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 "1izfrk5yahsz6s69wanfspn72qdffjglbr5305akj72ig9fnladq"))))
832 (build-system r-build-system)
834 `(("r-knitr" ,r-knitr)))
835 (home-page "https://arxiv.org/abs/1403.2805")
836 (synopsis "Robust, high performance JSON parser and generator for R")
838 "The jsonlite package provides a fast JSON parser and generator optimized
839 for statistical data and the web. It offers flexible, robust, high
840 performance tools for working with JSON in R and is particularly powerful for
841 building pipelines and interacting with a web API. In addition to converting
842 JSON data from/to R objects, jsonlite contains functions to stream, validate,
843 and prettify JSON data. The unit tests included with the package verify that
844 all edge cases are encoded and decoded consistently for use with dynamic data
845 in systems and applications.")
846 (license license:expat)))
848 (define-public r-servr
854 (uri (cran-uri "servr" version))
857 "0lxkjr7mwdk96cdpx66j92nn4w2vkgn2j2bbg7kd4238jsk9srs7"))))
858 (build-system r-build-system)
860 `(("r-httpuv" ,r-httpuv)
861 ("r-jsonlite" ,r-jsonlite)
864 (home-page "https://github.com/yihui/servr")
865 (synopsis "Simple HTTP server to serve static files or dynamic documents")
867 "Servr provides an HTTP server in R to serve static files, or dynamic
868 documents that can be converted to HTML files (e.g., R Markdown) under a given
870 (license license:expat)))
872 (define-public r-htmltools
878 (uri (cran-uri "htmltools" version))
881 "07fjznax5sin563ddnzlb7iwc8b39wzf7ymjn66pbmxgskijq2pz"))))
882 (build-system r-build-system)
884 `(("r-base64enc" ,r-base64enc)
885 ("r-digest" ,r-digest)
886 ("r-rlang" ,r-rlang)))
887 (home-page "https://cran.r-project.org/web/packages/htmltools")
888 (synopsis "R tools for HTML")
890 "This package provides tools for HTML generation and output in R.")
891 (license license:expat)))
893 (define-public r-htmlwidgets
895 (name "r-htmlwidgets")
899 (uri (cran-uri "htmlwidgets" version))
902 "10fp306l1nybkah6jrlrqwwdb6zvklbddp8i3w9v9naj8la5jbnl"))))
903 (build-system r-build-system)
905 `(("r-htmltools" ,r-htmltools)
906 ("r-jsonlite" ,r-jsonlite)
908 (home-page "https://github.com/ramnathv/htmlwidgets")
909 (synopsis "HTML Widgets for R")
911 "HTML widgets is a framework for creating HTML widgets that render in
912 various contexts including the R console, R Markdown documents, and Shiny web
914 (license license:expat)))
916 (define-public r-htmltable
923 (uri (cran-uri "htmlTable" version))
926 "1a1al4kld7lrapc2i086crr78kbgrskahs221iy9v77x0nhin2q3"))))
927 (properties `((upstream-name . "htmlTable")))
928 (build-system r-build-system)
930 `(("r-checkmate" ,r-checkmate)
931 ("r-htmltools" ,r-htmltools)
932 ("r-htmlwidgets" ,r-htmlwidgets)
934 ("r-magrittr" ,r-magrittr)
935 ("r-rstudioapi" ,r-rstudioapi)
936 ("r-stringr" ,r-stringr)))
938 `(("r-knitr" ,r-knitr)))
939 (home-page "http://gforge.se/packages/")
940 (synopsis "Advanced tables for Markdown/HTML")
942 "This package provides functions to build tables with advanced layout
943 elements such as row spanners, column spanners, table spanners, zebra
944 striping, and more. While allowing advanced layout, the underlying
945 CSS-structure is simple in order to maximize compatibility with word
946 processors such as LibreOffice. The package also contains a few text
947 formatting functions that help outputting text compatible with HTML or
949 (license license:gpl3+)))
951 (define-public r-curl
957 (uri (cran-uri "curl" version))
960 "1nrf6md41b37j424y6rvifdj9zb3j14f60fj7q71k9jhpf2x81kl"))))
961 (build-system r-build-system)
964 (modify-phases %standard-phases
965 ;; The environment variable CURL_CA_BUNDLE is only respected when
966 ;; running Windows, so we disable the platform checks.
967 ;; This can be removed once the libcurl has been patched.
968 (add-after 'unpack 'allow-CURL_CA_BUNDLE
970 (substitute* "R/onload.R"
971 (("if \\(!grepl\\(\"mingw\".*")
973 (substitute* "src/handle.c"
976 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
977 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
984 `(("pkg-config" ,pkg-config)))
985 (home-page "https://github.com/jeroenooms/curl")
986 (synopsis "HTTP client for R")
988 "The @code{curl()} and @code{curl_download()} functions provide highly
989 configurable drop-in replacements for base @code{url()} and
990 @code{download.file()} with better performance, support for encryption, gzip
991 compression, authentication, and other @code{libcurl} goodies. The core of
992 the package implements a framework for performing fully customized requests
993 where data can be processed either in memory, on disk, or streaming via the
994 callback or connection interfaces.")
995 (license license:expat)))
997 (define-public r-hwriter
1004 (uri (cran-uri "hwriter" version))
1007 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1008 (build-system r-build-system)
1009 (home-page "https://cran.r-project.org/web/packages/hwriter")
1010 (synopsis "Output R objects in HTML format")
1012 "This package provides easy-to-use and versatile functions to output R
1013 objects in HTML format.")
1014 (license license:lgpl2.1+)))
1016 (define-public r-rjson
1023 (uri (cran-uri "rjson" version))
1026 "0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
1027 (build-system r-build-system)
1028 (home-page "https://cran.r-project.org/web/packages/rjson")
1029 (synopsis "JSON library for R")
1031 "This package provides functions to convert R objects into JSON objects
1033 (license license:gpl2+)))
1035 (define-public r-fastmap
1042 (uri (cran-uri "fastmap" version))
1045 "1v7sp56xiha0bh78g3w92k52p9vkp7ryzpw0z66nyddxzrfv0y27"))))
1046 (properties `((upstream-name . "fastmap")))
1047 (build-system r-build-system)
1048 (home-page "https://r-lib.github.io/fastmap/")
1049 (synopsis "Fast implementation of a key-value store")
1051 "This package provides a fast implementation of a key-value store.
1052 Environments are commonly used as key-value stores, but every time a new key
1053 is used, it is added to R's global symbol table, causing a small amount of
1054 memory leakage. This can be problematic in cases where many different keys
1055 are used. Fastmap avoids this memory leak issue by implementing the map using
1056 data structures in C++.")
1057 (license license:expat)))
1059 (define-public r-shiny
1067 (url "https://github.com/rstudio/shiny.git")
1068 (commit (string-append "v" version))))
1069 (file-name (git-file-name name version))
1072 "005wgcxq7f2q9g6wvfk29n2nms262w0abpz93sfvx79yv6qxppzs"))))
1073 (build-system r-build-system)
1075 `(#:modules ((guix build r-build-system)
1076 (guix build minify-build-system)
1079 #:imported-modules (,@%r-build-system-modules
1080 (guix build minify-build-system))
1082 (modify-phases (@ (guix build r-build-system) %standard-phases)
1083 (add-after 'unpack 'replace-bundled-minified-JavaScript
1084 (lambda* (#:key inputs #:allow-other-keys)
1085 (let ((replace-file (lambda (old new)
1086 (format #t "replacing ~a with ~a\n" old new)
1088 (symlink new old))))
1089 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
1090 ;; contain just data. They are not minified code, so we don't
1092 (with-directory-excursion "inst/www/shared"
1093 (replace-file "bootstrap/shim/respond.min.js"
1094 (string-append (assoc-ref inputs "js-respond")
1095 "/share/javascript/respond.min.js"))
1096 (replace-file "bootstrap/shim/html5shiv.min.js"
1097 (string-append (assoc-ref inputs "js-html5shiv")
1098 "/share/javascript/html5shiv.min.js"))
1099 (replace-file "json2-min.js"
1100 (string-append (assoc-ref inputs "js-json2")
1101 "/share/javascript/json2-min.js"))
1102 (replace-file "strftime/strftime-min.js"
1103 (string-append (assoc-ref inputs "js-strftime")
1104 "/share/javascript/strftime.min.js"))
1105 (replace-file "highlight/highlight.pack.js"
1106 (string-append (assoc-ref inputs "js-highlight")
1107 "/share/javascript/highlight.min.js"))
1108 (replace-file "datatables/js/jquery.dataTables.min.js"
1109 (string-append (assoc-ref inputs "js-datatables")
1110 "/share/javascript/jquery.dataTables.min.js"))
1111 (replace-file "selectize/js/selectize.min.js"
1112 (string-append (assoc-ref inputs "js-selectize")
1113 "/share/javascript/selectize.min.js"))
1114 (replace-file "selectize/js/es5-shim.min.js"
1115 (string-append (assoc-ref inputs "js-es5-shim")
1116 "/share/javascript/es5-shim.min.js"))
1117 (for-each (match-lambda
1119 (delete-file target)
1120 (minify source #:target target)))
1121 '(("jqueryui/jquery-ui.js" .
1122 "jqueryui/jquery-ui.min.js")
1123 ("datepicker/js/bootstrap-datepicker.js" .
1124 "datepicker/js/bootstrap-datepicker.min.js")
1125 ("ionrangeslider/js/ion.rangeSlider.js" .
1126 "ionrangeslider/js/ion.rangeSlider.min.js")
1127 ("bootstrap/js/bootstrap.js" .
1128 "bootstrap/js/bootstrap.min.js")
1133 ("legacy/jquery.js" .
1134 "legacy/jquery.min.js")
1135 ("showdown/src/showdown.js" .
1136 "showdown/compressed/showdown.js")))))
1139 `(("r-crayon" ,r-crayon)
1140 ("r-digest" ,r-digest)
1141 ("r-fastmap" ,r-fastmap)
1142 ("r-htmltools" ,r-htmltools)
1143 ("r-httpuv" ,r-httpuv)
1144 ("r-jsonlite" ,r-jsonlite)
1145 ("r-later" ,r-later)
1147 ("r-promises" ,r-promises)
1149 ("r-rlang" ,r-rlang)
1150 ("r-sourcetools" ,r-sourcetools)
1151 ("r-withr" ,r-withr)
1152 ("r-xtable" ,r-xtable)))
1154 `(("js-datatables" ,js-datatables)
1155 ("js-html5shiv" ,js-html5shiv)
1156 ("js-json2" ,js-json2)
1157 ("js-respond" ,js-respond)
1158 ("js-selectize" ,js-selectize)
1159 ("js-strftime" ,js-strftime)
1160 ("js-highlight" ,js-highlight)
1161 ("js-es5-shim" ,js-es5-shim)))
1163 `(("uglify-js" ,uglify-js)
1164 ("gfortran" ,gfortran)))
1165 (home-page "http://shiny.rstudio.com")
1166 (synopsis "Easy interactive web applications with R")
1168 "Makes it incredibly easy to build interactive web applications
1169 with R. Automatic \"reactive\" binding between inputs and outputs and
1170 extensive prebuilt widgets make it possible to build beautiful,
1171 responsive, and powerful applications with minimal effort.")
1172 (license license:artistic2.0)))
1174 ;; This package includes minified JavaScript files. When upgrading please
1175 ;; check that there are no new minified JavaScript files.
1176 (define-public r-shinytree
1178 (name "r-shinytree")
1183 (uri (cran-uri "shinyTree" version))
1186 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
1187 (modules '((guix build utils)))
1190 ;; Delete minified JavaScript
1191 (for-each delete-file
1192 '("inst/www/jsTree-3.3.7/libs/require.js"
1193 "inst/www/jsTree-3.3.7/libs/jquery.js"
1194 "inst/www/jsTree-3.3.7/jstree.min.js"))
1196 (properties `((upstream-name . "shinyTree")))
1197 (build-system r-build-system)
1199 `(#:modules ((guix build utils)
1200 (guix build r-build-system)
1204 (modify-phases %standard-phases
1205 (add-after 'unpack 'replace-minified-javascript
1206 (lambda* (#:key inputs #:allow-other-keys)
1207 (with-directory-excursion "inst/www/jsTree-3.3.7/"
1208 (symlink (string-append (assoc-ref inputs "js-requirejs")
1209 "/share/javascript/require.min.js")
1214 `((,(assoc-ref inputs "js-jquery")
1218 (lambda (sources targets)
1219 (for-each (lambda (source target)
1220 (format #t "Processing ~a --> ~a~%"
1222 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1223 (call-with-output-file target
1225 (dump-port minified port)))))
1229 `(("r-htmlwidgets" ,r-htmlwidgets)
1230 ("r-jsonlite" ,r-jsonlite)
1231 ("r-promises" ,r-promises)
1232 ("r-shiny" ,r-shiny)
1233 ("r-stringr" ,r-stringr)))
1235 `(("js-requirejs" ,js-requirejs)))
1237 `(("uglify-js" ,uglify-js)
1241 (uri "https://code.jquery.com/jquery-3.3.1.js")
1244 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
1245 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
1246 (synopsis "jsTree bindings for Shiny")
1248 "This package exposes R bindings to jsTree, a JavaScript library that
1249 supports interactive trees, to enable rich, editable trees in Shiny.")
1250 (license license:expat)))
1252 (define-public r-shinydashboard
1254 (name "r-shinydashboard")
1258 (uri (cran-uri "shinydashboard" version))
1261 "0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
1262 (build-system r-build-system)
1263 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
1264 ;; Regenerate it from the included sources.
1266 `(#:modules ((guix build utils)
1267 (guix build r-build-system)
1270 (modify-phases %standard-phases
1271 (add-after 'unpack 'generate-minified-javascript
1273 (with-directory-excursion "inst/AdminLTE"
1274 (delete-file "app.min.js")
1275 (let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
1276 (call-with-output-file "app.min.js"
1278 (dump-port minified port))))))))))
1280 `(("r-htmltools" ,r-htmltools)
1281 ("r-promises" ,r-promises)
1282 ("r-shiny" ,r-shiny)))
1284 `(("uglify-js" ,uglify-js)))
1285 (home-page "https://rstudio.github.io/shinydashboard/")
1286 (synopsis "Create dashboards with shiny")
1287 (description "This package provides an extension to the Shiny web
1288 application framework for R, making it easy to create attractive dashboards.")
1289 ;; This package includes software that was released under the Expat
1290 ;; license, but the whole package is released under GPL version 2 or
1292 (license license:gpl2+)))
1294 (define-public r-shinyfiles
1296 (name "r-shinyfiles")
1301 (uri (cran-uri "shinyFiles" version))
1303 (base32 "0gwyx37f2r86cldsyknws9pafpj8g5mg3mchlyl9ymgnk5f4b88w"))))
1304 (properties `((upstream-name . "shinyFiles")))
1305 (build-system r-build-system)
1308 ("r-htmltools" ,r-htmltools)
1309 ("r-jsonlite" ,r-jsonlite)
1310 ("r-shiny" ,r-shiny)
1311 ("r-tibble" ,r-tibble)))
1312 (home-page "https://github.com/thomasp85/shinyFiles")
1313 (synopsis "Server-side file system viewer for Shiny")
1315 "This package provides functionality for client-side navigation of the
1316 server side file system in shiny apps. In case the app is running locally
1317 this gives the user direct access to the file system without the need to
1318 \"download\" files to a temporary location. Both file and folder selection as
1319 well as file saving is available.")
1320 (license license:gpl2+)))
1322 (define-public r-shinythemes
1324 (name "r-shinythemes")
1329 (uri (cran-uri "shinythemes" version))
1332 "12miz44n2zxfswnia7p8dirxj3miw0aqn4pkx2111ikz67ax84rf"))))
1333 (properties `((upstream-name . "shinythemes")))
1334 (build-system r-build-system)
1335 (propagated-inputs `(("r-shiny" ,r-shiny)))
1336 (home-page "https://rstudio.github.io/shinythemes/")
1337 (synopsis "Themes for Shiny")
1339 "This package provides themes for use with Shiny. It includes several
1340 Bootstrap themes, which are packaged for use with Shiny applications.")
1341 ;; The package is released under version 3 of the GPL, but it includes
1342 ;; source files that are covered by the Expat license. It also includes
1343 ;; fonts under SIL or the ASL.
1344 (license (list license:gpl3 license:expat
1345 license:silofl1.1 license:asl2.0))))
1347 ;; The package sources include minified variants of d3.js and non-minified
1348 ;; source code of d3-jetpack.
1349 (define-public r-d3r
1356 (uri (cran-uri "d3r" version))
1359 "0vd1qk8yr18xdfkv5ybhqvf0mmccpi721wqa7c881nzm9nnlzc4y"))))
1360 (build-system r-build-system)
1362 `(#:modules ((guix build utils)
1363 (guix build r-build-system)
1367 (modify-phases %standard-phases
1368 (add-after 'unpack 'process-javascript
1369 (lambda* (#:key inputs #:allow-other-keys)
1370 (with-directory-excursion "inst/www/d3/"
1374 `((,(assoc-ref inputs "d3.v3.js")
1375 "v3/dist/d3.min.js")
1376 (,(assoc-ref inputs "d3.v4.js")
1377 "v4/dist/d3.min.js")
1378 (,(assoc-ref inputs "d3.v5.js")
1379 "v5/dist/d3.min.js"))))
1380 (lambda (sources targets)
1381 (for-each (lambda (source target)
1382 (format #t "Processing ~a --> ~a~%"
1384 (delete-file target)
1385 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
1386 (call-with-output-file target
1388 (dump-port minified port)))))
1392 `(("r-dplyr" ,r-dplyr)
1393 ("r-htmltools" ,r-htmltools)
1394 ("r-rlang" ,r-rlang)
1395 ("r-tidyr" ,r-tidyr)))
1397 `(("uglify-js" ,uglify-js)
1401 (uri "https://d3js.org/d3.v3.js")
1404 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
1408 (uri "https://d3js.org/d3.v4.js")
1411 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
1415 (uri "https://d3js.org/d3.v5.js")
1418 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))))
1419 (home-page "https://github.com/timelyportfolio/d3r")
1420 (synopsis "d3.js utilities for R")
1422 "This package provides a suite of functions to help ease the use of the
1423 d3.js visualization library in R. These helpers include
1424 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
1425 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
1426 R objects into the JSON format that the d3.js library expects.")
1427 (license license:bsd-3)))
1429 ;; We use the latest commit here because the last release was in 2016 while
1430 ;; the latest commit was in 2018.
1431 (define-public r-sankeyd3
1432 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
1436 (version (git-version "0.3.2" revision commit))
1441 (url "https://github.com/fbreitwieser/sankeyD3.git")
1443 (file-name (git-file-name name version))
1446 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
1447 (build-system r-build-system)
1450 ("r-htmlwidgets" ,r-htmlwidgets)
1451 ("r-shiny" ,r-shiny)
1452 ("r-magrittr" ,r-magrittr)))
1453 (home-page "https://github.com/fbreitwieser/sankeyD3")
1454 (synopsis "Sankey network graphs from R")
1456 "This package provides an R library to generate Sankey network graphs
1457 in R and Shiny via the D3 visualization library.")
1458 ;; The R code is licensed under GPLv3+. It includes the non-minified
1459 ;; JavaScript source code of d3-sankey, which is released under the
1460 ;; 3-clause BSD license.
1461 (license (list license:gpl3+ license:bsd-3)))))
1463 (define-public r-crosstalk
1465 (name "r-crosstalk")
1470 (uri (cran-uri "crosstalk" version))
1473 "03ihj7cimkklrbad9zic78xsrfcisygmgy859hqnx0hiph80p9rn"))))
1474 (build-system r-build-system)
1476 `(("r-htmltools" ,r-htmltools)
1477 ("r-jsonlite" ,r-jsonlite)
1478 ("r-lazyeval" ,r-lazyeval)
1480 (home-page "https://rstudio.github.io/crosstalk/")
1481 (synopsis "Inter-widget interactivity for HTML widgets")
1483 "This package provides building blocks for allowing HTML widgets to
1484 communicate with each other, with Shiny or without (i.e. static @code{.html}
1485 files). It currently supports linked brushing and filtering.")
1486 (license license:expat)))
1488 (define-public r-rook
1495 (uri (cran-uri "Rook" version))
1498 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
1499 (properties `((upstream-name . "Rook")))
1500 (build-system r-build-system)
1501 (propagated-inputs `(("r-brew" ,r-brew)))
1502 (home-page "https://cran.r-project.org/web/packages/Rook")
1503 (synopsis "Web server interface for R")
1505 "This package contains the Rook specification and convenience software
1506 for building and running Rook applications. A Rook application is an R
1507 reference class object that implements a @code{call} method or an R closure
1508 that takes exactly one argument, an environment, and returns a list with three
1509 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
1510 (license license:gpl2)))
1512 (define-public r-miniui
1519 (uri (cran-uri "miniUI" version))
1522 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
1523 (properties `((upstream-name . "miniUI")))
1524 (build-system r-build-system)
1526 `(("r-htmltools" ,r-htmltools)
1527 ("r-shiny" ,r-shiny)))
1528 (home-page "https://cran.r-project.org/web/packages/miniUI/")
1529 (synopsis "Shiny UI widgets for small screens")
1531 "This package provides UI widget and layout functions for writing Shiny apps that
1532 work well on small screens.")
1533 (license license:gpl3)))
1535 (define-public r-feather
1542 (uri (cran-uri "feather" version))
1545 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
1546 (build-system r-build-system)
1550 ("r-tibble" ,r-tibble)))
1551 (home-page "https://github.com/wesm/feather")
1552 (synopsis "R Bindings to the Feather API")
1553 (description "Read and write feather files, a lightweight binary columnar
1554 data store designed for maximum speed.")
1555 (license license:asl2.0)))
1557 (define-public r-maps
1564 (uri (cran-uri "maps" version))
1567 "05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
1568 (build-system r-build-system)
1569 (home-page "https://cran.r-project.org/web/packages/maps")
1570 (synopsis "Draw geographical maps")
1571 (description "This package provides an R module for display of maps.
1572 Projection code and larger maps are in separate packages (@code{mapproj} and
1574 (license license:gpl2)))
1576 (define-public r-mapproj
1583 (uri (cran-uri "mapproj" version))
1586 "0nscsfq8md6ri9258xz57c3dj81wdl6kdwf4a9qcrwwbn20i427h"))))
1587 (build-system r-build-system)
1588 (propagated-inputs `(("r-maps" ,r-maps)))
1589 (home-page "https://cran.r-project.org/web/packages/mapproj")
1590 (synopsis "Map projection in R")
1591 (description "This package converts latitude/longitude into projected
1593 (license (list license:gpl2 ; The R interface
1594 (license:non-copyleft ; The C code
1595 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
1596 "Lucent Public License Version 1.02")))))
1598 (define-public r-rgooglemaps
1600 (name "r-rgooglemaps")
1605 (uri (cran-uri "RgoogleMaps" version))
1608 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
1609 (properties `((upstream-name . "RgoogleMaps")))
1610 (build-system r-build-system)
1614 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
1615 (synopsis "Use Google Maps in R")
1616 (description "This package serves two purposes:
1618 @item Provide a comfortable R interface to query the Google server for static
1620 @item Use the map as a background image to overlay plots within R. This
1621 requires proper coordinate scaling.
1623 (license license:gpl2+)))
1625 (define-public r-geosphere
1627 (name "r-geosphere")
1632 (uri (cran-uri "geosphere" version))
1635 "15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
1636 (build-system r-build-system)
1637 (propagated-inputs `(("r-sp" ,r-sp)))
1638 (home-page "https://cran.r-project.org/web/packages/geosphere")
1639 (synopsis "Spherical trigonometry")
1640 (description "This package computes spherical trigonometry for geographic
1641 applications. That is, compute distances and related measures for angular
1642 (longitude/latitude) locations.")
1643 (license license:gpl3+)))
1645 (define-public r-jpeg
1652 (uri (cran-uri "jpeg" version))
1655 "1a8mi70x79a691r40yiw684jkg1mr9n8agkxlcksxcnrdybs9c0x"))))
1656 (build-system r-build-system)
1657 (inputs `(("libjpeg" ,libjpeg-turbo)))
1658 (home-page "https://www.rforge.net/jpeg/")
1659 (synopsis "Read and write JPEG images with R")
1660 (description "This package provides a way to read, write and display
1661 bitmap images stored in the JPEG format with R. It can read and write both
1662 files and in-memory raw vectors.")
1663 (license license:gpl2+)))
1665 (define-public r-ggmap
1672 (uri (cran-uri "ggmap" version))
1675 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
1676 (build-system r-build-system)
1678 `(("r-bitops" ,r-bitops)
1679 ("r-digest" ,r-digest)
1680 ("r-dplyr" ,r-dplyr)
1681 ("r-ggplot2" ,r-ggplot2)
1685 ("r-magrittr" ,r-magrittr)
1688 ("r-purrr" ,r-purrr)
1689 ("r-rgooglemaps" ,r-rgooglemaps)
1690 ("r-rjson" ,r-rjson)
1691 ("r-scales" ,r-scales)
1692 ("r-stringr" ,r-stringr)
1693 ("r-tibble" ,r-tibble)
1694 ("r-tidyr" ,r-tidyr)))
1695 (home-page "https://github.com/dkahle/ggmap")
1696 (synopsis "Spatial visualization with ggplot2")
1697 (description "This package provides a collection of functions to visualize
1698 spatial data and models on top of static maps from various online sources (e.g
1699 Google Maps and Stamen Maps). It includes tools common to those tasks,
1700 including functions for geolocation and routing.")
1701 (license license:gpl2)))
1703 (define-public r-haven
1710 (uri (cran-uri "haven" version))
1713 "03cypgqhdkrfbfpl1yx2wb7flczrbak1w654wkicmd5ajwr9zvkf"))))
1714 (build-system r-build-system)
1718 `(("r-knitr" ,r-knitr)))
1720 `(("r-forcats" ,r-forcats)
1723 ("r-rlang" ,r-rlang)
1724 ("r-readr" ,r-readr)
1725 ("r-tibble" ,r-tibble)
1726 ("r-tidyselect" ,r-tidyselect)
1727 ("r-vctrs" ,r-vctrs)))
1728 (home-page "https://haven.tidyverse.org")
1729 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
1731 "This package lets you mport foreign statistical formats into R via the
1732 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
1733 (license license:expat)))
1735 (define-public r-amap
1741 (uri (cran-uri "amap" version))
1744 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
1745 (build-system r-build-system)
1747 `(("gfortran" ,gfortran)))
1748 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
1749 (synopsis "Another multidimensional analysis package")
1750 (description "This package provides tools for clustering and principal
1751 component analysis (with robust methods, and parallelized functions).")
1752 (license license:gpl2+)))
1754 (define-public r-ape
1761 (uri (cran-uri "ape" version))
1764 "0f74x9vx9sxpns2hlq4w2x80cd2gw42isfgncvs9pqbjf4hiyqnr"))))
1765 (build-system r-build-system)
1767 `(("r-lattice" ,r-lattice)
1769 ("r-rcpp" ,r-rcpp)))
1770 (home-page "http://ape-package.ird.fr/")
1771 (synopsis "Analyses of phylogenetics and evolution")
1773 "This package provides functions for reading, writing, plotting, and
1774 manipulating phylogenetic trees, analyses of comparative data in a
1775 phylogenetic framework, ancestral character analyses, analyses of
1776 diversification and macroevolution, computing distances from DNA sequences,
1777 and several other tools.")
1778 (license license:gpl2+)))
1780 (define-public r-abbyyr
1787 (uri (cran-uri "abbyyR" version))
1790 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
1791 (properties `((upstream-name . "abbyyR")))
1792 (build-system r-build-system)
1794 `(("r-curl" ,r-curl)
1797 ("r-progress" ,r-progress)
1798 ("r-readr" ,r-readr)
1800 (home-page "https://github.com/soodoku/abbyyR")
1801 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
1803 "This package provides tools to get text from images of text using Abbyy
1804 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
1805 OCR images, barcodes, forms, documents with machine readable zones, e.g.
1806 passports and get the results in a variety of formats including plain text and
1807 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
1808 (license license:expat)))
1810 (define-public r-colorspace
1812 (name "r-colorspace")
1817 (uri (cran-uri "colorspace" version))
1819 (base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
1820 (build-system r-build-system)
1821 (home-page "https://cran.r-project.org/web/packages/colorspace")
1822 (synopsis "Color space manipulation")
1824 "This package carries out a mapping between assorted color spaces
1825 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
1826 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
1827 colors are provided.")
1828 (license license:bsd-3)))
1830 (define-public r-glue
1837 (uri (cran-uri "glue" version))
1840 "1j1va4vi3g9sl0cyjdwxvh5lvh10x8k9qvnsr9zyxddcbk9qgdpq"))))
1841 (build-system r-build-system)
1842 ;; knitr depends on glue, so we can't add knitr here to build the
1846 `(("r-knitr" ,r-knitr)))
1847 (home-page "https://github.com/tidyverse/glue")
1848 (synopsis "Interpreted string literals")
1850 "This package provides an implementation of interpreted string literals,
1851 inspired by Python's Literal String Interpolation (PEP-0498) and
1852 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
1853 (license license:expat)))
1855 (define-public r-pastecs
1861 (uri (cran-uri "pastecs" version))
1864 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
1865 (build-system r-build-system)
1867 `(("r-boot" ,r-boot)))
1868 (home-page "http://www.sciviews.org/pastecs")
1869 (synopsis "Analysis of space-time ecological series")
1871 "This package provides functions for regulation, decomposition and analysis
1872 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
1873 initiative to bring PASSTEC 2000 functionalities to R.")
1874 (license license:gpl2+)))
1876 (define-public r-plogr
1883 (uri (cran-uri "plogr" version))
1886 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
1887 (build-system r-build-system)
1888 (home-page "https://github.com/krlmlr/plogr")
1889 (synopsis "R bindings for the plog C++ logging library")
1891 "This package provides the header files for a stripped-down version of
1892 the plog header-only C++ logging library, and a method to log to R's standard
1894 (license license:expat)))
1896 (define-public r-pls
1903 (uri (cran-uri "pls" version))
1905 (base32 "121byimd6bg7jbrq5wz5fpi0vxq0vh8g724vkhnjzszbvcv1xsb7"))))
1906 (build-system r-build-system)
1907 (home-page "https://mevik.net/work/software/pls.html")
1908 (synopsis "Partial Least Squares and Principal Component Regression")
1910 "The pls package implements multivariate regression methods: Partial Least
1911 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
1912 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
1915 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
1916 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
1917 @item multi-response models (or @dfn{PLS2})
1918 @item flexible cross-validation
1919 @item Jackknife variance estimates of regression coefficients
1920 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
1921 (R)MSEP, R², and correlation loadings
1922 @item formula interface, modelled after @code{lm()}, with methods for predict,
1923 print, summary, plot, update, etc.
1924 @item extraction functions for coefficients, scores, and loadings
1925 @item MSEP, RMSEP, and R² estimates
1926 @item multiplicative scatter correction (@dfn{MSC})
1928 (license license:gpl2)))
1937 (uri (cran-uri "ps" version))
1939 (base32 "1x10zgvq75gnkmzqhbqn6jyvp9h1y4qxgnbdds0bwmc8ad8md903"))))
1940 (build-system r-build-system)
1941 (home-page "https://ps.r-lib.org")
1942 (synopsis "List, query, and manipulate system processes")
1944 "The ps package implements an API to list, query, and manipulate system
1945 processes. Most of its code is based on the @code{psutil} Python package.")
1946 (license license:bsd-3)))
1948 (define-public r-pkgbuild
1955 (uri (cran-uri "pkgbuild" version))
1957 (base32 "188r2ba7y5j80mnfqdf210af40yd28jjgx7rbya4iwcfx7rzqjdi"))))
1958 (build-system r-build-system)
1960 `(("r-callr" ,r-callr)
1962 ("r-crayon" ,r-crayon)
1964 ("r-prettyunits" ,r-prettyunits)
1966 ("r-rprojroot" ,r-rprojroot)
1967 ("r-withr" ,r-withr)))
1968 (home-page "https://github.com/r-pkgs/pkgbuild")
1969 (synopsis "Find tools needed to build R packages")
1971 "This package provides functions used to build R packages. It locates
1972 compilers needed to build R packages on various platforms and ensures the PATH
1973 is configured appropriately so R can use them.")
1974 (license license:gpl3)))
1976 (define-public r-pkgload
1983 (uri (cran-uri "pkgload" version))
1986 "03bv8xq4s6s7m34y1kjs99jzlb95vwrfi76mbnhmzcx2pc6ld78q"))))
1987 (build-system r-build-system)
1990 ("r-crayon" ,r-crayon)
1992 ("r-pkgbuild" ,r-pkgbuild)
1993 ("r-rlang" ,r-rlang)
1994 ("r-rprojroot" ,r-rprojroot)
1995 ("r-rstudioapi" ,r-rstudioapi)
1996 ("r-withr" ,r-withr)))
1997 (home-page "https://github.com/r-lib/pkgload")
1998 (synopsis "Simulate package installation and attach")
2000 "This package simulates the process of installing a package and then
2001 attaching it. This is a key part of the @code{devtools} package as it allows
2002 you to rapidly iterate while developing a package.")
2003 (license license:gpl3)))
2005 (define-public r-rcpp
2012 (uri (cran-uri "Rcpp" version))
2014 (base32 "00mk23zmrqn1c4mk9d6csjcbnl12wd7yicjk2ikmw5dyvdfngbs5"))))
2015 (build-system r-build-system)
2016 (home-page "http://www.rcpp.org")
2017 (synopsis "Seamless R and C++ integration")
2019 "The Rcpp package provides R functions as well as C++ classes which offer
2020 a seamless integration of R and C++. Many R data types and objects can be
2021 mapped back and forth to C++ equivalents which facilitates both writing of new
2022 code as well as easier integration of third-party libraries. Documentation
2023 about Rcpp is provided by several vignettes included in this package, via the
2024 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
2025 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
2026 @code{citation(\"Rcpp\")} for details on these last two.")
2027 (license license:gpl2+)))
2029 (define-public r-bindr
2036 (uri (cran-uri "bindr" version))
2039 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
2040 (build-system r-build-system)
2041 (home-page "https://github.com/krlmlr/bindr")
2042 (synopsis "Parametrized active bindings")
2044 "This package provides a simple interface for creating active bindings
2045 where the bound function accepts additional arguments.")
2046 (license license:expat)))
2048 (define-public r-bindrcpp
2055 (uri (cran-uri "bindrcpp" version))
2058 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
2059 (build-system r-build-system)
2061 `(("r-bindr" ,r-bindr)
2062 ("r-plogr" ,r-plogr)
2063 ("r-rcpp" ,r-rcpp)))
2064 (home-page "https://github.com/krlmlr/bindrcpp")
2065 (synopsis "Rcpp interface to active bindings")
2067 "This package provides an easy way to fill an environment with active
2068 bindings that call a C++ function.")
2069 (license license:expat)))
2071 (define-public r-auc
2078 (uri (cran-uri "AUC" version))
2081 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
2082 (properties `((upstream-name . "AUC")))
2083 (build-system r-build-system)
2084 (home-page "https://cran.r-project.org/web/packages/AUC")
2085 (synopsis "Compute the area under the curve of selected measures")
2087 "This package includes functions to compute the area under the curve of
2088 selected measures: the area under the sensitivity curve (AUSEC), the area
2089 under the specificity curve (AUSPC), the area under the accuracy
2090 curve (AUACC), and the area under the receiver operating characteristic
2091 curve (AUROC). The curves can also be visualized. Support for partial areas
2093 (license license:gpl2+)))
2095 (define-public r-calibrate
2097 (name "r-calibrate")
2102 (uri (cran-uri "calibrate" version))
2104 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
2105 (build-system r-build-system)
2107 `(("r-mass" ,r-mass)))
2108 (home-page "https://cran.r-project.org/web/packages/calibrate")
2109 (synopsis "Calibration of scatterplot and biplot axes")
2111 "This is a package for drawing calibrated scales with tick marks
2112 on (non-orthogonal) variable vectors in scatterplots and biplots.")
2113 (license license:gpl2)))
2115 (define-public r-shape
2122 (uri (cran-uri "shape" version))
2125 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
2126 (build-system r-build-system)
2127 (home-page "https://cran.r-project.org/web/packages/shape")
2128 (synopsis "Functions for plotting graphical shapes")
2130 "This package provides functions for plotting graphical shapes such as
2131 ellipses, circles, cylinders, arrows, ...")
2132 (license license:gpl3+)))
2134 (define-public r-globaloptions
2136 (name "r-globaloptions")
2141 (uri (cran-uri "GlobalOptions" version))
2143 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
2144 (properties `((upstream-name . "GlobalOptions")))
2145 (build-system r-build-system)
2147 `(("r-knitr" ,r-knitr)))
2148 (home-page "https://github.com/jokergoo/GlobalOptions")
2149 (synopsis "Generate functions to get or set global options")
2151 "This package provides more controls on the option values such as
2152 validation and filtering on the values, making options invisible or private.")
2153 (license license:gpl2+)))
2155 (define-public r-circlize
2162 (uri (cran-uri "circlize" version))
2165 "1xb1jq3mg4kw1513zv1i09vhn7rj7f8vp0bnms2qml74s47wxsgk"))))
2166 (build-system r-build-system)
2168 `(("r-colorspace" ,r-colorspace)
2169 ("r-globaloptions" ,r-globaloptions)
2170 ("r-shape" ,r-shape)))
2172 `(("r-knitr" ,r-knitr)))
2173 (home-page "https://github.com/jokergoo/circlize")
2174 (synopsis "Circular visualization")
2176 "Circular layout is an efficient way to visualise huge amounts of
2177 information. This package provides an implementation of circular layout
2178 generation in R as well as an enhancement of available software. Its
2179 flexibility is based on the usage of low-level graphics functions such that
2180 self-defined high-level graphics can be easily implemented by users for
2181 specific purposes. Together with the seamless connection between the powerful
2182 computational and visual environment in R, it gives users more convenience and
2183 freedom to design figures for better understanding complex patterns behind
2184 multi-dimensional data.")
2185 (license license:gpl2+)))
2187 (define-public r-powerlaw
2194 (uri (cran-uri "poweRlaw" version))
2196 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
2197 (properties `((upstream-name . "poweRlaw")))
2198 (build-system r-build-system)
2200 `(("r-pracma" ,r-pracma)))
2202 `(("r-knitr" ,r-knitr)))
2203 (home-page "https://github.com/csgillespie/poweRlaw")
2204 (synopsis "Tools for the analysis of heavy tailed distributions")
2206 "This package provides an implementation of maximum likelihood estimators
2207 for a variety of heavy tailed distributions, including both the discrete and
2208 continuous power law distributions. Additionally, a goodness-of-fit based
2209 approach is used to estimate the lower cut-off for the scaling region.")
2210 ;; Any of these GPL versions.
2211 (license (list license:gpl2 license:gpl3))))
2213 (define-public r-compare
2220 (uri (cran-uri "compare" version))
2223 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
2224 (build-system r-build-system)
2225 (home-page "https://cran.r-project.org/web/packages/compare")
2226 (synopsis "Comparing objects for differences")
2228 "This package provides functions to compare a model object to a
2229 comparison object. If the objects are not identical, the functions can be
2230 instructed to explore various modifications of the objects (e.g., sorting
2231 rows, dropping names) to see if the modified versions are identical.")
2232 (license license:gpl2+)))
2234 (define-public r-dendextend
2236 (name "r-dendextend")
2241 (uri (cran-uri "dendextend" version))
2244 "1pjbz6sb4pgh3d5pm53vmf3q8y6lq3hrgjd6547xxs3m63sb8mn4"))))
2245 (build-system r-build-system)
2247 `(("r-ggplot2" ,r-ggplot2)
2248 ("r-magrittr" ,r-magrittr)
2249 ("r-viridis" ,r-viridis)))
2250 (home-page "https://cran.r-project.org/web/packages/dendextend")
2251 (synopsis "Extending 'dendrogram' functionality in R")
2253 "This package offers a set of functions for extending @code{dendrogram}
2254 objects in R, letting you visualize and compare trees of hierarchical
2255 clusterings. You can adjust a tree's graphical parameters (the color, size,
2256 type, etc of its branches, nodes and labels) and visually and statistically
2257 compare different dendrograms to one another.")
2258 ;; Any of these versions
2259 (license (list license:gpl2 license:gpl3))))
2261 (define-public r-getoptlong
2263 (name "r-getoptlong")
2268 (uri (cran-uri "GetoptLong" version))
2271 "1fswgy5j4xaipqs7nk7nzrl66vrchhxrk0w7hcsbyij3sxgn3z9j"))))
2272 (properties `((upstream-name . "GetoptLong")))
2273 (build-system r-build-system)
2277 `(("r-crayon" ,r-crayon)
2278 ("r-globaloptions" ,r-globaloptions)
2279 ("r-rjson" ,r-rjson)))
2281 `(("r-knitr" ,r-knitr)))
2282 (home-page "https://github.com/jokergoo/GetoptLong")
2283 (synopsis "Parsing command-line arguments and variable interpolation")
2285 "This is yet another command-line argument parser which wraps the
2286 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
2287 use in R. It also provides a simple way for variable interpolation in R.")
2288 (license license:gpl2+)))
2290 (define-public r-fastmatch
2292 (name "r-fastmatch")
2297 (uri (cran-uri "fastmatch" version))
2300 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
2301 (build-system r-build-system)
2302 (home-page "https://www.rforge.net/fastmatch")
2303 (synopsis "Fast match function")
2305 "This package provides a fast @code{match} replacement for cases that
2306 require repeated look-ups. It is slightly faster that R's built-in
2307 @code{match} function on first match against a table, but extremely fast on
2308 any subsequent lookup as it keeps the hash table in memory.")
2309 (license license:gpl2)))
2314 (version "2.2-14.2")
2318 (uri (cran-uri "ff" version))
2321 "1r1pbrf5s4rdm3msxxr8fy1f2xjihqciclsnvxf59qzz6g1nmh7q"))))
2322 (build-system r-build-system)
2323 (propagated-inputs `(("r-bit" ,r-bit)))
2324 (home-page "http://ff.r-forge.r-project.org/")
2325 (synopsis "Memory-efficient storage of large data on disk and access functions")
2327 "This package provides data structures that are stored on disk but
2328 behave (almost) as if they were in RAM by transparently mapping only a section
2330 ;; error Architecture not supported.
2331 (supported-systems (delete "aarch64-linux" %supported-systems))
2332 (license license:gpl2)))
2334 (define-public r-ffbase
2341 (uri (cran-uri "ffbase" version))
2344 "0mjk7dkq1ginqqfvngzny747ggf9a8fd7kblq96n5ys1jrwjyqhq"))))
2345 (build-system r-build-system)
2348 ("r-fastmatch" ,r-fastmatch)
2350 (home-page "http://github.com/edwindj/ffbase")
2351 (synopsis "Basic statistical functions for package 'ff'")
2353 "This package extends the out of memory vectors of @code{ff} with
2354 statistical functions and other utilities to ease their usage.")
2355 (license license:gpl3)))
2357 (define-public r-prettyunits
2359 (name "r-prettyunits")
2364 (uri (cran-uri "prettyunits" version))
2367 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
2368 (build-system r-build-system)
2369 (home-page "https://github.com/gaborcsardi/prettyunits")
2370 (synopsis "Pretty, human readable formatting of quantities")
2372 "This package provides tools for pretty, human readable formatting of
2374 (license license:expat)))
2376 (define-public r-reshape
2383 (uri (cran-uri "reshape" version))
2386 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
2387 (build-system r-build-system)
2389 `(("r-plyr" ,r-plyr)
2390 ("r-rcpp" ,r-rcpp)))
2391 (home-page "http://had.co.nz/reshape")
2392 (synopsis "Flexibly reshape data")
2394 "Flexibly restructure and aggregate data using just two functions:
2395 @code{melt} and @code{cast}. This package provides them.")
2396 (license license:expat)))
2398 (define-public r-progress
2405 (uri (cran-uri "progress" version))
2408 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
2409 (build-system r-build-system)
2411 `(("r-crayon" ,r-crayon)
2413 ("r-prettyunits" ,r-prettyunits)
2415 (home-page "https://github.com/gaborcsardi/progress")
2416 (synopsis "Terminal progress bars")
2418 "This package provides configurable progress bars. They may include
2419 percentage, elapsed time, and/or the estimated completion time. They work in
2420 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
2421 package also provides a C++ API, that works with or without Rcpp.")
2422 (license license:expat)))
2424 (define-public r-ggally
2431 (uri (cran-uri "GGally" version))
2434 "1gkmpzh1yvwvypkw0nwqv3gsf6za3220wig3rfv8g23kss60rl1s"))))
2435 (properties `((upstream-name . "GGally")))
2436 (build-system r-build-system)
2438 `(("libressl" ,libressl)))
2440 `(("r-ggplot2" ,r-ggplot2)
2441 ("r-gtable" ,r-gtable)
2442 ("r-lifecycle" ,r-lifecycle)
2444 ("r-progress" ,r-progress)
2445 ("r-rcolorbrewer" ,r-rcolorbrewer)
2446 ("r-reshape" ,r-reshape)
2447 ("r-rlang" ,r-rlang)
2448 ("r-scales" ,r-scales)))
2449 (home-page "https://ggobi.github.io/ggally")
2450 (synopsis "Extension to ggplot2")
2452 "The R package ggplot2 is a plotting system based on the grammar of
2453 graphics. GGally extends ggplot2 by adding several functions to reduce the
2454 complexity of combining geometric objects with transformed data. Some of
2455 these functions include a pairwise plot matrix, a two group pairwise plot
2456 matrix, a parallel coordinates plot, a survival plot, and several functions to
2458 (license license:gpl2+)))
2460 (define-public r-proxy
2467 (uri (cran-uri "proxy" version))
2470 "0z4wdnpv5x135nssxnmkkba7fivd5xgbpaabqjkl2na76vq9pzwc"))))
2471 (build-system r-build-system)
2472 (home-page "https://cran.r-project.org/web/packages/proxy")
2473 (synopsis "Distance and similarity measures")
2475 "This package provides an extensible framework for the efficient
2476 calculation of auto- and cross-proximities, along with implementations of the
2477 most popular ones.")
2478 (license license:gpl2)))
2487 (uri (cran-uri "sp" version))
2489 (base32 "02jxsd30apzjbdbssirysq70d4svdwzn931jhxr0ladl72g9bqvk"))))
2490 (build-system r-build-system)
2492 `(("r-lattice" ,r-lattice)))
2493 (home-page "https://cran.r-project.org/web/packages/sp")
2494 (synopsis "Classes and methods for spatial data")
2496 "This package provides classes and methods for spatial data; the classes
2497 document where the spatial location information resides, for 2D or 3D data.
2498 Utility functions are provided, e.g. for plotting data as maps, spatial
2499 selection, as well as methods for retrieving coordinates, for subsetting,
2500 print, summary, etc.")
2501 (license license:gpl2+)))
2503 (define-public r-rmtstat
2510 (uri (cran-uri "RMTstat" version))
2513 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
2514 (properties `((upstream-name . "RMTstat")))
2515 (build-system r-build-system)
2516 (home-page "https://cran.r-project.org/web/packages/RMTstat")
2517 (synopsis "Distributions, statistics and tests derived from random matrix theory")
2519 "This package provides functions for working with the Tracy-Widom laws
2520 and other distributions related to the eigenvalues of large Wishart
2522 (license license:bsd-3)))
2524 (define-public r-rmpi
2530 (uri (cran-uri "Rmpi" version))
2533 "1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
2534 (properties `((upstream-name . "Rmpi")))
2535 (build-system r-build-system)
2537 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
2538 #:phases (modify-phases %standard-phases
2539 (add-before 'install 'mpi-setup
2542 `(("openmpi" ,openmpi)))
2544 `(("pkg-config" ,pkg-config)))
2545 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
2546 (synopsis "R interface to message-passing interface (MPI)")
2548 "This package provides an interface (wrapper) to MPI APIs. It also
2549 provides an interactive R manager and worker environment.")
2550 (license license:gpl2+)))
2552 (define-public r-lmoments
2559 (uri (cran-uri "Lmoments" version))
2562 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
2563 (properties `((upstream-name . "Lmoments")))
2564 (build-system r-build-system)
2566 `(("r-rcpp" ,r-rcpp)
2567 ("r-rcpparmadillo" ,r-rcpparmadillo)))
2568 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
2569 (synopsis "L-moments and quantile mixtures")
2571 "This package contains functions to estimate L-moments and trimmed
2572 L-moments from the data. It also contains functions to estimate the
2573 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
2574 quantile mixture from L-moments and trimmed L-moments.")
2575 (license license:gpl2)))
2577 (define-public r-distillery
2579 (name "r-distillery")
2584 (uri (cran-uri "distillery" version))
2587 "0w72vb3p51m0hwms9icwgy1xg3dplmpjrxibl2s92lpdrv737249"))))
2588 (build-system r-build-system)
2589 (home-page "https://ral.ucar.edu/staff/ericg/")
2590 (synopsis "Functions for confidence intervals and object information")
2592 "This package provides some very simple method functions for confidence
2593 interval calculation and to distill pertinent information from a potentially
2594 complex object; primarily used in common with the packages extRemes and
2596 (license license:gpl2+)))
2598 (define-public r-extremes
2605 (uri (cran-uri "extRemes" version))
2608 "0wldzvj1h93jksq31dw9zgnr1wrqwmfr9qwmg7qk7nznsn2yy1h2"))))
2609 (properties `((upstream-name . "extRemes")))
2610 (build-system r-build-system)
2612 `(("r-distillery" ,r-distillery)
2613 ("r-lmoments" ,r-lmoments)))
2614 (home-page "https://www.assessment.ucar.edu/toolkit/")
2615 (synopsis "Extreme value analysis")
2617 "ExtRemes is a suite of functions for carrying out analyses on the
2618 extreme values of a process of interest; be they block maxima over long blocks
2619 or excesses over a high threshold.")
