgohel.github.io/flextable")
7055 (synopsis "Functions for tabular reporting")
7057 "This package provides tools to create pretty tables for HTML documents
7058 and other formats. Functions are provided to let users create tables, modify
7059 and format their content. It extends the @code{officer} package and can be
7060 used within R markdown documents when rendering to HTML and to Word
7062 (license license:gpl3)))
7064 (define-public r-writexl
7071 (uri (cran-uri "writexl" version))
7074 "0lah0r2pd996s0vdbi614j3h52dbxmifha6f19v53p2b7fr32wjd"))))
7075 (build-system r-build-system)
7076 (inputs `(("zlib" ,zlib)))
7077 (home-page "https://github.com/ropensci/writexl")
7078 (synopsis "Export data frames to xlsx format")
7080 "This package provides a data frame to xlsx exporter based on
7082 (license license:bsd-2)))
7084 (define-public r-biasedurn
7086 (name "r-biasedurn")
7091 (uri (cran-uri "BiasedUrn" version))
7094 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7095 (properties `((upstream-name . "BiasedUrn")))
7096 (build-system r-build-system)
7097 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7098 (synopsis "Biased Urn model distributions")
7100 "This package provides statistical models of biased sampling in the form
7101 of univariate and multivariate noncentral hypergeometric distributions,
7102 including Wallenius' noncentral hypergeometric distribution and Fisher's
7103 noncentral hypergeometric distribution (also called extended hypergeometric
7105 (license license:gpl3)))
7107 (define-public r-goplot
7114 (uri (cran-uri "GOplot" version))
7117 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7118 (properties `((upstream-name . "GOplot")))
7119 (build-system r-build-system)
7121 `(("r-ggdendro" ,r-ggdendro)
7122 ("r-ggplot2" ,r-ggplot2)
7123 ("r-gridextra" ,r-gridextra)
7124 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7125 (home-page "https://github.com/wencke/wencke.github.io")
7126 (synopsis "Visualization of functional analysis data")
7128 "This package provides an implementation of multilayered visualizations
7129 for enhanced graphical representation of functional analysis data. It
7130 combines and integrates omics data derived from expression and functional
7131 annotation enrichment analyses. Its plotting functions have been developed
7132 with an hierarchical structure in mind: starting from a general overview to
7133 identify the most enriched categories (modified bar plot, bubble plot) to a
7134 more detailed one displaying different types of relevant information for the
7135 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7136 Venn diagram, heatmap).")
7137 (license license:gpl2)))
7139 (define-public r-getopt
7146 (uri (cran-uri "getopt" version))
7149 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7150 (build-system r-build-system)
7151 (home-page "https://github.com/trevorld/getopt")
7152 (synopsis "Command-line option processor for R")
7154 "This package is designed to be used with Rscript to write shebang
7155 scripts that accept short and long options. Many users will prefer to
7156 use the packages @code{optparse} or @code{argparse} which add extra
7157 features like automatically generated help options and usage texts,
7158 support for default values, positional argument support, etc.")
7159 (license license:gpl2+)))
7161 (define-public r-findpython
7163 (name "r-findpython")
7168 (uri (cran-uri "findpython" version))
7171 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7172 (build-system r-build-system)
7173 (home-page "https://github.com/trevorld/findpython")
7174 (synopsis "Functions to find an acceptable Python binary")
7176 "This package was designed to find an acceptable Python binary that
7177 matches version and feature constraints.")
7178 (license license:expat)))
7180 ;; This in not the same as "r-argparser"
7181 (define-public r-argparse
7188 (uri (cran-uri "argparse" version))
7191 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7192 (build-system r-build-system)
7193 (inputs `(("python" ,python)))
7195 `(("r-findpython" ,r-findpython)
7196 ("r-jsonlite" ,r-jsonlite)
7198 (home-page "https://github.com/trevorld/argparse")
7199 (synopsis "Command line optional and positional argument parser")
7201 "This package provides a command line parser to be used with Rscript to
7202 write shebang scripts that gracefully accept positional and optional arguments
7203 and automatically generate usage notices.")
7204 (license license:gpl2+)))
7206 (define-public r-hash
7213 (uri (cran-uri "hash" version))
7216 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7217 (build-system r-build-system)
7218 (home-page "https://cran.r-project.org/web/packages/hash/")
7219 (synopsis "Implementation of hash/associated arrays/dictionaries")
7221 "This package implements a data structure similar to hashes in Perl and
7222 dictionaries in Python but with a purposefully R flavor. For objects of
7223 appreciable size, access using hashes outperforms native named lists and
7225 (license license:gpl2+)))
7227 (define-public r-orddom
7234 (uri (cran-uri "orddom" version))
7237 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7238 (build-system r-build-system)
7239 (propagated-inputs `(("r-psych" ,r-psych)))
7240 (home-page "https://cran.r-project.org/web/packages/orddom/")
7241 (synopsis "Ordinal dominance statistics")
7243 "This package provides tools to compute ordinal, statistics and effect
7244 sizes as an alternative to mean comparison: Cliff's delta or success rate
7245 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7246 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7247 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7248 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7249 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7250 Group (Non-)Overlap considerations.")
7251 (license license:gpl2)))
7253 (define-public r-deriv
7260 (uri (cran-uri "Deriv" version))
7263 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
7264 (properties `((upstream-name . "Deriv")))
7265 (build-system r-build-system)
7266 (home-page "https://cran.r-project.org/web/packages/Deriv")
7267 (synopsis "Symbolic differentiation")
7269 "This package provides an R-based solution for symbolic differentiation.
7270 It admits user-defined functions as well as function substitution in arguments
7271 of functions to be differentiated. Some symbolic simplification is part of
7273 (license license:gpl3+)))
7275 (define-public r-doby
7282 (uri (cran-uri "doBy" version))
7285 "0wz1vmsf1545r1m42q88s675ncwvm8figjn7kzbngjn9aqck9qbq"))))
7286 (properties `((upstream-name . "doBy")))
7287 (build-system r-build-system)
7289 `(("r-broom" ,r-broom)
7290 ("r-deriv" ,r-deriv)
7291 ("r-magrittr" ,r-magrittr)
7293 ("r-matrix" ,r-matrix)
7294 ("r-pbkrtest" ,r-pbkrtest)
7295 ("r-tibble" ,r-tibble)))
7297 `(("r-knitr" ,r-knitr)))
7298 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7299 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7301 "This package contains:
7304 @item facilities for working with grouped data: @code{do}
7305 something to data stratified @code{by} some variables.
7306 @item implementations of least-squares means, general linear contrasts, and
7307 @item miscellaneous other utilities.
7309 (license license:gpl2+)))
7311 (define-public r-refgenome
7313 (name "r-refgenome")
7318 (uri (cran-uri "refGenome" version))
7321 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7322 (properties `((upstream-name . "refGenome")))
7323 (build-system r-build-system)
7327 ("r-rsqlite" ,r-rsqlite)))
7328 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7330 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7332 "This package contains functionality for importing and managing of
7333 downloaded genome annotation data from the Ensembl genome browser (European
7334 Bioinformatics Institute) and from the UCSC genome browser (University of
7335 California, Santa Cruz) and annotation routines for genomic positions and
7336 splice site positions.")
7337 (license license:gpl2)))
7339 (define-public r-basix
7346 (uri (cran-uri "BASIX" version))
7349 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7350 (properties `((upstream-name . "BASIX")))
7351 (build-system r-build-system)
7352 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7353 (synopsis "Efficient C/C++ toolset for R")
7355 "BASIX provides some efficient C/C++ implementations of native R
7356 procedures to speed up calculations in R.")
7357 (license license:gpl2)))
7359 (define-public r-blockfest
7361 (name "r-blockfest")
7366 (uri (cran-uri "BlockFeST" version))
7369 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7370 (properties `((upstream-name . "BlockFeST")))
7371 (build-system r-build-system)
7372 (propagated-inputs `(("r-basix" ,r-basix)))
7373 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7374 (synopsis "Bayesian calculation of region-specific fixation index")
7376 "This package provides an R implementation of an extension of the
7377 BayeScan software for codominant markers, adding the option to group
7378 individual SNPs into pre-defined blocks. A typical application of this new
7379 approach is the identification of genomic regions, genes, or gene sets
7380 containing one or more SNPs that evolved under directional selection.")
7381 (license license:gpl2)))
7383 (define-public r-proc
7390 (uri (cran-uri "pROC" version))
7393 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7394 (properties `((upstream-name . "pROC")))
7395 (build-system r-build-system)
7397 `(("r-plyr" ,r-plyr)
7398 ("r-rcpp" ,r-rcpp)))
7399 (home-page "https://web.expasy.org/pROC/")
7400 (synopsis "Display and analyze ROC curves")
7402 "This package provides tools for visualizing, smoothing and comparing
7403 receiver operating characteristic (ROC curves). The area under the
7404 curve (AUC) can be compared with statistical tests based on U-statistics or
7405 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7406 (license license:gpl3+)))
7408 (define-public r-rootsolve
7410 (name "r-rootsolve")
7415 (uri (cran-uri "rootSolve" version))
7418 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7419 (properties `((upstream-name . "rootSolve")))
7420 (build-system r-build-system)
7421 (native-inputs `(("gfortran" ,gfortran)))
7422 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7423 (synopsis "Tools for the analysis of ordinary differential equations")
7425 "This package provides routines to find the root of nonlinear functions,
7426 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7427 differential equations} (ODE). It includes routines that:
7430 @item generate gradient and jacobian matrices (full and banded),
7431 @item find roots of non-linear equations by the Newton-Raphson method,
7432 @item estimate steady-state conditions of a system of (differential) equations
7433 in full, banded or sparse form, using the Newton-Raphson method, or by
7434 dynamically running,
7435 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7436 and 3-D partial differential equations, that have been converted to ordinary
7437 differential equations by numerical differencing (using the method-of-lines
7440 (license license:gpl2+)))
7442 (define-public r-abcanalysis
7444 (name "r-abcanalysis")
7449 (uri (cran-uri "ABCanalysis" version))
7451 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7452 (properties `((upstream-name . "ABCanalysis")))
7453 (build-system r-build-system)
7454 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7455 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7456 (synopsis "Computed ABC Analysis")
7458 "Multivariate data sets often differ in several factors or derived statistical
7459 parameters, which have to be selected for a valid interpretation. Basing this
7460 selection on traditional statistical limits leads occasionally to the perception
7461 of losing information from a data set. This package provides tools to calculate
7462 these limits on the basis of the mathematical properties of the distribution of
7463 the analyzed items.")
7464 (license license:gpl3)))
7466 (define-public r-slam
7473 (uri (cran-uri "slam" version))
7475 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7476 (build-system r-build-system)
7477 (home-page "https://cran.r-project.org/web/packages/slam/")
7478 (synopsis "Sparse lightweight arrays and matrices")
7480 "This package contains data structures and algorithms for sparse arrays and matrices,
7481 based on index arrays and simple triplet representations, respectively.")
7482 (license license:gpl2)))
7484 (define-public r-manipulatewidget
7486 (name "r-manipulatewidget")
7491 (uri (cran-uri "manipulateWidget" version))
7493 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7495 `((upstream-name . "manipulateWidget")))
7496 (build-system r-build-system)
7498 `(("r-base64enc" ,r-base64enc)
7499 ("r-codetools" ,r-codetools)
7500 ("r-htmltools" ,r-htmltools)
7501 ("r-htmlwidgets" ,r-htmlwidgets)
7502 ("r-knitr" ,r-knitr)
7503 ("r-miniui" ,r-miniui)
7504 ("r-shiny" ,r-shiny)
7505 ("r-webshot" ,r-webshot)))
7506 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7507 (synopsis "Add even more interactivity to interactive charts")
7509 "This package lets you create in just a few lines of R code a nice user interface to
7510 modify the data or the graphical parameters of one or multiple interactive
7511 charts. It is useful to quickly explore visually some data or for package
7512 developers to generate user interfaces easy to maintain.")
7513 (license license:gpl2+)))
7522 (uri (cran-uri "A3" version))
7524 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7525 (properties `((upstream-name . "A3")))
7526 (build-system r-build-system)
7528 `(("r-pbapply" ,r-pbapply)
7529 ("r-xtable" ,r-xtable)))
7530 (home-page "https://cran.r-project.org/web/packages/A3/")
7531 (synopsis "Error metrics for predictive models")
7533 "This package supplies tools for tabulating and analyzing the results of predictive
7534 models. The methods employed are applicable to virtually any predictive model
7535 and make comparisons between different methodologies straightforward.")
7536 (license license:gpl2+)))
7538 (define-public r-infotheo
7545 (uri (cran-uri "infotheo" version))
7548 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7549 (build-system r-build-system)
7550 (home-page "http://homepage.meyerp.com/software")
7551 (synopsis "Information-theoretic measures")
7553 "This package implements various measures of information theory based on
7554 several entropy estimators.")
7555 (license license:gpl3+)))
7557 (define-public r-abcoptim
7564 (uri (cran-uri "ABCoptim" version))
7566 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7567 (properties `((upstream-name . "ABCoptim")))
7568 (build-system r-build-system)
7569 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7570 (home-page "https://github.com/gvegayon/ABCoptim/")
7571 (synopsis "Optimization of Artificial Bee Colony algorithm")
7573 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7574 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7575 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7576 algorithms, and uses only common control parameters such as colony size and
7577 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7578 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7579 This version is a work-in-progress and is written in R code.")
7580 (license license:expat)))
7582 (define-public r-abcp2
7589 (uri (cran-uri "ABCp2" version))
7591 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7592 (properties `((upstream-name . "ABCp2")))
7593 (build-system r-build-system)
7594 (propagated-inputs `(("r-mass" ,r-mass)))
7595 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7596 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7598 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7599 Poisson, and Gamma distribution and estimates the proportional paternity of the
7600 second male (P2) based on the best fit distribution.")
7601 (license license:gpl2)))
7603 (define-public r-abcrf
7610 (uri (cran-uri "abcrf" version))
7612 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7613 (build-system r-build-system)
7615 `(("r-doparallel" ,r-doparallel)
7616 ("r-foreach" ,r-foreach)
7618 ("r-matrixstats" ,r-matrixstats)
7619 ("r-ranger" ,r-ranger)
7621 ("r-rcpparmadillo" ,r-rcpparmadillo)
7622 ("r-readr" ,r-readr)
7623 ("r-stringr" ,r-stringr)))
7624 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7625 (synopsis "Approximate bayesian computation via random forests")
7627 "This package performs approximate bayesian computation (ABC) model choice and
7628 parameter inference via random forests. This machine learning tool named random
7629 forests (RF) can conduct selection among the highly complex models covered by
7631 (license license:gpl2+)))
7633 (define-public r-abctools
7640 (uri (cran-uri "abctools" version))
7642 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7643 (build-system r-build-system)
7646 ("r-abind" ,r-abind)
7647 ("r-hmisc" ,r-hmisc)
7648 ("r-plyr" ,r-plyr)))
7649 (home-page "https://github.com/dennisprangle/abctools/")
7650 (synopsis "Tools for ABC analyses")
7652 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7653 including summary statistic selection and assessing coverage. This includes
7654 recent dimension reduction algorithms to tune the choice of summary statistics,
7655 and coverage methods to tune the choice of threshold.")
7656 (license license:gpl2+)))
7658 (define-public r-ggstance
7665 (uri (cran-uri "ggstance" version))
7667 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7668 (build-system r-build-system)
7670 `(("r-ggplot2" ,r-ggplot2)
7672 ("r-rlang" ,r-rlang)
7673 ("r-withr" ,r-withr)))
7674 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7675 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7677 "This package is a @code{r-ggplot2} extension that provides flipped components:
7679 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7680 @item vertical versions of @code{r-ggplot2} positions.
7682 (license license:gpl3)))
7684 (define-public r-mosaiccore
7686 (name "r-mosaiccore")
7691 (uri (cran-uri "mosaicCore" version))
7693 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7694 (properties `((upstream-name . "mosaicCore")))
7695 (build-system r-build-system)
7697 `(("r-dplyr" ,r-dplyr)
7698 ("r-lazyeval" ,r-lazyeval)
7700 ("r-rlang" ,r-rlang)
7701 ("r-tidyr" ,r-tidyr)))
7702 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7703 (synopsis "Common utilities for mosaic family packages")
7705 "Common utilities used in other Mosaic family packages are collected here.")
7706 (license license:gpl2+)))
7708 (define-public r-ggformula
7710 (name "r-ggformula")
7715 (uri (cran-uri "ggformula" version))
7717 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7718 (build-system r-build-system)
7720 `(("r-ggforce" ,r-ggforce)
7721 ("r-ggplot2" ,r-ggplot2)
7722 ("r-ggstance" ,r-ggstance)
7723 ("r-magrittr" ,r-magrittr)
7724 ("r-mosaiccore" ,r-mosaiccore)
7725 ("r-rlang" ,r-rlang)
7726 ("r-stringr" ,r-stringr)
7727 ("r-tibble" ,r-tibble)))
7728 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7729 (synopsis "Formula interface for the @code{r-ggplot2}")
7731 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7732 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7733 and extends the excellent simplicity of the lattice-graphics formula interface,
7734 while providing the intuitive capabilities of @code{r-ggplot2}.")
7735 (license license:expat)))
7737 (define-public r-mosaicdata
7739 (name "r-mosaicdata")
7744 (uri (cran-uri "mosaicData" version))
7746 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7747 (properties `((upstream-name . "mosaicData")))
7748 (build-system r-build-system)
7749 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7750 (synopsis "Data sets for project Mosaic")
7752 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7753 used to teach mathematics, statistics, computation and modeling.")
7754 (license license:gpl2+)))
7756 (define-public r-raster
7763 (uri (cran-uri "raster" version))
7766 "010sq00ijpmwac280ip9rryw0pxk0al8g675v2lc9rdrbgaj4rnv"))))
7767 (build-system r-build-system)
7769 `(("r-rcpp" ,r-rcpp)
7771 (home-page "https://www.rspatial.org/")
7772 (synopsis "Geographic data analysis and modeling")
7774 "The package implements basic and high-level functions for reading,
7775 writing, manipulating, analyzing and modeling of gridded spatial data.
7776 Processing of very large files is supported.")
7777 (license license:gpl3+)))
7779 (define-public r-mosaic
7786 (uri (cran-uri "mosaic" version))
7788 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7789 (build-system r-build-system)
7791 `(("r-broom" ,r-broom)
7792 ("r-dplyr" ,r-dplyr)
7793 ("r-ggdendro" ,r-ggdendro)
7794 ("r-ggformula" ,r-ggformula)
7795 ("r-ggplot2" ,r-ggplot2)
7796 ("r-ggrepel" ,r-ggrepel)
7798 ("r-gridextra" ,r-gridextra)
7799 ("r-lattice" ,r-lattice)
7800 ("r-latticeextra" ,r-latticeextra)
7801 ("r-lazyeval" ,r-lazyeval)
7803 ("r-matrix" ,r-matrix)
7804 ("r-mosaiccore" ,r-mosaiccore)
7805 ("r-mosaicdata" ,r-mosaicdata)
7806 ("r-readr" ,r-readr)
7807 ("r-tidyr" ,r-tidyr)))
7809 `(("r-knitr" ,r-knitr)))
7810 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7811 (synopsis "Mathematics, statistics, and computation teaching utilities")
7813 "This package contain data sets and utilities from
7814 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7815 statistics, computation and modeling. Project MOSAIC is a community of
7816 educators working to tie together aspects of quantitative work that students
7817 in science, technology, engineering and mathematics will need in their
7818 professional lives, but which are usually taught in isolation, if at all.")
7819 (license license:gpl2+)))
7821 (define-public r-abd
7828 (uri (cran-uri "abd" version))
7830 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7831 (build-system r-build-system)
7833 `(("r-lattice" ,r-lattice)
7834 ("r-mosaic" ,r-mosaic)
7835 ("r-nlme" ,r-nlme)))
7836 (home-page "https://cran.r-project.org/web/packages/abd/")
7837 (synopsis "Analysis of biological data")
7839 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7840 biological data by Michael Whitlock and Dolph Schluter.")
7841 (license license:gpl2)))
7843 (define-public r-svgui
7850 (uri (cran-uri "svGUI" version))
7852 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7853 (properties `((upstream-name . "svGUI")))
7854 (build-system r-build-system)
7855 (home-page "https://github.com/SciViews/svGUI/")
7856 (synopsis "Functions for managing GUI clients in R")
7858 "The SciViews @code{svGUI} package eases the management of Graphical User
7859 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7860 centralizes info about GUI elements currently used, and it dispatches GUI
7861 calls to the particular toolkits in use in function of the context.")
7862 (license license:gpl2)))
7864 (define-public r-svdialogs
7866 (name "r-svdialogs")
7871 (uri (cran-uri "svDialogs" version))
7873 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7874 (properties `((upstream-name . "svDialogs")))
7875 (build-system r-build-system)
7878 ("zenity" ,zenity)))
7880 `(("r-rstudioapi" ,r-rstudioapi)
7881 ("r-svgui" ,r-svgui)))
7882 (home-page "https://github.com/SciViews/svDialogs/")
7883 (synopsis "Portable dialog boxes")
7885 "This package helps to construct standard dialog boxes for your GUI, including
7886 message boxes, input boxes, list, file or directory selection, and others. In
7887 case R cannot display GUI dialog boxes, a simpler command line version of these
7888 interactive elements is also provided as a fallback solution.")
7889 (license license:gpl2)))
7891 (define-public r-abe
7898 (uri (cran-uri "abe" version))
7901 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7902 (build-system r-build-system)
7903 (home-page "https://cran.r-project.org/web/packages/abe/")
7904 (synopsis "Augmented backward elimination")
7906 "This package performs augmented backward elimination and checks the
7907 stability of the obtained model. Augmented backward elimination combines
7908 significance or information based criteria with the change in estimate to
7909 either select the optimal model for prediction purposes or to serve as a tool
7910 to obtain a practically sound, highly interpretable model.")
7911 (license license:gpl2+)))
7913 (define-public r-abf2
7920 (uri (cran-uri "abf2" version))
7922 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7923 (build-system r-build-system)
7924 (home-page "https://cran.r-project.org/web/packages/abf2/")
7925 (synopsis "Load gap-free axon @code{r-abf2} files")
7927 "This package loads electrophysiology data from ABF2 files, as created by
7928 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7929 mode are currently supported.")
7930 (license license:artistic2.0)))
7932 (define-public r-abhgenotyper
7934 (name "r-abhgenotyper")
7939 (uri (cran-uri "ABHgenotypeR" version))
7941 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7942 (properties `((upstream-name . "ABHgenotypeR")))
7943 (build-system r-build-system)
7945 `(("r-ggplot2" ,r-ggplot2)
7946 ("r-reshape2" ,r-reshape2)))
7947 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7948 (synopsis "Visualize and manipulate ABH genotypes")
7950 "The @code{r-abhgenotyper} package provides simple imputation,
7951 error-correction and plotting capacities for genotype data. The package is
7952 supposed to serve as an intermediate but independent analysis tool between the
7953 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7954 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7955 genotypes as \"graphical genotypes\".")
7956 (license license:gpl3)))
7958 (define-public r-furrr
7965 (uri (cran-uri "furrr" version))
7968 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7969 (build-system r-build-system)
7971 `(("r-future" ,r-future)
7972 ("r-globals" ,r-globals)
7973 ("r-purrr" ,r-purrr)
7974 ("r-rlang" ,r-rlang)))
7975 (home-page "https://github.com/DavisVaughan/furrr")
7976 (synopsis "Apply mapping functions in parallel using futures")
7978 "This package provides implementations of the family of @code{map()}
7979 functions from the @code{purrr} package that can be resolved using any
7980 @code{future}-supported backend, e.g. parallel on the local machine or
7981 distributed on a compute cluster.")
7982 (license license:lgpl2.1+)))
7984 (define-public r-abjutils
7991 (uri (cran-uri "abjutils" version))
7993 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7994 (build-system r-build-system)
7996 `(("r-devtools" ,r-devtools)
7997 ("r-dplyr" ,r-dplyr)
7998 ("r-furrr" ,r-furrr)
7999 ("r-future" ,r-future)
8002 ("r-magrittr" ,r-magrittr)
8003 ("r-progress" ,r-progress)
8004 ("r-purrr" ,r-purrr)
8005 ("r-readr" ,r-readr)
8006 ("r-rlang" ,r-rlang)
8007 ("r-rstudioapi" ,r-rstudioapi)
8008 ("r-scales" ,r-scales)
8009 ("r-stringi" ,r-stringi)
8010 ("r-stringr" ,r-stringr)
8011 ("r-tibble" ,r-tibble)
8012 ("r-tidyr" ,r-tidyr)))
8013 (home-page "https://github.com/abjur/abjutils/")
8014 (synopsis "Collection of tools for jurimetrical analysis")
8016 "This package implements general purpose tools, such as functions for
8017 sampling and basic manipulation of Brazilian lawsuits identification number.
8018 It also implements functions for text cleaning, such as accentuation
8020 (license license:expat)))
8022 (define-public r-abnormality
8024 (name "r-abnormality")
8029 (uri (cran-uri "abnormality" version))
8031 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8032 (build-system r-build-system)
8034 `(("r-mass" ,r-mass)
8035 ("r-matrix" ,r-matrix)))
8036 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8037 (synopsis "Measure a subject's abnormality with respect to a reference population")
8039 "This package contains functions to implement the methodology and
8040 considerations laid out by Marks et al. in the article \"Measuring abnormality
8041 in high dimensional spaces: applications in biomechanical gait analysis\".
8042 Using high-dimensional datasets to measure a subject's overall level of
8043 abnormality as compared to a reference population is often needed in outcomes
8045 (license license:expat)))
8047 (define-public r-abodoutlier
8049 (name "r-abodoutlier")
8054 (uri (cran-uri "abodOutlier" version))
8056 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8057 (properties `((upstream-name . "abodOutlier")))
8058 (build-system r-build-system)
8060 `(("r-cluster" ,r-cluster)))
8061 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8062 (synopsis "Angle-based outlier detection")
8064 "This package performs angle-based outlier detection on a given data
8065 frame. It offers three methods to process data:
8067 @item full but slow implementation using all the data that has cubic
8069 @item a fully randomized method;
8070 @item a method using k-nearest neighbours.
8072 These algorithms are well suited for high dimensional data outlier
8074 (license license:expat)))
8076 (define-public r-abps
8083 (uri (cran-uri "ABPS" version))
8085 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8086 (properties `((upstream-name . "ABPS")))
8087 (build-system r-build-system)
8088 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8089 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8090 (synopsis "Abnormal blood profile score to detect blood doping")
8092 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8093 The ABPS is a part of the Athlete biological passport program of the World
8094 anti-doping agency, which combines several blood parameters into a single
8095 score in order to detect blood doping. The package also contains functions to
8096 calculate other scores used in anti-doping programs, such as the ratio of
8097 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8098 (license license:gpl2+)))
8100 (define-public r-parmigene
8102 (name "r-parmigene")
8107 (uri (cran-uri "parmigene" version))
8110 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
8111 (build-system r-build-system)
8112 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8113 (synopsis "Mutual information estimation for gene network reconstruction")
8115 "This package provides a parallel estimation of the mutual information
8116 based on entropy estimates from k-nearest neighbors distances and algorithms
8117 for the reconstruction of gene regulatory networks.")
8118 (license license:agpl3+)))
8120 (define-public r-pscl
8127 (uri (cran-uri "pscl" version))
8129 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8130 (build-system r-build-system)
8132 `(("r-mass" ,r-mass)))
8133 (home-page "https://github.com/atahk/pscl/")
8134 (synopsis "Political science computational laboratory")
8136 "The @code{pscl} is an R package providing classes and methods for:
8138 @item Bayesian analysis of roll call data (item-response models);
8139 @item elementary Bayesian statistics;
8140 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8142 @item utility functions.
8144 (license license:gpl2)))
8146 (define-public r-accelmissing
8148 (name "r-accelmissing")
8153 (uri (cran-uri "accelmissing" version))
8155 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8156 (build-system r-build-system)
8158 `(("r-mice" ,r-mice)
8159 ("r-pscl" ,r-pscl)))
8160 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8161 (synopsis "Missing value imputation for accelerometer data")
8163 "This package provides a statistical method to impute the missing values in
8164 accelerometer data. The methodology includes both parametric and
8165 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8166 model. It also provides multiple functions to preprocess the accelerometer data
8167 previous to the missing data imputation. These include detecting the wearing
8168 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8169 (license license:gpl2+)))
8171 (define-public r-mhsmm
8178 (uri (cran-uri "mhsmm" version))
8180 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8181 (build-system r-build-system)
8182 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8183 (home-page "https://github.com/jaredo/mhsmm/")
8184 (synopsis "Inference for hidden Markov and semi-Markov models")
8186 "The @code{r-mhsmm} package implements estimation and prediction methods for
8187 hidden Markov and semi-Markov models for multiple observation sequences. Such
8188 techniques are of interest when observed data is thought to be dependent on some
8189 unobserved (or hidden) state. Also, this package is suitable for equidistant
8190 time series data, with multivariate and/or missing data. Allows user defined
8191 emission distributions.")
8192 (license license:gpl2+)))
8194 (define-public r-nleqslv
8201 (uri (cran-uri "nleqslv" version))
8203 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8204 (build-system r-build-system)
8205 (native-inputs `(("gfortran" ,gfortran)))
8206 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8207 (synopsis "Solve systems of nonlinear equations")
8209 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8210 Broyden or a Newton method with a choice of global strategies such as line
8211 search and trust region. There are options for using a numerical or user
8212 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8213 singular or ill-conditioned Jacobian.")
8214 (license license:gpl2+)))
8216 (define-public r-physicalactivity
8218 (name "r-physicalactivity")
8223 (uri (cran-uri "PhysicalActivity" version))
8225 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8227 `((upstream-name . "PhysicalActivity")))
8228 (build-system r-build-system)
8229 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8230 (synopsis "Procesing accelerometer data for physical activity measurement")
8232 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8233 for classification of monitor wear and nonwear time intervals in accelerometer
8234 data collected to assess physical activity. The package also contains functions
8235 for making plots of accelerometer data and obtaining the summary of various
8236 information including daily monitor wear time and the mean monitor wear time
8237 during valid days. The revised package version 0.2-1 improved the functions
8238 regarding speed, robustness and add better support for time zones and daylight
8239 saving. In addition, several functions were added:
8241 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8242 @item the @code{markPAI} can categorize physical activity intensity level based
8243 on user-defined cut-points of accelerometer counts.
8245 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8246 @code{queryActigraph} functions.")
8247 (license license:gpl3+)))
8249 (define-public r-acc
8256 (uri (cran-uri "acc" version))
8258 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8259 (build-system r-build-system)
8261 `(("r-circlize" ,r-circlize)
8263 ("r-ggplot2" ,r-ggplot2)
8264 ("r-iterators" ,r-iterators)
8265 ("r-mhsmm" ,r-mhsmm)
8266 ("r-nleqslv" ,r-nleqslv)
8267 ("r-physicalactivity" ,r-physicalactivity)
8269 ("r-r-utils" ,r-r-utils)
8271 ("r-rcpparmadillo" ,r-rcpparmadillo)
8272 ("r-rsqlite" ,r-rsqlite)
8274 (home-page "https://cran.r-project.org/web/packages/acc/")
8275 (synopsis "Exploring accelerometer data")
8277 "This package processes accelerometer data from uni-axial and tri-axial devices
8278 and generates data summaries. Also, includes functions to plot, analyze, and
8279 simulate accelerometer data.")
8280 (license license:gpl2+)))
8282 (define-public r-rbenchmark
8284 (name "r-rbenchmark")
8289 (uri (cran-uri "rbenchmark" version))
8291 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8292 (build-system r-build-system)
8293 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8294 (synopsis "Benchmarking routine for R")
8296 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8297 and is intended to facilitate benchmarking of arbitrary R code. The library
8298 consists of just one function, benchmark, which is a simple wrapper around
8299 system.time. Given a specification of the benchmarking process (counts of
8300 replications, evaluation environment) and an arbitrary number of expressions,
8301 benchmark evaluates each of the expressions in the specified environment,
8302 replicating the evaluation as many times as specified, and returning the results
8303 conveniently wrapped into a data frame.")
8304 (license license:gpl2+)))
8306 (define-public r-mitools
8313 (uri (cran-uri "mitools" version))
8316 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8317 (build-system r-build-system)
8318 (propagated-inputs `(("r-dbi" ,r-dbi)))
8319 (home-page "https://cran.r-project.org/web/packages/mitools/")
8320 (synopsis "Tools for multiple imputation of missing data")
8322 "This package provides tools to perform analyses and combine results from
8323 multiple-imputation datasets.")
8324 (license license:gpl2)))
8326 (define-public r-magick
8333 (uri (cran-uri "magick" version))
8336 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8337 (build-system r-build-system)
8339 `(("imagemagick" ,imagemagick)
8342 `(("r-curl" ,r-curl)
8343 ("r-magrittr" ,r-magrittr)
8344 ("r-rcpp" ,r-rcpp)))
8346 `(("pkg-config" ,pkg-config)
8347 ("r-knitr" ,r-knitr)))
8348 (home-page "https://github.com/ropensci/magick")
8349 (synopsis "Advanced graphics and image-processing in R")
8351 "This package provides bindings to ImageMagick, a comprehensive image
8352 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8353 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8354 operations are vectorized via the Magick++ STL meaning they operate either on
8355 a single frame or a series of frames for working with layers, collages, or
8356 animation. In RStudio, images are automatically previewed when printed to the
8357 console, resulting in an interactive editing environment.")
8358 (license license:expat)))
8360 (define-public r-survey
8367 (uri (cran-uri "survey" version))
8370 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8371 (build-system r-build-system)
8373 `(("r-lattice" ,r-lattice)
8374 ("r-matrix" ,r-matrix)
8375 ("r-minqa" ,r-minqa)
8376 ("r-mitools" ,r-mitools)
8377 ("r-numderiv" ,r-numderiv)
8378 ("r-survival" ,r-survival)))
8379 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8380 (synopsis "Analysis of complex survey samples")
8382 "This package provides tools for the analysis of complex survey samples.
8383 The provided features include: summary statistics, two-sample tests, rank
8384 tests, generalised linear models, cumulative link models, Cox models,
8385 loglinear models, and general maximum pseudolikelihood estimation for
8386 multistage stratified, cluster-sampled, unequally weighted survey samples;
8387 variances by Taylor series linearisation or replicate weights;
8388 post-stratification, calibration, and raking; two-phase subsampling designs;
8389 graphics; PPS sampling without replacement; principal components, and factor
8391 ;; Either version of the GPL.
8392 (license (list license:gpl2 license:gpl3))))
8394 (define-public r-gee
8401 (uri (cran-uri "gee" version))
8404 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8405 (properties `((upstream-name . "gee")))
8406 (build-system r-build-system)
8408 `(("gfortran" ,gfortran)))
8409 (home-page "https://cran.r-project.org/web/packages/gee/")
8410 (synopsis "Generalized estimation equation solver")
8412 "This package provides a solver for generalized estimation equations.")
8413 (license license:gpl2)))
8415 (define-public r-tab
8422 (uri (cran-uri "tab" version))
8425 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8426 (properties `((upstream-name . "tab")))
8427 (build-system r-build-system)
8429 `(("r-dplyr" ,r-dplyr)
8431 ("r-knitr" ,r-knitr)
8433 ("r-survey" ,r-survey)
8434 ("r-survival" ,r-survival)
8435 ("r-xtable" ,r-xtable)))
8436 (home-page "https://cran.r-project.org/web/packages/tab/")
8437 (synopsis "Create summary tables for statistical reports")
8439 "This package contains functions for creating various types of summary
8440 tables, e.g. comparing characteristics across levels of a categorical variable
8441 and summarizing fitted generalized linear models, generalized estimating
8442 equations, and Cox proportional hazards models. Functions are available to
8443 handle data from simple random samples as well as complex surveys.")
8444 (license license:gpl3+)))
8446 (define-public r-dvmisc
8453 (uri (cran-uri "dvmisc" version))
8455 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8456 (build-system r-build-system)
8458 `(("r-cubature" ,r-cubature)
8459 ("r-data-table" ,r-data-table)
8460 ("r-dplyr" ,r-dplyr)
8461 ("r-ggplot2" ,r-ggplot2)
8463 ("r-mvtnorm" ,r-mvtnorm)
8464 ("r-pracma" ,r-pracma)
8465 ("r-rbenchmark" ,r-rbenchmark)
8467 ("r-survey" ,r-survey)
8469 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8470 (synopsis "Faster computation of common statistics and miscellaneous functions")
8472 "This package implements faster versions of base R functions (e.g. mean, standard
8473 deviation, covariance, weighted mean), mostly written in C++, along with
8474 miscellaneous functions for various purposes (e.g. create the histogram with
8475 fitted probability density function or probability mass function curve, create
8476 the body mass index groups, assess the linearity assumption in logistic
8478 (license license:gpl2)))
8480 (define-public r-accelerometry
8482 (name "r-accelerometry")
8487 (uri (cran-uri "accelerometry" version))
8489 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8490 (build-system r-build-system)
8492 `(("r-dvmisc" ,r-dvmisc)
8493 ("r-rcpp" ,r-rcpp)))
8494 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8495 (synopsis "Functions for processing accelerometer data")
8497 "This package provides a collection of functions that perform operations on
8498 time-series accelerometer data, such as identify the non-wear time, flag minutes
8499 that are part of an activity bout, and find the maximum 10-minute average count
8500 value. The functions are generally very flexible, allowing for a variety of
8501 algorithms to be implemented.")
8502 (license license:gpl3)))
8504 (define-public r-absim
8511 (uri (cran-uri "AbSim" version))
8513 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8514 (properties `((upstream-name . "AbSim")))
8515 (build-system r-build-system)
8518 ("r-powerlaw" ,r-powerlaw)))
8519 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8520 (synopsis "Time resolved simulations of antibody repertoires")
8522 "This package provides simulation methods for the evolution of antibody repertoires.
8523 The heavy and light chain variable region of both human and C57BL/6 mice can
8524 be simulated in a time-dependent fashion. Both single lineages using one set of
8525 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8526 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8527 Upon completion, the main loop of the algorithm begins, with each iteration
8528 representing one simulated time step. Various mutation events are possible at
8529 each time step, contributing to a diverse final repertoire.")
8530 (license license:gpl2)))
8532 (define-public r-quic
8539 (uri (cran-uri "QUIC" version))
8541 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8542 (properties `((upstream-name . "QUIC")))
8543 (build-system r-build-system)
8544 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8545 (synopsis "Regularized sparse inverse covariance matrix estimation")
8547 "This package implements the regularized Gaussian maximum likelihood
8548 estimation of the inverse of a covariance matrix. It uses Newton's method and
8549 coordinate descent to solve the regularized inverse covariance matrix
8550 estimation problem.")
8551 ;; The project home page states that the release is under GPLv3 or later.
8552 ;; The CRAN page only says GPL-3.
8553 (license license:gpl3+)))
8555 (define-public r-abundant
8562 (uri (cran-uri "abundant" version))
8564 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8565 (build-system r-build-system)
8567 `(("r-quic" ,r-quic)))
8568 (home-page "https://cran.r-project.org/web/packages/abundant/")
8569 (synopsis "Abundant regression and high-dimensional principal fitted components")
8571 "This package provides tools to fit and predict with the high-dimensional
8572 principal fitted components model. This model is described by Cook, Forzani,
8573 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8574 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8575 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8576 (license license:gpl2+)))
8578 (define-public r-ac3net
8585 (uri (cran-uri "Ac3net" version))
8587 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8588 (properties `((upstream-name . "Ac3net")))
8589 (build-system r-build-system)
8591 `(("r-data-table" ,r-data-table)))
8592 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8593 (synopsis "Inferring directional conservative causal core gene networks")
8594 (description "This package infers directional Conservative causal core
8595 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8596 directional network.")
8597 (license license:gpl3+)))
8599 (define-public r-aca
8606 (uri (cran-uri "ACA" version))
8608 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8609 (properties `((upstream-name . "ACA")))
8610 (build-system r-build-system)
8611 (home-page "https://cran.r-project.org/web/packages/ACA/")
8612 (synopsis "Abrupt change-point or aberration detection in point series")
8614 "This package offers an interactive function for the detection of breakpoints in
8616 ;; Any version of the GPL
8617 (license (list license:gpl2+ license:gpl3+))))
8619 (define-public r-acceptancesampling
8621 (name "r-acceptancesampling")
8626 (uri (cran-uri "AcceptanceSampling" version))
8628 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8630 `((upstream-name . "AcceptanceSampling")))
8631 (build-system r-build-system)
8632 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8633 (synopsis "Creation and evaluation of acceptance sampling plans")
8635 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8636 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8637 in quality control and improvement. International standards of acceptance
8638 sampling provide sampling plans for specific circumstances. The aim of this
8639 package is to provide an easy-to-use interface to visualize single, double or
8640 multiple sampling plans. In addition, methods have been provided to enable the
8641 user to assess sampling plans against pre-specified levels of performance, as
8642 measured by the probability of acceptance for a given level of quality in the
8644 (license license:gpl3+)))
8646 (define-public r-acclma
8653 (uri (cran-uri "ACCLMA" version))
8655 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8656 (properties `((upstream-name . "ACCLMA")))
8657 (build-system r-build-system)
8658 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8659 (synopsis "ACC & LMA graph plotting")
8661 "This package contains a function that imports data from a @acronym{CSV,
8662 Comma-Separated Values} file, or uses manually entered data from the format (x,
8663 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8664 Curve} vs @acronym{LOI, Line of Independence} graph and
8665 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8666 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8667 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8668 string) was passed, a manual data entry window is opened. The header parameter
8669 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8670 a header row or not. The dataset should contain only one independent variable
8671 (x) and one dependent variable (y) and can contain a weight for each
8673 (license license:gpl2)))
8675 (define-public r-aspi
8682 (uri (cran-uri "aspi" version))
8684 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8685 (build-system r-build-system)
8687 "https://cran.r-project.org/web/packages/aspi/")
8689 "Analysis of symmetry of parasitic infections")
8691 "This package provides tools for the analysis and visualization of bilateral
8692 asymmetry in parasitic infections.")
8693 (license license:gpl3+)))
8695 (define-public r-sandwich
8702 (uri (cran-uri "sandwich" version))
8705 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8706 (build-system r-build-system)
8708 `(("r-zoo" ,r-zoo)))
8709 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8710 (synopsis "Robust Covariance Matrix Estimators")
8712 "This package provides model-robust standard error estimators for
8713 cross-sectional, time series, clustered, panel, and longitudinal data.")
8714 ;; Either version of the license.
8715 (license (list license:gpl2 license:gpl3))))
8717 (define-public r-th-data
8724 (uri (cran-uri "TH.data" version))
8727 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8728 (properties `((upstream-name . "TH.data")))
8729 (build-system r-build-system)
8731 `(("r-mass" ,r-mass)
8732 ("r-survival" ,r-survival)))
8733 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8734 (synopsis "Shared data sets")
8736 "This package contains supporting data sets that are used in other
8737 packages maintained by Torsten Hothorn.")
8738 (license license:gpl3)))
8740 (define-public r-multcomp
8747 (uri (cran-uri "multcomp" version))
8750 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8751 (build-system r-build-system)
8753 `(("r-codetools" ,r-codetools)
8754 ("r-mvtnorm" ,r-mvtnorm)
8755 ("r-sandwich" ,r-sandwich)
8756 ("r-survival" ,r-survival)
8757 ("r-th-data" ,r-th-data)))
8758 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8759 (synopsis "Simultaneous inference in general parametric models")
8761 "Simultaneous tests and confidence intervals for general linear
8762 hypotheses in parametric models, including linear, generalized linear, linear
8763 mixed effects, and survival models. The package includes demos reproducing
8764 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8765 Hothorn, Westfall, 2010, CRC Press).")
8766 (license license:gpl2)))
8768 (define-public r-emmeans
8775 (uri (cran-uri "emmeans" version))
8778 "0jh7l1rzsb2ihbnh4r4388kwm629z17rcapvdws1hnkklhr8j74k"))))
8779 (build-system r-build-system)
8781 `(("r-estimability" ,r-estimability)
8782 ("r-mvtnorm" ,r-mvtnorm)
8783 ("r-numderiv" ,r-numderiv)
8785 ("r-xtable" ,r-xtable)))
8787 `(("r-knitr" ,r-knitr)))
8788 (home-page "https://github.com/rvlenth/emmeans")
8789 (synopsis "Estimated marginal means, aka least-squares means")
8791 "This package provides tools to obtain @dfn{estimated marginal
8792 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8793 be used to compute contrasts or linear functions of EMMs, trends, and
8794 comparisons of slopes.")
8795 ;; Either version of the license.
8796 (license (list license:gpl2 license:gpl3))))
8798 (define-public r-pwr
8805 (uri (cran-uri "pwr" version))
8808 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8809 (build-system r-build-system)
8811 `(("r-knitr" ,r-knitr)))
8812 (home-page "https://github.com/heliosdrm/pwr")
8813 (synopsis "Basic functions for power analysis")
8815 "This package provides power analysis functions along the lines of
8817 (license license:gpl3+)))
8819 (define-public r-libcoin
8826 (uri (cran-uri "libcoin" version))
8829 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8830 (build-system r-build-system)
8831 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8832 (home-page "https://cran.r-project.org/web/packages/libcoin")
8833 (synopsis "Linear test statistics for permutation inference")
8835 "This package provides basic infrastructure for linear test statistics
8836 and permutation inference in the framework of Strasser and Weber (1999).")
8837 (license license:gpl2)))
8839 (define-public r-coin
8846 (uri (cran-uri "coin" version))
8849 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8850 (build-system r-build-system)
8852 `(("r-libcoin" ,r-libcoin)
8853 ("r-matrixstats" ,r-matrixstats)
8854 ("r-modeltools" ,r-modeltools)
8855 ("r-multcomp" ,r-multcomp)
8856 ("r-mvtnorm" ,r-mvtnorm)
8857 ("r-survival" ,r-survival)))
8858 (home-page "http://coin.r-forge.r-project.org")
8859 (synopsis "Conditional inference procedures in a permutation test framework")
8861 "This package provides conditional inference procedures for the general
8862 independence problem including two-sample, K-sample (non-parametric ANOVA),
8863 correlation, censored, ordered and multivariate problems.")
8864 (license license:gpl2)))
8866 (define-public r-bayesplot
8868 (name "r-bayesplot")
8873 (uri (cran-uri "bayesplot" version))
8876 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
8877 (build-system r-build-system)
8879 `(("pandoc" ,ghc-pandoc)
8880 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8882 `(("r-knitr" ,r-knitr)))
8884 `(("r-dplyr" ,r-dplyr)
8885 ("r-ggplot2" ,r-ggplot2)
8886 ("r-ggridges" ,r-ggridges)
8888 ("r-reshape2" ,r-reshape2)
8889 ("r-rlang" ,r-rlang)
8890 ("r-tibble" ,r-tibble)
8891 ("r-tidyselect" ,r-tidyselect)))
8892 (home-page "https://mc-stan.org/bayesplot")
8893 (synopsis "Plotting for Bayesian models")
8895 "This package provides plotting functions for posterior analysis, model
8896 checking, and MCMC diagnostics. The package is designed not only to provide
8897 convenient functionality for users, but also a common set of functions that
8898 can be easily used by developers working on a variety of R packages for
8899 Bayesian modeling.")
8900 (license license:gpl3+)))
8902 (define-public r-tmb
8909 (uri (cran-uri "TMB" version))
8912 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8913 (properties `((upstream-name . "TMB")))
8914 (build-system r-build-system)
8916 `(("r-matrix" ,r-matrix)
8917 ("r-rcppeigen" ,r-rcppeigen)))
8918 (home-page "http://tmb-project.org")
8919 (synopsis "Template model builder: a general random effect tool")
8921 "With this tool, a user should be able to quickly implement complex
8922 random effect models through simple C++ templates. The package combines
8923 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8924 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8925 from R) to obtain an efficient implementation of the applied Laplace
8926 approximation with exact derivatives. Key features are: Automatic sparseness
8927 detection, parallelism through BLAS and parallel user templates.")
8928 (license license:gpl2)))
8930 (define-public r-sjstats
8937 (uri (cran-uri "sjstats" version))
8939 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
8940 (build-system r-build-system)
8942 `(("r-bayestestr" ,r-bayestestr)
8943 ("r-broom" ,r-broom)
8944 ("r-dplyr" ,r-dplyr)
8945 ("r-effectsize" ,r-effectsize)
8946 ("r-emmeans" ,r-emmeans)
8947 ("r-insight" ,r-insight)
8949 ("r-magrittr" ,r-magrittr)
8951 ("r-modelr" ,r-modelr)
8952 ("r-parameters" ,r-parameters)
8953 ("r-performance" ,r-performance)
8954 ("r-purrr" ,r-purrr)
8955 ("r-rlang" ,r-rlang)
8956 ("r-sjlabelled" ,r-sjlabelled)
8957 ("r-sjmisc" ,r-sjmisc)
8958 ("r-tidyr" ,r-tidyr)))
8959 (home-page "https://github.com/strengejacke/sjstats")
8960 (synopsis "Functions for common statistical computations")
8962 "This package provides a collection of convenient functions for common
8963 statistical computations, which are not directly provided by R's @code{base}
8964 or @code{stats} packages. This package aims at providing, first, shortcuts
8965 for statistical measures, which otherwise could only be calculated with
8966 additional effort. Second, these shortcut functions are generic, and can be
8967 applied not only to vectors, but also to other objects as well. The focus of
8968 most functions lies on summary statistics or fit measures for regression
8969 models, including generalized linear models, mixed effects models and Bayesian
8971 (license license:gpl3)))
8973 (define-public r-glmmtmb
8980 (uri (cran-uri "glmmTMB" version))
8983 "0sdx1q7wc7895xh8747r4p0wkij0xjgn5ij62ipi9423zd0sr0mm"))))
8984 (properties `((upstream-name . "glmmTMB")))
8985 (build-system r-build-system)
8987 `(("r-lme4" ,r-lme4)
8988 ("r-matrix" ,r-matrix)
8990 ("r-rcppeigen" ,r-rcppeigen)
8993 `(("r-knitr" ,r-knitr))) ; for vignettes
8994 (home-page "https://github.com/glmmTMB")
8995 (synopsis "Generalized linear mixed models")
8997 "Fit linear and generalized linear mixed models with various extensions,
8998 including zero-inflation. The models are fitted using maximum likelihood
8999 estimation via the Template Model Builder. Random effects are assumed to be
9000 Gaussian on the scale of the linear predictor and are integrated out using the
9001 Laplace approximation. Gradients are calculated using automatic
9003 (license license:agpl3+)))
9005 (define-public r-bayestestr
9007 (name "r-bayestestr")
9012 (uri (cran-uri "bayestestR" version))
9015 "1nrycyzznzrlwnfwk1w3ixdq0bj82nri9kb2qiaiw8wwzwrsl1hd"))))
9016 (properties `((upstream-name . "bayestestR")))
9017 (build-system r-build-system)
9019 `(("r-insight" ,r-insight)))
9021 `(("r-knitr" ,r-knitr)))
9022 (home-page "https://github.com/easystats/bayestestR")
9023 (synopsis "Describe Bayesian models and posterior distributions")
9025 "This package provides utilities to understand and describe posterior
9026 distributions and Bayesian models. It includes point-estimates such as
9027 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9028 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9029 ROPE percentage and pd).")
9030 (license license:gpl3)))
9032 (define-public r-performance
9034 (name "r-performance")
9039 (uri (cran-uri "performance" version))
9042 "0gw165wm2a0vjsvyll8z9k6qd156z3jf4priy1r745v63x4mnb5k"))))
9043 (build-system r-build-system)
9045 `(("r-bayestestr" ,r-bayestestr)
9046 ("r-insight" ,r-insight)))
9047 (home-page "https://easystats.github.io/performance/")
9048 (synopsis "Assessment of regression models performance")
9050 "This package provides utilities for computing measures to assess model
9051 quality, which are not directly provided by R's @code{base} or @code{stats}
9052 packages. These include e.g. measures like r-squared, intraclass correlation
9053 coefficient, root mean squared error or functions to check models for
9054 overdispersion, singularity or zero-inflation and more. Functions apply to a
9055 large variety of regression models, including generalized linear models, mixed
9056 effects models and Bayesian models.")
9057 (license license:gpl3)))
9059 (define-public r-ggeffects
9061 (name "r-ggeffects")
9066 (uri (cran-uri "ggeffects" version))
9069 "1bqvbhw5la3cj3v0gwava117ff24b1p450azln402gsxgfl3vw7r"))))
9070 (build-system r-build-system)
9072 `(("r-insight" ,r-insight)
9074 ("r-sjlabelled" ,r-sjlabelled)))
9076 `(("r-knitr" ,r-knitr)))
9077 (home-page "https://github.com/strengejacke/ggeffects")
9078 (synopsis "Create tidy data frames of marginal effects for ggplot")
9080 "This package provides tools to compute marginal effects from statistical
9081 models and return the result as tidy data frames. These data frames are ready
9082 to use with the @code{ggplot2} package. Marginal effects can be calculated
9083 for many different models. Interaction terms, splines and polynomial terms
9084 are also supported. The two main functions are @code{ggpredict()} and
9085 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9086 results using @code{ggplot2}.")
9087 (license license:gpl3)))
9089 (define-public r-effectsize
9091 (name "r-effectsize")
9096 (uri (cran-uri "effectsize" version))
9099 "1n5b5434sd8f1v95bfjwg92v879rkaj8zpm6ldnrg0kgfb0gy6q4"))))
9100 (properties `((upstream-name . "effectsize")))
9101 (build-system r-build-system)
9103 `(("r-bayestestr" ,r-bayestestr)
9104 ("r-insight" ,r-insight)
9105 ("r-parameters" ,r-parameters)))
9107 `(("r-knitr" ,r-knitr)))
9108 (home-page "https://github.com/easystats/effectsize")
9109 (synopsis "Indices of effect size and standardized parameters")
9111 "This package provides utilities to work with indices of effect size and
9112 standardized parameters for a wide variety of models, allowing computation and
9113 conversion of indices such as Cohen's d, r, odds, etc.")
9114 (license license:gpl3)))
9116 (define-public r-sjplot
9123 (uri (cran-uri "sjPlot" version))
9125 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9126 (properties `((upstream-name . "sjPlot")))
9127 (build-system r-build-system)
9129 `(("r-bayestestr" ,r-bayestestr)
9130 ("r-dplyr" ,r-dplyr)
9131 ("r-effectsize" ,r-effectsize)
9132 ("r-ggeffects" ,r-ggeffects)
9133 ("r-ggplot2" ,r-ggplot2)
9134 ("r-insight" ,r-insight)
9135 ("r-knitr" ,r-knitr)
9137 ("r-parameters" ,r-parameters)
9138 ("r-performance" ,r-performance)
9139 ("r-purrr" ,r-purrr)
9140 ("r-rlang" ,r-rlang)
9141 ("r-scales" ,r-scales)
9142 ("r-sjlabelled" ,r-sjlabelled)
9143 ("r-sjmisc" ,r-sjmisc)
9144 ("r-sjstats" ,r-sjstats)
9145 ("r-tidyr" ,r-tidyr)))
9147 `(("r-knitr" ,r-knitr)))
9148 (home-page "https://strengejacke.github.io/sjPlot/")
9149 (synopsis "Data visualization for statistics in social science")
9151 "This package represents a collection of plotting and table output
9152 functions for data visualization. Results of various statistical
9153 analyses (that are commonly used in social sciences) can be visualized using
9154 this package, including simple and cross tabulated frequencies, histograms,
9155 box plots, (generalized) linear models, mixed effects models, principal
9156 component analysis and correlation matrices, cluster analyses, scatter plots,
9157 stacked scales, effects plots of regression models (including interaction
9158 terms) and much more. This package supports labelled data.")
9159 (license license:gpl3)))
9161 (define-public r-ini
9168 (uri (cran-uri "ini" version))
9171 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9172 (build-system r-build-system)
9173 (home-page "https://github.com/dvdscripter/ini")
9174 (synopsis "Read and write configuration files")
9176 "This package provides tools to parse simple @code{.ini} configuration
9177 files to an structured list. Users can manipulate this resulting list with
9178 @code{lapply()} functions. This same structured list can be used to write
9179 back to file after modifications.")
9180 (license license:gpl3)))
9189 (uri (cran-uri "gh" version))
9192 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9193 (build-system r-build-system)
9198 ("r-jsonlite" ,r-jsonlite)))
9199 (home-page "https://github.com/r-lib/gh#readme")
9200 (synopsis "Access the GitHub API via R")
9202 "This package provides a minimal R client to access the GitHub API.")
9203 (license license:expat)))
9212 (uri (cran-uri "fs" version))
9215 "0kksig9pk8aid9l6r250na8z8j9919jvs20lj0s6m9bcybgh74df"))))
9216 (build-system r-build-system)
9218 `(("pkg-config" ,pkg-config)
9219 ("r-knitr" ,r-knitr)))
9220 (home-page "https://fs.r-lib.org")
9221 (synopsis "Cross-platform file system operations based on libuv")
9223 "This package provides a cross-platform interface to file system
9224 operations, built on top of the libuv C library.")
9225 (license license:gpl3)))
9227 (define-public r-clisymbols
9229 (name "r-clisymbols")
9234 (uri (cran-uri "clisymbols" version))
9237 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9238 (build-system r-build-system)
9239 (home-page "https://github.com/gaborcsardi/clisymbols")
9240 (synopsis "Unicode symbols at the R prompt")
9242 "This package provides a small subset of Unicode symbols, that are useful
9243 when building command line applications. They fall back to alternatives on
9244 terminals that do not support Unicode.")
9245 (license license:expat)))
9247 (define-public r-usethis
9254 (uri (cran-uri "usethis" version))
9257 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9258 (build-system r-build-system)
9261 ("r-clipr" ,r-clipr)
9262 ("r-crayon" ,r-crayon)
9267 ("r-git2r" ,r-git2r)
9269 ("r-purrr" ,r-purrr)
9270 ("r-rematch2" ,r-rematch2)
9271 ("r-rlang" ,r-rlang)
9272 ("r-rprojroot" ,r-rprojroot)
9273 ("r-rstudioapi" ,r-rstudioapi)
9274 ("r-whisker" ,r-whisker)
9275 ("r-withr" ,r-withr)
9276 ("r-yaml" ,r-yaml)))
9277 (home-page "https://github.com/r-lib/usethis")
9278 (synopsis "Automate R package and project setup")
9280 "This package helps you to automate R package and project setup tasks
9281 that are otherwise performed manually. This includes setting up unit testing,
9282 test coverage, continuous integration, Git, GitHub integration, licenses,
9283 Rcpp, RStudio projects, and more.")
9284 (license license:gpl3)))
9286 (define-public r-sessioninfo
9288 (name "r-sessioninfo")
9293 (uri (cran-uri "sessioninfo" version))
9296 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9297 (build-system r-build-system)
9300 ("r-withr" ,r-withr)))
9301 (home-page "https://github.com/r-lib/sessioninfo#readme")
9302 (synopsis "R session information")
9304 "This package provides tools to query and print information about the
9305 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9306 more information about packages, and where they were installed from.")
9307 (license license:gpl2)))
9309 (define-public r-remotes
9316 (uri (cran-uri "remotes" version))
9319 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
9320 (build-system r-build-system)
9321 (home-page "https://github.com/r-lib/remotes#readme")
9322 (synopsis "R package installation from remote repositories")
9324 "Download and install R packages stored in GitHub, BitBucket, or plain
9325 subversion or git repositories. This package is a lightweight replacement of
9326 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9327 the code was copied over from @code{devtools}.")
9328 (license license:gpl2+)))
9330 (define-public r-xopen
9337 (uri (cran-uri "xopen" version))
9340 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9341 (build-system r-build-system)
9343 `(("r-processx" ,r-processx)))
9344 (home-page "https://github.com/r-lib/xopen#readme")
9345 (synopsis "Open system files, URLs, anything")
9347 "This package provides a cross-platform solution to open files,
9348 directories or URLs with their associated programs.")
9349 (license license:expat)))
9351 (define-public r-rcmdcheck
9353 (name "r-rcmdcheck")
9358 (uri (cran-uri "rcmdcheck" version))
9361 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9362 (build-system r-build-system)
9364 `(("r-callr" ,r-callr)
9366 ("r-crayon" ,r-crayon)
9368 ("r-digest" ,r-digest)
9369 ("r-pkgbuild" ,r-pkgbuild)
9370 ("r-prettyunits" ,r-prettyunits)
9372 ("r-rprojroot" ,r-rprojroot)
9373 ("r-sessioninfo" ,r-sessioninfo)
9374 ("r-withr" ,r-withr)
9375 ("r-xopen" ,r-xopen)))
9376 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9377 (synopsis "Run R CMD check from R and capture results")
9379 "Run @code{R CMD check} from R programmatically, and capture the results
9380 of the individual checks.")
9381 (license license:expat)))
9383 (define-public r-rapportools
9385 (name "r-rapportools")
9390 (uri (cran-uri "rapportools" version))
9393 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9394 (build-system r-build-system)
9396 `(("r-pander" ,r-pander)
9398 ("r-reshape" ,r-reshape)))
9399 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9400 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9402 "This package provides helper functions that act as wrappers to more
9403 advanced statistical methods with the advantage of having sane defaults for
9405 (license license:agpl3+)))
9407 (define-public r-pander
9414 (uri (cran-uri "pander" version))
9417 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9418 (build-system r-build-system)
9420 `(("r-digest" ,r-digest)
9421 ("r-rcpp" ,r-rcpp)))
9422 (home-page "https://rapporter.github.io/pander")
9423 (synopsis "Render R objects into Pandoc's markdown")
9425 "The main aim of the pander R package is to provide a minimal and easy
9426 tool for rendering R objects into Pandoc's markdown. The package is also
9427 capable of exporting/converting complex Pandoc documents (reports) in various
9429 ;; This package is licensed under either the AGPLv3+ or the very rarely
9431 (license license:agpl3+)))
9433 (define-public r-summarytools
9435 (name "r-summarytools")
9440 (uri (cran-uri "summarytools" version))
9443 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9444 (build-system r-build-system)
9446 `(("r-base64enc" ,r-base64enc)
9447 ("r-checkmate" ,r-checkmate)
9448 ("r-dplyr" ,r-dplyr)
9449 ("r-htmltools" ,r-htmltools)
9450 ("r-lubridate" ,r-lubridate)
9451 ("r-magick" ,r-magick)
9452 ("r-matrixstats" ,r-matrixstats)
9453 ("r-pander" ,r-pander)
9455 ("r-rapportools" ,r-rapportools)
9456 ("r-tibble" ,r-tibble)
9457 ("r-tidyr" ,r-tidyr)))
9458 (home-page "https://github.com/dcomtois/summarytools")
9459 (synopsis "Tools to quickly and neatly summarize data")
9461 "This package provides tools for data frame summaries, cross-tabulations,
9462 weight-enabled frequency tables and common univariate statistics in concise
9463 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9464 good point-of-entry for exploring data, both for experienced and new R
9466 (license license:gpl2)))
9468 (define-public r-lsei
9475 (uri (cran-uri "lsei" version))
9478 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9479 (build-system r-build-system)
9481 `(("gfortran" ,gfortran)))
9482 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9483 (synopsis "Solve regression problems under equality/inequality constraints")
9485 "It contains functions that solve least squares linear regression
9486 problems under linear equality/inequality constraints. Functions for solving
9487 quadratic programming problems are also available, which transform such
9488 problems into least squares ones first.")
9489 (license license:gpl2+)))
9491 (define-public r-npsurv
9498 (uri (cran-uri "npsurv" version))
9501 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9502 (build-system r-build-system)
9504 `(("r-lsei" ,r-lsei)))
9505 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9506 (synopsis "Nonparametric survival analysis")
9508 "This package contains functions for non-parametric survival analysis of
9509 exact and interval-censored observations.")
9510 (license license:gpl2+)))
9512 (define-public r-clusteval
9514 (name "r-clusteval")
9519 (uri (cran-uri "clusteval" version))
9522 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9523 (build-system r-build-system)
9525 `(("r-mvtnorm" ,r-mvtnorm)
9526 ("r-rcpp" ,r-rcpp)))
9527 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9528 (synopsis "Evaluation of clustering algorithms")
9530 "This R package provides a suite of tools to evaluate clustering
9531 algorithms, clusterings, and individual clusters.")
9532 (license license:expat)))
9534 (define-public r-tweedie
9541 (uri (cran-uri "tweedie" version))
9544 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9545 (build-system r-build-system)
9546 (native-inputs `(("gfortran" ,gfortran)))
9547 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9548 (synopsis "Evaluation of Tweedie exponential family models")
9550 "Maximum likelihood computations for Tweedie families, including the
9551 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9552 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9553 and related methods.")
9554 (license license:gpl2+)))
9556 (define-public r-rcppgsl
9563 (uri (cran-uri "RcppGSL" version))
9565 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9566 (properties `((upstream-name . "RcppGSL")))
9567 (build-system r-build-system)
9569 `(("r-rcpp" ,r-rcpp)
9571 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9572 (synopsis "Rcpp integration for GSL vectors and matrices")
9574 "The GNU Scientific Library (or GSL) is a collection of numerical
9575 routines for scientific computing. It is particularly useful for C and C++
9576 programs as it provides a standard C interface to a wide range of mathematical
9577 routines. There are over 1000 functions in total with an extensive test
9578 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9579 structures and R using concepts from Rcpp which is itself a package that eases
9580 the interfaces between R and C++.")
9581 (license license:gpl2+)))
9583 (define-public r-mvabund
9590 (uri (cran-uri "mvabund" version))
9593 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9594 (build-system r-build-system)
9596 `(("r-mass" ,r-mass)
9598 ("r-rcppgsl" ,r-rcppgsl)
9599 ("r-statmod" ,r-statmod)
9600 ("r-tweedie" ,r-tweedie)))
9601 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9602 (synopsis "Statistical methods for analysing multivariate abundance data")
9604 "This package provides a set of tools for displaying, modeling and
9605 analysing multivariate abundance data in community ecology.")
9606 (license license:lgpl2.1+)))
9608 (define-public r-afex
9615 (uri (cran-uri "afex" version))
9618 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9619 (build-system r-build-system)
9623 ("r-lmertest" ,r-lmertest)
9624 ("r-pbkrtest" ,r-pbkrtest)
9625 ("r-reshape2" ,r-reshape2)))
9627 `(("r-knitr" ,r-knitr)))
9628 (home-page "https://afex.singmann.science/")
9629 (synopsis "Analysis of factorial experiments")
9631 "This package provides convenience functions for analyzing factorial
9632 experiments using ANOVA or mixed models.")
9633 (license license:gpl2+)))
9635 (define-public r-lmertest
9642 (uri (cran-uri "lmerTest" version))
9645 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9646 (properties `((upstream-name . "lmerTest")))
9647 (build-system r-build-system)
9649 `(("r-ggplot2" ,r-ggplot2)
9652 ("r-numderiv" ,r-numderiv)))
9653 (home-page "https://github.com/runehaubo/lmerTestR")
9654 (synopsis "Tests in linear mixed effects models")
9656 "This package provides p-values in type I, II or III anova and summary
9657 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9658 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9659 package. Model selection methods include step, drop1 and anova-like tables
9660 for random effects (ranova). Methods for Least-Square means (LS-means) and
9661 tests of linear contrasts of fixed effects are also available.")
9662 (license license:gpl2+)))
9664 (define-public r-r2glmm
9671 (uri (cran-uri "r2glmm" version))
9674 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9675 (build-system r-build-system)
9677 `(("r-afex" ,r-afex)
9678 ("r-data-table" ,r-data-table)
9679 ("r-dplyr" ,r-dplyr)
9680 ("r-ggplot2" ,r-ggplot2)
9681 ("r-gridextra" ,r-gridextra)
9682 ("r-lmertest" ,r-lmertest)
9684 ("r-matrix" ,r-matrix)
9686 ("r-pbkrtest" ,r-pbkrtest)))
9687 (home-page "https://github.com/bcjaeger/r2glmm")
9688 (synopsis "Compute R squared for mixed (multilevel) models")
9690 "This package computes model and semi partial R squared with confidence
9691 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9692 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9693 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9695 (license license:gpl2)))
9697 (define-public r-weights
9704 (uri (cran-uri "weights" version))
9707 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9708 (build-system r-build-system)
9710 `(("r-gdata" ,r-gdata)
9711 ("r-hmisc" ,r-hmisc)
9712 ("r-mice" ,r-mice)))
9714 "https://cran.r-project.org/web/packages/weights/")
9715 (synopsis "Weighting and weighted statistics")
9716 (description "This package Provides a variety of functions for producing
9717 simple weighted statistics, such as weighted Pearson's correlations, partial
9718 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9719 includes some software for quickly recoding survey data and plotting point
9720 estimates from interaction terms in regressions (and multiply imputed
9721 regressions). NOTE: Weighted partial correlation calculations pulled to
9723 (license license:gpl2+)))
9725 (define-public r-rcppannoy
9727 (name "r-rcppannoy")
9732 (uri (cran-uri "RcppAnnoy" version))
9735 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9736 (properties `((upstream-name . "RcppAnnoy")))
9737 (build-system r-build-system)
9739 `(("r-rcpp" ,r-rcpp)))
9740 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9741 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9743 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9744 for efficient memory usage as well an ability to load from and save to disk.
9745 This package provides an R interface.")
9746 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9748 (license (list license:gpl2+ license:asl2.0))))
9750 (define-public r-rcpphnsw
9757 (uri (cran-uri "RcppHNSW" version))
9760 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9761 (properties `((upstream-name . "RcppHNSW")))
9762 (build-system r-build-system)
9763 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9764 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9765 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9767 "Hnswlib is a C++ library for approximate nearest neighbors. This
9768 package provides a minimal R interface by relying on the Rcpp package.")
9769 ;; hnswlib is released under Version 2.0 of the Apache License.
9770 (license (list license:gpl3 license:asl2.0))))
9772 (define-public r-rcppparallel
9774 (name "r-rcppparallel")
9779 (uri (cran-uri "RcppParallel" version))
9782 "029yyjnixggqmddazwxh1wqid1h7xpwpi4sgixyhbb4kmvqlwfkd"))))
9783 (properties `((upstream-name . "RcppParallel")))
9784 (build-system r-build-system)
9785 (home-page "https://rcppcore.github.io/RcppParallel/")
9786 (synopsis "Parallel programming tools for Rcpp")
9788 "This package provides high level functions for parallel programming with
9789 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9790 the work of a standard serial @code{for} loop into a parallel one and the
9791 @code{parallelReduce()} function can be used for accumulating aggregates or
9793 (license license:gpl2)))
9795 (define-public r-ncdf4
9802 (uri (cran-uri "ncdf4" version))
9805 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9806 (build-system r-build-system)
9808 `(("netcdf" ,netcdf)
9810 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9811 (synopsis "R interface to Unidata netCDF format data files")
9813 "This package provides a high-level R interface to data files written
9814 using Unidata's netCDF library (version 4 or earlier), which are binary data
9815 files that are portable across platforms and include metadata information in
9816 addition to the data sets. Using this package, netCDF files can be opened and
9817 data sets read in easily. It is also easy to create new netCDF dimensions,
9818 variables, and files, in either version 3 or 4 format, and manipulate existing
9820 (license license:gpl3+)))
9822 (define-public r-biocmanager
9824 (name "r-biocmanager")
9829 (uri (cran-uri "BiocManager" version))
9831 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9832 (properties `((upstream-name . "BiocManager")))
9833 (build-system r-build-system)
9834 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9835 (synopsis "Access the Bioconductor project package repository")
9837 "This package provides a convenient tool to install and update
9838 Bioconductor packages.")
9839 (license license:artistic2.0)))
9841 (define-public r-rgl
9844 (version "0.100.54")
9848 (uri (cran-uri "rgl" version))
9851 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9852 (build-system r-build-system)
9854 `(("pkg-config" ,pkg-config)))
9856 `(("freetype" ,freetype)
9860 ("ghc-pandoc" ,ghc-pandoc)
9863 `(("r-crosstalk" ,r-crosstalk)
9864 ("r-htmltools" ,r-htmltools)
9865 ("r-htmlwidgets" ,r-htmlwidgets)
9866 ("r-jsonlite" ,r-jsonlite)
9867 ("r-knitr" ,r-knitr)
9868 ("r-magrittr" ,r-magrittr)
9869 ("r-manipulatewidget" ,r-manipulatewidget)
9870 ("r-shiny" ,r-shiny)))
9871 (home-page "https://r-forge.r-project.org/projects/rgl/")
9872 (synopsis "3D visualization using OpenGL")
9874 "This package provides medium to high level functions for 3D interactive graphics,
9875 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9876 as functions for constructing representations of geometric
9877 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9878 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9879 image formats, including PNG, Postscript, SVG, PGF.")
9880 ;; Any version of the GPL.
9881 (license (list license:gpl2+ license:gpl3+))))
9883 (define-public r-multicool
9885 (name "r-multicool")
9890 (uri (cran-uri "multicool" version))
9893 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9894 (build-system r-build-system)
9895 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9896 (home-page "https://cran.r-project.org/web/packages/multicool/")
9897 (synopsis "Permutations of multisets in cool-lex order")
9899 "This package provides a set of tools to permute multisets without loops
9900 or hash tables and to generate integer partitions. Cool-lex order is similar
9901 to colexicographical order.")
9902 (license license:gpl2)))
9904 (define-public r-misc3d
9911 (uri (cran-uri "misc3d" version))
9914 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9915 (build-system r-build-system)
9916 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9917 (synopsis "Miscellaneous 3D Plots")
9919 "This package provides a collection of miscellaneous 3d plots, including
9921 ;; Any version of the GPL.
9922 (license (list license:gpl2+ license:gpl3+))))
9931 (uri (cran-uri "ks" version))
9933 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9934 (build-system r-build-system)
9937 ("r-kernlab" ,r-kernlab)
9938 ("r-kernsmooth" ,r-kernsmooth)
9939 ("r-matrix" ,r-matrix)
9940 ("r-mclust" ,r-mclust)
9942 ("r-multicool" ,r-multicool)
9943 ("r-mvtnorm" ,r-mvtnorm)))
9944 (home-page "http://www.mvstat.net/tduong/")
9945 (synopsis "Kernel smoothing")
9947 "This package provides kernel smoothers for univariate and multivariate
9948 data, including density functions, density derivatives, cumulative
9949 distributions, modal clustering, discriminant analysis, and two-sample
9950 hypothesis testing.")
9951 ;; Either version of the GPL.
9952 (license (list license:gpl2 license:gpl3))))
9954 (define-public r-feature
9961 (uri (cran-uri "feature" version))
9964 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9965 (build-system r-build-system)
9968 ("r-misc3d" ,r-misc3d)
9970 (home-page "http://www.mvstat.net/tduong/")
9971 (synopsis "Inferential feature significance for kernel density estimation")
9973 "The feature package contains functions to display and compute kernel
9974 density estimates, significant gradient and significant curvature regions.
9975 Significant gradient and/or curvature regions often correspond to significant
9976 features (e.g. local modes).")
9977 ;; Either version of the GPL.
9978 (license (list license:gpl2 license:gpl3))))
9980 (define-public r-arm
9987 (uri (cran-uri "arm" version))
9990 "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
9991 (build-system r-build-system)
9993 `(("r-abind" ,r-abind)
9997 ("r-matrix" ,r-matrix)
9998 ("r-nlme" ,r-nlme)))
9999 (home-page "https://cran.r-project.org/web/packages/arm/")
10000 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10002 "This package provides functions to accompany A. Gelman and J. Hill,
10003 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10004 University Press, 2007.")
10005 (license license:gpl3+)))
10007 (define-public r-circular
10009 (name "r-circular")
10014 (uri (cran-uri "circular" version))
10017 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10018 (build-system r-build-system)
10020 `(("r-boot" ,r-boot)
10021 ("r-mvtnorm" ,r-mvtnorm)))
10023 `(("gfortran" ,gfortran)))
10024 (home-page "https://cran.r-project.org/web/packages/circular/")
10025 (synopsis "Circular statistics")
10027 "This package provides tools for circular statistics, from \"Topics in
10028 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10030 (license license:gpl2+)))
10032 (define-public r-activity
10034 (name "r-activity")
10039 (uri (cran-uri "activity" version))
10042 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10043 (build-system r-build-system)
10045 `(("r-circular" ,r-circular)
10046 ("r-insol" ,r-insol)
10047 ("r-pbapply" ,r-pbapply)))
10048 (home-page "https://cran.r-project.org/web/packages/activity/")
10049 (synopsis "Animal activity statistics")
10051 "This package provides functions to fit kernel density functions to
10052 animal activity time data; plot activity distributions; quantify overall
10053 levels of activity; statistically compare activity metrics through
10054 bootstrapping; and evaluate variation in linear variables with time (or other
10055 circular variables).")
10056 (license license:gpl3)))
10058 (define-public r-ouch
10065 (uri (cran-uri "ouch" version))
10068 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10069 (build-system r-build-system)
10070 (propagated-inputs `(("r-subplex" ,r-subplex)))
10071 (home-page "https://kingaa.github.io/ouch/")
10072 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10074 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10075 for evolution along a phylogenetic tree.")
10076 (license license:gpl2+)))
10078 (define-public r-fmsb
10085 (uri (cran-uri "fmsb" version))
10088 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10089 (build-system r-build-system)
10090 (home-page "http://minato.sip21c.org/msb/")
10091 (synopsis "Functions for medical statistics book with demographic data")
10093 "This package provides several utility functions for the book entitled
10094 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10095 Japan, 2007) with Japanese demographic data and some demographic analysis
10096 related functions.")
10097 (license license:gpl2+)))
10099 (define-public r-stabledist
10101 (name "r-stabledist")
10106 (uri (cran-uri "stabledist" version))
10109 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10110 (build-system r-build-system)
10111 (home-page "https://www.rmetrics.org")
10112 (synopsis "Stable distribution functions")
10114 "This package provides density, probability and quantile functions, and
10115 random number generation for (skew) stable distributions, using the
10116 parametrizations of Nolan.")
10117 (license license:gpl2+)))
10119 (define-public r-gsl
10126 (uri (cran-uri "gsl" version))
10129 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10130 (build-system r-build-system)
10133 (home-page "https://cran.r-project.org/web/packages/gsl")
10134 (synopsis "Wrapper for the GNU Scientific Library")
10136 "This package provides an R wrapper for the special functions and quasi
10137 random number generators of the GNU Scientific Library.")
10138 (license license:gpl2+)))
10140 (define-public r-adgoftest
10142 (name "r-adgoftest")
10147 (uri (cran-uri "ADGofTest" version))
10150 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10151 (properties `((upstream-name . "ADGofTest")))
10152 (build-system r-build-system)
10153 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10154 (synopsis "Anderson-Darling GoF test")
10156 "This package provides an implementation of the Anderson-Darling GoF test
10157 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10158 Anderson-Darling Distribution\".")
10159 ;; Any version of the GPL.
10160 (license license:gpl3+)))
10162 (define-public r-softimpute
10164 (name "r-softimpute")
10169 (uri (cran-uri "softImpute" version))
10172 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10173 (properties `((upstream-name . "softImpute")))
10174 (build-system r-build-system)
10176 `(("r-matrix" ,r-matrix)))
10178 `(("gfortran" ,gfortran)))
10179 (home-page "https://cran.r-project.org/web/packages/softImpute")
10180 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10182 "This package provides iterative methods for matrix completion that use
10183 nuclear-norm regularization. The package includes procedures for centering
10184 and scaling rows, columns or both, and for computing low-rank @dfn{single
10185 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10187 (license license:gpl2)))
10189 (define-public r-fftwtools
10191 (name "r-fftwtools")
10196 (uri (cran-uri "fftwtools" version))
10199 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10200 (build-system r-build-system)
10201 (inputs `(("fftw" ,fftw)))
10202 (home-page "https://github.com/krahim/fftwtools")
10203 (synopsis "Wrapper for FFTW3")
10205 "This package provides a wrapper for several FFTW functions. It provides
10206 access to the two-dimensional FFT, the multivariate FFT, and the
10207 one-dimensional real to complex FFT using the FFTW3 library. The package
10208 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10209 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10210 The FFT functions have a parameter that allows them to not return the
10211 redundant complex conjugate when the input is real data.")
10212 (license license:gpl2+)))
10214 (define-public r-tiff
10221 (uri (cran-uri "tiff" version))
10224 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10225 (build-system r-build-system)
10227 `(("libtiff" ,libtiff)
10228 ("libjpeg" ,libjpeg-turbo)
10230 (home-page "https://www.rforge.net/tiff/")
10231 (synopsis "Read and write TIFF images")
10233 "This package provides an easy and simple way to read, write and display
10234 bitmap images stored in the TIFF format. It can read and write both files and
10235 in-memory raw vectors.")
10236 ;; Either of these two license versions.
10237 (license (list license:gpl2 license:gpl3))))
10239 (define-public r-nlp
10246 (uri (cran-uri "NLP" version))
10249 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10250 (properties `((upstream-name . "NLP")))
10251 (build-system r-build-system)
10252 (home-page "https://cran.r-project.org/web/packages/NLP/")
10253 (synopsis "Natural language processing infrastructure")
10255 "This package provides basic classes and methods for Natural Language
10257 (license license:gpl3)))
10259 (define-public r-tm
10266 (uri (cran-uri "tm" version))
10269 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10270 (properties `((upstream-name . "tm")))
10271 (build-system r-build-system)
10277 ("r-xml2" ,r-xml2)))
10278 (home-page "http://tm.r-forge.r-project.org/")
10279 (synopsis "Text mining package")
10281 "This package provides a framework for text mining applications within R.")
10282 (license license:gpl3)))
10284 (define-public r-waveslim
10286 (name "r-waveslim")
10291 (uri (cran-uri "waveslim" version))
10294 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10295 (build-system r-build-system)
10297 `(("gfortran" ,gfortran)))
10298 (home-page "http://waveslim.blogspot.com")
10299 (synopsis "Basic wavelet routines for signal processing")
10301 "This package provides basic wavelet routines for time series (1D),
10302 image (2D) and array (3D) analysis. The code provided here is based on
10303 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10304 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10305 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10306 pairs (Selesnick 2001, 2002).")
10307 (license license:bsd-3)))
10309 (define-public r-wordcloud
10311 (name "r-wordcloud")
10316 (uri (cran-uri "wordcloud" version))
10319 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10320 (build-system r-build-system)
10322 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10324 ;; The "tm" package is only "suggested" according to CRAN, but the
10325 ;; wordcloud package cannot be loaded without it.
10327 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10328 (synopsis "Word clouds")
10330 "This package provides functionality to create pretty word clouds,
10331 visualize differences and similarity between documents, and avoid
10332 over-plotting in scatter plots with text.")
10333 (license license:lgpl2.1)))
10335 (define-public r-colorramps
10337 (name "r-colorramps")
10342 (uri (cran-uri "colorRamps" version))
10345 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10346 (properties `((upstream-name . "colorRamps")))
10347 (build-system r-build-system)
10348 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10349 (synopsis "Build color tables")
10350 (description "This package provides features to build gradient color
10352 ;; Any version of the GPL
10353 (license license:gpl3+)))
10355 (define-public r-tidytree
10357 (name "r-tidytree")
10362 (uri (cran-uri "tidytree" version))
10364 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10365 (build-system r-build-system)
10368 ("r-dplyr" ,r-dplyr)
10369 ("r-lazyeval" ,r-lazyeval)
10370 ("r-magrittr" ,r-magrittr)
10371 ("r-rlang" ,r-rlang)
10372 ("r-tibble" ,r-tibble)))
10374 `(("r-knitr" ,r-knitr)))
10375 (home-page "https://github.com/GuangchuangYu/tidytree")
10376 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10378 "Phylogenetic trees generally contain multiple components including nodes,
10379 edges, branches and associated data. This package provides an approach to
10380 convert tree objects to tidy data frames. It also provides tidy interfaces to
10381 manipulate tree data.")
10382 (license license:artistic2.0)))
10384 (define-public r-rvcheck
10391 (uri (cran-uri "rvcheck" version))
10393 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10394 (build-system r-build-system)
10396 `(("r-biocmanager" ,r-biocmanager)
10397 ("r-rlang" ,r-rlang)))
10398 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10399 (synopsis "R package version check")
10401 "This package provides tools to check the latest release version of R and
10402 R packages (on CRAN, Bioconductor or Github).")
10403 (license license:artistic2.0)))
10405 (define-public r-docopt
10412 (uri (cran-uri "docopt" version))
10415 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10416 (build-system r-build-system)
10417 (home-page "https://github.com/docopt/docopt.R")
10418 (synopsis "Command-line interface specification language")
10420 "This package enables you to define a command-line interface by just
10421 giving it a description in the specific format.")
10422 (license license:expat)))
10424 (define-public r-sparsesvd
10426 (name "r-sparsesvd")
10431 (uri (cran-uri "sparsesvd" version))
10434 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10435 (build-system r-build-system)
10436 (propagated-inputs `(("r-matrix" ,r-matrix)))
10437 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10438 (synopsis "Sparse truncated singular value decomposition")
10440 "This package provides a Wrapper around the SVDLIBC library
10441 for (truncated) singular value decomposition of a sparse matrix. Currently,
10442 only sparse real matrices in Matrix package format are supported.")
10443 ;; SVDLIBC is released under BSD-2. The R interface is released under
10445 (license (list license:bsd-3 license:bsd-2))))
10447 (define-public r-speedglm
10449 (name "r-speedglm")
10454 (uri (cran-uri "speedglm" version))
10457 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10458 (build-system r-build-system)
10460 `(("r-mass" ,r-mass)
10461 ("r-matrix" ,r-matrix)))
10462 (home-page "https://cran.r-project.org/web/packages/speedglm")
10463 (synopsis "Fit linear and generalized linear models to large data sets")
10465 "This package provides tools for fitting linear models and generalized
10466 linear models to large data sets by updating algorithms.")
10467 ;; Any version of the GPL
10468 (license license:gpl2+)))
10470 (define-public r-densityclust
10472 (name "r-densityclust")
10477 (uri (cran-uri "densityClust" version))
10480 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10481 (properties `((upstream-name . "densityClust")))
10482 (build-system r-build-system)
10485 ("r-ggplot2" ,r-ggplot2)
10486 ("r-ggrepel" ,r-ggrepel)
10487 ("r-gridextra" ,r-gridextra)
10488 ("r-rcolorbrewer" ,r-rcolorbrewer)
10490 ("r-rtsne" ,r-rtsne)))
10491 (home-page "https://cran.r-project.org/web/packages/densityClust")
10492 (synopsis "Clustering by fast search and find of density peaks")
10494 "This package provides an improved implementation (based on k-nearest
10495 neighbors) of the density peak clustering algorithm, originally described by
10496 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10497 large datasets (> 100,000 samples) very efficiently.")
10498 (license license:gpl2+)))
10500 (define-public r-combinat
10502 (name "r-combinat")
10507 (uri (cran-uri "combinat" version))
10510 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10511 (build-system r-build-system)
10512 (home-page "https://cran.r-project.org/web/packages/combinat")
10513 (synopsis "Combinatorics utilities")
10514 (description "This package provides assorted routines for combinatorics.")
10515 (license license:gpl2)))
10517 (define-public r-qlcmatrix
10519 (name "r-qlcmatrix")
10524 (uri (cran-uri "qlcMatrix" version))
10527 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10528 (properties `((upstream-name . "qlcMatrix")))
10529 (build-system r-build-system)
10531 `(("r-docopt" ,r-docopt)
10532 ("r-matrix" ,r-matrix)
10534 ("r-sparsesvd" ,r-sparsesvd)))
10535 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10536 (synopsis "Sparse matrix functions for quantitative language comparison")
10538 "This package provides an extension of the functionality of the Matrix
10539 package for using sparse matrices. Some of the functions are very general,
10540 while other are highly specific for the special data format used for
10541 @dfn{quantitative language comparison} (QLC).")
10542 (license license:gpl3)))
10544 (define-public r-ddrtree
10551 (uri (cran-uri "DDRTree" version))
10554 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10555 (properties `((upstream-name . "DDRTree")))
10556 (build-system r-build-system)
10559 ("r-irlba" ,r-irlba)
10561 ("r-rcppeigen" ,r-rcppeigen)))
10562 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10563 (synopsis "Learning principal graphs with DDRTree")
10565 "This package provides an implementation of the framework of
10566 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10567 dimensional space while constructs a principal tree which passes through the
10568 middle of the data simultaneously. DDRTree shows superiority to
10569 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10570 intrinsic structure of single cell genomics data. In general, it could be
10571 used to reconstruct the temporal progression as well as the bifurcation
10572 structure of any data type.")
10573 (license license:asl2.0)))
10575 (define-public r-corpcor
10582 (uri (cran-uri "corpcor" version))
10585 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10586 (build-system r-build-system)
10587 (home-page "http://strimmerlab.org/software/corpcor/")
10588 (synopsis "Efficient estimation of covariance and (partial) correlation")
10590 "This package implements a James-Stein-type shrinkage estimator for the
10591 covariance matrix, with separate shrinkage for variances and correlations.
10592 Furthermore, functions are available for fast singular value decomposition,
10593 for computing the pseudoinverse, and for checking the rank and positive
10594 definiteness of a matrix.")
10595 (license license:gpl3+)))
10597 (define-public r-rspectra
10599 (name "r-rspectra")
10604 (uri (cran-uri "RSpectra" version))
10607 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10608 (properties `((upstream-name . "RSpectra")))
10609 (build-system r-build-system)
10611 `(("r-matrix" ,r-matrix)
10613 ("r-rcppeigen" ,r-rcppeigen)))
10614 (home-page "https://github.com/yixuan/RSpectra")
10615 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10617 "This package provides an R interface to the Spectra library for
10618 large-scale eigenvalue and SVD problems. It is typically used to compute a
10619 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10620 which is usually more efficient than @code{eigen()} if k << n.")
10622 (license license:mpl2.0)))
10624 (define-public r-vbsr
10631 (uri (cran-uri "vbsr" version))
10634 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10635 (build-system r-build-system)
10636 (home-page "https://cran.r-project.org/web/packages/vbsr")
10637 (synopsis "Variational Bayes spike regression regularized linear models")
10639 "This package provides an efficient algorithm for solving ultra-sparse
10640 regularized regression models using a variational Bayes algorithm with a spike
10641 prior. The algorithm is solved on a path, with coordinate updates, and is
10642 capable of generating very sparse models. Very general model
10643 diagnostics for controlling type-1 errors are also provided.")
10644 (license license:gpl2)))
10646 (define-public r-flare
10649 (version "1.6.0.2")
10653 (uri (cran-uri "flare" version))
10656 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10657 (build-system r-build-system)
10659 `(("r-igraph" ,r-igraph)
10660 ("r-lattice" ,r-lattice)
10662 ("r-matrix" ,r-matrix)))
10663 (home-page "https://cran.r-project.org/web/packages/flare")
10664 (synopsis "Family of Lasso regression implementations")
10666 "This package provides implementations of a family of Lasso variants
10667 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10668 high dimensional sparse linear models.")
10669 (license license:gpl2)))
10671 (define-public r-lassopv
10678 (uri (cran-uri "lassopv" version))
10681 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10682 (build-system r-build-system)
10683 (propagated-inputs `(("r-lars" ,r-lars)))
10684 (home-page "https://github.com/lingfeiwang/lassopv")
10685 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10687 "This package enables you to estimate the p-values for predictors x
10688 against target variable y in Lasso regression, using the regularization
10689 strength when each predictor enters the active set of regularization path for
10690 the first time as the statistic.")
10691 (license license:gpl3)))
10693 (define-public r-splitstackshape
10695 (name "r-splitstackshape")
10700 (uri (cran-uri "splitstackshape" version))
10703 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10704 (build-system r-build-system)
10706 `(("r-data-table" ,r-data-table)))
10707 (home-page "https://github.com/mrdwab/splitstackshape")
10708 (synopsis "Stack and reshape datasets after splitting concatenated values")
10710 "Online data collection tools like Google Forms often export
10711 multiple-response questions with data concatenated in cells. The
10712 @code{concat.split} (cSplit) family of functions provided by this package
10713 splits such data into separate cells. This package also includes functions to
10714 stack groups of columns and to reshape wide data, even when the data are
10715 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10716 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10718 (license license:gpl3)))
10720 (define-public r-tfmpvalue
10722 (name "r-tfmpvalue")
10727 (uri (cran-uri "TFMPvalue" version))
10730 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10731 (properties `((upstream-name . "TFMPvalue")))
10732 (build-system r-build-system)
10733 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10734 (home-page "https://github.com/ge11232002/TFMPvalue")
10735 (synopsis "P-value computation for position weight matrices")
10737 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10738 identification from sequence/alignments, we are interested in the significance
10739 of certain match scores. TFMPvalue provides the accurate calculation of a
10740 p-value with a score threshold for position weight matrices, or the score with
10741 a given p-value. It is an interface to code originally made available by
10742 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10743 Touzet and Varre (2007).")
10744 (license license:gpl2)))
10746 (define-public r-rnifti
10753 (uri (cran-uri "RNifti" version))
10756 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10757 (properties `((upstream-name . "RNifti")))
10758 (build-system r-build-system)
10759 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10760 (home-page "https://github.com/jonclayden/RNifti")
10761 (synopsis "Fast R and C++ access to NIfTI images")
10763 "This package provides very fast read and write access to images stored
10764 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10765 compiled C and interpreted R code. It also provides a C/C++ API that can be
10766 used by other packages.")
10767 (license license:gpl2)))
10769 (define-public r-shades
10776 (uri (cran-uri "shades" version))
10779 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10780 (build-system r-build-system)
10781 (home-page "https://github.com/jonclayden/shades")
10782 (synopsis "Simple color manipulation")
10784 "This package provides functions for easily manipulating colors,
10785 creating color scales and calculating color distances.")
10786 (license license:bsd-3)))
10788 (define-public r-ore
10795 (uri (cran-uri "ore" version))
10797 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10798 (build-system r-build-system)
10799 (home-page "https://github.com/jonclayden/ore")
10800 (synopsis "R interface to the Onigmo regular expression library")
10802 "This package provides an alternative to R's built-in functionality for
10803 handling regular expressions, based on the Onigmo library. It offers
10804 first-class compiled regex objects, partial matching and function-based
10805 substitutions, amongst other features.")
10806 (license license:bsd-3)))
10808 (define-public r-reportr
10815 (uri (cran-uri "reportr" version))
10818 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10819 (build-system r-build-system)
10820 (propagated-inputs `(("r-ore" ,r-ore)))
10821 (home-page "https://github.com/jonclayden/reportr")
10822 (synopsis "General message and error reporting system")
10824 "This package provides a system for reporting messages, which offers
10825 certain useful features over the standard R system, such as the incorporation
10826 of output consolidation, message filtering, assertions, expression
10827 substitution, automatic generation of stack traces for debugging, and
10828 conditional reporting based on the current \"output level\".")
10829 (license license:gpl2)))
10831 (define-public r-tractor-base
10833 (name "r-tractor-base")
10838 (uri (cran-uri "tractor.base" version))
10841 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10842 (properties `((upstream-name . "tractor.base")))
10843 (build-system r-build-system)
10846 ("r-reportr" ,r-reportr)
10847 ("r-rnifti" ,r-rnifti)
10848 ("r-shades" ,r-shades)))
10849 (home-page "https://www.tractor-mri.org.uk")
10850 (synopsis "Read, manipulate and visualize magnetic resonance images")
10852 "This package provides functions for working with magnetic resonance
10853 images. It supports reading and writing of popular file formats (DICOM,
10854 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10855 visualization; flexible image manipulation; metadata and sparse image
10857 (license license:gpl2)))
10859 (define-public r-grimport
10861 (name "r-grimport")
10866 (uri (cran-uri "grImport" version))
10869 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10870 (properties `((upstream-name . "grImport")))
10871 (build-system r-build-system)
10873 `(("ghostscript" ,ghostscript)))
10875 `(("r-xml" ,r-xml)))
10876 (home-page "https://cran.r-project.org/web/packages/grImport")
10877 (synopsis "Convert, import, and draw PostScript pictures")
10879 "This package provides functions for converting, importing, and drawing
10880 PostScript pictures in R plots.")
10881 (license license:gpl2+)))
10883 (define-public r-grimport2
10885 (name "r-grimport2")
10890 (uri (cran-uri "grImport2" version))
10893 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10894 (properties `((upstream-name . "grImport2")))
10895 (build-system r-build-system)
10897 `(("r-base64enc" ,r-base64enc)
10901 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10902 (synopsis "Import SVG graphics")
10904 "This package provides functions for importing external vector images and
10905 drawing them as part of R plots. This package is different from the
10906 @code{grImport} package because, where that package imports PostScript format
10907 images, this package imports SVG format images. Furthermore, this package
10908 imports a specific subset of SVG, so external images must be preprocessed
10909 using a package like @code{rsvg} to produce SVG that this package can import.
10910 SVG features that are not supported by R graphics, such as gradient fills, can
10911 be imported and then exported via the @code{gridSVG} package.")
10912 (license license:gpl2+)))
10914 (define-public r-kohonen
10921 (uri (cran-uri "kohonen" version))
10924 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10925 (build-system r-build-system)
10927 `(("r-rcpp" ,r-rcpp)))
10928 (home-page "https://cran.r-project.org/web/packages/kohonen")
10929 (synopsis "Supervised and unsupervised self-organising maps")
10931 "This package provides functions to train @dfn{self-organising
10932 maps} (SOMs). Also interrogation of the maps and prediction using trained
10933 maps are supported. The name of the package refers to Teuvo Kohonen, the
10934 inventor of the SOM.")
10935 (license license:gpl2+)))
10937 (define-public r-nnls
10944 (uri (cran-uri "nnls" version))
10947 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10948 (build-system r-build-system)
10949 (native-inputs `(("gfortran" ,gfortran)))
10950 (home-page "https://cran.r-project.org/web/packages/nnls")
10951 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10953 "This package provides an R interface to the Lawson-Hanson implementation
10954 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10955 the combination of non-negative and non-positive constraints.")