2620 (license license:gpl2+)))
2622 (define-public r-lmtest
2629 (uri (cran-uri "lmtest" version))
2632 "02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
2633 (build-system r-build-system)
2635 `(("r-zoo" ,r-zoo)))
2637 `(("gfortran" ,gfortran)))
2638 (home-page "https://cran.r-project.org/web/packages/lmtest")
2639 (synopsis "Testing linear regression models")
2641 "This package provides a collection of tests, data sets, and examples for
2642 diagnostic checking in linear regression models. Furthermore, some generic
2643 tools for inference in parametric models are provided.")
2644 ;; Either version is okay
2645 (license (list license:gpl2 license:gpl3))))
2647 (define-public r-idr
2653 (uri (cran-uri "idr" version))
2656 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
2657 (build-system r-build-system)
2658 (home-page "https://cran.r-project.org/web/packages/idr/")
2659 (synopsis "Irreproducible discovery rate")
2661 "This is a package for estimating the copula mixture model and plotting
2662 correspondence curves in \"Measuring reproducibility of high-throughput
2663 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
2664 by Li, Brown, Huang, and Bickel")
2665 (license license:gpl2+)))
2667 (define-public r-inline
2673 (uri (cran-uri "inline" version))
2676 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
2677 (build-system r-build-system)
2678 (home-page "https://cran.r-project.org/web/packages/inline")
2679 (synopsis "Functions to inline C, C++, Fortran function calls from R")
2681 "This package provides functionality to dynamically define R functions
2682 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
2683 @code{.Call} calling conventions.")
2684 ;; Any version of the LGPL.
2685 (license license:lgpl3+)))
2687 (define-public r-inum
2693 (uri (cran-uri "inum" version))
2696 "16d09391l65w557dkzhhx1aqn1ljamcmjj3yh42pwq037k0r8brw"))))
2697 (build-system r-build-system)
2699 `(("r-libcoin" ,r-libcoin)))
2700 (home-page "https://cran.r-project.org/web/packages/inum/")
2701 (synopsis "Interval and enum-type representation of vectors")
2703 "This package provides an enum-type representation of vectors and
2704 representation of intervals, including a method of coercing variables
2706 (license license:gpl2)))
2708 (define-public r-bdsmatrix
2710 (name "r-bdsmatrix")
2715 (uri (cran-uri "bdsmatrix" version))
2718 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
2719 (properties `((upstream-name . "bdsmatrix")))
2720 (build-system r-build-system)
2721 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
2722 (synopsis "Routines for block diagonal symmetric matrices")
2724 "This package provides procedures to work with block diagonal symmetric
2725 matrices, a special case of sparse matrices.")
2726 (license license:lgpl2.0)))
2728 (define-public r-bbmle
2731 (version "1.0.23.1")
2735 (uri (cran-uri "bbmle" version))
2738 "0p3l9shbr2846qmw8n0fyzf4j7gmi08aypl82jml3dwh26q1whk0"))))
2739 (build-system r-build-system)
2741 `(("r-bdsmatrix" ,r-bdsmatrix)
2742 ("r-lattice" ,r-lattice)
2744 ("r-matrix" ,r-matrix)
2745 ("r-mvtnorm" ,r-mvtnorm)
2746 ("r-numderiv" ,r-numderiv)))
2747 (home-page "https://cran.r-project.org/web/packages/bbmle")
2748 (synopsis "Tools for General Maximum Likelihood Estimation")
2750 "This package provides methods and functions for fitting maximum
2751 likelihood models in R. This package modifies and extends the @code{mle}
2752 classes in the @code{stats4} package.")
2753 ;; Any version of the GPL
2754 (license license:gpl2+)))
2756 (define-public r-emdbook
2763 (uri (cran-uri "emdbook" version))
2766 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
2767 (build-system r-build-system)
2769 `(("r-bbmle" ,r-bbmle)
2771 ("r-lattice" ,r-lattice)
2773 ("r-plyr" ,r-plyr)))
2774 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
2775 (synopsis "Support functions and data for \"Ecological Models and Data\"")
2777 "This package provides auxiliary functions and data sets for \"Ecological
2778 Models and Data\", a book presenting maximum likelihood estimation and related
2779 topics for ecologists (ISBN 978-0-691-12522-0).")
2781 (license (list license:gpl2 license:gpl3))))
2783 (define-public r-lpsolve
2790 (uri (cran-uri "lpSolve" version))
2793 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
2794 (properties `((upstream-name . "lpSolve")))
2795 (build-system r-build-system)
2796 (home-page "https://cran.r-project.org/web/packages/lpSolve")
2797 (synopsis "R interface to Lp_solve to solve linear/integer programs")
2799 "Lp_solve is software for solving linear, integer and mixed integer
2800 programs. This implementation supplies a \"wrapper\" function in C and some R
2801 functions that solve general linear/integer problems, assignment problems, and
2802 transportation problems.")
2803 (license license:lgpl2.0)))
2805 (define-public r-limsolve
2812 (uri (cran-uri "limSolve" version))
2815 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
2816 (properties `((upstream-name . "limSolve")))
2817 (build-system r-build-system)
2819 `(("r-lpsolve" ,r-lpsolve)
2821 ("r-quadprog" ,r-quadprog)))
2822 (native-inputs `(("gfortran" ,gfortran)))
2823 (home-page "https://cran.r-project.org/web/packages/limSolve")
2824 (synopsis "Solving linear inverse models")
2826 "This package provides functions that:
2829 @item find the minimum/maximum of a linear or quadratic function,
2830 @item sample an underdetermined or overdetermined system,
2831 @item solve a linear system Ax=B for the unknown x.
2834 It includes banded and tridiagonal linear systems. The package calls Fortran
2835 functions from LINPACK.")
2837 (license (list license:gpl2+ license:gpl3+))))
2839 (define-public r-fitdistrplus
2841 (name "r-fitdistrplus")
2846 (uri (cran-uri "fitdistrplus" version))
2849 "1rnfnwmxa495fql7q0h9018cnwygwhj8gfh6ryz1vbf474570vjl"))))
2850 (build-system r-build-system)
2852 `(("r-mass" ,r-mass)
2853 ("r-survival" ,r-survival)))
2855 `(("r-knitr" ,r-knitr)))
2856 (home-page "http://riskassessment.r-forge.r-project.org")
2857 (synopsis "Fitting a parametric distribution from data")
2859 "This package extends the @code{fitdistr} function of the MASS package
2860 with several functions to help the fit of a parametric distribution to
2861 non-censored or censored data. Censored data may contain left-censored,
2862 right-censored and interval-censored values, with several lower and upper
2863 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
2864 provides moment matching (MME), quantile matching (QME) and maximum
2865 goodness-of-fit estimation (MGE) methods (available only for non-censored
2866 data). Weighted versions of MLE, MME and QME are available.")
2867 (license license:gpl2+)))
2869 (define-public r-energy
2876 (uri (cran-uri "energy" version))
2879 "13wnx5nwk7nsv7vf5sxhz4y0rxrnzm76ldgywk1bxrz67srqzf37"))))
2880 (build-system r-build-system)
2882 `(("r-boot" ,r-boot)
2883 ("r-rcpp" ,r-rcpp)))
2884 (home-page "https://cran.r-project.org/web/packages/energy")
2885 (synopsis "Multivariate inference via the energy of data")
2887 "This package provides e-statistics (energy) tests and statistics for
2888 multivariate and univariate inference, including distance correlation,
2889 one-sample, two-sample, and multi-sample tests for comparing multivariate
2890 distributions, are implemented. Measuring and testing multivariate
2891 independence based on distance correlation, partial distance correlation,
2892 multivariate goodness-of-fit tests, clustering based on energy distance,
2893 testing for multivariate normality, distance components (disco) for
2894 non-parametric analysis of structured data, and other energy
2895 statistics/methods are implemented.")
2896 (license license:gpl2+)))
2898 (define-public r-suppdists
2900 (name "r-suppdists")
2905 (uri (cran-uri "SuppDists" version))
2908 "01j6p94m1g363nph2158fq2rmd6z3h5dvcv6aidh2d6syw131xak"))))
2909 (properties `((upstream-name . "SuppDists")))
2910 (build-system r-build-system)
2911 (home-page "https://cran.r-project.org/web/packages/SuppDists")
2912 (synopsis "Supplementary distributions")
2914 "This package provides ten distributions supplementing those built into
2915 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
2916 Spearman's rho, maximum F ratio, the Pearson product moment correlation
2917 coefficient, Johnson distributions, normal scores and generalized
2918 hypergeometric distributions. In addition two random number generators of
2919 George Marsaglia are included.")
2920 (license license:gpl2+)))
2922 (define-public r-ksamples
2929 (uri (cran-uri "kSamples" version))
2932 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
2933 (properties `((upstream-name . "kSamples")))
2934 (build-system r-build-system)
2936 `(("r-suppdists" ,r-suppdists)))
2937 (home-page "https://cran.r-project.org/web/packages/kSamples")
2938 (synopsis "K-Sample rank tests and their combinations")
2940 "This package provides tools to compares k samples using the
2941 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
2942 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
2943 test. It computes asymptotic, simulated or (limited) exact P-values, all
2944 valid under randomization, with or without ties, or conditionally under random
2945 sampling from populations, given the observed tie pattern. Except for Steel's
2946 test and the JT test it also combines these tests across several blocks of
2948 (license license:gpl2+)))
2950 (define-public r-cvst
2957 (uri (cran-uri "CVST" version))
2960 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
2961 (properties `((upstream-name . "CVST")))
2962 (build-system r-build-system)
2964 `(("r-kernlab" ,r-kernlab)
2965 ("r-matrix" ,r-matrix)))
2966 (home-page "https://cran.r-project.org/web/packages/CVST")
2967 (synopsis "Fast cross-validation via sequential testing")
2969 "This package implements the fast cross-validation via sequential
2970 testing (CVST) procedure. CVST is an improved cross-validation procedure
2971 which uses non-parametric testing coupled with sequential analysis to
2972 determine the best parameter set on linearly increasing subsets of the data.
2973 Additionally to the CVST the package contains an implementation of the
2974 ordinary k-fold cross-validation with a flexible and powerful set of helper
2975 objects and methods to handle the overall model selection process. The
2976 implementations of the Cochran's Q test with permutations and the sequential
2977 testing framework of Wald are generic and can therefore also be used in other
2979 (license license:gpl2+)))
2981 (define-public r-squarem
2988 (uri (cran-uri "SQUAREM" version))
2991 "17l05i87vwvcsk79fbg52zrx04zdlwiiyl3ga8qafs7mqx0j976q"))))
2992 (properties `((upstream-name . "SQUAREM")))
2993 (build-system r-build-system)
2994 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
2995 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
2997 "This package provides algorithms for accelerating the convergence of
2998 slow, monotone sequences from smooth, contraction mapping such as the EM
2999 algorithm. It can be used to accelerate any smooth, linearly convergent
3000 acceleration scheme. A tutorial style introduction to this package is
3001 available in a vignette.")
3002 (license license:gpl2+)))
3004 (define-public r-lava
3011 (uri (cran-uri "lava" version))
3014 "0ffzxbb8pvfh1m6j61az4ga37snyhylq2941fyc76w7w9i2sixv3"))))
3015 (build-system r-build-system)
3017 `(("r-numderiv" ,r-numderiv)
3018 ("r-squarem" ,r-squarem)
3019 ("r-survival" ,r-survival)))
3020 (home-page "https://github.com/kkholst/lava")
3021 (synopsis "Latent variable models")
3023 "This package provides tools for the estimation and simulation of latent
3025 (license license:gpl3)))
3027 (define-public r-drr
3034 (uri (cran-uri "DRR" version))
3037 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
3038 (properties `((upstream-name . "DRR")))
3039 (build-system r-build-system)
3041 `(("r-cvst" ,r-cvst)
3042 ("r-kernlab" ,r-kernlab)
3043 ("r-matrix" ,r-matrix)))
3044 (home-page "https://cran.r-project.org/web/packages/DRR")
3045 (synopsis "Dimensionality reduction via regression")
3047 "This package provides an implementation of dimensionality reduction via
3048 regression using Kernel Ridge Regression.")
3049 (license license:gpl3)))
3051 (define-public r-prodlim
3054 (version "2019.11.13")
3058 (uri (cran-uri "prodlim" version))
3061 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
3062 (build-system r-build-system)
3064 `(("r-kernsmooth" ,r-kernsmooth)
3067 ("r-survival" ,r-survival)))
3068 (home-page "https://cran.r-project.org/web/packages/prodlim")
3069 (synopsis "Product-limit estimation for censored event history analysis")
3071 "This package provides a fast and user-friendly implementation of
3072 nonparametric estimators for censored event history (survival) analysis with
3073 the Kaplan-Meier and Aalen-Johansen methods.")
3074 (license license:gpl2+)))
3076 (define-public r-dimred
3083 (uri (cran-uri "dimRed" version))
3086 "110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
3087 (properties `((upstream-name . "dimRed")))
3088 (build-system r-build-system)
3091 ("r-magrittr" ,r-magrittr)))
3092 (home-page "https://github.com/gdkrmr/dimRed")
3093 (synopsis "Framework for dimensionality reduction")
3095 "This package provides a collection of dimensionality reduction
3096 techniques from R packages and provides a common interface for calling the
3098 (license license:gpl3)))
3100 (define-public r-timedate
3103 (version "3043.102")
3107 (uri (cran-uri "timeDate" version))
3110 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
3111 (properties `((upstream-name . "timeDate")))
3112 (build-system r-build-system)
3113 (home-page "https://www.rmetrics.org")
3114 (synopsis "Chronological and calendar objects")
3116 "This package provides an environment for teaching \"Financial
3117 Engineering and Computational Finance\" and for managing chronological and
3119 (license license:gpl2+)))
3121 (define-public r-magic
3128 (uri (cran-uri "magic" version))
3131 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
3132 (build-system r-build-system)
3134 `(("r-abind" ,r-abind)))
3135 (home-page "https://github.com/RobinHankin/magic.git")
3136 (synopsis "Create and investigate magic squares")
3138 "This package provides a collection of efficient, vectorized algorithms
3139 for the creation and investigation of magic squares and hypercubes, including
3140 a variety of functions for the manipulation and analysis of arbitrarily
3141 dimensioned arrays.")
3142 (license license:gpl2)))
3144 (define-public r-rmysql
3151 (uri (cran-uri "RMySQL" version))
3154 "0lv9m6zpm8dgv7yixr6xhw379vbq45d7n7gkrmjrppdj8vcih77i"))))
3155 (properties `((upstream-name . "RMySQL")))
3156 (build-system r-build-system)
3158 `(("mariadb" ,mariadb "lib")
3159 ("mariadb-dev" ,mariadb "dev")
3162 `(("r-dbi" ,r-dbi)))
3163 (home-page "https://github.com/r-dbi/RMySQL")
3164 (synopsis "Database interface and MySQL driver for R")
3166 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
3167 package contains an old implementation based on legacy code from S-PLUS which
3168 is being phased out. A modern MySQL client based on Rcpp is available from
3169 the RMariaDB package.")
3170 (license license:gpl2)))
3172 (define-public r-rpostgresql
3174 (name "r-rpostgresql")
3179 (uri (cran-uri "RPostgreSQL" version))
3182 "1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
3183 (properties `((upstream-name . "RPostgreSQL")))
3184 (build-system r-build-system)
3186 `(("postgresql" ,postgresql)))
3188 `(("r-dbi" ,r-dbi)))
3189 (home-page "https://github.com/tomoakin/RPostgreSQL")
3190 (synopsis "R interface to the PostgreSQL database system")
3192 "This package provides a Database Interface (DBI) compliant driver for R
3193 to access PostgreSQL database systems.")
3194 ;; The whole package is released under GPL version 2. It includes code
3195 ;; under the PostgreSQL license.
3196 (license license:gpl2)))
3198 (define-public r-linprog
3205 (uri (cran-uri "linprog" version))
3208 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
3209 (build-system r-build-system)
3210 (propagated-inputs `(("r-lpsolve" ,r-lpsolve)))
3211 (home-page "http://linprog.r-forge.r-project.org/")
3212 (synopsis "Linear programming and optimization")
3214 "This package can be used to solve Linear Programming / Linear
3215 Optimization problems by using the simplex algorithm.")
3216 (license license:gpl2+)))
3218 (define-public r-geometry
3225 (uri (cran-uri "geometry" version))
3228 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
3229 (build-system r-build-system)
3231 `(("r-magic" ,r-magic)
3232 ("r-linprog" ,r-linprog)
3233 ("r-lpsolve" ,r-lpsolve)
3235 ("r-rcppprogress" ,r-rcppprogress)))
3236 (home-page "http://geometry.r-forge.r-project.org/")
3237 (synopsis "Mesh generation and surface tesselation")
3239 "This package makes the qhull library available in R, in a similar manner
3240 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
3241 intersections about a point, Voronoi diagrams, furthest-site Delaunay
3242 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
3243 and higher dimensions. It implements the Quickhull algorithm for computing
3244 the convex hull. Qhull does not support constrained Delaunay triangulations,
3245 or mesh generation of non-convex objects, but the package does include some R
3246 functions that allow for this. Currently the package only gives access to
3247 Delaunay triangulation and convex hull computation.")
3248 ;; The Qhull sources are included and are distributed under a custom
3249 ;; non-copyleft license. The R sources are released under GPL version 2.
3250 (license (list license:gpl2
3251 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
3253 (define-public r-ddalpha
3260 (uri (cran-uri "ddalpha" version))
3263 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
3264 (build-system r-build-system)
3267 ("r-class" ,r-class)
3268 ("r-geometry" ,r-geometry)
3271 ("r-robustbase" ,r-robustbase)
3272 ("r-sfsmisc" ,r-sfsmisc)))
3274 `(("gfortran" ,gfortran)))
3275 (home-page "https://cran.r-project.org/web/packages/ddalpha")
3276 (synopsis "Depth-Based classification and calculation of data depth")
3278 "This package contains procedures for depth-based supervised learning,
3279 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
3280 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
3281 statistical depth function to a compact low-dimensional space, where the final
3282 classification is done. It also offers an extension to functional data and
3283 routines for calculating certain notions of statistical depth functions. 50
3284 multivariate and 5 functional classification problems are included.")
3285 (license license:gpl2)))
3287 (define-public r-gower
3294 (uri (cran-uri "gower" version))
3297 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
3298 (build-system r-build-system)
3299 (home-page "https://github.com/markvanderloo/gower")
3300 (synopsis "Gower's distance")
3302 "This package provides tools to compute Gower's distance (or similarity)
3303 coefficient between records, and to compute the top-n matches between records.
3304 Core algorithms are executed in parallel on systems supporting OpenMP.")
3305 (license license:gpl3)))
3307 (define-public r-rcpproll
3314 (uri (cran-uri "RcppRoll" version))
3317 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
3318 (properties `((upstream-name . "RcppRoll")))
3319 (build-system r-build-system)
3321 `(("r-rcpp" ,r-rcpp)))
3322 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
3323 (synopsis "Efficient rolling and windowed operations")
3325 "This package provides fast and efficient routines for common rolling /
3326 windowed operations. Routines for the efficient computation of windowed mean,
3327 median, sum, product, minimum, maximum, standard deviation and variance are
3329 (license license:gpl2+)))
3331 (define-public r-ipred
3338 (uri (cran-uri "ipred" version))
3341 "0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
3342 (build-system r-build-system)
3344 `(("r-class" ,r-class)
3347 ("r-prodlim" ,r-prodlim)
3348 ("r-rpart" ,r-rpart)
3349 ("r-survival" ,r-survival)))
3350 (home-page "https://cran.r-project.org/web/packages/ipred")
3351 (synopsis "Improved predictors")
3353 "This package provides improved predictive models by indirect
3354 classification and bagging for classification, regression and survival
3355 problems as well as resampling based estimators of prediction error.")
3356 (license license:gpl2+)))
3358 (define-public r-psych
3361 (version "1.9.12.31")
3365 (uri (cran-uri "psych" version))
3368 "02i9p6appf15hjdsi58g39bzs9as40f9qhy8m7ki30hd1fz1vrr5"))))
3369 (build-system r-build-system)
3371 `(("r-lattice" ,r-lattice)
3372 ("r-mnormt" ,r-mnormt)
3373 ("r-nlme" ,r-nlme)))
3374 (home-page "https://cran.r-project.org/web/packages/psych/")
3375 (synopsis "Procedures for psychological, psychometric, and personality research")
3377 "This package provides a general purpose toolbox for personality,
3378 psychometric theory and experimental psychology. Functions are primarily for
3379 multivariate analysis and scale construction using factor analysis, principal
3380 component analysis, cluster analysis and reliability analysis, although others
3381 provide basic descriptive statistics. Item Response Theory is done using
3382 factor analysis of tetrachoric and polychoric correlations. Functions for
3383 analyzing data at multiple levels include within and between group statistics,
3384 including correlations and factor analysis. Functions for simulating and
3385 testing particular item and test structures are included. Several functions
3386 serve as a useful front end for structural equation modeling. Graphical
3387 displays of path diagrams, factor analysis and structural equation models are
3388 created using basic graphics.")
3389 (license license:gpl2+)))
3391 (define-public r-generics
3398 (uri (cran-uri "generics" version))
3401 "0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
3402 (build-system r-build-system)
3403 (home-page "https://github.com/r-lib/generics")
3404 (synopsis "Common S3 generics not provided by base R methods")
3406 "In order to reduce potential package dependencies and conflicts,
3407 generics provides a number of commonly used S3 generics that are not provided
3408 by base R methods related to model fitting.")
3409 (license license:gpl2)))
3411 (define-public r-broom
3418 (uri (cran-uri "broom" version))
3421 "0da3jsb02xckrk6alznicn6l5lnyvdhc64qklyarnd77miqgc1hb"))))
3422 (build-system r-build-system)
3424 `(("r-backports" ,r-backports)
3425 ("r-dplyr" ,r-dplyr)
3426 ("r-generics" ,r-generics)
3428 ("r-purrr" ,r-purrr)
3429 ("r-reshape2" ,r-reshape2)
3430 ("r-stringr" ,r-stringr)
3431 ("r-tibble" ,r-tibble)
3432 ("r-tidyr" ,r-tidyr)))
3434 `(("r-knitr" ,r-knitr)))
3435 (home-page "https://github.com/tidyverse/broom")
3436 (synopsis "Convert statistical analysis objects into tidy data frames")
3438 "This package provides tools to convert statistical analysis objects from
3439 R into tidy data frames, so that they can more easily be combined, reshaped
3440 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
3441 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
3442 summarizes a model's statistical findings such as coefficients of a
3443 regression; @code{augment}, which adds columns to the original data such as
3444 predictions, residuals and cluster assignments; and @code{glance}, which
3445 provides a one-row summary of model-level statistics.")
3446 (license license:expat)))
3448 (define-public r-recipes
3455 (uri (cran-uri "recipes" version))
3458 "1d3pmprkiz60w7lq5q4lpl5zlwf7fg7qghf7sq6xs1294w54gzbs"))))
3459 (build-system r-build-system)
3461 `(("r-dplyr" ,r-dplyr)
3462 ("r-generics" ,r-generics)
3464 ("r-gower" ,r-gower)
3465 ("r-ipred" ,r-ipred)
3466 ("r-lifecycle" ,r-lifecycle)
3467 ("r-lubridate" ,r-lubridate)
3468 ("r-magrittr" ,r-magrittr)
3469 ("r-matrix" ,r-matrix)
3470 ("r-purrr" ,r-purrr)
3471 ("r-rlang" ,r-rlang)
3472 ("r-tibble" ,r-tibble)
3473 ("r-tidyr" ,r-tidyr)
3474 ("r-tidyselect" ,r-tidyselect)
3475 ("r-timedate" ,r-timedate)
3476 ("r-withr" ,r-withr)))
3478 `(("r-knitr" ,r-knitr)))
3479 (home-page "https://github.com/topepo/recipes")
3480 (synopsis "Preprocessing tools to create design matrices")
3482 "Recipes is an extensible framework to create and preprocess design
3483 matrices. Recipes consist of one or more data manipulation and analysis
3484 \"steps\". Statistical parameters for the steps can be estimated from an
3485 initial data set and then applied to other data sets. The resulting design
3486 matrices can then be used as inputs into statistical or machine learning
3488 (license license:gpl2)))
3490 (define-public r-pdist
3497 (uri (cran-uri "pdist" version))
3500 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
3501 (build-system r-build-system)
3502 (home-page "https://github.com/jeffwong/pdist")
3503 (synopsis "Partitioned distance function")
3505 "Pdist computes the euclidean distance between rows of a matrix X and
3506 rows of another matrix Y. Previously, this could be done by binding the two
3507 matrices together and calling @code{dist}, but this creates unnecessary
3508 computation by computing the distances between a row of X and another row of
3509 X, and likewise for Y. Pdist strictly computes distances across the two
3510 matrices, not within the same matrix, making computations significantly faster
3511 for certain use cases.")
3512 (license license:gpl3+)))
3514 (define-public r-ggrepel
3521 (uri (cran-uri "ggrepel" version))
3524 "1qaifn3dazdqbqlii210xhw7yf142iw7g9p2axmmxbz90p0by08d"))))
3525 (build-system r-build-system)
3527 `(("r-ggplot2" ,r-ggplot2)
3529 ("r-scales" ,r-scales)))
3531 `(("r-knitr" ,r-knitr))) ; for vignettes
3532 (home-page "http://github.com/slowkow/ggrepel")
3533 (synopsis "Repulsive text and label geometries for ggplot2")
3535 "This package provides text and label geometries for ggplot2 that help to
3536 avoid overlapping text labels. Labels repel away from each other and away
3537 from the data points.")
3538 (license license:gpl3)))
3540 (define-public r-corrplot
3547 (uri (cran-uri "corrplot" version))
3550 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
3551 (build-system r-build-system)
3552 (home-page "https://github.com/taiyun/corrplot")
3553 (synopsis "Visualization of a correlation matrix")
3555 "This package provides a graphical display of a correlation matrix or
3556 general matrix. It also contains some algorithms to do matrix reordering. In
3557 addition, corrplot is good at details, including choosing color, text labels,
3558 color labels, layout, etc.")
3559 ;; Any version of the GPL
3560 (license license:gpl2+)))
3562 (define-public r-stringdist
3564 (name "r-stringdist")
3569 (uri (cran-uri "stringdist" version))
3571 (base32 "1dqfakclzaf878x7mhwmqrcpcql2h9cv19fz5f3ygpajf3si5kqi"))))
3572 (build-system r-build-system)
3573 (home-page "https://github.com/markvanderloo/stringdist")
3574 (synopsis "Approximate string matching and string distance functions")
3576 "This package implements an approximate string matching version of R's
3577 native @code{match} function. It can calculate various string distances based
3578 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
3579 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
3580 Jaro-Winkler). An implementation of soundex is provided as well. Distances
3581 can be computed between character vectors while taking proper care of encoding
3582 or between integer vectors representing generic sequences.")
3583 (license license:gpl3+)))
3585 (define-public r-ucminf
3592 (uri (cran-uri "ucminf" version))
3595 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
3596 (build-system r-build-system)
3597 (native-inputs `(("gfortran" ,gfortran)))
3598 (home-page "https://cran.r-project.org/web/packages/ucminf/")
3599 (synopsis "General-purpose unconstrained non-linear optimization")
3601 "This package provides an implementation of an algorithm for
3602 general-purpose unconstrained non-linear optimization. The algorithm is of
3603 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
3604 search with a trust region type monitoring of the input to the line search
3605 algorithm. The interface of @code{ucminf} is designed for easy interchange
3606 with the package @code{optim}.")
3607 (license license:gpl2+)))
3609 (define-public r-ordinal
3612 (version "2019.12-10")
3616 (uri (cran-uri "ordinal" version))
3619 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
3620 (build-system r-build-system)
3622 `(("r-mass" ,r-mass)
3623 ("r-matrix" ,r-matrix)
3624 ("r-numderiv" ,r-numderiv)
3625 ("r-ucminf" ,r-ucminf)))
3626 (home-page "https://github.com/runehaubo/ordinal")
3627 (synopsis "Regression models for ordinal data")
3629 "This package provides an implementation of cumulative link (mixed)
3630 models also known as ordered regression models, proportional odds models,
3631 proportional hazards models for grouped survival times and ordered models.
3632 Estimation is via maximum likelihood and mixed models are fitted with the
3633 Laplace approximation and adaptive Gauss-Hermite quadrature.")
3634 (license license:gpl2+)))
3636 (define-public r-jomo
3643 (uri (cran-uri "jomo" version))
3646 "0cdy9m4ylarkk9d0v1s61k2d877l4bbxly8a4jwhfy43fdvskz1w"))))
3647 (build-system r-build-system)
3649 `(("r-lme4" ,r-lme4)
3651 ("r-ordinal" ,r-ordinal)
3652 ("r-survival" ,r-survival)))
3653 (home-page "https://cran.r-project.org/web/packages/jomo/")
3654 (synopsis "Multilevel Joint Modelling Multiple Imputation")
3656 "Similarly to Schafer's package pan, jomo is a package for multilevel
3657 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
3658 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
3659 possibility of handling binary and categorical data through latent normal
3660 variables, the option to use cluster-specific covariance matrices and to
3661 impute compatibly with the substantive model.")
3662 (license license:gpl2)))
3664 (define-public r-pan
3671 (uri (cran-uri "pan" version))
3674 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
3675 (build-system r-build-system)
3676 (native-inputs `(("gfortran" ,gfortran)))
3677 (home-page "https://cran.r-project.org/web/packages/pan/")
3678 (synopsis "Multiple imputation for multivariate panel or clustered data")
3680 "This package implements multiple imputation for multivariate panel or
3682 (license license:gpl3)))
3684 (define-public r-mitml
3691 (uri (cran-uri "mitml" version))
3694 "0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
3695 (build-system r-build-system)
3697 `(("r-haven" ,r-haven)
3700 (home-page "https://cran.r-project.org/web/packages/mitml/")
3701 (synopsis "Tools for multiple imputation in multilevel modeling")
3703 "This package provides tools for multiple imputation of missing data in
3704 multilevel modeling. It includes a user-friendly interface to the packages
3705 pan and jomo, and several functions for visualization, data management and the
3706 analysis of multiply imputed data sets.")
3707 (license license:gpl2+)))
3709 (define-public r-mice
3716 (uri (cran-uri "mice" version))
3719 "1wycbc2iqp68gfzvqx1gsn5n1k1h4bg79dy8m5msqf226hy83ncn"))))
3720 (build-system r-build-system)
3722 `(("r-broom" ,r-broom)
3723 ("r-dplyr" ,r-dplyr)
3724 ("r-lattice" ,r-lattice)
3726 ("r-tidyr" ,r-tidyr)))
3727 (home-page "https://cran.r-project.org/web/packages/mice/")
3728 (synopsis "Multivariate imputation by chained equations")
3730 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
3731 implemented by the MICE algorithm as described in @url{Van Buuren and
3732 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
3733 variable has its own imputation model. Built-in imputation models are
3734 provided for continuous data (predictive mean matching, normal), binary
3735 data (logistic regression), unordered categorical data (polytomous logistic
3736 regression) and ordered categorical data (proportional odds). MICE can also
3737 impute continuous two-level data (normal model, pan, second-level variables).
3738 Passive imputation can be used to maintain consistency between variables.
3739 Various diagnostic plots are available to inspect the quality of the
3741 ;; Any of these two versions.
3742 (license (list license:gpl2 license:gpl3))))
3744 (define-public r-truncnorm
3746 (name "r-truncnorm")
3751 (uri (cran-uri "truncnorm" version))
3754 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
3755 (build-system r-build-system)
3756 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
3757 (synopsis "Truncated normal distribution")
3758 (description "This package provides functions for the truncated normal
3759 distribution with mean equal to @code{mean} and standard deviation equal to
3760 @code{sd}. It includes density, distribution, quantile, and expected value
3761 functions, as well as a random generation function.")
3762 (license license:gpl2)))
3764 (define-public r-rsolnp
3771 (uri (cran-uri "Rsolnp" version))
3774 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
3775 (properties `((upstream-name . "Rsolnp")))
3776 (build-system r-build-system)
3778 `(("r-truncnorm" ,r-truncnorm)))
3779 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
3780 (synopsis "General non-linear optimization")
3781 (description "The Rsolnp package implements a general non-linear augmented
3782 Lagrange multiplier method solver, a @dfn{sequential quadratic
3783 programming} (SQP) based solver).")
3784 ;; Any version of the GPL.
3785 (license license:gpl2+)))
3787 (define-public r-hardyweinberg
3789 (name "r-hardyweinberg")
3794 (uri (cran-uri "HardyWeinberg" version))
3797 "1irz44q6nf95h37av868f47aakwv3jgwgw217xfsfw0afkm7s25f"))))
3798 (properties `((upstream-name . "HardyWeinberg")))
3799 (build-system r-build-system)
3801 `(("r-mice" ,r-mice)
3803 ("r-rsolnp" ,r-rsolnp)))
3804 (home-page "https://cran.r-project.org/package=HardyWeinberg")
3805 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
3807 "This package contains tools for exploring Hardy-Weinberg equilibrium for
3808 diallelic genetic marker data. All classical tests (chi-square, exact,
3809 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
3810 included in the package, as well as functions for power computation and for
3811 the simulation of marker data under equilibrium and disequilibrium. Routines
3812 for dealing with markers on the X-chromosome are included. Functions for
3813 testing equilibrium in the presence of missing data by using multiple
3814 imputation are also provided. Implements several graphics for exploring the
3815 equilibrium status of a large set of diallelic markers: ternary plots with
3816 acceptance regions, log-ratio plots and Q-Q plots.")
3817 (license license:gpl2+)))
3826 (uri (cran-uri "sm" version))
3829 "0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
3830 (build-system r-build-system)
3831 (native-inputs `(("gfortran" ,gfortran)))
3832 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
3833 (synopsis "Smoothing methods for nonparametric regression and density estimation")
3835 "This is software accompanying the book 'Applied Smoothing Techniques for
3836 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
3837 University Press. It provides smoothing methods for nonparametric regression
3838 and density estimation")
3839 (license license:gpl2+)))
3841 (define-public r-venndiagram
3843 (name "r-venndiagram")
3847 (uri (cran-uri "VennDiagram" version))
3850 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
3851 (properties `((upstream-name . "VennDiagram")))
3852 (build-system r-build-system)
3854 `(("r-futile-logger" ,r-futile-logger)))
3855 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
3856 (synopsis "Generate High-Resolution Venn and Euler Plots")
3858 "This package provides a set of functions to generate high-resolution
3859 Venn and Euler plots. It includes handling for several special cases,
3860 including two-case scaling, and extensive customization of plot shape and
3862 (license license:gpl2+)))
3864 (define-public r-vioplot
3871 (uri (cran-uri "vioplot" version))
3874 "0aiy615kn9lpr2cs757g3pklg81n01yhqh0wrwv111fn3cy86r0v"))))
3875 (build-system r-build-system)
3880 `(("r-knitr" ,r-knitr)))
3881 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
3882 (synopsis "Violin plot")
3884 "This package provides a violin plot, which is a combination of a box
3885 plot and a kernel density plot.")
3886 (license license:bsd-3)))
3888 (define-public r-rsofia
3894 ;; This package has been removed from CRAN, so we can
3895 ;; only fetch it from the archives.
3896 (uri (string-append "https://cran.r-project.org/src/"
3897 "contrib/Archive/RSofia/RSofia_"
3901 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
3902 (properties `((upstream-name . "RSofia")))
3903 (build-system r-build-system)
3905 `(("r-rcpp" ,r-rcpp)))
3906 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
3907 (synopsis "Port of sofia-ml to R")
3908 (description "This package is a port of sofia-ml to R. Sofia-ml is a
3909 suite of fast incremental algorithms for machine learning that can be used for
3910 training models for classification or ranking.")
3911 (license license:asl2.0)))
3913 (define-public r-xts
3920 (uri (cran-uri "xts" version))
3923 "0q4cc8ynp7ndmgll1jj3lxyl6wmgg89ad3wq09kjc2ngszdfc4fz"))))
3924 (build-system r-build-system)
3925 (propagated-inputs `(("r-zoo" ,r-zoo)))
3926 (home-page "https://github.com/joshuaulrich/xts")
3927 (synopsis "Extensible time series")
3929 "This package provides for uniform handling of R's different time-based
3930 data classes by extending @code{zoo}, maximizing native format information
3931 preservation and allowing for user-level customization and extension, while
3932 simplifying cross-class interoperability.")
3933 (license license:gpl2+)))
3935 (define-public r-performanceanalytics
3937 (name "r-performanceanalytics")
3942 (uri (cran-uri "PerformanceAnalytics" version))
3945 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
3947 `((upstream-name . "PerformanceAnalytics")))
3948 (build-system r-build-system)
3950 `(("r-quadprog" ,r-quadprog)
3953 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
3954 (synopsis "Econometric tools for performance and risk analysis")
3955 (description "This is a collection of econometric functions for
3956 performance and risk analysis. This package aims to aid practitioners and
3957 researchers in utilizing the latest research in analysis of non-normal return
3958 streams. In general, it is most tested on return (rather than price) data on
3959 a regular scale, but most functions will work with irregular return data as
3960 well, and increasing numbers of functions will work with P&L or price data
3962 ;; Either version may be picked.
3963 (license (list license:gpl2 license:gpl3))))
3965 (define-public r-laeken
3972 (uri (cran-uri "laeken" version))
3975 "199rjkhjjygpr6cjzab87as46acb5npi44m4yycvk7lnd0blma8s"))))
3976 (build-system r-build-system)
3978 `(("r-boot" ,r-boot)
3979 ("r-mass" ,r-mass)))
3980 (home-page "https://cran.r-project.org/web/packages/laeken/")
3981 (synopsis "Estimation of indicators on social exclusion and poverty")
3982 (description "This package provides tools for the estimation of indicators
3983 on social exclusion and poverty, as well as an implementation of Pareto tail
3984 modeling for empirical income distributions.")
3985 (license license:gpl2+)))
3987 (define-public r-vcd
3994 (uri (cran-uri "vcd" version))
3997 "16aj688nhlcvdxzfsqh4s375v8f8vl8997dl8h1xg29b42nv52gc"))))
3998 (build-system r-build-system)
4000 `(("r-colorspace" ,r-colorspace)
4001 ("r-lmtest" ,r-lmtest)
4002 ("r-mass" ,r-mass)))
4003 (home-page "https://cran.r-project.org/web/packages/vcd/")
4004 (synopsis "Visualizing categorical data")
4005 (description "This package provides visualization techniques, data sets,
4006 summary and inference procedures aimed particularly at categorical data.
4007 Special emphasis is given to highly extensible grid graphics. The package was
4008 originally inspired by the book \"Visualizing Categorical Data\" by Michael
4009 Friendly and is now the main support package for a new book, \"Discrete Data
4010 Analysis with R\" by Michael Friendly and David Meyer (2015).")
4011 (license license:gpl2)))
4013 (define-public r-ica
4020 (uri (cran-uri "ica" version))
4023 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
4024 (build-system r-build-system)
4025 (home-page "https://cran.r-project.org/web/packages/ica/")
4026 (synopsis "Independent component analysis")
4027 (description "This package provides tools for @dfn{Independent Component
4028 Analysis} (ICA) using various algorithms: FastICA,
4029 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
4030 of Eigenmatrices} (JADE).")
4031 (license license:gpl2+)))
4033 (define-public r-dtw
4040 (uri (cran-uri "dtw" version))
4043 "02hyhx1sy5h3vzh9zixy18a7d47df4k5d0wyflcvlcbsbcl6p90s"))))
4044 (build-system r-build-system)
4045 (propagated-inputs `(("r-proxy" ,r-proxy)))
4046 (home-page "http://dtw.r-forge.r-project.org/")
4047 (synopsis "Dynamic Time Warping Algorithms")
4048 (description "This package provides a comprehensive implementation of
4049 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
4050 optimal (least cumulative distance) alignment between points of two time
4051 series. Common DTW variants covered include local (slope) and global (window)
4052 constraints, subsequence matches, arbitrary distance definitions,
4053 normalizations, minimum variance matching, and so on.")
4054 (license license:gpl2+)))
4056 (define-public r-sdmtools
4059 (version "1.1-221.2")
4063 (uri (cran-uri "SDMTools" version))
4066 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
4067 (properties `((upstream-name . "SDMTools")))
4068 (build-system r-build-system)
4069 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
4070 (home-page "https://www.rforge.net/SDMTools/")
4071 (synopsis "Species distribution modelling tools")
4072 (description "This package provides a set of tools for post processing
4073 the outcomes of species distribution modeling exercises. It includes novel
4074 methods for comparing models and tracking changes in distributions through
4075 time. It further includes methods for visualizing outcomes, selecting
4076 thresholds, calculating measures of accuracy and landscape fragmentation
4078 (license license:gpl3+)))
4080 (define-public r-scatterplot3d
4082 (name "r-scatterplot3d")
4087 (uri (cran-uri "scatterplot3d" version))
4090 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
4091 (build-system r-build-system)
4092 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
4093 (synopsis "3D scatter plot")
4094 (description "This package provides an implementation of scatter plots for
4095 plotting. a three dimensional point cloud.")
4096 (license license:gpl2)))
4098 (define-public r-ggridges
4105 (uri (cran-uri "ggridges" version))
4108 "03pz257aw0mkh5k75rby9givkc1ky3n5scvhjhjiz9vry9fpffmh"))))
4109 (build-system r-build-system)
4111 `(("r-ggplot2" ,r-ggplot2)
4113 ("r-scales" ,r-scales)
4114 ("r-withr" ,r-withr)))
4115 (home-page "https://github.com/clauswilke/ggridges")
4116 (synopsis "Ridgeline plots in ggplot2")
4118 "Ridgeline plots provide a convenient way of visualizing changes in
4119 distributions over time or space. This package enables the creation of such
4120 plots in @code{ggplot2}.")
4121 (license license:gpl2)))
4123 (define-public r-ggjoy
4130 (uri (cran-uri "ggjoy" version))
4133 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
4134 (build-system r-build-system)
4136 `(("r-ggplot2" ,r-ggplot2)
4137 ("r-ggridges" ,r-ggridges)))
4138 (home-page "https://github.com/clauswilke/ggjoy")
4139 (synopsis "Joyplots in ggplot2")
4140 (description "Joyplots provide a convenient way of visualizing changes in
4141 distributions over time or space. This package enables the creation of such
4142 plots in @code{ggplot2}.")
4143 (license license:gpl2)))
4145 (define-public r-cli
4152 (uri (cran-uri "cli" version))
4155 "1dhkah6jvr96k4h4agcc2rfls75bpjb0j58fzaz3dc0fp3jk8229"))))
4156 (build-system r-build-system)
4158 `(("r-assertthat" ,r-assertthat)
4159 ("r-crayon" ,r-crayon)
4160 ("r-fansi" ,r-fansi)
4161 ("r-glue" ,r-glue)))
4162 (home-page "https://github.com/r-lib/cli#readme")
4163 (synopsis "Helpers for developing command line interfaces")
4164 (description "This package provides a suite of tools designed to build
4165 attractive command line interfaces (CLIs). It includes tools for drawing
4166 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
4167 (license license:expat)))
4169 (define-public r-argparser
4171 (name "r-argparser")
4176 (uri (cran-uri "argparser" version))
4179 "1pxiz9jlhlnpzqn1lz349r07i7glw708w202x6dlnxp112fg7k4x"))))
4180 (build-system r-build-system)
4181 (home-page "https://bitbucket.org/djhshih/argparser")
4182 (synopsis "Command-line argument parser")
4184 "This package provides a cross-platform command-line argument parser
4185 written purely in R with no external dependencies. It is useful with the
4186 Rscript front-end and facilitates turning an R script into an executable
4188 (license license:gpl3+)))
4190 (define-public r-debugme
4197 (uri (cran-uri "debugme" version))
4200 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
4201 (build-system r-build-system)
4202 (propagated-inputs `(("r-crayon" ,r-crayon)))
4203 (home-page "https://github.com/r-lib/debugme#readme")
4204 (synopsis "Debug R packages")
4206 "This package allows the user to specify debug messages as special string
4207 constants, and control debugging of packages via environment variables.")
4208 (license license:expat)))
4210 (define-public r-processx
4217 (uri (cran-uri "processx" version))
4220 "02awswxq6wh3rl99dncw5n6c1xmd0v81xcdp2dfyi6vm6b3gz84l"))))
4221 (build-system r-build-system)
4225 (home-page "https://github.com/r-lib/processx3")
4226 (synopsis "Execute and control system processes")
4228 "This package provides portable tools to run system processes in the
4229 background. It can check if a background process is running; wait on a
4230 background process to finish; get the exit status of finished processes; kill
4231 background processes and their children; restart processes. It can read the
4232 standard output and error of the processes, using non-blocking connections.
4233 @code{processx} can poll a process for standard output or error, with a
4234 timeout. It can also poll several processes at once.")
4235 (license license:expat)))
4237 (define-public r-tsp
4244 (uri (cran-uri "TSP" version))
4247 "0z1v6m0vqjzxc4az3zyjaayygx0jr3mdmc56jjd421iqh0b9z5s4"))))
4248 (properties `((upstream-name . "TSP")))
4249 (build-system r-build-system)
4250 (propagated-inputs `(("r-foreach" ,r-foreach)))
4251 (home-page "https://cran.r-project.org/web/packages/TSP/")
4252 (synopsis "Traveling salesperson problem (TSP)")
4253 (description "This package provides basic infrastructure and some
4254 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
4255 traveling salesman problem).")
4256 (license license:gpl3)))
4258 (define-public r-qap
4265 (uri (cran-uri "qap" version))
4268 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
4269 (build-system r-build-system)
4270 (native-inputs `(("gfortran" ,gfortran)))
4271 (home-page "https://cran.r-project.org/web/packages/qap/")
4272 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
4273 (description "This package implements heuristics for the @dfn{quadratic
4274 assignment problem} (QAP). Currently only a simulated annealing heuristic is
4276 (license license:gpl3)))
4278 (define-public r-gclus
4285 (uri (cran-uri "gclus" version))
4288 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
4289 (build-system r-build-system)
4290 (propagated-inputs `(("r-cluster" ,r-cluster)))
4291 (home-page "https://cran.r-project.org/web/packages/gclus/")
4292 (synopsis "Clustering graphics")
4293 (description "This package orders panels in scatterplot matrices and
4294 parallel coordinate displays by some merit index. It contains various indices
4295 of merit, ordering functions, and enhanced versions of @code{pairs} and
4296 @code{parcoord} which color panels according to their merit level.")
4297 (license license:gpl2+)))
4299 (define-public r-webshot
4306 (uri (cran-uri "webshot" version))
4309 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
4310 (build-system r-build-system)
4312 `(("r-callr" ,r-callr)
4313 ("r-jsonlite" ,r-jsonlite)
4314 ("r-magrittr" ,r-magrittr)))
4315 (home-page "https://github.com/wch/webshot/")
4316 (synopsis "Take screenshots of web pages")
4318 "Webshot makes it easy to take screenshots of web pages from within R.
4319 It can also run Shiny applications locally and take screenshots of the
4320 application; and it can render and screenshot static as well as interactive R
4321 Markdown documents.")
4322 (license license:gpl2)))
4324 (define-public r-seriation
4326 (name "r-seriation")
4331 (uri (cran-uri "seriation" version))
4334 "1zbdxq0s5rc5v307b69fw9k52m0654ls7pf22lh35ggirig6lwsk"))))
4335 (build-system r-build-system)
4337 `(("r-cluster" ,r-cluster)
4338 ("r-colorspace" ,r-colorspace)
4339 ("r-dendextend" ,r-dendextend)
4340 ("r-gclus" ,r-gclus)
4341 ("r-gplots" ,r-gplots)
4344 ("r-registry" ,r-registry)
4346 (native-inputs `(("gfortran" ,gfortran)))
4347 (home-page "https://s2.smu.edu/IDA/seriation/")
4348 (synopsis "Infrastructure for ordering objects using seriation")
4350 "This package provides infrastructure for seriation with an
4351 implementation of several seriation/sequencing techniques to reorder matrices,
4352 dissimilarity matrices, and dendrograms. It also provides (optimally)
4353 reordered heatmaps, color images and clustering visualizations like
4354 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
4356 (license license:gpl3)))
4358 (define-public r-xfun
4365 (uri (cran-uri "xfun" version))
4367 (base32 "1fdipwrl45bznb17da4169ria5jax0f2649yj5accw6qr6wsc8bj"))))
4368 (build-system r-build-system)
4369 ;; knitr itself depends on xfun
4372 `(("r-knitr" ,r-knitr)))
4373 (home-page "https://github.com/yihui/xfun")
4374 (synopsis "Miscellaneous functions")
4376 "This package provides miscellaneous functions commonly used in other
4377 packages maintained by Yihui Xie.")