10956 (license license:gpl2+)))
10958 (define-public r-iso
10961 (version "0.0-18.1")
10965 (uri (cran-uri "Iso" version))
10968 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
10969 (properties `((upstream-name . "Iso")))
10970 (build-system r-build-system)
10971 (native-inputs `(("gfortran" ,gfortran)))
10972 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10973 (synopsis "Functions to perform isotonic regression")
10975 "This package provides support for linear order and unimodal
10976 order (univariate) isotonic regression and bivariate isotonic regression with
10977 linear order on both variables.")
10978 (license license:gpl2+)))
10980 (define-public r-chemometricswithr
10982 (name "r-chemometricswithr")
10987 (uri (cran-uri "ChemometricsWithR" version))
10990 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10992 `((upstream-name . "ChemometricsWithR")))
10993 (build-system r-build-system)
10995 `(("r-devtools" ,r-devtools)
10996 ("r-kohonen" ,r-kohonen)
10999 (home-page "https://github.com/rwehrens/CWR")
11000 (synopsis "Chemometrics with R")
11002 "This package provides functions and scripts used in the book
11003 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11004 Life Sciences\" by Ron Wehrens, Springer (2011).")
11005 (license license:gpl2+)))
11007 (define-public r-als
11014 (uri (cran-uri "ALS" version))
11017 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11018 (properties `((upstream-name . "ALS")))
11019 (build-system r-build-system)
11022 ("r-nnls" ,r-nnls)))
11023 (home-page "https://cran.r-project.org/web/packages/ALS")
11024 (synopsis "Multivariate curve resolution alternating least squares")
11026 "Alternating least squares is often used to resolve components
11027 contributing to data with a bilinear structure; the basic technique may be
11028 extended to alternating constrained least squares. This package provides an
11029 implementation of @dfn{multivariate curve resolution alternating least
11030 squares} (MCR-ALS).
11032 Commonly applied constraints include unimodality, non-negativity, and
11033 normalization of components. Several data matrices may be decomposed
11034 simultaneously by assuming that one of the two matrices in the bilinear
11035 decomposition is shared between datasets.")
11036 (license license:gpl2+)))
11038 (define-public r-strucchange
11040 (name "r-strucchange")
11045 (uri (cran-uri "strucchange" version))
11048 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11049 (build-system r-build-system)
11051 `(("r-sandwich" ,r-sandwich)
11053 (home-page "https://cran.r-project.org/web/packages/strucchange")
11054 (synopsis "Testing, monitoring, and dating structural changes")
11056 "This package provides tools for testing, monitoring and dating
11057 structural changes in (linear) regression models. It features tests/methods
11058 from the generalized fluctuation test framework as well as from the F
11059 test (Chow test) framework. This includes methods to fit, plot and test
11060 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11061 statistics, respectively. It is possible to monitor incoming data online
11062 using fluctuation processes. Finally, the breakpoints in regression models
11063 with structural changes can be estimated together with confidence intervals.
11064 Emphasis is always given to methods for visualizing the data.")
11065 ;; Either of these two GPL versions
11066 (license (list license:gpl2 license:gpl3))))
11068 (define-public r-pixmap
11075 (uri (cran-uri "pixmap" version))
11078 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11079 (build-system r-build-system)
11080 (home-page "https://cran.r-project.org/web/packages/pixmap")
11081 (synopsis "Tools for bitmap images")
11083 "This package provides functions for importing, exporting, plotting and
11084 other manipulations of bitmapped images.")
11085 (license license:gpl2)))
11087 (define-public r-rapidjsonr
11089 (name "r-rapidjsonr")
11094 (uri (cran-uri "rapidjsonr" version))
11097 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11098 (build-system r-build-system)
11099 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11100 (synopsis "JSON parser")
11102 "This package provides JSON parsing capability through the Rapidjson
11104 (license license:expat)))
11106 (define-public r-ontologyindex
11108 (name "r-ontologyindex")
11113 (uri (cran-uri "ontologyIndex" version))
11116 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11117 (properties `((upstream-name . "ontologyIndex")))
11118 (build-system r-build-system)
11119 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11120 (synopsis "Functions for processing ontologies in R")
11122 "This package provides functions for reading ontologies into R as lists
11123 and manipulating sets of ontological terms.")
11124 (license license:gpl2+)))
11126 (define-public r-gargle
11133 (uri (cran-uri "gargle" version))
11136 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11137 (build-system r-build-system)
11142 ("r-jsonlite" ,r-jsonlite)
11143 ("r-rlang" ,r-rlang)
11144 ("r-withr" ,r-withr)))
11146 `(("r-knitr" ,r-knitr)))
11147 (home-page "https://gargle.r-lib.org")
11148 (synopsis "Utilities for working with Google APIs")
11150 "This package provides utilities for working with Google APIs. This
11151 includes functions and classes for handling common credential types and for
11152 preparing, executing, and processing HTTP requests.")
11153 (license license:expat)))
11155 (define-public r-bigrquery
11157 (name "r-bigrquery")
11162 (uri (cran-uri "bigrquery" version))
11165 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11166 (build-system r-build-system)
11168 `(("r-assertthat" ,r-assertthat)
11169 ("r-bit64" ,r-bit64)
11172 ("r-gargle" ,r-gargle)
11175 ("r-jsonlite" ,r-jsonlite)
11176 ("r-prettyunits" ,r-prettyunits)
11177 ("r-progress" ,r-progress)
11178 ("r-rapidjsonr" ,r-rapidjsonr)
11180 ("r-rlang" ,r-rlang)
11181 ("r-tibble" ,r-tibble)))
11182 (home-page "https://github.com/rstats-db/bigrquery")
11183 (synopsis "R interface to Google's BigQuery API")
11185 "This package provides an R interface to Google's BigQuery database.")
11186 (license license:gpl3)))
11188 (define-public r-gmp
11195 (uri (cran-uri "gmp" version))
11198 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11199 (build-system r-build-system)
11202 (modify-phases %standard-phases
11203 (add-after 'unpack 'set-CC
11204 (lambda _ (setenv "CC" "gcc") #t)))))
11205 (inputs `(("gmp" ,gmp)))
11206 (home-page "https://cran.r-project.org/web/packages/gmp")
11207 (synopsis "Multiple precision arithmetic")
11209 "This package supports multiple precision arithmetic (big integers and
11210 rationals, prime number tests, matrix computation), \"arithmetic without
11211 limitations\" using the GNU Multiple Precision library.")
11212 ;; Any version of the GPL.
11213 (license license:gpl3+)))
11215 (define-public r-rmpfr
11222 (uri (cran-uri "Rmpfr" version))
11225 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11226 (properties `((upstream-name . "Rmpfr")))
11227 (build-system r-build-system)
11232 `(("r-gmp" ,r-gmp)))
11234 `(("pkg-config" ,pkg-config)))
11235 (home-page "http://rmpfr.r-forge.r-project.org/")
11236 (synopsis "R bindings to the MPFR library")
11238 "This package supports arithmetic (via S4 classes and methods) for
11239 arbitrary precision floating point numbers, including transcendental
11240 functions. To this end, the package interfaces with the @dfn{Multiple
11241 Precision Floating-Point Reliable} (MPFR) library.")
11242 (license license:gpl2+)))
11244 (define-public r-assertive-base
11246 (name "r-assertive-base")
11251 (uri (cran-uri "assertive.base" version))
11254 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11256 `((upstream-name . "assertive.base")))
11257 (build-system r-build-system)
11258 (home-page "https://bitbucket.org/richierocks/assertive.base")
11259 (synopsis "Core of the assertive package")
11261 "This package provides a minimal set of predicates and assertions used by
11262 the assertive package. This is mainly for use by other package developers who
11263 want to include run-time testing features in their own packages.")
11264 (license license:gpl3+)))
11266 (define-public r-assertive-properties
11268 (name "r-assertive-properties")
11273 (uri (cran-uri "assertive.properties" version))
11276 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11278 `((upstream-name . "assertive.properties")))
11279 (build-system r-build-system)
11281 `(("r-assertive-base" ,r-assertive-base)))
11282 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11283 (synopsis "Assertions to check properties of variables")
11285 "This package provides a set of predicates and assertions for checking
11286 the properties of variables, such as length, names and attributes. This is
11287 mainly for use by other package developers who want to include run-time
11288 testing features in their own packages.")
11289 (license license:gpl3+)))
11291 (define-public r-assertive-numbers
11293 (name "r-assertive-numbers")
11298 (uri (cran-uri "assertive.numbers" version))
11301 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11303 `((upstream-name . "assertive.numbers")))
11304 (build-system r-build-system)
11306 `(("r-assertive-base" ,r-assertive-base)))
11307 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11308 (synopsis "Assertions to check properties of numbers")
11310 "This package provides a set of predicates and assertions for checking
11311 the properties of numbers. This is mainly for use by other package developers
11312 who want to include run-time testing features in their own packages.")
11313 (license license:gpl3+)))
11315 (define-public r-assertive-sets
11317 (name "r-assertive-sets")
11322 (uri (cran-uri "assertive.sets" version))
11325 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11327 `((upstream-name . "assertive.sets")))
11328 (build-system r-build-system)
11330 `(("r-assertive-base" ,r-assertive-base)))
11331 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11332 (synopsis "Assertions to check properties of sets")
11334 "This package provides a set of predicates and assertions for checking
11335 the properties of sets. This is mainly for use by other package developers
11336 who want to include run-time testing features in their own packages.")
11337 (license license:gpl3+)))
11339 (define-public r-assertive-matrices
11341 (name "r-assertive-matrices")
11346 (uri (cran-uri "assertive.matrices" version))
11349 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11351 `((upstream-name . "assertive.matrices")))
11352 (build-system r-build-system)
11354 `(("r-assertive-base" ,r-assertive-base)))
11355 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11356 (synopsis "Assertions to check properties of matrices")
11358 "This package provides a set of predicates and assertions for checking
11359 the properties of matrices. This is mainly for use by other package
11360 developers who want to include run-time testing features in their own
11362 (license license:gpl3+)))
11364 (define-public r-assertive-models
11366 (name "r-assertive-models")
11371 (uri (cran-uri "assertive.models" version))
11374 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11376 `((upstream-name . "assertive.models")))
11377 (build-system r-build-system)
11379 `(("r-assertive-base" ,r-assertive-base)))
11380 (home-page "https://bitbucket.org/richierocks/assertive.models")
11381 (synopsis "Assertions to check properties of models")
11383 "This package provides a set of predicates and assertions for checking
11384 the properties of models. This is mainly for use by other package developers
11385 who want to include run-time testing features in their own packages.")
11386 (license license:gpl3+)))
11388 (define-public r-assertive-reflection
11390 (name "r-assertive-reflection")
11395 (uri (cran-uri "assertive.reflection" version))
11398 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
11400 `((upstream-name . "assertive.reflection")))
11401 (build-system r-build-system)
11403 `(("r-assertive-base" ,r-assertive-base)))
11404 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11405 (synopsis "Assertions for checking the state of R")
11407 "This package provides a set of predicates and assertions for checking
11408 the state and capabilities of R, the operating system it is running on, and
11409 the IDE being used. This is mainly for use by other package developers who
11410 want to include run-time testing features in their own packages.")
11411 (license license:gpl3+)))
11413 (define-public r-assertive-types
11415 (name "r-assertive-types")
11420 (uri (cran-uri "assertive.types" version))
11423 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11425 `((upstream-name . "assertive.types")))
11426 (build-system r-build-system)
11428 `(("r-assertive-base" ,r-assertive-base)
11429 ("r-assertive-properties" ,r-assertive-properties)
11430 ("r-codetools" ,r-codetools)))
11431 (home-page "https://bitbucket.org/richierocks/assertive.types")
11432 (synopsis "Assertions to check types of variables")
11434 "This package provides a set of predicates and assertions for checking
11435 the types of variables. This is mainly for use by other package developers
11436 who want to include run-time testing features in their own packages.")
11437 (license license:gpl3+)))
11439 (define-public r-assertive-files
11441 (name "r-assertive-files")
11446 (uri (cran-uri "assertive.files" version))
11449 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11451 `((upstream-name . "assertive.files")))
11452 (build-system r-build-system)
11454 `(("r-assertive-base" ,r-assertive-base)
11455 ("r-assertive-numbers" ,r-assertive-numbers)))
11456 (home-page "https://bitbucket.org/richierocks/assertive.files")
11457 (synopsis "Assertions to check properties of files")
11459 "This package provides a set of predicates and assertions for checking
11460 the properties of files and connections. This is mainly for use by other
11461 package developers who want to include run-time testing features in their own
11463 (license license:gpl3+)))
11465 (define-public r-assertive-code
11467 (name "r-assertive-code")
11472 (uri (cran-uri "assertive.code" version))
11475 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11477 `((upstream-name . "assertive.code")))
11478 (build-system r-build-system)
11480 `(("r-assertive-base" ,r-assertive-base)
11481 ("r-assertive-properties" ,r-assertive-properties)
11482 ("r-assertive-types" ,r-assertive-types)))
11483 (home-page "https://bitbucket.org/richierocks/assertive.code")
11484 (synopsis "Assertions to check properties of code")
11486 "This package provides a set of predicates and assertions for checking
11487 the properties of code. This is mainly for use by other package developers
11488 who want to include run-time testing features in their own packages.")
11489 (license license:gpl3+)))
11491 (define-public r-assertive-datetimes
11493 (name "r-assertive-datetimes")
11498 (uri (cran-uri "assertive.datetimes" version))
11501 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11503 `((upstream-name . "assertive.datetimes")))
11504 (build-system r-build-system)
11506 `(("r-assertive-base" ,r-assertive-base)
11507 ("r-assertive-types" ,r-assertive-types)))
11508 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11509 (synopsis "Assertions to check properties of dates and times")
11511 "This package provides a set of predicates and assertions for checking
11512 the properties of dates and times. This is mainly for use by other package
11513 developers who want to include run-time testing features in their own
11515 (license license:gpl3+)))
11517 (define-public r-assertive-strings
11519 (name "r-assertive-strings")
11524 (uri (cran-uri "assertive.strings" version))
11527 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11529 `((upstream-name . "assertive.strings")))
11530 (build-system r-build-system)
11532 `(("r-assertive-base" ,r-assertive-base)
11533 ("r-assertive-types" ,r-assertive-types)
11534 ("r-stringi" ,r-stringi)))
11535 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11536 (synopsis "Assertions to check properties of strings")
11538 "This package provides a set of predicates and assertions for checking
11539 the properties of strings. This is mainly for use by other package developers
11540 who want to include run-time testing features in their own packages.")
11541 (license license:gpl3+)))
11543 (define-public r-assertive-data-us
11545 (name "r-assertive-data-us")
11550 (uri (cran-uri "assertive.data.us" version))
11553 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11555 `((upstream-name . "assertive.data.us")))
11556 (build-system r-build-system)
11558 `(("r-assertive-base" ,r-assertive-base)
11559 ("r-assertive-strings" ,r-assertive-strings)))
11560 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11561 (synopsis "Assertions to check properties of strings")
11563 "This package provides a set of predicates and assertions for checking
11564 the properties of US-specific complex data types. This is mainly for use by
11565 other package developers who want to include run-time testing features in
11566 their own packages.")
11567 (license license:gpl3+)))
11569 (define-public r-assertive-data-uk
11571 (name "r-assertive-data-uk")
11576 (uri (cran-uri "assertive.data.uk" version))
11579 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11581 `((upstream-name . "assertive.data.uk")))
11582 (build-system r-build-system)
11584 `(("r-assertive-base" ,r-assertive-base)
11585 ("r-assertive-strings" ,r-assertive-strings)))
11586 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11587 (synopsis "Assertions to check properties of strings")
11589 "This package provides a set of predicates and assertions for checking
11590 the properties of UK-specific complex data types. This is mainly for use by
11591 other package developers who want to include run-time testing features in
11592 their own packages.")
11593 (license license:gpl3+)))
11595 (define-public r-assertive-data
11597 (name "r-assertive-data")
11602 (uri (cran-uri "assertive.data" version))
11605 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11607 `((upstream-name . "assertive.data")))
11608 (build-system r-build-system)
11610 `(("r-assertive-base" ,r-assertive-base)
11611 ("r-assertive-strings" ,r-assertive-strings)))
11612 (home-page "https://bitbucket.org/richierocks/assertive.data")
11613 (synopsis "Assertions to check properties of data")
11615 "This package provides a set of predicates and assertions for checking
11616 the properties of (country independent) complex data types. This is mainly
11617 for use by other package developers who want to include run-time testing
11618 features in their own packages.")
11619 (license license:gpl3+)))
11621 (define-public r-assertive
11623 (name "r-assertive")
11628 (uri (cran-uri "assertive" version))
11631 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11632 (build-system r-build-system)
11634 `(("r-assertive-base" ,r-assertive-base)
11635 ("r-assertive-code" ,r-assertive-code)
11636 ("r-assertive-data" ,r-assertive-data)
11637 ("r-assertive-data-uk" ,r-assertive-data-uk)
11638 ("r-assertive-data-us" ,r-assertive-data-us)
11639 ("r-assertive-datetimes" ,r-assertive-datetimes)
11640 ("r-assertive-files" ,r-assertive-files)
11641 ("r-assertive-matrices" ,r-assertive-matrices)
11642 ("r-assertive-models" ,r-assertive-models)
11643 ("r-assertive-numbers" ,r-assertive-numbers)
11644 ("r-assertive-properties" ,r-assertive-properties)
11645 ("r-assertive-reflection" ,r-assertive-reflection)
11646 ("r-assertive-sets" ,r-assertive-sets)
11647 ("r-assertive-strings" ,r-assertive-strings)
11648 ("r-assertive-types" ,r-assertive-types)
11649 ("r-knitr" ,r-knitr)))
11650 (home-page "https://bitbucket.org/richierocks/assertive")
11651 (synopsis "Readable check functions to ensure code integrity")
11653 "This package provides lots of predicates (@code{is_*} functions) to
11654 check the state of your variables, and assertions (@code{assert_*} functions)
11655 to throw errors if they aren't in the right form.")
11656 (license license:gpl3+)))
11658 (define-public r-dotcall64
11660 (name "r-dotcall64")
11665 (uri (cran-uri "dotCall64" version))
11668 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11669 (properties `((upstream-name . "dotCall64")))
11670 (build-system r-build-system)
11671 (native-inputs `(("gfortran" ,gfortran)))
11672 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11673 (synopsis "Enhanced foreign function interface supporting long vectors")
11675 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11676 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11677 supports long vectors, arguments of type 64-bit integer, and provides a
11678 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11679 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11680 (license license:gpl2+)))
11682 (define-public r-spam
11689 (uri (cran-uri "spam" version))
11691 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11692 (build-system r-build-system)
11694 `(("r-dotcall64" ,r-dotcall64)))
11695 (native-inputs `(("gfortran" ,gfortran)))
11696 (home-page "https://www.math.uzh.ch/pages/spam/")
11697 (synopsis "Sparse matrix algebra")
11699 "This package provides a set of functions for sparse matrix algebra.
11700 Differences with other sparse matrix packages are:
11703 @item it only supports (essentially) one sparse matrix format;
11704 @item it is based on transparent and simple structure(s);
11705 @item it is tailored for MCMC calculations within G(M)RF;
11706 @item and it is fast and scalable (with the extension package @code{spam64}).
11708 ;; Either of these licenses
11709 (license (list license:bsd-3 license:lgpl2.0))))
11711 (define-public r-fields
11718 (uri (cran-uri "fields" version))
11720 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11721 (build-system r-build-system)
11723 `(("r-maps" ,r-maps)
11724 ("r-spam" ,r-spam)))
11726 `(("gfortran" ,gfortran)))
11727 (home-page "https://www.image.ucar.edu/fields")
11728 (synopsis "Tools for spatial data")
11730 "This is a package for curve, surface and function fitting with an
11731 emphasis on splines, spatial data and spatial statistics. The major methods
11732 include cubic, and thin plate splines, Kriging, and compactly supported
11733 covariance functions for large data sets.")
11734 (license license:gpl2+)))
11736 (define-public r-spatialextremes
11738 (name "r-spatialextremes")
11743 (uri (cran-uri "SpatialExtremes" version))
11746 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11748 `((upstream-name . "SpatialExtremes")))
11749 (build-system r-build-system)
11751 `(("r-fields" ,r-fields)
11752 ("r-maps" ,r-maps)))
11753 (home-page "http://spatialextremes.r-forge.r-project.org/")
11754 (synopsis "Modelling spatial extremes")
11756 "This package provides tools for the statistical modelling of spatial
11757 extremes using max-stable processes, copula or Bayesian hierarchical models.
11758 More precisely, this package allows (conditional) simulations from various
11759 parametric max-stable models, analysis of the extremal spatial dependence, the
11760 fitting of such processes using composite likelihoods or least square (simple
11761 max-stable processes only), model checking and selection and prediction.")
11762 (license license:gpl2+)))
11764 (define-public r-drc
11771 (uri (cran-uri "drc" version))
11774 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11775 (build-system r-build-system)
11778 ("r-gtools" ,r-gtools)
11780 ("r-multcomp" ,r-multcomp)
11781 ("r-plotrix" ,r-plotrix)
11782 ("r-scales" ,r-scales)))
11783 (home-page "https://cran.r-project.org/web/packages/drc")
11784 (synopsis "Analysis of dose-response curves")
11786 "This package provides a suite of flexible and versatile model fitting
11787 and after-fitting functions for the analysis of dose-response data.")
11788 (license license:gpl2+)))
11790 (define-public r-rmeta
11797 (uri (cran-uri "rmeta" version))
11800 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11801 (build-system r-build-system)
11802 (home-page "https://cran.r-project.org/web/packages/rmeta")
11803 (synopsis "Tools for meta-analysis")
11805 "This package provides functions for simple fixed and random effects
11806 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11807 draws standard summary plots, funnel plots, and computes summaries and tests
11808 for association and heterogeneity.")
11809 (license license:gpl2)))
11811 (define-public r-bootstrap
11813 (name "r-bootstrap")
11818 (uri (cran-uri "bootstrap" version))
11821 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11822 (build-system r-build-system)
11823 (native-inputs `(("gfortran" ,gfortran)))
11824 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11825 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11827 "This package provides software and data for the book \"An Introduction
11828 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11829 This package is primarily provided for projects already based on it, and for
11830 support of the book. New projects should preferentially use the recommended
11831 package \"boot\".")
11832 (license license:bsd-3)))
11834 (define-public r-survivalroc
11836 (name "r-survivalroc")
11841 (uri (cran-uri "survivalROC" version))
11844 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11845 (properties `((upstream-name . "survivalROC")))
11846 (build-system r-build-system)
11847 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11848 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11850 "Compute time-dependent ROC curve from censored survival data using
11851 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11852 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11853 (license license:gpl2+)))
11855 (define-public r-longitudinal
11857 (name "r-longitudinal")
11862 (uri (cran-uri "longitudinal" version))
11865 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11866 (build-system r-build-system)
11867 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11868 (home-page "http://strimmerlab.org/software/longitudinal/")
11869 (synopsis "Analysis of multiple time course data")
11871 "This package contains general data structures and functions for
11872 longitudinal data with multiple variables, repeated measurements, and
11873 irregularly spaced time points. It also implements a shrinkage estimator of
11874 dynamical correlation and dynamical covariance.")
11875 (license license:gpl3+)))
11877 (define-public r-genenet
11884 (uri (cran-uri "GeneNet" version))
11887 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
11888 (properties `((upstream-name . "GeneNet")))
11889 (build-system r-build-system)
11891 `(("r-corpcor" ,r-corpcor)
11892 ("r-fdrtool" ,r-fdrtool)
11893 ("r-longitudinal" ,r-longitudinal)))
11894 (home-page "http://strimmerlab.org/software/genenet/")
11895 (synopsis "Modeling and inferring gene networks")
11897 "This package analyzes gene expression (time series) data with focus on
11898 the inference of gene networks. In particular, GeneNet implements the methods
11899 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11900 for learning large-scale gene association networks (including assignment of
11901 putative directions).")
11902 (license license:gpl3+)))
11904 (define-public r-rbamtools
11906 (name "r-rbamtools")
11907 (version "2.16.17")
11911 (uri (cran-uri "rbamtools" version))
11914 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11915 (build-system r-build-system)
11916 (inputs `(("zlib" ,zlib)))
11918 `(("r-refgenome" ,r-refgenome)))
11919 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11920 (synopsis "Read and write BAM (binary alignment) files")
11922 "This package provides an R interface to functions of the SAMtools
11924 (license license:artistic2.0)))
11926 (define-public r-protviz
11933 (uri (cran-uri "protViz" version))
11936 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
11937 (properties `((upstream-name . "protViz")))
11938 (build-system r-build-system)
11939 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11940 (home-page "https://github.com/protViz/protViz/")
11941 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11943 "This package helps with quality checks, visualizations and analysis of
11944 mass spectrometry data, coming from proteomics experiments. The package is
11945 developed, tested and used at the Functional Genomics Center Zurich, where it
11946 is used mainly for prototyping, teaching, and having fun with proteomics data.
11947 But it can also be used to do data analysis for small scale data sets.")
11948 (license license:gpl3)))
11950 (define-public r-cmprsk
11957 (uri (cran-uri "cmprsk" version))
11959 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
11960 (build-system r-build-system)
11962 `(("r-survival" ,r-survival)))
11964 `(("gfortran" ,gfortran)))
11965 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11966 (synopsis "Subdistribution analysis of competing risks")
11968 "This package provides tool for estimation, testing and regression
11969 modeling of subdistribution functions in competing risks, as described in
11970 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11971 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11972 A proportional hazards model for the subdistribution of a competing risk,
11973 JASA, 94:496-509.")
11974 (license license:gpl2+)))
11976 (define-public r-etm
11983 (uri (cran-uri "etm" version))
11986 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
11987 (build-system r-build-system)
11989 `(("r-data-table" ,r-data-table)
11990 ("r-lattice" ,r-lattice)
11992 ("r-rcpparmadillo" ,r-rcpparmadillo)
11993 ("r-survival" ,r-survival)))
11994 (home-page "https://cran.r-project.org/web/packages/etm")
11995 (synopsis "Empirical transition matrix")
11997 "The @dfn{empirical transition matrix} (etm) package estimates
11998 the matrix of transition probabilities for any time-inhomogeneous multistate
11999 model with finite state space using the Aalen-Johansen estimator.")
12000 (license license:expat)))
12002 (define-public r-epi
12009 (uri (cran-uri "Epi" version))
12012 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
12013 (properties `((upstream-name . "Epi")))
12014 (build-system r-build-system)
12016 `(("r-cmprsk" ,r-cmprsk)
12017 ("r-data-table" ,r-data-table)
12020 ("r-matrix" ,r-matrix)
12022 ("r-numderiv" ,r-numderiv)
12024 ("r-survival" ,r-survival)
12026 (home-page "https://BendixCarstensen.com/Epi/")
12027 (synopsis "Statistical analysis in epidemiology")
12029 "This package provides functions for demographic and epidemiological
12030 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12031 particular representation, manipulation and simulation of multistate data -
12032 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12033 @code{etm} and @code{cmprsk} packages. It also contains functions for
12034 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12035 data and some useful functions for tabulation and plotting, as well as a
12036 number of epidemiological data sets.")
12037 (license license:gpl2)))
12039 (define-public r-ppls
12042 (version "1.6-1.1")
12046 (uri (cran-uri "ppls" version))
12049 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12050 (build-system r-build-system)
12051 (propagated-inputs `(("r-mass" ,r-mass)))
12052 (home-page "https://cran.r-project.org/web/packages/ppls")
12053 (synopsis "Penalized partial least squares")
12055 "This package contains linear and nonlinear regression methods based on
12056 partial least squares and penalization techniques. Model parameters are
12057 selected via cross-validation, and confidence intervals ans tests for the
12058 regression coefficients can be conducted via jackknifing.")
12059 (license license:gpl2+)))
12061 (define-public r-huge
12064 (version "1.3.4.1")
12068 (uri (cran-uri "huge" version))
12070 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12071 (build-system r-build-system)
12073 `(("r-igraph" ,r-igraph)
12075 ("r-matrix" ,r-matrix)
12077 ("r-rcppeigen" ,r-rcppeigen)))
12078 (home-page "https://cran.r-project.org/web/packages/huge")
12079 (synopsis "High-dimensional undirected graph estimation")
12081 "This package provides a general framework for high-dimensional
12082 undirected graph estimation. It integrates data preprocessing, neighborhood
12083 screening, graph estimation, and model selection techniques into a pipeline.")
12084 (license license:gpl2)))
12086 (define-public r-parcor
12093 (uri (cran-uri "parcor" version))
12096 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12097 (build-system r-build-system)
12100 ("r-genenet" ,r-genenet)
12101 ("r-glmnet" ,r-glmnet)
12103 ("r-ppls" ,r-ppls)))
12104 (home-page "https://cran.r-project.org/web/packages/parcor")
12105 (synopsis "Regularized estimation of partial correlation matrices")
12107 "This package estimates the matrix of partial correlations based on
12108 different regularized regression methods: lasso, adaptive lasso, PLS, and
12109 Ridge Regression. In addition, the package provides model selection for
12110 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12111 (license license:gpl2+)))
12113 (define-public r-mcmc
12120 (uri (cran-uri "mcmc" version))
12123 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12124 (build-system r-build-system)
12125 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12126 (synopsis "Markov chain Monte Carlo")
12128 "This package simulates continuous distributions of random vectors using
12129 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12130 function that evaluates the log unnormalized density. Algorithms are random
12131 walk Metropolis algorithm (function @code{metrop}), simulated
12132 tempering (function @code{temper}), and morphometric random walk
12133 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12134 by change of variable.")
12135 (license license:expat)))
12137 (define-public r-listenv
12144 (uri (cran-uri "listenv" version))
12147 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12148 (build-system r-build-system)
12150 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12151 (home-page "https://github.com/HenrikBengtsson/listenv")
12152 (synopsis "Environments behaving (almost) as lists")
12154 "This package implements list environments. List environments are
12155 environments that have list-like properties. For instance, the elements of a
12156 list environment are ordered and can be accessed and iterated over using index
12158 (license license:lgpl2.1+)))
12160 (define-public r-globals
12167 (uri (cran-uri "globals" version))
12170 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12171 (build-system r-build-system)
12173 `(("r-codetools" ,r-codetools)))
12174 (home-page "https://github.com/HenrikBengtsson/globals")
12175 (synopsis "Identify global objects in R expressions")
12177 "This package provides tools to identify global (\"unknown\" or \"free\")
12178 objects in R expressions by code inspection using various strategies, e.g.
12179 conservative or liberal. The objective of this package is to make it as
12180 simple as possible to identify global objects for the purpose of exporting
12181 them in distributed compute environments.")
12182 (license license:lgpl2.1+)))
12184 (define-public r-future
12191 (uri (cran-uri "future" version))
12194 "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
12195 (build-system r-build-system)
12197 `(("r-digest" ,r-digest)
12198 ("r-globals" ,r-globals)
12199 ("r-listenv" ,r-listenv)))
12201 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12202 (home-page "https://github.com/HenrikBengtsson/future")
12203 (synopsis "Unified parallel and distributed processing in R")
12205 "The purpose of this package is to provide a lightweight and unified
12206 Future API for sequential and parallel processing of R expression via futures.
12207 This package implements sequential, multicore, multisession, and cluster
12208 futures. With these, R expressions can be evaluated on the local machine, in
12209 parallel a set of local machines, or distributed on a mix of local and remote
12210 machines. Extensions to this package implement additional backends for
12211 processing futures via compute cluster schedulers etc. Because of its unified
12212 API, there is no need to modify any code in order to switch from sequential on
12213 the local machine to, say, distributed processing on a remote compute cluster.")
12214 (license license:lgpl2.1+)))
12216 (define-public r-future-apply
12218 (name "r-future-apply")
12223 (uri (cran-uri "future.apply" version))
12226 "095a681ngbwbp7v53ladwya7ar8fgwnlgr3r1yklf3vdxwd54xll"))))
12227 (properties `((upstream-name . "future.apply")))
12228 (build-system r-build-system)
12230 `(("r-future" ,r-future)
12231 ("r-globals" ,r-globals)))
12233 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12234 (home-page "https://github.com/HenrikBengtsson/future.apply")
12235 (synopsis "Apply function to elements in parallel using futures")
12237 "This package provides implementations of @code{apply()},
12238 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12239 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12240 can be resolved using any future-supported backend, e.g. parallel on the local
12241 machine or distributed on a compute cluster.")
12242 (license license:gpl2+)))
12244 (define-public r-rsvd
12251 (uri (cran-uri "rsvd" version))
12254 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12255 (build-system r-build-system)
12257 `(("r-matrix" ,r-matrix)))
12258 (home-page "https://github.com/erichson/rSVD")
12259 (synopsis "Randomized singular value decomposition")
12261 "Low-rank matrix decompositions are fundamental tools and widely used for
12262 data analysis, dimension reduction, and data compression. Classically, highly
12263 accurate deterministic matrix algorithms are used for this task. However, the
12264 emergence of large-scale data has severely challenged our computational
12265 ability to analyze big data. The concept of randomness has been demonstrated
12266 as an effective strategy to quickly produce approximate answers to familiar
12267 problems such as the @dfn{singular value decomposition} (SVD). This package
12268 provides several randomized matrix algorithms such as the randomized singular
12269 value decomposition (@code{rsvd}), randomized principal component
12270 analysis (@code{rpca}), randomized robust principal component
12271 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12272 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12273 functions are provided.")
12274 (license license:gpl3+)))
12276 (define-public r-sloop
12283 (uri (cran-uri "sloop" version))
12286 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12287 (build-system r-build-system)
12289 `(("r-codetools" ,r-codetools)
12290 ("r-crayon" ,r-crayon)
12291 ("r-purrr" ,r-purrr)
12292 ("r-rlang" ,r-rlang)
12293 ("r-tibble" ,r-tibble)))
12294 (home-page "https://github.com/r-lib/sloop")
12295 (synopsis "Helpers for object-oriented programming in R")
12297 "This package provides a collection of helper functions designed to
12298 help you to better understand object oriented programming in R, particularly
12300 (license license:gpl3)))
12302 (define-public r-capushe
12309 (uri (cran-uri "capushe" version))
12312 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12313 (build-system r-build-system)
12314 (propagated-inputs `(("r-mass" ,r-mass)))
12315 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12316 (synopsis "Calibrating penalties using slope heuristics")
12318 "This package provides tools for the calibration of penalized criteria
12319 for model selection. The calibration methods available are based on the slope
12321 (license license:gpl2+)))
12323 (define-public r-dorng
12330 (uri (cran-uri "doRNG" version))
12333 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12334 (properties `((upstream-name . "doRNG")))
12335 (build-system r-build-system)
12337 `(("r-foreach" ,r-foreach)
12338 ("r-iterators" ,r-iterators)
12339 ("r-rngtools" ,r-rngtools)))
12340 (home-page "https://renozao.github.io/doRNG/")
12341 (synopsis "Generic reproducible parallel backend for foreach loops")
12343 "This package provides functions to perform reproducible parallel
12344 @code{foreach} loops, using independent random streams as generated by
12345 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12346 convert standard @code{%dopar%} loops into fully reproducible loops,
12347 independently of the number of workers, the task scheduling strategy, or the
12348 chosen parallel environment and associated foreach backend.")
12349 (license license:gpl2+)))
12351 (define-public r-blockmodeling
12353 (name "r-blockmodeling")
12358 (uri (cran-uri "blockmodeling" version))
12361 "12paf76l3wlxad14bkxn37lw9rg6ka473m86wlcf3yhriw8kbaiz"))))
12362 (build-system r-build-system)
12364 `(("r-matrix" ,r-matrix)))
12365 (native-inputs `(("gfortran" ,gfortran)))
12366 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12367 (synopsis "Generalized and classical blockmodeling of valued networks")
12369 "This package is primarily meant as an implementation of generalized
12370 blockmodeling for valued networks. In addition, measures of similarity or
12371 dissimilarity based on structural equivalence and regular equivalence (REGE
12372 algorithms) can be computed and partitioned matrices can be plotted.")
12373 (license license:gpl2+)))
12375 (define-public r-upsetr
12382 (uri (cran-uri "UpSetR" version))
12385 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12386 (properties `((upstream-name . "UpSetR")))
12387 (build-system r-build-system)
12389 `(("r-ggplot2" ,r-ggplot2)
12390 ("r-gridextra" ,r-gridextra)
12392 ("r-scales" ,r-scales)))
12393 (home-page "https://github.com/hms-dbmi/UpSetR")
12394 (synopsis "Visualize intersecting sets")
12396 "This package provides a more scalable alternative to Venn and Euler
12397 diagrams for visualizing intersecting sets. Create visualizations of
12398 intersecting sets using a novel matrix design, along with visualizations of
12399 several common set, element and attribute related tasks.")
12400 (license license:expat)))
12402 ;; This package includes a JavaScript file, which is not minified. When
12403 ;; upgrading please check that there are no new minified JavaScript files.
12404 (define-public r-shinybs
12411 (uri (cran-uri "shinyBS" version))
12414 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12415 (properties `((upstream-name . "shinyBS")))
12416 (build-system r-build-system)
12417 ;; The tests spawn Shiny browser apps. They cannot be run
12418 ;; non-interactively.
12419 (arguments '(#:tests? #f))
12421 `(("r-htmltools" ,r-htmltools)
12422 ("r-shiny" ,r-shiny)))
12423 (home-page "https://ebailey78.github.io/shinyBS/")
12424 (synopsis "Twitter Bootstrap components for Shiny")
12426 "This package adds additional Twitter Bootstrap components to Shiny.")
12427 (license license:gpl3)))
12429 (define-public r-outliers
12431 (name "r-outliers")
12436 (uri (cran-uri "outliers" version))
12439 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12440 (build-system r-build-system)
12441 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12442 (synopsis "Tests for outliers")
12444 "This package provides a collection of some tests commonly used for
12445 identifying outliers.")
12446 (license license:gpl2+)))
12448 (define-public r-bayesm
12455 (uri (cran-uri "bayesm" version))
12457 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12458 (build-system r-build-system)
12460 `(("r-rcpp" ,r-rcpp)
12461 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12462 (home-page "http://www.perossi.org/home/bsm-1")
12463 (synopsis "Bayesian inference for marketing/micro-econometrics")
12465 "This package covers many important models used in marketing and
12466 micro-econometrics applications, including Bayes Regression (univariate or
12467 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12468 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12469 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12470 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12471 Estimation with normal base, Hierarchical Linear Models with normal prior and
12472 covariates, Hierarchical Linear Models with a mixture of normals prior and
12473 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12474 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12475 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12476 analysis of choice-based conjoint data, Bayesian treatment of linear
12477 instrumental variables models, Analysis of Multivariate Ordinal survey data
12478 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12479 Coefficient Logit Models.")
12480 (license license:gpl2+)))
12482 (define-public r-tensora
12489 (uri (cran-uri "tensorA" version))
12492 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12493 (properties `((upstream-name . "tensorA")))
12494 (build-system r-build-system)
12495 (home-page "http://www.stat.boogaart.de/tensorA")
12496 (synopsis "Advanced tensor arithmetic with named indices")
12498 "This package provides convenience functions for advanced linear algebra
12499 with tensors and computation with datasets of tensors on a higher level
12500 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12501 co- and contravariate indices, and parallel computations on sequences of
12503 (license license:gpl2+)))
12505 (define-public r-rarpack
12512 (uri (cran-uri "rARPACK" version))
12515 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12516 (properties `((upstream-name . "rARPACK")))
12517 (build-system r-build-system)
12518 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12519 (home-page "https://github.com/yixuan/rARPACK")
12520 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12522 "This package was previously an R wrapper of the ARPACK library, and now
12523 a shell of the R package RSpectra, an R interface to the Spectra library for
12524 solving large scale eigenvalue/vector problems. The current version of
12525 rARPACK simply imports and exports the functions provided by RSpectra. New
12526 users of rARPACK are advised to switch to the RSpectra package.")
12527 (license license:bsd-3)))
12529 (define-public r-compositions
12531 (name "r-compositions")
12536 (uri (cran-uri "compositions" version))
12539 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12540 (build-system r-build-system)
12542 `(("r-bayesm" ,r-bayesm)
12543 ("r-robustbase" ,r-robustbase)
12544 ("r-tensora" ,r-tensora)))
12545 (home-page "http://www.stat.boogaart.de/compositions")
12546 (synopsis "Compositional data analysis")
12548 "This package provides functions for the consistent analysis of
12549 compositional data (e.g. portions of substances) and positive
12550 numbers (e.g. concentrations).")
12551 (license license:gpl2+)))
12553 (define-public r-cobs
12560 (uri (cran-uri "cobs" version))
12563 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12564 (build-system r-build-system)
12566 `(("r-quantreg" ,r-quantreg)
12567 ("r-sparsem" ,r-sparsem)))
12568 (home-page "https://cran.r-project.org/web/packages/cobs")
12569 (synopsis "Constrained B-Splines (sparse matrix based)")
12571 "This package provides qualitatively constrained (regression) smoothing
12572 splines via linear programming and sparse matrices.")
12573 (license license:gpl2+)))
12575 (define-public r-drimpute
12577 (name "r-drimpute")
12582 (uri (cran-uri "DrImpute" version))
12585 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12586 (properties `((upstream-name . "DrImpute")))
12587 (build-system r-build-system)
12589 `(("r-rcpp" ,r-rcpp)
12590 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12591 (home-page "https://github.com/ikwak2/DrImpute")
12592 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12594 "This is an R package for imputing dropout events. Many statistical
12595 methods in cell type identification, visualization and lineage reconstruction
12596 do not account for dropout events. DrImpute can improve the performance of
12597 such software by imputing dropout events.")
12598 (license license:gpl3)))
12600 (define-public r-gamlss-dist
12602 (name "r-gamlss-dist")
12607 (uri (cran-uri "gamlss.dist" version))
12609 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12610 (properties `((upstream-name . "gamlss.dist")))
12611 (build-system r-build-system)
12612 (propagated-inputs `(("r-mass" ,r-mass)))
12613 (home-page "http://www.gamlss.org/")
12614 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12616 "This package provides a set of distributions which can be used for
12617 modelling the response variables in Generalized Additive Models for Location
12618 Scale and Shape. The distributions can be continuous, discrete or mixed
12619 distributions. Extra distributions can be created, by transforming, any
12620 continuous distribution defined on the real line, to a distribution defined on
12621 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12622 transformation, respectively.")
12623 ;; Either version of the GPL.
12624 (license (list license:gpl2 license:gpl3))))
12626 ;; This package includes JavaScript files, which are not minified. When
12627 ;; upgrading please check that there are no new minified JavaScript files.
12628 (define-public r-shinyjs
12635 (uri (cran-uri "shinyjs" version))
12638 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12639 (build-system r-build-system)
12641 `(("r-digest" ,r-digest)
12642 ("r-htmltools" ,r-htmltools)
12643 ("r-jsonlite" ,r-jsonlite)
12644 ("r-shiny" ,r-shiny)))
12645 (home-page "https://deanattali.com/shinyjs")
12646 (synopsis "Improve the user experience of your Shiny apps")
12648 "Perform common useful JavaScript operations in Shiny apps that will
12649 greatly improve your apps without having to know any JavaScript. Examples
12650 include: hiding an element, disabling an input, resetting an input back to its
12651 original value, delaying code execution by a few seconds, and many more useful
12652 functions for both the end user and the developer. Shinyjs can also be used
12653 to easily call your own custom JavaScript functions from R.")
12654 (license license:agpl3+)))
12656 ;; This package includes minified JavaScript files. When upgrading please
12657 ;; check that there are no new minified JavaScript files.
12658 (define-public r-colourpicker
12660 (name "r-colourpicker")
12665 (uri (cran-uri "colourpicker" version))
12668 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12669 (build-system r-build-system)
12671 `(#:modules ((guix build utils)
12672 (guix build r-build-system)
12676 (modify-phases %standard-phases
12677 (add-after 'unpack 'process-javascript
12678 (lambda* (#:key inputs #:allow-other-keys)
12679 (with-directory-excursion "inst"
12683 `((,(assoc-ref inputs "js-salvattore")
12684 "examples/colourInput/www/salvattore.min.js")
12685 (,(assoc-ref inputs "js-jquery")
12686 "htmlwidgets/lib/jquery/jquery.min.js")
12687 ("www/shared/colourpicker/js/colourpicker.js"
12688 "www/shared/colourpicker/js/colourpicker.min.js"))))
12689 (lambda (sources targets)
12690 (for-each (lambda (source target)
12691 (format #t "Processing ~a --> ~a~%"
12693 (delete-file target)
12694 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12695 (call-with-output-file target
12697 (dump-port minified port)))))
12698 sources targets))))
12701 `(("r-ggplot2" ,r-ggplot2)
12702 ("r-htmltools" ,r-htmltools)
12703 ("r-htmlwidgets" ,r-htmlwidgets)
12704 ("r-jsonlite" ,r-jsonlite)
12705 ("r-miniui" ,r-miniui)
12706 ("r-shiny" ,r-shiny)
12707 ("r-shinyjs" ,r-shinyjs)))
12709 `(("uglify-js" ,uglify-js)
12713 (uri "https://code.jquery.com/jquery-3.3.1.js")
12716 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12720 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12723 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12724 (home-page "https://github.com/daattali/colourpicker")
12725 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12727 "This package provides a color picker that can be used as an input in
12728 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12729 custom color palettes, and many more options. A plot color helper tool is
12730 available as an RStudio Addin, which helps you pick colors to use in your
12731 plots. A more generic color picker RStudio Addin is also provided to let you
12732 select colors to use in your R code.")
12733 (license license:expat)))
12735 (define-public r-ggextra
12742 (uri (cran-uri "ggExtra" version))
12745 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12746 (properties `((upstream-name . "ggExtra")))
12747 (build-system r-build-system)
12749 `(("r-colourpicker" ,r-colourpicker)
12750 ("r-ggplot2" ,r-ggplot2)
12751 ("r-gtable" ,r-gtable)
12752 ("r-miniui" ,r-miniui)
12754 ("r-scales" ,r-scales)
12755 ("r-shiny" ,r-shiny)
12756 ("r-shinyjs" ,r-shinyjs)))
12758 `(("r-knitr" ,r-knitr)))
12759 (home-page "https://github.com/daattali/ggExtra")
12760 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12762 "This package is a collection of functions and layers to enhance ggplot2.
12763 The flagship function is @code{ggMarginal()}, which can be used to add
12764 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12765 (license license:expat)))
12767 (define-public r-minpack-lm
12769 (name "r-minpack-lm")
12774 (uri (cran-uri "minpack.lm" version))
12777 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12778 (properties `((upstream-name . "minpack.lm")))
12779 (build-system r-build-system)
12780 (native-inputs `(("gfortran" ,gfortran)))
12781 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12782 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12784 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12785 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12786 problems by a modification of the Levenberg-Marquardt algorithm, with support
12787 for lower and upper parameter bounds. The implementation can be used via
12788 @code{nls}-like calls using the @code{nlsLM} function.")
12789 (license license:gpl3)))
12791 (define-public r-moments
12798 (uri (cran-uri "moments" version))
12801 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12802 (build-system r-build-system)
12803 (home-page "https://cran.r-project.org/web/packages/moments")
12804 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12806 "This package provides functions to calculate: moments, Pearson's
12807 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12808 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12809 (license license:gpl2+)))
12811 (define-public r-msir
12818 (uri (cran-uri "msir" version))
12821 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12822 (build-system r-build-system)
12824 `(("r-mclust" ,r-mclust)))
12825 (home-page "https://cran.r-project.org/web/packages/msir")
12826 (synopsis "Model-based sliced inverse regression")
12828 "This is an R package for dimension reduction based on finite Gaussian
12829 mixture modeling of inverse regression.")
12830 (license license:gpl2+)))
12832 (define-public r-pbivnorm
12834 (name "r-pbivnorm")
12839 (uri (cran-uri "pbivnorm" version))
12842 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12843 (build-system r-build-system)
12844 (native-inputs `(("gfortran" ,gfortran)))
12845 (home-page "https://github.com/brentonk/pbivnorm")
12846 (synopsis "Vectorized bivariate normal CDF")
12848 "This package provides a vectorized R function for calculating
12849 probabilities from a standard bivariate normal CDF.")
12850 (license license:gpl2+)))
12852 (define-public r-lavaan
12859 (uri (cran-uri "lavaan" version))
12862 "0sfv58r2kxinax62bx6j3kkfx07qm16ddwf5qz392q33h9zs009h"))))
12863 (build-system r-build-system)
12865 `(("r-mass" ,r-mass)
12866 ("r-mnormt" ,r-mnormt)
12867 ("r-numderiv" ,r-numderiv)
12868 ("r-pbivnorm" ,r-pbivnorm)))
12869 (home-page "http://lavaan.ugent.be")
12870 (synopsis "Latent variable analysis")
12872 "This package provides tools to fit a variety of latent variable models,
12873 including confirmatory factor analysis, structural equation modeling and
12874 latent growth curve models.")