4378 (license license:expat)))
4380 (define-public r-utf8
4387 (uri (cran-uri "utf8" version))
4390 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
4391 (build-system r-build-system)
4392 (home-page "https://github.com/patperry/r-utf8")
4393 (synopsis "Unicode text processing")
4395 "This package provides tools to process and print UTF-8 encoded
4396 international text (Unicode). Input, validate, normalize, encode, format, and
4398 (license license:asl2.0)))
4400 (define-public r-zeallot
4407 (uri (cran-uri "zeallot" version))
4410 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
4411 (build-system r-build-system)
4412 (home-page "https://github.com/nteetor/zeallot")
4413 (synopsis "Multiple, unpacking, and destructuring assignment")
4415 "This package provides a @code{%<-%} operator to perform multiple,
4416 unpacking, and destructuring assignment in R. The operator unpacks the
4417 right-hand side of an assignment into multiple values and assigns these values
4418 to variables on the left-hand side of the assignment.")
4419 (license license:expat)))
4421 (define-public r-vctrs
4428 (uri (cran-uri "vctrs" version))
4431 "025si8gqwsj79lna3s0hdzxmymjyzbjq3ddan7n6chah6n3kbrhp"))))
4432 (build-system r-build-system)
4434 `(("r-digest" ,r-digest)
4435 ("r-ellipsis" ,r-ellipsis)
4437 ("r-rlang" ,r-rlang)))
4439 `(("r-knitr" ,r-knitr)))
4440 (home-page "https://github.com/r-lib/vctrs")
4441 (synopsis "Vector helpers")
4443 "There are three main goals to the @code{vctrs} package:
4446 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
4447 @code{length()} and @code{class()}. These definitions are paired with a
4448 framework for type-coercion and size-recycling.
4449 @item To define type- and size-stability as desirable function properties, use
4450 them to analyse existing base function, and to propose better alternatives.
4451 This work has been particularly motivated by thinking about the ideal
4452 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
4453 @item To provide a new @code{vctr} base class that makes it easy to create new
4454 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
4455 a few new @code{vctrs} generics, making implementation considerably simpler
4458 (license license:gpl3)))
4460 (define-public r-pillar
4467 (uri (cran-uri "pillar" version))
4470 "0viymfp1rkr7ig3m1b016r75hk8qbr9cqsjc6c20ks9pm5svmsp1"))))
4471 (build-system r-build-system)
4474 ("r-crayon" ,r-crayon)
4475 ("r-fansi" ,r-fansi)
4476 ("r-rlang" ,r-rlang)
4478 ("r-vctrs" ,r-vctrs)))
4479 (home-page "https://github.com/r-lib/pillar")
4480 (synopsis "Coloured formatting for columns")
4482 "This package provides a @code{pillar} generic designed for formatting
4483 columns of data using the full range of colours provided by modern
4485 (license license:gpl3)))
4487 (define-public r-uuid
4494 (uri (cran-uri "uuid" version))
4497 "0gm9ii7ncvllxbvyk6srsiinjmqyj7lmh84w43x4nhqpvafj9q4q"))))
4498 (build-system r-build-system)
4499 (home-page "https://www.rforge.net/uuid")
4500 (synopsis "Tools for generating and handling of UUIDs")
4502 "This package provides tools for generating and handling of
4503 @dfn{Universally Unique Identifiers} (UUIDs).")
4504 (license license:expat)))
4506 (define-public r-tinytex
4513 (uri (cran-uri "tinytex" version))
4516 "0mc9i7r45s5kagcfig508dbyf6jir6q4ghq9cxqvnpxp6ymh4qpr"))))
4517 (build-system r-build-system)
4519 `(("r-xfun" ,r-xfun)))
4520 (home-page "https://github.com/yihui/tinytex")
4521 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
4523 "This package provides helper functions to install and maintain the LaTeX
4524 distribution named TinyTeX, a lightweight, cross-platform, portable, and
4525 easy-to-maintain version of TeX Live. This package also contains helper
4526 functions to compile LaTeX documents, and install missing LaTeX packages
4528 (license license:expat)))
4530 (define-public r-network
4537 (uri (cran-uri "network" version))
4540 "0dnf1wl3za2lhx2lwd8smhlijl1cfhckgr8zz9piiirrfi2m2kx2"))))
4541 (build-system r-build-system)
4543 `(("r-magrittr" ,r-magrittr)
4544 ("r-tibble" ,r-tibble)))
4545 (home-page "https://statnet.org/")
4546 (synopsis "Classes for relational data")
4548 "This package provides tools to create and modify network objects. The
4549 @code{network} class can represent a range of relational data types, and
4550 supports arbitrary vertex/edge/graph attributes.")
4551 (license license:gpl2+)))
4553 (define-public r-statnet-common
4555 (name "r-statnet-common")
4560 (uri (cran-uri "statnet.common" version))
4563 "0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
4565 `((upstream-name . "statnet.common")))
4566 (build-system r-build-system)
4568 `(("r-coda" ,r-coda)))
4569 (home-page "https://statnet.org")
4570 (synopsis "R scripts and utilities used by the Statnet software")
4571 (description "This package provides non-statistical utilities used by the
4572 software developed by the Statnet Project.")
4573 (license license:gpl3)))
4575 (define-public r-statcheck
4577 (name "r-statcheck")
4582 (uri (cran-uri "statcheck" version))
4585 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
4586 (build-system r-build-system)
4588 `(("r-ggplot2" ,r-ggplot2)
4590 ("r-rmarkdown" ,r-rmarkdown)))
4591 (home-page "https://cran.r-project.org/web/packages/statcheck/")
4592 (synopsis "Extract statistics from articles and recompute p-values")
4593 (description "This package can automatically extract statistical
4594 null-hypothesis significant testing (NHST) results from articles and recompute
4595 the p-values based on the reported test statistic and degrees of freedom to
4596 detect possible inconsistencies.")
4597 (license license:gpl2)))
4599 (define-public r-sna
4606 (uri (cran-uri "sna" version))
4609 "1j3i6300m686qqfmyvadim377cd3mplzgj6mandygw8brg50id8k"))))
4610 (build-system r-build-system)
4612 `(("r-network" ,r-network)
4613 ("r-statnet-common" ,r-statnet-common)))
4614 (home-page "https://statnet.org")
4615 (synopsis "Tools for social network analysis")
4617 "This package provides a range of tools for social network analysis,
4618 including node and graph-level indices, structural distance and covariance
4619 methods, structural equivalence detection, network regression, random graph
4620 generation, and 2D/3D network visualization.")
4621 (license license:gpl2+)))
4623 (define-public r-tfisher
4630 (uri (cran-uri "TFisher" version))
4633 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
4634 (properties `((upstream-name . "TFisher")))
4635 (build-system r-build-system)
4637 `(("r-matrix" ,r-matrix)
4638 ("r-mvtnorm" ,r-mvtnorm)
4640 (home-page "https://cran.r-project.org/web/packages/TFisher/")
4641 (synopsis "Optimal thresholding Fisher's p-value combination method")
4643 "This package provides the @dfn{cumulative distribution function} (CDF),
4644 quantile, and statistical power calculator for a collection of thresholding
4645 Fisher's p-value combination methods, including Fisher's p-value combination
4646 method, truncated product method and, in particular, soft-thresholding
4647 Fisher's p-value combination method which is proven to be optimal in some
4648 context of signal detection. The p-value calculator for the omnibus version
4649 of these tests are also included.")
4650 (license license:gpl2)))
4652 (define-public r-ttr
4659 (uri (cran-uri "TTR" version))
4662 "0rg22ma3x07s9djlxscfw5jcq1gbir05cwhgvwfi53x1sf4hmhdg"))))
4663 (properties `((upstream-name . "TTR")))
4664 (build-system r-build-system)
4666 `(("r-curl" ,r-curl)
4669 (home-page "https://github.com/joshuaulrich/TTR")
4670 (synopsis "Technical trading rules")
4672 "This package provides functions and data to construct technical trading
4674 (license license:gpl2)))
4676 (define-public r-leaps
4683 (uri (cran-uri "leaps" version))
4686 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
4687 (build-system r-build-system)
4688 (native-inputs `(("gfortran" ,gfortran)))
4689 (home-page "https://cran.r-project.org/web/packages/leaps/")
4690 (synopsis "Regression subset selection")
4692 "This package provides tools for regression subset selection, including
4693 exhaustive search.")
4694 (license license:gpl2+)))
4696 (define-public r-splus2r
4703 (uri (cran-uri "splus2R" version))
4706 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
4707 (properties `((upstream-name . "splus2R")))
4708 (build-system r-build-system)
4709 (native-inputs `(("gfortran" ,gfortran)))
4710 (home-page "https://cran.r-project.org/web/packages/splus2R/")
4711 (synopsis "Supplemental S-PLUS functionality in R")
4713 "Currently there are many functions in S-PLUS that are missing in R. To
4714 facilitate the conversion of S-PLUS packages to R packages, this package
4715 provides some missing S-PLUS functionality in R.")
4716 (license license:gpl2)))
4718 (define-public r-ifultools
4720 (name "r-ifultools")
4725 (uri (cran-uri "ifultools" version))
4728 "040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
4729 (build-system r-build-system)
4731 `(("r-mass" ,r-mass)
4732 ("r-splus2r" ,r-splus2r)))
4733 (home-page "https://cran.r-project.org/web/packages/ifultools/")
4734 (synopsis "Insightful research tools")
4735 (description "This package provides C code used by the wmtsa, fractal, and
4737 (license license:gpl2)))
4739 (define-public r-sapa
4746 (uri (cran-uri "sapa" version))
4749 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
4750 (build-system r-build-system)
4752 `(("r-ifultools" ,r-ifultools)
4753 ("r-splus2r" ,r-splus2r)))
4754 (home-page "https://cran.r-project.org/web/packages/sapa/")
4755 (synopsis "Spectral analysis for physical applications")
4756 (description "This package provides software for the book Spectral
4757 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
4758 Cambridge University Press, 1993.")
4759 (license license:gpl2)))
4761 (define-public r-aggregation
4763 (name "r-aggregation")
4768 (uri (cran-uri "aggregation" version))
4771 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
4772 (build-system r-build-system)
4773 (home-page "https://cran.r-project.org/web/packages/aggregation/")
4774 (synopsis "Methods for p-value aggregation")
4776 "This package contains functionality for performing the following methods
4777 of p-value aggregation: Fisher's method, the Lancaster method (weighted
4778 Fisher's method), and Sidak correction.")
4779 (license license:gpl3)))
4781 (define-public r-quantmod
4788 (uri (cran-uri "quantmod" version))
4791 "1ss441rwlr88kz212m0wgx0hwgwi41rhy1jncg2lgqzqfvr5dzqa"))))
4792 (build-system r-build-system)
4794 `(("r-curl" ,r-curl)
4798 (home-page "https://cran.r-project.org/web/packages/quantmod/")
4799 (synopsis "Quantitative financial modelling framework")
4800 (description "This package provides a quantitative financial modelling
4801 framework to allow users to specify, build, trade, and analyse quantitative
4802 financial trading strategies.")
4803 (license license:gpl3)))
4805 (define-public r-tseries
4812 (uri (cran-uri "tseries" version))
4815 "0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
4816 (build-system r-build-system)
4818 `(("r-quadprog" ,r-quadprog)
4819 ("r-quantmod" ,r-quantmod)
4822 `(("gfortran" ,gfortran)))
4823 (home-page "https://cran.r-project.org/web/packages/tseries/")
4824 (synopsis "Time series analysis and computational finance")
4826 "This package provides functions relating to time series analysis and
4827 computational finance.")
4828 (license license:gpl2)))
4830 (define-public r-wmtsa
4837 (uri (cran-uri "wmtsa" version))
4840 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
4841 (build-system r-build-system)
4843 `(("r-ifultools" ,r-ifultools)
4845 ("r-splus2r" ,r-splus2r)))
4846 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
4847 (synopsis "Wavelet methods for time series analysis")
4849 "This package provides software to accompany the book \"Wavelet Methods
4850 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
4851 University Press, 2000.")
4852 (license license:gpl2)))
4854 (define-public r-tsa
4861 (uri (cran-uri "TSA" version))
4864 "0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
4865 (properties `((upstream-name . "TSA")))
4866 (build-system r-build-system)
4868 `(("r-leaps" ,r-leaps)
4869 ("r-locfit" ,r-locfit)
4870 ("r-mgcv" ,r-mgcv)))
4871 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
4872 (synopsis "Time series analysis")
4874 "This package contains R functions and datasets detailed in the book
4875 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
4876 Cryer and Kung-Sik Chan.")
4877 (license license:gpl2+)))
4879 (define-public r-extradistr
4881 (name "r-extradistr")
4886 (uri (cran-uri "extraDistr" version))
4889 "1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
4890 (properties `((upstream-name . "extraDistr")))
4891 (build-system r-build-system)
4893 `(("r-rcpp" ,r-rcpp)))
4894 (home-page "https://github.com/twolodzko/extraDistr")
4895 (synopsis "Additional univariate and multivariate distributions")
4897 "This package implements density, distribution functions, quantile
4898 functions and random generation functions for a large number of univariate and
4899 multivariate distributions.")
4900 (license license:gpl2)))
4902 (define-public r-fractal
4909 (uri (cran-uri "fractal" version))
4912 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
4913 (build-system r-build-system)
4915 `(("r-ifultools" ,r-ifultools)
4918 ("r-scatterplot3d" ,r-scatterplot3d)
4919 ("r-splus2r" ,r-splus2r)
4920 ("r-wmtsa" ,r-wmtsa)))
4921 (home-page "https://cran.r-project.org/web/packages/fractal/")
4922 (synopsis "Fractal time series modeling and analysis")
4924 "This package provides tools for stochastic fractal and deterministic
4925 chaotic time series analysis.")
4926 (license license:gpl2)))
4928 (define-public r-urca
4935 (uri (cran-uri "urca" version))
4938 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
4939 (build-system r-build-system)
4940 (propagated-inputs `(("r-nlme" ,r-nlme)))
4941 (native-inputs `(("gfortran" ,gfortran)))
4942 (home-page "https://cran.r-project.org/web/packages/urca/")
4943 (synopsis "Unit root and cointegration tests for time series data")
4945 "This package provides unit root and cointegration tests encountered in
4946 applied econometric analysis.")
4947 (license license:gpl2+)))
4949 (define-public r-cubature
4956 (uri (cran-uri "cubature" version))
4959 "0jpyq8j7x06dpiz29w48av879ygldzgls9z810192hsymkmfaz6r"))))
4960 (build-system r-build-system)
4962 `(("r-rcpp" ,r-rcpp)))
4963 (home-page "https://github.com/bnaras/cubature")
4964 (synopsis "Adaptive multivariate integration over hypercubes")
4966 "This package is an R wrapper around the cubature C library for adaptive
4967 multivariate integration over hypercubes. This version provides both
4968 @code{hcubature} and @code{pcubature} routines in addition to a vector
4970 ;; The included cubature C library is released under GPLv2+, but the
4971 ;; wrapper declares the license to be GPLv3+.
4972 (license (list license:gpl2+ license:gpl3+))))
4974 (define-public r-trend
4981 (uri (cran-uri "trend" version))
4984 "09b6ycyfgs4xlhx6kn6qm5rl2acp58hzhv8qclzn3kb1wjjyvxy5"))))
4985 (build-system r-build-system)
4987 `(("r-extradistr" ,r-extradistr)))
4989 `(("gfortran" ,gfortran)))
4990 (home-page "https://cran.r-project.org/web/packages/trend/")
4991 (synopsis "Non-parametric trend tests and change-point detection")
4993 "The analysis of environmental data often requires the detection of
4994 trends and change-points. This package includes tests for trend
4995 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
4996 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
4997 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
4998 correlation trend test), change-point detection (Lanzante's test procedures,
4999 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
5000 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
5001 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
5002 sample Robust Rank-Order Distributional Test.")
5003 (license license:gpl3)))
5005 (define-public r-expm
5012 (uri (cran-uri "expm" version))
5015 "15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
5016 (build-system r-build-system)
5017 (propagated-inputs `(("r-matrix" ,r-matrix)))
5018 (native-inputs `(("gfortran" ,gfortran)))
5019 (home-page "https://r-forge.r-project.org/projects/expm/")
5020 (synopsis "Tools for matrix exponentials and related quantities")
5022 "This package provides tools for the computation of the matrix
5023 exponential, logarithm, square root, and related quantities.")
5024 (license license:gpl2+)))
5026 (define-public r-complexplus
5028 (name "r-complexplus")
5033 (uri (cran-uri "complexplus" version))
5036 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
5037 (build-system r-build-system)
5039 `(("r-expm" ,r-expm)
5040 ("r-matrix" ,r-matrix)))
5041 (home-page "https://cran.r-project.org/web/packages/complexplus/")
5042 (synopsis "Functions of complex or real variables")
5044 "This package extends several functions to the complex domain, including
5045 the matrix exponential and logarithm, and the determinant.")
5046 (license license:gpl2)))
5048 (define-public r-phontools
5050 (name "r-phontools")
5055 (uri (cran-uri "phonTools" version))
5058 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
5059 (properties `((upstream-name . "phonTools")))
5060 (build-system r-build-system)
5061 (home-page "http://www.santiagobarreda.com/rscripts.html")
5062 (synopsis "Tools for phonetic and acoustic analyses")
5064 "This package contains tools for the organization, display, and analysis
5065 of the sorts of data frequently encountered in phonetics research and
5066 experimentation, including the easy creation of IPA vowel plots, and the
5067 creation and manipulation of WAVE audio files.")
5068 (license license:bsd-2)))
5077 (uri (cran-uri "np" version))
5080 "06h8k0kdv5s258jr6s08fabvlycrbs7iq34jk2f2hfmqm2y4nyx2"))))
5081 (build-system r-build-system)
5083 `(("r-boot" ,r-boot)
5084 ("r-cubature" ,r-cubature)
5085 ("r-quadprog" ,r-quadprog)
5086 ("r-quantreg" ,r-quantreg)))
5087 (home-page "https://github.com/JeffreyRacine/R-Package-np")
5088 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
5089 (description "This package provides non-parametric (and semi-parametric)
5090 kernel methods that seamlessly handle a mix of continuous, unordered, and
5091 ordered factor data types.")
5092 ;; Any version of the GPL.
5093 (license license:gpl3+)))
5095 (define-public r-powerplus
5097 (name "r-powerplus")
5102 (uri (cran-uri "powerplus" version))
5105 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
5106 (build-system r-build-system)
5108 `(("r-complexplus" ,r-complexplus)
5111 ("r-matrix" ,r-matrix)
5112 ("r-phontools" ,r-phontools)))
5113 (home-page "https://cran.r-project.org/web/packages/powerplus/")
5114 (synopsis "Exponentiation operations")
5116 "This package provides tools for the computation of matrix and scalar
5118 (license license:gpl2)))
5120 (define-public r-egg
5127 (uri (cran-uri "egg" version))
5130 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
5131 (properties `((upstream-name . "egg")))
5132 (build-system r-build-system)
5134 `(("r-ggplot2" ,r-ggplot2)
5135 ("r-gridextra" ,r-gridextra)
5136 ("r-gtable" ,r-gtable)))
5137 (home-page "https://cran.r-project.org/web/packages/egg")
5138 (synopsis "Extensions for ggplot2")
5140 "This package provides miscellaneous functions to help customize ggplot2
5141 objects. High-level functions are provided to post-process ggplot2 layouts
5142 and allow alignment between plot panels, as well as setting panel sizes to
5143 fixed values. Other functions include a custom @code{geom}, and helper
5144 functions to enforce symmetric scales or add tags to facetted plots.")
5145 (license license:gpl3)))
5147 (define-public r-heatmaply
5149 (name "r-heatmaply")
5154 (uri (cran-uri "heatmaply" version))
5157 "133q8ir45vhfxs2lnd96k97g21ihg2arfhp349kmk339pk32fcxz"))))
5158 (build-system r-build-system)
5160 `(("r-assertthat" ,r-assertthat)
5161 ("r-colorspace" ,r-colorspace)
5162 ("r-dendextend" ,r-dendextend)
5164 ("r-ggplot2" ,r-ggplot2)
5165 ("r-htmlwidgets" ,r-htmlwidgets)
5166 ("r-magrittr" ,r-magrittr)
5167 ("r-plotly" ,r-plotly)
5168 ("r-rcolorbrewer" ,r-rcolorbrewer)
5169 ("r-reshape2" ,r-reshape2)
5170 ("r-scales" ,r-scales)
5171 ("r-seriation" ,r-seriation)
5172 ("r-viridis" ,r-viridis)
5173 ("r-webshot" ,r-webshot)))
5175 `(("r-knitr" ,r-knitr)))
5176 (home-page "https://cran.r-project.org/package=heatmaply")
5177 (synopsis "Interactive cluster heat maps using plotly")
5179 "This package enables you to create interactive cluster heatmaps that can
5180 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
5181 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
5182 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
5183 a popular graphical method for visualizing high-dimensional data, in which a
5184 table of numbers is encoded as a grid of colored cells. The rows and columns
5185 of the matrix are ordered to highlight patterns and are often accompanied by
5187 ;; Either version of the license.
5188 (license (list license:gpl2 license:gpl3))))
5197 (uri (cran-uri "h5" version))
5200 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
5201 (build-system r-build-system)
5206 `(("which" ,which)))
5208 `(("r-rcpp" ,r-rcpp)))
5209 (home-page "https://github.com/mannau/h5")
5210 (synopsis "Interface to the HDF5 Library")
5212 "This package provides an S4 interface to the HDF5 library supporting
5213 fast storage and retrieval of R-objects like vectors, matrices and arrays to
5214 binary files in a language independent format. The HDF5 format can therefore
5215 be used as an alternative to R's save/load mechanism. Since h5 is able to
5216 access only subsets of stored data it can also handle data sets which do not
5218 (license license:bsd-2)))
5220 (define-public r-cgdsr
5227 (uri (cran-uri "cgdsr" version))
5230 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
5231 (build-system r-build-system)
5233 `(("r-httr" ,r-httr)
5234 ("r-r-methodss3" ,r-r-methodss3)
5235 ("r-r-oo" ,r-r-oo)))
5236 (home-page "https://github.com/cBioPortal/cgdsr")
5237 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
5239 "This package provides a basic set of R functions for querying the Cancer
5240 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
5241 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
5242 (license license:lgpl3)))
5244 (define-public r-import
5251 (uri (cran-uri "import" version))
5254 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
5255 (build-system r-build-system)
5256 (home-page "https://github.com/smbache/import")
5257 (synopsis "Import mechanism for R")
5259 "This is an alternative mechanism for importing objects from packages.
5260 The syntax allows for importing multiple objects from a package with a single
5261 command in an expressive way. The import package bridges some of the gap
5262 between using @code{library} (or @code{require}) and direct (single-object)
5263 imports. Furthermore the imported objects are not placed in the current
5264 environment. It is also possible to import objects from stand-alone @code{.R}
5266 (license license:expat)))
5268 (define-public r-shinyace
5275 (uri (cran-uri "shinyAce" version))
5278 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
5279 (properties `((upstream-name . "shinyAce")))
5280 (build-system r-build-system)
5282 `(("r-shiny" ,r-shiny)
5283 ("r-jsonlite" ,r-jsonlite)))
5284 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
5285 (synopsis "Ace editor bindings for Shiny")
5287 "This package provides Ace editor bindings to enable a rich text editing
5288 environment within Shiny.")
5289 (license license:expat)))
5291 (define-public r-randomizr
5293 (name "r-randomizr")
5298 (uri (cran-uri "randomizr" version))
5301 "0dljyfldnardaps3fq6vi5wcs9x6qfaq5apapa78c51lnaa6fn9h"))))
5302 (properties `((upstream-name . "randomizr")))
5303 (build-system r-build-system)
5305 `(("r-knitr" ,r-knitr)))
5306 (home-page "https://declaredesign.org/r/randomizr/")
5307 (synopsis "Tools for common forms of random assignment and sampling")
5309 "This package provides tools for generating random assignments for common
5310 experimental designs and random samples for common sampling designs.")
5311 (license license:expat)))
5313 (define-public r-base64url
5315 (name "r-base64url")
5320 (uri (cran-uri "base64url" version))
5323 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
5324 (build-system r-build-system)
5326 `(("r-backports" ,r-backports)))
5327 (home-page "https://github.com/mllg/base64url")
5328 (synopsis "Fast and URL-safe base64 encoder and decoder")
5330 "This package provides a URL-safe base64 encoder and decoder. In
5331 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
5332 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
5333 encoder does not fill the string with trailing @code{=}. The resulting
5334 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
5335 and thus are safe to use in URLs or for file names. The package also comes
5336 with a simple base32 encoder/decoder suited for case insensitive file
5338 (license license:gpl3)))
5340 (define-public r-radiant-data
5342 (name "r-radiant-data")
5347 (uri (cran-uri "radiant.data" version))
5350 "19gbc7k1hsi6hg6ka8i70wlw8j9fs9wkpn36761lzbcyam6vgqn0"))
5351 (modules '((guix build utils)))
5354 ;; Delete files that are under CC-NC-SA.
5355 (delete-file-recursively "inst/app/tools/help")
5357 (properties `((upstream-name . "radiant.data")))
5358 (build-system r-build-system)
5360 `(("r-base64enc" ,r-base64enc)
5361 ("r-broom" ,r-broom)
5364 ("r-dplyr" ,r-dplyr)
5367 ("r-ggplot2" ,r-ggplot2)
5368 ("r-import" ,r-import)
5369 ("r-jsonlite" ,r-jsonlite)
5370 ("r-knitr" ,r-knitr)
5371 ("r-lubridate" ,r-lubridate)
5372 ("r-magrittr" ,r-magrittr)
5373 ("r-markdown" ,r-markdown)
5375 ("r-patchwork" ,r-patchwork)
5376 ("r-plotly" ,r-plotly)
5377 ("r-psych" ,r-psych)
5378 ("r-randomizr" ,r-randomizr)
5379 ("r-readr" ,r-readr)
5380 ("r-readxl" ,r-readxl)
5381 ("r-rlang" ,r-rlang)
5382 ("r-rmarkdown" ,r-rmarkdown)
5383 ("r-rstudioapi" ,r-rstudioapi)
5384 ("r-scales" ,r-scales)
5385 ("r-shiny" ,r-shiny)
5386 ("r-shinyfiles" ,r-shinyfiles)
5387 ("r-shinyace" ,r-shinyace)
5388 ("r-stringi" ,r-stringi)
5389 ("r-tibble" ,r-tibble)
5390 ("r-tidyr" ,r-tidyr)
5391 ("r-writexl" ,r-writexl)))
5392 (home-page "https://github.com/radiant-rstats/radiant.data")
5393 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
5395 "The Radiant Data menu includes interfaces for loading, saving, viewing,
5396 visualizing, summarizing, transforming, and combining data. It also contains
5397 functionality to generate reproducible reports of the analyses conducted in
5399 (license license:agpl3)))
5401 (define-public r-algdesign
5403 (name "r-algdesign")
5408 (uri (cran-uri "AlgDesign" version))
5410 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
5411 (properties `((upstream-name . "AlgDesign")))
5412 (build-system r-build-system)
5413 (home-page "https://github.com/jvbraun/AlgDesign")
5414 (synopsis "Algorithmic experimental design")
5416 "This package provides tools to calculate exact and approximate theory
5417 experimental designs for D, A, and I criteria. Very large designs may be
5418 created. Experimental designs may be blocked or blocked designs created from
5419 a candidate list, using several criteria. The blocking can be done when whole
5420 and within plot factors interact.")
5421 (license license:gpl2+)))
5423 (define-public r-signal
5430 (uri (cran-uri "signal" version))
5433 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
5434 (build-system r-build-system)
5435 (propagated-inputs `(("r-mass" ,r-mass)))
5436 (native-inputs `(("gfortran" ,gfortran)))
5437 (home-page "https://cran.r-project.org/web/packages/signal/")
5438 (synopsis "Signal processing")
5440 "This package provides a set of signal processing functions originally
5441 written for Matlab and GNU Octave. It includes filter generation utilities,
5442 filtering functions, resampling routines, and visualization of filter models.
5443 It also includes interpolation functions.")
5444 (license license:gpl2)))
5446 (define-public r-gsubfn
5453 (uri (cran-uri "gsubfn" version))
5456 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
5457 (build-system r-build-system)
5458 (propagated-inputs `(("r-proto" ,r-proto)))
5459 (home-page "https://code.google.com/archive/p/gsubfn/")
5460 (synopsis "Utilities for strings and function arguments.")
5462 "This package provides @code{gsubfn} which is like @code{gsub} but can
5463 take a replacement function or certain other objects instead of the
5464 replacement string. Matches and back references are input to the replacement
5465 function and replaced by the function output. @code{gsubfn} can be used to
5466 split strings based on content rather than delimiters and for quasi-perl-style
5467 string interpolation. The package also has facilities for translating
5468 formulas to functions and allowing such formulas in function calls instead of
5470 (license license:gpl2+)))
5472 (define-public r-sqldf
5479 (uri (cran-uri "sqldf" version))
5482 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
5483 (build-system r-build-system)
5485 `(("r-chron" ,r-chron)
5487 ("r-gsubfn" ,r-gsubfn)
5488 ("r-proto" ,r-proto)
5489 ("r-rsqlite" ,r-rsqlite)))
5490 (home-page "https://github.com/ggrothendieck/sqldf")
5491 (synopsis "Manipulate R data frames using SQL")
5493 "The @code{sqldf} function is typically passed a single argument which is
5494 an SQL select statement where the table names are ordinary R data frame names.
5495 @code{sqldf} transparently sets up a database, imports the data frames into
5496 that database, performs the SQL statement and returns the result using a
5497 heuristic to determine which class to assign to each column of the returned
5498 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
5499 used to read filtered files into R even if the original files are larger than
5500 R itself can handle.")
5501 (license license:gpl2)))
5503 (define-public r-abind
5510 (uri (cran-uri "abind" version))
5513 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
5514 (build-system r-build-system)
5515 (home-page "https://cran.r-project.org/web/packages/abind/")
5516 (synopsis "Combine multidimensional arrays")
5518 "This package provides tools to combine multidimensional arrays into a
5519 single array. This is a generalization of @code{cbind} and @code{rbind}. It
5520 works with vectors, matrices, and higher-dimensional arrays. It also provides
5521 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
5522 extracting and replacing data in arrays.")
5523 (license license:lgpl2.0+)))
5525 (define-public r-prroc
5532 (uri (cran-uri "PRROC" version))
5535 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
5536 (properties `((upstream-name . "PRROC")))
5537 (build-system r-build-system)
5538 (home-page "https://cran.r-project.org/web/packages/PRROC/")
5539 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
5541 "This package computes the areas under the @dfn{precision-recall} (PR)
5542 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
5543 contrast to other implementations, the interpolation between points of the PR
5544 curve is done by a non-linear piecewise function. In addition to the areas
5545 under the curves, the curves themselves can also be computed and plotted by a
5546 specific S3-method.")
5547 (license license:gpl3)))
5549 (define-public r-vim
5556 (uri (cran-uri "VIM" version))
5559 "0ddhca4v912q82rjpf1qld6i6g2c381g0v5b4hbnygr3lm6a7wiv"))))
5560 (properties `((upstream-name . "VIM")))
5561 (build-system r-build-system)
5564 ("r-colorspace" ,r-colorspace)
5565 ("r-data-table" ,r-data-table)
5566 ("r-e1071" ,r-e1071)
5567 ("r-laeken" ,r-laeken)
5568 ("r-magrittr" ,r-magrittr)
5571 ("r-ranger" ,r-ranger)
5573 ("r-robustbase" ,r-robustbase)
5577 `(("r-knitr" ,r-knitr)))
5578 (home-page "https://github.com/alexkowa/VIM")
5579 (synopsis "Visualization and imputation of missing values")
5581 "This package provides tools for the visualization of missing and/or
5582 imputed values are introduced, which can be used for exploring the data and
5583 the structure of the missing and/or imputed values. Depending on this
5584 structure of the missing values, the corresponding methods may help to
5585 identify the mechanism generating the missing values and allows to explore the
5586 data including missing values. In addition, the quality of imputation can be
5587 visually explored using various univariate, bivariate, multiple and
5588 multivariate plot methods.")
5589 (license license:gpl2+)))
5591 (define-public r-fnn
5598 (uri (cran-uri "FNN" version))
5601 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
5602 (properties `((upstream-name . "FNN")))
5603 (build-system r-build-system)
5604 (home-page "https://cran.r-project.org/web/packages/FNN")
5605 (synopsis "Fast nearest neighbor search algorithms and applications")
5607 "This package provides cover-tree and kd-tree fast k-nearest neighbor
5608 search algorithms. Related applications including KNN classification,
5609 regression and information measures are implemented.")
5610 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
5611 ;; later can be used.
5612 (license license:gpl2+)))
5614 (define-public r-smoother
5621 (uri (cran-uri "smoother" version))
5624 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
5625 (build-system r-build-system)
5627 `(("r-ttr" ,r-ttr)))
5628 (home-page "https://cran.r-project.org/web/packages/smoother")
5629 (synopsis "Functions relating to the smoothing of numerical data")
5631 "This package provides a collection of methods for smoothing numerical
5632 data, commencing with a port of the Matlab gaussian window smoothing function.
5633 In addition, several functions typically used in smoothing of financial data
5635 (license license:gpl2)))
5637 (define-public r-riverplot
5639 (name "r-riverplot")
5644 (uri (cran-uri "riverplot" version))
5647 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
5648 (build-system r-build-system)
5649 (home-page "https://logfc.wordpress.com")
5650 (synopsis "Sankey or ribbon plots")
5652 "Sankey plots are a type of diagram that is convenient to illustrate how
5653 flow of information, resources etc. separates and joins, much like observing
5654 how rivers split and merge. For example, they can be used to compare
5655 different clusterings. This package provides an implementation of Sankey
5657 (license license:gpl2+)))
5659 (define-public r-dyn
5666 (uri (cran-uri "dyn" version))
5669 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
5670 (build-system r-build-system)
5672 `(("r-zoo" ,r-zoo)))
5673 (home-page "https://cran.r-project.org/web/packages/dyn")
5674 (synopsis "Time series regression")
5676 "This package provides the dyn class interfaces @code{ts}, @code{irts},
5677 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
5678 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
5679 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
5680 @code{randomForest::randomForest()} and other regression functions, allowing
5681 those functions to be used with time series including specifications that may
5682 contain lags, diffs and missing values.")
5684 (license license:gpl2+)))
5686 (define-public r-catdap
5693 (uri (cran-uri "catdap" version))
5696 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
5697 (build-system r-build-system)
5699 `(("gfortran" ,gfortran)))
5700 (home-page "https://cran.r-project.org/web/packages/catdap/")
5701 (synopsis "Tools for categorical data analysis")
5703 "This package provides functions for analyzing multivariate data.
5704 Dependencies of the distribution of the specified variable (response
5705 variable) to other variables (explanatory variables) are derived and
5706 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
5707 (license license:gpl2+)))
5709 (define-public r-arules
5716 (uri (cran-uri "arules" version))
5719 "1pk3jjizn2m5rwi7qkdkbq9f07acgpy0qdzzqmx0agg47cwahlkm"))))
5720 (build-system r-build-system)
5722 `(("r-matrix" ,r-matrix)))
5723 (home-page "https://github.com/mhahsler/arules")
5724 (synopsis "Mining association rules and frequent itemsets")
5726 "This package provides an infrastructure for representing, manipulating
5727 and analyzing transaction data and patterns (frequent itemsets and association rules).
5728 It also provides C implementations of the association mining algorithms Apriori
5730 (license license:gpl3)))
5732 (define-public r-parsedate
5734 (name "r-parsedate")
5739 (uri (cran-uri "parsedate" version))
5742 "0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
5743 (build-system r-build-system)
5745 `(("r-rematch2" ,r-rematch2)))
5746 (home-page "https://github.com/gaborcsardi/parsedate")
5748 "Recognize and parse dates in various formats")
5750 "This package provides three functions for dealing with dates:
5751 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
5752 time formats, @code{parse_date} parses dates in unspecified formats,
5753 and @code{format_iso_8601} formats a date in ISO 8601 format.")
5754 (license license:gpl2)))
5756 (define-public r-abc-data
5763 (uri (cran-uri "abc.data" version))
5766 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
5767 (properties `((upstream-name . "abc.data")))
5768 (build-system r-build-system)
5769 (home-page "https://cran.r-project.org/web/packages/abc.data/")
5770 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
5772 "This package contains data which are used by functions of the abc
5773 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
5774 algorithms for performing parameter estimation, model selection, and
5776 (license license:gpl3+)))
5778 (define-public r-abc
5785 (uri (cran-uri "abc" version))
5788 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
5789 (build-system r-build-system)
5791 `(("r-abc-data" ,r-abc-data)
5792 ("r-locfit" ,r-locfit)
5795 ("r-quantreg" ,r-quantreg)))
5796 (home-page "https://cran.r-project.org/web/packages/abc/")
5797 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
5799 "This package implements several @dfn{Approximate Bayesian
5800 Computation} (ABC) algorithms for performing parameter estimation, model
5801 selection, and goodness-of-fit. Cross-validation tools are also available for
5802 measuring the accuracy of ABC estimates, and to calculate the
5803 misclassification probabilities of different models.")
5804 (license license:gpl3+)))
5806 (define-public r-zip
5813 (uri (cran-uri "zip" version))
5816 "1c02amk3pl6xir5jnbfiwiv2wvpkpbkkb1w71y6lf2yk7g3d0pdb"))))
5817 (build-system r-build-system)
5818 (home-page "https://github.com/gaborcsardi/zip")
5819 (synopsis "Cross-platform Zip compression")
5821 "This package provides a cross-platform Zip compression library for R.
5822 It is a replacement for the @code{zip} function, that does not require any
5823 additional external tools on any platform.")
5824 (license license:cc0)))
5826 (define-public r-openxlsx
5833 (uri (cran-uri "openxlsx" version))
5836 "0wkpa3wsd8rs0pib7cp67iv0s6jn99frcrw7clypqxmvvdwyb9kq"))))
5837 (build-system r-build-system)
5839 `(("r-rcpp" ,r-rcpp)
5840 ("r-stringi" ,r-stringi)
5843 `(("r-knitr" ,r-knitr)))
5844 (home-page "https://github.com/awalker89/openxlsx")
5845 (synopsis "Read, write and edit XLSX files")
5847 "This package simplifies the creation of Excel @code{.xlsx} files by
5848 providing a high level interface to writing, styling and editing worksheets.
5849 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
5850 and @code{XLConnect} packages with the added benefit of removing the
5851 dependency on Java.")
5852 (license license:gpl3)))
5854 (define-public r-rio
5861 (uri (cran-uri "rio" version))
5864 "0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
5865 (build-system r-build-system)
5867 `(("r-curl" ,r-curl)
5868 ("r-data-table" ,r-data-table)
5869 ("r-foreign" ,r-foreign)
5870 ("r-haven" ,r-haven)
5871 ("r-openxlsx" ,r-openxlsx)
5872 ("r-readxl" ,r-readxl)
5873 ("r-tibble" ,r-tibble)))
5874 (home-page "https://github.com/leeper/rio")
5875 (synopsis "Swiss-army knife for data I/O")
5877 "This package provides streamlined data import and export infrastructure
5878 by making assumptions that the user is probably willing to make: @code{import}
5879 and @code{export} determine the data structure from the file extension,
5880 reasonable defaults are used for data import and export (e.g.,
5881 @code{stringsAsFactors=FALSE}), web-based import is natively
5882 supported (including from SSL/HTTPS), compressed files can be read directly
5883 without explicit decompression, and fast import packages are used where
5884 appropriate. An additional convenience function, @code{convert}, provides a
5885 simple method for converting between file types.")
5886 (license license:gpl2)))
5888 (define-public r-maptools
5895 (uri (cran-uri "maptools" version))
5898 "0fs1y3cbymcq4f76wd27h5a7ihdmxii3ca8x29x32xgxhmasni4l"))))
5899 (build-system r-build-system)
5901 `(("r-foreign" ,r-foreign)
5902 ("r-lattice" ,r-lattice)
5904 (home-page "https://r-forge.r-project.org/projects/maptools/")
5905 (synopsis "Tools for reading and handling spatial objects")
5907 "This package provides a set of tools for manipulating and reading
5908 geographic data, in particular ESRI Shapefiles. It includes binary access to
5909 GSHHG shoreline files. The package also provides interface wrappers for
5910 exchanging spatial objects with other R packages.")
5911 ;; The C source files from shapelib are released under the Expat license.
5912 ;; The R code is released under GPL version 2 or later.
5913 (license (list license:gpl2+
5916 (define-public r-later
5923 (uri (cran-uri "later" version))
5926 "1k9n2j7zxw9gfclnx8zfqp6w64c5d6apn7g02yhkajkpmszagfki"))))
5927 (build-system r-build-system)
5931 ("r-rlang" ,r-rlang)))
5933 `(("r-knitr" ,r-knitr)))
5934 (home-page "https://github.com/r-lib/later")
5935 (synopsis "Utilities for delaying function execution")
5937 "This package provides tools to execute arbitrary R or C functions some
5938 time after the current time, after the R execution stack has emptied.")
5939 (license license:gpl2+)))
5941 (define-public r-promises
5948 (uri (cran-uri "promises" version))
5951 "002qkhcn3ri6a3w5fizjvdvrjgvqiw8i7rl9jglcnqik5kmwc61p"))))
5952 (build-system r-build-system)
5954 `(("r-later" ,r-later)
5955 ("r-magrittr" ,r-magrittr)
5958 ("r-rlang" ,r-rlang)))
5960 `(("r-knitr" ,r-knitr)))
5961 (home-page "https://rstudio.github.io/promises")
5962 (synopsis "Abstractions for promise-based asynchronous programming")
5964 "This package provides fundamental abstractions for doing asynchronous
5965 programming in R using promises. Asynchronous programming is useful for
5966 allowing a single R process to orchestrate multiple tasks in the background
5967 while also attending to something else. Semantics are similar to JavaScript
5968 promises, but with a syntax that is idiomatic R.")
5969 (license license:expat)))
5971 (define-public r-dosnow
5978 (uri (cran-uri "doSNOW" version))
5981 "0rj72z5505cprh6wykhhiz08l9bmd966srqh2qypwivf321bvrvh"))))
5982 (properties `((upstream-name . "doSNOW")))
5983 (build-system r-build-system)
5985 `(("r-foreach" ,r-foreach)
5986 ("r-iterators" ,r-iterators)
5987 ("r-snow" ,r-snow)))
5988 (home-page "https://cran.r-project.org/web/packages/doSNOW")
5989 (synopsis "Foreach parallel adaptor for the snow package")
5991 "This package provides a parallel backend for the @code{%dopar%} function
5992 using the @code{snow} package.")
5993 (license license:gpl2)))
5995 (define-public r-snowfall
5998 (version "1.84-6.1")
6001 (uri (cran-uri "snowfall" version))
6003 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
6004 (build-system r-build-system)
6006 `(("r-snow" ,r-snow)))
6007 (home-page "https://cran.r-project.org/web/packages/snowfall/")
6008 (synopsis "Easier cluster computing")
6009 (description "This package is a usability wrapper around snow for easier
6010 development of parallel R programs. This package offers e.g. extended error
6011 checks, and additional functions. All functions work in sequential mode, too,
6012 if no cluster is present or wished. The package is also designed as connector
6013 to the cluster management tool @code{sfCluster}, but can also used without
6015 (license license:gpl2+)))
6017 (define-public r-rappdirs
6024 (uri (cran-uri "rappdirs" version))
6027 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
6028 (build-system r-build-system)
6029 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
6030 (synopsis "Determine where to save data, caches, and logs")
6032 "This package provides an easy way to determine which directories on the
6033 user's computer should be used to save data, caches and logs. It is a port of
6034 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
6035 (license license:expat)))
6037 (define-public r-renv
6044 (uri (cran-uri "renv" version))
6047 "0dd63jr240pg95a6p058s5kcclfmscihdy89v212msihmwvylwh3"))))
6048 (properties `((upstream-name . "renv")))
6049 (build-system r-build-system)
6051 `(("r-knitr" ,r-knitr)))
6052 (home-page "https://rstudio.github.io/renv")
6053 (synopsis "Project environments")
6055 "This package provides a dependency management toolkit for R. Using
6056 renv, you can create and manage project-local R libraries, save the state of
6057 these libraries to a lockfile, and later restore your library as required.
6058 Together, these tools can help make your projects more isolated, portable, and
6060 (license license:expat)))
6062 (define-public r-learnr
6069 (uri (cran-uri "learnr" version))
6072 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
6073 (build-system r-build-system)
6075 `(("r-checkmate" ,r-checkmate)
6076 ("r-ellipsis" ,r-ellipsis)
6077 ("r-evaluate" ,r-evaluate)
6078 ("r-htmltools" ,r-htmltools)
6079 ("r-htmlwidgets" ,r-htmlwidgets)
6080 ("r-jsonlite" ,r-jsonlite)
6081 ("r-knitr" ,r-knitr)
6082 ("r-markdown" ,r-markdown)
6083 ("r-rappdirs" ,r-rappdirs)
6085 ("r-rmarkdown" ,r-rmarkdown)
6086 ("r-rprojroot" ,r-rprojroot)
6087 ("r-shiny" ,r-shiny)
6088 ("r-withr" ,r-withr)))
6089 (home-page "https://rstudio.github.io/learnr/")
6090 (synopsis "Interactive tutorials for R")
6092 "This package provides tools to create interactive tutorials using R
6093 Markdown. Use a combination of narrative, figures, videos, exercises, and
6094 quizzes to create self-paced tutorials for learning about R and R packages.")
6095 (license license:asl2.0)))
6097 (define-public r-analytics
6099 (name "r-analytics")
6104 (uri (cran-uri "analytics" version))
6107 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
6108 (build-system r-build-system)
6111 ("r-cluster" ,r-cluster)
6112 ("r-fractal" ,r-fractal)
6113 ("r-lmtest" ,r-lmtest)
6116 ("r-powerplus" ,r-powerplus)
6117 ("r-robust" ,r-robust)
6118 ("r-trend" ,r-trend)
6122 (home-page "https://cran.r-project.org/web/packages/analytics/")
6123 (synopsis "Collection of data analysis tools")
6125 "This package is a collection of data analysis tools. It includes tools
6126 for regression outlier detection in a fitted linear model, stationary
6127 bootstrap using a truncated geometric distribution, a comprehensive test for
6128 weak stationarity, column means by group, weighted biplots, and a heuristic to
6129 obtain a better initial configuration in non-metric MDS.")
6130 (license license:gpl2)))
6132 (define-public r-reticulate
6134 (name "r-reticulate")
6139 (uri (cran-uri "reticulate" version))
6142 "0ddx3xrlw55d8d3w7pxap618w2c5pd1n2jw4xsa185s8mf1zifkl"))))
6143 (build-system r-build-system)
6144 (inputs `(("python" ,python)))
6146 `(("r-rappdirs" ,r-rappdirs)
6147 ("r-jsonlite" ,r-jsonlite)
6148 ("r-matrix" ,r-matrix)
6149 ("r-rcpp" ,r-rcpp)))
6151 `(("r-knitr" ,r-knitr)))
6152 (home-page "https://github.com/rstudio/reticulate")
6153 (synopsis "R interface to Python")
6155 "This package provides an interface from R to Python modules, classes,
6156 and functions. When calling into Python, R data types are automatically
6157 converted to their equivalent Python types. When values are returned from
6158 Python to R they are converted back to R types.")
6159 (license license:asl2.0)))
6161 (define-public r-bibtex
6168 (uri (cran-uri "bibtex" version))
6171 "140hkjzdp3033cvji861rd06z1ixgpnn4n5amygqsmhnixk8ff07"))))
6172 (build-system r-build-system)
6173 (propagated-inputs `(("r-stringr" ,r-stringr)))
6174 (home-page "https://github.com/romainfrancois/bibtex")
6175 (synopsis "Bibtex parser")
6176 (description "This package provides a utility for R to parse a bibtex
6178 (license license:gpl2+)))
6180 (define-public r-ggseqlogo
6182 (name "r-ggseqlogo")
6187 (uri (cran-uri "ggseqlogo" version))
6190 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
6191 (build-system r-build-system)
6192 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
6193 (home-page "https://github.com/omarwagih/ggseqlogo")
6194 (synopsis "ggplot2 extension for drawing genetic sequence logos")
6196 "The range of functions provided by this package makes it possible to
6197 draw highly versatile genomic sequence logos. Features include, but are not
6198 limited to, modifying colour schemes and fonts used to draw the logo,
6199 generating multiple logo plots, and aiding the visualisation with annotations.
6200 Sequence logos can easily be combined with other ggplot2 plots.")
6201 ;; Unspecified version of the LGPL.
6202 (license license:lgpl3+)))
6204 (define-public r-ggsci
6211 (uri (cran-uri "ggsci" version))
6214 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
6215 (build-system r-build-system)
6217 `(("r-ggplot2" ,r-ggplot2)
6218 ("r-scales" ,r-scales)))
6219 (home-page "https://nanx.me/ggsci/")
6220 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
6222 "This package provides a collection of ggplot2 color palettes inspired by
6223 plots in scientific journals, data visualization libraries, science fiction
6224 movies, and TV shows.")
6225 (license license:gpl3)))
6227 (define-public r-ggsignif
6234 (uri (cran-uri "ggsignif" version))
6237 "17j9hg967k1wp9xw3x84mqss58jkb8pvlrnlchz4i1hklgykxqbg"))))
6238 (build-system r-build-system)
6240 `(("r-knitr" ,r-knitr)))
6242 `(("r-ggplot2" ,r-ggplot2)))
6243 (home-page "https://github.com/const-ae/ggsignif")
6244 (synopsis "Significance brackets for ggplot2")
6246 "Enrich your ggplots with group-wise comparisons. This package provides
6247 an easy way to indicate if two groups are significantly different. Commonly
6248 this is shown by a bracket on top connecting the groups of interest which
6249 itself is annotated with the level of significance. The package provides a
6250 single layer that takes the groups for comparison and the test as arguments
6251 and adds the annotation to the plot.")