12875 (license license:gpl2+)))
12877 (define-public r-nonnest2
12879 (name "r-nonnest2")
12884 (uri (cran-uri "nonnest2" version))
12887 "07nr54hxdnc4k022nd4a2g9w9l9ym2ikfr978rrnqc71wx750i0z"))))
12888 (build-system r-build-system)
12890 `(("r-compquadform" ,r-compquadform)
12891 ("r-lavaan" ,r-lavaan)
12892 ("r-mvtnorm" ,r-mvtnorm)
12893 ("r-sandwich" ,r-sandwich)))
12895 `(("r-knitr" ,r-knitr)))
12896 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12897 (synopsis "Tests of non-nested models")
12899 "This package allows for testing of non-nested models. It includes tests
12900 of model distinguishability and of model fit that can be applied to both
12901 nested and non-nested models. The package also includes functionality to
12902 obtain confidence intervals associated with AIC and BIC.")
12903 ;; Either version of the GPL.
12904 (license (list license:gpl2 license:gpl3))))
12906 (define-public r-penalized
12908 (name "r-penalized")
12913 (uri (cran-uri "penalized" version))
12916 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12917 (build-system r-build-system)
12919 `(("r-rcpp" ,r-rcpp)
12920 ("r-rcpparmadillo" ,r-rcpparmadillo)
12921 ("r-survival" ,r-survival)))
12922 (home-page "https://cran.r-project.org/web/packages/penalized/")
12923 (synopsis "Penalized estimation in GLMs and in the Cox model")
12925 "This package provides tools for fitting possibly high dimensional
12926 penalized regression models. The penalty structure can be any combination of
12927 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12928 constraint on the regression coefficients. The supported regression models
12929 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12930 model. Cross-validation routines allow optimization of the tuning
12932 (license license:gpl2+)))
12934 (define-public r-zim
12941 (uri (cran-uri "ZIM" version))
12944 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12945 (properties `((upstream-name . "ZIM")))
12946 (build-system r-build-system)
12947 (propagated-inputs `(("r-mass" ,r-mass)))
12948 (home-page "https://github.com/biostatstudio/ZIM")
12949 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12951 "Analyze count time series with excess zeros. Two types of statistical
12952 models are supported: Markov regression and state-space models. They are also
12953 known as observation-driven and parameter-driven models respectively in the
12954 time series literature. The functions used for Markov regression or
12955 observation-driven models can also be used to fit ordinary regression models
12956 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12957 negative binomial (ZINB) assumption. The package also contains miscellaneous
12958 functions to compute density, distribution, quantile, and generate random
12959 numbers from ZIP and ZINB distributions.")
12960 (license license:gpl3)))
12962 (define-public r-nor1mix
12969 (uri (cran-uri "nor1mix" version))
12972 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12973 (build-system r-build-system)
12974 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12975 (synopsis "Normal (1-d) mixture models")
12977 "This package provides S3 classes and methods for one-dimensional normal
12978 mixture models, for, e.g., density estimation or clustering algorithms
12979 research and teaching; it provides the widely used Marron-Wand densities. It
12980 also provides tools for efficient random number generation and graphics.")
12981 (license license:gpl2+)))
12983 (define-public r-beanplot
12985 (name "r-beanplot")
12990 (uri (cran-uri "beanplot" version))
12993 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12994 (build-system r-build-system)
12995 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12996 (synopsis "Visualization via beanplots")
12998 "This package provides beanplots, an alternative to
12999 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13001 (license license:gpl2)))
13003 (define-public r-pbdzmq
13010 (uri (cran-uri "pbdZMQ" version))
13013 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13014 (properties `((upstream-name . "pbdZMQ")))
13015 (build-system r-build-system)
13017 `(("zeromq" ,zeromq)
13020 `(("pkg-config" ,pkg-config)))
13021 (home-page "https://pbdr.org/")
13022 (synopsis "R interface to ZeroMQ")
13024 "ZeroMQ is a well-known library for high-performance asynchronous
13025 messaging in scalable, distributed applications. This package provides high
13026 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13027 interactive client/server programming frameworks. A few wrapper functions
13028 compatible with @code{rzmq} are also provided.")
13029 (license license:gpl3)))
13031 (define-public r-repr
13038 (uri (cran-uri "repr" version))
13041 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13042 (build-system r-build-system)
13044 `(("r-base64enc" ,r-base64enc)
13045 ("r-htmltools" ,r-htmltools)
13046 ("r-jsonlite" ,r-jsonlite)
13047 ("r-pillar" ,r-pillar)))
13048 (home-page "https://cran.r-project.org/web/packages/repr/")
13049 (synopsis "Serializable representations")
13051 "This package provides string and binary representations of objects for
13052 several formats and MIME types.")
13053 (license license:gpl3)))
13055 (define-public r-irdisplay
13057 (name "r-irdisplay")
13062 (uri (cran-uri "IRdisplay" version))
13065 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13066 (properties `((upstream-name . "IRdisplay")))
13067 (build-system r-build-system)
13069 `(("r-repr" ,r-repr)))
13070 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13071 (synopsis "Jupyter display machinery")
13073 "This package provides an interface to the rich display capabilities of
13074 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13075 running IRkernel session.")
13076 (license license:expat)))
13078 (define-public r-irkernel
13080 (name "r-irkernel")
13085 (uri (cran-uri "IRkernel" version))
13088 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
13089 (properties `((upstream-name . "IRkernel")))
13090 (build-system r-build-system)
13093 (modify-phases %standard-phases
13094 (add-after 'install 'install-kernelspec
13095 (lambda* (#:key outputs #:allow-other-keys)
13096 (let ((out (assoc-ref outputs "out")))
13097 (setenv "HOME" "/tmp")
13098 (invoke "jupyter" "kernelspec" "install"
13101 (string-append out "/site-library/IRkernel/kernelspec"))
13102 ;; Record the absolute file name of the 'R' executable in
13104 (substitute* (string-append out "/share/jupyter"
13105 "/kernels/ir/kernel.json")
13107 (string-append "[\"" (which "R") "\",")))
13110 `(("jupyter" ,jupyter)))
13112 `(("r-crayon" ,r-crayon)
13113 ("r-digest" ,r-digest)
13114 ("r-evaluate" ,r-evaluate)
13115 ("r-irdisplay" ,r-irdisplay)
13116 ("r-jsonlite" ,r-jsonlite)
13117 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13118 ("r-minimal" ,r-minimal)
13119 ("r-pbdzmq" ,r-pbdzmq)
13121 ("r-uuid" ,r-uuid)))
13122 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13123 (synopsis "Native R kernel for Jupyter")
13125 "The R kernel for the Jupyter environment executes R code which the
13126 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13128 (license license:expat)))
13130 (define-public r-gmodels
13137 (uri (cran-uri "gmodels" version))
13140 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13141 (build-system r-build-system)
13143 `(("r-gdata" ,r-gdata)
13144 ("r-mass" ,r-mass)))
13145 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13146 (synopsis "Various R programming tools for model fitting")
13148 "This package provides various R programming tools for model fitting.")
13149 (license license:gpl2)))
13151 (define-public r-apcluster
13153 (name "r-apcluster")
13158 (uri (cran-uri "apcluster" version))
13161 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13162 (build-system r-build-system)
13164 `(("r-matrix" ,r-matrix)
13165 ("r-rcpp" ,r-rcpp)))
13166 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13167 (synopsis "Affinity propagation clustering")
13169 "This package implements affinity propagation clustering introduced by
13170 Frey and Dueck (2007). The package further provides leveraged affinity
13171 propagation and an algorithm for exemplar-based agglomerative clustering that
13172 can also be used to join clusters obtained from affinity propagation. Various
13173 plotting functions are available for analyzing clustering results.")
13174 (license license:gpl2+)))
13176 (define-public r-valr
13183 (uri (cran-uri "valr" version))
13186 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13187 (build-system r-build-system)
13189 `(("r-broom" ,r-broom)
13190 ("r-dplyr" ,r-dplyr)
13191 ("r-ggplot2" ,r-ggplot2)
13193 ("r-readr" ,r-readr)
13194 ("r-rlang" ,r-rlang)
13195 ("r-stringr" ,r-stringr)
13196 ("r-tibble" ,r-tibble)))
13198 `(("r-knitr" ,r-knitr)))
13199 (home-page "http://github.com/rnabioco/valr")
13200 (synopsis "Genome interval arithmetic in R")
13202 "This package enables you to read and manipulate genome intervals and
13203 signals. It provides functionality similar to command-line tool suites within
13204 R, enabling interactive analysis and visualization of genome-scale data.")
13205 (license license:expat)))
13207 (define-public r-rematch2
13209 (name "r-rematch2")
13214 (uri (cran-uri "rematch2" version))
13217 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13218 (build-system r-build-system)
13220 `(("r-tibble" ,r-tibble)))
13221 (home-page "https://github.com/r-lib/rematch2")
13222 (synopsis "Tidy output from regular expression matching")
13224 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13225 return the match results in tidy data frames.")
13226 (license license:expat)))
13228 (define-public r-picante
13235 (uri (cran-uri "picante" version))
13238 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13239 (build-system r-build-system)
13243 ("r-vegan" ,r-vegan)))
13244 (home-page "https://cran.r-project.org/web/packages/picante/")
13245 (synopsis "Integrating phylogenies and ecology")
13247 "This package provides functions for phylocom integration, community
13248 analyses, null-models, traits and evolution. It implements numerous
13249 ecophylogenetic approaches including measures of community phylogenetic and
13250 trait diversity, phylogenetic signal, estimation of trait values for
13251 unobserved taxa, null models for community and phylogeny randomizations, and
13252 utility functions for data input/output and phylogeny plotting. A full
13253 description of package functionality and methods are provided by Kembel et
13255 (license license:gpl2)))
13257 (define-public r-reinforcelearn
13259 (name "r-reinforcelearn")
13264 (uri (cran-uri "reinforcelearn" version))
13267 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13268 (build-system r-build-system)
13270 `(("r-checkmate" ,r-checkmate)
13272 ("r-purrr" ,r-purrr)
13274 (home-page "https://markusdumke.github.io/reinforcelearn")
13275 (synopsis "Reinforcement learning")
13277 "This package implements reinforcement learning environments and
13278 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13279 can be used with function approximation, eligibility traces (Singh & Sutton,
13280 1996) and experience replay (Mnih et al., 2013).")
13281 (license license:expat)))
13283 (define-public r-lemon
13290 (uri (cran-uri "lemon" version))
13293 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13294 (build-system r-build-system)
13296 `(("r-ggplot2" ,r-ggplot2)
13297 ("r-gridextra" ,r-gridextra)
13298 ("r-gtable" ,r-gtable)
13299 ("r-knitr" ,r-knitr)
13300 ("r-lattice" ,r-lattice)
13302 ("r-rlang" ,r-rlang)
13303 ("r-scales" ,r-scales)))
13305 `(("r-knitr" ,r-knitr)))
13306 (home-page "https://github.com/stefanedwards/lemon")
13307 (synopsis "Freshen up your ggplot2 plots")
13309 "This package provides functions for working with legends and axis lines
13310 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13312 (license license:gpl3)))
13314 (define-public r-wgaim
13321 (uri (cran-uri "wgaim" version))
13323 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13324 (build-system r-build-system)
13326 `(("r-ggplot2" ,r-ggplot2)
13328 (home-page "https://cran.r-project.org/web/packages/wgaim")
13329 (synopsis "Whole genome average interval mapping for QTL detection")
13331 "This package integrates sophisticated mixed modelling methods with a
13332 whole genome approach to detecting significant QTL in linkage maps.")
13333 (license license:gpl2+)))
13335 (define-public r-bedr
13342 (uri (cran-uri "bedr" version))
13345 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13346 (build-system r-build-system)
13348 `(("r-data-table" ,r-data-table)
13349 ("r-r-utils" ,r-r-utils)
13350 ("r-testthat" ,r-testthat)
13351 ("r-venndiagram" ,r-venndiagram)
13354 ("bedtools" ,bedtools)
13355 ("htslib" ,htslib))) ; for tabix
13357 `(("r-knitr" ,r-knitr))) ; for vignettes
13358 (home-page "https://cran.r-project.org/web/packages/bedr")
13359 (synopsis "Genomic region processing")
13361 "This package is for genomic regions processing using command line tools
13362 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13363 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13364 The bedr package's API enhances access to these tools as well as offers
13365 additional utilities for genomic regions processing.")
13366 (license license:gpl2)))
13368 (define-public r-sets
13375 (uri (cran-uri "sets" version))
13378 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13379 (properties `((upstream-name . "sets")))
13380 (build-system r-build-system)
13381 (home-page "https://cran.r-project.org/web/packages/sets")
13382 (synopsis "Sets, generalized sets, customizable sets and intervals")
13384 "This package provides data structures and basic operations for ordinary
13385 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13386 customizable sets, and intervals.")
13387 (license license:gpl2)))
13389 (define-public r-partitions
13391 (name "r-partitions")
13396 (uri (cran-uri "partitions" version))
13399 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13400 (build-system r-build-system)
13403 ("r-polynom" ,r-polynom)
13404 ("r-sets" ,r-sets)))
13405 (home-page "https://cran.r-project.org/web/packages/partitions")
13406 (synopsis "Additive partitions of integers")
13408 "This package provides tools to enumerates the partitions, unequal
13409 partitions, and restricted partitions of an integer; the three corresponding
13410 partition functions are also given.")
13411 ;; Any version of the GPL
13412 (license license:gpl2+)))
13414 (define-public r-brobdingnag
13416 (name "r-brobdingnag")
13421 (uri (cran-uri "Brobdingnag" version))
13424 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13425 (properties `((upstream-name . "Brobdingnag")))
13426 (build-system r-build-system)
13427 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13428 (synopsis "Very large numbers in R")
13430 "This package handles very large numbers in R. Real numbers are held
13431 using their natural logarithms, plus a logical flag indicating sign. The
13432 package includes a vignette that gives a step-by-step introduction to using S4
13434 ;; Any version of the GPL
13435 (license license:gpl2+)))
13437 (define-public r-untb
13444 (uri (cran-uri "untb" version))
13447 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13448 (build-system r-build-system)
13450 `(("r-brobdingnag" ,r-brobdingnag)
13451 ("r-partitions" ,r-partitions)
13452 ("r-polynom" ,r-polynom)))
13453 (home-page "https://github.com/RobinHankin/untb.git")
13454 (synopsis "Ecological drift under the UNTB")
13456 "This package provides numerical simulations, and visualizations, of
13457 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13458 (license license:gpl2+)))
13460 (define-public r-stepwise
13462 (name "r-stepwise")
13467 (uri (cran-uri "stepwise" version))
13470 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13471 (build-system r-build-system)
13472 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13473 (synopsis "Stepwise detection of recombination breakpoints")
13475 "This package provides a stepwise approach to identifying recombination
13476 breakpoints in a genomic sequence alignment.")
13477 (license license:gpl2+)))
13479 (define-public r-snpmaxsel
13481 (name "r-snpmaxsel")
13486 (uri (cran-uri "SNPmaxsel" version))
13489 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13490 (properties `((upstream-name . "SNPmaxsel")))
13491 (build-system r-build-system)
13493 `(("r-combinat" ,r-combinat)
13494 ("r-mvtnorm" ,r-mvtnorm)))
13495 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13496 (synopsis "Maximally selected statistics for SNP data")
13498 "This package implements asymptotic methods related to maximally selected
13499 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13501 (license license:gpl2+)))
13503 (define-public r-acsnminer
13505 (name "r-acsnminer")
13506 (version "0.16.8.25")
13509 (uri (cran-uri "ACSNMineR" version))
13512 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13513 (properties `((upstream-name . "ACSNMineR")))
13514 (build-system r-build-system)
13516 `(("r-ggplot2" ,r-ggplot2)
13517 ("r-gridextra" ,r-gridextra)))
13518 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13519 (synopsis "Gene enrichment analysis")
13521 "This package provides tools to compute and represent gene set enrichment
13522 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13523 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13524 enrichment can be run with hypergeometric test or Fisher exact test, and can
13525 use multiple corrections. Visualization of data can be done either by
13526 barplots or heatmaps.")
13527 (license license:gpl2+)))
13529 (define-public r-seqinr
13536 (uri (cran-uri "seqinr" version))
13539 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13540 (build-system r-build-system)
13542 `(("r-ade4" ,r-ade4)
13543 ("r-segmented" ,r-segmented)))
13546 (home-page "http://seqinr.r-forge.r-project.org/")
13547 (synopsis "Biological sequences retrieval and analysis")
13549 "This package provides tools for exploratory data analysis and data
13550 visualization of biological sequence (DNA and protein) data. It also includes
13551 utilities for sequence data management under the ACNUC system.")
13552 (license license:gpl2+)))
13554 (define-public r-units
13561 (uri (cran-uri "units" version))
13564 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13565 (build-system r-build-system)
13567 `(("udunits" ,udunits)))
13569 `(("r-rcpp" ,r-rcpp)))
13571 `(("r-knitr" ,r-knitr)))
13572 (home-page "https://github.com/r-quantities/units/")
13573 (synopsis "Measurement Units for R Vectors")
13575 "This package provides support for measurement units in R vectors,
13576 matrices and arrays: automatic propagation, conversion, derivation and
13577 simplification of units; raising errors in case of unit incompatibility. It
13578 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13580 (license license:gpl2)))
13582 (define-public r-classint
13584 (name "r-classint")
13589 (uri (cran-uri "classInt" version))
13592 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13593 (properties `((upstream-name . "classInt")))
13594 (build-system r-build-system)
13596 `(("r-class" ,r-class)
13597 ("r-e1071" ,r-e1071)
13598 ("r-kernsmooth" ,r-kernsmooth)))
13600 `(("gfortran" ,gfortran)
13601 ("r-knitr" ,r-knitr)))
13602 (home-page "https://github.com/r-spatial/classInt/")
13603 (synopsis "Choose univariate class intervals")
13605 "This package provides selected commonly used methods for choosing
13606 univariate class intervals for mapping or other graphics purposes.")
13607 (license license:gpl2+)))
13609 (define-public r-spdata
13616 (uri (cran-uri "spData" version))
13619 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13620 (properties `((upstream-name . "spData")))
13621 (build-system r-build-system)
13623 `(("r-raster" ,r-raster)
13625 (home-page "https://github.com/Nowosad/spData")
13626 (synopsis "Datasets for spatial analysis")
13628 "This a package containing diverse spatial datasets for demonstrating,
13629 benchmarking and teaching spatial data analysis. It includes R data of class
13630 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13631 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13632 of the datasets are designed to illustrate specific analysis techniques.
13633 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13634 illustrate point pattern analysis techniques.")
13635 (license license:cc0)))
13637 (define-public r-learnbayes
13639 (name "r-learnbayes")
13644 (uri (cran-uri "LearnBayes" version))
13647 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13648 (properties `((upstream-name . "LearnBayes")))
13649 (build-system r-build-system)
13650 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13651 (synopsis "Functions for learning Bayesian inference")
13653 "This package provides a collection of functions helpful in learning the
13654 basic tenets of Bayesian statistical inference. It contains functions for
13655 summarizing basic one and two parameter posterior distributions and predictive
13656 distributions. It contains MCMC algorithms for summarizing posterior
13657 distributions defined by the user. It also contains functions for regression
13658 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13660 (license license:gpl2+)))
13662 (define-public r-deldir
13669 (uri (cran-uri "deldir" version))
13672 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13673 (build-system r-build-system)
13674 (native-inputs `(("gfortran" ,gfortran)))
13675 (home-page "https://cran.r-project.org/web/packages/deldir")
13676 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13678 "This package provides tools for calculating the Delaunay triangulation
13679 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13680 of a planar point set. It plots triangulations and tessellations in various
13681 ways, clips tessellations to sub-windows, calculates perimeters of
13682 tessellations, and summarizes information about the tiles of the
13684 (license license:gpl2+)))
13686 (define-public r-sf
13693 (uri (cran-uri "sf" version))
13696 "1xgmnz01pxvpg2ins1h65mlcrafqihlljcjlag8spq9ii7d5i7mx"))))
13697 (build-system r-build-system)
13704 `(("r-classint" ,r-classint)
13706 ("r-magrittr" ,r-magrittr)
13708 ("r-units" ,r-units)))
13710 `(("pkg-config" ,pkg-config)
13711 ("r-knitr" ,r-knitr)))
13712 (home-page "https://github.com/r-spatial/sf/")
13713 (synopsis "Simple features for R")
13715 "This package provides support for simple features, a standardized way to
13716 encode spatial vector data. It binds to GDAL for reading and writing data, to
13717 GEOS for geometrical operations, and to PROJ for projection conversions and
13718 datum transformations.")
13719 ;; Either of these licenses
13720 (license (list license:gpl2 license:expat))))
13722 (define-public r-spdep
13729 (uri (cran-uri "spdep" version))
13732 "1f8cjffqqc6rnb3n4qym70ca6nz2kvrsd3g587wrqdr79nnbwnrk"))))
13733 (build-system r-build-system)
13735 `(("r-boot" ,r-boot)
13737 ("r-deldir" ,r-deldir)
13739 ("r-gmodels" ,r-gmodels)
13740 ("r-learnbayes" ,r-learnbayes)
13742 ("r-matrix" ,r-matrix)
13746 ("r-spdata" ,r-spdata)))
13747 (home-page "https://github.com/r-spatial/spdep/")
13748 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13750 "This package provides a collection of functions to create spatial
13751 weights matrix objects from polygon contiguities, from point patterns by
13752 distance and tessellations, for summarizing these objects, and for permitting
13753 their use in spatial data analysis, including regional aggregation by minimum
13755 (license license:gpl2+)))
13757 (define-public r-adegenet
13759 (name "r-adegenet")
13764 (uri (cran-uri "adegenet" version))
13767 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13768 (build-system r-build-system)
13770 `(("r-ade4" ,r-ade4)
13773 ("r-dplyr" ,r-dplyr)
13774 ("r-ggplot2" ,r-ggplot2)
13775 ("r-igraph" ,r-igraph)
13777 ("r-reshape2" ,r-reshape2)
13778 ("r-seqinr" ,r-seqinr)
13779 ("r-shiny" ,r-shiny)
13780 ("r-spdep" ,r-spdep)
13781 ("r-vegan" ,r-vegan)))
13782 (home-page "https://github.com/thibautjombart/adegenet")
13783 (synopsis "Exploratory analysis of genetic and genomic data")
13785 "This package provides a toolset for the exploration of genetic and
13786 genomic data. Adegenet provides formal (S4) classes for storing and handling
13787 various genetic data, including genetic markers with varying ploidy and
13788 hierarchical population structure (@code{genind} class), alleles counts by
13789 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13790 also implements original multivariate methods (DAPC, sPCA), graphics,
13791 statistical tests, simulation tools, distance and similarity measures, and
13792 several spatial methods. A range of both empirical and simulated datasets is
13793 also provided to illustrate various methods.")
13794 (license license:gpl2+)))
13796 (define-public r-pegas
13803 (uri (cran-uri "pegas" version))
13805 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13806 (build-system r-build-system)
13808 `(("r-adegenet" ,r-adegenet)
13810 (home-page "http://ape-package.ird.fr/pegas.html")
13811 (synopsis "Population and evolutionary genetics analysis system")
13813 "This package provides functions for reading, writing, plotting,
13814 analysing, and manipulating allelic and haplotypic data, including from VCF
13815 files, and for the analysis of population nucleotide sequences and
13816 micro-satellites including coalescent analyses, linkage disequilibrium,
13817 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13818 minimum spanning tree and network, and median-joining networks.")
13819 (license license:gpl2+)))
13821 (define-public r-rmetasim
13823 (name "r-rmetasim")
13828 (uri (cran-uri "rmetasim" version))
13831 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13832 (build-system r-build-system)
13834 `(("r-ade4" ,r-ade4)
13835 ("r-adegenet" ,r-adegenet)
13836 ("r-gtools" ,r-gtools)
13837 ("r-pegas" ,r-pegas)))
13838 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13839 (synopsis "Individual-based population genetic simulation environment")
13841 "This package provides an interface between R and the metasim simulation
13842 engine. The simulation environment is documented in: Strand, A.(2002),
13843 Metasim 1.0: an individual-based environment for simulating population
13844 genetics of complex population dynamics.")
13846 (license license:gpl2+)))
13848 (define-public r-genetics
13850 (name "r-genetics")
13851 (version "1.3.8.1.2")
13855 (uri (cran-uri "genetics" version))
13858 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13859 (build-system r-build-system)
13861 `(("r-combinat" ,r-combinat)
13862 ("r-gdata" ,r-gdata)
13863 ("r-gtools" ,r-gtools)
13865 ("r-mvtnorm" ,r-mvtnorm)))
13866 (home-page "https://cran.r-project.org/web/packages/genetics/")
13867 (synopsis "Population genetics")
13869 "This package provides classes and methods for handling genetic data.
13870 It includes classes to represent genotypes and haplotypes at single markers up
13871 to multiple markers on multiple chromosomes. Function include allele
13872 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13873 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13874 and testing for linkage disequilibrium, ...")
13875 ;; Any GPL version.
13876 (license license:gpl2+)))
13878 (define-public r-snp-plotter
13880 (name "r-snp-plotter")
13885 (uri (cran-uri "snp.plotter" version))
13888 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13889 (properties `((upstream-name . "snp.plotter")))
13890 (build-system r-build-system)
13891 (propagated-inputs `(("r-genetics" ,r-genetics)))
13892 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13893 (synopsis "Plot p-values using single SNP and/or haplotype data")
13895 "This package helps you create plots of p-values using single SNP and/or
13896 haplotype data. Main features of the package include options to display a
13897 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13898 datasets simultaneously. Plots can be created using global and/or individual
13899 haplotype p-values along with single SNP p-values. Images are created as
13900 either PDF/EPS files.")
13901 (license license:gpl2+)))
13903 (define-public r-polspline
13905 (name "r-polspline")
13910 (uri (cran-uri "polspline" version))
13912 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
13913 (build-system r-build-system)
13914 (native-inputs `(("gfortran" ,gfortran)))
13915 (home-page "https://cran.r-project.org/web/packages/polspline/")
13916 (synopsis "Polynomial spline routines")
13918 "This package provides routines for the polynomial spline fitting
13919 routines hazard regression, hazard estimation with flexible tails, logspline,
13920 lspec, polyclass, and polymars.")
13921 (license license:gpl2+)))
13923 (define-public r-rms
13930 (uri (cran-uri "rms" version))
13932 (base32 "0m88m63d19qz03x8v56h4rrblln3d2943spi1v4wxxnbcdk22np9"))))
13933 (build-system r-build-system)
13935 `(("r-cluster" ,r-cluster)
13936 ("r-digest" ,r-digest)
13937 ("r-ggplot2" ,r-ggplot2)
13938 ("r-hmisc" ,r-hmisc)
13939 ("r-htmltable" ,r-htmltable)
13940 ("r-htmltools" ,r-htmltools)
13941 ("r-lattice" ,r-lattice)
13943 ("r-multcomp" ,r-multcomp)
13945 ("r-polspline" ,r-polspline)
13946 ("r-quantreg" ,r-quantreg)
13947 ("r-rpart" ,r-rpart)
13948 ("r-sparsem" ,r-sparsem)
13949 ("r-survival" ,r-survival)))
13950 (native-inputs `(("gfortran" ,gfortran)))
13951 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13952 (synopsis "Regression modeling strategies")
13954 "This is a package for regression modeling, testing, estimation,
13955 validation, graphics, prediction, and typesetting by storing enhanced model
13956 design attributes in the fit. The rms package is a collection of functions
13957 that assist with and streamline modeling. It also contains functions for
13958 binary and ordinal logistic regression models, ordinal models for continuous Y
13959 with a variety of distribution families, and the Buckley-James multiple
13960 regression model for right-censored responses, and implements penalized
13961 maximum likelihood estimation for logistic and ordinary linear models. The
13962 package works with almost any regression model, but it was especially written
13963 to work with binary or ordinal regression models, Cox regression, accelerated
13964 failure time models, ordinary linear models, the Buckley-James model,
13965 generalized least squares for serially or spatially correlated observations,
13966 generalized linear models, and quantile regression.")
13967 (license license:gpl2+)))
13969 (define-public r-haplo-stats
13971 (name "r-haplo-stats")
13976 (uri (cran-uri "haplo.stats" version))
13979 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13980 (properties `((upstream-name . "haplo.stats")))
13981 (build-system r-build-system)
13983 `(("r-rms" ,r-rms)))
13985 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13986 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13987 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13989 "This package provides routines for the analysis of indirectly measured
13990 haplotypes. The statistical methods assume that all subjects are unrelated
13991 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13992 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13993 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13994 examples in the vignette.")
13995 (license license:gpl2+)))
13997 (define-public r-bqtl
14004 (uri (cran-uri "bqtl" version))
14007 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14008 (build-system r-build-system)
14009 (native-inputs `(("gfortran" ,gfortran)))
14010 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14011 (synopsis "Bayesian QTL mapping toolkit")
14013 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14014 lines. It includes maximum likelihood and Bayesian tools.")
14015 (license license:gpl2+)))
14017 (define-public r-ibdreg
14024 (uri (cran-uri "ibdreg" version))
14027 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
14028 (build-system r-build-system)
14029 (home-page "https://www.mayo.edu/research/labs/\
14030 statistical-genetics-genetic-epidemiology/software")
14031 (synopsis "Regression methods for IBD linkage with covariates")
14033 "This package provides a method to test genetic linkage with covariates
14034 by regression methods with response IBD sharing for relative pairs. Account
14035 for correlations of IBD statistics and covariates for relative pairs within
14036 the same pedigree.")
14037 (license license:gpl2+)))
14039 (define-public r-dlmap
14046 (uri (cran-uri "dlmap" version))
14049 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14050 (build-system r-build-system)
14052 `(("r-ibdreg" ,r-ibdreg)
14056 ("r-wgaim" ,r-wgaim)))
14057 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14058 (synopsis "Detection localization mapping for QTL")
14060 "This is package for QTL mapping in a mixed model framework with separate
14061 detection and localization stages. The first stage detects the number of QTL
14062 on each chromosome based on the genetic variation due to grouped markers on
14063 the chromosome; the second stage uses this information to determine the most
14064 likely QTL positions. The mixed model can accommodate general fixed and
14065 random effects, including spatial effects in field trials and pedigree
14066 effects. It is applicable to backcrosses, doubled haploids, recombinant
14067 inbred lines, F2 intercrosses, and association mapping populations.")
14068 (license license:gpl2)))
14070 (define-public r-ldheatmap
14072 (name "r-ldheatmap")
14077 (uri (cran-uri "LDheatmap" version))
14080 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14081 (properties `((upstream-name . "LDheatmap")))
14082 (build-system r-build-system)
14084 `(("r-genetics" ,r-genetics)
14086 ("r-snpstats" ,r-snpstats)))
14087 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14088 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14090 "This package provides tools to produce a graphical display, as a heat
14091 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14092 optionally include the physical locations or genetic map distances of each SNP
14094 (license license:gpl3)))
14096 (define-public r-hwde
14103 (uri (cran-uri "hwde" version))
14106 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14107 (build-system r-build-system)
14108 (home-page "https://cran.r-project.org/web/packages/hwde/")
14109 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14111 "This package fits models for genotypic disequilibria, as described in
14112 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14113 terms are available that account for first order interactions between loci.
14114 It also implements, for a single locus in a single population, a conditional
14115 exact test for Hardy-Weinberg equilibrium.")
14116 (license license:gpl2+)))
14118 (define-public r-tdthap
14125 (uri (cran-uri "tdthap" version))
14128 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14129 (build-system r-build-system)
14130 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14131 (synopsis "TDT tests for extended haplotypes")
14133 "Functions and examples are provided for transmission/disequilibrium
14134 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14135 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14136 (license license:artistic2.0)))
14138 (define-public r-sparql
14144 (uri (cran-uri "SPARQL" version))
14147 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14148 (properties `((upstream-name . "SPARQL")))
14149 (build-system r-build-system)
14151 `(("r-rcurl" ,r-rcurl)
14153 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14154 (synopsis "SPARQL client for R")
14155 (description "This package provides an interface to use SPARQL to pose
14156 SELECT or UPDATE queries to an end-point.")
14157 ;; The only license indication is found in the DESCRIPTION file,
14158 ;; which states GPL-3. So we cannot assume GPLv3+.
14159 (license license:gpl3)))
14161 (define-public r-bookdown
14163 (name "r-bookdown")
14167 (uri (cran-uri "bookdown" version))
14170 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14171 (build-system r-build-system)
14173 `(("r-htmltools" ,r-htmltools)
14174 ("r-knitr" ,r-knitr)
14175 ("r-rmarkdown" ,r-rmarkdown)
14176 ("r-tinytex" ,r-tinytex)
14178 ("pandoc" ,ghc-pandoc)))
14179 (home-page "https://github.com/rstudio/bookdown")
14180 (synopsis "Authoring books and technical documents with R markdown")
14181 (description "This package provides output formats and utilities for
14182 authoring books and technical documents with R Markdown.")
14183 (license license:gpl3)))
14185 (define-public r-optparse
14187 (name "r-optparse")
14192 (uri (cran-uri "optparse" version))
14195 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14196 (build-system r-build-system)
14198 `(("r-getopt" ,r-getopt)))
14200 `(("r-knitr" ,r-knitr)))
14201 (home-page "https://github.com/trevorld/optparse")
14202 (synopsis "Command line option parser")
14204 "This package provides a command line parser inspired by Python's
14205 @code{optparse} library to be used with Rscript to write shebang scripts
14206 that accept short and long options.")
14207 (license license:gpl2+)))
14209 (define-public r-wgcna
14216 (uri (cran-uri "WGCNA" version))
14219 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14220 (properties `((upstream-name . "WGCNA")))
14221 (build-system r-build-system)
14223 `(("r-annotationdbi" ,r-annotationdbi)
14224 ("r-doparallel" ,r-doparallel)
14225 ("r-dynamictreecut" ,r-dynamictreecut)
14226 ("r-fastcluster" ,r-fastcluster)
14227 ("r-foreach" ,r-foreach)
14228 ("r-go-db" ,r-go-db)
14229 ("r-hmisc" ,r-hmisc)
14230 ("r-impute" ,r-impute)
14232 ("r-survival" ,r-survival)
14233 ("r-matrixstats" ,r-matrixstats)
14234 ("r-preprocesscore" ,r-preprocesscore)))
14236 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14237 (synopsis "Weighted correlation network analysis")
14239 "This package provides functions necessary to perform Weighted
14240 Correlation Network Analysis on high-dimensional data. It includes functions
14241 for rudimentary data cleaning, construction and summarization of correlation
14242 networks, module identification and functions for relating both variables and
14243 modules to sample traits. It also includes a number of utility functions for
14244 data manipulation and visualization.")
14245 (license license:gpl2+)))
14247 (define-public r-kernlab
14254 (uri (cran-uri "kernlab" version))
14256 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14257 (build-system r-build-system)
14258 (home-page "https://cran.r-project.org/web/packages/kernlab")
14259 (synopsis "Kernel-based machine learning tools")
14261 "This package provides kernel-based machine learning methods for
14262 classification, regression, clustering, novelty detection, quantile regression
14263 and dimensionality reduction. Among other methods @code{kernlab} includes
14264 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14266 (license license:gpl2)))
14268 (define-public r-hierfstat
14270 (name "r-hierfstat")
14271 (version "0.04-22")
14275 (uri (cran-uri "hierfstat" version))
14278 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
14279 (build-system r-build-system)
14281 `(("r-ade4" ,r-ade4)
14282 ("r-adegenet" ,r-adegenet)
14283 ("r-gtools" ,r-gtools)))
14284 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14285 (synopsis "Estimation and tests of hierarchical F-statistics")
14287 "This package allows the estimation of hierarchical F-statistics from
14288 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14289 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14290 are also given to test via randomisations the significance of each F and
14291 variance components, using the likelihood-ratio statistics G.")
14292 (license license:gpl2+)))
14294 (define-public r-hapassoc
14296 (name "r-hapassoc")
14301 (uri (cran-uri "hapassoc" version))
14304 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14305 (build-system r-build-system)
14306 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14307 (synopsis "Inference of trait associations with SNP haplotypes")
14309 "Hapassoc performs likelihood inference of trait associations with
14310 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14311 functions are developed primarily for data collected in cohort or
14312 cross-sectional studies. They can accommodate uncertain haplotype phase and
14313 handle missing genotypes at some SNPs.")
14314 (license license:gpl2)))
14316 (define-public r-sampling
14318 (name "r-sampling")
14323 (uri (cran-uri "sampling" version))
14326 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14327 (build-system r-build-system)
14329 `(("r-lpsolve" ,r-lpsolve)
14330 ("r-mass" ,r-mass)))
14331 (home-page "https://cran.r-project.org/web/packages/sampling/")
14332 (synopsis "Survey sampling")
14334 "This package provides functions for drawing and calibrating samples.")
14335 (license license:gpl2+)))
14337 (define-public r-r2html
14344 (uri (cran-uri "R2HTML" version))
14347 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14348 (properties `((upstream-name . "R2HTML")))
14349 (build-system r-build-system)
14350 (home-page "https://github.com/nalimilan/R2HTML")
14351 (synopsis "HTML export for R objects")
14353 "This package includes HTML functions and methods to write in an HTML
14354 file. Thus, making HTML reports is easy. It includes a function that allows
14355 redirection on the fly, which appears to be very useful for teaching purposes,
14356 as the student can keep a copy of the produced output to keep all that they
14357 did during the course. The package comes with a vignette describing how to
14358 write HTML reports for statistical analysis. Finally, a driver for Sweave
14359 parses HTML flat files containing R code and to automatically write
14360 the corresponding outputs (tables and graphs).")
14361 (license license:gpl2+)))
14363 (define-public r-rjava
14370 (uri (cran-uri "rJava" version))
14373 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
14374 (properties `((upstream-name . "rJava")))
14375 (build-system r-build-system)
14377 `(#:modules ((guix build utils)
14378 (guix build r-build-system)
14381 (modify-phases %standard-phases
14382 (add-after 'unpack 'set-JAVA_HOME
14383 (lambda* (#:key inputs #:allow-other-keys)
14384 (let ((jdk (assoc-ref inputs "jdk")))
14385 (setenv "JAVA_HOME" jdk)
14386 (setenv "JAVA" (which "java"))
14387 (setenv "JAR" (which "jar"))
14388 (setenv "JAVAC" (which "javac"))
14389 (setenv "JAVAH" (which "javah"))
14390 (setenv "JAVA_CPPFLAGS"
14391 (string-append "-I" jdk "/include "
14392 "-I" jdk "/include/linux"))
14393 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14394 ((lib) (setenv "JAVA_LIBS" lib))
14395 (_ (error "Could not find libjvm.so"))))
14399 ("jdk" ,icedtea-8 "jdk")
14402 (home-page "https://www.rforge.net/rJava/")
14403 (synopsis "Low-Level R to Java interface")
14405 "This package provides a low-level interface to the Java VM very much
14406 like .C/.Call and friends. It allows the creation of objects, calling methods
14407 and accessing fields.")
14408 (license license:gpl2)))
14410 (define-public r-svmisc
14417 (uri (cran-uri "svMisc" version))
14420 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14421 (properties `((upstream-name . "svMisc")))
14422 (build-system r-build-system)
14423 (home-page "https://github.com/SciViews/svMisc")
14424 (synopsis "Miscellaneous functions for SciViews")
14426 "This package provides miscellaneous functions for SciViews or general
14427 use, including tools to manage a temporary environment attached to the search
14428 path for temporary variables you do not want to @code{save()} or
14429 @code{load()}; test the current platform; showing progress bars, etc.")
14430 (license license:gpl2)))
14432 (define-public r-xyz
14439 (uri (cran-uri "xyz" version))
14442 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14443 (build-system r-build-system)
14445 `(("r-rcpp" ,r-rcpp)))
14446 (home-page "https://cran.r-project.org/web/packages/xyz/")
14447 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14449 "High dimensional interaction search by brute force requires a quadratic
14450 computational cost in the number of variables. The xyz algorithm provably
14451 finds strong interactions in almost linear time. For details of the algorithm
14452 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14453 interaction search in high-dimensional data.")
14454 ;; Any version of the GPL.
14455 (license license:gpl2+)))
14457 (define-public r-rttf2pt1
14459 (name "r-rttf2pt1")
14464 (uri (cran-uri "Rttf2pt1" version))
14467 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14468 (properties `((upstream-name . "Rttf2pt1")))
14469 (build-system r-build-system)
14470 (home-page "https://github.com/wch/Rttf2pt1")
14471 (synopsis "Font conversion utility")
14473 "This package contains the program @code{ttf2pt1}, for use with the
14474 @code{extrafont} package.")
14475 ;; Most of the files are covered under the Expat license. Some files are
14476 ;; covered under BSD-3. Deviations for individual files are recorded in
14477 ;; the LICENSE file.
14478 (license (list license:bsd-3 license:expat
14479 (license:non-copyleft "file://LICENSE")))))
14481 (define-public r-extrafontdb
14483 (name "r-extrafontdb")
14488 (uri (cran-uri "extrafontdb" version))
14491 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14492 (build-system r-build-system)
14493 (home-page "https://github.com/wch/extrafontdb")
14494 (synopsis "Database for the extrafont package")
14496 "This package holds the database for the @code{extrafont} package.")
14497 (license license:gpl2)))
14499 (define-public r-extrafont
14501 (name "r-extrafont")
14506 (uri (cran-uri "extrafont" version))
14509 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14510 (build-system r-build-system)
14512 `(("r-extrafontdb" ,r-extrafontdb)
14513 ("r-rttf2pt1" ,r-rttf2pt1)))
14514 (home-page "https://github.com/wch/extrafont")
14515 (synopsis "Tools for using fonts in R")
14517 "The extrafont package makes it easier to use fonts other than the basic
14518 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14519 used with PDF or PostScript output files. There are two hurdles for using
14520 fonts in PDF (or Postscript) output files:
14523 @item Making R aware of the font and the dimensions of the characters.
14524 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14525 properly on a device that doesn't have the font. This is usually needed if
14526 you want to print the PDF file or share it with others.
14529 The extrafont package makes both of these things easier.")
14530 (license license:gpl2)))
14532 (define-public r-xkcd
14539 (uri (cran-uri "xkcd" version))
14542 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14543 (build-system r-build-system)
14545 `(("r-extrafont" ,r-extrafont)
14546 ("r-ggplot2" ,r-ggplot2)
14547 ("r-hmisc" ,r-hmisc)))
14548 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14549 (synopsis "Plot ggplot2 graphics in the XKCD style")
14551 "This package provides the means to plot ggplot2 graphs in the style of
14552 the XKCD web comic.")
14553 (license license:gpl3)))
14555 (define-public r-msigdbr
14562 (uri (cran-uri "msigdbr" version))
14565 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14566 (build-system r-build-system)
14568 `(("r-dplyr" ,r-dplyr)
14569 ("r-magrittr" ,r-magrittr)
14570 ("r-rlang" ,r-rlang)
14571 ("r-tibble" ,r-tibble)))
14573 `(("r-knitr" ,r-knitr)))
14574 (home-page "https://github.com/igordot/msigdbr")
14575 (synopsis "MSigDB gene sets for multiple organisms")
14577 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14578 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14579 software in a standard R data frame with key-value pairs. Included are the
14580 original human gene symbols and Entrez IDs as well as the equivalents for
14581 various frequently studied model organisms such as mouse, rat, pig, fly, and
14583 ;; The package is covered under the Expat license, but the upstream MSigDB
14584 ;; files are made available under the Creative Commons Attribution 4.0
14585 ;; International license.
14586 (license (list license:expat license:cc-by4.0))))
14588 (define-public r-gridgraphics
14590 (name "r-gridgraphics")
14595 (uri (cran-uri "gridGraphics" version))
14598 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14599 (properties `((upstream-name . "gridGraphics")))
14600 (build-system r-build-system)
14601 (home-page "https://github.com/pmur002/gridgraphics")
14602 (synopsis "Redraw base graphics using @code{grid} graphics")
14604 "This package provides functions to convert a page of plots drawn with
14605 the @code{graphics} package into identical output drawn with the @code{grid}
14606 package. The result looks like the original @code{graphics}-based plot, but
14607 consists of @code{grid} grobs and viewports that can then be manipulated with
14608 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14609 (license license:gpl2+)))
14611 (define-public r-farver
14618 (uri (cran-uri "farver" version))
14621 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14622 (build-system r-build-system)
14623 (home-page "https://github.com/thomasp85/farver")
14624 (synopsis "Vectorized color conversion and comparison")
14626 "The encoding of color can be handled in many different ways, using
14627 different color spaces. As different color spaces have different uses,
14628 efficient conversion between these representations are important. This
14629 package provides a set of functions that gives access to very fast color space
14630 conversion and comparisons implemented in C++, and offers 100-fold speed
14631 improvements over the @code{convertColor} function in the @code{grDevices}
14633 (license license:expat)))
14635 (define-public r-ggplotify
14637 (name "r-ggplotify")
14642 (uri (cran-uri "ggplotify" version))
14645 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14646 (build-system r-build-system)
14648 `(("r-ggplot2" ,r-ggplot2)
14649 ("r-gridgraphics" ,r-gridgraphics)
14650 ("r-rvcheck" ,r-rvcheck)))
14652 `(("r-knitr" ,r-knitr)))
14653 (home-page "https://github.com/GuangchuangYu/ggplotify")
14654 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14656 "This package provides tools to convert plot function calls (using
14657 expression or formula) to @code{grob} or @code{ggplot} objects that are
14658 compatible with the @code{grid} and @code{ggplot2} environment. With this
14659 package, we are able to e.g. use @code{cowplot} to align plots produced by
14660 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14661 converting them to @code{ggplot} objects.")
14662 (license license:artistic2.0)))
14664 (define-public r-triebeard
14666 (name "r-triebeard")
14671 (uri (cran-uri "triebeard" version))
14674 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14675 (build-system r-build-system)
14676 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14677 (home-page "https://github.com/Ironholds/triebeard/")
14678 (synopsis "Radix trees in Rcpp")
14680 "Radix trees, or tries, are key-value data structures optimized for
14681 efficient lookups, similar in purpose to hash tables. This package provides
14682 an implementation of radix trees for use in R programming and in developing
14683 packages with Rcpp.")
14684 (license license:expat)))
14686 (define-public r-tweenr
14693 (uri (cran-uri "tweenr" version))
14696 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14697 (build-system r-build-system)
14699 `(("r-farver" ,r-farver)
14700 ("r-magrittr" ,r-magrittr)
14702 ("r-rlang" ,r-rlang)))
14703 (home-page "https://github.com/thomasp85/tweenr")
14704 (synopsis "Interpolate data for smooth animations")
14706 "In order to create smooth animation between states of data, tweening is
14707 necessary. This package provides a range of functions for creating tweened
14708 data that can be used as basis for animation. Furthermore it adds a number of
14709 vectorized interpolaters for common R data types such as numeric, date and
14711 (license license:expat)))
14713 (define-public r-polyclip
14715 (name "r-polyclip")
14720 (uri (cran-uri "polyclip" version))
14723 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14724 (build-system r-build-system)
14725 (native-inputs `(("pkg-config" ,pkg-config)))
14726 (home-page "http://www.angusj.com/delphi/clipper.php")
14727 (synopsis "Polygon clipping")
14729 "This package provides an R port of the library Clipper. It performs
14730 polygon clipping operations (intersection, union, set minus, set difference)
14731 for polygonal regions of arbitrary complexity, including holes. It computes
14732 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14733 dilations) for polygonal regions and polygonal lines. It computes the
14734 Minkowski Sum of general polygons. There is a function for removing
14735 self-intersections from polygon data.")
14736 (license license:boost1.0)))
14738 (define-public r-urltools
14740 (name "r-urltools")
14745 (uri (cran-uri "urltools" version))
14748 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14749 (build-system r-build-system)
14751 `(("r-rcpp" ,r-rcpp)
14752 ("r-triebeard" ,r-triebeard)))
14753 (home-page "https://github.com/Ironholds/urltools/")
14754 (synopsis "Vectorized tools for URL handling and parsing")
14756 "This package provides a toolkit for all URL-handling needs, including
14757 encoding and decoding, parsing, parameter extraction and modification. All
14758 functions are designed to be both fast and entirely vectorized. It is
14759 intended to be useful for people dealing with web-related datasets, such as
14760 server-side logs, although may be useful for other situations involving large
14762 (license license:expat)))
14764 (define-public r-ggforce
14771 (uri (cran-uri "ggforce" version))
14774 "04926cqrda6psvy2nzkkw4czwyxdp7fnxg76byp14v12kgd72lm0"))))
14775 (build-system r-build-system)
14777 `(("r-ggplot2" ,r-ggplot2)
14778 ("r-gtable" ,r-gtable)
14780 ("r-polyclip" ,r-polyclip)
14782 ("r-rcppeigen" ,r-rcppeigen)
14783 ("r-rlang" ,r-rlang)
14784 ("r-scales" ,r-scales)
14785 ("r-tidyselect" ,r-tidyselect)
14786 ("r-tweenr" ,r-tweenr)
14787 ("r-withr" ,r-withr)))
14788 (home-page "https://ggforce.data-imaginist.com")
14789 (synopsis "Accelerating ggplot2")
14791 "The aim of the ggplot2 package is to aid in visual data investigations.