6252 (license license:gpl3)))
6254 (define-public r-rstatix
6261 (uri (cran-uri "rstatix" version))
6264 "0nwwvxwr4z3j4n9z8cnvwghppc836g47n0ia98chk272qwh8xcpb"))))
6265 (properties `((upstream-name . "rstatix")))
6266 (build-system r-build-system)
6268 `(("r-broom" ,r-broom)
6270 ("r-corrplot" ,r-corrplot)
6271 ("r-dplyr" ,r-dplyr)
6272 ("r-generics" ,r-generics)
6273 ("r-magrittr" ,r-magrittr)
6274 ("r-purrr" ,r-purrr)
6275 ("r-rlang" ,r-rlang)
6276 ("r-tibble" ,r-tibble)
6277 ("r-tidyr" ,r-tidyr)
6278 ("r-tidyselect" ,r-tidyselect)))
6279 (home-page "https://rpkgs.datanovia.com/rstatix/")
6280 (synopsis "Pipe-friendly framework for basic statistical tests")
6282 "This package provides a simple and intuitive pipe-friendly framework,
6283 coherent with the @code{tidyverse} design philosophy, for performing basic
6284 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
6285 correlation analyses. The output of each test is automatically transformed
6286 into a tidy data frame to facilitate visualization. Additional functions are
6287 available for reshaping, reordering, manipulating and visualizing correlation
6289 (license license:gpl2)))
6291 (define-public r-ggpubr
6298 (uri (cran-uri "ggpubr" version))
6301 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
6302 (build-system r-build-system)
6304 `(("r-cowplot" ,r-cowplot)
6305 ("r-dplyr" ,r-dplyr)
6306 ("r-ggplot2" ,r-ggplot2)
6307 ("r-ggrepel" ,r-ggrepel)
6308 ("r-ggsci" ,r-ggsci)
6309 ("r-ggsignif" ,r-ggsignif)
6311 ("r-gridextra" ,r-gridextra)
6312 ("r-magrittr" ,r-magrittr)
6313 ("r-polynom" ,r-polynom)
6314 ("r-purrr" ,r-purrr)
6315 ("r-rlang" ,r-rlang)
6316 ("r-scales" ,r-scales)
6317 ("r-rstatix" ,r-rstatix)
6318 ("r-tibble" ,r-tibble)
6319 ("r-tidyr" ,r-tidyr)))
6320 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
6321 (synopsis "ggplot2-based publication-ready plots")
6323 "The ggplot2 package is an excellent and flexible package for elegant
6324 data visualization in R. However the default generated plots require some
6325 formatting before we can send them for publication. The ggpubr package
6326 provides some easy-to-use functions for creating and customizing ggplot2-based
6327 publication-ready plots.")
6328 (license license:gpl2)))
6330 (define-public r-ellipse
6337 (uri (cran-uri "ellipse" version))
6340 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
6341 (build-system r-build-system)
6342 (home-page "https://cran.r-project.org/web/packages/ellipse/")
6343 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
6345 "This package contains various routines for drawing ellipses and
6346 ellipse-like confidence regions, implementing the plots described in Murdoch
6347 and Chow (1996), A graphical display of large correlation matrices, The
6348 American Statistician 50, 178-180. There are also routines implementing the
6349 profile plots described in Bates and Watts (1988), Nonlinear Regression
6350 Analysis and its Applications.")
6351 (license license:gpl2+)))
6353 (define-public r-flashclust
6355 (name "r-flashclust")
6360 (uri (cran-uri "flashClust" version))
6363 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
6364 (properties `((upstream-name . "flashClust")))
6365 (build-system r-build-system)
6366 (native-inputs `(("gfortran" ,gfortran)))
6367 (home-page "https://cran.r-project.org/web/packages/flashClust/")
6368 (synopsis "Implementation of optimal hierarchical clustering")
6370 "This package provides a fast implementation of hierarchical
6372 (license license:gpl2+)))
6374 (define-public r-factominer
6376 (name "r-factominer")
6381 (uri (cran-uri "FactoMineR" version))
6384 "0ldgf3daksh6lpblhqys67m4mxqx3q9s9n5plfam6dwshfik0ky6"))))
6385 (properties `((upstream-name . "FactoMineR")))
6386 (build-system r-build-system)
6389 ("r-cluster" ,r-cluster)
6390 ("r-ellipse" ,r-ellipse)
6391 ("r-flashclust" ,r-flashclust)
6392 ("r-ggplot2" ,r-ggplot2)
6393 ("r-ggrepel" ,r-ggrepel)
6394 ("r-lattice" ,r-lattice)
6395 ("r-leaps" ,r-leaps)
6397 ("r-scatterplot3d" ,r-scatterplot3d)))
6398 (home-page "http://factominer.free.fr")
6399 (synopsis "Multivariate exploratory data analysis and data mining")
6401 "This package provides exploratory data analysis methods to summarize,
6402 visualize and describe datasets. The main principal component methods are
6403 available, those with the largest potential in terms of applications:
6404 principal component analysis (PCA) when variables are quantitative,
6405 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
6406 variables are categorical, Multiple Factor Analysis when variables are
6407 structured in groups, etc. and hierarchical cluster analysis.")
6408 (license license:gpl2+)))
6410 (define-public r-factoextra
6412 (name "r-factoextra")
6417 (uri (cran-uri "factoextra" version))
6420 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
6421 (build-system r-build-system)
6423 `(("r-abind" ,r-abind)
6424 ("r-cluster" ,r-cluster)
6425 ("r-dendextend" ,r-dendextend)
6426 ("r-factominer" ,r-factominer)
6427 ("r-ggplot2" ,r-ggplot2)
6428 ("r-ggpubr" ,r-ggpubr)
6429 ("r-ggrepel" ,r-ggrepel)
6430 ("r-reshape2" ,r-reshape2)
6431 ("r-tidyr" ,r-tidyr)))
6432 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
6433 (synopsis "Extract and visualize the results of multivariate data analyses")
6435 "This package provides some easy-to-use functions to extract and
6436 visualize the output of multivariate data analyses, including
6437 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
6438 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
6439 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
6440 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
6441 packages. It contains also functions for simplifying some clustering analysis
6442 steps and provides ggplot2-based elegant data visualization.")
6443 (license license:gpl2)))
6445 (define-public r-fansi
6452 (uri (cran-uri "fansi" version))
6455 "028ywjy538psnmdnddvy5jr3idzffr4hikzr4x97x0m30g4fws9w"))))
6456 (build-system r-build-system)
6458 `(("r-knitr" ,r-knitr))) ; for vignettes
6459 (home-page "https://github.com/brodieG/fansi")
6460 (synopsis "ANSI control sequence aware string functions")
6462 "This package provides counterparts to R string manipulation functions
6463 that account for the effects of ANSI text formatting control sequences.")
6464 (license license:gpl2+)))
6466 (define-public r-nbclust
6473 (uri (cran-uri "NbClust" version))
6476 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
6477 (properties `((upstream-name . "NbClust")))
6478 (build-system r-build-system)
6479 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
6480 (synopsis "Determine the best number of clusters in a data set")
6482 "NbClust provides 30 indexes for determining the optimal number of
6483 clusters in a data set and offers the best clustering scheme from different
6484 results to the user.")
6485 (license license:gpl2)))
6487 (define-public r-hdf5r
6494 (uri (cran-uri "hdf5r" version))
6497 "0c2p06k9bp9rf0fyavnxw5d8jr2bbgx3gjblahz581cpvsfksj9i"))))
6498 (build-system r-build-system)
6503 `(("r-bit64" ,r-bit64)
6506 `(("r-knitr" ,r-knitr)))
6507 (home-page "https://hhoeflin.github.io/hdf5r")
6508 (synopsis "Interface to the HDF5 binary data format")
6510 "HDF5 is a data model, library and file format for storing and managing
6511 large amounts of data. This package provides a nearly feature complete,
6512 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
6513 functionality is added so that HDF5 objects behave very similar to their
6514 corresponding R counterparts.")
6515 (license license:asl2.0)))
6517 (define-public r-itertools
6519 (name "r-itertools")
6524 (uri (cran-uri "itertools" version))
6527 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
6528 (build-system r-build-system)
6530 `(("r-iterators" ,r-iterators)))
6531 (home-page "https://cran.r-project.org/web/packages/itertools/")
6532 (synopsis "Iterator tools")
6534 "This package provides various tools for creating iterators, many
6535 patterned after functions in the Python @code{itertools} module, and others
6536 patterned after functions in the snow package.")
6537 (license license:gpl2)))
6539 (define-public r-polynom
6546 (uri (cran-uri "polynom" version))
6549 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
6550 (build-system r-build-system)
6551 (home-page "https://cran.r-project.org/web/packages/polynom/")
6552 (synopsis "Functions for univariate polynomial manipulations")
6554 "This package provides a collection of functions to implement a class for
6555 univariate polynomial manipulations.")
6556 (license license:gpl2)))
6558 (define-public r-gbrd
6565 (uri (cran-uri "gbRd" version))
6568 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
6569 (properties `((upstream-name . "gbRd")))
6570 (build-system r-build-system)
6571 (home-page "https://cran.r-project.org/web/packages/gbRd/")
6572 (synopsis "Utilities for processing Rd objects and files")
6574 "This package provides utilities for processing Rd objects and files.
6575 Extract argument descriptions and other parts of the help pages of
6577 (license license:gpl2+)))
6579 (define-public r-rjags
6586 (uri (cran-uri "rjags" version))
6589 "1nhaim84ww8fd6m8xlpmngqcnp2qpql29ahc38366fxja3ghngmx"))))
6590 (build-system r-build-system)
6592 `(("r-coda" ,r-coda)))
6596 `(("pkg-config" ,pkg-config)))
6597 (home-page "http://mcmc-jags.sourceforge.net")
6598 (synopsis "Bayesian graphical models using MCMC")
6600 "This package provides an R interface to the JAGS MCMC library. JAGS is
6601 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
6602 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
6603 (license license:gpl2)))
6605 (define-public r-rdpack
6612 (uri (cran-uri "Rdpack" version))
6615 "069yh9h57z3gjl5ih1r6wyiwmgmfzkpjxrpxg8mfq7y6zr1mynsw"))))
6616 (properties `((upstream-name . "Rdpack")))
6617 (build-system r-build-system)
6619 `(("r-bibtex" ,r-bibtex)
6620 ("r-gbrd" ,r-gbrd)))
6621 (home-page "https://github.com/GeoBosh/Rdpack")
6622 (synopsis "Update and manipulate Rd documentation objects")
6624 "This package provides functions for manipulation of R documentation
6625 objects, including functions @code{reprompt()} and @code{ereprompt()} for
6626 updating Rd documentation for functions, methods and classes; it also includes
6627 Rd macros for citations and import of references from bibtex files for use in
6628 Rd files and roxygen2 comments, as well as many functions for manipulation of
6629 references and Rd files.")
6630 (license license:gpl2+)))
6632 (define-public r-officer
6639 (uri (cran-uri "officer" version))
6642 "1wk9h6bz77s5j6lgksmlrmi1vyaa35c766gq6hgb1dp0dz0x342x"))))
6643 (build-system r-build-system)
6645 `(("r-magrittr" ,r-magrittr)
6651 `(("r-knitr" ,r-knitr)))
6652 (home-page "https://davidgohel.github.io/officer")
6653 (synopsis "Manipulation of Word and PowerPoint documents")
6655 "This package provides tools to access and manipulate Word and PowerPoint
6656 documents from R. The package focuses on tabular and graphical reporting from
6657 R; it also provides two functions that let users get document content into
6658 data objects. A set of functions lets add and remove images, tables and
6659 paragraphs of text in new or existing documents. When working with PowerPoint
6660 presentations, slides can be added or removed; shapes inside slides can also
6661 be added or removed. When working with Word documents, a cursor can be used
6662 to help insert or delete content at a specific location in the document.")
6663 (license license:gpl3)))
6665 (define-public r-profilemodel
6667 (name "r-profilemodel")
6672 (uri (cran-uri "profileModel" version))
6675 "0yq8hy43h62hlz8bbf9ila4a3xcwizi1if27b78xc5y857ncwad8"))))
6676 (properties `((upstream-name . "profileModel")))
6677 (build-system r-build-system)
6678 (home-page "https://github.com/ikosmidis/profileModel")
6679 (synopsis "Profiling inference functions for various model classes")
6681 "This package provides tools that can be used to calculate, evaluate,
6682 plot and use for inference the profiles of *arbitrary* inference functions for
6683 arbitrary @code{glm}-like fitted models with linear predictors. More information
6684 on the methods that are implemented can be found in Kosmidis (2008)
6685 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
6686 (license license:gpl2+)))
6688 (define-public r-brglm
6695 (uri (cran-uri "brglm" version))
6698 "0c9ngscc6zlfm90fqyggnj04qfkhp5qgf5q3wnfpxwyc8cm47by2"))))
6699 (properties `((upstream-name . "brglm")))
6700 (build-system r-build-system)
6702 `(("r-profilemodel" ,r-profilemodel)))
6703 (home-page "https://github.com/ikosmidis/brglm")
6704 (synopsis "Bias reduction in binomial-response generalized linear models")
6706 "Fit generalized linear models with binomial responses using either an
6707 adjusted-score approach to bias reduction or maximum penalized likelihood
6708 where penalization is by Jeffreys invariant prior. These procedures return
6709 estimates with improved frequentist properties (bias, mean squared error) that
6710 are always finite even in cases where the maximum likelihood estimates are
6711 infinite (data separation). Fitting takes place by fitting generalized linear
6712 models on iteratively updated pseudo-data. The interface is essentially the
6713 same as @code{glm}. More flexibility is provided by the fact that custom
6714 pseudo-data representations can be specified and used for model fitting.
6715 Functions are provided for the construction of confidence intervals for the
6716 reduced-bias estimates.")
6717 (license license:gpl2+)))
6719 (define-public r-entropy
6726 (uri (cran-uri "entropy" version))
6729 "10vg4818q5g54pv2nn9x5i7pvky5nsv96syy47pz2mgqp1273cpd"))))
6730 (properties `((upstream-name . "entropy")))
6731 (build-system r-build-system)
6732 (home-page "https://www.strimmerlab.org/software/entropy/")
6733 (synopsis "Estimation of entropy, mutual information and related quantities")
6735 "This package implements various estimators of entropy, such as the
6736 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
6737 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
6738 estimator. It also offers an R interface to the NSB estimator. Furthermore,
6739 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
6740 mutual information, and chi-squared statistic of independence. In addition
6741 there are functions for discretizing continuous random variables.")
6742 (license license:gpl3+)))
6744 (define-public r-abn
6751 (uri (cran-uri "abn" version))
6754 "1wwnzv5yir8cyl0f0arxagbsg9ndgs0799m42wbjkpr8cg9sfdhc"))))
6755 (build-system r-build-system)
6759 `(("r-boot" ,r-boot)
6760 ("r-brglm" ,r-brglm)
6761 ("r-entropy" ,r-entropy)
6764 ("r-moments" ,r-moments)
6767 ("r-rcpparmadillo" ,r-rcpparmadillo)
6768 ("r-rjags" ,r-rjags)))
6769 (home-page "https://r-bayesian-networks.org/")
6770 (synopsis "Modelling multivariate data with additive bayesian networks")
6772 "Bayesian network analysis is a form of probabilistic graphical models
6773 which derives from empirical data a directed acyclic graph, DAG, describing
6774 the dependency structure between random variables. An additive Bayesian
6775 network model consists of a form of a DAG where each node comprises a
6776 @dfn{generalized linear model} (GLM). Additive Bayesian network models are
6777 equivalent to Bayesian multivariate regression using graphical modelling, they
6778 generalises the usual multivariable regression, GLM, to multiple dependent
6779 variables. This package provides routines to help determine optimal Bayesian
6780 network models for a given data set, where these models are used to identify
6781 statistical dependencies in messy, complex data.")
6782 (license license:gpl2+)))
6784 (define-public r-acd
6791 (uri (cran-uri "ACD" version))
6794 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
6795 (properties `((upstream-name . "ACD")))
6796 (build-system r-build-system)
6797 (home-page "https://cran.r-project.org/web/packages/ACD/")
6798 (synopsis "Categorical data analysis with complete or missing responses")
6800 "This package provides tools for categorical data analysis with complete
6801 or missing responses.")
6802 (license license:gpl2+)))
6804 (define-public r-acdm
6811 (uri (cran-uri "ACDm" version))
6814 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
6815 (properties `((upstream-name . "ACDm")))
6816 (build-system r-build-system)
6818 `(("r-dplyr" ,r-dplyr)
6819 ("r-ggplot2" ,r-ggplot2)
6821 ("r-rsolnp" ,r-rsolnp)
6823 (home-page "https://cran.r-project.org/web/packages/ACDm/")
6824 (synopsis "Tools for Autoregressive Conditional Duration Models")
6826 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
6827 and Russell, 1998) models. It creates trade, price or volume durations from
6828 transactions (tic) data, performs diurnal adjustments, fits various ACD models
6830 (license license:gpl2+)))
6832 (define-public r-overlap
6839 (uri (cran-uri "overlap" version))
6842 "17cnr4qin1qy0df4k491267acna12gpbbps6w3gi8nccqxfrb1pd"))))
6843 (build-system r-build-system)
6844 (home-page "https://cran.r-project.org/web/packages/overlap/")
6845 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
6847 "This package provides functions to fit kernel density functions to data
6848 on temporal activity patterns of animals; estimate coefficients of overlapping
6849 of densities for two species; and calculate bootstrap estimates of confidence
6851 (license license:gpl3+)))
6853 (define-public r-snakecase
6855 (name "r-snakecase")
6860 (uri (cran-uri "snakecase" version))
6863 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
6864 (build-system r-build-system)
6866 `(("r-stringi" ,r-stringi)
6867 ("r-stringr" ,r-stringr)))
6868 (home-page "https://github.com/Tazinho/snakecase")
6869 (synopsis "Convert strings into any case")
6871 "This package provides a consistent, flexible and easy to use tool to
6872 parse and convert strings into cases like snake or camel among others.")
6873 (license license:gpl3)))
6875 (define-public r-prediction
6877 (name "r-prediction")
6882 (uri (cran-uri "prediction" version))
6885 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
6886 (build-system r-build-system)
6888 `(("r-data-table" ,r-data-table)))
6889 (home-page "https://github.com/leeper/prediction")
6890 (synopsis "Tidy, type-safe prediction methods")
6892 "This package provides the @code{prediction()} function, a type-safe
6893 alternative to @code{predict()} that always returns a data frame. The package
6894 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
6895 from the @code{stats} package, as well as numerous other model classes from
6896 other add-on packages.")
6897 (license license:expat)))
6899 (define-public r-insight
6906 (uri (cran-uri "insight" version))
6909 "0ggczjd112kclknyxxqvjkzwzazfhjwglchafzamk4zb08ww7y7k"))))
6910 (build-system r-build-system)
6912 `(("r-knitr" ,r-knitr)))
6913 (home-page "https://easystats.github.io/insight/")
6914 (synopsis "Easy access to model information for various model objects")
6916 "This package provides a tool to provide an easy, intuitive and
6917 consistent access to information contained in various R models, like model
6918 formulas, model terms, information about random effects, data that was used to
6919 fit the model or data from response variables. The package mainly revolves
6920 around two types of functions: Functions that find (the names of) information,
6921 starting with @code{find_}, and functions that get the underlying data,
6922 starting with @code{get_}. The package has a consistent syntax and works with
6923 many different model objects, where otherwise functions to access these
6924 information are missing.")
6925 (license license:gpl3)))
6927 (define-public r-sjlabelled
6929 (name "r-sjlabelled")
6934 (uri (cran-uri "sjlabelled" version))
6937 "0xvb0yi7c7wiiqjbnbisyb2cjinm11i373jacfv1yzyc9cznzyzq"))))
6938 (build-system r-build-system)
6940 `(("r-insight" ,r-insight)))
6942 `(("r-knitr" ,r-knitr)))
6943 (home-page "https://github.com/strengejacke/sjlabelled")
6944 (synopsis "Labelled data utility functions")
6946 "This package provides a collection of functions dealing with labelled
6947 data, like reading and writing data between R and other statistical software
6948 packages. This includes easy ways to get, set or change value and variable
6949 label attributes, to convert labelled vectors into factors or numeric (and
6950 vice versa), or to deal with multiple declared missing values.")
6951 (license license:gpl3)))
6953 (define-public r-sjmisc
6960 (uri (cran-uri "sjmisc" version))
6963 "0xl0s56d13bia89ai619rcr0fzbvc2k8f7hjxik4qp0g4v87zzlk"))))
6964 (build-system r-build-system)
6966 `(("r-dplyr" ,r-dplyr)
6967 ("r-insight" ,r-insight)
6968 ("r-magrittr" ,r-magrittr)
6969 ("r-purrr" ,r-purrr)
6970 ("r-rlang" ,r-rlang)
6971 ("r-sjlabelled" ,r-sjlabelled)
6972 ("r-tidyselect" ,r-tidyselect)))
6974 `(("r-knitr" ,r-knitr)))
6975 (home-page "https://github.com/strengejacke/sjmisc")
6976 (synopsis "Data and variable transformation functions")
6978 "This package is a collection of miscellaneous utility functions,
6979 supporting data transformation tasks like recoding, dichotomizing or grouping
6980 variables, setting and replacing missing values. The data transformation
6981 functions also support labelled data, and all integrate seamlessly into a
6982 tidyverse workflow.")
6983 (license license:gpl3)))
6985 (define-public r-nortest
6992 (uri (cran-uri "nortest" version))
6995 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
6996 (build-system r-build-system)
6997 (home-page "https://cran.r-project.org/web/packages/nortest/")
6998 (synopsis "Tests for normality")
7000 "This package provides five omnibus tests for testing the composite
7001 hypothesis of normality.")
7002 (license license:gpl2+)))
7004 (define-public r-moonbook
7011 (uri (cran-uri "moonBook" version))
7014 "0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
7015 (properties `((upstream-name . "moonBook")))
7016 (build-system r-build-system)
7018 `(("r-magrittr" ,r-magrittr)
7019 ("r-nortest" ,r-nortest)
7020 ("r-purrr" ,r-purrr)
7021 ("r-sjmisc" ,r-sjmisc)
7022 ("r-stringr" ,r-stringr)
7023 ("r-survival" ,r-survival)))
7024 (home-page "https://github.com/cardiomoon/moonBook")
7025 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
7027 "This package provides several analysis-related functions for the book
7028 entitled \"R statistics and graph for medical articles\" (written in Korean),
7029 version 1, by Keon-Woong Moon with Korean demographic data with several plot
7031 (license license:gpl2)))
7033 (define-public r-flextable
7035 (name "r-flextable")
7040 (uri (cran-uri "flextable" version))
7043 "1j7yvjiavar21ywck6nyz0p6bd66fnj99bq8lljdz4rrl3314yb8"))))
7044 (build-system r-build-system)
7046 `(("r-base64enc" ,r-base64enc)
7047 ("r-data-table" ,r-data-table)
7048 ("r-gdtools" ,r-gdtools)
7049 ("r-htmltools" ,r-htmltools)
7050 ("r-knitr" ,r-knitr)
7051 ("r-officer" ,r-officer)
7052 ("r-rlang" ,r-rlang)
7053 ("r-rmarkdown" ,r-rmarkdown)
7055 ("r-xml2" ,r-xml2)))
7056 (home-page "https://davidgohel.github.io/flextable")
7057 (synopsis "Functions for tabular reporting")
7059 "This package provides tools to create pretty tables for HTML documents
7060 and other formats. Functions are provided to let users create tables, modify
7061 and format their content. It extends the @code{officer} package and can be
7062 used within R markdown documents when rendering to HTML and to Word
7064 (license license:gpl3)))
7066 (define-public r-writexl
7073 (uri (cran-uri "writexl" version))
7076 "0lah0r2pd996s0vdbi614j3h52dbxmifha6f19v53p2b7fr32wjd"))))
7077 (build-system r-build-system)
7078 (inputs `(("zlib" ,zlib)))
7079 (home-page "https://github.com/ropensci/writexl")
7080 (synopsis "Export data frames to xlsx format")
7082 "This package provides a data frame to xlsx exporter based on
7084 (license license:bsd-2)))
7086 (define-public r-biasedurn
7088 (name "r-biasedurn")
7093 (uri (cran-uri "BiasedUrn" version))
7096 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
7097 (properties `((upstream-name . "BiasedUrn")))
7098 (build-system r-build-system)
7099 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
7100 (synopsis "Biased Urn model distributions")
7102 "This package provides statistical models of biased sampling in the form
7103 of univariate and multivariate noncentral hypergeometric distributions,
7104 including Wallenius' noncentral hypergeometric distribution and Fisher's
7105 noncentral hypergeometric distribution (also called extended hypergeometric
7107 (license license:gpl3)))
7109 (define-public r-goplot
7116 (uri (cran-uri "GOplot" version))
7119 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
7120 (properties `((upstream-name . "GOplot")))
7121 (build-system r-build-system)
7123 `(("r-ggdendro" ,r-ggdendro)
7124 ("r-ggplot2" ,r-ggplot2)
7125 ("r-gridextra" ,r-gridextra)
7126 ("r-rcolorbrewer" ,r-rcolorbrewer)))
7127 (home-page "https://github.com/wencke/wencke.github.io")
7128 (synopsis "Visualization of functional analysis data")
7130 "This package provides an implementation of multilayered visualizations
7131 for enhanced graphical representation of functional analysis data. It
7132 combines and integrates omics data derived from expression and functional
7133 annotation enrichment analyses. Its plotting functions have been developed
7134 with an hierarchical structure in mind: starting from a general overview to
7135 identify the most enriched categories (modified bar plot, bubble plot) to a
7136 more detailed one displaying different types of relevant information for the
7137 molecules in a given set of categories (circle plot, chord plot, cluster plot,
7138 Venn diagram, heatmap).")
7139 (license license:gpl2)))
7141 (define-public r-getopt
7148 (uri (cran-uri "getopt" version))
7151 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
7152 (build-system r-build-system)
7153 (home-page "https://github.com/trevorld/getopt")
7154 (synopsis "Command-line option processor for R")
7156 "This package is designed to be used with Rscript to write shebang
7157 scripts that accept short and long options. Many users will prefer to
7158 use the packages @code{optparse} or @code{argparse} which add extra
7159 features like automatically generated help options and usage texts,
7160 support for default values, positional argument support, etc.")
7161 (license license:gpl2+)))
7163 (define-public r-findpython
7165 (name "r-findpython")
7170 (uri (cran-uri "findpython" version))
7173 "0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
7174 (build-system r-build-system)
7175 (home-page "https://github.com/trevorld/findpython")
7176 (synopsis "Functions to find an acceptable Python binary")
7178 "This package was designed to find an acceptable Python binary that
7179 matches version and feature constraints.")
7180 (license license:expat)))
7182 ;; This in not the same as "r-argparser"
7183 (define-public r-argparse
7190 (uri (cran-uri "argparse" version))
7193 "1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
7194 (build-system r-build-system)
7195 (inputs `(("python" ,python)))
7197 `(("r-findpython" ,r-findpython)
7198 ("r-jsonlite" ,r-jsonlite)
7200 (home-page "https://github.com/trevorld/argparse")
7201 (synopsis "Command line optional and positional argument parser")
7203 "This package provides a command line parser to be used with Rscript to
7204 write shebang scripts that gracefully accept positional and optional arguments
7205 and automatically generate usage notices.")
7206 (license license:gpl2+)))
7208 (define-public r-hash
7215 (uri (cran-uri "hash" version))
7218 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
7219 (build-system r-build-system)
7220 (home-page "https://cran.r-project.org/web/packages/hash/")
7221 (synopsis "Implementation of hash/associated arrays/dictionaries")
7223 "This package implements a data structure similar to hashes in Perl and
7224 dictionaries in Python but with a purposefully R flavor. For objects of
7225 appreciable size, access using hashes outperforms native named lists and
7227 (license license:gpl2+)))
7229 (define-public r-orddom
7236 (uri (cran-uri "orddom" version))
7239 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
7240 (build-system r-build-system)
7241 (propagated-inputs `(("r-psych" ,r-psych)))
7242 (home-page "https://cran.r-project.org/web/packages/orddom/")
7243 (synopsis "Ordinal dominance statistics")
7245 "This package provides tools to compute ordinal, statistics and effect
7246 sizes as an alternative to mean comparison: Cliff's delta or success rate
7247 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
7248 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
7249 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
7250 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
7251 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
7252 Group (Non-)Overlap considerations.")
7253 (license license:gpl2)))
7255 (define-public r-deriv
7262 (uri (cran-uri "Deriv" version))
7265 "03mlfy8jzzzbh2l18gnmw0a71n9savx4cw72yhkxq93v2xj8fy3n"))))
7266 (properties `((upstream-name . "Deriv")))
7267 (build-system r-build-system)
7268 (home-page "https://cran.r-project.org/web/packages/Deriv")
7269 (synopsis "Symbolic differentiation")
7271 "This package provides an R-based solution for symbolic differentiation.
7272 It admits user-defined functions as well as function substitution in arguments
7273 of functions to be differentiated. Some symbolic simplification is part of
7275 (license license:gpl3+)))
7277 (define-public r-doby
7284 (uri (cran-uri "doBy" version))
7287 "0wz1vmsf1545r1m42q88s675ncwvm8figjn7kzbngjn9aqck9qbq"))))
7288 (properties `((upstream-name . "doBy")))
7289 (build-system r-build-system)
7291 `(("r-broom" ,r-broom)
7292 ("r-deriv" ,r-deriv)
7293 ("r-magrittr" ,r-magrittr)
7295 ("r-matrix" ,r-matrix)
7296 ("r-pbkrtest" ,r-pbkrtest)
7297 ("r-tibble" ,r-tibble)))
7299 `(("r-knitr" ,r-knitr)))
7300 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
7301 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
7303 "This package contains:
7306 @item facilities for working with grouped data: @code{do}
7307 something to data stratified @code{by} some variables.
7308 @item implementations of least-squares means, general linear contrasts, and
7309 @item miscellaneous other utilities.
7311 (license license:gpl2+)))
7313 (define-public r-refgenome
7315 (name "r-refgenome")
7320 (uri (cran-uri "refGenome" version))
7323 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
7324 (properties `((upstream-name . "refGenome")))
7325 (build-system r-build-system)
7329 ("r-rsqlite" ,r-rsqlite)))
7330 (home-page "https://cran.r-project.org/web/packages/refGenome/")
7332 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
7334 "This package contains functionality for importing and managing of
7335 downloaded genome annotation data from the Ensembl genome browser (European
7336 Bioinformatics Institute) and from the UCSC genome browser (University of
7337 California, Santa Cruz) and annotation routines for genomic positions and
7338 splice site positions.")
7339 (license license:gpl2)))
7341 (define-public r-basix
7348 (uri (cran-uri "BASIX" version))
7351 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
7352 (properties `((upstream-name . "BASIX")))
7353 (build-system r-build-system)
7354 (home-page "https://cran.r-project.org/web/packages/BASIX/")
7355 (synopsis "Efficient C/C++ toolset for R")
7357 "BASIX provides some efficient C/C++ implementations of native R
7358 procedures to speed up calculations in R.")
7359 (license license:gpl2)))
7361 (define-public r-blockfest
7363 (name "r-blockfest")
7368 (uri (cran-uri "BlockFeST" version))
7371 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
7372 (properties `((upstream-name . "BlockFeST")))
7373 (build-system r-build-system)
7374 (propagated-inputs `(("r-basix" ,r-basix)))
7375 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
7376 (synopsis "Bayesian calculation of region-specific fixation index")
7378 "This package provides an R implementation of an extension of the
7379 BayeScan software for codominant markers, adding the option to group
7380 individual SNPs into pre-defined blocks. A typical application of this new
7381 approach is the identification of genomic regions, genes, or gene sets
7382 containing one or more SNPs that evolved under directional selection.")
7383 (license license:gpl2)))
7385 (define-public r-proc
7392 (uri (cran-uri "pROC" version))
7395 "0apwa5zzqh74pjnvf5a1s5qf6i9r5h44jdllfrwymkd2v479d2xn"))))
7396 (properties `((upstream-name . "pROC")))
7397 (build-system r-build-system)
7399 `(("r-plyr" ,r-plyr)
7400 ("r-rcpp" ,r-rcpp)))
7401 (home-page "https://web.expasy.org/pROC/")
7402 (synopsis "Display and analyze ROC curves")
7404 "This package provides tools for visualizing, smoothing and comparing
7405 receiver operating characteristic (ROC curves). The area under the
7406 curve (AUC) can be compared with statistical tests based on U-statistics or
7407 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
7408 (license license:gpl3+)))
7410 (define-public r-rootsolve
7412 (name "r-rootsolve")
7417 (uri (cran-uri "rootSolve" version))
7420 "0c9hhgq1pgqdg80a6n2ssfbj5nyaf97y4iiya7j7l6b34qc53128"))))
7421 (properties `((upstream-name . "rootSolve")))
7422 (build-system r-build-system)
7423 (native-inputs `(("gfortran" ,gfortran)))
7424 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
7425 (synopsis "Tools for the analysis of ordinary differential equations")
7427 "This package provides routines to find the root of nonlinear functions,
7428 and to perform steady-state and equilibrium analysis of @dfn{ordinary
7429 differential equations} (ODE). It includes routines that:
7432 @item generate gradient and jacobian matrices (full and banded),
7433 @item find roots of non-linear equations by the Newton-Raphson method,
7434 @item estimate steady-state conditions of a system of (differential) equations
7435 in full, banded or sparse form, using the Newton-Raphson method, or by
7436 dynamically running,
7437 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
7438 and 3-D partial differential equations, that have been converted to ordinary
7439 differential equations by numerical differencing (using the method-of-lines
7442 (license license:gpl2+)))
7444 (define-public r-abcanalysis
7446 (name "r-abcanalysis")
7451 (uri (cran-uri "ABCanalysis" version))
7453 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
7454 (properties `((upstream-name . "ABCanalysis")))
7455 (build-system r-build-system)
7456 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
7457 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
7458 (synopsis "Computed ABC Analysis")
7460 "Multivariate data sets often differ in several factors or derived statistical
7461 parameters, which have to be selected for a valid interpretation. Basing this
7462 selection on traditional statistical limits leads occasionally to the perception
7463 of losing information from a data set. This package provides tools to calculate
7464 these limits on the basis of the mathematical properties of the distribution of
7465 the analyzed items.")
7466 (license license:gpl3)))
7468 (define-public r-slam
7475 (uri (cran-uri "slam" version))
7477 (base32 "12fggw2c7hz3bpvsaqm24g3r6lbpq6jgli24g7x5j859iak5cqv9"))))
7478 (build-system r-build-system)
7479 (home-page "https://cran.r-project.org/web/packages/slam/")
7480 (synopsis "Sparse lightweight arrays and matrices")
7482 "This package contains data structures and algorithms for sparse arrays and matrices,
7483 based on index arrays and simple triplet representations, respectively.")
7484 (license license:gpl2)))
7486 (define-public r-manipulatewidget
7488 (name "r-manipulatewidget")
7493 (uri (cran-uri "manipulateWidget" version))
7495 (base32 "1vi71sjh7z1a880wffk8qqw7iysvk42q78giqxmm2sqz2a912qlx"))))
7497 `((upstream-name . "manipulateWidget")))
7498 (build-system r-build-system)
7500 `(("r-base64enc" ,r-base64enc)
7501 ("r-codetools" ,r-codetools)
7502 ("r-htmltools" ,r-htmltools)
7503 ("r-htmlwidgets" ,r-htmlwidgets)
7504 ("r-knitr" ,r-knitr)
7505 ("r-miniui" ,r-miniui)
7506 ("r-shiny" ,r-shiny)
7507 ("r-webshot" ,r-webshot)))
7508 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
7509 (synopsis "Add even more interactivity to interactive charts")
7511 "This package lets you create in just a few lines of R code a nice user interface to
7512 modify the data or the graphical parameters of one or multiple interactive
7513 charts. It is useful to quickly explore visually some data or for package
7514 developers to generate user interfaces easy to maintain.")
7515 (license license:gpl2+)))
7524 (uri (cran-uri "A3" version))
7526 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
7527 (properties `((upstream-name . "A3")))
7528 (build-system r-build-system)
7530 `(("r-pbapply" ,r-pbapply)
7531 ("r-xtable" ,r-xtable)))
7532 (home-page "https://cran.r-project.org/web/packages/A3/")
7533 (synopsis "Error metrics for predictive models")
7535 "This package supplies tools for tabulating and analyzing the results of predictive
7536 models. The methods employed are applicable to virtually any predictive model
7537 and make comparisons between different methodologies straightforward.")
7538 (license license:gpl2+)))
7540 (define-public r-infotheo
7547 (uri (cran-uri "infotheo" version))
7550 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
7551 (build-system r-build-system)
7552 (home-page "http://homepage.meyerp.com/software")
7553 (synopsis "Information-theoretic measures")
7555 "This package implements various measures of information theory based on
7556 several entropy estimators.")
7557 (license license:gpl3+)))
7559 (define-public r-abcoptim
7566 (uri (cran-uri "ABCoptim" version))
7568 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
7569 (properties `((upstream-name . "ABCoptim")))
7570 (build-system r-build-system)
7571 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
7572 (home-page "https://github.com/gvegayon/ABCoptim/")
7573 (synopsis "Optimization of Artificial Bee Colony algorithm")
7575 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
7576 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
7577 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
7578 algorithms, and uses only common control parameters such as colony size and
7579 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
7580 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
7581 This version is a work-in-progress and is written in R code.")
7582 (license license:expat)))
7584 (define-public r-abcp2
7591 (uri (cran-uri "ABCp2" version))
7593 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
7594 (properties `((upstream-name . "ABCp2")))
7595 (build-system r-build-system)
7596 (propagated-inputs `(("r-mass" ,r-mass)))
7597 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
7598 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
7600 "This package tests the goodness of fit of a distribution of offspring to the Normal,
7601 Poisson, and Gamma distribution and estimates the proportional paternity of the
7602 second male (P2) based on the best fit distribution.")
7603 (license license:gpl2)))
7605 (define-public r-abcrf
7612 (uri (cran-uri "abcrf" version))
7614 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
7615 (build-system r-build-system)
7617 `(("r-doparallel" ,r-doparallel)
7618 ("r-foreach" ,r-foreach)
7620 ("r-matrixstats" ,r-matrixstats)
7621 ("r-ranger" ,r-ranger)
7623 ("r-rcpparmadillo" ,r-rcpparmadillo)
7624 ("r-readr" ,r-readr)
7625 ("r-stringr" ,r-stringr)))
7626 (home-page "https://cran.r-project.org/web/packages/abcrf/")
7627 (synopsis "Approximate bayesian computation via random forests")
7629 "This package performs approximate bayesian computation (ABC) model choice and
7630 parameter inference via random forests. This machine learning tool named random
7631 forests (RF) can conduct selection among the highly complex models covered by
7633 (license license:gpl2+)))
7635 (define-public r-abctools
7642 (uri (cran-uri "abctools" version))
7644 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
7645 (build-system r-build-system)
7648 ("r-abind" ,r-abind)
7649 ("r-hmisc" ,r-hmisc)
7650 ("r-plyr" ,r-plyr)))
7651 (home-page "https://github.com/dennisprangle/abctools/")
7652 (synopsis "Tools for ABC analyses")
7654 "This @code{r-abctools} package provides tools for approximate Bayesian computation
7655 including summary statistic selection and assessing coverage. This includes
7656 recent dimension reduction algorithms to tune the choice of summary statistics,
7657 and coverage methods to tune the choice of threshold.")
7658 (license license:gpl2+)))
7660 (define-public r-ggstance
7667 (uri (cran-uri "ggstance" version))
7669 (base32 "0aqz3dn02cgij018a4sglqwrwr9dzzj12l8xr1064q7hfd4f64m1"))))
7670 (build-system r-build-system)
7672 `(("r-ggplot2" ,r-ggplot2)
7674 ("r-rlang" ,r-rlang)
7675 ("r-withr" ,r-withr)))
7676 (home-page "https://cran.r-project.org/web/packages/ggstance/")
7677 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
7679 "This package is a @code{r-ggplot2} extension that provides flipped components:
7681 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
7682 @item vertical versions of @code{r-ggplot2} positions.
7684 (license license:gpl3)))
7686 (define-public r-mosaiccore
7688 (name "r-mosaiccore")
7693 (uri (cran-uri "mosaicCore" version))
7695 (base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
7696 (properties `((upstream-name . "mosaicCore")))
7697 (build-system r-build-system)
7699 `(("r-dplyr" ,r-dplyr)
7700 ("r-lazyeval" ,r-lazyeval)
7702 ("r-rlang" ,r-rlang)
7703 ("r-tidyr" ,r-tidyr)))
7704 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
7705 (synopsis "Common utilities for mosaic family packages")
7707 "Common utilities used in other Mosaic family packages are collected here.")
7708 (license license:gpl2+)))
7710 (define-public r-ggformula
7712 (name "r-ggformula")
7717 (uri (cran-uri "ggformula" version))
7719 (base32 "04vdhg1bbc1psrx9ggaphz7cx4fw5xsmhkqpqfcg2w4ba2bjy46f"))))
7720 (build-system r-build-system)
7722 `(("r-ggforce" ,r-ggforce)
7723 ("r-ggplot2" ,r-ggplot2)
7724 ("r-ggstance" ,r-ggstance)
7725 ("r-magrittr" ,r-magrittr)
7726 ("r-mosaiccore" ,r-mosaiccore)
7727 ("r-rlang" ,r-rlang)
7728 ("r-stringr" ,r-stringr)
7729 ("r-tibble" ,r-tibble)))
7730 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
7731 (synopsis "Formula interface for the @code{r-ggplot2}")
7733 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
7734 gf_density(), and so on, bring the formula interface to ggplot(). This captures
7735 and extends the excellent simplicity of the lattice-graphics formula interface,
7736 while providing the intuitive capabilities of @code{r-ggplot2}.")
7737 (license license:expat)))
7739 (define-public r-mosaicdata
7741 (name "r-mosaicdata")
7746 (uri (cran-uri "mosaicData" version))
7748 (base32 "0cx5dg26ha7nzkdyghkbbd6ikncj60qv1538az77lfgn2jylvkbz"))))
7749 (properties `((upstream-name . "mosaicData")))
7750 (build-system r-build-system)
7751 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
7752 (synopsis "Data sets for project Mosaic")
7754 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
7755 used to teach mathematics, statistics, computation and modeling.")
7756 (license license:gpl2+)))
7758 (define-public r-raster
7765 (uri (cran-uri "raster" version))
7768 "144mva2dx7ffkq7z0fixr4z76ci1s4lizlyv5r7v07fd4nzg5hby"))))
7769 (build-system r-build-system)
7771 `(("r-rcpp" ,r-rcpp)
7773 (home-page "https://www.rspatial.org/")
7774 (synopsis "Geographic data analysis and modeling")
7776 "The package implements basic and high-level functions for reading,
7777 writing, manipulating, analyzing and modeling of gridded spatial data.
7778 Processing of very large files is supported.")
7779 (license license:gpl3+)))
7781 (define-public r-mosaic
7788 (uri (cran-uri "mosaic" version))
7790 (base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
7791 (build-system r-build-system)
7793 `(("r-broom" ,r-broom)
7794 ("r-dplyr" ,r-dplyr)
7795 ("r-ggdendro" ,r-ggdendro)
7796 ("r-ggformula" ,r-ggformula)
7797 ("r-ggplot2" ,r-ggplot2)
7798 ("r-ggrepel" ,r-ggrepel)
7800 ("r-gridextra" ,r-gridextra)
7801 ("r-lattice" ,r-lattice)
7802 ("r-latticeextra" ,r-latticeextra)
7803 ("r-lazyeval" ,r-lazyeval)
7805 ("r-matrix" ,r-matrix)
7806 ("r-mosaiccore" ,r-mosaiccore)
7807 ("r-mosaicdata" ,r-mosaicdata)
7808 ("r-readr" ,r-readr)
7809 ("r-tidyr" ,r-tidyr)))
7811 `(("r-knitr" ,r-knitr)))
7812 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
7813 (synopsis "Mathematics, statistics, and computation teaching utilities")
7815 "This package contain data sets and utilities from
7816 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
7817 statistics, computation and modeling. Project MOSAIC is a community of
7818 educators working to tie together aspects of quantitative work that students
7819 in science, technology, engineering and mathematics will need in their
7820 professional lives, but which are usually taught in isolation, if at all.")
7821 (license license:gpl2+)))
7823 (define-public r-abd
7830 (uri (cran-uri "abd" version))
7832 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
7833 (build-system r-build-system)
7835 `(("r-lattice" ,r-lattice)
7836 ("r-mosaic" ,r-mosaic)
7837 ("r-nlme" ,r-nlme)))
7838 (home-page "https://cran.r-project.org/web/packages/abd/")
7839 (synopsis "Analysis of biological data")
7841 "The @code{r-abd} package contains data sets and sample code for the Analysis of
7842 biological data by Michael Whitlock and Dolph Schluter.")
7843 (license license:gpl2)))
7845 (define-public r-svgui
7852 (uri (cran-uri "svGUI" version))
7854 (base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
7855 (properties `((upstream-name . "svGUI")))
7856 (build-system r-build-system)
7857 (home-page "https://github.com/SciViews/svGUI/")
7858 (synopsis "Functions for managing GUI clients in R")
7860 "The SciViews @code{svGUI} package eases the management of Graphical User
7861 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
7862 centralizes info about GUI elements currently used, and it dispatches GUI
7863 calls to the particular toolkits in use in function of the context.")
7864 (license license:gpl2)))
7866 (define-public r-svdialogs
7868 (name "r-svdialogs")
7873 (uri (cran-uri "svDialogs" version))
7875 (base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
7876 (properties `((upstream-name . "svDialogs")))
7877 (build-system r-build-system)
7880 ("zenity" ,zenity)))
7882 `(("r-rstudioapi" ,r-rstudioapi)
7883 ("r-svgui" ,r-svgui)))
7884 (home-page "https://github.com/SciViews/svDialogs/")
7885 (synopsis "Portable dialog boxes")
7887 "This package helps to construct standard dialog boxes for your GUI, including
7888 message boxes, input boxes, list, file or directory selection, and others. In
7889 case R cannot display GUI dialog boxes, a simpler command line version of these
7890 interactive elements is also provided as a fallback solution.")
7891 (license license:gpl2)))
7893 (define-public r-abe
7900 (uri (cran-uri "abe" version))
7903 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
7904 (build-system r-build-system)
7905 (home-page "https://cran.r-project.org/web/packages/abe/")
7906 (synopsis "Augmented backward elimination")
7908 "This package performs augmented backward elimination and checks the
7909 stability of the obtained model. Augmented backward elimination combines
7910 significance or information based criteria with the change in estimate to
7911 either select the optimal model for prediction purposes or to serve as a tool
7912 to obtain a practically sound, highly interpretable model.")
7913 (license license:gpl2+)))
7915 (define-public r-abf2
7922 (uri (cran-uri "abf2" version))
7924 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
7925 (build-system r-build-system)
7926 (home-page "https://cran.r-project.org/web/packages/abf2/")
7927 (synopsis "Load gap-free axon @code{r-abf2} files")
7929 "This package loads electrophysiology data from ABF2 files, as created by
7930 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
7931 mode are currently supported.")
7932 (license license:artistic2.0)))
7934 (define-public r-abhgenotyper
7936 (name "r-abhgenotyper")
7941 (uri (cran-uri "ABHgenotypeR" version))
7943 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
7944 (properties `((upstream-name . "ABHgenotypeR")))
7945 (build-system r-build-system)
7947 `(("r-ggplot2" ,r-ggplot2)
7948 ("r-reshape2" ,r-reshape2)))
7949 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
7950 (synopsis "Visualize and manipulate ABH genotypes")
7952 "The @code{r-abhgenotyper} package provides simple imputation,
7953 error-correction and plotting capacities for genotype data. The package is
7954 supposed to serve as an intermediate but independent analysis tool between the
7955 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
7956 not found in either TASSEL or @code{r-qtl} in addition to visualization of
7957 genotypes as \"graphical genotypes\".")
7958 (license license:gpl3)))
7960 (define-public r-furrr
7967 (uri (cran-uri "furrr" version))
7970 "1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
7971 (build-system r-build-system)
7973 `(("r-future" ,r-future)
7974 ("r-globals" ,r-globals)
7975 ("r-purrr" ,r-purrr)
7976 ("r-rlang" ,r-rlang)))
7977 (home-page "https://github.com/DavisVaughan/furrr")
7978 (synopsis "Apply mapping functions in parallel using futures")
7980 "This package provides implementations of the family of @code{map()}
7981 functions from the @code{purrr} package that can be resolved using any
7982 @code{future}-supported backend, e.g. parallel on the local machine or
7983 distributed on a compute cluster.")
7984 (license license:lgpl2.1+)))
7986 (define-public r-abjutils
7993 (uri (cran-uri "abjutils" version))
7995 (base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
7996 (build-system r-build-system)
7998 `(("r-devtools" ,r-devtools)
7999 ("r-dplyr" ,r-dplyr)
8000 ("r-furrr" ,r-furrr)
8001 ("r-future" ,r-future)
8004 ("r-magrittr" ,r-magrittr)
8005 ("r-progress" ,r-progress)
8006 ("r-purrr" ,r-purrr)
8007 ("r-readr" ,r-readr)
8008 ("r-rlang" ,r-rlang)
8009 ("r-rstudioapi" ,r-rstudioapi)
8010 ("r-scales" ,r-scales)
8011 ("r-stringi" ,r-stringi)
8012 ("r-stringr" ,r-stringr)
8013 ("r-tibble" ,r-tibble)
8014 ("r-tidyr" ,r-tidyr)))
8015 (home-page "https://github.com/abjur/abjutils/")
8016 (synopsis "Collection of tools for jurimetrical analysis")
8018 "This package implements general purpose tools, such as functions for
8019 sampling and basic manipulation of Brazilian lawsuits identification number.