14792 This focus has led to a lack of facilities for composing specialized plots.
14793 Thi package aims to be a collection of mainly new statistics and geometries
14794 that fills this gap.")
14795 (license license:expat)))
14797 (define-public r-europepmc
14799 (name "r-europepmc")
14804 (uri (cran-uri "europepmc" version))
14807 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
14808 (build-system r-build-system)
14810 `(("r-dplyr" ,r-dplyr)
14812 ("r-jsonlite" ,r-jsonlite)
14814 ("r-progress" ,r-progress)
14815 ("r-purrr" ,r-purrr)
14816 ("r-rlang" ,r-rlang)
14817 ("r-tibble" ,r-tibble)
14818 ("r-tidyr" ,r-tidyr)
14819 ("r-urltools" ,r-urltools)
14820 ("r-xml2" ,r-xml2)))
14822 `(("r-knitr" ,r-knitr)))
14823 (home-page "https://github.com/ropensci/europepmc/")
14824 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14826 "This package provides an R Client for the
14827 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14828 Service}. It gives access to both metadata on life science literature and
14829 open access full texts. Europe PMC indexes all PubMed content and other
14830 literature sources including Agricola, a bibliographic database of citations
14831 to the agricultural literature, or Biological Patents. In addition to
14832 bibliographic metadata, the client allows users to fetch citations and
14833 reference lists. Links between life-science literature and other EBI
14834 databases, including ENA, PDB or ChEMBL are also accessible.")
14835 (license license:gpl3)))
14837 (define-public r-ggraph
14844 (uri (cran-uri "ggraph" version))
14847 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
14848 (build-system r-build-system)
14850 `(("r-digest" ,r-digest)
14851 ("r-dplyr" ,r-dplyr)
14852 ("r-ggforce" ,r-ggforce)
14853 ("r-ggplot2" ,r-ggplot2)
14854 ("r-ggrepel" ,r-ggrepel)
14855 ("r-graphlayouts" ,r-graphlayouts)
14856 ("r-gtable" ,r-gtable)
14857 ("r-igraph" ,r-igraph)
14860 ("r-rlang" ,r-rlang)
14861 ("r-scales" ,r-scales)
14862 ("r-tidygraph" ,r-tidygraph)
14863 ("r-viridis" ,r-viridis)))
14865 `(("r-knitr" ,r-knitr)))
14866 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14867 (synopsis "Implementation of grammar of graphics for graphs and networks")
14869 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14870 graph and network visualizations due to its reliance on tabular data input.
14871 The ggraph package is an extension of the ggplot2 API tailored to graph
14872 visualizations and provides the same flexible approach to building up plots
14874 (license license:gpl3)))
14876 (define-public r-varselrf
14878 (name "r-varselrf")
14883 (uri (cran-uri "varSelRF" version))
14886 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14887 (properties `((upstream-name . "varSelRF")))
14888 (build-system r-build-system)
14890 `(("r-randomforest" ,r-randomforest)))
14891 (home-page "https://www.ligarto.org/rdiaz/software/software")
14892 (synopsis "Variable selection using random forests")
14894 "This package provides tools for the variable selection from random
14895 forests using both backwards variable elimination (for the selection of small
14896 sets of non-redundant variables) and selection based on the importance
14897 spectrum (somewhat similar to scree plots; for the selection of large,
14898 potentially highly-correlated variables). The main applications are in
14899 high-dimensional data (e.g., microarray data, and other genomics and
14900 proteomics applications).")
14901 (license license:gpl2+)))
14903 (define-public r-pamr
14910 (uri (cran-uri "pamr" version))
14913 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14914 (build-system r-build-system)
14916 `(("r-cluster" ,r-cluster)
14917 ("r-survival" ,r-survival)))
14918 (native-inputs `(("gfortran" ,gfortran)))
14919 (home-page "https://cran.r-project.org/web/packages/pamr/")
14920 (synopsis "Prediction Analysis for Microarrays")
14922 "This package provides some functions for sample classification in
14924 (license license:gpl2)))
14926 (define-public r-rda
14929 (version "1.0.2-2.1")
14933 (uri (cran-uri "rda" version))
14936 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14937 (build-system r-build-system)
14938 (home-page "https://cran.r-project.org/web/packages/rda/")
14939 (synopsis "Shrunken centroids regularized discriminant analysis")
14941 "This package provides tools for shrunken centroids regularized
14942 discriminant analysis for the purpose of classifying high dimensional data.")
14943 (license license:gpl2+)))
14945 (define-public r-ggvis
14952 (uri (cran-uri "ggvis" version))
14955 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14956 (build-system r-build-system)
14958 `(("r-assertthat" ,r-assertthat)
14959 ("r-dplyr" ,r-dplyr)
14960 ("r-htmltools" ,r-htmltools)
14961 ("r-jsonlite" ,r-jsonlite)
14962 ("r-lazyeval" ,r-lazyeval)
14963 ("r-magrittr" ,r-magrittr)
14964 ("r-shiny" ,r-shiny)))
14965 (home-page "https://ggvis.rstudio.com/")
14966 (synopsis "Interactive grammar of graphics")
14968 "This package is a data visualization package for R providing an
14969 implementation of an interactive grammar of graphics, taking the best parts of
14970 ggplot2, combining them with the reactive framework of Shiny and drawing web
14971 graphics using Vega.")
14972 (license license:gpl2)))
14974 (define-public r-gbm
14981 (uri (cran-uri "gbm" version))
14984 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14985 (build-system r-build-system)
14987 `(("r-gridextra" ,r-gridextra)
14988 ("r-lattice" ,r-lattice)
14989 ("r-survival" ,r-survival)))
14990 (home-page "https://github.com/gbm-developers/gbm")
14991 (synopsis "Generalized boosted regression models")
14993 "This package is an implementation of extensions to Freund and Schapire's
14994 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14995 regression methods for least squares, absolute loss, t-distribution loss,
14996 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
14997 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
14998 and Learning to Rank measures (LambdaMart).")
14999 (license license:gpl2+)))
15001 (define-public r-threejs
15008 (uri (cran-uri "threejs" version))
15011 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15012 (build-system r-build-system)
15014 `(#:modules ((guix build utils)
15015 (guix build r-build-system)
15019 (modify-phases %standard-phases
15020 (add-after 'unpack 'process-javascript
15021 (lambda* (#:key inputs #:allow-other-keys)
15022 (with-directory-excursion "inst"
15026 `((,(assoc-ref inputs "js-jquery")
15027 "htmlwidgets/lib/jquery/jquery.min.js")
15028 (,(assoc-ref inputs "js-threejs-111")
15029 "htmlwidgets/lib/threejs-111/three.min.js"))))
15030 (lambda (sources targets)
15031 (for-each (lambda (source target)
15032 (format #t "Processing ~a --> ~a~%"
15034 (delete-file target)
15035 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15036 (call-with-output-file target
15038 (dump-port minified port)))))
15039 sources targets))))
15042 `(("r-base64enc" ,r-base64enc)
15043 ("r-crosstalk" ,r-crosstalk)
15044 ("r-htmlwidgets" ,r-htmlwidgets)
15045 ("r-igraph" ,r-igraph)))
15047 `(("uglify-js" ,uglify-js)
15051 (uri "https://code.jquery.com/jquery-1.12.4.js")
15054 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15058 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15061 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15062 (home-page "https://bwlewis.github.io/rthreejs")
15063 (synopsis "Interactive 3D scatter plots, networks and globes")
15065 "Create interactive 3D scatter plots, network plots, and globes in R
15066 using the three.js visualization library.")
15067 (license license:expat)))
15069 (define-public r-mlbench
15076 (uri (cran-uri "mlbench" version))
15079 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15080 (build-system r-build-system)
15081 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15082 (synopsis "Machine learning benchmark problems")
15084 "This package provides a collection of artificial and real-world machine
15085 learning benchmark problems, including, e.g., several data sets from the UCI
15087 (license license:gpl2)))
15089 (define-public r-mpm
15096 (uri (cran-uri "mpm" version))
15099 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15100 (build-system r-build-system)
15102 `(("r-kernsmooth" ,r-kernsmooth)
15103 ("r-mass" ,r-mass)))
15104 (home-page "http://mpm.r-forge.r-project.org")
15105 (synopsis "Multivariate projection methods")
15107 "This is a package for exploratory graphical analysis of multivariate
15108 data, specifically gene expression data with different projection methods:
15109 principal component analysis, correspondence analysis, spectral map
15111 (license license:gpl2+)))
15113 (define-public r-png
15119 (uri (cran-uri "png" version))
15122 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15123 (build-system r-build-system)
15125 `(("libpng" ,libpng)
15127 (home-page "https://www.rforge.net/png/")
15128 (synopsis "Read and write PNG images")
15130 "This package provides an easy and simple way to read, write and display
15131 bitmap images stored in the PNG format. It can read and write both files and
15132 in-memory raw vectors.")
15133 ;; Any of these GPL versions.
15134 (license (list license:gpl2 license:gpl3))))
15136 (define-public r-ggcorrplot
15138 (name "r-ggcorrplot")
15143 (uri (cran-uri "ggcorrplot" version))
15146 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15147 (build-system r-build-system)
15149 `(("r-ggplot2" ,r-ggplot2)
15150 ("r-reshape2" ,r-reshape2)))
15151 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15152 (synopsis "Visualization of a correlation matrix using ggplot2")
15154 "The ggcorrplot package can be used to visualize easily a correlation
15155 matrix using ggplot2. It provides a solution for reordering the correlation
15156 matrix and displays the significance level on the plot. It also includes a
15157 function for computing a matrix of correlation p-values.")
15158 (license license:gpl2)))
15160 (define-public r-flexdashboard
15162 (name "r-flexdashboard")
15163 (version "0.5.1.1")
15167 (uri (cran-uri "flexdashboard" version))
15170 "0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
15171 (build-system r-build-system)
15173 `(#:modules ((guix build utils)
15174 (guix build r-build-system)
15178 (ice-9 textual-ports))
15180 (modify-phases %standard-phases
15181 (add-after 'unpack 'process-javascript
15182 (lambda* (#:key inputs #:allow-other-keys)
15183 (with-directory-excursion "inst"
15184 ;; Concatenate all components of prism.js
15185 (let ((contents (string-join
15186 (map (lambda (name)
15187 (call-with-input-file
15188 (assoc-ref inputs name)
15192 "js-prism-line-numbers"))
15194 (call-with-output-file "prism-src.js"
15195 (cut display contents <>)))
15199 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15200 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15202 "www/sly/sly.min.js")
15204 "www/prism/prism.js")
15205 (,(assoc-ref inputs "js-raphael")
15206 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15207 (,(assoc-ref inputs "js-featherlight")
15208 "www/featherlight/featherlight.min.js"))))
15209 (lambda (sources targets)
15210 (for-each (lambda (source target)
15211 (format #t "Processing ~a --> ~a~%"
15213 (delete-file target)
15214 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15215 (call-with-output-file target
15217 (dump-port minified port)))))
15218 sources targets))))
15221 `(("r-htmltools" ,r-htmltools)
15222 ("r-htmlwidgets" ,r-htmlwidgets)
15223 ("r-jsonlite" ,r-jsonlite)
15224 ("r-knitr" ,r-knitr)
15225 ("r-rmarkdown" ,r-rmarkdown)
15226 ("r-shiny" ,r-shiny)))
15228 `(("uglify-js" ,uglify-js)
15232 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15235 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15239 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15242 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15246 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15249 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15250 ("js-prism-line-numbers"
15253 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15256 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15260 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15263 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15264 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15265 (synopsis "R Markdown format for flexible dashboards")
15267 "This package provides an R Markdown format for converting an R Markdown
15268 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15269 of its components to the containing web page.")
15270 (license license:expat)))
15272 (define-public r-preseqr
15279 (uri (cran-uri "preseqR" version))
15282 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15283 (properties `((upstream-name . "preseqR")))
15284 (build-system r-build-system)
15286 `(("r-polynom" ,r-polynom)))
15287 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15288 (synopsis "Predicting species accumulation curves")
15290 "This package can be used to predict the r-species accumulation
15291 curve (r-SAC), which is the number of species represented at least r times as
15292 a function of the sampling effort. When r = 1, the curve is known as the
15293 species accumulation curve, or the library complexity curve in high-throughput
15294 genomic sequencing. The package includes both parametric and nonparametric
15295 methods, as described by Deng C, et al. (2018).")
15296 (license license:gpl3)))
15298 (define-public r-mapplots
15300 (name "r-mapplots")
15305 (uri (cran-uri "mapplots" version))
15308 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15309 (build-system r-build-system)
15310 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15311 (synopsis "Data visualization on maps")
15313 "This package helps you create simple maps; add sub-plots like pie plots
15314 to a map or any other plot; format, plot and export gridded data. The package
15315 was developed for displaying fisheries data but most functions can be used for
15316 more generic data visualisation.")
15317 (license license:gpl2+)))
15319 (define-public r-pmcmr
15326 (uri (cran-uri "PMCMR" version))
15329 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15330 (properties `((upstream-name . "PMCMR")))
15331 (build-system r-build-system)
15332 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15333 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15335 "This is a deprecated package for calculating pairwise multiple
15336 comparisons of mean rank sums. This package is superseded by the novel
15337 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15338 compatibility of dependent packages for some time.")
15339 (license license:gpl3+)))
15341 (define-public r-downloader
15343 (name "r-downloader")
15348 (uri (cran-uri "downloader" version))
15351 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15352 (build-system r-build-system)
15354 `(("r-digest" ,r-digest)))
15355 (home-page "https://github.com/wch/downloader")
15356 (synopsis "Download files over HTTP and HTTPS")
15358 "This package provides a wrapper for the @code{download.file} function,
15359 making it possible to download files over HTTPS across platforms. The
15360 @code{RCurl} package provides this functionality (and much more) but has
15361 external dependencies. This package has is implemented purely in R.")
15362 (license license:gpl2)))
15364 (define-public r-rex
15371 (uri (cran-uri "rex" version))
15374 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15375 (build-system r-build-system)
15377 `(("r-lazyeval" ,r-lazyeval)))
15379 `(("r-knitr" ,r-knitr)))
15380 (home-page "https://github.com/kevinushey/rex")
15381 (synopsis "Friendly regular expressions")
15383 "This package provides a friendly interface for the construction of
15384 regular expressions. Regular expressions are a very powerful feature, however
15385 they are often difficult to interpret. Rex allows you to build complex
15386 regular expressions from human readable expressions")
15387 (license license:expat)))
15389 (define-public r-xmlparsedata
15391 (name "r-xmlparsedata")
15396 (uri (cran-uri "xmlparsedata" version))
15399 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15400 (properties `((upstream-name . "xmlparsedata")))
15401 (build-system r-build-system)
15402 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15403 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15405 "This package provides tools to convert the output of
15406 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15407 @code{XPath}, and is easier to manipulate in general.")
15408 (license license:expat)))
15410 (define-public r-cyclocomp
15412 (name "r-cyclocomp")
15417 (uri (cran-uri "cyclocomp" version))
15420 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15421 (properties `((upstream-name . "cyclocomp")))
15422 (build-system r-build-system)
15424 `(("r-callr" ,r-callr)
15425 ("r-crayon" ,r-crayon)
15427 ("r-remotes" ,r-remotes)
15428 ("r-withr" ,r-withr)))
15429 (home-page "https://github.com/MangoTheCat/cyclocomp")
15430 (synopsis "Cyclomatic complexity of R code")
15432 "Cyclomatic complexity is a software metric, used to indicate the
15433 complexity of a program. It is a quantitative measure of the number of
15434 linearly independent paths through a program's source code. This package
15435 provides tools to compute this metric.")
15436 (license license:expat)))
15438 (define-public r-lintr
15445 (uri (cran-uri "lintr" version))
15448 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15449 (properties `((upstream-name . "lintr")))
15450 (build-system r-build-system)
15452 `(("r-codetools" ,r-codetools)
15453 ("r-crayon" ,r-crayon)
15454 ("r-cyclocomp" ,r-cyclocomp)
15455 ("r-digest" ,r-digest)
15457 ("r-jsonlite" ,r-jsonlite)
15458 ("r-knitr" ,r-knitr)
15460 ("r-rstudioapi" ,r-rstudioapi)
15461 ("r-testthat" ,r-testthat)
15463 ("r-xmlparsedata" ,r-xmlparsedata)))
15464 (home-page "https://github.com/jimhester/lintr")
15465 (synopsis "Linter for R code")
15466 (description "This package checks adherence to a given style, syntax
15467 errors and possible semantic issues. It supports on the fly checking of R
15468 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15469 (license license:expat)))
15471 (define-public r-sctransform
15473 (name "r-sctransform")
15478 (uri (cran-uri "sctransform" version))
15481 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15482 (build-system r-build-system)
15484 `(("r-future-apply" ,r-future-apply)
15485 ("r-ggplot2" ,r-ggplot2)
15486 ("r-gridextra" ,r-gridextra)
15488 ("r-matrix" ,r-matrix)
15490 ("r-rcppeigen" ,r-rcppeigen)
15491 ("r-reshape2" ,r-reshape2)))
15492 (home-page "https://github.com/ChristophH/sctransform")
15493 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15495 "This package provides a normalization method for single-cell UMI count
15496 data using a variance stabilizing transformation. The transformation is based
15497 on a negative binomial regression model with regularized parameters. As part
15498 of the same regression framework, this package also provides functions for
15499 batch correction, and data correction.")
15500 (license license:gpl3)))
15502 (define-public r-styler
15509 (uri (cran-uri "styler" version))
15512 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15513 (build-system r-build-system)
15515 `(("r-backports" ,r-backports)
15517 ("r-magrittr" ,r-magrittr)
15518 ("r-purrr" ,r-purrr)
15519 ("r-r-cache" ,r-r-cache)
15520 ("r-rematch2" ,r-rematch2)
15521 ("r-rlang" ,r-rlang)
15522 ("r-rprojroot" ,r-rprojroot)
15523 ("r-tibble" ,r-tibble)
15524 ("r-withr" ,r-withr)
15525 ("r-xfun" ,r-xfun)))
15526 (home-page "https://github.com/r-lib/styler")
15527 (synopsis "Non-invasive pretty printing of R code")
15529 "This is a package for pretty-printing R code without changing the user's
15530 formatting intent.")
15531 (license license:gpl3)))
15533 (define-public r-scrime
15540 (uri (cran-uri "scrime" version))
15543 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15544 (build-system r-build-system)
15545 (home-page "https://cran.r-project.org/web/packages/scrime/")
15546 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15548 "This package provides tools for the analysis of high-dimensional data
15549 developed/implemented at the group \"Statistical Complexity Reduction In
15550 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15551 the functions can also be applied to other types of categorical data.")
15552 (license license:gpl2)))
15554 (define-public r-pbmcapply
15556 (name "r-pbmcapply")
15561 (uri (cran-uri "pbmcapply" version))
15564 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15565 (build-system r-build-system)
15566 (home-page "https://github.com/kvnkuang/pbmcapply")
15567 (synopsis "Track the progress of apply procedures with a progress bar")
15569 "This light-weight package helps you track and visualize the progress of
15570 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15571 (license license:expat)))
15573 (define-public r-blme
15580 (uri (cran-uri "blme" version))
15583 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15584 (build-system r-build-system)
15585 (propagated-inputs `(("r-lme4" ,r-lme4)))
15586 (home-page "https://github.com/vdorie/blme")
15587 (synopsis "Bayesian linear mixed-effects models")
15589 "This package provides tools for maximum a posteriori estimation for
15590 linear and generalized linear mixed-effects models in a Bayesian setting. It
15591 extends the lme4 package.")
15592 (license license:gpl2+)))
15594 (define-public r-batchtools
15596 (name "r-batchtools")
15601 (uri (cran-uri "batchtools" version))
15604 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15605 (build-system r-build-system)
15607 `(("r-backports" ,r-backports)
15608 ("r-base64url" ,r-base64url)
15610 ("r-checkmate" ,r-checkmate)
15611 ("r-data-table" ,r-data-table)
15612 ("r-digest" ,r-digest)
15614 ("r-progress" ,r-progress)
15616 ("r-rappdirs" ,r-rappdirs)
15617 ("r-stringi" ,r-stringi)
15618 ("r-withr" ,r-withr)))
15620 `(("r-knitr" ,r-knitr)))
15621 (home-page "https://github.com/mllg/batchtools")
15622 (synopsis "Tools for computation on batch systems")
15624 "As a successor of the packages BatchJobs and BatchExperiments, this
15625 package provides a parallel implementation of the Map function for high
15626 performance computing systems managed by various schedulers. A multicore and
15627 socket mode allow the parallelization on a local machines, and multiple
15628 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15629 the package provides an abstraction mechanism to define large-scale computer
15630 experiments in a well-organized and reproducible way.")
15631 (license license:lgpl3)))
15633 (define-public r-clue
15640 (uri (cran-uri "clue" version))
15643 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15644 (build-system r-build-system)
15645 (propagated-inputs `(("r-cluster" ,r-cluster)))
15646 (home-page "https://cran.r-project.org/web/packages/clue/")
15647 (synopsis "Tools for analyzing cluster ensembles")
15648 (description "Cluster ensembles are collections of individual solutions to
15649 a given clustering problem which are useful or necessary to consider in a wide
15650 range of applications. This R package provides an extensible computational
15651 environment for creating and analyzing cluster ensembles, with basic data
15652 structures for representing partitions and hierarchies, and facilities for
15653 computing on them, including methods for measuring proximity and obtaining
15654 consensus and secondary clusterings.")
15655 (license license:gpl2)))
15657 (define-public r-sitmo
15664 (uri (cran-uri "sitmo" version))
15667 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15668 (build-system r-build-system)
15669 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15670 (home-page "https://github.com/coatless/sitmo/")
15671 (synopsis "Parallel pseudo random number generator header files")
15673 "This package provides two high quality and fast PPRNGs that may be used
15674 in an OpenMP parallel environment. In addition, there is a generator for one
15675 dimensional low-discrepancy sequence.")
15676 (license license:expat)))
15678 (define-public r-dqrng
15685 (uri (cran-uri "dqrng" version))
15688 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15689 (build-system r-build-system)
15693 ("r-sitmo" ,r-sitmo)))
15694 (home-page "https://www.daqana.org/dqrng")
15695 (synopsis "Fast pseudo random number generators")
15697 "Several fast random number generators are provided as C++ header-only
15698 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15699 Additionally, fast functions for generating random numbers according to a
15700 uniform, normal and exponential distribution are included. The latter two use
15701 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15702 functions are exported to R and as a C++ interface and are enabled for use
15703 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15704 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15705 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15706 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15707 ;; whole is distributed under the terms of the AGPL 3.
15708 (license license:agpl3)))
15710 (define-public r-ingredients
15712 (name "r-ingredients")
15717 (uri (cran-uri "ingredients" version))
15720 "1q196y9xzn4wk44fa1bvh0hcbizgm93rwir82nyk31k5pgixk967"))))
15721 (properties `((upstream-name . "ingredients")))
15722 (build-system r-build-system)
15724 `(("r-ggplot2" ,r-ggplot2)
15725 ("r-gridextra" ,r-gridextra)
15726 ("r-scales" ,r-scales)))
15727 (native-inputs `(("r-knitr" ,r-knitr)))
15728 (home-page "https://ModelOriented.github.io/ingredients/")
15729 (synopsis "Effects and importances of model ingredients")
15731 "This is a collection of tools for assessment of feature importance and
15732 feature effects. Key functions are:
15735 @item @code{feature_importance()} for assessment of global level feature
15737 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15738 @item @code{partial_dependence()} for partial dependence plots,
15739 @item @code{conditional_dependence()} for conditional dependence plots,
15740 @item @code{accumulated_dependence()} for accumulated local effects plots,
15741 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15742 aggregation of ceteris paribus profiles,
15743 @item generic @code{print()} and @code{plot()} for better usability of
15744 selected explainers,
15745 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15746 @item generic @code{describe()} for explanations in natural language.
15748 (license license:gpl3)))
15750 (define-public r-ibreakdown
15752 (name "r-ibreakdown")
15757 (uri (cran-uri "iBreakDown" version))
15760 "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
15761 (properties `((upstream-name . "iBreakDown")))
15762 (build-system r-build-system)
15763 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15764 (native-inputs `(("r-knitr" ,r-knitr)))
15765 (home-page "https://ModelOriented.github.io/iBreakDown/")
15766 (synopsis "Model agnostic instance level variable attributions")
15768 "This package provides a model agnostic tool for decomposition of
15769 predictions from black boxes. It supports additive attributions and
15770 attributions with interactions. The Break Down Table shows contributions of
15771 every variable to a final prediction. The Break Down Plot presents variable
15772 contributions in a concise graphical way. This package works for
15773 classification and regression models.")
15774 (license license:gpl3)))
15776 (define-public r-dalex
15783 (uri (cran-uri "DALEX" version))
15786 "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
15787 (properties `((upstream-name . "DALEX")))
15788 (build-system r-build-system)
15790 `(("r-ggplot2" ,r-ggplot2)
15791 ("r-ibreakdown" ,r-ibreakdown)
15792 ("r-ingredients" ,r-ingredients)))
15793 (home-page "https://pbiecek.github.io/DALEX/")
15794 (synopsis "Descriptive machine learning explanations")
15796 "Machine Learning models are widely used and have various applications in
15797 classification or regression. Models created with boosting, bagging, stacking
15798 or similar techniques are often used due to their high performance, but such
15799 black-box models usually lack interpretability. The DALEX package contains
15800 various explainers that help to understand the link between input variables
15801 and model output.")
15802 ;; Any version of the GPL
15803 (license license:gpl3+)))
15805 (define-public r-enrichr
15812 (uri (cran-uri "enrichR" version))
15815 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15816 (properties `((upstream-name . "enrichR")))
15817 (build-system r-build-system)
15819 `(("r-httr" ,r-httr)
15820 ("r-rjson" ,r-rjson)))
15821 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15822 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15824 "This package provides an R interface to all Enrichr databases, a
15825 web-based tool for analyzing gene sets and returns any enrichment of common
15826 annotated biological functions.")
15827 (license license:gpl2+)))
15829 (define-public r-plot3d
15836 (uri (cran-uri "plot3D" version))
15839 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15840 (properties `((upstream-name . "plot3D")))
15841 (build-system r-build-system)
15842 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15843 (home-page "https://cran.r-project.org/web/packages/plot3D")
15844 (synopsis "Plot multi-dimensional data")
15846 "This package provides functions for viewing 2D and 3D data, including
15847 perspective plots, slice plots, surface plots, scatter plots, etc. It
15848 includes data sets from oceanography.")
15849 (license license:gpl3+)))
15851 (define-public r-ggfortify
15853 (name "r-ggfortify")
15858 (uri (cran-uri "ggfortify" version))
15861 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15862 (build-system r-build-system)
15864 `(("r-dplyr" ,r-dplyr)
15865 ("r-ggplot2" ,r-ggplot2)
15866 ("r-gridextra" ,r-gridextra)
15867 ("r-scales" ,r-scales)
15868 ("r-stringr" ,r-stringr)
15869 ("r-tibble" ,r-tibble)
15870 ("r-tidyr" ,r-tidyr)))
15872 `(("r-knitr" ,r-knitr)))
15873 (home-page "https://github.com/sinhrks/ggfortify")
15874 (synopsis "Data visualization tools for statistical analysis results")
15876 "This package provides unified plotting tools for statistics commonly
15877 used, such as GLM, time series, PCA families, clustering and survival
15878 analysis. The package offers a single plotting interface for these analysis
15879 results and plots in a unified style using the @code{ggplot2} package.")
15880 (license license:gpl2)))
15882 (define-public r-refmanager
15884 (name "r-refmanager")
15889 (uri (cran-uri "RefManageR" version))
15892 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15893 (properties `((upstream-name . "RefManageR")))
15894 (build-system r-build-system)
15896 `(("r-bibtex" ,r-bibtex)
15898 ("r-jsonlite" ,r-jsonlite)
15899 ("r-lubridate" ,r-lubridate)
15901 ("r-stringr" ,r-stringr)
15902 ("r-xml2" ,r-xml2)))
15903 (home-page "https://github.com/ropensci/RefManageR/")
15904 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15906 "This package provides tools for importing and working with bibliographic
15907 references. It greatly enhances the @code{bibentry} class by providing a
15908 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15909 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15910 by various formats for name lists (author by last names, translator by full
15911 names, etc.). Entries can be updated, combined, sorted, printed in a number
15912 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15913 into R and converted to @code{BibEntry} objects.")
15914 ;; Any of these licenses may be picked.
15915 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15917 (define-public r-citr
15924 (uri (cran-uri "citr" version))
15927 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15928 (build-system r-build-system)
15930 `(("r-assertthat" ,r-assertthat)
15933 ("r-miniui" ,r-miniui)
15934 ("r-refmanager" ,r-refmanager)
15935 ("r-rstudioapi" ,r-rstudioapi)
15936 ("r-shiny" ,r-shiny)
15937 ("r-shinyjs" ,r-shinyjs)
15938 ("r-yaml" ,r-yaml)))
15939 (home-page "https://github.com/crsh/citr")
15940 (synopsis "RStudio add-in to insert Markdown citations")
15942 "This package provides functions and an RStudio add-in that search a
15943 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15944 the current document.")
15945 (license license:expat)))
15947 (define-public r-xgboost
15950 (version "1.1.1.1")
15954 (uri (cran-uri "xgboost" version))
15957 "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
15958 (build-system r-build-system)
15960 `(("r-data-table" ,r-data-table)
15961 ("r-magrittr" ,r-magrittr)
15962 ("r-matrix" ,r-matrix)
15963 ("r-stringi" ,r-stringi)))
15965 `(("r-knitr" ,r-knitr)))
15966 (home-page "https://github.com/dmlc/xgboost")
15967 (synopsis "Extreme gradient boosting")
15969 "This package provides an R interface to Extreme Gradient Boosting, which
15970 is an efficient implementation of the gradient boosting framework from Chen
15971 and Guestrin (2016). The package includes efficient linear model solver and
15972 tree learning algorithms. The package can automatically do parallel
15973 computation on a single machine. It supports various objective functions,
15974 including regression, classification and ranking. The package is made to be
15975 extensible, so that users are also allowed to define their own objectives
15977 (license license:asl2.0)))
15979 (define-public r-umap
15982 (version "0.2.6.0")
15986 (uri (cran-uri "umap" version))
15989 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
15990 (build-system r-build-system)
15992 `(("r-openssl" ,r-openssl)
15994 ("r-reticulate" ,r-reticulate)
15995 ("r-rspectra" ,r-rspectra)))
15997 `(("r-knitr" ,r-knitr)))
15998 (home-page "https://github.com/tkonopka/umap")
15999 (synopsis "Uniform manifold approximation and projection")
16001 "Uniform manifold approximation and projection is a technique for
16002 dimension reduction. This package provides an interface to the UMAP algorithm
16003 in R, including a translation of the original algorithm into R.")
16004 (license license:expat)))
16006 (define-public r-uwot
16013 (uri (cran-uri "uwot" version))
16016 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16017 (build-system r-build-system)
16019 `(("r-dqrng" ,r-dqrng)
16021 ("r-irlba" ,r-irlba)
16022 ("r-matrix" ,r-matrix)
16024 ("r-rcppannoy" ,r-rcppannoy)
16025 ("r-rcppprogress" ,r-rcppprogress)
16026 ("r-rspectra" ,r-rspectra)))
16027 (home-page "https://github.com/jlmelville/uwot")
16028 (synopsis "Uniform manifold approximation and projection")
16030 "This package provides an implementation of the Uniform Manifold
16031 Approximation and Projection dimensionality reduction by McInnes et
16032 al. (2018). It also provides means to transform new data and to carry out
16033 supervised dimensionality reduction. An implementation of the related
16034 LargeVis method of Tang et al. (2016) is also provided.")
16035 (license license:gpl3)))
16037 (define-public r-kableextra
16039 (name "r-kableextra")
16044 (uri (cran-uri "kableExtra" version))
16047 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
16048 (properties `((upstream-name . "kableExtra")))
16049 (build-system r-build-system)
16051 `(("r-digest" ,r-digest)
16053 ("r-htmltools" ,r-htmltools)
16054 ("r-knitr" ,r-knitr)
16055 ("r-magrittr" ,r-magrittr)
16056 ("r-readr" ,r-readr)
16057 ("r-rmarkdown" ,r-rmarkdown)
16058 ("r-rstudioapi" ,r-rstudioapi)
16059 ("r-rvest" ,r-rvest)
16060 ("r-scales" ,r-scales)
16061 ("r-stringr" ,r-stringr)
16062 ("r-viridislite" ,r-viridislite)
16063 ("r-webshot" ,r-webshot)
16064 ("r-xml2" ,r-xml2)))
16065 (home-page "https://haozhu233.github.io/kableExtra/")
16066 (synopsis "Construct complex tables with pipe syntax")
16068 "Build complex HTML or LaTeX tables using @code{kable()} from
16069 @code{knitr} and the piping syntax from @code{magrittr}. The function
16070 @code{kable()} is a light weight table generator coming from @code{knitr}.
16071 This package simplifies the way to manipulate the HTML or LaTeX codes
16072 generated by @code{kable()} and allows users to construct complex tables and
16073 customize styles using a readable syntax.")
16074 (license license:expat)))
16076 (define-public r-glasso
16083 (uri (cran-uri "glasso" version))
16085 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16086 (build-system r-build-system)
16087 (native-inputs `(("gfortran" ,gfortran)))
16088 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16089 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16091 "This is a package for estimation of a sparse inverse covariance matrix
16092 using a lasso (L1) penalty. Facilities are provided for estimates along a
16093 path of values for the regularization parameter.")
16094 (license license:gpl2)))
16096 (define-public r-rhpcblasctl
16098 (name "r-rhpcblasctl")
16099 (version "0.20-137")
16103 (uri (cran-uri "RhpcBLASctl" version))
16106 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16107 (properties `((upstream-name . "RhpcBLASctl")))
16108 (build-system r-build-system)
16109 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16110 (synopsis "Control the number of threads on BLAS")
16112 "This package allows you to control the number of threads the BLAS
16113 library uses. It is also possible to control the number of threads in
16115 (license license:agpl3+)))
16117 (define-public r-lda
16124 (uri (cran-uri "lda" version))
16127 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16128 (build-system r-build-system)
16129 (home-page "https://cran.r-project.org/web/packages/lda/")
16130 (synopsis "Collapsed Gibbs sampling methods for topic models")
16132 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16133 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16134 mixed-membership stochastic blockmodel. Inference for all of these models is
16135 implemented via a fast collapsed Gibbs sampler written in C. Utility
16136 functions for reading/writing data typically used in topic models, as well as
16137 tools for examining posterior distributions are also included.")
16138 ;; Any version of the LGPL
16139 (license license:lgpl3+)))
16141 (define-public r-rann-l1
16148 (uri (cran-uri "RANN.L1" version))
16151 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16152 (properties `((upstream-name . "RANN.L1")))
16153 (build-system r-build-system)
16154 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16155 (synopsis "Fast nearest neighbour search using L1 metric")
16157 "This package provides tools to find the k nearest neighbours for every
16158 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16159 library. There is support for approximate as well as exact searches, fixed
16160 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16161 computed using the L1 (Manhattan, taxicab) metric.")
16162 (license license:gpl3+)))
16164 (define-public r-leiden
16171 (uri (cran-uri "leiden" version))
16174 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16175 (properties `((upstream-name . "leiden")))
16176 (build-system r-build-system)
16178 `(("r-igraph" ,r-igraph)
16179 ("r-matrix" ,r-matrix)
16180 ("r-reticulate" ,r-reticulate)))
16181 (home-page "https://github.com/TomKellyGenetics/leiden")
16182 (synopsis "R implementation of Leiden clustering algorithm")
16184 "This package implements the Python @code{leidenalg} module to be called
16185 in R. It enables clustering using the Leiden algorithm for partitioning a
16186 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16187 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16188 (license license:gpl3)))
16190 (define-public r-patchwork
16192 (name "r-patchwork")
16197 (uri (cran-uri "patchwork" version))
16200 "0qrwbcswh7ylrmghi17k6wk7w51cz6mcmvcyyd41hy3m2ywmkywb"))))
16201 (build-system r-build-system)
16203 `(("r-ggplot2" ,r-ggplot2)
16204 ("r-gtable" ,r-gtable)))
16206 `(("r-knitr" ,r-knitr)))
16207 (home-page "https://github.com/thomasp85/patchwork")
16208 (synopsis "Compose ggplot2 plots")
16210 "The @code{ggplot2} package provides a strong API for sequentially
16211 building up a plot, but does not concern itself with composition of multiple
16212 plots. Patchwork is a package that expands the API to allow for arbitrarily
16213 complex composition of plots by providing mathmatical operators for combining
16215 (license license:expat)))
16217 (define-public r-liger
16224 (uri (git-reference
16225 (url "https://github.com/MacoskoLab/liger.git")
16226 (commit (string-append "v" version))))
16227 (file-name (git-file-name name version))
16230 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16231 (modules '((guix build utils)))
16234 (delete-file "inst/java/ModularityOptimizer.jar")
16236 (build-system r-build-system)
16239 (modify-phases %standard-phases
16240 (add-after 'unpack 'build-java-part
16241 (lambda* (#:key inputs #:allow-other-keys)
16242 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16243 (for-each (lambda (file) (invoke "javac" file))
16244 (find-files "." "\\.java$"))
16245 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16246 (find-files "." "\\.class$"))
16249 `(("r-cowplot" ,r-cowplot)
16250 ("r-dosnow" ,r-dosnow)
16251 ("r-dplyr" ,r-dplyr)
16253 ("r-foreach" ,r-foreach)
16254 ("r-ggplot2" ,r-ggplot2)
16255 ("r-ggrepel" ,r-ggrepel)
16256 ("r-hmisc" ,r-hmisc)
16258 ("r-irlba" ,r-irlba)
16259 ("r-matrix" ,r-matrix)
16260 ("r-mclust" ,r-mclust)
16261 ("r-patchwork" ,r-patchwork)
16263 ("r-rann-l1" ,r-rann-l1)
16265 ("r-rcpparmadillo" ,r-rcpparmadillo)
16266 ("r-riverplot" ,r-riverplot)
16267 ("r-rtsne" ,r-rtsne)
16268 ("r-snow" ,r-snow)))
16270 `(("jdk" ,icedtea "jdk")
16271 ;; See https://github.com/MacoskoLab/liger/issues/96
16272 ;; The optimizer is released under the Expat license.
16276 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16279 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16281 ("r-knitr" ,r-knitr))) ; for vignettes
16282 (home-page "https://github.com/MacoskoLab/liger")
16283 (synopsis "Integrate and analyze multiple single-cell datasets")
16285 "LIGER is a package for integrating and analyzing multiple single-cell
16286 datasets, developed and maintained by the Macosko lab. It relies on
16287 integrative non-negative matrix factorization to identify shared and
16288 dataset-specific factors.")
16289 (license license:gpl3)))
16291 (define-public r-harmony
16298 (uri (git-reference
16299 (url "https://github.com/immunogenomics/harmony")
16301 (file-name (git-file-name name version))
16304 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16305 (modules '((guix build utils)))
16308 (for-each delete-file '("config.status" "configure"))
16310 (build-system r-build-system)
16312 `(("r-cowplot" ,r-cowplot)
16313 ("r-dplyr" ,r-dplyr)
16314 ("r-ggplot2" ,r-ggplot2)
16315 ("r-irlba" ,r-irlba)
16316 ("r-matrix" ,r-matrix)
16318 ("r-rcpparmadillo" ,r-rcpparmadillo)
16319 ("r-rcppprogress" ,r-rcppprogress)
16320 ("r-rlang" ,r-rlang)
16321 ("r-tibble" ,r-tibble)
16322 ("r-tidyr" ,r-tidyr)))
16324 `(("autoconf" ,autoconf)))
16325 (home-page "https://github.com/immunogenomics/harmony")
16326 (synopsis "Integration of single cell sequencing data")
16328 "This package provides an implementation of the Harmony algorithm for
16329 single cell integration, described in Korsunsky et al
16330 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16331 function and interfaces to external frameworks.")
16332 (license license:gpl3)))
16334 (define-public r-covr
16341 (uri (cran-uri "covr" version))
16343 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16344 (properties `((upstream-name . "covr")))
16345 (build-system r-build-system)
16347 `(("r-crayon" ,r-crayon)
16348 ("r-digest" ,r-digest)
16350 ("r-jsonlite" ,r-jsonlite)
16352 ("r-withr" ,r-withr)
16353 ("r-yaml" ,r-yaml)))
16355 `(("r-knitr" ,r-knitr))) ; for vignettes
16356 (home-page "https://github.com/r-lib/covr")
16357 (synopsis "Test coverage for R packages")
16359 "Thisp package enables you to track and report code coverage for your
16360 package and (optionally) upload the results to a coverage service. Code
16361 coverage is a measure of the amount of code being exercised by a set of tests.
16362 It is an indirect measure of test quality and completeness. This package is
16363 compatible with any testing methodology or framework and tracks coverage of
16364 both R code and compiled C/C++/FORTRAN code.")
16365 (license license:gpl3)))
16367 (define-public r-systemfonts
16369 (name "r-systemfonts")
16374 (uri (cran-uri "systemfonts" version))
16377 "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
16378 (properties `((upstream-name . "systemfonts")))
16379 (build-system r-build-system)
16381 `(("fontconfig" ,fontconfig)
16384 `(("pkg-config" ,pkg-config)
16385 ("r-knitr" ,r-knitr)))
16386 (home-page "https://github.com/r-lib/systemfonts")
16387 (synopsis "System native font finding")
16389 "This package provides system native access to the font catalogue. As
16390 font handling varies between systems it is difficult to correctly locate
16391 installed fonts across different operating systems. The 'systemfonts' package
16392 provides bindings to the native libraries for finding font files that can then
16393 be used further by e.g. graphic devices.")
16394 (license license:expat)))
16396 (define-public r-graphlayouts
16398 (name "r-graphlayouts")
16403 (uri (cran-uri "graphlayouts" version))
16406 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16407 (properties `((upstream-name . "graphlayouts")))
16408 (build-system r-build-system)
16410 `(("r-igraph" ,r-igraph)
16412 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16413 (home-page "https://github.com/schochastics/graphlayouts")
16414 (synopsis "Additional layout algorithms for network visualizations")
16416 "This package provides several layout algorithms to visualize networks
16417 which are not part of the igraph library. Most are based on the concept of
16418 stress majorization by Gansner et al. (2004)
16419 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16420 emphasize hidden group structures in networks or focus on specific nodes.")
16421 (license license:expat)))
16423 (define-public r-tidygraph
16425 (name "r-tidygraph")
16430 (uri (cran-uri "tidygraph" version))
16433 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16434 (properties `((upstream-name . "tidygraph")))
16435 (build-system r-build-system)
16437 `(("r-dplyr" ,r-dplyr)
16438 ("r-igraph" ,r-igraph)
16439 ("r-magrittr" ,r-magrittr)
16440 ("r-pillar" ,r-pillar)
16443 ("r-rlang" ,r-rlang)
16444 ("r-tibble" ,r-tibble)
16445 ("r-tidyr" ,r-tidyr)))
16446 (home-page "https://github.com/thomasp85/tidygraph")
16447 (synopsis "Tidy API for graph manipulation")
16449 "This package provides a graph implementation that can be thought of as
16450 two tidy data frames describing node and edge data respectively. It provides
16451 an approach to manipulate these two virtual data frames using the API defined
16452 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16453 common graph algorithms.")
16454 (license license:expat)))
16456 (define-public r-soupx
16457 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16461 (version (git-version "0.3.1" revision commit))
16465 (uri (git-reference
16466 (url "https://github.com/constantAmateur/SoupX")
16468 (file-name (git-file-name name version))
16471 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16472 (properties `((upstream-name . "SoupX")))
16473 (build-system r-build-system)
16475 `(("r-ggplot2" ,r-ggplot2)
16476 ("r-matrix" ,r-matrix)
16477 ("r-seurat" ,r-seurat)))
16478 (home-page "https://github.com/constantAmateur/SoupX")
16479 (synopsis "Single cell mRNA Soup eXterminator")
16481 "This package provides a package for quantifying, profiling and
16482 removing cell free mRNA contamination (the \"soup\") from droplet based single
16483 cell RNA-seq experiments.")
16484 (license license:gpl2))))
16486 (define-public r-assertr
16493 (uri (cran-uri "assertr" version))
16496 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16497 (build-system r-build-system)
16499 `(("r-dplyr" ,r-dplyr)
16501 ("r-rlang" ,r-rlang)))
16503 `(("r-knitr" ,r-knitr))) ; needed for vignette
16504 (home-page "https://github.com/ropensci/assertr")
16505 (synopsis "Assertive programming for R analysis pipelines")
16507 "This package provides functionality to assert conditions that have to be
16508 met so that errors in data used in analysis pipelines can fail quickly. It is
16509 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16511 (license license:expat)))
16513 (define-public r-parameters
16515 (name "r-parameters")
16520 (uri (cran-uri "parameters" version))
16523 "1cmb2hc6f4qdx9aj586zhllckzs6s5sznbqrywvgmhp6a2saaqax"))))
16524 (properties `((upstream-name . "parameters")))
16525 (build-system r-build-system)
16527 `(("r-bayestestr" ,r-bayestestr)
16528 ("r-insight" ,r-insight)))
16530 `(("r-knitr" ,r-knitr)))
16531 (home-page "https://cran.r-project.org/web/packages/parameters")
16532 (synopsis "Processing of model parameters")
16534 "This package provides utilities for processing the parameters of various
16535 statistical models. Beyond computing p values, CIs, and other indices for a
16536 wide variety of models, this package implements features like standardization
16537 or bootstrapping of parameters and models, feature reduction (feature
16538 extraction and variable selection) as well as conversion between indices of
16540 (license license:gpl3)))
16542 (define-public r-rgdal
16549 (uri (cran-uri "rgdal" version))
16551 (base32 "02z7rhpizzmymiqpi90nm15bjdz0411bqlavlk0lhwxb42ilhif6"))))
16552 (properties `((upstream-name . "rgdal")))
16553 (build-system r-build-system)
16561 `(("pkg-config" ,pkg-config)
16562 ("r-knitr" ,r-knitr)))
16563 (home-page "http://rgdal.r-forge.r-project.org")
16564 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16566 "This package provides bindings to the Geospatial Data Abstraction
16567 Library (GDAL) and access to projection/transformation operations from the
16569 (license license:gpl2+)))
16571 (define-public r-insol
16578 (uri (cran-uri "insol" version))
16581 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16582 (properties `((upstream-name . "insol")))
16583 (build-system r-build-system)
16585 `(("r-raster" ,r-raster)))
16587 `(("gfortran" ,gfortran)))
16588 (home-page "https://meteoexploration.com/R/insol/index.html")
16589 (synopsis "Tools for calculating solar radiation")
16591 "This package provides functions to compute insolation on tilted
16592 surfaces, computes atmospheric transmittance and related parameters such as:
16593 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16594 time, vector in the direction of the sun, vector normal to surface, and some
16595 atmospheric physics.")
16596 (license license:gpl2+)))
16598 (define-public r-lifecycle
16600 (name "r-lifecycle")
16605 (uri (cran-uri "lifecycle" version))
16608 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16609 (properties `((upstream-name . "lifecycle")))
16610 (build-system r-build-system)
16612 `(("r-glue" ,r-glue)
16613 ("r-rlang" ,r-rlang)))
16615 `(("r-knitr" ,r-knitr))) ; for vignettes
16616 (home-page "https://github.com/r-lib/lifecycle")
16617 (synopsis "Manage the life cycle of your package functions")
16619 "Manage the life cycle of your exported functions with shared
16620 conventions, documentation badges, and non-invasive deprecation warnings. The
16621 lifecycle package defines four development stages (experimental, maturing,
16622 stable, and questioning) and three deprecation stages (soft-deprecated,
16623 deprecated, and defunct). It makes it easy to insert badges corresponding to
16624 these stages in your documentation. Usage of deprecated functions are
16625 signalled with increasing levels of non-invasive verbosity.")
16626 (license license:gpl3)))
16628 (define-public r-assertable
16630 (name "r-assertable")
16635 (uri (cran-uri "assertable" version))
16638 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16639 (build-system r-build-system)
16641 `(("r-data-table" ,r-data-table)))
16642 (home-page "https://cran.r-project.org/web/packages/assertable/")
16643 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16644 (description "This package provides simple, flexible assertions on
16645 data.frame or data.table objects with verbose output for vetting. While other
16646 assertion packages apply towards more general use-cases, @code{assertable} is
16647 tailored towards tabular data. It includes functions to check variable names
16648 and values, whether the dataset contains all combinations of a given set of
16649 unique identifiers, and whether it is a certain length. In addition,
16650 @code{assertable} includes utility functions to check the existence of target
16651 files and to efficiently import multiple tabular data files into one
16653 (license license:gpl3)))
16655 (define-public r-quadprog
16657 (name "r-quadprog")
16662 (uri (cran-uri "quadprog" version))
16664 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16665 (build-system r-build-system)
16667 `(("gfortran" ,gfortran)))
16668 (home-page "https://cran.r-project.org/web/packages/quadprog")
16669 (synopsis "Functions to solve quadratic programming problems")
16671 "This package contains routines and documentation for solving quadratic
16672 programming problems.")
16673 (license license:gpl3+)))
16675 (define-public r-desolve
16682 (uri (cran-uri "deSolve" version))
16684 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16685 (properties `((upstream-name . "deSolve")))
16686 (build-system r-build-system)
16688 `(("gfortran" ,gfortran)))
16689 (home-page "https://desolve.r-forge.r-project.org/")
16690 (synopsis "Solvers for initial value problems of differential equations")
16691 (description "This package provides functions that solve initial value
16692 problems of a system of first-order @dfn{ordinary differential
16693 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16694 @dfn{differential algebraic equations} (DAE), and of delay differential
16695 equations. The functions provide an interface to the FORTRAN functions
16696 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16697 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16698 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16699 time steps. The package contains routines designed for solving ODEs resulting
16700 from 1-D, 2-D and 3-D partial differential equations that have been converted
16701 to ODEs by numerical differencing.")
16702 (license license:gpl2+)))
16704 (define-public r-pracma
16710 (uri (cran-uri "pracma" version))
16712 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16713 (build-system r-build-system)
16714 (home-page "https://cran.r-project.org/web/packages/pracma/")
16715 (synopsis "Practical numerical math functions")
16716 (description "This package provides functions for numerical analysis and
16717 linear algebra, numerical optimization, differential equations, plus some
16718 special functions. It uses Matlab function names where appropriate to simplify
16720 (license license:gpl3+)))
16722 (define-public r-subplex
16729 (uri (cran-uri "subplex" version))
16732 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16733 (build-system r-build-system)
16735 `(("gfortran" ,gfortran)))
16736 (home-page "https://cran.r-project.org/web/packages/subplex")
16737 (synopsis "Unconstrained optimization using the subplex algorithm")
16739 "This package implements the Subplex optimization algorithm.
16740 It solves unconstrained optimization problems using a simplex method on
16741 subspaces. The method is well suited for optimizing objective functions that
16742 are noisy or are discontinuous at the solution.")
16743 (license license:gpl3+)))
16745 (define-public r-txtplot
16752 (uri (cran-uri "txtplot" version))
16755 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16756 (build-system r-build-system)
16757 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16758 (synopsis "Text-based plotting")
16759 (description "This package provides functions to produce rudimentary ASCII
16760 graphics directly in the terminal window. This package provides a basic
16761 plotting function (and equivalents of curve, density, acf and barplot) as well
16762 as a boxplot function.")
16763 (license license:lgpl3+)))
16765 (define-public r-bio3d
16772 (uri (cran-uri "bio3d" version))
16775 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16776 (properties `((upstream-name . "bio3d")))
16777 (build-system r-build-system)
16778 (inputs `(("zlib" ,zlib)))
16779 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16780 (home-page "http://thegrantlab.org/bio3d/")
16781 (synopsis "Biological structure analysis")
16783 "This package provides utilities to process, organize and explore protein
16784 structure, sequence and dynamics data. Features include the ability to read
16785 and write structure, sequence and dynamic trajectory data, perform sequence
16786 and structure database searches, data summaries, atom selection, alignment,
16787 superposition, rigid core identification, clustering, torsion analysis,
16788 distance matrix analysis, structure and sequence conservation analysis, normal
16789 mode analysis, principal component analysis of heterogeneous structure data,
16790 and correlation network analysis from normal mode and molecular dynamics data.
16791 In addition, various utility functions are provided to enable the statistical
16792 and graphical power of the R environment to work with biological sequence and
16794 (license license:gpl2+)))
16796 (define-public r-bios2cor
16798 (name "r-bios2cor")
16803 (uri (cran-uri "Bios2cor" version))
16806 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16807 (properties `((upstream-name . "Bios2cor")))
16808 (build-system r-build-system)
16810 `(("r-bigmemory" ,r-bigmemory)
16811 ("r-bio3d" ,r-bio3d)
16812 ("r-circular" ,r-circular)
16813 ("r-igraph" ,r-igraph)))
16814 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16815 (synopsis "From biological sequences and simulations to correlation analysis")
16817 "This package provides utilities for computation and analysis of
16818 correlation/covariation in multiple sequence alignments and in side chain
16819 motions during molecular dynamics simulations. Features include the
16820 computation of correlation/covariation scores using a variety of scoring
16821 functions between either sequence positions in alignments or side chain
16822 dihedral angles in molecular dynamics simulations and utilities to analyze the
16823 correlation/covariation matrix through a variety of tools including network
16824 representation and principal components analysis. In addition, several
16825 utility functions are based on the R graphical environment to provide friendly
16826 tools for help in data interpretation.")
16827 (license license:gpl2+)))
16829 ;; This package includes minified JavaScript files. When upgrading please
16830 ;; check that there are no new minified JavaScript files.
16831 (define-public r-networkd3
16833 (name "r-networkd3")
16838 (uri (cran-uri "networkD3" version))
16841 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16844 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16846 (properties `((upstream-name . "networkD3")))
16847 (build-system r-build-system)
16849 `(#:modules ((guix build utils)
16850 (guix build r-build-system)
16854 (modify-phases %standard-phases
16855 (add-after 'unpack 'process-javascript
16856 (lambda* (#:key inputs #:allow-other-keys)
16857 (with-directory-excursion "inst/htmlwidgets/lib/"
16861 `((,(assoc-ref inputs "d3.v4.js")
16862 "d3-4.5.0/d3.min.js"))))
16863 (lambda (sources targets)
16864 (for-each (lambda (source target)
16865 (format #t "Processing ~a --> ~a~%"
16867 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16868 (call-with-output-file target
16870 (dump-port minified port)))))
16871 sources targets))))
16874 `(("uglify-js" ,uglify-js)
16875 ;; NOTE: Make sure that this version of d3 is still valid when
16876 ;; upgrading the package.
16880 (uri "https://d3js.org/d3.v4.js")
16883 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16885 `(("r-htmlwidgets" ,r-htmlwidgets)
16886 ("r-igraph" ,r-igraph)
16887 ("r-magrittr" ,r-magrittr)))
16888 (home-page "https://cran.r-project.org/package=networkD3")
16889 (synopsis "D3 JavaScript network graphs from R")
16891 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16893 (license license:gpl3+)))
16895 (define-public r-aasea
16902 (uri (cran-uri "aaSEA" version))
16905 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16906 (properties `((upstream-name . "aaSEA")))
16907 (build-system r-build-system)
16909 `(("r-bios2cor" ,r-bios2cor)
16911 ("r-hmisc" ,r-hmisc)
16912 ("r-magrittr" ,r-magrittr)
16913 ("r-networkd3" ,r-networkd3)
16914 ("r-plotly" ,r-plotly)
16915 ("r-seqinr" ,r-seqinr)
16916 ("r-shiny" ,r-shiny)
16917 ("r-shinydashboard" ,r-shinydashboard)))
16918 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16919 (synopsis "Amino acid substitution effect analyzer")
16921 "Given a protein multiple sequence alignment, it is a daunting task to
16922 assess the effects of substitutions along sequence length. The aaSEA package
16923 is intended to help researchers to rapidly analyze property changes caused by
16924 single, multiple and correlated amino acid substitutions in proteins.")
16925 (license license:gpl3)))
16927 (define-public r-abacus
16934 (uri (cran-uri "ABACUS" version))
16937 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16938 (properties `((upstream-name . "ABACUS")))
16939 (build-system r-build-system)
16941 `(("r-ggplot2" ,r-ggplot2)
16942 ("r-shiny" ,r-shiny)))
16943 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16944 (synopsis "Apps-based activities for communicating and understanding statistics")
16946 "This package provides a set of Shiny apps for effective communication
16947 and understanding in statistics. The current version includes properties of
16948 normal distribution, properties of sampling distribution, one-sample z and t
16949 tests, two samples independent (unpaired) t test and analysis of variance.")
16950 (license license:gpl3)))
16952 (define-public r-abc-rap
16959 (uri (cran-uri "ABC.RAP" version))
16962 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16963 (properties `((upstream-name . "ABC.RAP")))
16964 (build-system r-build-system)
16965 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16966 (synopsis "Array-based CpG region analysis pipeline")
16968 "This package aims to identify candidate genes that are differentially
16969 methylated between cases and controls. It applies Student's t-test and delta
16970 beta analysis to identify candidate genes containing multiple CpG sites.")
16971 (license license:gpl3)))
16973 (define-public r-abcadm
16980 (uri (cran-uri "abcADM" version))
16983 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16984 (properties `((upstream-name . "abcADM")))
16985 (build-system r-build-system)
16988 ("r-rcpp" ,r-rcpp)))
16989 (home-page "https://cran.r-project.org/web/packages/abcADM/")
16990 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
16992 "This package provides tools to estimate parameters of accumulated
16993 damage (load duration) models based on failure time data under a Bayesian
16994 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
16995 long-term reliability under stochastic load profiles.")
16996 (license license:gpl3)))
16998 (define-public r-rglpk
17005 (uri (cran-uri "Rglpk" version))
17008 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17009 (properties `((upstream-name . "Rglpk")))
17010 (build-system r-build-system)
17012 `(("r-slam" ,r-slam)))
17015 (home-page "https://r-forge.r-project.org/projects/rglp/")
17016 (synopsis "R interface to the GNU Linear Programming Kit")
17018 "This package provides an R interface to the GNU Linear Programming Kit,
17019 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17020 integer linear programming} (MILP) and other related problems.")
17022 (license (list license:gpl2 license:gpl3))))
17024 (define-public r-abcdefba
17026 (name "r-abcdefba")
17031 (uri (cran-uri "abcdeFBA" version))
17034 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17035 (properties `((upstream-name . "abcdeFBA")))
17036 (build-system r-build-system)
17038 `(("r-corrplot" ,r-corrplot)
17039 ("r-lattice" ,r-lattice)
17041 ("r-rglpk" ,r-rglpk)))
17042 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17043 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17045 "This package provides functions for Constraint Based Simulation using
17046 Flux Balance Analysis and informative analysis of the data generated during
17048 (license license:gpl2)))
17050 (define-public r-abcrlda
17057 (uri (cran-uri "abcrlda" version))
17060 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17061 (properties `((upstream-name . "abcrlda")))
17062 (build-system r-build-system)
17063 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17064 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17066 "This package offers methods to perform @dfn{asymptotically
17067 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17068 cost-sensitive binary classification. The bias-correction is an estimate of
17069 the bias term added to regularized discriminant analysis that minimizes the
17071 (license license:gpl3)))
17073 (define-public r-abemus
17080 (uri (cran-uri "abemus" version))
17083 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17084 (properties `((upstream-name . "abemus")))
17085 (build-system r-build-system)
17087 `(("r-data-table" ,r-data-table)))
17088 (home-page "https://cran.r-project.org/web/packages/abemus/")
17089 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17091 "This package provides an implementation of @dfn{Adaptive Base Error
17092 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17093 platform-specific genetic knowledge and empirical signal to readily detect and
17094 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17095 cell free DNA} (cfDNA).")
17096 (license license:gpl3)))
17098 ;; This package includes minified JavaScript files. When upgrading please
17099 ;; check that there are no new minified JavaScript files.
17100 (define-public r-rintrojs
17102 (name "r-rintrojs")
17107 (uri (cran-uri "rintrojs" version))
17110 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17111 (properties `((upstream-name . "rintrojs")))
17112 (build-system r-build-system)
17114 `(#:modules ((guix build utils)
17115 (guix build r-build-system)
17119 (modify-phases %standard-phases
17120 (add-after 'unpack 'process-javascript
17121 (lambda* (#:key inputs #:allow-other-keys)
17122 (with-directory-excursion "inst/javascript/introjs/"
17126 `((,(assoc-ref inputs "intro.js")
17128 (lambda (sources targets)
17129 (for-each (lambda (source target)
17130 (format #t "Processing ~a --> ~a~%"
17132 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17133 (call-with-output-file target
17135 (dump-port minified port)))))
17136 sources targets))))
17139 `(("uglify-js" ,uglify-js)
17143 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17146 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17148 `(("r-jsonlite" ,r-jsonlite)
17149 ("r-shiny" ,r-shiny)))
17150 (home-page "https://github.com/carlganz/rintrojs")
17151 (synopsis "Wrapper for the Intro.js library")
17153 "This package provides a wrapper for the @url{http://www.introjs.com,
17154 Intro.js} library. This package makes it easy to include step-by-step
17155 introductions, and clickable hints in a Shiny application. It supports both
17156 static introductions in the UI, and programmatic introductions from the
17158 (license license:agpl3+)))
17160 (define-public r-sysfonts
17162 (name "r-sysfonts")
17167 (uri (cran-uri "sysfonts" version))
17170 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17171 (properties `((upstream-name . "sysfonts")))
17172 (build-system r-build-system)
17174 `(("freetype" ,freetype)
17178 `(("pkg-config" ,pkg-config)))
17179 (home-page "https://github.com/yixuan/sysfonts")
17180 (synopsis "Loading fonts into R")
17182 "This is a package to simplify loading of system fonts and Google Fonts
17183 into R, in order to support other packages.")
17184 (license license:gpl2)))
17186 (define-public r-showtextdb
17188 (name "r-showtextdb")
17193 (uri (cran-uri "showtextdb" version))
17196 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17197 (properties `((upstream-name . "showtextdb")))
17198 (build-system r-build-system)
17200 `(("r-sysfonts" ,r-sysfonts)))
17201 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17202 (synopsis "Font files for the 'showtext' package")
17204 "This package provides font files that can be used by the @code{showtext}
17206 (license license:asl2.0)))
17208 (define-public r-showtext
17210 (name "r-showtext")
17215 (uri (cran-uri "showtext" version))
17218 "1n1cd9f4zrv45k5953akclqh1jh7fy122dqkgmbfi5h122v6p2h0"))))
17219 (properties `((upstream-name . "showtext")))
17220 (build-system r-build-system)
17222 `(("freetype" ,freetype)
17226 `(("r-showtextdb" ,r-showtextdb)
17227 ("r-sysfonts" ,r-sysfonts)))
17229 `(("pkg-config" ,pkg-config)
17230 ("r-knitr" ,r-knitr)))
17231 (home-page "https://github.com/yixuan/showtext")
17232 (synopsis "Using fonts more easily in R graphs")
17234 "This package aims to make it easy to use various types of
17235 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17236 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17237 will be converted into polygons or raster images, hence after the plot has
17238 been created, it no longer relies on the font files. No external software
17239 such as Ghostscript is needed to use this package.")
17240 (license license:asl2.0)))
17242 (define-public r-emojifont
17244 (name "r-emojifont")
17249 (uri (cran-uri "emojifont" version))
17252 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17253 (properties `((upstream-name . "emojifont")))
17254 (build-system r-build-system)
17256 `(("r-ggplot2" ,r-ggplot2)
17257 ("r-proto" ,r-proto)
17258 ("r-showtext" ,r-showtext)
17259 ("r-sysfonts" ,r-sysfonts)))
17260 (home-page "https://guangchuangyu.github.io/emojifont")
17261 (synopsis "Emoji and Font Awesome in R graphics")
17263 "This package enables the use of emoji and the Font Awesome glyphs in
17264 both base and ggplot2 graphics.")
17265 (license license:artistic2.0)))
17267 (define-public r-abstractr
17269 (name "r-abstractr")
17274 (uri (cran-uri "abstractr" version))
17277 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17278 (properties `((upstream-name . "abstractr")))
17279 (build-system r-build-system)
17281 `(("r-colourpicker" ,r-colourpicker)
17282 ("r-emojifont" ,r-emojifont)
17283 ("r-ggplot2" ,r-ggplot2)
17284 ("r-gridextra" ,r-gridextra)
17285 ("r-rintrojs" ,r-rintrojs)
17286 ("r-shiny" ,r-shiny)
17287 ("r-shinythemes" ,r-shinythemes)))
17288 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17289 (synopsis "R-Shiny application for creating visual abstracts")
17291 "This package provides an R Shiny application to create visual abstracts
17292 for original research. A variety of user defined options and formatting are
17294 (license license:gpl3)))
17296 (define-public r-qgam
17303 (uri (cran-uri "qgam" version))
17306 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17307 (properties `((upstream-name . "qgam")))
17308 (build-system r-build-system)
17310 `(("r-doparallel" ,r-doparallel)
17313 ("r-shiny" ,r-shiny)))
17314 (native-inputs `(("r-knitr" ,r-knitr)))
17315 (home-page "https://cran.r-project.org/web/packages/qgam/")
17316 (synopsis "Smooth additive quantile regression models")
17318 "This package provides smooth additive quantile regression models, fitted
17319 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17320 the smoothing parameters are estimated automatically by marginal loss
17321 minimization, while the regression coefficients are estimated using either
17322 PIRLS or Newton algorithm. The learning rate is determined so that the
17323 Bayesian credible intervals of the estimated effects have approximately the
17324 correct coverage. The main function is @code{qgam()} which is similar to
17325 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17326 regression models.")
17327 (license license:gpl2+)))
17329 (define-public r-abtest
17336 (uri (cran-uri "abtest" version))
17339 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17340 (properties `((upstream-name . "abtest")))
17341 (build-system r-build-system)
17343 `(("r-matrix" ,r-matrix)
17344 ("r-mvtnorm" ,r-mvtnorm)
17345 ("r-plotrix" ,r-plotrix)
17347 ("r-rcolorbrewer" ,r-rcolorbrewer)
17350 ("r-truncnorm" ,r-truncnorm)))
17351 (home-page "https://cran.r-project.org/web/packages/abtest/")
17352 (synopsis "Bayesian A/B testing")
17354 "This package provides functions for Bayesian A/B testing including prior
17355 elicitation options based on Kass and Vaidyanathan (1992)
17356 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17357 (license license:gpl2+)))
17359 (define-public r-accept
17366 (uri (cran-uri "accept" version))
17369 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17370 (properties `((upstream-name . "accept")))
17371 (build-system r-build-system)
17373 `(("r-dplyr" ,r-dplyr)
17374 ("r-extrafont" ,r-extrafont)
17376 ("r-plotly" ,r-plotly)
17377 ("r-stringr" ,r-stringr)
17378 ("r-viridis" ,r-viridis)))
17379 (home-page "https://cran.r-project.org/web/packages/accept/")
17380 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17382 "This package allows clinicians to predict the rate and severity of
17383 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17384 Disease} (COPD) patients, based on the clinical prediction model published in
17385 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17386 (license license:gpl3)))
17388 (define-public r-smpracticals
17390 (name "r-smpracticals")
17395 (uri (cran-uri "SMPracticals" version))
17398 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17399 (properties `((upstream-name . "SMPracticals")))
17400 (build-system r-build-system)
17402 `(("r-ellipse" ,r-ellipse)
17405 ("r-survival" ,r-survival)))
17406 (home-page "http://statwww.epfl.ch/davison/SM/")
17407 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17409 "This package contains the datasets and a few functions for use with the
17410 practicals outlined in Appendix A of the book Statistical Models (Davison,
17411 2003, Cambridge University Press). The practicals themselves can be found at
17412 @url{http://statwww.epfl.ch/davison/SM/}.")
17413 (license license:gpl2+)))
17415 (define-public r-fgui
17422 (uri (cran-uri "fgui" version))
17425 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17426 (properties `((upstream-name . "fgui")))
17427 (build-system r-build-system)
17429 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17430 (synopsis "Create GUI for R functions")
17432 "Rapidly create a GUI for a function you created by automatically
17433 creating widgets for arguments of the function. This package automatically
17434 parses help routines for context-sensitive help to these arguments. The
17435 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17436 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17437 incorporated into the interface for greater customization for the more
17439 ;; Any version of the GPL.
17440 (license (list license:gpl2+ license:gpl3+))))
17442 (define-public r-tcltk2
17449 (uri (cran-uri "tcltk2" version))
17452 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17453 (properties `((upstream-name . "tcltk2")))
17454 (build-system r-build-system)
17458 (home-page "https://www.sciviews.org/SciViews-R")
17459 (synopsis "Tcl/Tk additions")
17461 "This package provides a series of additional Tcl commands and Tk widgets
17462 with style and various functions to supplement the tcltk package")
17463 (license license:lgpl3)))
17465 (define-public r-accrual
17472 (uri (cran-uri "accrual" version))
17475 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17476 (properties `((upstream-name . "accrual")))
17477 (build-system r-build-system)
17479 `(("r-fgui" ,r-fgui)
17480 ("r-smpracticals" ,r-smpracticals)
17481 ("r-tcltk2" ,r-tcltk2)))
17482 (home-page "https://cran.r-project.org/web/packages/accrual/")
17483 (synopsis "Bayesian accrual prediction")
17485 "Subject recruitment for medical research is challenging. Slow patient
17486 accrual leads to delay in research. Accrual monitoring during the process of
17487 recruitment is critical. Researchers need reliable tools to manage the
17488 accrual rate. This package provides an implementation of a Bayesian method
17489 that integrates researcher's experience on previous trials and data from the
17490 current study, providing reliable prediction on accrual rate for clinical
17491 studies. It provides functions for Bayesian accrual prediction which can be
17492 easily used by statisticians and clinical researchers.")
17493 (license license:gpl2)))
17495 (define-public r-accrued
17502 (uri (cran-uri "accrued" version))
17505 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17506 (properties `((upstream-name . "accrued")))
17507 (build-system r-build-system)
17508 (home-page "https://cran.r-project.org/web/packages/accrued/")
17509 (synopsis "Data quality visualization tools for partially accruing data")
17511 "This is a package for visualizing data quality of partially accruing
17513 (license license:gpl3)))
17515 (define-public r-mda
17522 (uri (cran-uri "mda" version))
17525 "01pjrz9xv1rx78ndy0x9dc32ws8brcvwyb500m1f0dqd42375vmx"))))
17526 (properties `((upstream-name . "mda")))
17527 (build-system r-build-system)
17528 (propagated-inputs `(("r-class" ,r-class)))
17529 (native-inputs `(("gfortran" ,gfortran)))
17530 (home-page "https://cran.r-project.org/web/packages/mda/")
17531 (synopsis "Mixture and flexible discriminant analysis")
17533 "This is a package for mixture and flexible discriminant analysis,
17534 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17535 (license license:gpl2)))
17537 (define-public r-elasticnet
17539 (name "r-elasticnet")
17544 (uri (cran-uri "elasticnet" version))
17547 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17548 (properties `((upstream-name . "elasticnet")))
17549 (build-system r-build-system)
17551 `(("r-lars" ,r-lars)))
17552 (home-page "http://users.stat.umn.edu/~zouxx019/")
17553 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17555 "This package provides functions for fitting the entire solution path of
17556 the Elastic-Net and also provides functions for estimating sparse Principal
17557 Components. The Lasso solution paths can be computed by the same function.")
17558 (license license:gpl2+)))
17560 (define-public r-sparselda
17562 (name "r-sparselda")
17567 (uri (cran-uri "sparseLDA" version))
17570 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17571 (properties `((upstream-name . "sparseLDA")))
17572 (build-system r-build-system)
17574 `(("r-elasticnet" ,r-elasticnet)
17577 (home-page "https://www.imm.dtu.dk/~lkhc/")
17578 (synopsis "Sparse discriminant analysis")
17580 "This package performs sparse linear discriminant analysis for Gaussians
17581 and mixture of Gaussian models.")
17582 (license license:gpl2+)))
17584 (define-public r-accsda
17591 (uri (cran-uri "accSDA" version))
17594 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17595 (properties `((upstream-name . "accSDA")))
17596 (build-system r-build-system)
17598 `(("r-ggplot2" ,r-ggplot2)
17599 ("r-ggthemes" ,r-ggthemes)
17600 ("r-gridextra" ,r-gridextra)
17602 ("r-rarpack" ,r-rarpack)
17603 ("r-sparselda" ,r-sparselda)))
17604 (home-page "https://github.com/gumeo/accSDA/wiki")
17605 (synopsis "Accelerated sparse discriminant analysis")
17607 "This package provides an implementation of sparse linear discriminant
17608 analysis, which is a supervised classification method for multiple classes.
17609 Various novel optimization approaches to this problem are implemented
17610 including @dfn{alternating direction method of multipliers} (ADMM),
17611 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17612 Functions for performing cross validation are also supplied along with basic
17613 prediction and plotting functions. @dfn{Sparse zero variance
17614 discriminant} (SZVD) analysis is also included in the package.")
17615 (license license:gpl2+)))
17617 (define-public r-ace2fastq
17619 (name "r-ace2fastq")
17624 (uri (cran-uri "ace2fastq" version))
17627 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17628 (properties `((upstream-name . "ace2fastq")))
17629 (build-system r-build-system)
17631 `(("r-stringr" ,r-stringr)))
17632 (home-page "https://github.com/c5sire/ace2fastq")
17633 (synopsis "ACE file to FASTQ converter")
17635 "The ACE file format is used in genomics to store contigs from sequencing
17636 machines. This tools converts it into FASTQ format. Both formats contain the
17637 sequence characters and their corresponding quality information. Unlike the
17638 FASTQ file, the ACE file stores the quality values numerically. The
17639 conversion algorithm uses the standard Sanger formula. The package
17640 facilitates insertion into pipelines, and content inspection.")
17641 (license license:gpl3)))
17643 (define-public r-rngwell
17650 (uri (cran-uri "rngWELL" version))
17653 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17654 (properties `((upstream-name . "rngWELL")))
17655 (build-system r-build-system)
17656 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17657 (synopsis "Toolbox for WELL random number generators")
17659 "This is a dedicated package to WELL pseudo random generators, which were
17660 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17661 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17662 (license license:bsd-3)))
17664 (define-public r-randtoolbox
17666 (name "r-randtoolbox")
17671 (uri (cran-uri "randtoolbox" version))
17674 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17675 (properties `((upstream-name . "randtoolbox")))
17676 (build-system r-build-system)
17678 `(("r-rngwell" ,r-rngwell)))
17680 `(("gfortran" ,gfortran)))
17681 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17682 (synopsis "Toolbox for pseudo and quasi random number generation")
17684 "This package provides
17687 @item pseudo random generators, such as general linear
17688 congruential generators, multiple recursive generators and generalized
17689 feedback shift register (SF-Mersenne Twister algorithm and WELL
17692 @item quasi random generators, such as the Torus algorithm, the Sobol
17693 sequence, the Halton sequence (including the Van der Corput sequence), and
17695 @item some generator tests: the gap test, the serial test, the poker test.
17698 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17699 (license license:bsd-3)))
17701 (define-public r-lhs
17708 (uri (cran-uri "lhs" version))
17711 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17712 (properties `((upstream-name . "lhs")))
17713 (build-system r-build-system)
17714 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17716 `(("r-knitr" ,r-knitr)))
17717 (home-page "https://github.com/bertcarnell/lhs")
17718 (synopsis "Latin Hypercube Samples")
17720 "This package provides a number of methods for creating and augmenting
17721 Latin Hypercube Samples.")
17722 (license license:gpl3)))
17724 (define-public r-acebayes
17726 (name "r-acebayes")
17731 (uri (cran-uri "acebayes" version))
17734 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17735 (properties `((upstream-name . "acebayes")))
17736 (build-system r-build-system)
17738 `(("r-compare" ,r-compare)
17740 ("r-randtoolbox" ,r-randtoolbox)
17742 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17743 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17744 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17746 "Finding an optimal Bayesian experimental design involves maximizing an
17747 objective function given by the expectation of some appropriately chosen
17748 utility function with respect to the joint distribution of unknown
17749 quantities (including responses). This objective function is usually not
17750 available in closed form and the design space can be continuous and of high
17751 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17752 to maximise an approximation to the expectation of the utility function.")
17753 (license license:gpl2)))
17755 (define-public r-acet
17762 (uri (cran-uri "ACEt" version))
17765 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17766 (properties `((upstream-name . "ACEt")))
17767 (build-system r-build-system)
17772 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17773 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17774 (synopsis "Estimating dynamic heritability and twin model comparison")
17776 "This package supports twin models that are able to estimate the dynamic
17777 behaviour of the variance components in the classical twin models with respect
17778 to age using B-splines and P-splines.")
17779 (license license:gpl2+)))
17781 (define-public r-acfmperiod
17783 (name "r-acfmperiod")
17788 (uri (cran-uri "acfMPeriod" version))
17791 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17792 (properties `((upstream-name . "acfMPeriod")))
17793 (build-system r-build-system)
17795 `(("r-mass" ,r-mass)))
17796 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17797 (synopsis "Estimation of the ACF from the M-periodogram")
17799 "This package support non-robust and robust computations of the sample
17800 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17801 univariate and multivariate processes. The methodology consists in reversing
17802 the diagonalization procedure involving the periodogram or the
17803 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17804 ACOVF or the ACF as discussed in Fuller (1995)
17805 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17806 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17807 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17808 (license license:gpl2+)))
17810 (define-public r-gamlss-data
17812 (name "r-gamlss-data")
17817 (uri (cran-uri "gamlss.data" version))
17820 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17821 (properties `((upstream-name . "gamlss.data")))
17822 (build-system r-build-system)
17823 (home-page "http://www.gamlss.org/")
17824 (synopsis "GAMLSS data")
17826 "This package provides data used as examples to demonstrate GAMLSS
17828 ;; Either version of the license
17829 (license (list license:gpl2 license:gpl3))))
17831 (define-public r-gamlss
17838 (uri (cran-uri "gamlss" version))
17841 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17842 (properties `((upstream-name . "gamlss")))
17843 (build-system r-build-system)
17845 `(("r-gamlss-data" ,r-gamlss-data)
17846 ("r-gamlss-dist" ,r-gamlss-dist)
17849 ("r-survival" ,r-survival)))
17850 (home-page "http://www.gamlss.org/")
17851 (synopsis "Generalized additive models for location scale and shape")
17853 "This package provides functions for fitting the generalized additive
17854 models for location scale and shape introduced by Rigby and
17855 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17856 use a distributional regression approach where all the parameters of the
17857 conditional distribution of the response variable are modelled using
17858 explanatory variables.")
17859 ;; Either version of the license
17860 (license (list license:gpl2 license:gpl3))))
17862 (define-public r-acid
17869 (uri (cran-uri "acid" version))
17872 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17873 (properties `((upstream-name . "acid")))
17874 (build-system r-build-system)
17876 `(("r-gamlss" ,r-gamlss)
17877 ("r-gamlss-dist" ,r-gamlss-dist)
17878 ("r-hmisc" ,r-hmisc)))
17879 (home-page "https://cran.r-project.org/web/packages/acid/")
17880 (synopsis "Analysing conditional income distributions")
17882 "This package provides functions for the analysis of income distributions
17883 for subgroups of the population as defined by a set of variables like age,
17884 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17885 distribution as well as functions for moments, inequality measures, entropy
17886 measures and polarisation measures of income distributions. This package thus
17887 aides the analysis of income inequality by offering tools for the exploratory
17888 analysis of income distributions at the disaggregated level.")
17889 (license license:gpl3)))
17891 (define-public r-acm4r
17898 (uri (cran-uri "acm4r" version))
17901 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17902 (properties `((upstream-name . "acm4r")))
17903 (build-system r-build-system)
17904 (propagated-inputs `(("r-mass" ,r-mass)))
17905 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17906 (synopsis "Align-and-count method comparisons of RFLP data")
17908 "This is a package to compare sequence fragment lengths or molecular
17909 weights from pairs of lanes. The number of matching bands in the
17910 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17911 the align-and-count method.")
17912 ;; Any version of the GPL
17913 (license (list license:gpl2+ license:gpl3+))))
17915 (define-public r-filematrix
17917 (name "r-filematrix")
17922 (uri (cran-uri "filematrix" version))
17925 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17926 (properties `((upstream-name . "filematrix")))
17927 (build-system r-build-system)
17928 ;; These inputs are needed for vignettes
17930 `(("r-knitr" ,r-knitr)
17931 ("r-rmarkdown" ,r-rmarkdown)
17932 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17933 (home-page "https://github.com/andreyshabalin/filematrix")
17934 (synopsis "File-backed matrix class with convenient read and write access")
17936 "This package provides an interface for working with large matrices
17937 stored in files, not in computer memory. It supports multiple non-character
17938 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17939 byte real values). Access to parts of the matrix is done by indexing, exactly
17940 as with usual R matrices. It supports very large matrices; the package has
17941 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17942 columns, ad allows for quick addition of extra columns to a filematrix.")
17943 (license license:lgpl3)))
17945 (define-public r-acmeeqtl
17947 (name "r-acmeeqtl")
17952 (uri (cran-uri "ACMEeqtl" version))
17955 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17956 (properties `((upstream-name . "ACMEeqtl")))
17957 (build-system r-build-system)
17959 `(("r-filematrix" ,r-filematrix)))
17960 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17961 (synopsis "Estimation of interpretable eQTL effect sizes")
17963 "This package provides a non-linear model, termed ACME, that reflects a
17964 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17965 With non-linear least-squares algorithm the maximum likelihood parameters can
17966 be estimated. The ACME model provides interpretable effect size estimates and
17967 p-values with well controlled Type-I error.")
17968 (license license:lgpl3)))
17970 (define-public r-acmer
17977 (uri (cran-uri "acmeR" version))
17980 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17981 (properties `((upstream-name . "acmeR")))
17982 (build-system r-build-system)
17983 (propagated-inputs `(("r-foreign" ,r-foreign)))
17984 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17985 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
17987 "This package provides an implementation of the ACME estimator, described
17988 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
17989 Mortality at Wind Turbines. Unlike most other models, this estimator supports
17990 decreasing-hazard Weibull model for persistence; decreasing search proficiency
17991 as carcasses age; variable bleed-through at successive searches; and interval
17992 mortality estimates. The package provides, based on search data, functions
17993 for estimating the mortality inflation factor in Frequentist and Bayesian
17995 (license license:expat)))
17997 (define-public r-r-huge
18004 (uri (cran-uri "R.huge" version))
18007 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18008 (properties `((upstream-name . "R.huge")))
18009 (build-system r-build-system)
18011 `(("r-r-methodss3" ,r-r-methodss3)
18013 ("r-r-utils" ,r-r-utils)))
18014 (home-page "https://github.com/HenrikBengtsson/R.huge")
18015 (synopsis "Methods for accessing huge amounts of data")
18017 "This is a deprecated package for accessing huge amounts of data.
18018 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18019 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18020 the @code{aroma.affymetrix} package.")
18021 (license license:lgpl2.1+)))
18023 (define-public r-r-filesets
18025 (name "r-r-filesets")
18030 (uri (cran-uri "R.filesets" version))
18033 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18034 (properties `((upstream-name . "R.filesets")))
18035 (build-system r-build-system)
18037 `(("r-digest" ,r-digest)
18038 ("r-r-cache" ,r-r-cache)
18039 ("r-r-methodss3" ,r-r-methodss3)
18041 ("r-r-utils" ,r-r-utils)))
18042 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18043 (synopsis "Easy handling of and access to files")
18045 "This package provides classes and methods to locate, setup, subset,
18046 navigate and iterate file sets, i.e. sets of files located in one or more
18047 directories on the file system. The API is designed such that these classes
18048 can be extended via inheritance to provide a richer API for special file
18049 formats. Moreover, a specific name format is defined such that filenames and
18050 directories can be considered to have full names which consists of a name
18051 followed by comma-separated tags. This adds additional flexibility to
18052 identify file sets and individual files.")
18053 (license license:lgpl2.1+)))
18055 (define-public r-r-devices
18057 (name "r-r-devices")
18062 (uri (cran-uri "R.devices" version))
18065 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18066 (properties `((upstream-name . "R.devices")))
18067 (build-system r-build-system)
18069 `(("r-base64enc" ,r-base64enc)
18070 ("r-r-methodss3" ,r-r-methodss3)
18072 ("r-r-utils" ,r-r-utils)))
18073 (home-page "https://github.com/HenrikBengtsson/R.devices")
18074 (synopsis "Unified handling of graphics devices")
18076 "This package provides functions for creating plots and image files in a
18077 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18078 Default device options as well as scales and aspect ratios are controlled in a
18079 uniform way across all device types. Switching output format requires minimal
18080 changes in code. This package is ideal for large-scale batch processing,
18081 because it will never leave open graphics devices or incomplete image files
18082 behind, even on errors or user interrupts.")
18083 (license license:lgpl2.1+)))
18085 (define-public r-acnr
18092 (uri (cran-uri "acnr" version))
18095 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18096 (properties `((upstream-name . "acnr")))
18097 (build-system r-build-system)
18098 (home-page "https://github.com/mpierrejean/acnr")
18099 (synopsis "Annotated copy-number regions")
18101 "This package provides SNP array data from different types of copy-number
18102 regions. These regions were identified manually by the authors of the package
18103 and may be used to generate realistic data sets with known truth.")
18104 (license license:lgpl2.1+)))
18106 (define-public r-acopula
18113 (uri (cran-uri "acopula" version))
18116 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18117 (properties `((upstream-name . "acopula")))
18118 (build-system r-build-system)
18119 (home-page "https://cran.r-project.org/web/packages/acopula/")
18120 (synopsis "Modelling dependence with multivariate Archimax copulas")
18122 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18123 package provides definitions of several parametric families of generator and
18124 dependence function, computes CDF and PDF, estimates parameters, tests for
18125 goodness of fit, generates random sample and checks copula properties for
18126 custom constructs. In the 2-dimensional case explicit formulas for density
18127 are used, contrary to higher dimensions when all derivatives are linearly
18128 approximated. Several non-archimax families (normal, FGM, Plackett) are
18129 provided as well.")
18130 (license license:gpl2)))
18132 (define-public r-tuner
18139 (uri (cran-uri "tuneR" version))
18142 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18143 (properties `((upstream-name . "tuneR")))
18144 (build-system r-build-system)
18145 (propagated-inputs `(("r-signal" ,r-signal)))
18146 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18147 (synopsis "Analysis of music and speech")
18149 "This is a package for the analysis of music and speech. Analyze music
18150 and speech, extract features like MFCCs, handle wave files and their
18151 representation in various ways, read MP3, read MIDI, perform steps of a
18152 transcription, ...")
18153 ;; Either of these versions.
18154 (license (list license:gpl2 license:gpl3))))
18156 (define-public r-seewave
18163 (uri (cran-uri "seewave" version))
18166 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18167 (properties `((upstream-name . "seewave")))
18168 (build-system r-build-system)
18170 `(("libsndfile" ,libsndfile)))
18172 `(("r-tuner" ,r-tuner)))
18173 (home-page "http://rug.mnhn.fr/seewave")
18174 (synopsis "Sound analysis and synthesis")
18176 "This package provides functions for analysing, manipulating, displaying,
18177 editing and synthesizing time waves (particularly sound). This package
18178 processes time analysis (oscillograms and envelopes), spectral content,
18179 resonance quality factor, entropy, cross correlation and autocorrelation,
18180 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18181 and 3D spectrograms and many other analyses.")
18182 (license license:gpl2+)))
18184 (define-public r-acousticndlcoder
18186 (name "r-acousticndlcoder")
18191 (uri (cran-uri "AcousticNDLCodeR" version))
18194 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18196 `((upstream-name . "AcousticNDLCodeR")))
18197 (build-system r-build-system)
18199 `(("r-seewave" ,r-seewave)
18200 ("r-tuner" ,r-tuner)
18202 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18203 (synopsis "Coding sound files for use with NDL")
18205 "Make acoustic cues to use with the R package @code{ndl}.
18206 The package implements functions used in the PLoS ONE paper \"Words from
18207 spontaneous conversational speech can be recognized with human-like accuracy
18208 by an error-driven learning algorithm that discriminates between meanings
18209 straight from smart acoustic features, bypassing the phoneme as recognition
18210 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18211 (license license:gpl2+)))
18213 (define-public r-acp
18220 (uri (cran-uri "acp" version))
18223 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18224 (properties `((upstream-name . "acp")))
18225 (build-system r-build-system)
18227 `(("r-quantmod" ,r-quantmod)
18228 ("r-tseries" ,r-tseries)))
18229 (home-page "https://cran.r-project.org/web/packages/acp/")
18230 (synopsis "Autoregressive conditional Poisson")
18232 "This package supports the analysis of count data exhibiting
18233 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18234 model (ACP(p,q)) proposed by Heinen (2003).")
18235 (license license:gpl2)))
18237 (define-public r-ada
18244 (uri (cran-uri "ada" version))
18247 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18248 (properties `((upstream-name . "ada")))
18249 (build-system r-build-system)
18250 (propagated-inputs `(("r-rpart" ,r-rpart)))
18251 (home-page "https://cran.r-project.org/web/packages/ada/")
18252 (synopsis "Stochastic boosting")
18254 "This package provides a straightforward, well-documented, and broad
18255 boosting routine for classification, ideally suited for small to
18256 moderate-sized data sets. It performs discrete, real, and gentle boost under
18257 both exponential and logistic loss on a given data set.")
18258 ;; Any version of the GPL.
18259 (license (list license:gpl2+ license:gpl3+))))
18261 (define-public r-genalg
18268 (uri (cran-uri "genalg" version))
18271 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18272 (properties `((upstream-name . "genalg")))
18273 (build-system r-build-system)
18274 (home-page "https://github.com/egonw/genalg")
18275 (synopsis "R based genetic algorithm")
18277 "This package provides an R based genetic algorithm for binary and
18278 floating point chromosomes.")
18279 (license license:gpl2)))
18281 (define-public r-kernelfactory
18283 (name "r-kernelfactory")
18288 (uri (cran-uri "kernelFactory" version))
18291 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18292 (properties `((upstream-name . "kernelFactory")))
18293 (build-system r-build-system)
18296 ("r-genalg" ,r-genalg)
18297 ("r-kernlab" ,r-kernlab)
18298 ("r-randomforest" ,r-randomforest)))
18299 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18300 (synopsis "Ensemble of kernel machines")
18302 "Kernel factory is an ensemble method where each base classifier (random
18303 forest) is fit on the kernel matrix of a subset of the training data.")
18304 (license license:gpl2+)))
18306 (define-public r-dummies
18313 (uri (cran-uri "dummies" version))
18316 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18317 (properties `((upstream-name . "dummies")))
18318 (build-system r-build-system)
18319 (home-page "https://decisionpatterns.com")
18320 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18322 "This package lets you expand factors, characters and other eligible
18323 classes into dummy/indicator variables.")
18324 (license license:gpl2+)))
18326 (define-public r-acrm
18333 (uri (cran-uri "aCRM" version))
18336 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18337 (properties `((upstream-name . "aCRM")))
18338 (build-system r-build-system)
18341 ("r-dummies" ,r-dummies)
18342 ("r-kernelfactory" ,r-kernelfactory)
18343 ("r-randomforest" ,r-randomforest)))
18344 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18345 (synopsis "Convenience functions for analytical customer relationship management")
18347 "This package provides convenience functions for data preparation and
18348 modeling often used in @dfn{analytical customer relationship
18349 management} (aCRM).")
18350 (license license:gpl2+)))
18352 (define-public r-treeclust
18354 (name "r-treeclust")
18359 (uri (cran-uri "treeClust" version))
18362 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18363 (properties `((upstream-name . "treeClust")))
18364 (build-system r-build-system)
18366 `(("r-cluster" ,r-cluster)
18367 ("r-rpart" ,r-rpart)))
18368 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18369 (synopsis "Cluster distances through trees")
18371 "This package provides tools to create a measure of inter-point
18372 dissimilarity useful for clustering mixed data, and, optionally, perform the
18374 (license license:gpl2+)))
18376 (define-public r-acrosstic
18378 (name "r-acrosstic")
18383 (uri (cran-uri "AcrossTic" version))
18386 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18387 (properties `((upstream-name . "AcrossTic")))
18388 (build-system r-build-system)
18390 `(("r-lpsolve" ,r-lpsolve)
18391 ("r-treeclust" ,r-treeclust)))
18392 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18393 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18395 "This is a package for constructing minimum-cost regular spanning
18396 subgraph as part of a non-parametric two-sample test for equality of
18398 (license license:gpl2+)))
18400 (define-public r-acrt
18407 (uri (cran-uri "acrt" version))
18410 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18411 (properties `((upstream-name . "acrt")))
18412 (build-system r-build-system)
18414 `(("r-rcpp" ,r-rcpp)
18415 ("r-rcppeigen" ,r-rcppeigen)
18416 ("r-sandwich" ,r-sandwich)))
18417 (home-page "https://cran.r-project.org/web/packages/acrt/")
18418 (synopsis "Autocorrelation robust testing")
18420 "This package provides functions for testing affine hypotheses on the
18421 regression coefficient vector in regression models with autocorrelated
18423 (license license:gpl2)))
18425 (define-public r-acs
18432 (uri (cran-uri "acs" version))
18435 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18436 (properties `((upstream-name . "acs")))
18437 (build-system r-build-system)
18439 `(("r-httr" ,r-httr)
18442 ("r-stringr" ,r-stringr)
18444 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18445 (synopsis "Work with data from the US Census")
18447 "This package provides a general toolkit for downloading, managing,
18448 analyzing, and presenting data from the
18449 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18450 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18451 American Community Survey (ACS). Confidence intervals provided with ACS data
18452 are converted to standard errors to be bundled with estimates in complex
18453 @code{acs} objects. The package provides new methods to conduct standard
18454 operations on @code{acs} objects and present/plot data in statistically
18455 appropriate ways.")
18456 (license license:gpl3)))
18458 (define-public r-acss-data
18460 (name "r-acss-data")
18465 (uri (cran-uri "acss.data" version))
18468 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18469 (properties `((upstream-name . "acss.data")))
18470 (build-system r-build-system)
18471 (home-page "http://complexitycalculator.com/methodology.html")
18472 (synopsis "Data for algorithmic complexity of short strings")
18474 "This is a data only package providing the algorithmic complexity of
18475 short strings, computed using the coding theorem method. For a given set of
18476 symbols in a string, all possible or a large number of random samples of
18477 Turing machines with a given number of states (e.g., 5) and number of symbols
18478 corresponding to the number of symbols in the strings were simulated until
18479 they reached a halting state or failed to end. This package contains data on
18480 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18481 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18482 distribution of the halting states.")
18483 (license license:gpl2+)))
18485 (define-public r-acss
18492 (uri (cran-uri "acss" version))
18495 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18496 (properties `((upstream-name . "acss")))
18497 (build-system r-build-system)
18499 `(("r-acss-data" ,r-acss-data)
18501 (home-page "http://complexitycalculator.com/methodology.html")
18502 (synopsis "Algorithmic complexity for short strings")
18504 "The main purpose of this package is to provide the algorithmic
18505 complexity for short strings, an approximation of the Kolmogorov Complexity of
18506 a short string using the coding theorem method. While the database containing
18507 the complexity is provided in the data only package @code{acss.data}, this
18508 package provides functions accessing the data such as @code{prob_random}
18509 returning the posterior probability that a given string was produced by a
18510 random process. In addition, two traditional (but problematic) measures of
18511 complexity are also provided: entropy and change complexity.")
18512 (license license:gpl2+)))
18514 (define-public r-acswr
18521 (uri (cran-uri "ACSWR" version))
18524 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18525 (properties `((upstream-name . "ACSWR")))
18526 (build-system r-build-system)
18528 `(("r-mass" ,r-mass)))
18529 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18530 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18532 "This is a companion package for the book \"A Course in Statistics with
18533 R\" (ISBN 978-1-119-15272-9.)")
18534 (license license:gpl2)))
18536 (define-public r-alabama
18539 (version "2015.3-1")
18543 (uri (cran-uri "alabama" version))
18546 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18547 (properties `((upstream-name . "alabama")))
18548 (build-system r-build-system)
18549 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18550 (home-page "https://cran.r-project.org/web/packages/alabama/")
18551 (synopsis "Constrained nonlinear optimization")
18553 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18554 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18555 constraints. Linear or nonlinear equality and inequality constraints are
18557 (license license:gpl2+)))
18559 (define-public r-gdina
18566 (uri (cran-uri "GDINA" version))
18569 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18570 (properties `((upstream-name . "GDINA")))
18571 (build-system r-build-system)
18573 `(("r-alabama" ,r-alabama)
18574 ("r-ggplot2" ,r-ggplot2)
18576 ("r-nloptr" ,r-nloptr)
18577 ("r-numderiv" ,r-numderiv)
18579 ("r-rcpparmadillo" ,r-rcpparmadillo)
18580 ("r-rsolnp" ,r-rsolnp)
18581 ("r-shiny" ,r-shiny)
18582 ("r-shinydashboard" ,r-shinydashboard)))
18584 `(("r-knitr" ,r-knitr)))
18585 (home-page "https://github.com/Wenchao-Ma/GDINA")
18586 (synopsis "Generalized DINA model framework")
18588 "This package provides a set of psychometric tools for cognitive
18589 diagnosis modeling based on the generalized deterministic inputs, noisy and
18590 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18591 and its extensions, including the sequential G-DINA model by Ma and de la
18592 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18593 polytomous G-DINA model by Chen and de la Torre
18594 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18595 distribution can be independent, saturated, higher-order, loglinear smoothed
18596 or structured. Q-matrix validation, item and model fit statistics, model
18597 comparison at test and item level and differential item functioning can also
18598 be conducted. A graphical user interface is also provided.")