8020 It also implements functions for text cleaning, such as accentuation
8022 (license license:expat)))
8024 (define-public r-abnormality
8026 (name "r-abnormality")
8031 (uri (cran-uri "abnormality" version))
8033 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
8034 (build-system r-build-system)
8036 `(("r-mass" ,r-mass)
8037 ("r-matrix" ,r-matrix)))
8038 (home-page "https://cran.r-project.org/web/packages/abnormality/")
8039 (synopsis "Measure a subject's abnormality with respect to a reference population")
8041 "This package contains functions to implement the methodology and
8042 considerations laid out by Marks et al. in the article \"Measuring abnormality
8043 in high dimensional spaces: applications in biomechanical gait analysis\".
8044 Using high-dimensional datasets to measure a subject's overall level of
8045 abnormality as compared to a reference population is often needed in outcomes
8047 (license license:expat)))
8049 (define-public r-abodoutlier
8051 (name "r-abodoutlier")
8056 (uri (cran-uri "abodOutlier" version))
8058 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
8059 (properties `((upstream-name . "abodOutlier")))
8060 (build-system r-build-system)
8062 `(("r-cluster" ,r-cluster)))
8063 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
8064 (synopsis "Angle-based outlier detection")
8066 "This package performs angle-based outlier detection on a given data
8067 frame. It offers three methods to process data:
8069 @item full but slow implementation using all the data that has cubic
8071 @item a fully randomized method;
8072 @item a method using k-nearest neighbours.
8074 These algorithms are well suited for high dimensional data outlier
8076 (license license:expat)))
8078 (define-public r-abps
8085 (uri (cran-uri "ABPS" version))
8087 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
8088 (properties `((upstream-name . "ABPS")))
8089 (build-system r-build-system)
8090 (propagated-inputs `(("r-kernlab" ,r-kernlab)))
8091 (home-page "https://cran.r-project.org/web/packages/ABPS/")
8092 (synopsis "Abnormal blood profile score to detect blood doping")
8094 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
8095 The ABPS is a part of the Athlete biological passport program of the World
8096 anti-doping agency, which combines several blood parameters into a single
8097 score in order to detect blood doping. The package also contains functions to
8098 calculate other scores used in anti-doping programs, such as the ratio of
8099 hemoglobin to reticulocytes (OFF-score), as well as example data.")
8100 (license license:gpl2+)))
8102 (define-public r-parmigene
8104 (name "r-parmigene")
8109 (uri (cran-uri "parmigene" version))
8112 "1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
8113 (build-system r-build-system)
8114 (home-page "https://cran.r-project.org/web/packages/parmigene/")
8115 (synopsis "Mutual information estimation for gene network reconstruction")
8117 "This package provides a parallel estimation of the mutual information
8118 based on entropy estimates from k-nearest neighbors distances and algorithms
8119 for the reconstruction of gene regulatory networks.")
8120 (license license:agpl3+)))
8122 (define-public r-pscl
8129 (uri (cran-uri "pscl" version))
8131 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
8132 (build-system r-build-system)
8134 `(("r-mass" ,r-mass)))
8135 (home-page "https://github.com/atahk/pscl/")
8136 (synopsis "Political science computational laboratory")
8138 "The @code{pscl} is an R package providing classes and methods for:
8140 @item Bayesian analysis of roll call data (item-response models);
8141 @item elementary Bayesian statistics;
8142 @item maximum likelihood estimation of zero-inflated and hurdle models for count
8144 @item utility functions.
8146 (license license:gpl2)))
8148 (define-public r-accelmissing
8150 (name "r-accelmissing")
8155 (uri (cran-uri "accelmissing" version))
8157 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
8158 (build-system r-build-system)
8160 `(("r-mice" ,r-mice)
8161 ("r-pscl" ,r-pscl)))
8162 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
8163 (synopsis "Missing value imputation for accelerometer data")
8165 "This package provides a statistical method to impute the missing values in
8166 accelerometer data. The methodology includes both parametric and
8167 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
8168 model. It also provides multiple functions to preprocess the accelerometer data
8169 previous to the missing data imputation. These include detecting the wearing
8170 and the non-wearing time, selecting valid days and subjects, and creating plots.")
8171 (license license:gpl2+)))
8173 (define-public r-mhsmm
8180 (uri (cran-uri "mhsmm" version))
8182 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
8183 (build-system r-build-system)
8184 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8185 (home-page "https://github.com/jaredo/mhsmm/")
8186 (synopsis "Inference for hidden Markov and semi-Markov models")
8188 "The @code{r-mhsmm} package implements estimation and prediction methods for
8189 hidden Markov and semi-Markov models for multiple observation sequences. Such
8190 techniques are of interest when observed data is thought to be dependent on some
8191 unobserved (or hidden) state. Also, this package is suitable for equidistant
8192 time series data, with multivariate and/or missing data. Allows user defined
8193 emission distributions.")
8194 (license license:gpl2+)))
8196 (define-public r-nleqslv
8203 (uri (cran-uri "nleqslv" version))
8205 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
8206 (build-system r-build-system)
8207 (native-inputs `(("gfortran" ,gfortran)))
8208 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
8209 (synopsis "Solve systems of nonlinear equations")
8211 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
8212 Broyden or a Newton method with a choice of global strategies such as line
8213 search and trust region. There are options for using a numerical or user
8214 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
8215 singular or ill-conditioned Jacobian.")
8216 (license license:gpl2+)))
8218 (define-public r-physicalactivity
8220 (name "r-physicalactivity")
8225 (uri (cran-uri "PhysicalActivity" version))
8227 (base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
8229 `((upstream-name . "PhysicalActivity")))
8230 (build-system r-build-system)
8231 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
8232 (synopsis "Procesing accelerometer data for physical activity measurement")
8234 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
8235 for classification of monitor wear and nonwear time intervals in accelerometer
8236 data collected to assess physical activity. The package also contains functions
8237 for making plots of accelerometer data and obtaining the summary of various
8238 information including daily monitor wear time and the mean monitor wear time
8239 during valid days. The revised package version 0.2-1 improved the functions
8240 regarding speed, robustness and add better support for time zones and daylight
8241 saving. In addition, several functions were added:
8243 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
8244 @item the @code{markPAI} can categorize physical activity intensity level based
8245 on user-defined cut-points of accelerometer counts.
8247 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
8248 @code{queryActigraph} functions.")
8249 (license license:gpl3+)))
8251 (define-public r-acc
8258 (uri (cran-uri "acc" version))
8260 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
8261 (build-system r-build-system)
8263 `(("r-circlize" ,r-circlize)
8265 ("r-ggplot2" ,r-ggplot2)
8266 ("r-iterators" ,r-iterators)
8267 ("r-mhsmm" ,r-mhsmm)
8268 ("r-nleqslv" ,r-nleqslv)
8269 ("r-physicalactivity" ,r-physicalactivity)
8271 ("r-r-utils" ,r-r-utils)
8273 ("r-rcpparmadillo" ,r-rcpparmadillo)
8274 ("r-rsqlite" ,r-rsqlite)
8276 (home-page "https://cran.r-project.org/web/packages/acc/")
8277 (synopsis "Exploring accelerometer data")
8279 "This package processes accelerometer data from uni-axial and tri-axial devices
8280 and generates data summaries. Also, includes functions to plot, analyze, and
8281 simulate accelerometer data.")
8282 (license license:gpl2+)))
8284 (define-public r-rbenchmark
8286 (name "r-rbenchmark")
8291 (uri (cran-uri "rbenchmark" version))
8293 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
8294 (build-system r-build-system)
8295 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
8296 (synopsis "Benchmarking routine for R")
8298 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
8299 and is intended to facilitate benchmarking of arbitrary R code. The library
8300 consists of just one function, benchmark, which is a simple wrapper around
8301 system.time. Given a specification of the benchmarking process (counts of
8302 replications, evaluation environment) and an arbitrary number of expressions,
8303 benchmark evaluates each of the expressions in the specified environment,
8304 replicating the evaluation as many times as specified, and returning the results
8305 conveniently wrapped into a data frame.")
8306 (license license:gpl2+)))
8308 (define-public r-mitools
8315 (uri (cran-uri "mitools" version))
8318 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
8319 (build-system r-build-system)
8320 (propagated-inputs `(("r-dbi" ,r-dbi)))
8321 (home-page "https://cran.r-project.org/web/packages/mitools/")
8322 (synopsis "Tools for multiple imputation of missing data")
8324 "This package provides tools to perform analyses and combine results from
8325 multiple-imputation datasets.")
8326 (license license:gpl2)))
8328 (define-public r-magick
8335 (uri (cran-uri "magick" version))
8338 "1y1p2blkg0h6061ay7mdwssxbswgrc25raffp6d8d9cqhdmsa72s"))))
8339 (build-system r-build-system)
8341 `(("imagemagick" ,imagemagick)
8344 `(("r-curl" ,r-curl)
8345 ("r-magrittr" ,r-magrittr)
8346 ("r-rcpp" ,r-rcpp)))
8348 `(("pkg-config" ,pkg-config)
8349 ("r-knitr" ,r-knitr)))
8350 (home-page "https://github.com/ropensci/magick")
8351 (synopsis "Advanced graphics and image-processing in R")
8353 "This package provides bindings to ImageMagick, a comprehensive image
8354 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
8355 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
8356 operations are vectorized via the Magick++ STL meaning they operate either on
8357 a single frame or a series of frames for working with layers, collages, or
8358 animation. In RStudio, images are automatically previewed when printed to the
8359 console, resulting in an interactive editing environment.")
8360 (license license:expat)))
8362 (define-public r-survey
8369 (uri (cran-uri "survey" version))
8372 "1q9x0s86s72gl43zj49gypg6jj2b78xjvxr4lmy5147s9h7z8lxh"))))
8373 (build-system r-build-system)
8375 `(("r-lattice" ,r-lattice)
8376 ("r-matrix" ,r-matrix)
8377 ("r-minqa" ,r-minqa)
8378 ("r-mitools" ,r-mitools)
8379 ("r-numderiv" ,r-numderiv)
8380 ("r-survival" ,r-survival)))
8381 (home-page "http://r-survey.r-forge.r-project.org/survey/")
8382 (synopsis "Analysis of complex survey samples")
8384 "This package provides tools for the analysis of complex survey samples.
8385 The provided features include: summary statistics, two-sample tests, rank
8386 tests, generalised linear models, cumulative link models, Cox models,
8387 loglinear models, and general maximum pseudolikelihood estimation for
8388 multistage stratified, cluster-sampled, unequally weighted survey samples;
8389 variances by Taylor series linearisation or replicate weights;
8390 post-stratification, calibration, and raking; two-phase subsampling designs;
8391 graphics; PPS sampling without replacement; principal components, and factor
8393 ;; Either version of the GPL.
8394 (license (list license:gpl2 license:gpl3))))
8396 (define-public r-gee
8403 (uri (cran-uri "gee" version))
8406 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
8407 (properties `((upstream-name . "gee")))
8408 (build-system r-build-system)
8410 `(("gfortran" ,gfortran)))
8411 (home-page "https://cran.r-project.org/web/packages/gee/")
8412 (synopsis "Generalized estimation equation solver")
8414 "This package provides a solver for generalized estimation equations.")
8415 (license license:gpl2)))
8417 (define-public r-tab
8424 (uri (cran-uri "tab" version))
8427 "0ds8n6gncidb66in7hlqkcmil5yfsf7ihqvmls789hrm2iz9xlfm"))))
8428 (properties `((upstream-name . "tab")))
8429 (build-system r-build-system)
8431 `(("r-dplyr" ,r-dplyr)
8433 ("r-knitr" ,r-knitr)
8435 ("r-survey" ,r-survey)
8436 ("r-survival" ,r-survival)
8437 ("r-xtable" ,r-xtable)))
8438 (home-page "https://cran.r-project.org/web/packages/tab/")
8439 (synopsis "Create summary tables for statistical reports")
8441 "This package contains functions for creating various types of summary
8442 tables, e.g. comparing characteristics across levels of a categorical variable
8443 and summarizing fitted generalized linear models, generalized estimating
8444 equations, and Cox proportional hazards models. Functions are available to
8445 handle data from simple random samples as well as complex surveys.")
8446 (license license:gpl3+)))
8448 (define-public r-dvmisc
8455 (uri (cran-uri "dvmisc" version))
8457 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
8458 (build-system r-build-system)
8460 `(("r-cubature" ,r-cubature)
8461 ("r-data-table" ,r-data-table)
8462 ("r-dplyr" ,r-dplyr)
8463 ("r-ggplot2" ,r-ggplot2)
8465 ("r-mvtnorm" ,r-mvtnorm)
8466 ("r-pracma" ,r-pracma)
8467 ("r-rbenchmark" ,r-rbenchmark)
8469 ("r-survey" ,r-survey)
8471 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
8472 (synopsis "Faster computation of common statistics and miscellaneous functions")
8474 "This package implements faster versions of base R functions (e.g. mean, standard
8475 deviation, covariance, weighted mean), mostly written in C++, along with
8476 miscellaneous functions for various purposes (e.g. create the histogram with
8477 fitted probability density function or probability mass function curve, create
8478 the body mass index groups, assess the linearity assumption in logistic
8480 (license license:gpl2)))
8482 (define-public r-accelerometry
8484 (name "r-accelerometry")
8489 (uri (cran-uri "accelerometry" version))
8491 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
8492 (build-system r-build-system)
8494 `(("r-dvmisc" ,r-dvmisc)
8495 ("r-rcpp" ,r-rcpp)))
8496 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
8497 (synopsis "Functions for processing accelerometer data")
8499 "This package provides a collection of functions that perform operations on
8500 time-series accelerometer data, such as identify the non-wear time, flag minutes
8501 that are part of an activity bout, and find the maximum 10-minute average count
8502 value. The functions are generally very flexible, allowing for a variety of
8503 algorithms to be implemented.")
8504 (license license:gpl3)))
8506 (define-public r-absim
8513 (uri (cran-uri "AbSim" version))
8515 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
8516 (properties `((upstream-name . "AbSim")))
8517 (build-system r-build-system)
8520 ("r-powerlaw" ,r-powerlaw)))
8521 (home-page "https://cran.r-project.org/web/packages/AbSim/")
8522 (synopsis "Time resolved simulations of antibody repertoires")
8524 "This package provides simulation methods for the evolution of antibody repertoires.
8525 The heavy and light chain variable region of both human and C57BL/6 mice can
8526 be simulated in a time-dependent fashion. Both single lineages using one set of
8527 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
8528 with an initial V-D-J recombination event, starting the first phylogenetic tree.
8529 Upon completion, the main loop of the algorithm begins, with each iteration
8530 representing one simulated time step. Various mutation events are possible at
8531 each time step, contributing to a diverse final repertoire.")
8532 (license license:gpl2)))
8534 (define-public r-quic
8541 (uri (cran-uri "QUIC" version))
8543 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
8544 (properties `((upstream-name . "QUIC")))
8545 (build-system r-build-system)
8546 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
8547 (synopsis "Regularized sparse inverse covariance matrix estimation")
8549 "This package implements the regularized Gaussian maximum likelihood
8550 estimation of the inverse of a covariance matrix. It uses Newton's method and
8551 coordinate descent to solve the regularized inverse covariance matrix
8552 estimation problem.")
8553 ;; The project home page states that the release is under GPLv3 or later.
8554 ;; The CRAN page only says GPL-3.
8555 (license license:gpl3+)))
8557 (define-public r-abundant
8564 (uri (cran-uri "abundant" version))
8566 (base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
8567 (build-system r-build-system)
8569 `(("r-quic" ,r-quic)))
8570 (home-page "https://cran.r-project.org/web/packages/abundant/")
8571 (synopsis "Abundant regression and high-dimensional principal fitted components")
8573 "This package provides tools to fit and predict with the high-dimensional
8574 principal fitted components model. This model is described by Cook, Forzani,
8575 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
8576 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
8577 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
8578 (license license:gpl2+)))
8580 (define-public r-ac3net
8587 (uri (cran-uri "Ac3net" version))
8589 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
8590 (properties `((upstream-name . "Ac3net")))
8591 (build-system r-build-system)
8593 `(("r-data-table" ,r-data-table)))
8594 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
8595 (synopsis "Inferring directional conservative causal core gene networks")
8596 (description "This package infers directional Conservative causal core
8597 (gene) networks (C3NET). This is a version of the algorithm C3NET with
8598 directional network.")
8599 (license license:gpl3+)))
8601 (define-public r-aca
8608 (uri (cran-uri "ACA" version))
8610 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
8611 (properties `((upstream-name . "ACA")))
8612 (build-system r-build-system)
8613 (home-page "https://cran.r-project.org/web/packages/ACA/")
8614 (synopsis "Abrupt change-point or aberration detection in point series")
8616 "This package offers an interactive function for the detection of breakpoints in
8618 ;; Any version of the GPL
8619 (license (list license:gpl2+ license:gpl3+))))
8621 (define-public r-acceptancesampling
8623 (name "r-acceptancesampling")
8628 (uri (cran-uri "AcceptanceSampling" version))
8630 (base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
8632 `((upstream-name . "AcceptanceSampling")))
8633 (build-system r-build-system)
8634 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
8635 (synopsis "Creation and evaluation of acceptance sampling plans")
8637 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
8638 acceptance sampling plans. Acceptance sampling is a methodology commonly used
8639 in quality control and improvement. International standards of acceptance
8640 sampling provide sampling plans for specific circumstances. The aim of this
8641 package is to provide an easy-to-use interface to visualize single, double or
8642 multiple sampling plans. In addition, methods have been provided to enable the
8643 user to assess sampling plans against pre-specified levels of performance, as
8644 measured by the probability of acceptance for a given level of quality in the
8646 (license license:gpl3+)))
8648 (define-public r-acclma
8655 (uri (cran-uri "ACCLMA" version))
8657 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
8658 (properties `((upstream-name . "ACCLMA")))
8659 (build-system r-build-system)
8660 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
8661 (synopsis "ACC & LMA graph plotting")
8663 "This package contains a function that imports data from a @acronym{CSV,
8664 Comma-Separated Values} file, or uses manually entered data from the format (x,
8665 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
8666 Curve} vs @acronym{LOI, Line of Independence} graph and
8667 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
8668 function is @code{plotLMA} (source file, header) that takes a data set and plots the
8669 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
8670 string) was passed, a manual data entry window is opened. The header parameter
8671 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
8672 a header row or not. The dataset should contain only one independent variable
8673 (x) and one dependent variable (y) and can contain a weight for each
8675 (license license:gpl2)))
8677 (define-public r-aspi
8684 (uri (cran-uri "aspi" version))
8686 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
8687 (build-system r-build-system)
8689 "https://cran.r-project.org/web/packages/aspi/")
8691 "Analysis of symmetry of parasitic infections")
8693 "This package provides tools for the analysis and visualization of bilateral
8694 asymmetry in parasitic infections.")
8695 (license license:gpl3+)))
8697 (define-public r-sandwich
8704 (uri (cran-uri "sandwich" version))
8707 "1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
8708 (build-system r-build-system)
8710 `(("r-zoo" ,r-zoo)))
8711 (home-page "https://cran.r-project.org/web/packages/sandwich/")
8712 (synopsis "Robust Covariance Matrix Estimators")
8714 "This package provides model-robust standard error estimators for
8715 cross-sectional, time series, clustered, panel, and longitudinal data.")
8716 ;; Either version of the license.
8717 (license (list license:gpl2 license:gpl3))))
8719 (define-public r-th-data
8726 (uri (cran-uri "TH.data" version))
8729 "0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
8730 (properties `((upstream-name . "TH.data")))
8731 (build-system r-build-system)
8733 `(("r-mass" ,r-mass)
8734 ("r-survival" ,r-survival)))
8735 (home-page "https://cran.r-project.org/web/packages/TH.data/")
8736 (synopsis "Shared data sets")
8738 "This package contains supporting data sets that are used in other
8739 packages maintained by Torsten Hothorn.")
8740 (license license:gpl3)))
8742 (define-public r-multcomp
8749 (uri (cran-uri "multcomp" version))
8752 "1nszi22rcc551yc75h9cdfkdqsxw1rz30vadazmpyzihp1bh63yk"))))
8753 (build-system r-build-system)
8755 `(("r-codetools" ,r-codetools)
8756 ("r-mvtnorm" ,r-mvtnorm)
8757 ("r-sandwich" ,r-sandwich)
8758 ("r-survival" ,r-survival)
8759 ("r-th-data" ,r-th-data)))
8760 (home-page "https://cran.r-project.org/web/packages/multcomp/")
8761 (synopsis "Simultaneous inference in general parametric models")
8763 "Simultaneous tests and confidence intervals for general linear
8764 hypotheses in parametric models, including linear, generalized linear, linear
8765 mixed effects, and survival models. The package includes demos reproducing
8766 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
8767 Hothorn, Westfall, 2010, CRC Press).")
8768 (license license:gpl2)))
8770 (define-public r-emmeans
8777 (uri (cran-uri "emmeans" version))
8780 "0h884qn4cip03w0h5psrz5y9zkm2wppklrhdz2chm2xk13zqnq5k"))))
8781 (build-system r-build-system)
8783 `(("r-estimability" ,r-estimability)
8784 ("r-mvtnorm" ,r-mvtnorm)
8785 ("r-numderiv" ,r-numderiv)
8787 ("r-xtable" ,r-xtable)))
8789 `(("r-knitr" ,r-knitr)))
8790 (home-page "https://github.com/rvlenth/emmeans")
8791 (synopsis "Estimated marginal means, aka least-squares means")
8793 "This package provides tools to obtain @dfn{estimated marginal
8794 means} (EMMs) for many linear, generalized linear, and mixed models. It can
8795 be used to compute contrasts or linear functions of EMMs, trends, and
8796 comparisons of slopes.")
8797 ;; Either version of the license.
8798 (license (list license:gpl2 license:gpl3))))
8800 (define-public r-pwr
8807 (uri (cran-uri "pwr" version))
8810 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
8811 (build-system r-build-system)
8813 `(("r-knitr" ,r-knitr)))
8814 (home-page "https://github.com/heliosdrm/pwr")
8815 (synopsis "Basic functions for power analysis")
8817 "This package provides power analysis functions along the lines of
8819 (license license:gpl3+)))
8821 (define-public r-libcoin
8828 (uri (cran-uri "libcoin" version))
8831 "1cm9x1dlg9f7fh7n5nw3x4a7rl88c7ylrlc8x3rx4mq5w1j42x0a"))))
8832 (build-system r-build-system)
8833 (propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
8834 (home-page "https://cran.r-project.org/web/packages/libcoin")
8835 (synopsis "Linear test statistics for permutation inference")
8837 "This package provides basic infrastructure for linear test statistics
8838 and permutation inference in the framework of Strasser and Weber (1999).")
8839 (license license:gpl2)))
8841 (define-public r-coin
8848 (uri (cran-uri "coin" version))
8851 "0qi03fyqw42a2vnqcia5l2m1mzyarj2q1iblknx9n19bdsd53qjx"))))
8852 (build-system r-build-system)
8854 `(("r-libcoin" ,r-libcoin)
8855 ("r-matrixstats" ,r-matrixstats)
8856 ("r-modeltools" ,r-modeltools)
8857 ("r-multcomp" ,r-multcomp)
8858 ("r-mvtnorm" ,r-mvtnorm)
8859 ("r-survival" ,r-survival)))
8860 (home-page "http://coin.r-forge.r-project.org")
8861 (synopsis "Conditional inference procedures in a permutation test framework")
8863 "This package provides conditional inference procedures for the general
8864 independence problem including two-sample, K-sample (non-parametric ANOVA),
8865 correlation, censored, ordered and multivariate problems.")
8866 (license license:gpl2)))
8868 (define-public r-bayesplot
8870 (name "r-bayesplot")
8875 (uri (cran-uri "bayesplot" version))
8878 "0aqy4bfjq1fmds0vpacsmqih528cp8wk4v4w0balzkph6zqzpwcl"))))
8879 (build-system r-build-system)
8881 `(("pandoc" ,ghc-pandoc)
8882 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
8884 `(("r-knitr" ,r-knitr)))
8886 `(("r-dplyr" ,r-dplyr)
8887 ("r-ggplot2" ,r-ggplot2)
8888 ("r-ggridges" ,r-ggridges)
8890 ("r-reshape2" ,r-reshape2)
8891 ("r-rlang" ,r-rlang)
8892 ("r-tibble" ,r-tibble)
8893 ("r-tidyselect" ,r-tidyselect)))
8894 (home-page "https://mc-stan.org/bayesplot")
8895 (synopsis "Plotting for Bayesian models")
8897 "This package provides plotting functions for posterior analysis, model
8898 checking, and MCMC diagnostics. The package is designed not only to provide
8899 convenient functionality for users, but also a common set of functions that
8900 can be easily used by developers working on a variety of R packages for
8901 Bayesian modeling.")
8902 (license license:gpl3+)))
8904 (define-public r-tmb
8911 (uri (cran-uri "TMB" version))
8914 "0lly12hdi99iklwr0vg9xkyhi038w4gncbf895qcwbndmqp0lx44"))))
8915 (properties `((upstream-name . "TMB")))
8916 (build-system r-build-system)
8918 `(("r-matrix" ,r-matrix)
8919 ("r-rcppeigen" ,r-rcppeigen)))
8920 (home-page "http://tmb-project.org")
8921 (synopsis "Template model builder: a general random effect tool")
8923 "With this tool, a user should be able to quickly implement complex
8924 random effect models through simple C++ templates. The package combines
8925 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
8926 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
8927 from R) to obtain an efficient implementation of the applied Laplace
8928 approximation with exact derivatives. Key features are: Automatic sparseness
8929 detection, parallelism through BLAS and parallel user templates.")
8930 (license license:gpl2)))
8932 (define-public r-sjstats
8939 (uri (cran-uri "sjstats" version))
8941 (base32 "17b1fcrhgjw66qa8zk2jj1bvz3vp5bnjn3p4y1wsg5ng5nxq8jz0"))))
8942 (build-system r-build-system)
8944 `(("r-bayestestr" ,r-bayestestr)
8945 ("r-broom" ,r-broom)
8946 ("r-dplyr" ,r-dplyr)
8947 ("r-effectsize" ,r-effectsize)
8948 ("r-emmeans" ,r-emmeans)
8949 ("r-insight" ,r-insight)
8951 ("r-magrittr" ,r-magrittr)
8953 ("r-modelr" ,r-modelr)
8954 ("r-parameters" ,r-parameters)
8955 ("r-performance" ,r-performance)
8956 ("r-purrr" ,r-purrr)
8957 ("r-rlang" ,r-rlang)
8958 ("r-sjlabelled" ,r-sjlabelled)
8959 ("r-sjmisc" ,r-sjmisc)
8960 ("r-tidyr" ,r-tidyr)))
8961 (home-page "https://github.com/strengejacke/sjstats")
8962 (synopsis "Functions for common statistical computations")
8964 "This package provides a collection of convenient functions for common
8965 statistical computations, which are not directly provided by R's @code{base}
8966 or @code{stats} packages. This package aims at providing, first, shortcuts
8967 for statistical measures, which otherwise could only be calculated with
8968 additional effort. Second, these shortcut functions are generic, and can be
8969 applied not only to vectors, but also to other objects as well. The focus of
8970 most functions lies on summary statistics or fit measures for regression
8971 models, including generalized linear models, mixed effects models and Bayesian
8973 (license license:gpl3)))
8975 (define-public r-glmmtmb
8982 (uri (cran-uri "glmmTMB" version))
8985 "1a35hxcxz1cdm3zd5s7fyjaw2qs00hkacgr7h9130amygc1262ab"))))
8986 (properties `((upstream-name . "glmmTMB")))
8987 (build-system r-build-system)
8989 `(("r-lme4" ,r-lme4)
8990 ("r-matrix" ,r-matrix)
8992 ("r-rcppeigen" ,r-rcppeigen)
8995 `(("r-knitr" ,r-knitr))) ; for vignettes
8996 (home-page "https://github.com/glmmTMB")
8997 (synopsis "Generalized linear mixed models")
8999 "Fit linear and generalized linear mixed models with various extensions,
9000 including zero-inflation. The models are fitted using maximum likelihood
9001 estimation via the Template Model Builder. Random effects are assumed to be
9002 Gaussian on the scale of the linear predictor and are integrated out using the
9003 Laplace approximation. Gradients are calculated using automatic
9005 (license license:agpl3+)))
9007 (define-public r-bayestestr
9009 (name "r-bayestestr")
9014 (uri (cran-uri "bayestestR" version))
9017 "1nrycyzznzrlwnfwk1w3ixdq0bj82nri9kb2qiaiw8wwzwrsl1hd"))))
9018 (properties `((upstream-name . "bayestestR")))
9019 (build-system r-build-system)
9021 `(("r-insight" ,r-insight)))
9023 `(("r-knitr" ,r-knitr)))
9024 (home-page "https://github.com/easystats/bayestestR")
9025 (synopsis "Describe Bayesian models and posterior distributions")
9027 "This package provides utilities to understand and describe posterior
9028 distributions and Bayesian models. It includes point-estimates such as
9029 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
9030 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
9031 ROPE percentage and pd).")
9032 (license license:gpl3)))
9034 (define-public r-performance
9036 (name "r-performance")
9041 (uri (cran-uri "performance" version))
9044 "0gw165wm2a0vjsvyll8z9k6qd156z3jf4priy1r745v63x4mnb5k"))))
9045 (build-system r-build-system)
9047 `(("r-bayestestr" ,r-bayestestr)
9048 ("r-insight" ,r-insight)))
9049 (home-page "https://easystats.github.io/performance/")
9050 (synopsis "Assessment of regression models performance")
9052 "This package provides utilities for computing measures to assess model
9053 quality, which are not directly provided by R's @code{base} or @code{stats}
9054 packages. These include e.g. measures like r-squared, intraclass correlation
9055 coefficient, root mean squared error or functions to check models for
9056 overdispersion, singularity or zero-inflation and more. Functions apply to a
9057 large variety of regression models, including generalized linear models, mixed
9058 effects models and Bayesian models.")
9059 (license license:gpl3)))
9061 (define-public r-ggeffects
9063 (name "r-ggeffects")
9068 (uri (cran-uri "ggeffects" version))
9071 "1bqvbhw5la3cj3v0gwava117ff24b1p450azln402gsxgfl3vw7r"))))
9072 (build-system r-build-system)
9074 `(("r-insight" ,r-insight)
9076 ("r-sjlabelled" ,r-sjlabelled)))
9078 `(("r-knitr" ,r-knitr)))
9079 (home-page "https://github.com/strengejacke/ggeffects")
9080 (synopsis "Create tidy data frames of marginal effects for ggplot")
9082 "This package provides tools to compute marginal effects from statistical
9083 models and return the result as tidy data frames. These data frames are ready
9084 to use with the @code{ggplot2} package. Marginal effects can be calculated
9085 for many different models. Interaction terms, splines and polynomial terms
9086 are also supported. The two main functions are @code{ggpredict()} and
9087 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
9088 results using @code{ggplot2}.")
9089 (license license:gpl3)))
9091 (define-public r-effectsize
9093 (name "r-effectsize")
9098 (uri (cran-uri "effectsize" version))
9101 "1n5b5434sd8f1v95bfjwg92v879rkaj8zpm6ldnrg0kgfb0gy6q4"))))
9102 (properties `((upstream-name . "effectsize")))
9103 (build-system r-build-system)
9105 `(("r-bayestestr" ,r-bayestestr)
9106 ("r-insight" ,r-insight)
9107 ("r-parameters" ,r-parameters)))
9109 `(("r-knitr" ,r-knitr)))
9110 (home-page "https://github.com/easystats/effectsize")
9111 (synopsis "Indices of effect size and standardized parameters")
9113 "This package provides utilities to work with indices of effect size and
9114 standardized parameters for a wide variety of models, allowing computation and
9115 conversion of indices such as Cohen's d, r, odds, etc.")
9116 (license license:gpl3)))
9118 (define-public r-sjplot
9125 (uri (cran-uri "sjPlot" version))
9127 (base32 "0b7k0mshkk8k26w11xbxkb5v0klhq279zn2xdz83cn8k791xkqyd"))))
9128 (properties `((upstream-name . "sjPlot")))
9129 (build-system r-build-system)
9131 `(("r-bayestestr" ,r-bayestestr)
9132 ("r-dplyr" ,r-dplyr)
9133 ("r-effectsize" ,r-effectsize)
9134 ("r-ggeffects" ,r-ggeffects)
9135 ("r-ggplot2" ,r-ggplot2)
9136 ("r-insight" ,r-insight)
9137 ("r-knitr" ,r-knitr)
9139 ("r-parameters" ,r-parameters)
9140 ("r-performance" ,r-performance)
9141 ("r-purrr" ,r-purrr)
9142 ("r-rlang" ,r-rlang)
9143 ("r-scales" ,r-scales)
9144 ("r-sjlabelled" ,r-sjlabelled)
9145 ("r-sjmisc" ,r-sjmisc)
9146 ("r-sjstats" ,r-sjstats)
9147 ("r-tidyr" ,r-tidyr)))
9149 `(("r-knitr" ,r-knitr)))
9150 (home-page "https://strengejacke.github.io/sjPlot/")
9151 (synopsis "Data visualization for statistics in social science")
9153 "This package represents a collection of plotting and table output
9154 functions for data visualization. Results of various statistical
9155 analyses (that are commonly used in social sciences) can be visualized using
9156 this package, including simple and cross tabulated frequencies, histograms,
9157 box plots, (generalized) linear models, mixed effects models, principal
9158 component analysis and correlation matrices, cluster analyses, scatter plots,
9159 stacked scales, effects plots of regression models (including interaction
9160 terms) and much more. This package supports labelled data.")
9161 (license license:gpl3)))
9163 (define-public r-ini
9170 (uri (cran-uri "ini" version))
9173 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
9174 (build-system r-build-system)
9175 (home-page "https://github.com/dvdscripter/ini")
9176 (synopsis "Read and write configuration files")
9178 "This package provides tools to parse simple @code{.ini} configuration
9179 files to an structured list. Users can manipulate this resulting list with
9180 @code{lapply()} functions. This same structured list can be used to write
9181 back to file after modifications.")
9182 (license license:gpl3)))
9191 (uri (cran-uri "gh" version))
9194 "1bc9bn1078s664hc806dh0y1ncxif77q479rfmxfir9z7hwaz7yy"))))
9195 (build-system r-build-system)
9200 ("r-jsonlite" ,r-jsonlite)))
9201 (home-page "https://github.com/r-lib/gh#readme")
9202 (synopsis "Access the GitHub API via R")
9204 "This package provides a minimal R client to access the GitHub API.")
9205 (license license:expat)))
9214 (uri (cran-uri "fs" version))
9217 "09rpazjba9jy448j6rq989fw3wv3xhng7fn8p8gr22gyx0n0y1zr"))))
9218 (build-system r-build-system)
9220 `(("pkg-config" ,pkg-config)
9221 ("r-knitr" ,r-knitr)))
9222 (home-page "https://fs.r-lib.org")
9223 (synopsis "Cross-platform file system operations based on libuv")
9225 "This package provides a cross-platform interface to file system
9226 operations, built on top of the libuv C library.")
9227 (license license:gpl3)))
9229 (define-public r-clisymbols
9231 (name "r-clisymbols")
9236 (uri (cran-uri "clisymbols" version))
9239 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
9240 (build-system r-build-system)
9241 (home-page "https://github.com/gaborcsardi/clisymbols")
9242 (synopsis "Unicode symbols at the R prompt")
9244 "This package provides a small subset of Unicode symbols, that are useful
9245 when building command line applications. They fall back to alternatives on
9246 terminals that do not support Unicode.")
9247 (license license:expat)))
9249 (define-public r-usethis
9256 (uri (cran-uri "usethis" version))
9259 "0vwxsnq615mwc706a4a71gyy0hmvnllbh249gzm7vl3ym5cr0cv0"))))
9260 (build-system r-build-system)
9263 ("r-clipr" ,r-clipr)
9264 ("r-crayon" ,r-crayon)
9269 ("r-git2r" ,r-git2r)
9271 ("r-purrr" ,r-purrr)
9272 ("r-rematch2" ,r-rematch2)
9273 ("r-rlang" ,r-rlang)
9274 ("r-rprojroot" ,r-rprojroot)
9275 ("r-rstudioapi" ,r-rstudioapi)
9276 ("r-whisker" ,r-whisker)
9277 ("r-withr" ,r-withr)
9278 ("r-yaml" ,r-yaml)))
9279 (home-page "https://github.com/r-lib/usethis")
9280 (synopsis "Automate R package and project setup")
9282 "This package helps you to automate R package and project setup tasks
9283 that are otherwise performed manually. This includes setting up unit testing,
9284 test coverage, continuous integration, Git, GitHub integration, licenses,
9285 Rcpp, RStudio projects, and more.")
9286 (license license:gpl3)))
9288 (define-public r-sessioninfo
9290 (name "r-sessioninfo")
9295 (uri (cran-uri "sessioninfo" version))
9298 "0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
9299 (build-system r-build-system)
9302 ("r-withr" ,r-withr)))
9303 (home-page "https://github.com/r-lib/sessioninfo#readme")
9304 (synopsis "R session information")
9306 "This package provides tools to query and print information about the
9307 current R session. It is similar to @code{utils::sessionInfo()}, but includes
9308 more information about packages, and where they were installed from.")
9309 (license license:gpl2)))
9311 (define-public r-remotes
9318 (uri (cran-uri "remotes" version))
9321 "12qinl7jv54f2524ri13gcrv6d523rg1harpi500j676zi30fnaf"))))
9322 (build-system r-build-system)
9323 (home-page "https://github.com/r-lib/remotes#readme")
9324 (synopsis "R package installation from remote repositories")
9326 "Download and install R packages stored in GitHub, BitBucket, or plain
9327 subversion or git repositories. This package is a lightweight replacement of
9328 the @code{install_*} functions in the @code{devtools} package. Indeed most of
9329 the code was copied over from @code{devtools}.")
9330 (license license:gpl2+)))
9332 (define-public r-xopen
9339 (uri (cran-uri "xopen" version))
9342 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
9343 (build-system r-build-system)
9345 `(("r-processx" ,r-processx)))
9346 (home-page "https://github.com/r-lib/xopen#readme")
9347 (synopsis "Open system files, URLs, anything")
9349 "This package provides a cross-platform solution to open files,
9350 directories or URLs with their associated programs.")
9351 (license license:expat)))
9353 (define-public r-rcmdcheck
9355 (name "r-rcmdcheck")
9360 (uri (cran-uri "rcmdcheck" version))
9363 "1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
9364 (build-system r-build-system)
9366 `(("r-callr" ,r-callr)
9368 ("r-crayon" ,r-crayon)
9370 ("r-digest" ,r-digest)
9371 ("r-pkgbuild" ,r-pkgbuild)
9372 ("r-prettyunits" ,r-prettyunits)
9374 ("r-rprojroot" ,r-rprojroot)
9375 ("r-sessioninfo" ,r-sessioninfo)
9376 ("r-withr" ,r-withr)
9377 ("r-xopen" ,r-xopen)))
9378 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
9379 (synopsis "Run R CMD check from R and capture results")
9381 "Run @code{R CMD check} from R programmatically, and capture the results
9382 of the individual checks.")
9383 (license license:expat)))
9385 (define-public r-rapportools
9387 (name "r-rapportools")
9392 (uri (cran-uri "rapportools" version))
9395 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
9396 (build-system r-build-system)
9398 `(("r-pander" ,r-pander)
9400 ("r-reshape" ,r-reshape)))
9401 (home-page "https://cran.r-project.org/web/packages/rapportools/")
9402 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
9404 "This package provides helper functions that act as wrappers to more
9405 advanced statistical methods with the advantage of having sane defaults for
9407 (license license:agpl3+)))
9409 (define-public r-pander
9416 (uri (cran-uri "pander" version))
9419 "1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
9420 (build-system r-build-system)
9422 `(("r-digest" ,r-digest)
9423 ("r-rcpp" ,r-rcpp)))
9424 (home-page "https://rapporter.github.io/pander")
9425 (synopsis "Render R objects into Pandoc's markdown")
9427 "The main aim of the pander R package is to provide a minimal and easy
9428 tool for rendering R objects into Pandoc's markdown. The package is also
9429 capable of exporting/converting complex Pandoc documents (reports) in various
9431 ;; This package is licensed under either the AGPLv3+ or the very rarely
9433 (license license:agpl3+)))
9435 (define-public r-summarytools
9437 (name "r-summarytools")
9442 (uri (cran-uri "summarytools" version))
9445 "03pcb2ild1rb9f15yq8b68p9bg10z5wk2x7ahgyzkwdh5f81vbq2"))))
9446 (build-system r-build-system)
9448 `(("r-base64enc" ,r-base64enc)
9449 ("r-checkmate" ,r-checkmate)
9450 ("r-dplyr" ,r-dplyr)
9451 ("r-htmltools" ,r-htmltools)
9452 ("r-lubridate" ,r-lubridate)
9453 ("r-magick" ,r-magick)
9454 ("r-matrixstats" ,r-matrixstats)
9455 ("r-pander" ,r-pander)
9457 ("r-rapportools" ,r-rapportools)
9458 ("r-tibble" ,r-tibble)
9459 ("r-tidyr" ,r-tidyr)))
9460 (home-page "https://github.com/dcomtois/summarytools")
9461 (synopsis "Tools to quickly and neatly summarize data")
9463 "This package provides tools for data frame summaries, cross-tabulations,
9464 weight-enabled frequency tables and common univariate statistics in concise
9465 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
9466 good point-of-entry for exploring data, both for experienced and new R
9468 (license license:gpl2)))
9470 (define-public r-lsei
9477 (uri (cran-uri "lsei" version))
9480 "1rvzdb33x9ykl5qfwxkps1iylxqzlf1qla3l88420nbq7pxp7m87"))))
9481 (build-system r-build-system)
9483 `(("gfortran" ,gfortran)))
9484 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9485 (synopsis "Solve regression problems under equality/inequality constraints")
9487 "It contains functions that solve least squares linear regression
9488 problems under linear equality/inequality constraints. Functions for solving
9489 quadratic programming problems are also available, which transform such
9490 problems into least squares ones first.")
9491 (license license:gpl2+)))
9493 (define-public r-npsurv
9500 (uri (cran-uri "npsurv" version))
9503 "09nxibp93bp9v8qcx0gnazk7fkvyh0fq9vlgxl639m6ndr7fwp88"))))
9504 (build-system r-build-system)
9506 `(("r-lsei" ,r-lsei)))
9507 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
9508 (synopsis "Nonparametric survival analysis")
9510 "This package contains functions for non-parametric survival analysis of
9511 exact and interval-censored observations.")
9512 (license license:gpl2+)))
9514 (define-public r-clusteval
9516 (name "r-clusteval")
9521 (uri (cran-uri "clusteval" version))
9524 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
9525 (build-system r-build-system)
9527 `(("r-mvtnorm" ,r-mvtnorm)
9528 ("r-rcpp" ,r-rcpp)))
9529 (home-page "https://cran.r-project.org/web/packages/clusteval/")
9530 (synopsis "Evaluation of clustering algorithms")
9532 "This R package provides a suite of tools to evaluate clustering
9533 algorithms, clusterings, and individual clusters.")
9534 (license license:expat)))
9536 (define-public r-tweedie
9543 (uri (cran-uri "tweedie" version))
9546 "10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
9547 (build-system r-build-system)
9548 (native-inputs `(("gfortran" ,gfortran)))
9549 (home-page "https://cran.r-project.org/web/packages/tweedie/")
9550 (synopsis "Evaluation of Tweedie exponential family models")
9552 "Maximum likelihood computations for Tweedie families, including the
9553 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
9554 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
9555 and related methods.")
9556 (license license:gpl2+)))
9558 (define-public r-rcppgsl
9565 (uri (cran-uri "RcppGSL" version))
9567 (base32 "17nlayy6gvwb3v6l5aiqm84i75yf4dfi3zclxrgpqwf3j9v09yvz"))))
9568 (properties `((upstream-name . "RcppGSL")))
9569 (build-system r-build-system)
9571 `(("r-rcpp" ,r-rcpp)
9573 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
9574 (synopsis "Rcpp integration for GSL vectors and matrices")
9576 "The GNU Scientific Library (or GSL) is a collection of numerical
9577 routines for scientific computing. It is particularly useful for C and C++
9578 programs as it provides a standard C interface to a wide range of mathematical
9579 routines. There are over 1000 functions in total with an extensive test
9580 suite. The RcppGSL package provides an easy-to-use interface between GSL data
9581 structures and R using concepts from Rcpp which is itself a package that eases
9582 the interfaces between R and C++.")
9583 (license license:gpl2+)))
9585 (define-public r-mvabund
9592 (uri (cran-uri "mvabund" version))
9595 "1z58h4dk3mc2hfnfvc7pghk471cbp7ah2s1z2ria5igw4s80962b"))))
9596 (build-system r-build-system)
9598 `(("r-mass" ,r-mass)
9600 ("r-rcppgsl" ,r-rcppgsl)
9601 ("r-statmod" ,r-statmod)
9602 ("r-tweedie" ,r-tweedie)))
9603 (home-page "https://cran.r-project.org/web/packages/mvabund/")
9604 (synopsis "Statistical methods for analysing multivariate abundance data")
9606 "This package provides a set of tools for displaying, modeling and
9607 analysing multivariate abundance data in community ecology.")
9608 (license license:lgpl2.1+)))
9610 (define-public r-afex
9617 (uri (cran-uri "afex" version))
9620 "0qsmcddy4449qjj3ajmqvdiqdkhkswmz5dqf150wxwq897p3bvf2"))))
9621 (build-system r-build-system)
9625 ("r-lmertest" ,r-lmertest)
9626 ("r-pbkrtest" ,r-pbkrtest)
9627 ("r-reshape2" ,r-reshape2)))
9629 `(("r-knitr" ,r-knitr)))
9630 (home-page "https://afex.singmann.science/")
9631 (synopsis "Analysis of factorial experiments")
9633 "This package provides convenience functions for analyzing factorial
9634 experiments using ANOVA or mixed models.")
9635 (license license:gpl2+)))
9637 (define-public r-lmertest
9644 (uri (cran-uri "lmerTest" version))
9647 "1qkdxx5sri65zgpb9gw4nkfkdam51kgy4hxclk5c40yk7y3p0n1q"))))
9648 (properties `((upstream-name . "lmerTest")))
9649 (build-system r-build-system)
9651 `(("r-ggplot2" ,r-ggplot2)
9654 ("r-numderiv" ,r-numderiv)))
9655 (home-page "https://github.com/runehaubo/lmerTestR")
9656 (synopsis "Tests in linear mixed effects models")
9658 "This package provides p-values in type I, II or III anova and summary
9659 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
9660 method. A Kenward-Roger method is also available via the @code{pbkrtest}
9661 package. Model selection methods include step, drop1 and anova-like tables
9662 for random effects (ranova). Methods for Least-Square means (LS-means) and
9663 tests of linear contrasts of fixed effects are also available.")
9664 (license license:gpl2+)))
9666 (define-public r-r2glmm
9673 (uri (cran-uri "r2glmm" version))
9676 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
9677 (build-system r-build-system)
9679 `(("r-afex" ,r-afex)
9680 ("r-data-table" ,r-data-table)
9681 ("r-dplyr" ,r-dplyr)
9682 ("r-ggplot2" ,r-ggplot2)
9683 ("r-gridextra" ,r-gridextra)
9684 ("r-lmertest" ,r-lmertest)
9686 ("r-matrix" ,r-matrix)
9688 ("r-pbkrtest" ,r-pbkrtest)))
9689 (home-page "https://github.com/bcjaeger/r2glmm")
9690 (synopsis "Compute R squared for mixed (multilevel) models")
9692 "This package computes model and semi partial R squared with confidence
9693 limits for the linear and generalized linear mixed model (LMM and GLMM). The
9694 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
9695 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
9697 (license license:gpl2)))
9699 (define-public r-weights
9706 (uri (cran-uri "weights" version))
9709 "1ka2kvzg464vn80qziqy4mrciy9wwd3jfasgq0d33wbiblhmxkj5"))))
9710 (build-system r-build-system)
9712 `(("r-gdata" ,r-gdata)
9713 ("r-hmisc" ,r-hmisc)
9714 ("r-mice" ,r-mice)))
9716 "https://cran.r-project.org/web/packages/weights/")
9717 (synopsis "Weighting and weighted statistics")
9718 (description "This package Provides a variety of functions for producing
9719 simple weighted statistics, such as weighted Pearson's correlations, partial
9720 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
9721 includes some software for quickly recoding survey data and plotting point
9722 estimates from interaction terms in regressions (and multiply imputed
9723 regressions). NOTE: Weighted partial correlation calculations pulled to
9725 (license license:gpl2+)))
9727 (define-public r-rcppannoy
9729 (name "r-rcppannoy")
9734 (uri (cran-uri "RcppAnnoy" version))
9737 "0bfa35lp6vc4b0h3ymvdx50br233q8vvyjml34ngi81rj0imz3fr"))))
9738 (properties `((upstream-name . "RcppAnnoy")))
9739 (build-system r-build-system)
9741 `(("r-rcpp" ,r-rcpp)))
9742 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
9743 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
9745 "Annoy is a small C++ library for Approximate Nearest Neighbors written
9746 for efficient memory usage as well an ability to load from and save to disk.