18599 (license license:gpl3)))
18601 (define-public r-actcd
18608 (uri (cran-uri "ACTCD" version))
18611 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18612 (properties `((upstream-name . "ACTCD")))
18613 (build-system r-build-system)
18615 `(("r-gdina" ,r-gdina)
18616 ("r-r-methodss3" ,r-r-methodss3)))
18618 `(("gfortran" ,gfortran)))
18619 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18620 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18622 "This is a package supporting cluster analysis for cognitive diagnosis
18623 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18624 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18625 sum-scores, cluster analysis techniques can be used to classify examinees into
18626 latent classes based on their attribute patterns. In addition to the
18627 algorithms used to classify data, three labeling approaches are proposed to
18628 label clusters so that examinees' attribute profiles can be obtained.")
18629 (license license:gpl2+)))
18631 (define-public r-ineq
18638 (uri (cran-uri "ineq" version))
18641 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18642 (properties `((upstream-name . "ineq")))
18643 (build-system r-build-system)
18644 (home-page "https://cran.r-project.org/web/packages/ineq/")
18645 (synopsis "Measuring inequality, concentration, and poverty")
18647 "This package provides tools for measuring inequality, concentration, and
18648 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18649 ;; Either of these two versions.
18650 (license (list license:gpl2 license:gpl3))))
18652 (define-public r-actfrag
18659 (uri (cran-uri "ActFrag" version))
18662 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18663 (properties `((upstream-name . "ActFrag")))
18664 (build-system r-build-system)
18666 `(("r-accelerometry" ,r-accelerometry)
18667 ("r-dplyr" ,r-dplyr)
18669 ("r-survival" ,r-survival)
18670 ("r-tidyr" ,r-tidyr)))
18671 (home-page "https://github.com/junruidi/ActFrag")
18672 (synopsis "Activity fragmentation metrics extraction")
18674 "This package provides functions to extract commonly used fragmentation
18675 metrics to quantify time accumulation strategies based on minute level
18676 actigraphy-measured activity counts data.")
18677 (license license:gpl3)))
18679 (define-public r-fda
18686 (uri (cran-uri "fda" version))
18689 "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
18690 (properties `((upstream-name . "fda")))
18691 (build-system r-build-system)
18693 `(("r-matrix" ,r-matrix)))
18694 (home-page "https://www.functionaldata.org")
18695 (synopsis "Functional data analysis")
18697 "These functions were developed to support functional data analysis as
18698 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18699 Analysis. The package includes data sets and script files working many
18701 (license license:gpl2+)))
18703 (define-public r-actigraphy
18705 (name "r-actigraphy")
18710 (uri (cran-uri "Actigraphy" version))
18713 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18714 (properties `((upstream-name . "Actigraphy")))
18715 (build-system r-build-system)
18717 `(("r-fda" ,r-fda)))
18718 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18719 (synopsis "Actigraphy data analysis")
18721 "This package provides tools for functional linear modeling and analysis
18722 of actigraphy data.")
18723 (license license:asl2.0)))
18725 (define-public r-activedriver
18727 (name "r-activedriver")
18732 (uri (cran-uri "ActiveDriver" version))
18735 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18736 (properties `((upstream-name . "ActiveDriver")))
18737 (build-system r-build-system)
18739 `(("r-mass" ,r-mass)))
18740 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18741 (synopsis "Tools for finding cancer driver proteins")
18743 "This package provides a mutation analysis tool that discovers cancer
18744 driver genes with frequent mutations in protein signalling sites such as
18745 post-translational modifications (phosphorylation, ubiquitination, etc). The
18746 Poisson generalized linear regression model identifies genes where cancer
18747 mutations in signalling sites are more frequent than expected from the
18748 sequence of the entire gene. Integration of mutations with signalling
18749 information helps find new driver genes and propose candidate mechanisms to
18751 (license license:gpl2+)))
18753 (define-public r-activitycounts
18755 (name "r-activitycounts")
18760 (uri (cran-uri "activityCounts" version))
18763 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18765 `((upstream-name . "activityCounts")))
18766 (build-system r-build-system)
18768 `(("r-lubridate" ,r-lubridate)
18769 ("r-magrittr" ,r-magrittr)
18770 ("r-seewave" ,r-seewave)
18771 ("r-signal" ,r-signal)
18772 ("r-tibble" ,r-tibble)))
18773 (home-page "https://github.com/walkabillylab/activityCounts")
18774 (synopsis "Generate ActiLife counts")
18776 "ActiLife generates activity counts from data collected by Actigraph
18777 accelerometers. Actigraph is one of the most common research-grade
18778 accelerometers. There is considerable research validating and developing
18779 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18780 counts are proprietary and difficult to implement if researchers use different
18781 accelerometer brands. The code creates ActiLife counts from raw acceleration
18782 data for different accelerometer brands.")
18783 (license license:gpl3)))
18785 (define-public r-activityindex
18787 (name "r-activityindex")
18792 (uri (cran-uri "ActivityIndex" version))
18795 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18796 (properties `((upstream-name . "ActivityIndex")))
18797 (build-system r-build-system)
18799 `(("r-data-table" ,r-data-table)
18800 ("r-matrixstats" ,r-matrixstats)
18801 ("r-r-utils" ,r-r-utils)))
18802 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18803 (synopsis "Activity Index calculation using raw accelerometry data")
18805 "This is a package to read raw accelerometry from GT3X+ accelerometry
18806 data and plain table data to calculate the Activity Index from Bai et
18807 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18808 (license license:gpl3)))
18810 (define-public r-activpal
18812 (name "r-activpal")
18817 (uri (cran-uri "activPAL" version))
18820 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18821 (properties `((upstream-name . "activPAL")))
18822 (build-system r-build-system)
18824 `(("r-devtools" ,r-devtools)
18825 ("r-dplyr" ,r-dplyr)
18826 ("r-ggplot2" ,r-ggplot2)
18827 ("r-lubridate" ,r-lubridate)
18828 ("r-magrittr" ,r-magrittr)
18829 ("r-tidyr" ,r-tidyr)))
18830 (home-page "https://cran.r-project.org/web/packages/activPAL")
18831 (synopsis "Processing and chart generation from activPAL events files")
18833 "This package contains functions to generate pre-defined summary
18834 statistics from activPAL events files. The package also contains functions to
18835 produce informative graphics that visualize physical activity behaviour and
18836 trends. This includes generating graphs that align physical activity
18837 behaviour with additional time based observations described by other data
18838 sets, such as sleep diaries and continuous glucose monitoring data.")
18839 (license license:gpl3)))
18841 (define-public r-activpalprocessing
18843 (name "r-activpalprocessing")
18848 (uri (cran-uri "activpalProcessing" version))
18851 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18853 `((upstream-name . "activpalProcessing")))
18854 (build-system r-build-system)
18856 `(("r-chron" ,r-chron)))
18857 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18858 (synopsis "Process activPAL events files")
18860 "This package performs estimation of physical activity and sedentary
18861 behavior variables from activPAL events files.")
18862 ;; Either version of the GPL.
18863 (license (list license:gpl2 license:gpl3))))
18865 (define-public r-actogrammr
18867 (name "r-actogrammr")
18872 (uri (cran-uri "actogrammr" version))
18875 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18876 (properties `((upstream-name . "actogrammr")))
18877 (build-system r-build-system)
18879 `(("r-dplyr" ,r-dplyr)
18880 ("r-ggplot2" ,r-ggplot2)
18881 ("r-lubridate" ,r-lubridate)
18882 ("r-readr" ,r-readr)
18883 ("r-tidyr" ,r-tidyr)))
18884 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18885 (synopsis "Read in activity data and plot actograms")
18887 "Read in activity measurements from standard file formats used by
18888 circadian rhythm researchers, currently only ClockLab format, and process and
18889 plot the data. The central type of plot is the actogram, as first described
18890 in \"Activity and distribution of certain wild mice in relation to biotic
18891 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18892 (license license:gpl3)))
18894 (define-public r-expint
18901 (uri (cran-uri "expint" version))
18904 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18905 (properties `((upstream-name . "expint")))
18906 (build-system r-build-system)
18907 (home-page "https://gitlab.com/vigou3/expint")
18908 (synopsis "Exponential integral and incomplete Gamma function")
18910 "This package provides the exponential integrals @code{E_1(x)},
18911 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18912 function @code{G(a, x)} defined for negative values of its first argument.
18913 The package also gives easy access to the underlying C routines through an
18914 API; see the package vignette for details.")
18915 (license license:gpl2+)))
18917 (define-public r-actuar
18924 (uri (cran-uri "actuar" version))
18927 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
18928 (properties `((upstream-name . "actuar")))
18929 (build-system r-build-system)
18930 (propagated-inputs `(("r-expint" ,r-expint)))
18931 (home-page "https://gitlab.com/vigou3/actuar")
18932 (synopsis "Actuarial functions and heavy tailed distributions")
18934 "This package provides functions and data sets for actuarial science:
18935 modeling of loss distributions; risk theory and ruin theory; simulation of
18936 compound models, discrete mixtures and compound hierarchical models;
18937 credibility theory. It boasts support for many additional probability
18938 distributions to model insurance loss amounts and loss frequency: 19
18939 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18940 distribution; zero-truncated and zero-modified extensions of the standard
18941 discrete distributions. It also supports phase-type distributions commonly
18942 used to compute ruin probabilities.")
18943 (license license:gpl2+)))
18945 (define-public r-bmp
18952 (uri (cran-uri "bmp" version))
18955 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18956 (properties `((upstream-name . "bmp")))
18957 (build-system r-build-system)
18958 (home-page "https://cran.r-project.org/web/packages/bmp/")
18959 (synopsis "Read Bitmap (BMP) images")
18961 "This package provides pure R tools to read BMP format images. It is
18962 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18963 (license license:gpl2+)))
18965 (define-public r-readbitmap
18967 (name "r-readbitmap")
18972 (uri (cran-uri "readbitmap" version))
18975 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18976 (properties `((upstream-name . "readbitmap")))
18977 (build-system r-build-system)
18979 `(("libjpeg" ,libjpeg-turbo)
18980 ("libpng" ,libpng)))
18985 ("r-tiff" ,r-tiff)))
18986 (home-page "https://github.com/jefferis/readbitmap")
18987 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
18989 "This package provides tools to identify and read BMP, JPEG, PNG, and
18990 TIFF format bitmap images. Identification defaults to the use of the magic
18991 number embedded in the file rather than the file extension.")
18992 (license license:gpl2+)))
18994 (define-public r-imager
19001 (uri (cran-uri "imager" version))
19004 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19005 (properties `((upstream-name . "imager")))
19006 (build-system r-build-system)
19009 ("libtiff" ,libtiff)
19013 `(("r-downloader" ,r-downloader)
19014 ("r-igraph" ,r-igraph)
19016 ("r-magrittr" ,r-magrittr)
19018 ("r-purrr" ,r-purrr)
19020 ("r-readbitmap" ,r-readbitmap)
19021 ("r-stringr" ,r-stringr)))
19023 `(("pkg-config" ,pkg-config)
19024 ("r-knitr" ,r-knitr)))
19025 (home-page "https://dahtah.github.io/imager/")
19026 (synopsis "Image processing library")
19028 "This is a package for fast image processing for images in up to 4
19029 dimensions (two spatial dimensions, one time/depth dimension, one color
19030 dimension). It provides most traditional image processing tools (filtering,
19031 morphology, transformations, etc.) as well as various functions for easily
19032 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19033 simple, modern C++ library for image processing.")
19034 (license license:lgpl3)))
19036 (define-public r-acuityview
19038 (name "r-acuityview")
19043 (uri (cran-uri "AcuityView" version))
19046 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19047 (properties `((upstream-name . "AcuityView")))
19048 (build-system r-build-system)
19050 `(("r-fftwtools" ,r-fftwtools)
19051 ("r-imager" ,r-imager)
19052 ("r-plotrix" ,r-plotrix)))
19053 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19054 (synopsis "Display scenes as seen by an animal with less acute vision")
19056 "This package provides a simple method for representing a visual scene as
19057 it may be seen by an animal with less acute vision.")
19058 (license license:gpl2+)))
19060 (define-public r-caret
19067 (uri (cran-uri "caret" version))
19070 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19071 (build-system r-build-system)
19073 `(("r-foreach" ,r-foreach)
19074 ("r-ggplot2" ,r-ggplot2)
19075 ("r-lattice" ,r-lattice)
19076 ("r-modelmetrics" ,r-modelmetrics)
19080 ("r-recipes" ,r-recipes)
19081 ("r-reshape2" ,r-reshape2)
19082 ("r-withr" ,r-withr)))
19084 `(("r-knitr" ,r-knitr)))
19085 (home-page "https://github.com/topepo/caret")
19086 (synopsis "Classification and regression training")
19088 "This package provides miscellaneous functions for training and plotting
19089 classification and regression models.")
19090 (license license:gpl2+)))
19092 (define-public r-adabag
19099 (uri (cran-uri "adabag" version))
19102 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19103 (properties `((upstream-name . "adabag")))
19104 (build-system r-build-system)
19106 `(("r-caret" ,r-caret)
19107 ("r-doparallel" ,r-doparallel)
19108 ("r-foreach" ,r-foreach)
19109 ("r-rpart" ,r-rpart)))
19110 (home-page "https://cran.r-project.org/web/packages/adabag/")
19111 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19113 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19114 Breiman's Bagging algorithm using classification trees as individual
19115 classifiers. Once these classifiers have been trained, they can be used to
19116 predict on new data. Also, cross validation estimation of the error can be
19118 (license license:gpl2+)))
19120 (define-public r-adagio
19127 (uri (cran-uri "adagio" version))
19130 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19131 (properties `((upstream-name . "adagio")))
19132 (build-system r-build-system)
19133 (native-inputs `(("gfortran" ,gfortran)))
19134 (home-page "https://cran.r-project.org/web/packages/adagio/")
19135 (synopsis "Discrete and global optimization routines")
19137 "This package provides methods and algorithms for discrete optimization,
19138 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19139 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19141 (license license:gpl3+)))
19143 (define-public r-univoutl
19145 (name "r-univoutl")
19150 (uri (cran-uri "univOutl" version))
19153 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19154 (properties `((upstream-name . "univOutl")))
19155 (build-system r-build-system)
19157 `(("r-hmisc" ,r-hmisc)
19158 ("r-robustbase" ,r-robustbase)))
19159 (home-page "https://github.com/marcellodo/univOutl")
19160 (synopsis "Detection of univariate outliers")
19162 "This package provides well-known outlier detection techniques in the
19163 univariate case. Methods to deal with skewed distribution are included too.
19164 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19165 historical data is implemented as well. When available, survey weights can be
19166 used in outliers detection.")
19167 (license license:gpl2+)))
19169 (define-public r-tolerance
19171 (name "r-tolerance")
19176 (uri (cran-uri "tolerance" version))
19179 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19180 (properties `((upstream-name . "tolerance")))
19181 (build-system r-build-system)
19183 `(("r-mass" ,r-mass)
19185 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19186 (synopsis "Statistical tolerance intervals and regions")
19188 "This package provides functions for estimating tolerance
19189 limits (intervals) for various univariate distributions (binomial, Cauchy,
19190 discrete Pareto, exponential, two-parameter exponential, extreme value,
19191 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19192 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19193 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19194 nonparametric tolerance intervals, tolerance bands for regression
19195 settings (linear regression, nonlinear regression, nonparametric regression,
19196 and multivariate regression), and analysis of variance tolerance intervals.
19197 Visualizations are also available for most of these settings.")
19198 (license license:gpl2+)))
19200 (define-public r-additivitytests
19202 (name "r-additivitytests")
19207 (uri (cran-uri "additivityTests" version))
19210 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19212 `((upstream-name . "additivityTests")))
19213 (build-system r-build-system)
19214 (home-page "https://github.com/simecek/additivityTests")
19215 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19217 "This package provides an implementation of the Tukey, Mandel,
19218 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19219 (license license:gpl3)))
19221 (define-public r-flexclust
19223 (name "r-flexclust")
19228 (uri (cran-uri "flexclust" version))
19231 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19232 (properties `((upstream-name . "flexclust")))
19233 (build-system r-build-system)
19235 `(("r-class" ,r-class)
19236 ("r-lattice" ,r-lattice)
19237 ("r-modeltools" ,r-modeltools)))
19238 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19239 (synopsis "Flexible cluster algorithms")
19241 "The main function @code{kcca} implements a general framework for
19242 k-centroids cluster analysis supporting arbitrary distance measures and
19243 centroid computation. Further cluster methods include hard competitive
19244 learning, neural gas, and QT clustering. There are numerous visualization
19245 methods for cluster results (neighborhood graphs, convex cluster hulls,
19246 barcharts of centroids, ...), and bootstrap methods for the analysis of
19247 cluster stability.")
19248 (license license:gpl2)))
19250 (define-public r-biclust
19257 (uri (cran-uri "biclust" version))
19260 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19261 (properties `((upstream-name . "biclust")))
19262 (build-system r-build-system)
19264 `(("r-additivitytests" ,r-additivitytests)
19265 ("r-colorspace" ,r-colorspace)
19266 ("r-flexclust" ,r-flexclust)
19267 ("r-ggplot2" ,r-ggplot2)
19268 ("r-lattice" ,r-lattice)
19270 ("r-tidyr" ,r-tidyr)))
19271 (home-page "https://cran.r-project.org/web/packages/biclust/")
19272 (synopsis "BiCluster algorithms")
19274 "The main function @code{biclust()} provides several algorithms to find
19275 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19276 In addition, the package provides methods for data
19277 preprocessing (normalization and discretization), visualization, and
19278 validation of bicluster solutions.")
19279 (license license:gpl3)))
19281 (define-public r-icge
19288 (uri (cran-uri "ICGE" version))
19291 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19292 (properties `((upstream-name . "ICGE")))
19293 (build-system r-build-system)
19295 `(("r-cluster" ,r-cluster)
19296 ("r-mass" ,r-mass)))
19297 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19298 (synopsis "Cluster estimation and identification of atypical units")
19300 "ICGE is a package that helps to estimate the number of real clusters in
19301 data as well as to identify atypical units. The underlying methods are based
19302 on distances rather than on unit x variables.")
19303 (license license:gpl2+)))
19305 (define-public r-depth
19308 (version "2.1-1.1")
19312 (uri (cran-uri "depth" version))
19315 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19316 (properties `((upstream-name . "depth")))
19317 (build-system r-build-system)
19319 `(("r-abind" ,r-abind)
19320 ("r-circular" ,r-circular)
19323 `(("gfortran" ,gfortran)))
19324 (home-page "https://cran.r-project.org/web/packages/depth/")
19325 (synopsis "Nonparametric depth functions for multivariate analysis")
19327 "This package provides tools for depth functions methodology applied to
19328 multivariate analysis. Besides allowing calculation of depth values and
19329 depth-based location estimators, the package includes functions or drawing
19330 contour plots and perspective plots of depth functions. Euclidian and
19331 spherical depths are supported.")
19332 (license license:gpl2)))
19334 (define-public r-archetypes
19336 (name "r-archetypes")
19337 (version "2.2-0.1")
19341 (uri (cran-uri "archetypes" version))
19344 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19345 (properties `((upstream-name . "archetypes")))
19346 (build-system r-build-system)
19348 `(("r-modeltools" ,r-modeltools)
19349 ("r-nnls" ,r-nnls)))
19350 (home-page "https://cran.r-project.org/web/packages/archetypes")
19351 (synopsis "Archetypal analysis")
19353 "The main function @code{archetypes} implements a framework for
19354 archetypal analysis supporting arbitrary problem solving mechanisms for the
19355 different conceptual parts of the algorithm.")
19356 (license license:gpl2+)))
19358 (define-public r-shapes
19365 (uri (cran-uri "shapes" version))
19368 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19369 (properties `((upstream-name . "shapes")))
19370 (build-system r-build-system)
19372 `(("r-mass" ,r-mass)
19373 ("r-minpack-lm" ,r-minpack-lm)
19375 ("r-scatterplot3d" ,r-scatterplot3d)))
19376 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19377 (synopsis "Statistical shape analysis")
19379 "This package provides routines for the statistical analysis of landmark
19380 shapes, including Procrustes analysis, graphical displays, principal
19381 components analysis, permutation and bootstrap tests, thin-plate spline
19382 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19383 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19384 Edition), John Wiley and Sons.")
19385 (license license:gpl2)))
19387 (define-public r-anthropometry
19389 (name "r-anthropometry")
19394 (uri (cran-uri "Anthropometry" version))
19397 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19398 (properties `((upstream-name . "Anthropometry")))
19399 (build-system r-build-system)
19401 `(("r-archetypes" ,r-archetypes)
19402 ("r-biclust" ,r-biclust)
19403 ("r-cluster" ,r-cluster)
19404 ("r-depth" ,r-depth)
19409 ("r-shapes" ,r-shapes)))
19411 `(("r-knitr" ,r-knitr)))
19412 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19413 (synopsis "Statistical methods for anthropometric data")
19415 "This package provides statistical methods especially developed to
19416 analyze anthropometric data. These methods are aimed at providing effective
19417 solutions to some commons problems related to Ergonomics and Anthropometry.
19418 They are based on clustering, the statistical concept of data depth,
19419 statistical shape analysis and archetypal analysis.")
19420 (license license:gpl2+)))
19422 (define-public r-adamethods
19424 (name "r-adamethods")
19429 (uri (cran-uri "adamethods" version))
19432 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
19433 (properties `((upstream-name . "adamethods")))
19434 (build-system r-build-system)
19436 `(("r-anthropometry" ,r-anthropometry)
19437 ("r-archetypes" ,r-archetypes)
19439 ("r-foreach" ,r-foreach)
19441 ("r-tolerance" ,r-tolerance)
19442 ("r-univoutl" ,r-univoutl)))
19443 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19444 (synopsis "Archetypoid algorithms and anomaly detection")
19446 "This package is a collection of several algorithms to obtain
19447 archetypoids with small and large databases and with both classical
19448 multivariate data and functional data (univariate and multivariate). Some of
19449 these algorithms also allow to detect anomalies (outliers).")
19450 (license license:gpl2+)))
19452 (define-public r-idpmisc
19459 (uri (cran-uri "IDPmisc" version))
19462 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19463 (properties `((upstream-name . "IDPmisc")))
19464 (build-system r-build-system)
19466 `(("r-lattice" ,r-lattice)))
19467 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19468 (synopsis "Functions for data analyses and visualization")
19470 "This package provides different high-level graphics functions for
19471 displaying large datasets, displaying circular data in a very flexible way,
19472 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19473 2D-plots, creating figures with differently colored margin and plot region.
19474 In addition, the package contains auxiliary functions for data manipulation
19475 like omitting observations with irregular values or selecting data by logical
19476 vectors, which include NAs. Other functions are especially useful in
19477 spectroscopy and analyses of environmental data: robust baseline fitting,
19478 finding peaks in spectra, converting humidity measures.")
19479 (license license:gpl3+)))
19481 (define-public r-qqman
19488 (uri (cran-uri "qqman" version))
19491 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19492 (properties `((upstream-name . "qqman")))
19493 (build-system r-build-system)
19495 `(("r-calibrate" ,r-calibrate)))
19496 (home-page "https://cran.r-project.org/web/packages/qqman/")
19497 (synopsis "Q-Q and Manhattan plots for GWAS data")
19499 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19500 from PLINK results.")
19501 (license license:gpl3)))
19503 (define-public r-ggplot-multistats
19505 (name "r-ggplot-multistats")
19510 (uri (cran-uri "ggplot.multistats" version))
19513 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19515 `((upstream-name . "ggplot.multistats")))
19516 (build-system r-build-system)
19518 `(("r-ggplot2" ,r-ggplot2)
19519 ("r-hexbin" ,r-hexbin)
19520 ("r-rlang" ,r-rlang)
19521 ("r-scales" ,r-scales)))
19522 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19523 (synopsis "Multiple summary statistics for binned stats/geometries")
19525 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19526 which functions similar to its singular form, but allows the use of multiple
19527 statistics per bin. Those statistics can be mapped to multiple bin
19529 (license license:gpl3)))
19531 (define-public r-knn-covertree
19533 (name "r-knn-covertree")
19538 (uri (cran-uri "knn.covertree" version))
19541 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19542 (properties `((upstream-name . "knn.covertree")))
19543 (build-system r-build-system)
19545 `(("r-matrix" ,r-matrix)
19547 ("r-rcppeigen" ,r-rcppeigen)))
19548 (home-page "https://github.com/flying-sheep/knn.covertree")
19549 (synopsis "Accurate kNN Implementation with multiple distance measures")
19551 "Similarly to the FNN package, this package allows calculation of the k
19552 nearest neighbors (kNN) of a data matrix. The implementation is based on
19553 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19554 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19555 (license license:agpl3+)))
19557 (define-public r-poibin
19564 (uri (cran-uri "poibin" version))
19567 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19568 (properties `((upstream-name . "poibin")))
19569 (build-system r-build-system)
19570 (home-page "https://cran.r-project.org/web/packages/poibin/")
19571 (synopsis "Poisson binomial distribution")
19573 "This package provides an implementation of both the exact and
19574 approximation methods for computing the @dfn{cumulative distribution
19575 function} (CDF) of the Poisson binomial distribution. It also provides the
19576 @dfn{probability mass function} (PMF), quantile function, and random number
19577 generation for the Poisson binomial distribution.")
19578 (license license:gpl2)))
19580 (define-public r-diagram
19587 (uri (cran-uri "diagram" version))
19590 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19591 (properties `((upstream-name . "diagram")))
19592 (build-system r-build-system)
19594 `(("r-shape" ,r-shape)))
19595 (home-page "https://cran.r-project.org/web/packages/diagram/")
19596 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19598 "This package provides tools to visualize simple graphs (networks) based
19599 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19600 electrical networks, etc. It also includes supporting material for the book
19601 \"A practical guide to ecological modelling - using R as a simulation
19602 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19603 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19604 Francesca Mazzia (2012).")
19605 (license license:gpl2+)))
19607 (define-public r-lim
19614 (uri (cran-uri "LIM" version))
19617 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19618 (properties `((upstream-name . "LIM")))
19619 (build-system r-build-system)
19621 `(("r-diagram" ,r-diagram)
19622 ("r-limsolve" ,r-limsolve)))
19623 (home-page "https://cran.r-project.org/web/packages/LIM/")
19624 (synopsis "Linear inverse model examples and solution methods")
19626 "This package provides functions that read and solve linear inverse
19627 problems (food web problems, linear programming problems).")
19628 (license license:gpl2+)))
19630 (define-public r-shinycssloaders
19632 (name "r-shinycssloaders")
19637 (uri (cran-uri "shinycssloaders" version))
19640 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19642 `((upstream-name . "shinycssloaders")))
19643 (build-system r-build-system)
19645 `(("r-digest" ,r-digest)
19647 ("r-shiny" ,r-shiny)))
19648 (home-page "https://github.com/andrewsali/shinycssloaders")
19649 (synopsis "Add CSS loading animations to Shiny outputs")
19651 "This package provides tools to create a lightweight Shiny wrapper for
19652 the css-loaders created by Luke Hass
19653 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19654 automatically show a loader when the output is (re)calculating.")
19655 (license license:gpl3)))
19657 (define-public r-rsvg
19664 (uri (cran-uri "rsvg" version))
19667 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19668 (properties `((upstream-name . "rsvg")))
19669 (build-system r-build-system)
19671 `(("librsvg" ,librsvg)
19674 `(("pkg-config" ,pkg-config)
19675 ("r-knitr" ,r-knitr)))
19676 (home-page "https://github.com/jeroen/rsvg#readme")
19677 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19679 "This package allows you to render vector-based SVG images into
19680 high-quality custom-size bitmap arrays using the librsvg2 library. The
19681 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19682 addition, the package can convert images directly to various formats such as
19683 PDF or PostScript.")
19684 (license license:expat)))
19686 (define-public r-influencer
19688 (name "r-influencer")
19693 (uri (cran-uri "influenceR" version))
19696 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19697 (properties `((upstream-name . "influenceR")))
19698 (build-system r-build-system)
19700 `(("r-igraph" ,r-igraph)
19701 ("r-matrix" ,r-matrix)))
19702 (home-page "https://github.com/rcc-uchicago/influenceR")
19703 (synopsis "Tools to quantify structural importance of nodes in a network")
19705 "This package provides functionality to compute various node centrality
19706 measures on networks. Included are functions to compute betweenness
19707 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19708 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19709 algorithm to identify key players, and Valente's bridging metric. The
19710 betweenness, Key Players, and bridging implementations are parallelized with
19712 (license license:gpl2)))
19714 (define-public r-emplik
19721 (uri (cran-uri "emplik" version))
19724 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
19725 (properties `((upstream-name . "emplik")))
19726 (build-system r-build-system)
19728 `(("r-quantreg" ,r-quantreg)))
19729 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19730 (synopsis "Empirical likelihood ratio for censored/truncated data")
19732 "This package provides empirical likelihood ratio tests for
19733 means/quantiles/hazards from possibly censored and/or truncated data. It also
19735 (license license:gpl2+)))
19737 (define-public r-imputeyn
19739 (name "r-imputeyn")
19744 (uri (cran-uri "imputeYn" version))
19747 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19748 (properties `((upstream-name . "imputeYn")))
19749 (build-system r-build-system)
19751 `(("r-boot" ,r-boot)
19752 ("r-emplik" ,r-emplik)
19753 ("r-mvtnorm" ,r-mvtnorm)
19754 ("r-quadprog" ,r-quadprog)
19755 ("r-survival" ,r-survival)))
19756 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19757 (synopsis "Impute last largest censored observation under weighted least squares")
19759 "This package allows for the imputation of the last largest censored
19760 observantions. This method brings less bias and more efficient estimates for
19762 (license license:gpl2)))
19764 (define-public r-adapenetclass
19766 (name "r-adapenetclass")
19771 (uri (cran-uri "AdapEnetClass" version))
19774 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19775 (properties `((upstream-name . "AdapEnetClass")))
19776 (build-system r-build-system)
19778 `(("r-glmnet" ,r-glmnet)
19779 ("r-imputeyn" ,r-imputeyn)
19781 ("r-quadprog" ,r-quadprog)))
19782 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19783 (synopsis "Class of adaptive elastic net methods for censored data")
19785 "This package provides methods for variable selection for AFT models.")
19786 (license license:gpl2)))
19788 (define-public r-flock
19795 (uri (cran-uri "flock" version))
19798 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19799 (properties `((upstream-name . "flock")))
19800 (build-system r-build-system)
19801 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19802 (home-page "https://cran.r-project.org/web/packages/flock/")
19803 (synopsis "Process synchronization using file locks")
19805 "This package implements synchronization between R processes (spawned by
19806 using the @code{parallel} package for instance) using file locks. It supports
19807 both exclusive and shared locking.")
19808 (license license:asl2.0)))
19810 (define-public r-archivist
19812 (name "r-archivist")
19817 (uri (cran-uri "archivist" version))
19820 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19821 (properties `((upstream-name . "archivist")))
19822 (build-system r-build-system)
19825 ("r-digest" ,r-digest)
19826 ("r-flock" ,r-flock)
19828 ("r-lubridate" ,r-lubridate)
19829 ("r-magrittr" ,r-magrittr)
19830 ("r-rcurl" ,r-rcurl)
19831 ("r-rsqlite" ,r-rsqlite)))
19832 (home-page "https://pbiecek.github.io/archivist/")
19833 (synopsis "Tools for storing, restoring and searching for R objects")
19835 "Data exploration and modelling is a process in which a lot of data
19836 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19837 statistical models, different versions of data sets and different versions of
19838 results. Archivist helps to store and manage artifacts created in R. It
19839 allows you to store selected artifacts as binary files together with their
19840 metadata and relations. Archivist allows sharing artifacts with others. It
19841 can look for already created artifacts by using its class, name, date of the
19842 creation or other properties. It also makes it easy to restore such
19844 (license license:gpl2)))
19846 (define-public r-versions
19848 (name "r-versions")
19853 (uri (cran-uri "versions" version))
19856 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19857 (properties `((upstream-name . "versions")))
19858 (build-system r-build-system)
19859 (home-page "https://cran.r-project.org/web/packages/versions/")
19860 (synopsis "Query and install specific versions of CRAN packages")
19862 "This package allows you to install specified versions of R packages
19863 hosted on CRAN and provides functions to list available versions and the
19864 versions of currently installed packages.")
19865 (license license:bsd-3)))
19867 (define-public r-adapr
19874 (uri (cran-uri "adapr" version))
19877 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19878 (properties `((upstream-name . "adapr")))
19879 (build-system r-build-system)
19881 `(("r-archivist" ,r-archivist)
19882 ("r-devtools" ,r-devtools)
19883 ("r-digest" ,r-digest)
19884 ("r-doparallel" ,r-doparallel)
19885 ("r-gdata" ,r-gdata)
19886 ("r-ggplot2" ,r-ggplot2)
19887 ("r-git2r" ,r-git2r)
19888 ("r-igraph" ,r-igraph)
19889 ("r-knitr" ,r-knitr)
19890 ("r-plotly" ,r-plotly)
19892 ("r-rmarkdown" ,r-rmarkdown)
19893 ("r-shiny" ,r-shiny)
19894 ("r-shinydashboard" ,r-shinydashboard)
19895 ("r-versions" ,r-versions)))
19896 (home-page "https://cran.r-project.org/web/packages/adapr/")
19897 (synopsis "Implementation of an accountable data analysis process")
19899 "This package tracks reading and writing within R scripts that are
19900 organized into a directed acyclic graph. It contains an interactive Shiny
19901 application @code{adaprApp()}. It uses Git and file hashes to track version
19902 histories of inputs and outputs.")
19903 (license license:lgpl2.0)))
19905 (define-public r-adapsamp
19907 (name "r-adapsamp")
19912 (uri (cran-uri "AdapSamp" version))
19915 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19916 (properties `((upstream-name . "AdapSamp")))
19917 (build-system r-build-system)
19918 (propagated-inputs `(("r-pracma" ,r-pracma)))
19919 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19920 (synopsis "Adaptive sampling algorithms")
19922 "For distributions whose probability density functions are log-concave,
19923 the adaptive rejection sampling algorithm can be used to build envelope
19924 functions for sampling. For others, the modified adaptive rejection sampling
19925 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19926 adaptive slice sampling algorithm can be used. This R package mainly includes
19927 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19928 @code{rASS()}. These functions can realize sampling based on the algorithms
19930 (license license:gpl2)))
19932 (define-public r-adaptalint
19934 (name "r-adaptalint")
19939 (uri (cran-uri "adaptalint" version))
19942 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19943 (properties `((upstream-name . "adaptalint")))
19944 (build-system r-build-system)
19946 `(("r-dplyr" ,r-dplyr)
19947 ("r-lintr" ,r-lintr)
19948 ("r-purrr" ,r-purrr)))
19949 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19950 (synopsis "Check R code style")
19952 "This package provides tools to infer the code style (which style rules
19953 are followed and which ones are not) from one package and use it to check
19954 another. This makes it easier to find and correct the most important problems
19956 (license license:gpl3)))
19958 (define-public r-fracdiff
19960 (name "r-fracdiff")
19965 (uri (cran-uri "fracdiff" version))
19968 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19969 (properties `((upstream-name . "fracdiff")))
19970 (build-system r-build-system)
19971 (home-page "https://github.com/mmaechler/fracdiff")
19973 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19975 "This package provides tools for the maximum likelihood estimation of the
19976 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19977 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19978 (license license:gpl2+)))
19980 (define-public r-forecast
19982 (name "r-forecast")
19987 (uri (cran-uri "forecast" version))
19990 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
19991 (properties `((upstream-name . "forecast")))
19992 (build-system r-build-system)
19994 `(("r-colorspace" ,r-colorspace)
19995 ("r-fracdiff" ,r-fracdiff)
19996 ("r-ggplot2" ,r-ggplot2)
19997 ("r-lmtest" ,r-lmtest)
19998 ("r-magrittr" ,r-magrittr)
20001 ("r-rcpparmadillo" ,r-rcpparmadillo)
20002 ("r-timedate" ,r-timedate)
20003 ("r-tseries" ,r-tseries)
20007 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20008 (home-page "https://pkg.robjhyndman.com/forecast/")
20009 (synopsis "Forecasting functions for time series and linear models")
20011 "This package provides methods and tools for displaying and analysing
20012 univariate time series forecasts including exponential smoothing via state
20013 space models and automatic ARIMA modelling.")
20014 (license license:gpl3)))
20016 (define-public r-xmisc
20023 (uri (cran-uri "Xmisc" version))
20026 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20027 (properties `((upstream-name . "Xmisc")))
20028 (build-system r-build-system)
20029 (home-page "https://cran.r-project.org/package=Xmisc")
20031 "Xiaobei's miscellaneous classes and functions")
20033 "This package provides Xiaobei's miscellaneous classes and functions,
20034 which are useful when developing R packages for @dfn{object oriented
20035 programming} (OOP) using R Reference Class.")
20036 (license license:gpl2+)))
20038 (define-public r-proxyc
20045 (uri (cran-uri "proxyC" version))
20048 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20049 (properties `((upstream-name . "proxyC")))
20050 (build-system r-build-system)
20052 `(("r-matrix" ,r-matrix)
20054 ("r-rcpparmadillo" ,r-rcpparmadillo)
20055 ("r-rcppparallel" ,r-rcppparallel)))
20056 (home-page "https://cran.r-project.org/package=proxyC")
20057 (synopsis "Compute proximity in large sparse matrices")
20059 "This package provides efficient tools to compute the proximity between
20060 rows or columns of large matrices. Functions are optimised for large sparse
20061 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20062 similarity/distance measures, computation of correlation, cosine similarity
20063 and Euclidean distance is particularly fast.")
20064 (license license:gpl3)))
20066 (define-public r-isocodes
20068 (name "r-isocodes")
20069 (version "2020.03.16")
20073 (uri (cran-uri "ISOcodes" version))
20076 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20077 (properties `((upstream-name . "ISOcodes")))
20078 (build-system r-build-system)
20079 (home-page "https://cran.r-project.org/package=ISOcodes")
20080 (synopsis "Selected ISO codes")
20082 "This package provides ISO language, territory, currency, script and
20083 character codes. It provides ISO 639 language codes, ISO 3166 territory
20084 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20085 character codes as well as the UN M.49 area codes.")
20086 (license license:gpl2)))
20088 (define-public r-stopwords
20090 (name "r-stopwords")
20095 (uri (cran-uri "stopwords" version))
20098 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20099 (properties `((upstream-name . "stopwords")))
20100 (build-system r-build-system)
20102 `(("r-desc" ,r-desc)
20103 ("r-isocodes" ,r-isocodes)
20104 ("r-usethis" ,r-usethis)))
20105 (home-page "https://github.com/quanteda/stopwords")
20106 (synopsis "Multilingual stopword lists")
20108 "This package provides multiple sources of stopwords, for use in text
20109 analysis and natural language processing.")
20110 (license license:expat)))
20112 (define-public r-spacyr
20119 (uri (cran-uri "spacyr" version))
20122 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20123 (properties `((upstream-name . "spacyr")))
20124 (build-system r-build-system)
20126 `(("r-data-table" ,r-data-table)
20127 ("r-reticulate" ,r-reticulate)))
20128 (home-page "https://spacyr.quanteda.io")
20129 (synopsis "R wrapper for the spaCy NLP library")
20131 "This package provides an R wrapper to the Python @dfn{natural language
20132 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20133 (license license:gpl3)))
20135 (define-public r-snowballc
20137 (name "r-snowballc")
20142 (uri (cran-uri "SnowballC" version))
20145 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20146 (properties `((upstream-name . "SnowballC")))
20147 (build-system r-build-system)
20148 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20149 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20151 "This package provides an R interface to the C @code{libstemmer} library
20152 that implements Porter's word stemming algorithm for collapsing words to a
20153 common root to aid comparison of vocabulary. Currently supported languages
20154 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20155 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20156 (license license:bsd-3)))
20158 (define-public r-quanteda
20160 (name "r-quanteda")
20165 (uri (cran-uri "quanteda" version))
20168 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
20169 (properties `((upstream-name . "quanteda")))
20170 (build-system r-build-system)
20172 `(("r-data-table" ,r-data-table)
20173 ("r-extrafont" ,r-extrafont)
20174 ("r-fastmatch" ,r-fastmatch)
20175 ("r-ggplot2" ,r-ggplot2)
20176 ("r-ggrepel" ,r-ggrepel)
20177 ("r-jsonlite" ,r-jsonlite)
20178 ("r-magrittr" ,r-magrittr)
20179 ("r-matrix" ,r-matrix)
20180 ("r-network" ,r-network)
20181 ("r-proxyc" ,r-proxyc)
20183 ("r-rcpparmadillo" ,r-rcpparmadillo)
20184 ("r-rcppparallel" ,r-rcppparallel)
20186 ("r-snowballc" ,r-snowballc)
20187 ("r-stopwords" ,r-stopwords)
20188 ("r-stringi" ,r-stringi)
20190 ("r-yaml" ,r-yaml)))
20192 `(("r-knitr" ,r-knitr)))
20193 (home-page "https://quanteda.io")
20194 (synopsis "Quantitative analysis of textual data")
20196 "This package provides a fast, flexible, and comprehensive framework for
20197 quantitative text analysis in R. It provides functionality for corpus
20198 management, creating and manipulating tokens and ngrams, exploring keywords in
20199 context, forming and manipulating sparse matrices of documents by features and
20200 feature co-occurrences, analyzing keywords, computing feature similarities and
20201 distances, applying content dictionaries, applying supervised and unsupervised
20202 machine learning, visually representing text and text analyses, and more.")
20203 (license license:gpl3)))
20205 (define-public r-topicmodels
20207 (name "r-topicmodels")
20212 (uri (cran-uri "topicmodels" version))
20215 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20216 (properties `((upstream-name . "topicmodels")))
20217 (build-system r-build-system)
20221 `(("r-modeltools" ,r-modeltools)
20224 (home-page "https://cran.r-project.org/package=topicmodels")
20225 (synopsis "Topic models")
20227 "This package provides an interface to the C code for @dfn{Latent
20228 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20229 David M. Blei and co-authors and the C++ code for fitting LDA models using
20230 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20231 (license license:gpl2)))
20233 (define-public r-stm
20240 (uri (cran-uri "stm" version))
20243 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20244 (properties `((upstream-name . "stm")))
20245 (build-system r-build-system)
20247 `(("r-data-table" ,r-data-table)
20248 ("r-glmnet" ,r-glmnet)
20250 ("r-matrix" ,r-matrix)
20251 ("r-matrixstats" ,r-matrixstats)
20252 ("r-quadprog" ,r-quadprog)
20253 ("r-quanteda" ,r-quanteda)
20255 ("r-rcpparmadillo" ,r-rcpparmadillo)
20257 ("r-stringr" ,r-stringr)))
20258 (home-page "http://www.structuraltopicmodel.com/")
20259 (synopsis "Estimation of the Structural Topic Model")
20261 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20262 topic models with document-level covariates. The package also includes tools
20263 for model selection, visualization, and estimation of topic-covariate
20265 (license license:expat)))
20267 (define-public r-polycor
20274 (uri (cran-uri "polycor" version))
20277 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20278 (properties `((upstream-name . "polycor")))
20279 (build-system r-build-system)
20281 `(("r-matrix" ,r-matrix)
20282 ("r-mvtnorm" ,r-mvtnorm)))
20283 (home-page "https://r-forge.r-project.org/projects/polycor/")
20284 (synopsis "Polychoric and polyserial correlations")
20286 "This package provides tools to compute polychoric and polyserial
20287 correlations by quick \"two-step\" methods or ML, optionally with standard
20288 errors; tetrachoric and biserial correlations are special cases.")
20289 (license license:gpl2+)))
20291 (define-public r-msm
20298 (uri (cran-uri "msm" version))
20301 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20302 (properties `((upstream-name . "msm")))
20303 (build-system r-build-system)
20305 `(("r-expm" ,r-expm)
20306 ("r-mvtnorm" ,r-mvtnorm)
20307 ("r-survival" ,r-survival)))
20308 (home-page "https://github.com/chjackson/msm")
20309 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20311 "This package provides functions for fitting continuous-time Markov and
20312 hidden Markov multi-state models to longitudinal data. It was designed for
20313 processes observed at arbitrary times in continuous time (panel data) but some
20314 other observation schemes are supported. Both Markov transition rates and the
20315 hidden Markov output process can be modelled in terms of covariates, which may
20316 be constant or piecewise-constant in time.")
20317 (license license:gpl2+)))
20319 (define-public r-ltm
20326 (uri (cran-uri "ltm" version))
20329 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20330 (properties `((upstream-name . "ltm")))
20331 (build-system r-build-system)
20333 `(("r-mass" ,r-mass)
20335 ("r-polycor" ,r-polycor)))
20336 (home-page "https://github.com/drizopoulos/ltm")
20337 (synopsis "Latent trait models under IRT")
20339 "This is a package supporting the analysis of multivariate dichotomous
20340 and polytomous data using latent trait models under the Item Response Theory
20341 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20342 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20344 (license license:gpl2+)))
20346 (define-public r-mi
20353 (uri (cran-uri "mi" version))
20356 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20357 (properties `((upstream-name . "mi")))
20358 (build-system r-build-system)
20361 ("r-matrix" ,r-matrix)))
20362 (home-page "http://www.stat.columbia.edu/~gelman/")
20363 (synopsis "Missing data imputation and model checking")
20365 "This package provides functions for data manipulation, imputing missing
20366 values in an approximate Bayesian framework, diagnostics of the models used to
20367 generate the imputations, confidence-building mechanisms to validate some of
20368 the assumptions of the imputation algorithm, and functions to analyze multiply
20369 imputed data sets with the appropriate degree of sampling uncertainty.")
20370 (license license:gpl2+)))
20372 (define-public r-matrixcalc
20374 (name "r-matrixcalc")
20379 (uri (cran-uri "matrixcalc" version))
20382 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20383 (properties `((upstream-name . "matrixcalc")))
20384 (build-system r-build-system)
20385 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20386 (synopsis "Collection of functions for matrix calculations")
20388 "This package provides a collection of functions to support matrix
20389 calculations for probability, econometric and numerical analysis. There are
20390 additional functions that are comparable to APL functions which are useful for
20391 actuarial models such as pension mathematics.")
20392 (license license:gpl2+)))
20394 (define-public r-sem
20401 (uri (cran-uri "sem" version))
20404 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20405 (properties `((upstream-name . "sem")))
20406 (build-system r-build-system)
20408 `(("r-boot" ,r-boot)
20410 ("r-matrixcalc" ,r-matrixcalc)
20412 (home-page "https://cran.r-project.org/package=sem")
20413 (synopsis "Structural equation models")
20415 "This package provides functions for fitting general linear structural
20416 equation models (with observed and latent variables) using the RAM approach,
20417 and for fitting structural equations in observed-variable models by two-stage
20419 (license license:gpl2+)))
20421 (define-public r-semtools
20423 (name "r-semtools")
20428 (uri (cran-uri "semTools" version))
20431 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20432 (properties `((upstream-name . "semTools")))
20433 (build-system r-build-system)
20435 `(("r-lavaan" ,r-lavaan)))
20436 (home-page "https://github.com/simsem/semTools/wiki")
20437 (synopsis "Useful tools for structural equation modeling")
20439 "This package provides useful tools for structural equation modeling.")
20440 (license license:gpl2+)))
20442 (define-public r-regsem
20449 (uri (cran-uri "regsem" version))
20452 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20453 (properties `((upstream-name . "regsem")))
20454 (build-system r-build-system)
20456 `(("r-lavaan" ,r-lavaan)
20458 ("r-rcpparmadillo" ,r-rcpparmadillo)
20459 ("r-rsolnp" ,r-rsolnp)))
20460 (home-page "https://cran.r-project.org/package=regsem")
20461 (synopsis "Regularized structural equation modeling")
20463 "This package uses both ridge and lasso penalties (and extensions) to
20464 penalize specific parameters in structural equation models. The package
20465 offers additional cost functions, cross validation, and other extensions
20466 beyond traditional structural equation models. It also contains a function to
20467 perform @dfn{exploratory mediation} (XMed).")
20468 (license license:gpl2+)))
20470 (define-public r-stanheaders
20472 (name "r-stanheaders")
20473 (version "2.21.0-5")
20477 (uri (cran-uri "StanHeaders" version))
20480 "1zyph2x47x9a5baj5d79a1lzj7gajirisajvkrcngrjvw8bq7810"))))
20481 (properties `((upstream-name . "StanHeaders")))
20482 (build-system r-build-system)
20483 (inputs `(("pandoc" ,ghc-pandoc)))
20485 `(("r-rcppeigen" ,r-rcppeigen)
20486 ("r-rcppparallel" ,r-rcppparallel)))
20488 `(("gfortran" ,gfortran)
20489 ("r-knitr" ,r-knitr))) ; for vignettes
20490 (home-page "https://mc-stan.org/")
20491 (synopsis "C++ header files for Stan")
20493 "The C++ header files of the Stan project are provided by this package.