9747 This package provides an R interface.")
9748 ;; Annoy is released under ASL 2.0, but this wrapper is released under
9750 (license (list license:gpl2+ license:asl2.0))))
9752 (define-public r-rcpphnsw
9759 (uri (cran-uri "RcppHNSW" version))
9762 "0gqdkw7vkcm544rz45g0hplg836ygzbfwk9gh9wr0817icvdb3qv"))))
9763 (properties `((upstream-name . "RcppHNSW")))
9764 (build-system r-build-system)
9765 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9766 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
9767 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
9769 "Hnswlib is a C++ library for approximate nearest neighbors. This
9770 package provides a minimal R interface by relying on the Rcpp package.")
9771 ;; hnswlib is released under Version 2.0 of the Apache License.
9772 (license (list license:gpl3 license:asl2.0))))
9774 (define-public r-rcppparallel
9776 (name "r-rcppparallel")
9781 (uri (cran-uri "RcppParallel" version))
9784 "10bg4fw38m64dhy543rwq2nnjjc9y24iggk343xslrb3ij8018lc"))))
9785 (properties `((upstream-name . "RcppParallel")))
9786 (build-system r-build-system)
9787 (home-page "https://rcppcore.github.io/RcppParallel/")
9788 (synopsis "Parallel programming tools for Rcpp")
9790 "This package provides high level functions for parallel programming with
9791 Rcpp. For example, the @code{parallelFor()} function can be used to convert
9792 the work of a standard serial @code{for} loop into a parallel one and the
9793 @code{parallelReduce()} function can be used for accumulating aggregates or
9795 (license license:gpl2)))
9797 (define-public r-ncdf4
9804 (uri (cran-uri "ncdf4" version))
9807 "1xls44ln2zjrrlimxl8v4bk2ni3g45c9j0gxdnjx31rikmrc95fv"))))
9808 (build-system r-build-system)
9810 `(("netcdf" ,netcdf)
9812 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
9813 (synopsis "R interface to Unidata netCDF format data files")
9815 "This package provides a high-level R interface to data files written
9816 using Unidata's netCDF library (version 4 or earlier), which are binary data
9817 files that are portable across platforms and include metadata information in
9818 addition to the data sets. Using this package, netCDF files can be opened and
9819 data sets read in easily. It is also easy to create new netCDF dimensions,
9820 variables, and files, in either version 3 or 4 format, and manipulate existing
9822 (license license:gpl3+)))
9824 (define-public r-biocmanager
9826 (name "r-biocmanager")
9831 (uri (cran-uri "BiocManager" version))
9833 (base32 "03n9s2vf7vgpgb5alpxwamf9xfkn32cbzngwyn6spq1bnh9a9dzk"))))
9834 (properties `((upstream-name . "BiocManager")))
9835 (build-system r-build-system)
9836 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
9837 (synopsis "Access the Bioconductor project package repository")
9839 "This package provides a convenient tool to install and update
9840 Bioconductor packages.")
9841 (license license:artistic2.0)))
9843 (define-public r-rgl
9846 (version "0.100.54")
9850 (uri (cran-uri "rgl" version))
9853 "1mgs2d8igmcdzzymfwbqdrypmaidd4pra5n5gnhsn9pm6pqzidqp"))))
9854 (build-system r-build-system)
9856 `(("pkg-config" ,pkg-config)))
9858 `(("freetype" ,freetype)
9862 ("ghc-pandoc" ,ghc-pandoc)
9865 `(("r-crosstalk" ,r-crosstalk)
9866 ("r-htmltools" ,r-htmltools)
9867 ("r-htmlwidgets" ,r-htmlwidgets)
9868 ("r-jsonlite" ,r-jsonlite)
9869 ("r-knitr" ,r-knitr)
9870 ("r-magrittr" ,r-magrittr)
9871 ("r-manipulatewidget" ,r-manipulatewidget)
9872 ("r-shiny" ,r-shiny)))
9873 (home-page "https://r-forge.r-project.org/projects/rgl/")
9874 (synopsis "3D visualization using OpenGL")
9876 "This package provides medium to high level functions for 3D interactive graphics,
9877 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
9878 as functions for constructing representations of geometric
9879 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
9880 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
9881 image formats, including PNG, Postscript, SVG, PGF.")
9882 ;; Any version of the GPL.
9883 (license (list license:gpl2+ license:gpl3+))))
9885 (define-public r-multicool
9887 (name "r-multicool")
9892 (uri (cran-uri "multicool" version))
9895 "0xk408qbz9cxwf51j3pmy55gcjcnws8mc6j3vyn9zhramxj7x40w"))))
9896 (build-system r-build-system)
9897 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
9898 (home-page "https://cran.r-project.org/web/packages/multicool/")
9899 (synopsis "Permutations of multisets in cool-lex order")
9901 "This package provides a set of tools to permute multisets without loops
9902 or hash tables and to generate integer partitions. Cool-lex order is similar
9903 to colexicographical order.")
9904 (license license:gpl2)))
9906 (define-public r-misc3d
9913 (uri (cran-uri "misc3d" version))
9916 "0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
9917 (build-system r-build-system)
9918 (home-page "https://cran.r-project.org/web/packages/misc3d/")
9919 (synopsis "Miscellaneous 3D Plots")
9921 "This package provides a collection of miscellaneous 3d plots, including
9923 ;; Any version of the GPL.
9924 (license (list license:gpl2+ license:gpl3+))))
9933 (uri (cran-uri "ks" version))
9935 (base32 "1f6jvxy0hmngyvnvrknzbmhl42njk0vqyycvydm4qnp8cqirqvba"))))
9936 (build-system r-build-system)
9939 ("r-kernlab" ,r-kernlab)
9940 ("r-kernsmooth" ,r-kernsmooth)
9941 ("r-matrix" ,r-matrix)
9942 ("r-mclust" ,r-mclust)
9944 ("r-multicool" ,r-multicool)
9945 ("r-mvtnorm" ,r-mvtnorm)))
9946 (home-page "http://www.mvstat.net/tduong/")
9947 (synopsis "Kernel smoothing")
9949 "This package provides kernel smoothers for univariate and multivariate
9950 data, including density functions, density derivatives, cumulative
9951 distributions, modal clustering, discriminant analysis, and two-sample
9952 hypothesis testing.")
9953 ;; Either version of the GPL.
9954 (license (list license:gpl2 license:gpl3))))
9956 (define-public r-feature
9963 (uri (cran-uri "feature" version))
9966 "07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
9967 (build-system r-build-system)
9970 ("r-misc3d" ,r-misc3d)
9972 (home-page "http://www.mvstat.net/tduong/")
9973 (synopsis "Inferential feature significance for kernel density estimation")
9975 "The feature package contains functions to display and compute kernel
9976 density estimates, significant gradient and significant curvature regions.
9977 Significant gradient and/or curvature regions often correspond to significant
9978 features (e.g. local modes).")
9979 ;; Either version of the GPL.
9980 (license (list license:gpl2 license:gpl3))))
9982 (define-public r-arm
9989 (uri (cran-uri "arm" version))
9992 "0i2lnm09bqy1qw0ms5pw0rzw196xmnk5dxha3g8lc58lqpldp0kv"))))
9993 (build-system r-build-system)
9995 `(("r-abind" ,r-abind)
9999 ("r-matrix" ,r-matrix)
10000 ("r-nlme" ,r-nlme)))
10001 (home-page "https://cran.r-project.org/web/packages/arm/")
10002 (synopsis "Data analysis using regression and multilevel/hierarchical models")
10004 "This package provides functions to accompany A. Gelman and J. Hill,
10005 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
10006 University Press, 2007.")
10007 (license license:gpl3+)))
10009 (define-public r-circular
10011 (name "r-circular")
10016 (uri (cran-uri "circular" version))
10019 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
10020 (build-system r-build-system)
10022 `(("r-boot" ,r-boot)
10023 ("r-mvtnorm" ,r-mvtnorm)))
10025 `(("gfortran" ,gfortran)))
10026 (home-page "https://cran.r-project.org/web/packages/circular/")
10027 (synopsis "Circular statistics")
10029 "This package provides tools for circular statistics, from \"Topics in
10030 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
10032 (license license:gpl2+)))
10034 (define-public r-activity
10036 (name "r-activity")
10041 (uri (cran-uri "activity" version))
10044 "12imqj366dp6pam5gap6ji56p5wf1073xz5g4iikfxf5l8snxw92"))))
10045 (build-system r-build-system)
10047 `(("r-circular" ,r-circular)
10048 ("r-insol" ,r-insol)
10049 ("r-pbapply" ,r-pbapply)))
10050 (home-page "https://cran.r-project.org/web/packages/activity/")
10051 (synopsis "Animal activity statistics")
10053 "This package provides functions to fit kernel density functions to
10054 animal activity time data; plot activity distributions; quantify overall
10055 levels of activity; statistically compare activity metrics through
10056 bootstrapping; and evaluate variation in linear variables with time (or other
10057 circular variables).")
10058 (license license:gpl3)))
10060 (define-public r-ouch
10067 (uri (cran-uri "ouch" version))
10070 "0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
10071 (build-system r-build-system)
10072 (propagated-inputs `(("r-subplex" ,r-subplex)))
10073 (home-page "https://kingaa.github.io/ouch/")
10074 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
10076 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
10077 for evolution along a phylogenetic tree.")
10078 (license license:gpl2+)))
10080 (define-public r-fmsb
10087 (uri (cran-uri "fmsb" version))
10090 "0x1wkzfdvv4s5xmr0whcwjz4aac71gacwymj2c3mzj2bbswwlw45"))))
10091 (build-system r-build-system)
10092 (home-page "http://minato.sip21c.org/msb/")
10093 (synopsis "Functions for medical statistics book with demographic data")
10095 "This package provides several utility functions for the book entitled
10096 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
10097 Japan, 2007) with Japanese demographic data and some demographic analysis
10098 related functions.")
10099 (license license:gpl2+)))
10101 (define-public r-stabledist
10103 (name "r-stabledist")
10108 (uri (cran-uri "stabledist" version))
10111 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
10112 (build-system r-build-system)
10113 (home-page "https://www.rmetrics.org")
10114 (synopsis "Stable distribution functions")
10116 "This package provides density, probability and quantile functions, and
10117 random number generation for (skew) stable distributions, using the
10118 parametrizations of Nolan.")
10119 (license license:gpl2+)))
10121 (define-public r-gsl
10128 (uri (cran-uri "gsl" version))
10131 "0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
10132 (build-system r-build-system)
10135 (home-page "https://cran.r-project.org/web/packages/gsl")
10136 (synopsis "Wrapper for the GNU Scientific Library")
10138 "This package provides an R wrapper for the special functions and quasi
10139 random number generators of the GNU Scientific Library.")
10140 (license license:gpl2+)))
10142 (define-public r-adgoftest
10144 (name "r-adgoftest")
10149 (uri (cran-uri "ADGofTest" version))
10152 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
10153 (properties `((upstream-name . "ADGofTest")))
10154 (build-system r-build-system)
10155 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
10156 (synopsis "Anderson-Darling GoF test")
10158 "This package provides an implementation of the Anderson-Darling GoF test
10159 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
10160 Anderson-Darling Distribution\".")
10161 ;; Any version of the GPL.
10162 (license license:gpl3+)))
10164 (define-public r-softimpute
10166 (name "r-softimpute")
10171 (uri (cran-uri "softImpute" version))
10174 "07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
10175 (properties `((upstream-name . "softImpute")))
10176 (build-system r-build-system)
10178 `(("r-matrix" ,r-matrix)))
10180 `(("gfortran" ,gfortran)))
10181 (home-page "https://cran.r-project.org/web/packages/softImpute")
10182 (synopsis "Matrix completion via iterative soft-thresholded SVD")
10184 "This package provides iterative methods for matrix completion that use
10185 nuclear-norm regularization. The package includes procedures for centering
10186 and scaling rows, columns or both, and for computing low-rank @dfn{single
10187 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
10189 (license license:gpl2)))
10191 (define-public r-fftwtools
10193 (name "r-fftwtools")
10198 (uri (cran-uri "fftwtools" version))
10201 "1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
10202 (build-system r-build-system)
10203 (inputs `(("fftw" ,fftw)))
10204 (home-page "https://github.com/krahim/fftwtools")
10205 (synopsis "Wrapper for FFTW3")
10207 "This package provides a wrapper for several FFTW functions. It provides
10208 access to the two-dimensional FFT, the multivariate FFT, and the
10209 one-dimensional real to complex FFT using the FFTW3 library. The package
10210 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
10211 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
10212 The FFT functions have a parameter that allows them to not return the
10213 redundant complex conjugate when the input is real data.")
10214 (license license:gpl2+)))
10216 (define-public r-tiff
10223 (uri (cran-uri "tiff" version))
10226 "0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
10227 (build-system r-build-system)
10229 `(("libtiff" ,libtiff)
10230 ("libjpeg" ,libjpeg-turbo)
10232 (home-page "https://www.rforge.net/tiff/")
10233 (synopsis "Read and write TIFF images")
10235 "This package provides an easy and simple way to read, write and display
10236 bitmap images stored in the TIFF format. It can read and write both files and
10237 in-memory raw vectors.")
10238 ;; Either of these two license versions.
10239 (license (list license:gpl2 license:gpl3))))
10241 (define-public r-nlp
10248 (uri (cran-uri "NLP" version))
10251 "0xbhkrnxcbf322jfw31xcn4y2gnk5y7ccq1bz4h3prf44h0whr7w"))))
10252 (properties `((upstream-name . "NLP")))
10253 (build-system r-build-system)
10254 (home-page "https://cran.r-project.org/web/packages/NLP/")
10255 (synopsis "Natural language processing infrastructure")
10257 "This package provides basic classes and methods for Natural Language
10259 (license license:gpl3)))
10261 (define-public r-tm
10268 (uri (cran-uri "tm" version))
10271 "0pyics8j7a4wkh5gzin46l0qars5vgbb1886xqpdqjs1z0gy9nyh"))))
10272 (properties `((upstream-name . "tm")))
10273 (build-system r-build-system)
10279 ("r-xml2" ,r-xml2)))
10280 (home-page "http://tm.r-forge.r-project.org/")
10281 (synopsis "Text mining package")
10283 "This package provides a framework for text mining applications within R.")
10284 (license license:gpl3)))
10286 (define-public r-waveslim
10288 (name "r-waveslim")
10293 (uri (cran-uri "waveslim" version))
10296 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
10297 (build-system r-build-system)
10299 `(("gfortran" ,gfortran)))
10300 (home-page "http://waveslim.blogspot.com")
10301 (synopsis "Basic wavelet routines for signal processing")
10303 "This package provides basic wavelet routines for time series (1D),
10304 image (2D) and array (3D) analysis. The code provided here is based on
10305 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
10306 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
10307 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
10308 pairs (Selesnick 2001, 2002).")
10309 (license license:bsd-3)))
10311 (define-public r-wordcloud
10313 (name "r-wordcloud")
10318 (uri (cran-uri "wordcloud" version))
10321 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
10322 (build-system r-build-system)
10324 `(("r-rcolorbrewer" ,r-rcolorbrewer)
10326 ;; The "tm" package is only "suggested" according to CRAN, but the
10327 ;; wordcloud package cannot be loaded without it.
10329 (home-page "https://cran.r-project.org/web/packages/wordcloud")
10330 (synopsis "Word clouds")
10332 "This package provides functionality to create pretty word clouds,
10333 visualize differences and similarity between documents, and avoid
10334 over-plotting in scatter plots with text.")
10335 (license license:lgpl2.1)))
10337 (define-public r-colorramps
10339 (name "r-colorramps")
10344 (uri (cran-uri "colorRamps" version))
10347 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
10348 (properties `((upstream-name . "colorRamps")))
10349 (build-system r-build-system)
10350 (home-page "https://cran.r-project.org/web/packages/colorRamps")
10351 (synopsis "Build color tables")
10352 (description "This package provides features to build gradient color
10354 ;; Any version of the GPL
10355 (license license:gpl3+)))
10357 (define-public r-tidytree
10359 (name "r-tidytree")
10364 (uri (cran-uri "tidytree" version))
10366 (base32 "05b53dap0f784kl6s1wgck6m7brwmy6ifqp7v5l06s1spfspagl6"))))
10367 (build-system r-build-system)
10370 ("r-dplyr" ,r-dplyr)
10371 ("r-lazyeval" ,r-lazyeval)
10372 ("r-magrittr" ,r-magrittr)
10373 ("r-rlang" ,r-rlang)
10374 ("r-tibble" ,r-tibble)))
10376 `(("r-knitr" ,r-knitr)))
10377 (home-page "https://github.com/GuangchuangYu/tidytree")
10378 (synopsis "Tidy tool for phylogenetic tree data manipulation")
10380 "Phylogenetic trees generally contain multiple components including nodes,
10381 edges, branches and associated data. This package provides an approach to
10382 convert tree objects to tidy data frames. It also provides tidy interfaces to
10383 manipulate tree data.")
10384 (license license:artistic2.0)))
10386 (define-public r-rvcheck
10393 (uri (cran-uri "rvcheck" version))
10395 (base32 "0627bc8qmhxmd63yh6f90qni3qw1zwdpxjln2qbychzmzd4am9ac"))))
10396 (build-system r-build-system)
10398 `(("r-biocmanager" ,r-biocmanager)
10399 ("r-rlang" ,r-rlang)))
10400 (home-page "https://cran.r-project.org/web/packages/rvcheck")
10401 (synopsis "R package version check")
10403 "This package provides tools to check the latest release version of R and
10404 R packages (on CRAN, Bioconductor or Github).")
10405 (license license:artistic2.0)))
10407 (define-public r-docopt
10414 (uri (cran-uri "docopt" version))
10417 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
10418 (build-system r-build-system)
10419 (home-page "https://github.com/docopt/docopt.R")
10420 (synopsis "Command-line interface specification language")
10422 "This package enables you to define a command-line interface by just
10423 giving it a description in the specific format.")
10424 (license license:expat)))
10426 (define-public r-sparsesvd
10428 (name "r-sparsesvd")
10433 (uri (cran-uri "sparsesvd" version))
10436 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
10437 (build-system r-build-system)
10438 (propagated-inputs `(("r-matrix" ,r-matrix)))
10439 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
10440 (synopsis "Sparse truncated singular value decomposition")
10442 "This package provides a Wrapper around the SVDLIBC library
10443 for (truncated) singular value decomposition of a sparse matrix. Currently,
10444 only sparse real matrices in Matrix package format are supported.")
10445 ;; SVDLIBC is released under BSD-2. The R interface is released under
10447 (license (list license:bsd-3 license:bsd-2))))
10449 (define-public r-speedglm
10451 (name "r-speedglm")
10456 (uri (cran-uri "speedglm" version))
10459 "1b25zimk0z7ad62yacqdg0zk0qs0jja4i918ym942xfw4j1z3jjz"))))
10460 (build-system r-build-system)
10462 `(("r-mass" ,r-mass)
10463 ("r-matrix" ,r-matrix)))
10464 (home-page "https://cran.r-project.org/web/packages/speedglm")
10465 (synopsis "Fit linear and generalized linear models to large data sets")
10467 "This package provides tools for fitting linear models and generalized
10468 linear models to large data sets by updating algorithms.")
10469 ;; Any version of the GPL
10470 (license license:gpl2+)))
10472 (define-public r-densityclust
10474 (name "r-densityclust")
10479 (uri (cran-uri "densityClust" version))
10482 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
10483 (properties `((upstream-name . "densityClust")))
10484 (build-system r-build-system)
10487 ("r-ggplot2" ,r-ggplot2)
10488 ("r-ggrepel" ,r-ggrepel)
10489 ("r-gridextra" ,r-gridextra)
10490 ("r-rcolorbrewer" ,r-rcolorbrewer)
10492 ("r-rtsne" ,r-rtsne)))
10493 (home-page "https://cran.r-project.org/web/packages/densityClust")
10494 (synopsis "Clustering by fast search and find of density peaks")
10496 "This package provides an improved implementation (based on k-nearest
10497 neighbors) of the density peak clustering algorithm, originally described by
10498 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
10499 large datasets (> 100,000 samples) very efficiently.")
10500 (license license:gpl2+)))
10502 (define-public r-combinat
10504 (name "r-combinat")
10509 (uri (cran-uri "combinat" version))
10512 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
10513 (build-system r-build-system)
10514 (home-page "https://cran.r-project.org/web/packages/combinat")
10515 (synopsis "Combinatorics utilities")
10516 (description "This package provides assorted routines for combinatorics.")
10517 (license license:gpl2)))
10519 (define-public r-qlcmatrix
10521 (name "r-qlcmatrix")
10526 (uri (cran-uri "qlcMatrix" version))
10529 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
10530 (properties `((upstream-name . "qlcMatrix")))
10531 (build-system r-build-system)
10533 `(("r-docopt" ,r-docopt)
10534 ("r-matrix" ,r-matrix)
10536 ("r-sparsesvd" ,r-sparsesvd)))
10537 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
10538 (synopsis "Sparse matrix functions for quantitative language comparison")
10540 "This package provides an extension of the functionality of the Matrix
10541 package for using sparse matrices. Some of the functions are very general,
10542 while other are highly specific for the special data format used for
10543 @dfn{quantitative language comparison} (QLC).")
10544 (license license:gpl3)))
10546 (define-public r-ddrtree
10553 (uri (cran-uri "DDRTree" version))
10556 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
10557 (properties `((upstream-name . "DDRTree")))
10558 (build-system r-build-system)
10561 ("r-irlba" ,r-irlba)
10563 ("r-rcppeigen" ,r-rcppeigen)))
10564 (home-page "https://cran.r-project.org/web/packages/DDRTree")
10565 (synopsis "Learning principal graphs with DDRTree")
10567 "This package provides an implementation of the framework of
10568 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
10569 dimensional space while constructs a principal tree which passes through the
10570 middle of the data simultaneously. DDRTree shows superiority to
10571 alternatives (Wishbone, DPT) for inferring the ordering as well as the
10572 intrinsic structure of single cell genomics data. In general, it could be
10573 used to reconstruct the temporal progression as well as the bifurcation
10574 structure of any data type.")
10575 (license license:asl2.0)))
10577 (define-public r-corpcor
10584 (uri (cran-uri "corpcor" version))
10587 "1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
10588 (build-system r-build-system)
10589 (home-page "http://strimmerlab.org/software/corpcor/")
10590 (synopsis "Efficient estimation of covariance and (partial) correlation")
10592 "This package implements a James-Stein-type shrinkage estimator for the
10593 covariance matrix, with separate shrinkage for variances and correlations.
10594 Furthermore, functions are available for fast singular value decomposition,
10595 for computing the pseudoinverse, and for checking the rank and positive
10596 definiteness of a matrix.")
10597 (license license:gpl3+)))
10599 (define-public r-rspectra
10601 (name "r-rspectra")
10606 (uri (cran-uri "RSpectra" version))
10609 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
10610 (properties `((upstream-name . "RSpectra")))
10611 (build-system r-build-system)
10613 `(("r-matrix" ,r-matrix)
10615 ("r-rcppeigen" ,r-rcppeigen)))
10616 (home-page "https://github.com/yixuan/RSpectra")
10617 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
10619 "This package provides an R interface to the Spectra library for
10620 large-scale eigenvalue and SVD problems. It is typically used to compute a
10621 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
10622 which is usually more efficient than @code{eigen()} if k << n.")
10624 (license license:mpl2.0)))
10626 (define-public r-vbsr
10633 (uri (cran-uri "vbsr" version))
10636 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
10637 (build-system r-build-system)
10638 (home-page "https://cran.r-project.org/web/packages/vbsr")
10639 (synopsis "Variational Bayes spike regression regularized linear models")
10641 "This package provides an efficient algorithm for solving ultra-sparse
10642 regularized regression models using a variational Bayes algorithm with a spike
10643 prior. The algorithm is solved on a path, with coordinate updates, and is
10644 capable of generating very sparse models. Very general model
10645 diagnostics for controlling type-1 errors are also provided.")
10646 (license license:gpl2)))
10648 (define-public r-flare
10651 (version "1.6.0.2")
10655 (uri (cran-uri "flare" version))
10658 "1ybrsx1djqldw0l5l1iz4pfh6xxb8ckkg1ric7wnsr51wm9ljlh5"))))
10659 (build-system r-build-system)
10661 `(("r-igraph" ,r-igraph)
10662 ("r-lattice" ,r-lattice)
10664 ("r-matrix" ,r-matrix)))
10665 (home-page "https://cran.r-project.org/web/packages/flare")
10666 (synopsis "Family of Lasso regression implementations")
10668 "This package provides implementations of a family of Lasso variants
10669 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
10670 high dimensional sparse linear models.")
10671 (license license:gpl2)))
10673 (define-public r-lassopv
10680 (uri (cran-uri "lassopv" version))
10683 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
10684 (build-system r-build-system)
10685 (propagated-inputs `(("r-lars" ,r-lars)))
10686 (home-page "https://github.com/lingfeiwang/lassopv")
10687 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
10689 "This package enables you to estimate the p-values for predictors x
10690 against target variable y in Lasso regression, using the regularization
10691 strength when each predictor enters the active set of regularization path for
10692 the first time as the statistic.")
10693 (license license:gpl3)))
10695 (define-public r-splitstackshape
10697 (name "r-splitstackshape")
10702 (uri (cran-uri "splitstackshape" version))
10705 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
10706 (build-system r-build-system)
10708 `(("r-data-table" ,r-data-table)))
10709 (home-page "https://github.com/mrdwab/splitstackshape")
10710 (synopsis "Stack and reshape datasets after splitting concatenated values")
10712 "Online data collection tools like Google Forms often export
10713 multiple-response questions with data concatenated in cells. The
10714 @code{concat.split} (cSplit) family of functions provided by this package
10715 splits such data into separate cells. This package also includes functions to
10716 stack groups of columns and to reshape wide data, even when the data are
10717 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
10718 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
10720 (license license:gpl3)))
10722 (define-public r-tfmpvalue
10724 (name "r-tfmpvalue")
10729 (uri (cran-uri "TFMPvalue" version))
10732 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
10733 (properties `((upstream-name . "TFMPvalue")))
10734 (build-system r-build-system)
10735 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10736 (home-page "https://github.com/ge11232002/TFMPvalue")
10737 (synopsis "P-value computation for position weight matrices")
10739 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
10740 identification from sequence/alignments, we are interested in the significance
10741 of certain match scores. TFMPvalue provides the accurate calculation of a
10742 p-value with a score threshold for position weight matrices, or the score with
10743 a given p-value. It is an interface to code originally made available by
10744 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
10745 Touzet and Varre (2007).")
10746 (license license:gpl2)))
10748 (define-public r-rnifti
10755 (uri (cran-uri "RNifti" version))
10758 "1z8ninp3aq18w0slcfn8r2fp48cdz8l0k0namsrnvgyp8lzcpqpn"))))
10759 (properties `((upstream-name . "RNifti")))
10760 (build-system r-build-system)
10761 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
10762 (home-page "https://github.com/jonclayden/RNifti")
10763 (synopsis "Fast R and C++ access to NIfTI images")
10765 "This package provides very fast read and write access to images stored
10766 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
10767 compiled C and interpreted R code. It also provides a C/C++ API that can be
10768 used by other packages.")
10769 (license license:gpl2)))
10771 (define-public r-shades
10778 (uri (cran-uri "shades" version))
10781 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
10782 (build-system r-build-system)
10783 (home-page "https://github.com/jonclayden/shades")
10784 (synopsis "Simple color manipulation")
10786 "This package provides functions for easily manipulating colors,
10787 creating color scales and calculating color distances.")
10788 (license license:bsd-3)))
10790 (define-public r-ore
10797 (uri (cran-uri "ore" version))
10799 (base32 "1vh6w3arrhgkfjjjw7ci91xmz4wpfr3cmwd5zkqch89dgn07skkv"))))
10800 (build-system r-build-system)
10801 (home-page "https://github.com/jonclayden/ore")
10802 (synopsis "R interface to the Onigmo regular expression library")
10804 "This package provides an alternative to R's built-in functionality for
10805 handling regular expressions, based on the Onigmo library. It offers
10806 first-class compiled regex objects, partial matching and function-based
10807 substitutions, amongst other features.")
10808 (license license:bsd-3)))
10810 (define-public r-reportr
10817 (uri (cran-uri "reportr" version))
10820 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
10821 (build-system r-build-system)
10822 (propagated-inputs `(("r-ore" ,r-ore)))
10823 (home-page "https://github.com/jonclayden/reportr")
10824 (synopsis "General message and error reporting system")
10826 "This package provides a system for reporting messages, which offers
10827 certain useful features over the standard R system, such as the incorporation
10828 of output consolidation, message filtering, assertions, expression
10829 substitution, automatic generation of stack traces for debugging, and
10830 conditional reporting based on the current \"output level\".")
10831 (license license:gpl2)))
10833 (define-public r-tractor-base
10835 (name "r-tractor-base")
10840 (uri (cran-uri "tractor.base" version))
10843 "0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
10844 (properties `((upstream-name . "tractor.base")))
10845 (build-system r-build-system)
10848 ("r-reportr" ,r-reportr)
10849 ("r-rnifti" ,r-rnifti)
10850 ("r-shades" ,r-shades)))
10851 (home-page "https://www.tractor-mri.org.uk")
10852 (synopsis "Read, manipulate and visualize magnetic resonance images")
10854 "This package provides functions for working with magnetic resonance
10855 images. It supports reading and writing of popular file formats (DICOM,
10856 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
10857 visualization; flexible image manipulation; metadata and sparse image
10859 (license license:gpl2)))
10861 (define-public r-grimport
10863 (name "r-grimport")
10868 (uri (cran-uri "grImport" version))
10871 "109mrdvq06xq3zgn9ngz0c7zzgqkv5zbpvsb2i636vmlk6y4dpkd"))))
10872 (properties `((upstream-name . "grImport")))
10873 (build-system r-build-system)
10875 `(("ghostscript" ,ghostscript)))
10877 `(("r-xml" ,r-xml)))
10878 (home-page "https://cran.r-project.org/web/packages/grImport")
10879 (synopsis "Convert, import, and draw PostScript pictures")
10881 "This package provides functions for converting, importing, and drawing
10882 PostScript pictures in R plots.")
10883 (license license:gpl2+)))
10885 (define-public r-grimport2
10887 (name "r-grimport2")
10892 (uri (cran-uri "grImport2" version))
10895 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
10896 (properties `((upstream-name . "grImport2")))
10897 (build-system r-build-system)
10899 `(("r-base64enc" ,r-base64enc)
10903 (home-page "https://cran.r-project.org/web/packages/grImport2/")
10904 (synopsis "Import SVG graphics")
10906 "This package provides functions for importing external vector images and
10907 drawing them as part of R plots. This package is different from the
10908 @code{grImport} package because, where that package imports PostScript format
10909 images, this package imports SVG format images. Furthermore, this package
10910 imports a specific subset of SVG, so external images must be preprocessed
10911 using a package like @code{rsvg} to produce SVG that this package can import.
10912 SVG features that are not supported by R graphics, such as gradient fills, can
10913 be imported and then exported via the @code{gridSVG} package.")
10914 (license license:gpl2+)))
10916 (define-public r-kohonen
10923 (uri (cran-uri "kohonen" version))
10926 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
10927 (build-system r-build-system)
10929 `(("r-rcpp" ,r-rcpp)))
10930 (home-page "https://cran.r-project.org/web/packages/kohonen")
10931 (synopsis "Supervised and unsupervised self-organising maps")
10933 "This package provides functions to train @dfn{self-organising
10934 maps} (SOMs). Also interrogation of the maps and prediction using trained
10935 maps are supported. The name of the package refers to Teuvo Kohonen, the
10936 inventor of the SOM.")
10937 (license license:gpl2+)))
10939 (define-public r-nnls
10946 (uri (cran-uri "nnls" version))
10949 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
10950 (build-system r-build-system)
10951 (native-inputs `(("gfortran" ,gfortran)))
10952 (home-page "https://cran.r-project.org/web/packages/nnls")
10953 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
10955 "This package provides an R interface to the Lawson-Hanson implementation
10956 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
10957 the combination of non-negative and non-positive constraints.")
10958 (license license:gpl2+)))
10960 (define-public r-iso
10963 (version "0.0-18.1")
10967 (uri (cran-uri "Iso" version))
10970 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
10971 (properties `((upstream-name . "Iso")))
10972 (build-system r-build-system)
10973 (native-inputs `(("gfortran" ,gfortran)))
10974 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
10975 (synopsis "Functions to perform isotonic regression")
10977 "This package provides support for linear order and unimodal
10978 order (univariate) isotonic regression and bivariate isotonic regression with
10979 linear order on both variables.")
10980 (license license:gpl2+)))
10982 (define-public r-chemometricswithr
10984 (name "r-chemometricswithr")
10989 (uri (cran-uri "ChemometricsWithR" version))
10992 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
10994 `((upstream-name . "ChemometricsWithR")))
10995 (build-system r-build-system)
10997 `(("r-devtools" ,r-devtools)
10998 ("r-kohonen" ,r-kohonen)
11001 (home-page "https://github.com/rwehrens/CWR")
11002 (synopsis "Chemometrics with R")
11004 "This package provides functions and scripts used in the book
11005 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
11006 Life Sciences\" by Ron Wehrens, Springer (2011).")
11007 (license license:gpl2+)))
11009 (define-public r-als
11016 (uri (cran-uri "ALS" version))
11019 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
11020 (properties `((upstream-name . "ALS")))
11021 (build-system r-build-system)
11024 ("r-nnls" ,r-nnls)))
11025 (home-page "https://cran.r-project.org/web/packages/ALS")
11026 (synopsis "Multivariate curve resolution alternating least squares")
11028 "Alternating least squares is often used to resolve components
11029 contributing to data with a bilinear structure; the basic technique may be
11030 extended to alternating constrained least squares. This package provides an
11031 implementation of @dfn{multivariate curve resolution alternating least
11032 squares} (MCR-ALS).
11034 Commonly applied constraints include unimodality, non-negativity, and
11035 normalization of components. Several data matrices may be decomposed
11036 simultaneously by assuming that one of the two matrices in the bilinear
11037 decomposition is shared between datasets.")
11038 (license license:gpl2+)))
11040 (define-public r-strucchange
11042 (name "r-strucchange")
11047 (uri (cran-uri "strucchange" version))
11050 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
11051 (build-system r-build-system)
11053 `(("r-sandwich" ,r-sandwich)
11055 (home-page "https://cran.r-project.org/web/packages/strucchange")
11056 (synopsis "Testing, monitoring, and dating structural changes")
11058 "This package provides tools for testing, monitoring and dating
11059 structural changes in (linear) regression models. It features tests/methods
11060 from the generalized fluctuation test framework as well as from the F
11061 test (Chow test) framework. This includes methods to fit, plot and test
11062 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
11063 statistics, respectively. It is possible to monitor incoming data online
11064 using fluctuation processes. Finally, the breakpoints in regression models
11065 with structural changes can be estimated together with confidence intervals.
11066 Emphasis is always given to methods for visualizing the data.")
11067 ;; Either of these two GPL versions
11068 (license (list license:gpl2 license:gpl3))))
11070 (define-public r-pixmap
11077 (uri (cran-uri "pixmap" version))
11080 "04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
11081 (build-system r-build-system)
11082 (home-page "https://cran.r-project.org/web/packages/pixmap")
11083 (synopsis "Tools for bitmap images")
11085 "This package provides functions for importing, exporting, plotting and
11086 other manipulations of bitmapped images.")
11087 (license license:gpl2)))
11089 (define-public r-rapidjsonr
11091 (name "r-rapidjsonr")
11096 (uri (cran-uri "rapidjsonr" version))
11099 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
11100 (build-system r-build-system)
11101 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
11102 (synopsis "JSON parser")
11104 "This package provides JSON parsing capability through the Rapidjson
11106 (license license:expat)))
11108 (define-public r-ontologyindex
11110 (name "r-ontologyindex")
11115 (uri (cran-uri "ontologyIndex" version))
11118 "127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
11119 (properties `((upstream-name . "ontologyIndex")))
11120 (build-system r-build-system)
11121 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
11122 (synopsis "Functions for processing ontologies in R")
11124 "This package provides functions for reading ontologies into R as lists
11125 and manipulating sets of ontological terms.")
11126 (license license:gpl2+)))
11128 (define-public r-gargle
11135 (uri (cran-uri "gargle" version))
11138 "1fykmiv3x8c9ai31r9wr7qcca51h6kqn9cgwbxvxfj15fhwskh4n"))))
11139 (build-system r-build-system)
11144 ("r-jsonlite" ,r-jsonlite)
11145 ("r-rlang" ,r-rlang)
11146 ("r-withr" ,r-withr)))
11148 `(("r-knitr" ,r-knitr)))
11149 (home-page "https://gargle.r-lib.org")
11150 (synopsis "Utilities for working with Google APIs")
11152 "This package provides utilities for working with Google APIs. This
11153 includes functions and classes for handling common credential types and for
11154 preparing, executing, and processing HTTP requests.")
11155 (license license:expat)))
11157 (define-public r-bigrquery
11159 (name "r-bigrquery")
11164 (uri (cran-uri "bigrquery" version))
11167 "0mq03sqv5lkyn3dlxvyd6lqqwnryfdaqh05pjvngzp194fxmd9cy"))))
11168 (build-system r-build-system)
11170 `(("r-assertthat" ,r-assertthat)
11171 ("r-bit64" ,r-bit64)
11174 ("r-gargle" ,r-gargle)
11177 ("r-jsonlite" ,r-jsonlite)
11178 ("r-prettyunits" ,r-prettyunits)
11179 ("r-progress" ,r-progress)
11180 ("r-rapidjsonr" ,r-rapidjsonr)
11182 ("r-rlang" ,r-rlang)
11183 ("r-tibble" ,r-tibble)))
11184 (home-page "https://github.com/rstats-db/bigrquery")
11185 (synopsis "R interface to Google's BigQuery API")
11187 "This package provides an R interface to Google's BigQuery database.")
11188 (license license:gpl3)))
11190 (define-public r-gmp
11197 (uri (cran-uri "gmp" version))
11200 "1c9vpr6j6h5f6dm9l535nscl66rvr8sba5az2kswjhmzwb9xpjxc"))))
11201 (build-system r-build-system)
11204 (modify-phases %standard-phases
11205 (add-after 'unpack 'set-CC
11206 (lambda _ (setenv "CC" "gcc") #t)))))
11207 (inputs `(("gmp" ,gmp)))
11208 (home-page "https://cran.r-project.org/web/packages/gmp")
11209 (synopsis "Multiple precision arithmetic")
11211 "This package supports multiple precision arithmetic (big integers and
11212 rationals, prime number tests, matrix computation), \"arithmetic without
11213 limitations\" using the GNU Multiple Precision library.")
11214 ;; Any version of the GPL.
11215 (license license:gpl3+)))
11217 (define-public r-rmpfr
11224 (uri (cran-uri "Rmpfr" version))
11227 "09kw7hyca8xc09r2d88qj81cclar8acaq5q9q5rw9f49iffda0rr"))))
11228 (properties `((upstream-name . "Rmpfr")))
11229 (build-system r-build-system)
11234 `(("r-gmp" ,r-gmp)))
11236 `(("pkg-config" ,pkg-config)))
11237 (home-page "http://rmpfr.r-forge.r-project.org/")
11238 (synopsis "R bindings to the MPFR library")
11240 "This package supports arithmetic (via S4 classes and methods) for
11241 arbitrary precision floating point numbers, including transcendental
11242 functions. To this end, the package interfaces with the @dfn{Multiple
11243 Precision Floating-Point Reliable} (MPFR) library.")
11244 (license license:gpl2+)))
11246 (define-public r-assertive-base
11248 (name "r-assertive-base")
11253 (uri (cran-uri "assertive.base" version))
11256 "1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
11258 `((upstream-name . "assertive.base")))
11259 (build-system r-build-system)
11260 (home-page "https://bitbucket.org/richierocks/assertive.base")
11261 (synopsis "Core of the assertive package")
11263 "This package provides a minimal set of predicates and assertions used by
11264 the assertive package. This is mainly for use by other package developers who
11265 want to include run-time testing features in their own packages.")
11266 (license license:gpl3+)))
11268 (define-public r-assertive-properties
11270 (name "r-assertive-properties")
11275 (uri (cran-uri "assertive.properties" version))
11278 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
11280 `((upstream-name . "assertive.properties")))
11281 (build-system r-build-system)
11283 `(("r-assertive-base" ,r-assertive-base)))
11284 (home-page "https://bitbucket.org/richierocks/assertive.properties")
11285 (synopsis "Assertions to check properties of variables")
11287 "This package provides a set of predicates and assertions for checking
11288 the properties of variables, such as length, names and attributes. This is
11289 mainly for use by other package developers who want to include run-time
11290 testing features in their own packages.")
11291 (license license:gpl3+)))
11293 (define-public r-assertive-numbers
11295 (name "r-assertive-numbers")
11300 (uri (cran-uri "assertive.numbers" version))
11303 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
11305 `((upstream-name . "assertive.numbers")))
11306 (build-system r-build-system)
11308 `(("r-assertive-base" ,r-assertive-base)))
11309 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
11310 (synopsis "Assertions to check properties of numbers")
11312 "This package provides a set of predicates and assertions for checking
11313 the properties of numbers. This is mainly for use by other package developers
11314 who want to include run-time testing features in their own packages.")
11315 (license license:gpl3+)))
11317 (define-public r-assertive-sets
11319 (name "r-assertive-sets")
11324 (uri (cran-uri "assertive.sets" version))
11327 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
11329 `((upstream-name . "assertive.sets")))
11330 (build-system r-build-system)
11332 `(("r-assertive-base" ,r-assertive-base)))
11333 (home-page "https://bitbucket.org/richierocks/assertive.sets")
11334 (synopsis "Assertions to check properties of sets")
11336 "This package provides a set of predicates and assertions for checking
11337 the properties of sets. This is mainly for use by other package developers
11338 who want to include run-time testing features in their own packages.")
11339 (license license:gpl3+)))
11341 (define-public r-assertive-matrices
11343 (name "r-assertive-matrices")
11348 (uri (cran-uri "assertive.matrices" version))
11351 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
11353 `((upstream-name . "assertive.matrices")))
11354 (build-system r-build-system)
11356 `(("r-assertive-base" ,r-assertive-base)))
11357 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
11358 (synopsis "Assertions to check properties of matrices")
11360 "This package provides a set of predicates and assertions for checking
11361 the properties of matrices. This is mainly for use by other package
11362 developers who want to include run-time testing features in their own
11364 (license license:gpl3+)))
11366 (define-public r-assertive-models
11368 (name "r-assertive-models")
11373 (uri (cran-uri "assertive.models" version))
11376 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
11378 `((upstream-name . "assertive.models")))
11379 (build-system r-build-system)
11381 `(("r-assertive-base" ,r-assertive-base)))
11382 (home-page "https://bitbucket.org/richierocks/assertive.models")
11383 (synopsis "Assertions to check properties of models")
11385 "This package provides a set of predicates and assertions for checking
11386 the properties of models. This is mainly for use by other package developers
11387 who want to include run-time testing features in their own packages.")
11388 (license license:gpl3+)))
11390 (define-public r-assertive-reflection
11392 (name "r-assertive-reflection")
11397 (uri (cran-uri "assertive.reflection" version))
11400 "19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
11402 `((upstream-name . "assertive.reflection")))
11403 (build-system r-build-system)
11405 `(("r-assertive-base" ,r-assertive-base)))
11406 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
11407 (synopsis "Assertions for checking the state of R")
11409 "This package provides a set of predicates and assertions for checking
11410 the state and capabilities of R, the operating system it is running on, and
11411 the IDE being used. This is mainly for use by other package developers who
11412 want to include run-time testing features in their own packages.")
11413 (license license:gpl3+)))
11415 (define-public r-assertive-types
11417 (name "r-assertive-types")
11422 (uri (cran-uri "assertive.types" version))
11425 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
11427 `((upstream-name . "assertive.types")))
11428 (build-system r-build-system)
11430 `(("r-assertive-base" ,r-assertive-base)
11431 ("r-assertive-properties" ,r-assertive-properties)
11432 ("r-codetools" ,r-codetools)))
11433 (home-page "https://bitbucket.org/richierocks/assertive.types")
11434 (synopsis "Assertions to check types of variables")
11436 "This package provides a set of predicates and assertions for checking
11437 the types of variables. This is mainly for use by other package developers
11438 who want to include run-time testing features in their own packages.")
11439 (license license:gpl3+)))
11441 (define-public r-assertive-files
11443 (name "r-assertive-files")
11448 (uri (cran-uri "assertive.files" version))
11451 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
11453 `((upstream-name . "assertive.files")))
11454 (build-system r-build-system)
11456 `(("r-assertive-base" ,r-assertive-base)
11457 ("r-assertive-numbers" ,r-assertive-numbers)))
11458 (home-page "https://bitbucket.org/richierocks/assertive.files")
11459 (synopsis "Assertions to check properties of files")
11461 "This package provides a set of predicates and assertions for checking
11462 the properties of files and connections. This is mainly for use by other
11463 package developers who want to include run-time testing features in their own
11465 (license license:gpl3+)))
11467 (define-public r-assertive-code
11469 (name "r-assertive-code")
11474 (uri (cran-uri "assertive.code" version))
11477 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
11479 `((upstream-name . "assertive.code")))
11480 (build-system r-build-system)
11482 `(("r-assertive-base" ,r-assertive-base)
11483 ("r-assertive-properties" ,r-assertive-properties)
11484 ("r-assertive-types" ,r-assertive-types)))
11485 (home-page "https://bitbucket.org/richierocks/assertive.code")
11486 (synopsis "Assertions to check properties of code")
11488 "This package provides a set of predicates and assertions for checking
11489 the properties of code. This is mainly for use by other package developers
11490 who want to include run-time testing features in their own packages.")
11491 (license license:gpl3+)))
11493 (define-public r-assertive-datetimes
11495 (name "r-assertive-datetimes")
11500 (uri (cran-uri "assertive.datetimes" version))
11503 "00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
11505 `((upstream-name . "assertive.datetimes")))
11506 (build-system r-build-system)
11508 `(("r-assertive-base" ,r-assertive-base)
11509 ("r-assertive-types" ,r-assertive-types)))
11510 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
11511 (synopsis "Assertions to check properties of dates and times")
11513 "This package provides a set of predicates and assertions for checking
11514 the properties of dates and times. This is mainly for use by other package
11515 developers who want to include run-time testing features in their own
11517 (license license:gpl3+)))
11519 (define-public r-assertive-strings
11521 (name "r-assertive-strings")
11526 (uri (cran-uri "assertive.strings" version))
11529 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
11531 `((upstream-name . "assertive.strings")))
11532 (build-system r-build-system)
11534 `(("r-assertive-base" ,r-assertive-base)
11535 ("r-assertive-types" ,r-assertive-types)
11536 ("r-stringi" ,r-stringi)))
11537 (home-page "https://bitbucket.org/richierocks/assertive.strings")
11538 (synopsis "Assertions to check properties of strings")
11540 "This package provides a set of predicates and assertions for checking
11541 the properties of strings. This is mainly for use by other package developers
11542 who want to include run-time testing features in their own packages.")
11543 (license license:gpl3+)))
11545 (define-public r-assertive-data-us
11547 (name "r-assertive-data-us")
11552 (uri (cran-uri "assertive.data.us" version))
11555 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
11557 `((upstream-name . "assertive.data.us")))
11558 (build-system r-build-system)
11560 `(("r-assertive-base" ,r-assertive-base)
11561 ("r-assertive-strings" ,r-assertive-strings)))
11562 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
11563 (synopsis "Assertions to check properties of strings")
11565 "This package provides a set of predicates and assertions for checking
11566 the properties of US-specific complex data types. This is mainly for use by
11567 other package developers who want to include run-time testing features in
11568 their own packages.")
11569 (license license:gpl3+)))
11571 (define-public r-assertive-data-uk
11573 (name "r-assertive-data-uk")
11578 (uri (cran-uri "assertive.data.uk" version))
11581 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
11583 `((upstream-name . "assertive.data.uk")))
11584 (build-system r-build-system)
11586 `(("r-assertive-base" ,r-assertive-base)
11587 ("r-assertive-strings" ,r-assertive-strings)))
11588 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
11589 (synopsis "Assertions to check properties of strings")
11591 "This package provides a set of predicates and assertions for checking
11592 the properties of UK-specific complex data types. This is mainly for use by
11593 other package developers who want to include run-time testing features in
11594 their own packages.")
11595 (license license:gpl3+)))
11597 (define-public r-assertive-data
11599 (name "r-assertive-data")
11604 (uri (cran-uri "assertive.data" version))
11607 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
11609 `((upstream-name . "assertive.data")))
11610 (build-system r-build-system)
11612 `(("r-assertive-base" ,r-assertive-base)
11613 ("r-assertive-strings" ,r-assertive-strings)))
11614 (home-page "https://bitbucket.org/richierocks/assertive.data")
11615 (synopsis "Assertions to check properties of data")
11617 "This package provides a set of predicates and assertions for checking
11618 the properties of (country independent) complex data types. This is mainly
11619 for use by other package developers who want to include run-time testing
11620 features in their own packages.")