20494 There is a shared object containing part of the @code{CVODES} library, but it
20495 is not accessible from R. @code{r-stanheaders} is only useful for developers
20496 who want to utilize the @code{LinkingTo} directive of their package's
20497 DESCRIPTION file to build on the Stan library without incurring unnecessary
20500 The Stan project develops a probabilistic programming language that implements
20501 full or approximate Bayesian statistical inference via Markov Chain Monte
20502 Carlo or variational methods and implements (optionally penalized) maximum
20503 likelihood estimation via optimization. The Stan library includes an advanced
20504 automatic differentiation scheme, templated statistical and linear algebra
20505 functions that can handle the automatically differentiable scalar types (and
20506 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20507 package provides user-facing R functions to parse, compile, test, estimate,
20508 and analyze Stan models.")
20509 (license license:bsd-3)))
20511 (define-public r-rpf
20518 (uri (cran-uri "rpf" version))
20521 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20522 (properties `((upstream-name . "rpf")))
20523 (build-system r-build-system)
20525 `(("r-lifecycle" ,r-lifecycle)
20526 ("r-mvtnorm" ,r-mvtnorm)
20528 ("r-rcppeigen" ,r-rcppeigen)))
20530 `(("r-knitr" ,r-knitr)))
20531 (home-page "https://github.com/jpritikin/rpf")
20532 (synopsis "Response probability functions")
20534 "The purpose of this package is to factor out logic and math common to
20535 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20536 core support code suitable for more specialized IRT packages to build upon.
20537 Complete access to optimized C functions is made available with
20538 @code{R_RegisterCCallable()}.")
20539 (license license:gpl3+)))
20541 (define-public r-openmx
20548 (uri (cran-uri "OpenMx" version))
20551 "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
20552 (properties `((upstream-name . "OpenMx")))
20553 (build-system r-build-system)
20556 ("r-digest" ,r-digest)
20558 ("r-matrix" ,r-matrix)
20560 ("r-rcppeigen" ,r-rcppeigen)
20562 ("r-stanheaders" ,r-stanheaders)))
20563 (native-inputs `(("gfortran" ,gfortran)))
20564 (home-page "http://openmx.ssri.psu.edu")
20565 (synopsis "Extended structural equation modelling")
20567 "This package allows for the estimation of a wide variety of advanced
20568 multivariate statistical models. It consists of a library of functions and
20569 optimizers that allow you to quickly and flexibly define an SEM model and
20570 estimate parameters given observed data.")
20571 (license license:asl2.0)))
20573 (define-public r-kutils
20580 (uri (cran-uri "kutils" version))
20583 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20584 (properties `((upstream-name . "kutils")))
20585 (build-system r-build-system)
20587 `(("r-foreign" ,r-foreign)
20588 ("r-openxlsx" ,r-openxlsx)
20590 ("r-runit" ,r-runit)
20591 ("r-xtable" ,r-xtable)))
20592 (home-page "https://cran.r-project.org/package=kutils")
20593 (synopsis "Project management tools")
20595 "This package provides tools for data importation, recoding, and
20596 inspection. There are functions to create new project folders, R code
20597 templates, create uniquely named output directories, and to quickly obtain a
20598 visual summary for each variable in a data frame. The main feature here is
20599 the systematic implementation of the \"variable key\" framework for data
20600 importation and recoding.")
20601 (license license:gpl2)))
20603 (define-public r-rockchalk
20605 (name "r-rockchalk")
20606 (version "1.8.144")
20610 (uri (cran-uri "rockchalk" version))
20613 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20614 (properties `((upstream-name . "rockchalk")))
20615 (build-system r-build-system)
20617 `(("r-cardata" ,r-cardata)
20618 ("r-kutils" ,r-kutils)
20620 ("r-mass" ,r-mass)))
20621 (home-page "https://cran.r-project.org/package=rockchalk")
20622 (synopsis "Regression estimation and presentation")
20624 "This package provides a collection of functions for interpretation and
20625 presentation of regression analysis. These functions are used to produce the
20626 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20627 includes regression diagnostics, regression tables, and plots of interactions
20628 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20629 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20630 fairly comprehensive overview.")
20631 (license license:gpl3+)))
20633 (define-public r-lisreltor
20635 (name "r-lisreltor")
20640 (uri (cran-uri "lisrelToR" version))
20643 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20644 (properties `((upstream-name . "lisrelToR")))
20645 (build-system r-build-system)
20646 (home-page "https://cran.r-project.org/package=lisrelToR")
20647 (synopsis "Import output from LISREL into R")
20649 "This is an unofficial package aimed at automating the import of LISREL
20651 (license license:gpl2)))
20653 (define-public r-bdgraph
20660 (uri (cran-uri "BDgraph" version))
20663 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20664 (properties `((upstream-name . "BDgraph")))
20665 (build-system r-build-system)
20667 `(("r-igraph" ,r-igraph)))
20668 (home-page "https://www.uva.nl/profile/a.mohammadi")
20669 (synopsis "Bayesian structure learning in graphical models")
20671 "This package provides statistical tools for Bayesian structure learning
20672 in undirected graphical models for continuous, discrete, and mixed data. It
20673 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20674 on a continuous-time birth-death process.")
20675 (license license:gpl2+)))
20677 (define-public r-d3network
20679 (name "r-d3network")
20680 (version "0.5.2.1")
20684 (uri (cran-uri "d3Network" version))
20687 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20688 (properties `((upstream-name . "d3Network")))
20689 (build-system r-build-system)
20691 `(("r-plyr" ,r-plyr)
20692 ("r-rjson" ,r-rjson)
20693 ("r-whisker" ,r-whisker)))
20694 (home-page "http://christophergandrud.github.io/d3Network/")
20695 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20697 "This package is intended to make it easy to create D3 JavaScript
20698 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20699 (license license:gpl3+)))
20701 (define-public r-qgraph
20708 (uri (cran-uri "qgraph" version))
20711 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20712 (properties `((upstream-name . "qgraph")))
20713 (build-system r-build-system)
20715 `(("r-abind" ,r-abind)
20716 ("r-bdgraph" ,r-bdgraph)
20717 ("r-colorspace" ,r-colorspace)
20718 ("r-corpcor" ,r-corpcor)
20719 ("r-d3network" ,r-d3network)
20720 ("r-dplyr" ,r-dplyr)
20721 ("r-fdrtool" ,r-fdrtool)
20722 ("r-ggplot2" ,r-ggplot2)
20723 ("r-ggraph" ,r-ggraph)
20724 ("r-glasso" ,r-glasso)
20725 ("r-gtools" ,r-gtools)
20726 ("r-hmisc" ,r-hmisc)
20728 ("r-igraph" ,r-igraph)
20730 ("r-lavaan" ,r-lavaan)
20731 ("r-matrix" ,r-matrix)
20732 ("r-pbapply" ,r-pbapply)
20735 ("r-psych" ,r-psych)
20737 ("r-reshape2" ,r-reshape2)
20738 ("r-tidygraph" ,r-tidygraph)))
20739 (home-page "http://sachaepskamp.com/qgraph/")
20740 (synopsis "Weighted network visualization and analysis")
20742 "This package implements tools for weighted network visualization and
20743 analysis, as well as Gaussian graphical model computation. It contains graph
20744 plotting methods, and tools for psychometric data visualization and graphical
20745 model estimation. See Epskamp et al. (2012)
20746 @url{doi:10.18637/jss.v048.i04}.")
20747 (license license:gpl2)))
20749 (define-public r-semplot
20756 (uri (cran-uri "semPlot" version))
20759 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20760 (properties `((upstream-name . "semPlot")))
20761 (build-system r-build-system)
20763 `(("r-colorspace" ,r-colorspace)
20764 ("r-corpcor" ,r-corpcor)
20765 ("r-igraph" ,r-igraph)
20766 ("r-lavaan" ,r-lavaan)
20767 ("r-lisreltor" ,r-lisreltor)
20768 ("r-openmx" ,r-openmx)
20770 ("r-qgraph" ,r-qgraph)
20771 ("r-regsem" ,r-regsem)
20772 ("r-rockchalk" ,r-rockchalk)
20775 (home-page "https://github.com/SachaEpskamp/semPlot")
20776 (synopsis "Unified visualizations of structural equation models")
20778 "Structural equation modeling (SEM) has a long history of representing
20779 models graphically as path diagrams. The semPlot package for R fills the gap
20780 between advanced, but time-consuming, graphical software and the limited
20781 graphics produced automatically by SEM software. In addition, semPlot offers
20782 more functionality than drawing path diagrams: it can act as a common ground
20783 for importing SEM results into R. Any result usable as input to semPlot can
20784 also be represented in any of the three popular SEM frame-works, as well as
20785 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20786 (license license:gpl2)))
20788 (define-public r-cdm
20795 (uri (cran-uri "CDM" version))
20798 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20799 (properties `((upstream-name . "CDM")))
20800 (build-system r-build-system)
20802 `(("r-mvtnorm" ,r-mvtnorm)
20803 ("r-polycor" ,r-polycor)
20805 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20807 "https://github.com/alexanderrobitzsch/CDM")
20808 (synopsis "Cognitive diagnosis modeling")
20810 "This package provides functions for cognitive diagnosis modeling and
20811 multidimensional item response modeling for dichotomous and polytomous item
20812 responses. It enables the estimation of the DINA and DINO model, the multiple
20813 group (polytomous) GDINA model, the multiple choice DINA model, the general
20814 diagnostic model (GDM), the structured latent class model (SLCA), and
20815 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20816 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20817 estimation and the package structure. For tutorials on how to use the CDM
20818 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20819 well as Ravand and Robitzsch (2015).")
20820 (license license:gpl2+)))
20822 (define-public r-tam
20829 (uri (cran-uri "TAM" version))
20832 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
20833 (properties `((upstream-name . "TAM")))
20834 (build-system r-build-system)
20838 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20839 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20840 (synopsis "Test analysis modules")
20842 "This package includes tools for marginal maximum likelihood estimation
20843 and joint maximum likelihood estimation for unidimensional and
20844 multidimensional item response models. The package functionality covers the
20845 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20846 multi-faceted Rasch model, nominal item response model, structured latent
20847 class model, mixture distribution IRT models, and located latent class models.
20848 Latent regression models and plausible value imputation are also supported.")
20849 (license license:gpl2+)))
20851 (define-public r-erm
20858 (uri (cran-uri "eRm" version))
20861 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20862 (properties `((upstream-name . "eRm")))
20863 (build-system r-build-system)
20865 `(("r-colorspace" ,r-colorspace)
20866 ("r-lattice" ,r-lattice)
20868 ("r-matrix" ,r-matrix)
20869 ("r-psych" ,r-psych)))
20870 (native-inputs `(("gfortran" ,gfortran)))
20871 (home-page "https://cran.r-project.org/package=eRm")
20872 (synopsis "Extended Rasch modeling")
20874 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20875 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20876 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20877 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20878 data matrix. Additional features are the ML estimation of the person
20879 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20880 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20881 infit and outfit measures, ICC and other plots, automated stepwise item
20882 elimination, and a simulation module for various binary data matrices.")
20883 (license license:gpl3)))
20885 (define-public r-irtoys
20892 (uri (cran-uri "irtoys" version))
20895 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20896 (properties `((upstream-name . "irtoys")))
20897 (build-system r-build-system)
20901 (home-page "https://cran.r-project.org/package=irtoys")
20902 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20904 "This package provides a collection of functions useful in learning and
20905 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20906 programs. It provides basic CTT analysis, a simple common interface to the
20907 estimation of item parameters in IRT models for binary responses with three
20908 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20909 EAP, WLE, plausible values), item and person fit statistics, scaling
20910 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20911 array of parametric and non-parametric (kernel) plots. It estimates and plots
20912 Haberman's interaction model when all items are dichotomously scored.")
20913 (license license:gpl2+)))
20915 (define-public r-iheatmapr
20917 (name "r-iheatmapr")
20922 (uri (cran-uri "iheatmapr" version))
20925 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20926 (properties `((upstream-name . "iheatmapr")))
20927 (build-system r-build-system)
20929 `(("r-fastcluster" ,r-fastcluster)
20930 ("r-ggdendro" ,r-ggdendro)
20931 ("r-htmlwidgets" ,r-htmlwidgets)
20932 ("r-jsonlite" ,r-jsonlite)
20933 ("r-knitr" ,r-knitr)
20934 ("r-magrittr" ,r-magrittr)
20936 ("r-rcolorbrewer" ,r-rcolorbrewer)
20937 ("r-s4vectors" ,r-s4vectors)
20938 ("r-scales" ,r-scales)))
20939 (home-page "https://docs.ropensci.org/iheatmapr")
20940 (synopsis "Interactive, Complex Heatmaps")
20942 "iheatmapr is an R package for building complex, interactive heatmaps
20943 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20944 subplots along the rows or columns of the main heatmap add more information
20945 about each row or column. For example, a one column additional heatmap may
20946 indicate what group a particular row or column belongs to. Complex heatmaps
20947 may also include multiple side by side heatmaps which show different types of
20948 data for the same conditions. Interactivity can improve complex heatmaps by
20949 providing tooltips with information about each cell and enabling zooming into
20950 interesting features. iheatmapr uses the plotly library for interactivity.")
20951 (license license:expat)))
20953 (define-public r-packrat
20960 (uri (cran-uri "packrat" version))
20963 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20964 (properties `((upstream-name . "packrat")))
20965 (build-system r-build-system)
20966 (home-page "https://github.com/rstudio/packrat/")
20967 (synopsis "Dependency management R projects")
20969 "This package provides a dependency manager for R projects that allows
20970 you to manage the R packages your project depends on in an isolated, portable,
20971 and reproducible way.")
20972 (license license:gpl2)))
20974 (define-public r-rsconnect
20976 (name "r-rsconnect")
20981 (uri (cran-uri "rsconnect" version))
20984 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20985 (properties `((upstream-name . "rsconnect")))
20986 (build-system r-build-system)
20988 `(("r-curl" ,r-curl)
20989 ("r-digest" ,r-digest)
20990 ("r-jsonlite" ,r-jsonlite)
20991 ("r-openssl" ,r-openssl)
20992 ("r-packrat" ,r-packrat)
20993 ("r-rstudioapi" ,r-rstudioapi)
20994 ("r-yaml" ,r-yaml)))
20995 (home-page "https://github.com/rstudio/rsconnect")
20996 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
20998 "This package provides a programmatic deployment interface for RPubs,
20999 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21000 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21001 (license license:gpl2)))
21003 ;; This package includes minified JavaScript files. When upgrading please
21004 ;; check that there are no new minified JavaScript files.
21005 (define-public r-dygraphs
21007 (name "r-dygraphs")
21008 (version "1.1.1.6")
21012 (uri (cran-uri "dygraphs" version))
21015 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21016 (properties `((upstream-name . "dygraphs")))
21017 (build-system r-build-system)
21019 `(#:modules ((guix build utils)
21020 (guix build r-build-system)
21024 (modify-phases %standard-phases
21025 (add-after 'unpack 'process-javascript
21026 (lambda* (#:key inputs #:allow-other-keys)
21027 (with-directory-excursion "inst/htmlwidgets/lib/"
21031 `(("dygraphs/dygraph-combined-dev.js"
21032 "dygraph-combined.js")
21033 (,(assoc-ref inputs "js-jquery")
21034 "jquery/jquery.min.js")
21035 (,(assoc-ref inputs "js-fquarter")
21036 "fquarter/moment-fquarter.min.js"))))
21037 (lambda (sources targets)
21038 (for-each (lambda (source target)
21039 (format #t "Processing ~a --> ~a~%"
21041 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21042 (call-with-output-file target
21044 (dump-port minified port)))))
21045 sources targets))))
21048 `(("uglify-js" ,uglify-js)
21049 ;; They actually use version 1.11.1, but this more recent version
21050 ;; should be just fine.
21054 (uri "https://code.jquery.com/jquery-1.12.4.js")
21057 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21061 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21062 "moment-fquarter/1.0.1/moment-fquarter.js"))
21065 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21067 `(("r-htmltools" ,r-htmltools)
21068 ("r-htmlwidgets" ,r-htmlwidgets)
21069 ("r-magrittr" ,r-magrittr)
21072 (home-page "https://github.com/rstudio/dygraphs")
21073 (synopsis "Interface to Dygraphs interactive time series charting library")
21075 "This package provides an R interface to the dygraphs JavaScript charting
21076 library (a copy of which is included in the package). It provides rich
21077 facilities for charting time-series data in R, including highly configurable
21078 series- and axis-display and interactive features like zoom/pan and
21079 series/point highlighting.")
21080 (license license:expat)))
21082 (define-public r-shinystan
21084 (name "r-shinystan")
21089 (uri (cran-uri "shinystan" version))
21092 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21093 (properties `((upstream-name . "shinystan")))
21094 (build-system r-build-system)
21096 `(("r-bayesplot" ,r-bayesplot)
21097 ("r-colourpicker" ,r-colourpicker)
21099 ("r-dygraphs" ,r-dygraphs)
21100 ("r-ggplot2" ,r-ggplot2)
21101 ("r-gridextra" ,r-gridextra)
21102 ("r-gtools" ,r-gtools)
21103 ("r-markdown" ,r-markdown)
21104 ("r-reshape2" ,r-reshape2)
21105 ("r-rsconnect" ,r-rsconnect)
21106 ("r-rstan" ,r-rstan)
21107 ("r-shiny" ,r-shiny)
21108 ("r-shinyjs" ,r-shinyjs)
21109 ("r-shinythemes" ,r-shinythemes)
21110 ("r-threejs" ,r-threejs)
21111 ("r-xtable" ,r-xtable)
21113 (home-page "https://mc-stan.org/")
21114 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21116 "This package provides a graphical user interface for interactive
21117 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21118 for analyzing a posterior sample. The interface is powered by the Shiny web
21119 application framework and works with the output of MCMC programs written in
21120 any programming language (and has extended functionality for Stan models fit
21121 using the @code{rstan} and @code{rstanarm} packages).")
21122 (license license:gpl3+)))
21124 (define-public r-rstantools
21126 (name "r-rstantools")
21131 (uri (cran-uri "rstantools" version))
21134 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
21135 (properties `((upstream-name . "rstantools")))
21136 (build-system r-build-system)
21137 (inputs `(("pandoc" ,ghc-pandoc)))
21139 `(("r-desc" ,r-desc)
21140 ("r-rcpp" ,r-rcpp)))
21141 (home-page "https://mc-stan.org/rstantools/")
21142 (synopsis "Tools for developing R packages interfacing with Stan")
21144 "This package provides various tools for developers of R packages
21145 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21146 up the required package structure, S3 generics and default methods to unify
21147 function naming across Stan-based R packages, and vignettes with
21148 recommendations for developers.")
21149 (license license:gpl3+)))
21151 (define-public r-loo
21158 (uri (cran-uri "loo" version))
21161 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
21162 (properties `((upstream-name . "loo")))
21163 (build-system r-build-system)
21165 `(("pandoc" ,ghc-pandoc)
21166 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21168 `(("r-checkmate" ,r-checkmate)
21169 ("r-matrixstats" ,r-matrixstats)))
21170 (home-page "https://mc-stan.org/loo/")
21171 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21173 "This package provides an implementation of efficient approximate
21174 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21175 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21176 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21177 procedure for regularizing importance weights. As a byproduct of the
21178 calculations, we also obtain approximate standard errors for estimated
21179 predictive errors and for the comparison of predictive errors between models.
21180 The package also provides methods for using stacking and other model weighting
21181 techniques to average Bayesian predictive distributions.")
21182 (license license:gpl3+)))
21184 (define-public r-rstan
21191 (uri (cran-uri "rstan" version))
21194 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
21195 (properties `((upstream-name . "rstan")))
21196 (build-system r-build-system)
21199 (modify-phases %standard-phases
21200 (add-before 'install 'set-timezone
21201 ;; This package is picky about timezones.
21202 (lambda* (#:key inputs #:allow-other-keys)
21203 (setenv "TZ" "UTC+1")
21205 (string-append (assoc-ref inputs "tzdata")
21206 "/share/zoneinfo"))
21209 `(("tzdata" ,tzdata-for-tests)
21210 ("pandoc" ,ghc-pandoc)))
21213 ("r-ggplot2" ,r-ggplot2)
21214 ("r-gridextra" ,r-gridextra)
21215 ("r-inline" ,r-inline)
21217 ("r-pkgbuild" ,r-pkgbuild)
21219 ("r-rcppeigen" ,r-rcppeigen)
21220 ("r-stanheaders" ,r-stanheaders)))
21221 (home-page "https://discourse.mc-stan.org/")
21222 (synopsis "R interface to Stan")
21224 "User-facing R functions are provided to parse, compile, test, estimate,
21225 and analyze Stan models by accessing the header-only Stan library provided by
21226 the StanHeaders package. The Stan project develops a probabilistic
21227 programming language that implements full Bayesian statistical inference via
21228 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21229 approximation, and (optionally penalized) maximum likelihood estimation via
21230 optimization. In all three cases, automatic differentiation is used to
21231 quickly and accurately evaluate gradients without burdening the user with the
21232 need to derive the partial derivatives.")
21233 (license license:gpl3+)))
21235 (define-public r-rstanarm
21237 (name "r-rstanarm")
21242 (uri (cran-uri "rstanarm" version))
21245 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
21246 (properties `((upstream-name . "rstanarm")))
21247 (build-system r-build-system)
21249 `(("pandoc" ,ghc-pandoc)
21250 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21252 `(("r-bayesplot" ,r-bayesplot)
21254 ("r-ggplot2" ,r-ggplot2)
21257 ("r-matrix" ,r-matrix)
21260 ("r-rcppeigen" ,r-rcppeigen)
21261 ("r-rcppparallel" ,r-rcppparallel)
21262 ("r-rstan" ,r-rstan)
21263 ("r-rstantools" ,r-rstantools)
21264 ("r-shinystan" ,r-shinystan)
21265 ("r-stanheaders" ,r-stanheaders)
21266 ("r-survival" ,r-survival)))
21267 (home-page "https://mc-stan.org/rstanarm/")
21268 (synopsis "Bayesian applied regression modeling via Stan")
21270 "This package estimates previously compiled regression models using the
21271 @code{rstan} package, which provides the R interface to the Stan C++ library
21272 for Bayesian estimation. Users specify models via the customary R syntax with
21273 a formula and @code{data.frame} plus some additional arguments for priors.")
21274 (license license:gpl3+)))
21276 (define-public r-kendall
21283 (uri (cran-uri "Kendall" version))
21286 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21287 (properties `((upstream-name . "Kendall")))
21288 (build-system r-build-system)
21290 `(("r-boot" ,r-boot)))
21292 `(("gfortran" ,gfortran)))
21293 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21294 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21296 "This package computes the Kendall rank correlation and Mann-Kendall
21298 (license license:gpl2+)))
21300 (define-public r-zyp
21303 (version "0.10-1.1")
21307 (uri (cran-uri "zyp" version))
21310 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21311 (properties `((upstream-name . "zyp")))
21312 (build-system r-build-system)
21314 `(("r-kendall" ,r-kendall)))
21315 (home-page "https://cran.r-project.org/web/packages/zyp/")
21316 (synopsis "Zhang + Yue-Pilon Trends Package")
21318 "This package contains an efficient implementation of Sen's slope
21319 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21320 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21322 (license license:lgpl2.1)))
21324 (define-public r-rlinsolve
21326 (name "r-rlinsolve")
21331 (uri (cran-uri "Rlinsolve" version))
21334 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21335 (properties `((upstream-name . "Rlinsolve")))
21336 (build-system r-build-system)
21338 `(("r-matrix" ,r-matrix)
21340 ("r-rcpparmadillo" ,r-rcpparmadillo)
21341 ("r-rdpack" ,r-rdpack)))
21342 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21343 (synopsis "Iterative solvers for (sparse) linear system of equations")
21345 "Solving a system of linear equations is one of the most fundamental
21346 computational problems for many fields of mathematical studies, such as
21347 regression problems from statistics or numerical partial differential
21348 equations. This package provides basic stationary iterative solvers such as
21349 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21350 Nonstationary, also known as Krylov subspace methods are also provided.
21351 Sparse matrix computation is also supported in that solving large and sparse
21352 linear systems can be manageable using the @code{Matrix} package along with
21353 @code{RcppArmadillo}.")
21354 (license license:gpl3+)))
21356 (define-public r-zvcv
21363 (uri (cran-uri "ZVCV" version))
21366 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21367 (properties `((upstream-name . "ZVCV")))
21368 (build-system r-build-system)
21370 `(("r-abind" ,r-abind)
21372 ("r-dplyr" ,r-dplyr)
21373 ("r-glmnet" ,r-glmnet)
21374 ("r-magrittr" ,r-magrittr)
21375 ("r-mvtnorm" ,r-mvtnorm)
21377 ("r-rcpparmadillo" ,r-rcpparmadillo)
21378 ("r-rlinsolve" ,r-rlinsolve)))
21379 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21380 (synopsis "Zero-Variance Control Variates")
21382 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21383 to reduce the variance of Monte Carlo estimators of expectations using the
21384 derivatives of the log target. Once the derivatives are available, the only
21385 additional computational effort is in solving a linear regression problem.
21386 This method has been extended to higher dimensions using regularisation. This
21387 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21388 samples, derivatives and function evaluations are available. Additional
21389 functions for applying ZV-CV to two estimators for the normalising constant of
21390 the posterior distribution in Bayesian statistics are also supplied.")
21391 (license license:gpl2+)))
21393 (define-public r-ztype
21400 (uri (cran-uri "ztype" version))
21403 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21404 (properties `((upstream-name . "ztype")))
21405 (build-system r-build-system)
21407 `(("r-assertthat" ,r-assertthat)
21408 ("r-dplyr" ,r-dplyr)
21409 ("r-ggplot2" ,r-ggplot2)
21410 ("r-lubridate" ,r-lubridate)
21411 ("r-magrittr" ,r-magrittr)
21412 ("r-rvest" ,r-rvest)
21413 ("r-stringr" ,r-stringr)))
21414 (home-page "https://cran.r-project.org/web/packages/ztype/")
21415 (synopsis "Run a Ztype game loaded with R functions")
21417 "How fast can you type R functions on your keyboard? Find out by running
21418 a @code{zty.pe} game: export R functions as instructions to type to destroy
21419 opponents' vessels.")
21420 (license license:gpl3)))
21422 (define-public r-zseq
21429 (uri (cran-uri "Zseq" version))
21432 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21433 (properties `((upstream-name . "Zseq")))
21434 (build-system r-build-system)
21436 `(("r-gmp" ,r-gmp)))
21437 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21438 (synopsis "Integer sequence generator")
21440 "This package generates well-known integer sequences. The @code{gmp}
21441 package is adopted for computing with arbitrarily large numbers. Every
21442 function has a hyperlink to its corresponding item in the @dfn{On-Line
21443 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21444 (license license:gpl3+)))
21446 (define-public r-isoband
21453 (uri (cran-uri "isoband" version))
21456 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21457 (properties `((upstream-name . "isoband")))
21458 (build-system r-build-system)
21460 `(("r-testthat" ,r-testthat)))
21462 `(("r-knitr" ,r-knitr)))
21463 (home-page "https://github.com/wilkelab/isoband")
21464 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21466 "This package provides a fast C++ implementation to generate contour
21467 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21468 containing elevation data.")
21469 (license license:expat)))
21471 (define-public r-ppcor
21478 (uri (cran-uri "ppcor" version))
21481 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21482 (properties `((upstream-name . "ppcor")))
21483 (build-system r-build-system)
21485 `(("r-mass" ,r-mass)))
21486 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21487 (synopsis "Partial and semi-partial correlation")
21489 "This package provides users not only with a function to readily
21490 calculate the higher-order partial and semi-partial correlations but also with
21491 statistics and p-values of the correlation coefficients.")
21492 (license license:gpl2)))
21494 (define-public r-hrbrthemes
21496 (name "r-hrbrthemes")
21501 (uri (cran-uri "hrbrthemes" version))
21503 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21504 (properties `((upstream-name . "hrbrthemes")))
21505 (build-system r-build-system)
21507 `(("r-extrafont" ,r-extrafont)
21508 ("r-gdtools" ,r-gdtools)
21509 ("r-ggplot2" ,r-ggplot2)
21510 ("r-htmltools" ,r-htmltools)
21511 ("r-knitr" ,r-knitr)
21512 ("r-magrittr" ,r-magrittr)
21513 ("r-rmarkdown" ,r-rmarkdown)
21514 ("r-scales" ,r-scales)))
21516 `(("r-knitr" ,r-knitr)))
21517 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21518 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21520 "This package provides a compilation of extra @code{ggplot2} themes,
21521 scales and utilities, including a spell check function for plot label fields
21522 and an overall emphasis on typography.")
21523 (license license:expat)))
21525 (define-public r-crochet
21532 (uri (cran-uri "crochet" version))
21535 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21536 (build-system r-build-system)
21538 `(("r-knitr" ,r-knitr)))
21539 (home-page "https://github.com/agrueneberg/crochet")
21540 (synopsis "Implementation Helper for Matrix-Like Types")
21542 "Functions to help implement the extraction / subsetting / indexing
21543 function @code{[} and replacement function @code{[<-} of custom matrix-like
21544 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21545 as possible (with tests to prove it).")
21546 (license license:expat)))
21548 (define-public r-boa
21551 (version "1.1.8-2")
21555 (uri (cran-uri "boa" version))
21558 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21559 (properties `((upstream-name . "boa")))
21560 (build-system r-build-system)
21561 (home-page "http://www.jstatsoft.org/v21/i11")
21562 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21564 "This package provides a menu-driven program and library of functions for
21565 carrying out convergence diagnostics and statistical and graphical analysis of
21566 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21567 (license license:gpl2+)))
21569 (define-public r-httpcode
21571 (name "r-httpcode")
21575 (uri (cran-uri "httpcode" version))
21578 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21579 (build-system r-build-system)
21580 (home-page "https://github.com/sckott/httpcode")
21581 (synopsis "HTTP status code helper")
21582 (description "@code{httpcode} provides functionality for finding and
21583 explaining the meaning of @code{HTTP} status codes. Functions are included for
21584 searching for codes by full or partial number, by message, and to get
21585 appropriate dog and cat images for many status codes.")
21586 (license license:expat)))
21588 (define-public r-latex2exp
21590 (name "r-latex2exp")
21594 (uri (cran-uri "latex2exp" version))
21597 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21598 (build-system r-build-system)
21600 `(("r-stringr" ,r-stringr)
21601 ("r-magrittr", r-magrittr)))
21602 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21603 (synopsis "Use LaTeX expressions in plots")
21604 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21605 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21606 rendered as text, axis labels, etc. throughout R's plotting system.")
21607 (license license:expat)))
21609 (define-public r-oai
21615 (uri (cran-uri "oai" version))
21618 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21619 (build-system r-build-system)
21621 `(("r-xml2" ,r-xml2)
21624 ("r-stringr" ,r-stringr)
21625 ("r-tibble" ,r-tibble)))
21626 (home-page "https://github.com/ropensci/oai/")
21627 (synopsis "General purpose OAI-PMH services client")
21628 (description "@code{oai} provides a general purpose client to work with
21629 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21630 service. Functions are provided to work with the OAI-PMH verbs:
21631 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21632 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21633 (license license:expat)))
21635 (define-public r-argon2
21642 (uri (cran-uri "argon2" version))
21645 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21646 (properties `((upstream-name . "argon2")))
21647 (build-system r-build-system)
21648 (home-page "https://github.com/wrathematics/argon2")
21649 (synopsis "Secure password hashing based on the argon2 algorithm")
21651 "This package provides utilities for secure password hashing via the
21652 argon2 algorithm.")
21653 (license license:bsd-2)))
21655 (define-public r-getpass
21662 (uri (cran-uri "getPass" version))
21665 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21666 (properties `((upstream-name . "getPass")))
21667 (build-system r-build-system)
21669 `(("r-rstudioapi" ,r-rstudioapi)))
21670 (home-page "https://github.com/wrathematics/getPass")
21671 (synopsis "Masked user input")
21673 "This package provides a micro-package for reading \"passwords\", i.e.
21674 reading user input with masking, so that the input is not displayed as it is
21675 typed. Currently, RStudio, the command line (every OS), and any platform
21676 where tcltk is present are supported.")
21677 (license license:bsd-2)))
21679 (define-public r-remoter
21686 (uri (cran-uri "remoter" version))
21689 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21690 (properties `((upstream-name . "remoter")))
21691 (build-system r-build-system)
21693 `(("r-argon2" ,r-argon2)
21694 ("r-getpass" ,r-getpass)
21695 ("r-pbdzmq" ,r-pbdzmq)
21697 (home-page "https://github.com/RBigData/remoter")
21698 (synopsis "Control a remote R session from a local one")
21700 "This package provides a set of utilities for client/server computing
21701 with R, controlling a remote R session (the server) from a local one (the
21703 (license license:bsd-2)))
21705 (define-public r-asd
21712 (uri (cran-uri "asd" version))
21715 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21716 (properties `((upstream-name . "asd")))
21717 (build-system r-build-system)
21719 `(("r-mvtnorm" ,r-mvtnorm)))
21720 (home-page "https://cran.r-project.org/web/packages/asd")
21721 (synopsis "Simulations for Adaptive Seamless Designs")
21723 "This package provdes means to run simulations for adaptive seamless
21724 designs with and without early outcomes for treatment selection and
21725 subpopulation type designs.")
21726 (license license:gpl3)))
21728 (define-public r-nbconvertr
21730 (name "r-nbconvertr")
21735 (uri (cran-uri "nbconvertR" version))
21738 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21739 (properties `((upstream-name . "nbconvertR")))
21740 (build-system r-build-system)
21742 `(("jupyter" ,python-nbconvert)
21743 ("pandoc" ,ghc-pandoc)))
21744 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21745 (synopsis "Vignette engine wrapping Jupyter notebooks")
21747 "This package calls the Jupyter script @code{nbconvert} to create
21748 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21749 containing rich text, code, and its output. Code cells can be edited and
21750 evaluated interactively.")
21751 (license license:gpl3)))
21753 (define-public r-bridgesampling
21755 (name "r-bridgesampling")
21760 (uri (cran-uri "bridgesampling" version))
21763 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21765 `((upstream-name . "bridgesampling")))
21766 (build-system r-build-system)
21768 `(("r-brobdingnag" ,r-brobdingnag)
21770 ("r-matrix" ,r-matrix)
21771 ("r-mvtnorm" ,r-mvtnorm)
21772 ("r-scales" ,r-scales)
21773 ("r-stringr" ,r-stringr)))
21775 `(("r-knitr" ,r-knitr)))
21776 (home-page "https://github.com/quentingronau/bridgesampling")
21777 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21779 "This package provides functions for estimating marginal likelihoods,
21780 Bayes factors, posterior model probabilities, and normalizing constants in
21781 general, via different versions of bridge sampling.")
21782 (license license:gpl2+)))
21784 (define-public r-tea
21791 (uri (cran-uri "tea" version))
21794 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21796 `((upstream-name . "tea")))
21797 (build-system r-build-system)
21799 `(("r-matrix" ,r-matrix)))
21800 (home-page "https://cran.r-project.org/web/packages/tea/")
21801 (synopsis "Threshold estimation approaches")
21803 "This package provides different approaches for selecting the threshold
21804 in generalized Pareto distributions. Most of them are based on minimizing the
21805 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21806 Others are heuristically motivated by searching for stable sample paths, i.e.
21807 a nearly constant region of the tail index estimator with respect to k, which
21808 is the number of data in the tail. The third class is motivated by graphical
21809 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21810 is also implemented here.")
21811 (license license:gpl3)))
21813 (define-public r-awsmethods
21815 (name "r-awsmethods")
21820 (uri (cran-uri "awsMethods" version))
21823 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21825 `((upstream-name . "awsMethods")))
21826 (build-system r-build-system)
21827 (home-page "http://www.wias-berlin.de/software/imaging/")
21828 (synopsis "Class and methods definitions")
21830 "This package defines the generic method @code{extract} and provides
21831 @code{openMP} support as needed in several packages like
21832 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21833 (license license:gpl2+)))
21835 (define-public r-aws
21842 (uri (cran-uri "aws" version))
21845 "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
21847 `((upstream-name . "aws")))
21848 (build-system r-build-system)
21850 `(("r-awsmethods" ,r-awsmethods)
21853 `(("gfortran" ,gfortran)))
21854 (home-page "https://cran.r-project.org/web/packages/aws/")
21855 (synopsis "Adaptive weights smoothing")
21857 "This package provides a collection of R-functions implementing adaptive
21858 smoothing procedures in 1D, 2D and 3D. This includes the
21859 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
21860 Confidence Intervals} (ICI), variational approaches, and a non-local means
21862 (license license:gpl2+)))
21864 (define-public r-sgloptim
21866 (name "r-sgloptim")
21871 (uri (cran-uri "sglOptim" version))
21874 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
21876 `((upstream-name . "sglOptim")))
21877 (build-system r-build-system)
21880 ("r-doparallel" ,r-doparallel)
21881 ("r-foreach" ,r-foreach)
21882 ("r-matrix" ,r-matrix)
21884 ("r-rcpparmadillo" ,r-rcpparmadillo)
21885 ("r-rcppprogress" ,r-rcppprogress)))
21887 `(("r-knitr" ,r-knitr)))
21888 (home-page "https://github.com/nielsrhansen/sglOptim")
21889 (synopsis "Generic sparse group Lasso solver")
21891 "This package provides a fast generic solver for sparse group lasso
21892 optimization problems. The loss (objective) function must be defined in a C++
21893 module. The optimization problem is solved using a coordinate gradient
21894 descent algorithm. Convergence of the algorithm is established and the
21895 algorithm is applicable to a broad class of loss functions. Use of parallel
21896 computing for cross validation and subsampling is supported through the
21897 @code{foreach} and @code{doParallel} packages.")
21898 (license license:gpl2+)))
21900 (define-public r-grouped
21907 (uri (cran-uri "grouped" version))
21910 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
21912 `((upstream-name . "grouped")))
21913 (build-system r-build-system)
21915 `(("r-mass" ,r-mass)))
21916 (home-page "https://cran.r-project.org/web/packages/grouped/")
21917 (synopsis "Regression analysis of grouped and coarse data")
21919 "This package provides regression models for grouped and coarse data,
21920 under the coarsened at random assumption.")
21921 (license license:gpl2+)))
21923 (define-public r-stam
21930 (uri (cran-uri "stam" version))
21933 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
21935 `((upstream-name . "stam")))
21936 (build-system r-build-system)
21940 (home-page "https://cran.r-project.org/web/packages/stam")
21941 (synopsis "Spatio-temporal analysis and modelling")
21943 "This package provides various methods to conduct Spatio-Temporal
21944 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
21945 Inferred Spatio-Temporal Modelling.")
21946 (license license:gpl2+)))
21948 (define-public r-dcv
21955 (uri (cran-uri "dcv" version))
21958 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
21960 `((upstream-name . "dcv")))
21961 (build-system r-build-system)
21963 `(("r-lmtest" ,r-lmtest)))
21964 (home-page "https://cran.r-project.org/web/packages/dcv/")
21965 (synopsis "Conventional cross-validation statistics for climate-growth model")
21967 "This package performs several conventional cross-validation statistical
21968 methods for climate-growth model in the climate reconstruction from tree
21969 rings, including Sign Test statistic, Reduction of Error statistic, Product
21970 Mean Test, Durbin-Watson statistic etc.")
21971 (license license:gpl2)))
21973 (define-public r-rcdd
21980 (uri (cran-uri "rcdd" version))
21983 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
21985 `((upstream-name . "rcdd")))
21986 (build-system r-build-system)
21989 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
21990 (synopsis "Computational geometry")
21992 "This package converts back and forth between two representations of a
21993 convex polytope: as solution of a set of linear equalities and inequalities
21994 and as convex hull of set of points and rays. Also does linear programming
21995 and redundant generator elimination. All functions can use exact
21996 infinite-precision rational arithmetic.")
21997 (license license:gpl2)))
21999 (define-public r-rxnat
22006 (uri (cran-uri "Rxnat" version))
22009 "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
22011 `((upstream-name . "Rxnat")))
22012 (build-system r-build-system)
22014 `(("r-httr" ,r-httr)
22015 ("r-rcurl" ,r-rcurl)))
22017 `(("r-knitr" ,r-knitr)))
22018 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22019 (synopsis "Queries and extracts images from neuroimaging datasets")
22021 "This package allows communication with the Extensible Neuroimaging
22022 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22024 (license license:gpl2)))
22026 (define-public r-rserve
22033 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22034 version ".tar.gz"))
22037 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22038 (build-system r-build-system)
22040 `(("r-checkmate" ,r-checkmate)
22042 ("r-jsonlite" ,r-jsonlite)
22043 ("r-knitr" ,r-knitr)
22046 ("r-uuid" ,r-uuid)))
22048 `(("openssl" ,openssl)
22050 (home-page "https://github.com/s-u/Rserve")
22052 "Server providing access to R from many languages and systems")
22054 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22055 binary requests to be sent to R. Every connection has a separate workspace
22056 and working directory. Client-side implementations are available for popular
22057 languages such as C/C++ and Java, allowing any application to use facilities
22058 of R without the need of linking to R code. Rserve supports remote
22059 connection, user authentication and file transfer. A simple R client is
22060 included in this package as well.")
22061 (license license:gpl2)))
22063 (define-public r-brms
22070 (uri (cran-uri "brms" version))
22073 "0vdncdawxawi16f326qrgy9jjjipmqdjxh741y9p7xdzd4fwaxx3"))))
22074 (properties `((upstream-name . "brms")))
22075 (build-system r-build-system)
22077 `(("r-abind" ,r-abind)
22078 ("r-backports" ,r-backports)
22079 ("r-bayesplot" ,r-bayesplot)
22080 ("r-bridgesampling" ,r-bridgesampling)
22082 ("r-future" ,r-future)
22083 ("r-ggplot2" ,r-ggplot2)
22086 ("r-matrix" ,r-matrix)
22087 ("r-matrixstats" ,r-matrixstats)
22089 ("r-nleqslv" ,r-nleqslv)
22092 ("r-rstan" ,r-rstan)
22093 ("r-rstantools" ,r-rstantools)
22094 ("r-shinystan" ,r-shinystan)))
22095 (native-inputs `(("r-knitr" ,r-knitr)))
22097 "https://github.com/paul-buerkner/brms")
22099 "Bayesian Regression Models using 'Stan'")
22101 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22102 using 'Stan' for full Bayesian inference. A wide range of distributions and
22103 link functions are supported, allowing users to fit -- among others -- linear,
22104 robust linear, count data, survival, response times, ordinal, zero-inflated,
22105 hurdle, and even self-defined mixture models all in a multilevel context.
22106 Further modeling options include non-linear and smooth terms, auto-correlation
22107 structures, censored data, meta-analytic standard errors, and quite a few
22108 more. In addition, all parameters of the response distribution can be
22109 predicted in order to perform distributional regression. Prior specifications
22110 are flexible and explicitly encourage users to apply prior distributions that
22111 actually reflect their beliefs. Model fit can easily be assessed and compared
22112 with posterior predictive checks and leave-one-out cross-validation.")
22113 (license license:gpl2)))
22115 (define-public r-mstate
22122 (uri (cran-uri "mstate" version))
22125 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22126 (properties `((upstream-name . "mstate")))
22127 (build-system r-build-system)
22129 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22130 ("r-survival" ,r-survival)))
22132 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22134 "Data Preparation, Estimation and Prediction in Multi-State Models")
22136 "Contains functions for data preparation, descriptives, hazard estimation
22137 and prediction with Aalen-Johansen or simulation in competing risks and
22138 multi-state models.")
22139 (license license:gpl2+)))
22141 (define-public r-scatterpie
22143 (name "r-scatterpie")
22148 (uri (cran-uri "scatterpie" version))
22151 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22152 (properties `((upstream-name . "scatterpie")))
22153 (build-system r-build-system)
22155 `(("r-ggforce" ,r-ggforce)
22156 ("r-ggplot2" ,r-ggplot2)
22157 ("r-rlang" ,r-rlang)
22158 ("r-rvcheck" ,r-rvcheck)
22159 ("r-tidyr" ,r-tidyr)))
22161 `(("r-knitr" ,r-knitr)))
22162 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22163 (synopsis "Scatter pie plot")
22165 "This package creates scatterpie plots, especially useful for plotting
22167 (license license:artistic2.0)))
22169 (define-public r-boruta
22176 (uri (cran-uri "Boruta" version))
22179 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22180 (properties `((upstream-name . "Boruta")))
22181 (build-system r-build-system)
22182 (propagated-inputs `(("r-ranger" ,r-ranger)))
22183 (home-page "https://gitlab.com/mbq/Boruta/")
22184 (synopsis "Wrapper algorithm for all relevant feature selection")
22186 "This package provides an all relevant feature selection wrapper
22187 algorithm. It finds relevant features by comparing original attributes'
22188 importance with importance achievable at random, estimated using their
22189 permuted copies (shadows).")
22190 (license license:gpl2+)))
22192 (define-public r-directlabels
22194 (name "r-directlabels")
22195 (version "2020.1.31")
22199 (uri (cran-uri "directlabels" version))
22202 "08s1gnwp4bn8xahwjaq0f1qzhwh2dvybzhq3z7xyzn8cnyzmis6c"))))
22203 (build-system r-build-system)
22205 `(("r-quadprog" ,r-quadprog)))
22206 (home-page "http://directlabels.r-forge.r-project.org/")
22207 (synopsis "Direct labels for multicolor plots")
22209 "This package provides an extensible framework for automatically placing
22210 direct labels onto multicolor plots. Label positions are described using
22211 positioning methods that can be re-used across several different plots. There
22212 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22213 inferring an appropriate positioning method.")
22214 (license license:gpl3)))
22216 (define-public r-lsd
22223 (uri (cran-uri "LSD" version))
22225 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22226 (properties `((upstream-name . "LSD")))
22227 (build-system r-build-system)
22228 (home-page "https://cran.r-project.org/web/packages/LSD/")
22229 (synopsis "Lots of superior depictions tool creates colorful plots")
22231 "This package creates lots of colorful plots in a multitude of variations.
22232 Try a demo of the LSD by running @code{demotour()}.")
22234 (license (list license:gpl2 license:gpl3))))
22236 (define-public r-fourcseq
22238 (name "r-fourcseq")
22243 (uri (bioconductor-uri "FourCSeq" version))
22245 (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x"))))
22246 (properties `((upstream-name . "FourCSeq")))
22247 (build-system r-build-system)
22249 `(("r-biobase" ,r-biobase)
22250 ("r-biostrings" ,r-biostrings)
22251 ("r-deseq2" ,r-deseq2)
22253 ("r-genomicalignments" ,r-genomicalignments)
22254 ("r-genomicranges" ,r-genomicranges)
22255 ("r-ggbio" ,r-ggbio)
22256 ("r-ggplot2" ,r-ggplot2)
22257 ("r-gtools" ,r-gtools)
22259 ("r-matrix" ,r-matrix)
22260 ("r-reshape2" ,r-reshape2)
22261 ("r-rsamtools" ,r-rsamtools)
22262 ("r-rtracklayer" ,r-rtracklayer)
22263 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22265 `(("r-knitr" ,r-knitr)))
22267 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22268 (synopsis "Analysis of multiplexed 4C sequencing data")
22270 "This package is an R package dedicated to the analysis of (multiplexed)
22271 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22272 interactions between DNA elements and identify differential interactions
22273 between conditions. The statistical analysis in R starts with individual bam
22274 files for each sample as inputs. To obtain these files, the package contains
22275 a Python script to demultiplex libraries and trim off primer sequences. With
22276 a standard alignment software the required bam files can be then be
22278 (license license:gpl3+)))
22280 (define-public r-phylogram
22282 (name "r-phylogram")
22287 (uri (cran-uri "phylogram" version))
22289 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22290 (properties `((upstream-name . "phylogram")))
22291 (build-system r-build-system)
22292 (propagated-inputs `(("r-ape" ,r-ape)))
22293 (home-page "https://github.com/ropensci/phylogram/")
22294 (synopsis "Dendrograms for evolutionary analysis")
22296 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22297 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22298 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22299 as well as several tools for command-line tree manipulation and import/export
22300 via Newick parenthetic text. This improves accessibility to the comprehensive
22301 range of object-specific analytical and tree-visualization functions found
22302 across a wide array of bioinformatic R packages.")
22303 (license license:gpl3)))
22305 (define-public r-kmer
22312 (uri (cran-uri "kmer" version))
22314 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22315 (properties `((upstream-name . "kmer")))
22316 (build-system r-build-system)
22318 `(("r-openssl" ,r-openssl)
22319 ("r-phylogram" ,r-phylogram)
22320 ("r-rcpp" ,r-rcpp)))
22321 (home-page "https://github.com/shaunpwilkinson/kmer/")
22322 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22324 "@code{r-kmer} is an R package for rapidly computing distance matrices
22325 and clustering large sequence datasets using fast alignment-free k-mer
22326 counting and recursive k-means partitioning.")
22327 (license license:gpl3)))