11621 (license license:gpl3+)))
11623 (define-public r-assertive
11625 (name "r-assertive")
11630 (uri (cran-uri "assertive" version))
11633 "0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
11634 (build-system r-build-system)
11636 `(("r-assertive-base" ,r-assertive-base)
11637 ("r-assertive-code" ,r-assertive-code)
11638 ("r-assertive-data" ,r-assertive-data)
11639 ("r-assertive-data-uk" ,r-assertive-data-uk)
11640 ("r-assertive-data-us" ,r-assertive-data-us)
11641 ("r-assertive-datetimes" ,r-assertive-datetimes)
11642 ("r-assertive-files" ,r-assertive-files)
11643 ("r-assertive-matrices" ,r-assertive-matrices)
11644 ("r-assertive-models" ,r-assertive-models)
11645 ("r-assertive-numbers" ,r-assertive-numbers)
11646 ("r-assertive-properties" ,r-assertive-properties)
11647 ("r-assertive-reflection" ,r-assertive-reflection)
11648 ("r-assertive-sets" ,r-assertive-sets)
11649 ("r-assertive-strings" ,r-assertive-strings)
11650 ("r-assertive-types" ,r-assertive-types)
11651 ("r-knitr" ,r-knitr)))
11652 (home-page "https://bitbucket.org/richierocks/assertive")
11653 (synopsis "Readable check functions to ensure code integrity")
11655 "This package provides lots of predicates (@code{is_*} functions) to
11656 check the state of your variables, and assertions (@code{assert_*} functions)
11657 to throw errors if they aren't in the right form.")
11658 (license license:gpl3+)))
11660 (define-public r-dotcall64
11662 (name "r-dotcall64")
11667 (uri (cran-uri "dotCall64" version))
11670 "1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
11671 (properties `((upstream-name . "dotCall64")))
11672 (build-system r-build-system)
11673 (native-inputs `(("gfortran" ,gfortran)))
11674 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
11675 (synopsis "Enhanced foreign function interface supporting long vectors")
11677 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
11678 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
11679 supports long vectors, arguments of type 64-bit integer, and provides a
11680 mechanism to avoid unnecessary copies of read-only and write-only arguments.
11681 This makes it a convenient and fast interface to C/C++ and Fortran code.")
11682 (license license:gpl2+)))
11684 (define-public r-spam
11691 (uri (cran-uri "spam" version))
11693 (base32 "0ry0a76cljlmilrzcriiizcidxyhq1i7i9bqhvl1qda81ld8hifi"))))
11694 (build-system r-build-system)
11696 `(("r-dotcall64" ,r-dotcall64)))
11697 (native-inputs `(("gfortran" ,gfortran)))
11698 (home-page "https://www.math.uzh.ch/pages/spam/")
11699 (synopsis "Sparse matrix algebra")
11701 "This package provides a set of functions for sparse matrix algebra.
11702 Differences with other sparse matrix packages are:
11705 @item it only supports (essentially) one sparse matrix format;
11706 @item it is based on transparent and simple structure(s);
11707 @item it is tailored for MCMC calculations within G(M)RF;
11708 @item and it is fast and scalable (with the extension package @code{spam64}).
11710 ;; Either of these licenses
11711 (license (list license:bsd-3 license:lgpl2.0))))
11713 (define-public r-fields
11720 (uri (cran-uri "fields" version))
11722 (base32 "12k97vfjlz5h8vynirnvik1nyj1iw25n8xl7awmx9mpd6wvgy2s9"))))
11723 (build-system r-build-system)
11725 `(("r-maps" ,r-maps)
11726 ("r-spam" ,r-spam)))
11728 `(("gfortran" ,gfortran)))
11729 (home-page "https://www.image.ucar.edu/fields")
11730 (synopsis "Tools for spatial data")
11732 "This is a package for curve, surface and function fitting with an
11733 emphasis on splines, spatial data and spatial statistics. The major methods
11734 include cubic, and thin plate splines, Kriging, and compactly supported
11735 covariance functions for large data sets.")
11736 (license license:gpl2+)))
11738 (define-public r-spatialextremes
11740 (name "r-spatialextremes")
11745 (uri (cran-uri "SpatialExtremes" version))
11748 "0r2byz5xxc46zqnigdax28q7446ibmzmsmi10lmm2hdks3ml6sl3"))))
11750 `((upstream-name . "SpatialExtremes")))
11751 (build-system r-build-system)
11753 `(("r-fields" ,r-fields)
11754 ("r-maps" ,r-maps)))
11755 (home-page "http://spatialextremes.r-forge.r-project.org/")
11756 (synopsis "Modelling spatial extremes")
11758 "This package provides tools for the statistical modelling of spatial
11759 extremes using max-stable processes, copula or Bayesian hierarchical models.
11760 More precisely, this package allows (conditional) simulations from various
11761 parametric max-stable models, analysis of the extremal spatial dependence, the
11762 fitting of such processes using composite likelihoods or least square (simple
11763 max-stable processes only), model checking and selection and prediction.")
11764 (license license:gpl2+)))
11766 (define-public r-drc
11773 (uri (cran-uri "drc" version))
11776 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
11777 (build-system r-build-system)
11780 ("r-gtools" ,r-gtools)
11782 ("r-multcomp" ,r-multcomp)
11783 ("r-plotrix" ,r-plotrix)
11784 ("r-scales" ,r-scales)))
11785 (home-page "https://cran.r-project.org/web/packages/drc")
11786 (synopsis "Analysis of dose-response curves")
11788 "This package provides a suite of flexible and versatile model fitting
11789 and after-fitting functions for the analysis of dose-response data.")
11790 (license license:gpl2+)))
11792 (define-public r-rmeta
11799 (uri (cran-uri "rmeta" version))
11802 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
11803 (build-system r-build-system)
11804 (home-page "https://cran.r-project.org/web/packages/rmeta")
11805 (synopsis "Tools for meta-analysis")
11807 "This package provides functions for simple fixed and random effects
11808 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
11809 draws standard summary plots, funnel plots, and computes summaries and tests
11810 for association and heterogeneity.")
11811 (license license:gpl2)))
11813 (define-public r-bootstrap
11815 (name "r-bootstrap")
11820 (uri (cran-uri "bootstrap" version))
11823 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
11824 (build-system r-build-system)
11825 (native-inputs `(("gfortran" ,gfortran)))
11826 (home-page "https://cran.r-project.org/web/packages/bootstrap")
11827 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
11829 "This package provides software and data for the book \"An Introduction
11830 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
11831 This package is primarily provided for projects already based on it, and for
11832 support of the book. New projects should preferentially use the recommended
11833 package \"boot\".")
11834 (license license:bsd-3)))
11836 (define-public r-survivalroc
11838 (name "r-survivalroc")
11843 (uri (cran-uri "survivalROC" version))
11846 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
11847 (properties `((upstream-name . "survivalROC")))
11848 (build-system r-build-system)
11849 (home-page "https://cran.r-project.org/web/packages/survivalROC")
11850 (synopsis "Time-dependent ROC curve estimation from censored survival data")
11852 "Compute time-dependent ROC curve from censored survival data using
11853 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
11854 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
11855 (license license:gpl2+)))
11857 (define-public r-longitudinal
11859 (name "r-longitudinal")
11864 (uri (cran-uri "longitudinal" version))
11867 "1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
11868 (build-system r-build-system)
11869 (propagated-inputs `(("r-corpcor" ,r-corpcor)))
11870 (home-page "http://strimmerlab.org/software/longitudinal/")
11871 (synopsis "Analysis of multiple time course data")
11873 "This package contains general data structures and functions for
11874 longitudinal data with multiple variables, repeated measurements, and
11875 irregularly spaced time points. It also implements a shrinkage estimator of
11876 dynamical correlation and dynamical covariance.")
11877 (license license:gpl3+)))
11879 (define-public r-genenet
11886 (uri (cran-uri "GeneNet" version))
11889 "11ba6ahsk3x9alvcw8bai2bpg84ki1m8nadrjjdhjg65svhw8njm"))))
11890 (properties `((upstream-name . "GeneNet")))
11891 (build-system r-build-system)
11893 `(("r-corpcor" ,r-corpcor)
11894 ("r-fdrtool" ,r-fdrtool)
11895 ("r-longitudinal" ,r-longitudinal)))
11896 (home-page "http://strimmerlab.org/software/genenet/")
11897 (synopsis "Modeling and inferring gene networks")
11899 "This package analyzes gene expression (time series) data with focus on
11900 the inference of gene networks. In particular, GeneNet implements the methods
11901 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
11902 for learning large-scale gene association networks (including assignment of
11903 putative directions).")
11904 (license license:gpl3+)))
11906 (define-public r-rbamtools
11908 (name "r-rbamtools")
11909 (version "2.16.17")
11913 (uri (cran-uri "rbamtools" version))
11916 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
11917 (build-system r-build-system)
11918 (inputs `(("zlib" ,zlib)))
11920 `(("r-refgenome" ,r-refgenome)))
11921 (home-page "https://cran.r-project.org/web/packages/rbamtools")
11922 (synopsis "Read and write BAM (binary alignment) files")
11924 "This package provides an R interface to functions of the SAMtools
11926 (license license:artistic2.0)))
11928 (define-public r-protviz
11935 (uri (cran-uri "protViz" version))
11938 "0rn8fjg7791a4j2k1kk1jwx40xz20bfaavvflmhyzpl398vmmy3a"))))
11939 (properties `((upstream-name . "protViz")))
11940 (build-system r-build-system)
11941 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
11942 (home-page "https://github.com/protViz/protViz/")
11943 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
11945 "This package helps with quality checks, visualizations and analysis of
11946 mass spectrometry data, coming from proteomics experiments. The package is
11947 developed, tested and used at the Functional Genomics Center Zurich, where it
11948 is used mainly for prototyping, teaching, and having fun with proteomics data.
11949 But it can also be used to do data analysis for small scale data sets.")
11950 (license license:gpl3)))
11952 (define-public r-cmprsk
11959 (uri (cran-uri "cmprsk" version))
11961 (base32 "1xnx2zanw548prxsw2zw5cddkkg6kj97jgyzw67achq5mnsvfbg8"))))
11962 (build-system r-build-system)
11964 `(("r-survival" ,r-survival)))
11966 `(("gfortran" ,gfortran)))
11967 (home-page "https://cran.r-project.org/web/packages/cmprsk")
11968 (synopsis "Subdistribution analysis of competing risks")
11970 "This package provides tool for estimation, testing and regression
11971 modeling of subdistribution functions in competing risks, as described in
11972 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
11973 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
11974 A proportional hazards model for the subdistribution of a competing risk,
11975 JASA, 94:496-509.")
11976 (license license:gpl2+)))
11978 (define-public r-etm
11985 (uri (cran-uri "etm" version))
11988 "02yvh473l5qajaymhsxwb235a9r7q3nsig9a9mrfca68xih8yvgd"))))
11989 (build-system r-build-system)
11991 `(("r-data-table" ,r-data-table)
11992 ("r-lattice" ,r-lattice)
11994 ("r-rcpparmadillo" ,r-rcpparmadillo)
11995 ("r-survival" ,r-survival)))
11996 (home-page "https://cran.r-project.org/web/packages/etm")
11997 (synopsis "Empirical transition matrix")
11999 "The @dfn{empirical transition matrix} (etm) package estimates
12000 the matrix of transition probabilities for any time-inhomogeneous multistate
12001 model with finite state space using the Aalen-Johansen estimator.")
12002 (license license:expat)))
12004 (define-public r-epi
12011 (uri (cran-uri "Epi" version))
12014 "046y10vwks5y84pzccmrn6d4pd6qz70imvp1hw5ywp8fnwzfh4g5"))))
12015 (properties `((upstream-name . "Epi")))
12016 (build-system r-build-system)
12018 `(("r-cmprsk" ,r-cmprsk)
12019 ("r-data-table" ,r-data-table)
12022 ("r-matrix" ,r-matrix)
12024 ("r-numderiv" ,r-numderiv)
12026 ("r-survival" ,r-survival)
12028 (home-page "https://BendixCarstensen.com/Epi/")
12029 (synopsis "Statistical analysis in epidemiology")
12031 "This package provides functions for demographic and epidemiological
12032 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
12033 particular representation, manipulation and simulation of multistate data -
12034 the Lexis suite of functions, which includes interfaces to the @code{mstate},
12035 @code{etm} and @code{cmprsk} packages. It also contains functions for
12036 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
12037 data and some useful functions for tabulation and plotting, as well as a
12038 number of epidemiological data sets.")
12039 (license license:gpl2)))
12041 (define-public r-ppls
12044 (version "1.6-1.1")
12048 (uri (cran-uri "ppls" version))
12051 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
12052 (build-system r-build-system)
12053 (propagated-inputs `(("r-mass" ,r-mass)))
12054 (home-page "https://cran.r-project.org/web/packages/ppls")
12055 (synopsis "Penalized partial least squares")
12057 "This package contains linear and nonlinear regression methods based on
12058 partial least squares and penalization techniques. Model parameters are
12059 selected via cross-validation, and confidence intervals ans tests for the
12060 regression coefficients can be conducted via jackknifing.")
12061 (license license:gpl2+)))
12063 (define-public r-huge
12066 (version "1.3.4.1")
12070 (uri (cran-uri "huge" version))
12072 (base32 "11m80dnaxqw5v006q6kvhndl2y5ih5553fcqg4jcaljd8sp9xvvq"))))
12073 (build-system r-build-system)
12075 `(("r-igraph" ,r-igraph)
12077 ("r-matrix" ,r-matrix)
12079 ("r-rcppeigen" ,r-rcppeigen)))
12080 (home-page "https://cran.r-project.org/web/packages/huge")
12081 (synopsis "High-dimensional undirected graph estimation")
12083 "This package provides a general framework for high-dimensional
12084 undirected graph estimation. It integrates data preprocessing, neighborhood
12085 screening, graph estimation, and model selection techniques into a pipeline.")
12086 (license license:gpl2)))
12088 (define-public r-parcor
12095 (uri (cran-uri "parcor" version))
12098 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
12099 (build-system r-build-system)
12102 ("r-genenet" ,r-genenet)
12103 ("r-glmnet" ,r-glmnet)
12105 ("r-ppls" ,r-ppls)))
12106 (home-page "https://cran.r-project.org/web/packages/parcor")
12107 (synopsis "Regularized estimation of partial correlation matrices")
12109 "This package estimates the matrix of partial correlations based on
12110 different regularized regression methods: lasso, adaptive lasso, PLS, and
12111 Ridge Regression. In addition, the package provides model selection for
12112 lasso, adaptive lasso and Ridge regression based on cross-validation.")
12113 (license license:gpl2+)))
12115 (define-public r-mcmc
12122 (uri (cran-uri "mcmc" version))
12125 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
12126 (build-system r-build-system)
12127 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
12128 (synopsis "Markov chain Monte Carlo")
12130 "This package simulates continuous distributions of random vectors using
12131 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
12132 function that evaluates the log unnormalized density. Algorithms are random
12133 walk Metropolis algorithm (function @code{metrop}), simulated
12134 tempering (function @code{temper}), and morphometric random walk
12135 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
12136 by change of variable.")
12137 (license license:expat)))
12139 (define-public r-listenv
12146 (uri (cran-uri "listenv" version))
12149 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
12150 (build-system r-build-system)
12152 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12153 (home-page "https://github.com/HenrikBengtsson/listenv")
12154 (synopsis "Environments behaving (almost) as lists")
12156 "This package implements list environments. List environments are
12157 environments that have list-like properties. For instance, the elements of a
12158 list environment are ordered and can be accessed and iterated over using index
12160 (license license:lgpl2.1+)))
12162 (define-public r-globals
12169 (uri (cran-uri "globals" version))
12172 "1ha8iasgijp4q3v2b0b17y1wh7cd3nvzd9b03w49qm2bidkaf68m"))))
12173 (build-system r-build-system)
12175 `(("r-codetools" ,r-codetools)))
12176 (home-page "https://github.com/HenrikBengtsson/globals")
12177 (synopsis "Identify global objects in R expressions")
12179 "This package provides tools to identify global (\"unknown\" or \"free\")
12180 objects in R expressions by code inspection using various strategies, e.g.
12181 conservative or liberal. The objective of this package is to make it as
12182 simple as possible to identify global objects for the purpose of exporting
12183 them in distributed compute environments.")
12184 (license license:lgpl2.1+)))
12186 (define-public r-future
12193 (uri (cran-uri "future" version))
12196 "0d4y7gwcgqx2z0y6h5bh4lrz0m7b0inii5cjcq0kk8za762bi8rg"))))
12197 (build-system r-build-system)
12199 `(("r-digest" ,r-digest)
12200 ("r-globals" ,r-globals)
12201 ("r-listenv" ,r-listenv)))
12203 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12204 (home-page "https://github.com/HenrikBengtsson/future")
12205 (synopsis "Unified parallel and distributed processing in R")
12207 "The purpose of this package is to provide a lightweight and unified
12208 Future API for sequential and parallel processing of R expression via futures.
12209 This package implements sequential, multicore, multisession, and cluster
12210 futures. With these, R expressions can be evaluated on the local machine, in
12211 parallel a set of local machines, or distributed on a mix of local and remote
12212 machines. Extensions to this package implement additional backends for
12213 processing futures via compute cluster schedulers etc. Because of its unified
12214 API, there is no need to modify any code in order to switch from sequential on
12215 the local machine to, say, distributed processing on a remote compute cluster.")
12216 (license license:lgpl2.1+)))
12218 (define-public r-future-apply
12220 (name "r-future-apply")
12225 (uri (cran-uri "future.apply" version))
12228 "1zbfycjfvxnrigm6l2fd2zgnw96g0apiw426c73gkv3xv7bdy6ms"))))
12229 (properties `((upstream-name . "future.apply")))
12230 (build-system r-build-system)
12232 `(("r-future" ,r-future)
12233 ("r-globals" ,r-globals)))
12235 `(("r-r-rsp" ,r-r-rsp))) ; vignette builder
12236 (home-page "https://github.com/HenrikBengtsson/future.apply")
12237 (synopsis "Apply function to elements in parallel using futures")
12239 "This package provides implementations of @code{apply()},
12240 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
12241 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
12242 can be resolved using any future-supported backend, e.g. parallel on the local
12243 machine or distributed on a compute cluster.")
12244 (license license:gpl2+)))
12246 (define-public r-rsvd
12253 (uri (cran-uri "rsvd" version))
12256 "1fvrw46fl5xb2akaa4mp8nja4h7nn4bdhnjdrk22fsdfqc7hwmhk"))))
12257 (build-system r-build-system)
12259 `(("r-matrix" ,r-matrix)))
12260 (home-page "https://github.com/erichson/rSVD")
12261 (synopsis "Randomized singular value decomposition")
12263 "Low-rank matrix decompositions are fundamental tools and widely used for
12264 data analysis, dimension reduction, and data compression. Classically, highly
12265 accurate deterministic matrix algorithms are used for this task. However, the
12266 emergence of large-scale data has severely challenged our computational
12267 ability to analyze big data. The concept of randomness has been demonstrated
12268 as an effective strategy to quickly produce approximate answers to familiar
12269 problems such as the @dfn{singular value decomposition} (SVD). This package
12270 provides several randomized matrix algorithms such as the randomized singular
12271 value decomposition (@code{rsvd}), randomized principal component
12272 analysis (@code{rpca}), randomized robust principal component
12273 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
12274 and the randomized CUR decomposition (@code{rcur}). In addition several plot
12275 functions are provided.")
12276 (license license:gpl3+)))
12278 (define-public r-sloop
12285 (uri (cran-uri "sloop" version))
12288 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
12289 (build-system r-build-system)
12291 `(("r-codetools" ,r-codetools)
12292 ("r-crayon" ,r-crayon)
12293 ("r-purrr" ,r-purrr)
12294 ("r-rlang" ,r-rlang)
12295 ("r-tibble" ,r-tibble)))
12296 (home-page "https://github.com/r-lib/sloop")
12297 (synopsis "Helpers for object-oriented programming in R")
12299 "This package provides a collection of helper functions designed to
12300 help you to better understand object oriented programming in R, particularly
12302 (license license:gpl3)))
12304 (define-public r-capushe
12311 (uri (cran-uri "capushe" version))
12314 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
12315 (build-system r-build-system)
12316 (propagated-inputs `(("r-mass" ,r-mass)))
12317 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
12318 (synopsis "Calibrating penalties using slope heuristics")
12320 "This package provides tools for the calibration of penalized criteria
12321 for model selection. The calibration methods available are based on the slope
12323 (license license:gpl2+)))
12325 (define-public r-dorng
12332 (uri (cran-uri "doRNG" version))
12335 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
12336 (properties `((upstream-name . "doRNG")))
12337 (build-system r-build-system)
12339 `(("r-foreach" ,r-foreach)
12340 ("r-iterators" ,r-iterators)
12341 ("r-rngtools" ,r-rngtools)))
12342 (home-page "https://renozao.github.io/doRNG/")
12343 (synopsis "Generic reproducible parallel backend for foreach loops")
12345 "This package provides functions to perform reproducible parallel
12346 @code{foreach} loops, using independent random streams as generated by
12347 L'Ecuyer's combined multiple-recursive generator. It enables to easily
12348 convert standard @code{%dopar%} loops into fully reproducible loops,
12349 independently of the number of workers, the task scheduling strategy, or the
12350 chosen parallel environment and associated foreach backend.")
12351 (license license:gpl2+)))
12353 (define-public r-blockmodeling
12355 (name "r-blockmodeling")
12360 (uri (cran-uri "blockmodeling" version))
12363 "1z4w2kq0id0gb5d0lqcdaw3clplhzywarkpvvx3drivdypzl237i"))))
12364 (build-system r-build-system)
12366 `(("r-matrix" ,r-matrix)))
12367 (native-inputs `(("gfortran" ,gfortran)))
12368 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
12369 (synopsis "Generalized and classical blockmodeling of valued networks")
12371 "This package is primarily meant as an implementation of generalized
12372 blockmodeling for valued networks. In addition, measures of similarity or
12373 dissimilarity based on structural equivalence and regular equivalence (REGE
12374 algorithms) can be computed and partitioned matrices can be plotted.")
12375 (license license:gpl2+)))
12377 (define-public r-upsetr
12384 (uri (cran-uri "UpSetR" version))
12387 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
12388 (properties `((upstream-name . "UpSetR")))
12389 (build-system r-build-system)
12391 `(("r-ggplot2" ,r-ggplot2)
12392 ("r-gridextra" ,r-gridextra)
12394 ("r-scales" ,r-scales)))
12395 (home-page "https://github.com/hms-dbmi/UpSetR")
12396 (synopsis "Visualize intersecting sets")
12398 "This package provides a more scalable alternative to Venn and Euler
12399 diagrams for visualizing intersecting sets. Create visualizations of
12400 intersecting sets using a novel matrix design, along with visualizations of
12401 several common set, element and attribute related tasks.")
12402 (license license:expat)))
12404 ;; This package includes a JavaScript file, which is not minified. When
12405 ;; upgrading please check that there are no new minified JavaScript files.
12406 (define-public r-shinybs
12413 (uri (cran-uri "shinyBS" version))
12416 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
12417 (properties `((upstream-name . "shinyBS")))
12418 (build-system r-build-system)
12419 ;; The tests spawn Shiny browser apps. They cannot be run
12420 ;; non-interactively.
12421 (arguments '(#:tests? #f))
12423 `(("r-htmltools" ,r-htmltools)
12424 ("r-shiny" ,r-shiny)))
12425 (home-page "https://ebailey78.github.io/shinyBS/")
12426 (synopsis "Twitter Bootstrap components for Shiny")
12428 "This package adds additional Twitter Bootstrap components to Shiny.")
12429 (license license:gpl3)))
12431 (define-public r-outliers
12433 (name "r-outliers")
12438 (uri (cran-uri "outliers" version))
12441 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
12442 (build-system r-build-system)
12443 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
12444 (synopsis "Tests for outliers")
12446 "This package provides a collection of some tests commonly used for
12447 identifying outliers.")
12448 (license license:gpl2+)))
12450 (define-public r-bayesm
12457 (uri (cran-uri "bayesm" version))
12459 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
12460 (build-system r-build-system)
12462 `(("r-rcpp" ,r-rcpp)
12463 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12464 (home-page "http://www.perossi.org/home/bsm-1")
12465 (synopsis "Bayesian inference for marketing/micro-econometrics")
12467 "This package covers many important models used in marketing and
12468 micro-econometrics applications, including Bayes Regression (univariate or
12469 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
12470 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
12471 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
12472 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
12473 Estimation with normal base, Hierarchical Linear Models with normal prior and
12474 covariates, Hierarchical Linear Models with a mixture of normals prior and
12475 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
12476 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
12477 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
12478 analysis of choice-based conjoint data, Bayesian treatment of linear
12479 instrumental variables models, Analysis of Multivariate Ordinal survey data
12480 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
12481 Coefficient Logit Models.")
12482 (license license:gpl2+)))
12484 (define-public r-tensora
12491 (uri (cran-uri "tensorA" version))
12494 "176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
12495 (properties `((upstream-name . "tensorA")))
12496 (build-system r-build-system)
12497 (home-page "http://www.stat.boogaart.de/tensorA")
12498 (synopsis "Advanced tensor arithmetic with named indices")
12500 "This package provides convenience functions for advanced linear algebra
12501 with tensors and computation with datasets of tensors on a higher level
12502 abstraction. It includes Einstein and Riemann summing conventions, dragging,
12503 co- and contravariate indices, and parallel computations on sequences of
12505 (license license:gpl2+)))
12507 (define-public r-rarpack
12514 (uri (cran-uri "rARPACK" version))
12517 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
12518 (properties `((upstream-name . "rARPACK")))
12519 (build-system r-build-system)
12520 (propagated-inputs `(("r-rspectra" ,r-rspectra)))
12521 (home-page "https://github.com/yixuan/rARPACK")
12522 (synopsis "Solvers for large scale eigenvalue and SVD problems")
12524 "This package was previously an R wrapper of the ARPACK library, and now
12525 a shell of the R package RSpectra, an R interface to the Spectra library for
12526 solving large scale eigenvalue/vector problems. The current version of
12527 rARPACK simply imports and exports the functions provided by RSpectra. New
12528 users of rARPACK are advised to switch to the RSpectra package.")
12529 (license license:bsd-3)))
12531 (define-public r-compositions
12533 (name "r-compositions")
12538 (uri (cran-uri "compositions" version))
12541 "0l9ayz2nb2wqhl7v9hkfl7pd950ba0h6hma8zqncbcxh6xh2k7l7"))))
12542 (build-system r-build-system)
12544 `(("r-bayesm" ,r-bayesm)
12545 ("r-robustbase" ,r-robustbase)
12546 ("r-tensora" ,r-tensora)))
12547 (home-page "http://www.stat.boogaart.de/compositions")
12548 (synopsis "Compositional data analysis")
12550 "This package provides functions for the consistent analysis of
12551 compositional data (e.g. portions of substances) and positive
12552 numbers (e.g. concentrations).")
12553 (license license:gpl2+)))
12555 (define-public r-cobs
12562 (uri (cran-uri "cobs" version))
12565 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
12566 (build-system r-build-system)
12568 `(("r-quantreg" ,r-quantreg)
12569 ("r-sparsem" ,r-sparsem)))
12570 (home-page "https://cran.r-project.org/web/packages/cobs")
12571 (synopsis "Constrained B-Splines (sparse matrix based)")
12573 "This package provides qualitatively constrained (regression) smoothing
12574 splines via linear programming and sparse matrices.")
12575 (license license:gpl2+)))
12577 (define-public r-drimpute
12579 (name "r-drimpute")
12584 (uri (cran-uri "DrImpute" version))
12587 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
12588 (properties `((upstream-name . "DrImpute")))
12589 (build-system r-build-system)
12591 `(("r-rcpp" ,r-rcpp)
12592 ("r-rcpparmadillo" ,r-rcpparmadillo)))
12593 (home-page "https://github.com/ikwak2/DrImpute")
12594 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
12596 "This is an R package for imputing dropout events. Many statistical
12597 methods in cell type identification, visualization and lineage reconstruction
12598 do not account for dropout events. DrImpute can improve the performance of
12599 such software by imputing dropout events.")
12600 (license license:gpl3)))
12602 (define-public r-gamlss-dist
12604 (name "r-gamlss-dist")
12609 (uri (cran-uri "gamlss.dist" version))
12611 (base32 "1p904x0b07z4amaqdn2xhs7qzbq8lisr6lqc844s3pkxzmny7w1z"))))
12612 (properties `((upstream-name . "gamlss.dist")))
12613 (build-system r-build-system)
12614 (propagated-inputs `(("r-mass" ,r-mass)))
12615 (home-page "http://www.gamlss.org/")
12616 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
12618 "This package provides a set of distributions which can be used for
12619 modelling the response variables in Generalized Additive Models for Location
12620 Scale and Shape. The distributions can be continuous, discrete or mixed
12621 distributions. Extra distributions can be created, by transforming, any
12622 continuous distribution defined on the real line, to a distribution defined on
12623 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
12624 transformation, respectively.")
12625 ;; Either version of the GPL.
12626 (license (list license:gpl2 license:gpl3))))
12628 ;; This package includes JavaScript files, which are not minified. When
12629 ;; upgrading please check that there are no new minified JavaScript files.
12630 (define-public r-shinyjs
12637 (uri (cran-uri "shinyjs" version))
12640 "14k8y313ppj23m9rhlk8jc94x6sbn3qrsnx6xrijiyv8m8dii1l9"))))
12641 (build-system r-build-system)
12643 `(("r-digest" ,r-digest)
12644 ("r-htmltools" ,r-htmltools)
12645 ("r-jsonlite" ,r-jsonlite)
12646 ("r-shiny" ,r-shiny)))
12647 (home-page "https://deanattali.com/shinyjs")
12648 (synopsis "Improve the user experience of your Shiny apps")
12650 "Perform common useful JavaScript operations in Shiny apps that will
12651 greatly improve your apps without having to know any JavaScript. Examples
12652 include: hiding an element, disabling an input, resetting an input back to its
12653 original value, delaying code execution by a few seconds, and many more useful
12654 functions for both the end user and the developer. Shinyjs can also be used
12655 to easily call your own custom JavaScript functions from R.")
12656 (license license:agpl3+)))
12658 ;; This package includes minified JavaScript files. When upgrading please
12659 ;; check that there are no new minified JavaScript files.
12660 (define-public r-colourpicker
12662 (name "r-colourpicker")
12667 (uri (cran-uri "colourpicker" version))
12670 "0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
12671 (build-system r-build-system)
12673 `(#:modules ((guix build utils)
12674 (guix build r-build-system)
12678 (modify-phases %standard-phases
12679 (add-after 'unpack 'process-javascript
12680 (lambda* (#:key inputs #:allow-other-keys)
12681 (with-directory-excursion "inst"
12685 `((,(assoc-ref inputs "js-salvattore")
12686 "examples/colourInput/www/salvattore.min.js")
12687 (,(assoc-ref inputs "js-jquery")
12688 "htmlwidgets/lib/jquery/jquery.min.js")
12689 ("www/shared/colourpicker/js/colourpicker.js"
12690 "www/shared/colourpicker/js/colourpicker.min.js"))))
12691 (lambda (sources targets)
12692 (for-each (lambda (source target)
12693 (format #t "Processing ~a --> ~a~%"
12695 (delete-file target)
12696 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
12697 (call-with-output-file target
12699 (dump-port minified port)))))
12700 sources targets))))
12703 `(("r-ggplot2" ,r-ggplot2)
12704 ("r-htmltools" ,r-htmltools)
12705 ("r-htmlwidgets" ,r-htmlwidgets)
12706 ("r-jsonlite" ,r-jsonlite)
12707 ("r-miniui" ,r-miniui)
12708 ("r-shiny" ,r-shiny)
12709 ("r-shinyjs" ,r-shinyjs)))
12711 `(("uglify-js" ,uglify-js)
12715 (uri "https://code.jquery.com/jquery-3.3.1.js")
12718 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
12722 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
12725 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
12726 (home-page "https://github.com/daattali/colourpicker")
12727 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
12729 "This package provides a color picker that can be used as an input in
12730 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
12731 custom color palettes, and many more options. A plot color helper tool is
12732 available as an RStudio Addin, which helps you pick colors to use in your
12733 plots. A more generic color picker RStudio Addin is also provided to let you
12734 select colors to use in your R code.")
12735 (license license:expat)))
12737 (define-public r-ggextra
12744 (uri (cran-uri "ggExtra" version))
12747 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
12748 (properties `((upstream-name . "ggExtra")))
12749 (build-system r-build-system)
12751 `(("r-colourpicker" ,r-colourpicker)
12752 ("r-ggplot2" ,r-ggplot2)
12753 ("r-gtable" ,r-gtable)
12754 ("r-miniui" ,r-miniui)
12756 ("r-scales" ,r-scales)
12757 ("r-shiny" ,r-shiny)
12758 ("r-shinyjs" ,r-shinyjs)))
12760 `(("r-knitr" ,r-knitr)))
12761 (home-page "https://github.com/daattali/ggExtra")
12762 (synopsis "Marginal histograms for ggplot2 and other enhancements")
12764 "This package is a collection of functions and layers to enhance ggplot2.
12765 The flagship function is @code{ggMarginal()}, which can be used to add
12766 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
12767 (license license:expat)))
12769 (define-public r-minpack-lm
12771 (name "r-minpack-lm")
12776 (uri (cran-uri "minpack.lm" version))
12779 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
12780 (properties `((upstream-name . "minpack.lm")))
12781 (build-system r-build-system)
12782 (native-inputs `(("gfortran" ,gfortran)))
12783 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
12784 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
12786 "The @code{nls.lm} function provides an R interface to @code{lmder} and
12787 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
12788 problems by a modification of the Levenberg-Marquardt algorithm, with support
12789 for lower and upper parameter bounds. The implementation can be used via
12790 @code{nls}-like calls using the @code{nlsLM} function.")
12791 (license license:gpl3)))
12793 (define-public r-moments
12800 (uri (cran-uri "moments" version))
12803 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
12804 (build-system r-build-system)
12805 (home-page "https://cran.r-project.org/web/packages/moments")
12806 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
12808 "This package provides functions to calculate: moments, Pearson's
12809 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
12810 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
12811 (license license:gpl2+)))
12813 (define-public r-msir
12820 (uri (cran-uri "msir" version))
12823 "0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
12824 (build-system r-build-system)
12826 `(("r-mclust" ,r-mclust)))
12827 (home-page "https://cran.r-project.org/web/packages/msir")
12828 (synopsis "Model-based sliced inverse regression")
12830 "This is an R package for dimension reduction based on finite Gaussian
12831 mixture modeling of inverse regression.")
12832 (license license:gpl2+)))
12834 (define-public r-pbivnorm
12836 (name "r-pbivnorm")
12841 (uri (cran-uri "pbivnorm" version))
12844 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
12845 (build-system r-build-system)
12846 (native-inputs `(("gfortran" ,gfortran)))
12847 (home-page "https://github.com/brentonk/pbivnorm")
12848 (synopsis "Vectorized bivariate normal CDF")
12850 "This package provides a vectorized R function for calculating
12851 probabilities from a standard bivariate normal CDF.")
12852 (license license:gpl2+)))
12854 (define-public r-lavaan
12861 (uri (cran-uri "lavaan" version))
12864 "0sfv58r2kxinax62bx6j3kkfx07qm16ddwf5qz392q33h9zs009h"))))
12865 (build-system r-build-system)
12867 `(("r-mass" ,r-mass)
12868 ("r-mnormt" ,r-mnormt)
12869 ("r-numderiv" ,r-numderiv)
12870 ("r-pbivnorm" ,r-pbivnorm)))
12871 (home-page "http://lavaan.ugent.be")
12872 (synopsis "Latent variable analysis")
12874 "This package provides tools to fit a variety of latent variable models,
12875 including confirmatory factor analysis, structural equation modeling and
12876 latent growth curve models.")
12877 (license license:gpl2+)))
12879 (define-public r-nonnest2
12881 (name "r-nonnest2")
12886 (uri (cran-uri "nonnest2" version))
12889 "07nr54hxdnc4k022nd4a2g9w9l9ym2ikfr978rrnqc71wx750i0z"))))
12890 (build-system r-build-system)
12892 `(("r-compquadform" ,r-compquadform)
12893 ("r-lavaan" ,r-lavaan)
12894 ("r-mvtnorm" ,r-mvtnorm)
12895 ("r-sandwich" ,r-sandwich)))
12897 `(("r-knitr" ,r-knitr)))
12898 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
12899 (synopsis "Tests of non-nested models")
12901 "This package allows for testing of non-nested models. It includes tests
12902 of model distinguishability and of model fit that can be applied to both
12903 nested and non-nested models. The package also includes functionality to
12904 obtain confidence intervals associated with AIC and BIC.")
12905 ;; Either version of the GPL.
12906 (license (list license:gpl2 license:gpl3))))
12908 (define-public r-penalized
12910 (name "r-penalized")
12915 (uri (cran-uri "penalized" version))
12918 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
12919 (build-system r-build-system)
12921 `(("r-rcpp" ,r-rcpp)
12922 ("r-rcpparmadillo" ,r-rcpparmadillo)
12923 ("r-survival" ,r-survival)))
12924 (home-page "https://cran.r-project.org/web/packages/penalized/")
12925 (synopsis "Penalized estimation in GLMs and in the Cox model")
12927 "This package provides tools for fitting possibly high dimensional
12928 penalized regression models. The penalty structure can be any combination of
12929 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
12930 constraint on the regression coefficients. The supported regression models
12931 are linear, logistic and Poisson regression and the Cox Proportional Hazards
12932 model. Cross-validation routines allow optimization of the tuning
12934 (license license:gpl2+)))
12936 (define-public r-zim
12943 (uri (cran-uri "ZIM" version))
12946 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
12947 (properties `((upstream-name . "ZIM")))
12948 (build-system r-build-system)
12949 (propagated-inputs `(("r-mass" ,r-mass)))
12950 (home-page "https://github.com/biostatstudio/ZIM")
12951 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
12953 "Analyze count time series with excess zeros. Two types of statistical
12954 models are supported: Markov regression and state-space models. They are also
12955 known as observation-driven and parameter-driven models respectively in the
12956 time series literature. The functions used for Markov regression or
12957 observation-driven models can also be used to fit ordinary regression models
12958 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
12959 negative binomial (ZINB) assumption. The package also contains miscellaneous
12960 functions to compute density, distribution, quantile, and generate random
12961 numbers from ZIP and ZINB distributions.")
12962 (license license:gpl3)))
12964 (define-public r-nor1mix
12971 (uri (cran-uri "nor1mix" version))
12974 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
12975 (build-system r-build-system)
12976 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
12977 (synopsis "Normal (1-d) mixture models")
12979 "This package provides S3 classes and methods for one-dimensional normal
12980 mixture models, for, e.g., density estimation or clustering algorithms
12981 research and teaching; it provides the widely used Marron-Wand densities. It
12982 also provides tools for efficient random number generation and graphics.")
12983 (license license:gpl2+)))
12985 (define-public r-beanplot
12987 (name "r-beanplot")
12992 (uri (cran-uri "beanplot" version))
12995 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
12996 (build-system r-build-system)
12997 (home-page "https://cran.r-project.org/web/packages/beanplot/")
12998 (synopsis "Visualization via beanplots")
13000 "This package provides beanplots, an alternative to
13001 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
13003 (license license:gpl2)))
13005 (define-public r-pbdzmq
13012 (uri (cran-uri "pbdZMQ" version))
13015 "1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
13016 (properties `((upstream-name . "pbdZMQ")))
13017 (build-system r-build-system)
13019 `(("zeromq" ,zeromq)
13022 `(("pkg-config" ,pkg-config)))
13023 (home-page "https://pbdr.org/")
13024 (synopsis "R interface to ZeroMQ")
13026 "ZeroMQ is a well-known library for high-performance asynchronous
13027 messaging in scalable, distributed applications. This package provides high
13028 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
13029 interactive client/server programming frameworks. A few wrapper functions
13030 compatible with @code{rzmq} are also provided.")
13031 (license license:gpl3)))
13033 (define-public r-repr
13040 (uri (cran-uri "repr" version))
13043 "15jz780w4nd9qjd1g3gq8f5lkh60p2v3ig3hm5kl1rg3z4cf0gvl"))))
13044 (build-system r-build-system)
13046 `(("r-base64enc" ,r-base64enc)
13047 ("r-htmltools" ,r-htmltools)
13048 ("r-jsonlite" ,r-jsonlite)
13049 ("r-pillar" ,r-pillar)))
13050 (home-page "https://cran.r-project.org/web/packages/repr/")
13051 (synopsis "Serializable representations")
13053 "This package provides string and binary representations of objects for
13054 several formats and MIME types.")
13055 (license license:gpl3)))
13057 (define-public r-irdisplay
13059 (name "r-irdisplay")
13064 (uri (cran-uri "IRdisplay" version))
13067 "12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
13068 (properties `((upstream-name . "IRdisplay")))
13069 (build-system r-build-system)
13071 `(("r-repr" ,r-repr)))
13072 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
13073 (synopsis "Jupyter display machinery")
13075 "This package provides an interface to the rich display capabilities of
13076 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
13077 running IRkernel session.")
13078 (license license:expat)))
13080 (define-public r-irkernel
13082 (name "r-irkernel")
13087 (uri (cran-uri "IRkernel" version))
13090 "1viqxs91dys1z4cf7gb59rmqvzb8lc7jdp4azrpmhgwa8qf46s94"))))
13091 (properties `((upstream-name . "IRkernel")))
13092 (build-system r-build-system)
13095 (modify-phases %standard-phases
13096 (add-after 'install 'install-kernelspec
13097 (lambda* (#:key outputs #:allow-other-keys)
13098 (let ((out (assoc-ref outputs "out")))
13099 (setenv "HOME" "/tmp")
13100 (invoke "jupyter" "kernelspec" "install"
13103 (string-append out "/site-library/IRkernel/kernelspec"))
13104 ;; Record the absolute file name of the 'R' executable in
13106 (substitute* (string-append out "/share/jupyter"
13107 "/kernels/ir/kernel.json")
13109 (string-append "[\"" (which "R") "\",")))
13112 `(("jupyter" ,jupyter)))
13114 `(("r-crayon" ,r-crayon)
13115 ("r-digest" ,r-digest)
13116 ("r-evaluate" ,r-evaluate)
13117 ("r-irdisplay" ,r-irdisplay)
13118 ("r-jsonlite" ,r-jsonlite)
13119 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
13120 ("r-minimal" ,r-minimal)
13121 ("r-pbdzmq" ,r-pbdzmq)
13123 ("r-uuid" ,r-uuid)))
13124 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
13125 (synopsis "Native R kernel for Jupyter")
13127 "The R kernel for the Jupyter environment executes R code which the
13128 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
13130 (license license:expat)))
13132 (define-public r-gmodels
13139 (uri (cran-uri "gmodels" version))
13142 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
13143 (build-system r-build-system)
13145 `(("r-gdata" ,r-gdata)
13146 ("r-mass" ,r-mass)))
13147 (home-page "https://cran.r-project.org/web/packages/gmodels/")
13148 (synopsis "Various R programming tools for model fitting")
13150 "This package provides various R programming tools for model fitting.")
13151 (license license:gpl2)))
13153 (define-public r-apcluster
13155 (name "r-apcluster")
13160 (uri (cran-uri "apcluster" version))
13163 "0lzf2jqm56i74wif6x5sw3j0w2qc4sni49zq2fgbl89b7lwkvchj"))))
13164 (build-system r-build-system)
13166 `(("r-matrix" ,r-matrix)
13167 ("r-rcpp" ,r-rcpp)))
13168 (home-page "https://cran.r-project.org/web/packages/apcluster/")
13169 (synopsis "Affinity propagation clustering")
13171 "This package implements affinity propagation clustering introduced by
13172 Frey and Dueck (2007). The package further provides leveraged affinity
13173 propagation and an algorithm for exemplar-based agglomerative clustering that
13174 can also be used to join clusters obtained from affinity propagation. Various
13175 plotting functions are available for analyzing clustering results.")
13176 (license license:gpl2+)))
13178 (define-public r-valr
13185 (uri (cran-uri "valr" version))
13188 "1qxw6h63i2vfb2w6q453zzwk0ypma3xdwwpj15i06669vzgyy3bb"))))
13189 (build-system r-build-system)
13191 `(("r-broom" ,r-broom)
13192 ("r-dplyr" ,r-dplyr)
13193 ("r-ggplot2" ,r-ggplot2)
13195 ("r-readr" ,r-readr)
13196 ("r-rlang" ,r-rlang)
13197 ("r-stringr" ,r-stringr)
13198 ("r-tibble" ,r-tibble)))
13200 `(("r-knitr" ,r-knitr)))
13201 (home-page "http://github.com/rnabioco/valr")
13202 (synopsis "Genome interval arithmetic in R")
13204 "This package enables you to read and manipulate genome intervals and
13205 signals. It provides functionality similar to command-line tool suites within
13206 R, enabling interactive analysis and visualization of genome-scale data.")
13207 (license license:expat)))
13209 (define-public r-rematch2
13211 (name "r-rematch2")
13216 (uri (cran-uri "rematch2" version))
13219 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
13220 (build-system r-build-system)
13222 `(("r-tibble" ,r-tibble)))
13223 (home-page "https://github.com/r-lib/rematch2")
13224 (synopsis "Tidy output from regular expression matching")
13226 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
13227 return the match results in tidy data frames.")
13228 (license license:expat)))
13230 (define-public r-picante
13237 (uri (cran-uri "picante" version))
13240 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
13241 (build-system r-build-system)
13245 ("r-vegan" ,r-vegan)))
13246 (home-page "https://cran.r-project.org/web/packages/picante/")
13247 (synopsis "Integrating phylogenies and ecology")
13249 "This package provides functions for phylocom integration, community
13250 analyses, null-models, traits and evolution. It implements numerous
13251 ecophylogenetic approaches including measures of community phylogenetic and
13252 trait diversity, phylogenetic signal, estimation of trait values for
13253 unobserved taxa, null models for community and phylogeny randomizations, and
13254 utility functions for data input/output and phylogeny plotting. A full
13255 description of package functionality and methods are provided by Kembel et
13257 (license license:gpl2)))
13259 (define-public r-reinforcelearn
13261 (name "r-reinforcelearn")
13266 (uri (cran-uri "reinforcelearn" version))
13269 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
13270 (build-system r-build-system)
13272 `(("r-checkmate" ,r-checkmate)
13274 ("r-purrr" ,r-purrr)
13276 (home-page "https://markusdumke.github.io/reinforcelearn")
13277 (synopsis "Reinforcement learning")
13279 "This package implements reinforcement learning environments and
13280 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
13281 can be used with function approximation, eligibility traces (Singh & Sutton,
13282 1996) and experience replay (Mnih et al., 2013).")
13283 (license license:expat)))
13285 (define-public r-lemon
13292 (uri (cran-uri "lemon" version))
13295 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
13296 (build-system r-build-system)
13298 `(("r-ggplot2" ,r-ggplot2)
13299 ("r-gridextra" ,r-gridextra)
13300 ("r-gtable" ,r-gtable)
13301 ("r-knitr" ,r-knitr)
13302 ("r-lattice" ,r-lattice)
13304 ("r-rlang" ,r-rlang)
13305 ("r-scales" ,r-scales)))
13307 `(("r-knitr" ,r-knitr)))
13308 (home-page "https://github.com/stefanedwards/lemon")
13309 (synopsis "Freshen up your ggplot2 plots")
13311 "This package provides functions for working with legends and axis lines
13312 of ggplot2, facets that repeat axis lines on all panels, and some knitr
13314 (license license:gpl3)))
13316 (define-public r-wgaim
13323 (uri (cran-uri "wgaim" version))
13325 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
13326 (build-system r-build-system)
13328 `(("r-ggplot2" ,r-ggplot2)
13330 (home-page "https://cran.r-project.org/web/packages/wgaim")
13331 (synopsis "Whole genome average interval mapping for QTL detection")
13333 "This package integrates sophisticated mixed modelling methods with a
13334 whole genome approach to detecting significant QTL in linkage maps.")
13335 (license license:gpl2+)))
13337 (define-public r-bedr
13344 (uri (cran-uri "bedr" version))
13347 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
13348 (build-system r-build-system)
13350 `(("r-data-table" ,r-data-table)
13351 ("r-r-utils" ,r-r-utils)
13352 ("r-testthat" ,r-testthat)
13353 ("r-venndiagram" ,r-venndiagram)
13356 ("bedtools" ,bedtools)
13357 ("htslib" ,htslib))) ; for tabix
13359 `(("r-knitr" ,r-knitr))) ; for vignettes
13360 (home-page "https://cran.r-project.org/web/packages/bedr")
13361 (synopsis "Genomic region processing")
13363 "This package is for genomic regions processing using command line tools
13364 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
13365 utilities to perform genome arithmetic e.g indexing, formatting and merging.
13366 The bedr package's API enhances access to these tools as well as offers
13367 additional utilities for genomic regions processing.")
13368 (license license:gpl2)))
13370 (define-public r-sets
13377 (uri (cran-uri "sets" version))
13380 "16v7650p47khqrbbw0z98llmwmmhswqmhri0n7nrfhdqwmby1lbl"))))
13381 (properties `((upstream-name . "sets")))
13382 (build-system r-build-system)
13383 (home-page "https://cran.r-project.org/web/packages/sets")
13384 (synopsis "Sets, generalized sets, customizable sets and intervals")
13386 "This package provides data structures and basic operations for ordinary
13387 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
13388 customizable sets, and intervals.")
13389 (license license:gpl2)))
13391 (define-public r-partitions
13393 (name "r-partitions")
13398 (uri (cran-uri "partitions" version))
13401 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
13402 (build-system r-build-system)
13405 ("r-polynom" ,r-polynom)
13406 ("r-sets" ,r-sets)))
13407 (home-page "https://cran.r-project.org/web/packages/partitions")
13408 (synopsis "Additive partitions of integers")
13410 "This package provides tools to enumerates the partitions, unequal
13411 partitions, and restricted partitions of an integer; the three corresponding
13412 partition functions are also given.")
13413 ;; Any version of the GPL
13414 (license license:gpl2+)))
13416 (define-public r-brobdingnag
13418 (name "r-brobdingnag")
13423 (uri (cran-uri "Brobdingnag" version))
13426 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
13427 (properties `((upstream-name . "Brobdingnag")))
13428 (build-system r-build-system)
13429 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
13430 (synopsis "Very large numbers in R")
13432 "This package handles very large numbers in R. Real numbers are held
13433 using their natural logarithms, plus a logical flag indicating sign. The
13434 package includes a vignette that gives a step-by-step introduction to using S4
13436 ;; Any version of the GPL
13437 (license license:gpl2+)))
13439 (define-public r-untb
13446 (uri (cran-uri "untb" version))
13449 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
13450 (build-system r-build-system)
13452 `(("r-brobdingnag" ,r-brobdingnag)
13453 ("r-partitions" ,r-partitions)
13454 ("r-polynom" ,r-polynom)))
13455 (home-page "https://github.com/RobinHankin/untb.git")
13456 (synopsis "Ecological drift under the UNTB")
13458 "This package provides numerical simulations, and visualizations, of
13459 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
13460 (license license:gpl2+)))
13462 (define-public r-stepwise
13464 (name "r-stepwise")
13469 (uri (cran-uri "stepwise" version))
13472 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
13473 (build-system r-build-system)
13474 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
13475 (synopsis "Stepwise detection of recombination breakpoints")
13477 "This package provides a stepwise approach to identifying recombination
13478 breakpoints in a genomic sequence alignment.")
13479 (license license:gpl2+)))
13481 (define-public r-snpmaxsel
13483 (name "r-snpmaxsel")
13488 (uri (cran-uri "SNPmaxsel" version))
13491 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
13492 (properties `((upstream-name . "SNPmaxsel")))
13493 (build-system r-build-system)
13495 `(("r-combinat" ,r-combinat)
13496 ("r-mvtnorm" ,r-mvtnorm)))
13497 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
13498 (synopsis "Maximally selected statistics for SNP data")
13500 "This package implements asymptotic methods related to maximally selected
13501 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
13503 (license license:gpl2+)))
13505 (define-public r-acsnminer
13507 (name "r-acsnminer")
13508 (version "0.16.8.25")
13511 (uri (cran-uri "ACSNMineR" version))
13514 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
13515 (properties `((upstream-name . "ACSNMineR")))
13516 (build-system r-build-system)
13518 `(("r-ggplot2" ,r-ggplot2)
13519 ("r-gridextra" ,r-gridextra)))
13520 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
13521 (synopsis "Gene enrichment analysis")
13523 "This package provides tools to compute and represent gene set enrichment
13524 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
13525 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
13526 enrichment can be run with hypergeometric test or Fisher exact test, and can
13527 use multiple corrections. Visualization of data can be done either by
13528 barplots or heatmaps.")
13529 (license license:gpl2+)))
13531 (define-public r-seqinr
13538 (uri (cran-uri "seqinr" version))
13541 "0j30za6kji6y3v09cvcydiacnp65pv6ig8aw7cydl47l5s9chky4"))))
13542 (build-system r-build-system)
13544 `(("r-ade4" ,r-ade4)
13545 ("r-segmented" ,r-segmented)))
13548 (home-page "http://seqinr.r-forge.r-project.org/")
13549 (synopsis "Biological sequences retrieval and analysis")
13551 "This package provides tools for exploratory data analysis and data
13552 visualization of biological sequence (DNA and protein) data. It also includes
13553 utilities for sequence data management under the ACNUC system.")
13554 (license license:gpl2+)))
13556 (define-public r-units
13563 (uri (cran-uri "units" version))
13566 "1rdpbkiqcabz00fqzzs98v89v4cgvcd4pb00pwxzkq6vmwmscwrz"))))
13567 (build-system r-build-system)
13569 `(("udunits" ,udunits)))
13571 `(("r-rcpp" ,r-rcpp)))
13573 `(("r-knitr" ,r-knitr)))
13574 (home-page "https://github.com/r-quantities/units/")
13575 (synopsis "Measurement Units for R Vectors")
13577 "This package provides support for measurement units in R vectors,
13578 matrices and arrays: automatic propagation, conversion, derivation and
13579 simplification of units; raising errors in case of unit incompatibility. It
13580 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
13582 (license license:gpl2)))
13584 (define-public r-classint
13586 (name "r-classint")
13591 (uri (cran-uri "classInt" version))
13594 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
13595 (properties `((upstream-name . "classInt")))
13596 (build-system r-build-system)
13598 `(("r-class" ,r-class)
13599 ("r-e1071" ,r-e1071)
13600 ("r-kernsmooth" ,r-kernsmooth)))
13602 `(("gfortran" ,gfortran)
13603 ("r-knitr" ,r-knitr)))
13604 (home-page "https://github.com/r-spatial/classInt/")
13605 (synopsis "Choose univariate class intervals")
13607 "This package provides selected commonly used methods for choosing
13608 univariate class intervals for mapping or other graphics purposes.")
13609 (license license:gpl2+)))
13611 (define-public r-spdata
13618 (uri (cran-uri "spData" version))
13621 "09l9j1vjbfyc8mikb8kliqmdjkg4xigq3zhdx98mv51flh5q87lh"))))
13622 (properties `((upstream-name . "spData")))
13623 (build-system r-build-system)
13625 `(("r-raster" ,r-raster)
13627 (home-page "https://github.com/Nowosad/spData")
13628 (synopsis "Datasets for spatial analysis")
13630 "This a package containing diverse spatial datasets for demonstrating,
13631 benchmarking and teaching spatial data analysis. It includes R data of class
13632 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
13633 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
13634 of the datasets are designed to illustrate specific analysis techniques.
13635 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
13636 illustrate point pattern analysis techniques.")
13637 (license license:cc0)))
13639 (define-public r-learnbayes
13641 (name "r-learnbayes")
13646 (uri (cran-uri "LearnBayes" version))
13649 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
13650 (properties `((upstream-name . "LearnBayes")))
13651 (build-system r-build-system)
13652 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
13653 (synopsis "Functions for learning Bayesian inference")
13655 "This package provides a collection of functions helpful in learning the
13656 basic tenets of Bayesian statistical inference. It contains functions for
13657 summarizing basic one and two parameter posterior distributions and predictive
13658 distributions. It contains MCMC algorithms for summarizing posterior
13659 distributions defined by the user. It also contains functions for regression
13660 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
13662 (license license:gpl2+)))
13664 (define-public r-deldir
13671 (uri (cran-uri "deldir" version))
13674 "0kdglv8rc1pb4ilcid4xc9wpv5kkj2y6x6wg7919k3hya7mz58ph"))))
13675 (build-system r-build-system)
13676 (native-inputs `(("gfortran" ,gfortran)))
13677 (home-page "https://cran.r-project.org/web/packages/deldir")
13678 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
13680 "This package provides tools for calculating the Delaunay triangulation
13681 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
13682 of a planar point set. It plots triangulations and tessellations in various
13683 ways, clips tessellations to sub-windows, calculates perimeters of
13684 tessellations, and summarizes information about the tiles of the
13686 (license license:gpl2+)))
13688 (define-public r-sf
13695 (uri (cran-uri "sf" version))
13698 "1xgmnz01pxvpg2ins1h65mlcrafqihlljcjlag8spq9ii7d5i7mx"))))
13699 (build-system r-build-system)
13706 `(("r-classint" ,r-classint)
13708 ("r-magrittr" ,r-magrittr)
13710 ("r-units" ,r-units)))
13712 `(("pkg-config" ,pkg-config)
13713 ("r-knitr" ,r-knitr)))
13714 (home-page "https://github.com/r-spatial/sf/")
13715 (synopsis "Simple features for R")
13717 "This package provides support for simple features, a standardized way to
13718 encode spatial vector data. It binds to GDAL for reading and writing data, to
13719 GEOS for geometrical operations, and to PROJ for projection conversions and
13720 datum transformations.")
13721 ;; Either of these licenses
13722 (license (list license:gpl2 license:expat))))
13724 (define-public r-spdep
13731 (uri (cran-uri "spdep" version))
13734 "0pbd7wrg5v44p2yxsjp774lpyzap3madir5mn5p3ix7ibk7ldjs7"))))
13735 (build-system r-build-system)
13737 `(("r-boot" ,r-boot)
13739 ("r-deldir" ,r-deldir)
13741 ("r-gmodels" ,r-gmodels)
13742 ("r-learnbayes" ,r-learnbayes)
13744 ("r-matrix" ,r-matrix)
13748 ("r-spdata" ,r-spdata)))
13750 `(("r-knitr" ,r-knitr)))
13751 (home-page "https://github.com/r-spatial/spdep/")
13752 (synopsis "Spatial dependence: weighting schemes, statistics and models")
13754 "This package provides a collection of functions to create spatial
13755 weights matrix objects from polygon contiguities, from point patterns by
13756 distance and tessellations, for summarizing these objects, and for permitting
13757 their use in spatial data analysis, including regional aggregation by minimum
13759 (license license:gpl2+)))
13761 (define-public r-adegenet
13763 (name "r-adegenet")
13768 (uri (cran-uri "adegenet" version))
13771 "1ipnawi0qfd4rfwj37igvh36x1a9d8x4n7xynn1jcr12rd713407"))))
13772 (build-system r-build-system)
13774 `(("r-ade4" ,r-ade4)
13777 ("r-dplyr" ,r-dplyr)
13778 ("r-ggplot2" ,r-ggplot2)
13779 ("r-igraph" ,r-igraph)
13781 ("r-reshape2" ,r-reshape2)
13782 ("r-seqinr" ,r-seqinr)
13783 ("r-shiny" ,r-shiny)
13784 ("r-spdep" ,r-spdep)
13785 ("r-vegan" ,r-vegan)))
13786 (home-page "https://github.com/thibautjombart/adegenet")
13787 (synopsis "Exploratory analysis of genetic and genomic data")
13789 "This package provides a toolset for the exploration of genetic and
13790 genomic data. Adegenet provides formal (S4) classes for storing and handling
13791 various genetic data, including genetic markers with varying ploidy and
13792 hierarchical population structure (@code{genind} class), alleles counts by
13793 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
13794 also implements original multivariate methods (DAPC, sPCA), graphics,
13795 statistical tests, simulation tools, distance and similarity measures, and
13796 several spatial methods. A range of both empirical and simulated datasets is
13797 also provided to illustrate various methods.")
13798 (license license:gpl2+)))
13800 (define-public r-pegas
13807 (uri (cran-uri "pegas" version))
13809 (base32 "002i7s4g0nhnq0v05gs0yssqiyhpq2f7rw2rhn31hsbgxc86frvy"))))
13810 (build-system r-build-system)
13812 `(("r-adegenet" ,r-adegenet)
13814 (home-page "http://ape-package.ird.fr/pegas.html")
13815 (synopsis "Population and evolutionary genetics analysis system")
13817 "This package provides functions for reading, writing, plotting,
13818 analysing, and manipulating allelic and haplotypic data, including from VCF
13819 files, and for the analysis of population nucleotide sequences and
13820 micro-satellites including coalescent analyses, linkage disequilibrium,
13821 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
13822 minimum spanning tree and network, and median-joining networks.")
13823 (license license:gpl2+)))
13825 (define-public r-rmetasim
13827 (name "r-rmetasim")
13832 (uri (cran-uri "rmetasim" version))
13835 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
13836 (build-system r-build-system)
13838 `(("r-ade4" ,r-ade4)
13839 ("r-adegenet" ,r-adegenet)
13840 ("r-gtools" ,r-gtools)
13841 ("r-pegas" ,r-pegas)))
13842 (home-page "https://cran.r-project.org/web/packages/rmetasim")
13843 (synopsis "Individual-based population genetic simulation environment")
13845 "This package provides an interface between R and the metasim simulation
13846 engine. The simulation environment is documented in: Strand, A.(2002),
13847 Metasim 1.0: an individual-based environment for simulating population
13848 genetics of complex population dynamics.")
13850 (license license:gpl2+)))
13852 (define-public r-genetics
13854 (name "r-genetics")
13855 (version "1.3.8.1.2")
13859 (uri (cran-uri "genetics" version))
13862 "1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
13863 (build-system r-build-system)
13865 `(("r-combinat" ,r-combinat)
13866 ("r-gdata" ,r-gdata)
13867 ("r-gtools" ,r-gtools)
13869 ("r-mvtnorm" ,r-mvtnorm)))
13870 (home-page "https://cran.r-project.org/web/packages/genetics/")
13871 (synopsis "Population genetics")
13873 "This package provides classes and methods for handling genetic data.
13874 It includes classes to represent genotypes and haplotypes at single markers up
13875 to multiple markers on multiple chromosomes. Function include allele
13876 frequencies, flagging homo/heterozygotes, flagging carriers of certain
13877 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
13878 and testing for linkage disequilibrium, ...")
13879 ;; Any GPL version.
13880 (license license:gpl2+)))
13882 (define-public r-snp-plotter
13884 (name "r-snp-plotter")
13889 (uri (cran-uri "snp.plotter" version))
13892 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
13893 (properties `((upstream-name . "snp.plotter")))
13894 (build-system r-build-system)
13895 (propagated-inputs `(("r-genetics" ,r-genetics)))
13896 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
13897 (synopsis "Plot p-values using single SNP and/or haplotype data")
13899 "This package helps you create plots of p-values using single SNP and/or
13900 haplotype data. Main features of the package include options to display a
13901 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
13902 datasets simultaneously. Plots can be created using global and/or individual
13903 haplotype p-values along with single SNP p-values. Images are created as
13904 either PDF/EPS files.")
13905 (license license:gpl2+)))
13907 (define-public r-polspline
13909 (name "r-polspline")
13914 (uri (cran-uri "polspline" version))
13916 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
13917 (build-system r-build-system)
13918 (native-inputs `(("gfortran" ,gfortran)))
13919 (home-page "https://cran.r-project.org/web/packages/polspline/")
13920 (synopsis "Polynomial spline routines")
13922 "This package provides routines for the polynomial spline fitting
13923 routines hazard regression, hazard estimation with flexible tails, logspline,
13924 lspec, polyclass, and polymars.")
13925 (license license:gpl2+)))
13927 (define-public r-rms
13934 (uri (cran-uri "rms" version))
13936 (base32 "0m88m63d19qz03x8v56h4rrblln3d2943spi1v4wxxnbcdk22np9"))))
13937 (build-system r-build-system)
13939 `(("r-cluster" ,r-cluster)
13940 ("r-digest" ,r-digest)
13941 ("r-ggplot2" ,r-ggplot2)
13942 ("r-hmisc" ,r-hmisc)
13943 ("r-htmltable" ,r-htmltable)
13944 ("r-htmltools" ,r-htmltools)
13945 ("r-lattice" ,r-lattice)
13947 ("r-multcomp" ,r-multcomp)
13949 ("r-polspline" ,r-polspline)
13950 ("r-quantreg" ,r-quantreg)
13951 ("r-rpart" ,r-rpart)
13952 ("r-sparsem" ,r-sparsem)
13953 ("r-survival" ,r-survival)))
13954 (native-inputs `(("gfortran" ,gfortran)))
13955 (home-page "http://biostat.mc.vanderbilt.edu/rms")
13956 (synopsis "Regression modeling strategies")
13958 "This is a package for regression modeling, testing, estimation,
13959 validation, graphics, prediction, and typesetting by storing enhanced model
13960 design attributes in the fit. The rms package is a collection of functions
13961 that assist with and streamline modeling. It also contains functions for
13962 binary and ordinal logistic regression models, ordinal models for continuous Y
13963 with a variety of distribution families, and the Buckley-James multiple
13964 regression model for right-censored responses, and implements penalized
13965 maximum likelihood estimation for logistic and ordinary linear models. The
13966 package works with almost any regression model, but it was especially written
13967 to work with binary or ordinal regression models, Cox regression, accelerated
13968 failure time models, ordinary linear models, the Buckley-James model,
13969 generalized least squares for serially or spatially correlated observations,
13970 generalized linear models, and quantile regression.")
13971 (license license:gpl2+)))
13973 (define-public r-haplo-stats
13975 (name "r-haplo-stats")
13980 (uri (cran-uri "haplo.stats" version))
13983 "19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
13984 (properties `((upstream-name . "haplo.stats")))
13985 (build-system r-build-system)
13987 `(("r-rms" ,r-rms)))
13989 `(("r-r-rsp" ,r-r-rsp))) ; for vignettes
13990 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
13991 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
13993 "This package provides routines for the analysis of indirectly measured
13994 haplotypes. The statistical methods assume that all subjects are unrelated
13995 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
13996 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
13997 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
13998 examples in the vignette.")
13999 (license license:gpl2+)))
14001 (define-public r-bqtl
14008 (uri (cran-uri "bqtl" version))
14011 "0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
14012 (build-system r-build-system)
14013 (native-inputs `(("gfortran" ,gfortran)))
14014 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
14015 (synopsis "Bayesian QTL mapping toolkit")
14017 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
14018 lines. It includes maximum likelihood and Bayesian tools.")
14019 (license license:gpl2+)))
14021 (define-public r-ibdreg
14028 (uri (cran-uri "ibdreg" version))
14031 "1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
14032 (build-system r-build-system)
14033 (home-page "https://www.mayo.edu/research/labs/\
14034 statistical-genetics-genetic-epidemiology/software")
14035 (synopsis "Regression methods for IBD linkage with covariates")
14037 "This package provides a method to test genetic linkage with covariates
14038 by regression methods with response IBD sharing for relative pairs. Account
14039 for correlations of IBD statistics and covariates for relative pairs within
14040 the same pedigree.")
14041 (license license:gpl2+)))
14043 (define-public r-dlmap
14050 (uri (cran-uri "dlmap" version))
14053 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
14054 (build-system r-build-system)
14056 `(("r-ibdreg" ,r-ibdreg)
14060 ("r-wgaim" ,r-wgaim)))
14061 (home-page "https://cran.r-project.org/web/packages/dlmap/")
14062 (synopsis "Detection localization mapping for QTL")
14064 "This is package for QTL mapping in a mixed model framework with separate
14065 detection and localization stages. The first stage detects the number of QTL
14066 on each chromosome based on the genetic variation due to grouped markers on
14067 the chromosome; the second stage uses this information to determine the most
14068 likely QTL positions. The mixed model can accommodate general fixed and
14069 random effects, including spatial effects in field trials and pedigree
14070 effects. It is applicable to backcrosses, doubled haploids, recombinant
14071 inbred lines, F2 intercrosses, and association mapping populations.")
14072 (license license:gpl2)))
14074 (define-public r-ldheatmap
14076 (name "r-ldheatmap")
14081 (uri (cran-uri "LDheatmap" version))
14084 "1x3da3rbhyqb2ddngi48qv7vzb6vc347n9qhryr70qgcc1xvqj4z"))))
14085 (properties `((upstream-name . "LDheatmap")))
14086 (build-system r-build-system)
14088 `(("r-genetics" ,r-genetics)
14090 ("r-snpstats" ,r-snpstats)))
14091 (home-page "https://stat.sfu.ca/statgen/research/ldheatmap.html")
14092 (synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
14094 "This package provides tools to produce a graphical display, as a heat
14095 map, of measures of pairwise linkage disequilibria between SNPs. Users may
14096 optionally include the physical locations or genetic map distances of each SNP
14098 (license license:gpl3)))
14100 (define-public r-hwde
14107 (uri (cran-uri "hwde" version))
14110 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
14111 (build-system r-build-system)
14112 (home-page "https://cran.r-project.org/web/packages/hwde/")
14113 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
14115 "This package fits models for genotypic disequilibria, as described in
14116 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
14117 terms are available that account for first order interactions between loci.
14118 It also implements, for a single locus in a single population, a conditional
14119 exact test for Hardy-Weinberg equilibrium.")
14120 (license license:gpl2+)))
14122 (define-public r-tdthap
14129 (uri (cran-uri "tdthap" version))
14132 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
14133 (build-system r-build-system)
14134 (home-page "https://cran.r-project.org/web/packages/tdthap/")
14135 (synopsis "TDT tests for extended haplotypes")
14137 "Functions and examples are provided for transmission/disequilibrium
14138 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
14139 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
14140 (license license:artistic2.0)))
14142 (define-public r-sparql
14148 (uri (cran-uri "SPARQL" version))
14151 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
14152 (properties `((upstream-name . "SPARQL")))
14153 (build-system r-build-system)
14155 `(("r-rcurl" ,r-rcurl)
14157 (home-page "https://cran.r-project.org/web/packages/SPARQL")
14158 (synopsis "SPARQL client for R")
14159 (description "This package provides an interface to use SPARQL to pose
14160 SELECT or UPDATE queries to an end-point.")
14161 ;; The only license indication is found in the DESCRIPTION file,
14162 ;; which states GPL-3. So we cannot assume GPLv3+.
14163 (license license:gpl3)))
14165 (define-public r-bookdown
14167 (name "r-bookdown")
14171 (uri (cran-uri "bookdown" version))
14174 "0gnshkp1aj7f29sjkhzxn890hz39nwaqdln61x8apmrc658nacdg"))))
14175 (build-system r-build-system)
14177 `(("r-htmltools" ,r-htmltools)
14178 ("r-knitr" ,r-knitr)
14179 ("r-rmarkdown" ,r-rmarkdown)
14180 ("r-tinytex" ,r-tinytex)
14182 ("pandoc" ,ghc-pandoc)))
14183 (home-page "https://github.com/rstudio/bookdown")
14184 (synopsis "Authoring books and technical documents with R markdown")
14185 (description "This package provides output formats and utilities for
14186 authoring books and technical documents with R Markdown.")
14187 (license license:gpl3)))
14189 (define-public r-optparse
14191 (name "r-optparse")
14196 (uri (cran-uri "optparse" version))
14199 "1l301dy3gc8pn7j00awcjh41wmc1ks9kswak255kbsa6f54rsxsi"))))
14200 (build-system r-build-system)
14202 `(("r-getopt" ,r-getopt)))
14204 `(("r-knitr" ,r-knitr)))
14205 (home-page "https://github.com/trevorld/optparse")
14206 (synopsis "Command line option parser")
14208 "This package provides a command line parser inspired by Python's
14209 @code{optparse} library to be used with Rscript to write shebang scripts
14210 that accept short and long options.")
14211 (license license:gpl2+)))
14213 (define-public r-wgcna
14220 (uri (cran-uri "WGCNA" version))
14223 "022hkprnrafvggi8pkjffkvk1qlnibmbbxxrni00wkrdbga5589f"))))
14224 (properties `((upstream-name . "WGCNA")))
14225 (build-system r-build-system)
14227 `(("r-annotationdbi" ,r-annotationdbi)
14228 ("r-doparallel" ,r-doparallel)
14229 ("r-dynamictreecut" ,r-dynamictreecut)
14230 ("r-fastcluster" ,r-fastcluster)
14231 ("r-foreach" ,r-foreach)
14232 ("r-go-db" ,r-go-db)
14233 ("r-hmisc" ,r-hmisc)
14234 ("r-impute" ,r-impute)
14236 ("r-survival" ,r-survival)
14237 ("r-matrixstats" ,r-matrixstats)
14238 ("r-preprocesscore" ,r-preprocesscore)))
14240 "http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
14241 (synopsis "Weighted correlation network analysis")
14243 "This package provides functions necessary to perform Weighted
14244 Correlation Network Analysis on high-dimensional data. It includes functions
14245 for rudimentary data cleaning, construction and summarization of correlation
14246 networks, module identification and functions for relating both variables and
14247 modules to sample traits. It also includes a number of utility functions for
14248 data manipulation and visualization.")
14249 (license license:gpl2+)))
14251 (define-public r-kernlab
14258 (uri (cran-uri "kernlab" version))
14260 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
14261 (build-system r-build-system)
14262 (home-page "https://cran.r-project.org/web/packages/kernlab")
14263 (synopsis "Kernel-based machine learning tools")
14265 "This package provides kernel-based machine learning methods for
14266 classification, regression, clustering, novelty detection, quantile regression
14267 and dimensionality reduction. Among other methods @code{kernlab} includes
14268 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
14270 (license license:gpl2)))
14272 (define-public r-hierfstat
14274 (name "r-hierfstat")
14275 (version "0.04-22")
14279 (uri (cran-uri "hierfstat" version))
14282 "1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
14283 (build-system r-build-system)
14285 `(("r-ade4" ,r-ade4)
14286 ("r-adegenet" ,r-adegenet)
14287 ("r-gtools" ,r-gtools)))
14288 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
14289 (synopsis "Estimation and tests of hierarchical F-statistics")
14291 "This package allows the estimation of hierarchical F-statistics from
14292 haploid or diploid genetic data with any numbers of levels in the hierarchy,
14293 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
14294 are also given to test via randomisations the significance of each F and
14295 variance components, using the likelihood-ratio statistics G.")
14296 (license license:gpl2+)))
14298 (define-public r-hapassoc
14300 (name "r-hapassoc")
14305 (uri (cran-uri "hapassoc" version))
14308 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
14309 (build-system r-build-system)
14310 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
14311 (synopsis "Inference of trait associations with SNP haplotypes")
14313 "Hapassoc performs likelihood inference of trait associations with
14314 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
14315 functions are developed primarily for data collected in cohort or
14316 cross-sectional studies. They can accommodate uncertain haplotype phase and
14317 handle missing genotypes at some SNPs.")
14318 (license license:gpl2)))
14320 (define-public r-sampling
14322 (name "r-sampling")
14327 (uri (cran-uri "sampling" version))
14330 "06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
14331 (build-system r-build-system)
14333 `(("r-lpsolve" ,r-lpsolve)
14334 ("r-mass" ,r-mass)))
14335 (home-page "https://cran.r-project.org/web/packages/sampling/")
14336 (synopsis "Survey sampling")
14338 "This package provides functions for drawing and calibrating samples.")
14339 (license license:gpl2+)))
14341 (define-public r-r2html
14348 (uri (cran-uri "R2HTML" version))
14351 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
14352 (properties `((upstream-name . "R2HTML")))
14353 (build-system r-build-system)
14354 (home-page "https://github.com/nalimilan/R2HTML")
14355 (synopsis "HTML export for R objects")
14357 "This package includes HTML functions and methods to write in an HTML
14358 file. Thus, making HTML reports is easy. It includes a function that allows
14359 redirection on the fly, which appears to be very useful for teaching purposes,
14360 as the student can keep a copy of the produced output to keep all that they
14361 did during the course. The package comes with a vignette describing how to
14362 write HTML reports for statistical analysis. Finally, a driver for Sweave
14363 parses HTML flat files containing R code and to automatically write
14364 the corresponding outputs (tables and graphs).")
14365 (license license:gpl2+)))
14367 (define-public r-rjava
14374 (uri (cran-uri "rJava" version))
14377 "03vv0pj6san03c51iyqsyb1rwh3097dfpl2s8iswzzmc7k3shj12"))))
14378 (properties `((upstream-name . "rJava")))
14379 (build-system r-build-system)
14381 `(#:modules ((guix build utils)
14382 (guix build r-build-system)
14385 (modify-phases %standard-phases
14386 (add-after 'unpack 'set-JAVA_HOME
14387 (lambda* (#:key inputs #:allow-other-keys)
14388 (let ((jdk (assoc-ref inputs "jdk")))
14389 (setenv "JAVA_HOME" jdk)
14390 (setenv "JAVA" (which "java"))
14391 (setenv "JAR" (which "jar"))
14392 (setenv "JAVAC" (which "javac"))
14393 (setenv "JAVAH" (which "javah"))
14394 (setenv "JAVA_CPPFLAGS"
14395 (string-append "-I" jdk "/include "
14396 "-I" jdk "/include/linux"))
14397 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
14398 ((lib) (setenv "JAVA_LIBS" lib))
14399 (_ (error "Could not find libjvm.so"))))
14403 ("jdk" ,icedtea-8 "jdk")
14406 (home-page "https://www.rforge.net/rJava/")
14407 (synopsis "Low-Level R to Java interface")
14409 "This package provides a low-level interface to the Java VM very much
14410 like .C/.Call and friends. It allows the creation of objects, calling methods
14411 and accessing fields.")
14412 (license license:gpl2)))
14414 (define-public r-svmisc
14421 (uri (cran-uri "svMisc" version))
14424 "01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
14425 (properties `((upstream-name . "svMisc")))
14426 (build-system r-build-system)
14427 (home-page "https://github.com/SciViews/svMisc")
14428 (synopsis "Miscellaneous functions for SciViews")
14430 "This package provides miscellaneous functions for SciViews or general
14431 use, including tools to manage a temporary environment attached to the search
14432 path for temporary variables you do not want to @code{save()} or
14433 @code{load()}; test the current platform; showing progress bars, etc.")
14434 (license license:gpl2)))
14436 (define-public r-xyz
14443 (uri (cran-uri "xyz" version))
14446 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
14447 (build-system r-build-system)
14449 `(("r-rcpp" ,r-rcpp)))
14450 (home-page "https://cran.r-project.org/web/packages/xyz/")
14451 (synopsis "Algorithm for fast interaction search in high-dimensional data")
14453 "High dimensional interaction search by brute force requires a quadratic
14454 computational cost in the number of variables. The xyz algorithm provably
14455 finds strong interactions in almost linear time. For details of the algorithm
14456 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
14457 interaction search in high-dimensional data.")
14458 ;; Any version of the GPL.
14459 (license license:gpl2+)))
14461 (define-public r-rttf2pt1
14463 (name "r-rttf2pt1")
14468 (uri (cran-uri "Rttf2pt1" version))
14471 "0b3f2zkmbyshn19cnaaf042d0zwf43l9jnkqizfhxxwb93a4c1jn"))))
14472 (properties `((upstream-name . "Rttf2pt1")))
14473 (build-system r-build-system)
14474 (home-page "https://github.com/wch/Rttf2pt1")
14475 (synopsis "Font conversion utility")
14477 "This package contains the program @code{ttf2pt1}, for use with the
14478 @code{extrafont} package.")
14479 ;; Most of the files are covered under the Expat license. Some files are
14480 ;; covered under BSD-3. Deviations for individual files are recorded in
14481 ;; the LICENSE file.
14482 (license (list license:bsd-3 license:expat
14483 (license:non-copyleft "file://LICENSE")))))
14485 (define-public r-extrafontdb
14487 (name "r-extrafontdb")
14492 (uri (cran-uri "extrafontdb" version))
14495 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
14496 (build-system r-build-system)
14497 (home-page "https://github.com/wch/extrafontdb")
14498 (synopsis "Database for the extrafont package")
14500 "This package holds the database for the @code{extrafont} package.")
14501 (license license:gpl2)))
14503 (define-public r-extrafont
14505 (name "r-extrafont")
14510 (uri (cran-uri "extrafont" version))
14513 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
14514 (build-system r-build-system)
14516 `(("r-extrafontdb" ,r-extrafontdb)
14517 ("r-rttf2pt1" ,r-rttf2pt1)))
14518 (home-page "https://github.com/wch/extrafont")
14519 (synopsis "Tools for using fonts in R")
14521 "The extrafont package makes it easier to use fonts other than the basic
14522 PostScript fonts that R uses. Fonts that are imported into extrafont can be
14523 used with PDF or PostScript output files. There are two hurdles for using
14524 fonts in PDF (or Postscript) output files:
14527 @item Making R aware of the font and the dimensions of the characters.
14528 @item Embedding the fonts in the PDF file so that the PDF can be displayed
14529 properly on a device that doesn't have the font. This is usually needed if
14530 you want to print the PDF file or share it with others.
14533 The extrafont package makes both of these things easier.")
14534 (license license:gpl2)))
14536 (define-public r-xkcd
14543 (uri (cran-uri "xkcd" version))
14546 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
14547 (build-system r-build-system)
14549 `(("r-extrafont" ,r-extrafont)
14550 ("r-ggplot2" ,r-ggplot2)
14551 ("r-hmisc" ,r-hmisc)))
14552 (home-page "https://cran.r-project.org/web/packages/xkcd/")
14553 (synopsis "Plot ggplot2 graphics in the XKCD style")
14555 "This package provides the means to plot ggplot2 graphs in the style of
14556 the XKCD web comic.")
14557 (license license:gpl3)))
14559 (define-public r-msigdbr
14566 (uri (cran-uri "msigdbr" version))
14569 "0jvi49qa7616s58p0rx66pcw7h12rc8kgcg9225jk7pc3934hnzh"))))
14570 (build-system r-build-system)
14572 `(("r-dplyr" ,r-dplyr)
14573 ("r-magrittr" ,r-magrittr)
14574 ("r-rlang" ,r-rlang)
14575 ("r-tibble" ,r-tibble)))
14577 `(("r-knitr" ,r-knitr)))
14578 (home-page "https://github.com/igordot/msigdbr")
14579 (synopsis "MSigDB gene sets for multiple organisms")
14581 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
14582 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
14583 software in a standard R data frame with key-value pairs. Included are the
14584 original human gene symbols and Entrez IDs as well as the equivalents for
14585 various frequently studied model organisms such as mouse, rat, pig, fly, and
14587 ;; The package is covered under the Expat license, but the upstream MSigDB
14588 ;; files are made available under the Creative Commons Attribution 4.0
14589 ;; International license.
14590 (license (list license:expat license:cc-by4.0))))
14592 (define-public r-gridgraphics
14594 (name "r-gridgraphics")
14599 (uri (cran-uri "gridGraphics" version))
14602 "0rlyc3xk8kfrfzbfd8n4javq3yxqd7lsfmi4q5n6s61srnrl6c1r"))))
14603 (properties `((upstream-name . "gridGraphics")))
14604 (build-system r-build-system)
14605 (home-page "https://github.com/pmur002/gridgraphics")
14606 (synopsis "Redraw base graphics using @code{grid} graphics")
14608 "This package provides functions to convert a page of plots drawn with
14609 the @code{graphics} package into identical output drawn with the @code{grid}
14610 package. The result looks like the original @code{graphics}-based plot, but
14611 consists of @code{grid} grobs and viewports that can then be manipulated with
14612 @code{grid} functions (e.g., edit grobs and revisit viewports).")
14613 (license license:gpl2+)))
14615 (define-public r-farver
14622 (uri (cran-uri "farver" version))
14625 "1k75v07dsfkjra2gsgxg9s55cw3b46b1nh960kqphq7cg7gr058f"))))
14626 (build-system r-build-system)
14627 (home-page "https://github.com/thomasp85/farver")
14628 (synopsis "Vectorized color conversion and comparison")
14630 "The encoding of color can be handled in many different ways, using
14631 different color spaces. As different color spaces have different uses,
14632 efficient conversion between these representations are important. This
14633 package provides a set of functions that gives access to very fast color space
14634 conversion and comparisons implemented in C++, and offers 100-fold speed
14635 improvements over the @code{convertColor} function in the @code{grDevices}
14637 (license license:expat)))
14639 (define-public r-ggplotify
14641 (name "r-ggplotify")
14646 (uri (cran-uri "ggplotify" version))
14649 "0pfnp4lrissf21z7867kdm6slr979kchyva8iaf83i1302kscph3"))))
14650 (build-system r-build-system)
14652 `(("r-ggplot2" ,r-ggplot2)
14653 ("r-gridgraphics" ,r-gridgraphics)
14654 ("r-rvcheck" ,r-rvcheck)))
14656 `(("r-knitr" ,r-knitr)))
14657 (home-page "https://github.com/GuangchuangYu/ggplotify")
14658 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
14660 "This package provides tools to convert plot function calls (using
14661 expression or formula) to @code{grob} or @code{ggplot} objects that are
14662 compatible with the @code{grid} and @code{ggplot2} environment. With this
14663 package, we are able to e.g. use @code{cowplot} to align plots produced by
14664 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
14665 converting them to @code{ggplot} objects.")
14666 (license license:artistic2.0)))
14668 (define-public r-triebeard
14670 (name "r-triebeard")
14675 (uri (cran-uri "triebeard" version))
14678 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
14679 (build-system r-build-system)
14680 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
14681 (home-page "https://github.com/Ironholds/triebeard/")
14682 (synopsis "Radix trees in Rcpp")
14684 "Radix trees, or tries, are key-value data structures optimized for
14685 efficient lookups, similar in purpose to hash tables. This package provides
14686 an implementation of radix trees for use in R programming and in developing
14687 packages with Rcpp.")
14688 (license license:expat)))
14690 (define-public r-tweenr
14697 (uri (cran-uri "tweenr" version))
14700 "0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
14701 (build-system r-build-system)
14703 `(("r-farver" ,r-farver)
14704 ("r-magrittr" ,r-magrittr)
14706 ("r-rlang" ,r-rlang)))
14707 (home-page "https://github.com/thomasp85/tweenr")
14708 (synopsis "Interpolate data for smooth animations")
14710 "In order to create smooth animation between states of data, tweening is
14711 necessary. This package provides a range of functions for creating tweened
14712 data that can be used as basis for animation. Furthermore it adds a number of
14713 vectorized interpolaters for common R data types such as numeric, date and
14715 (license license:expat)))
14717 (define-public r-polyclip
14719 (name "r-polyclip")
14724 (uri (cran-uri "polyclip" version))
14727 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
14728 (build-system r-build-system)
14729 (native-inputs `(("pkg-config" ,pkg-config)))
14730 (home-page "http://www.angusj.com/delphi/clipper.php")
14731 (synopsis "Polygon clipping")
14733 "This package provides an R port of the library Clipper. It performs
14734 polygon clipping operations (intersection, union, set minus, set difference)
14735 for polygonal regions of arbitrary complexity, including holes. It computes
14736 offset polygons (spatial buffer zones, morphological dilations, Minkowski
14737 dilations) for polygonal regions and polygonal lines. It computes the
14738 Minkowski Sum of general polygons. There is a function for removing
14739 self-intersections from polygon data.")
14740 (license license:boost1.0)))
14742 (define-public r-urltools
14744 (name "r-urltools")
14749 (uri (cran-uri "urltools" version))
14752 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
14753 (build-system r-build-system)
14755 `(("r-rcpp" ,r-rcpp)
14756 ("r-triebeard" ,r-triebeard)))
14757 (home-page "https://github.com/Ironholds/urltools/")
14758 (synopsis "Vectorized tools for URL handling and parsing")
14760 "This package provides a toolkit for all URL-handling needs, including
14761 encoding and decoding, parsing, parameter extraction and modification. All
14762 functions are designed to be both fast and entirely vectorized. It is
14763 intended to be useful for people dealing with web-related datasets, such as
14764 server-side logs, although may be useful for other situations involving large
14766 (license license:expat)))
14768 (define-public r-ggforce
14775 (uri (cran-uri "ggforce" version))
14778 "1lplxyq5bgx90dgaimhynpcywag1gp6vlsy7q52ay1nfc35qmkjc"))))
14779 (build-system r-build-system)
14781 `(("r-ggplot2" ,r-ggplot2)
14782 ("r-gtable" ,r-gtable)
14784 ("r-polyclip" ,r-polyclip)
14786 ("r-rcppeigen" ,r-rcppeigen)
14787 ("r-rlang" ,r-rlang)
14788 ("r-scales" ,r-scales)
14789 ("r-tidyselect" ,r-tidyselect)
14790 ("r-tweenr" ,r-tweenr)
14791 ("r-withr" ,r-withr)))
14792 (home-page "https://ggforce.data-imaginist.com")
14793 (synopsis "Accelerating ggplot2")
14795 "The aim of the ggplot2 package is to aid in visual data investigations.
14796 This focus has led to a lack of facilities for composing specialized plots.
14797 Thi package aims to be a collection of mainly new statistics and geometries
14798 that fills this gap.")
14799 (license license:expat)))
14801 (define-public r-europepmc
14803 (name "r-europepmc")
14808 (uri (cran-uri "europepmc" version))
14811 "174nnyc2mbgqxb5kgqabn1vf71c2mps7ig2bclq4is0f7nb64pym"))))
14812 (build-system r-build-system)
14814 `(("r-dplyr" ,r-dplyr)
14816 ("r-jsonlite" ,r-jsonlite)
14818 ("r-progress" ,r-progress)
14819 ("r-purrr" ,r-purrr)
14820 ("r-rlang" ,r-rlang)
14821 ("r-tibble" ,r-tibble)
14822 ("r-tidyr" ,r-tidyr)
14823 ("r-urltools" ,r-urltools)
14824 ("r-xml2" ,r-xml2)))
14826 `(("r-knitr" ,r-knitr)))
14827 (home-page "https://github.com/ropensci/europepmc/")
14828 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
14830 "This package provides an R Client for the
14831 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
14832 Service}. It gives access to both metadata on life science literature and
14833 open access full texts. Europe PMC indexes all PubMed content and other
14834 literature sources including Agricola, a bibliographic database of citations
14835 to the agricultural literature, or Biological Patents. In addition to
14836 bibliographic metadata, the client allows users to fetch citations and
14837 reference lists. Links between life-science literature and other EBI
14838 databases, including ENA, PDB or ChEMBL are also accessible.")
14839 (license license:gpl3)))
14841 (define-public r-ggraph
14848 (uri (cran-uri "ggraph" version))
14851 "1pz06j0za4p6dc3fqjzcw8bpym70bmnfcvpv1q34r74rnwzjdyvq"))))
14852 (build-system r-build-system)
14854 `(("r-digest" ,r-digest)
14855 ("r-dplyr" ,r-dplyr)
14856 ("r-ggforce" ,r-ggforce)
14857 ("r-ggplot2" ,r-ggplot2)
14858 ("r-ggrepel" ,r-ggrepel)
14859 ("r-graphlayouts" ,r-graphlayouts)
14860 ("r-gtable" ,r-gtable)
14861 ("r-igraph" ,r-igraph)
14864 ("r-rlang" ,r-rlang)
14865 ("r-scales" ,r-scales)
14866 ("r-tidygraph" ,r-tidygraph)
14867 ("r-viridis" ,r-viridis)))
14869 `(("r-knitr" ,r-knitr)))
14870 (home-page "https://cran.r-project.org/web/packages/ggraph/")
14871 (synopsis "Implementation of grammar of graphics for graphs and networks")
14873 "The grammar of graphics as implemented in ggplot2 is a poor fit for
14874 graph and network visualizations due to its reliance on tabular data input.
14875 The ggraph package is an extension of the ggplot2 API tailored to graph
14876 visualizations and provides the same flexible approach to building up plots
14878 (license license:gpl3)))
14880 (define-public r-varselrf
14882 (name "r-varselrf")
14887 (uri (cran-uri "varSelRF" version))
14890 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
14891 (properties `((upstream-name . "varSelRF")))
14892 (build-system r-build-system)
14894 `(("r-randomforest" ,r-randomforest)))
14895 (home-page "https://www.ligarto.org/rdiaz/software/software")
14896 (synopsis "Variable selection using random forests")
14898 "This package provides tools for the variable selection from random
14899 forests using both backwards variable elimination (for the selection of small
14900 sets of non-redundant variables) and selection based on the importance
14901 spectrum (somewhat similar to scree plots; for the selection of large,
14902 potentially highly-correlated variables). The main applications are in
14903 high-dimensional data (e.g., microarray data, and other genomics and
14904 proteomics applications).")
14905 (license license:gpl2+)))
14907 (define-public r-pamr
14914 (uri (cran-uri "pamr" version))
14917 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
14918 (build-system r-build-system)
14920 `(("r-cluster" ,r-cluster)
14921 ("r-survival" ,r-survival)))
14922 (native-inputs `(("gfortran" ,gfortran)))
14923 (home-page "https://cran.r-project.org/web/packages/pamr/")
14924 (synopsis "Prediction Analysis for Microarrays")
14926 "This package provides some functions for sample classification in
14928 (license license:gpl2)))
14930 (define-public r-rda
14933 (version "1.0.2-2.1")
14937 (uri (cran-uri "rda" version))
14940 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
14941 (build-system r-build-system)
14942 (home-page "https://cran.r-project.org/web/packages/rda/")
14943 (synopsis "Shrunken centroids regularized discriminant analysis")
14945 "This package provides tools for shrunken centroids regularized
14946 discriminant analysis for the purpose of classifying high dimensional data.")
14947 (license license:gpl2+)))
14949 (define-public r-ggvis
14956 (uri (cran-uri "ggvis" version))
14959 "091i9f17912j8qcyxppjgwzjnyqj7769ixs9d2gjg6f2clskqdw2"))))
14960 (build-system r-build-system)
14962 `(("r-assertthat" ,r-assertthat)
14963 ("r-dplyr" ,r-dplyr)
14964 ("r-htmltools" ,r-htmltools)
14965 ("r-jsonlite" ,r-jsonlite)
14966 ("r-lazyeval" ,r-lazyeval)
14967 ("r-magrittr" ,r-magrittr)
14968 ("r-shiny" ,r-shiny)))
14969 (home-page "https://ggvis.rstudio.com/")
14970 (synopsis "Interactive grammar of graphics")
14972 "This package is a data visualization package for R providing an
14973 implementation of an interactive grammar of graphics, taking the best parts of
14974 ggplot2, combining them with the reactive framework of Shiny and drawing web
14975 graphics using Vega.")
14976 (license license:gpl2)))
14978 (define-public r-gbm
14985 (uri (cran-uri "gbm" version))
14988 "0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
14989 (build-system r-build-system)
14991 `(("r-gridextra" ,r-gridextra)
14992 ("r-lattice" ,r-lattice)
14993 ("r-survival" ,r-survival)))
14994 (home-page "https://github.com/gbm-developers/gbm")
14995 (synopsis "Generalized boosted regression models")
14997 "This package is an implementation of extensions to Freund and Schapire's
14998 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
14999 regression methods for least squares, absolute loss, t-distribution loss,
15000 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
15001 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
15002 and Learning to Rank measures (LambdaMart).")
15003 (license license:gpl2+)))
15005 (define-public r-threejs
15012 (uri (cran-uri "threejs" version))
15015 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
15016 (build-system r-build-system)
15018 `(#:modules ((guix build utils)
15019 (guix build r-build-system)
15023 (modify-phases %standard-phases
15024 (add-after 'unpack 'process-javascript
15025 (lambda* (#:key inputs #:allow-other-keys)
15026 (with-directory-excursion "inst"
15030 `((,(assoc-ref inputs "js-jquery")
15031 "htmlwidgets/lib/jquery/jquery.min.js")
15032 (,(assoc-ref inputs "js-threejs-111")
15033 "htmlwidgets/lib/threejs-111/three.min.js"))))
15034 (lambda (sources targets)
15035 (for-each (lambda (source target)
15036 (format #t "Processing ~a --> ~a~%"
15038 (delete-file target)
15039 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15040 (call-with-output-file target
15042 (dump-port minified port)))))
15043 sources targets))))
15046 `(("r-base64enc" ,r-base64enc)
15047 ("r-crosstalk" ,r-crosstalk)
15048 ("r-htmlwidgets" ,r-htmlwidgets)
15049 ("r-igraph" ,r-igraph)))
15051 `(("uglify-js" ,uglify-js)
15055 (uri "https://code.jquery.com/jquery-1.12.4.js")
15058 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
15062 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
15065 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
15066 (home-page "https://bwlewis.github.io/rthreejs")
15067 (synopsis "Interactive 3D scatter plots, networks and globes")
15069 "Create interactive 3D scatter plots, network plots, and globes in R
15070 using the three.js visualization library.")
15071 (license license:expat)))
15073 (define-public r-mlbench
15080 (uri (cran-uri "mlbench" version))
15083 "1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
15084 (build-system r-build-system)
15085 (home-page "https://cran.r-project.org/web/packages/mlbench/")
15086 (synopsis "Machine learning benchmark problems")
15088 "This package provides a collection of artificial and real-world machine
15089 learning benchmark problems, including, e.g., several data sets from the UCI
15091 (license license:gpl2)))
15093 (define-public r-mpm
15100 (uri (cran-uri "mpm" version))
15103 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
15104 (build-system r-build-system)
15106 `(("r-kernsmooth" ,r-kernsmooth)
15107 ("r-mass" ,r-mass)))
15108 (home-page "http://mpm.r-forge.r-project.org")
15109 (synopsis "Multivariate projection methods")
15111 "This is a package for exploratory graphical analysis of multivariate
15112 data, specifically gene expression data with different projection methods:
15113 principal component analysis, correspondence analysis, spectral map
15115 (license license:gpl2+)))
15117 (define-public r-png
15123 (uri (cran-uri "png" version))
15126 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
15127 (build-system r-build-system)
15129 `(("libpng" ,libpng)
15131 (home-page "https://www.rforge.net/png/")
15132 (synopsis "Read and write PNG images")
15134 "This package provides an easy and simple way to read, write and display
15135 bitmap images stored in the PNG format. It can read and write both files and
15136 in-memory raw vectors.")
15137 ;; Any of these GPL versions.
15138 (license (list license:gpl2 license:gpl3))))
15140 (define-public r-ggcorrplot
15142 (name "r-ggcorrplot")
15147 (uri (cran-uri "ggcorrplot" version))
15150 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
15151 (build-system r-build-system)
15153 `(("r-ggplot2" ,r-ggplot2)
15154 ("r-reshape2" ,r-reshape2)))
15155 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
15156 (synopsis "Visualization of a correlation matrix using ggplot2")
15158 "The ggcorrplot package can be used to visualize easily a correlation
15159 matrix using ggplot2. It provides a solution for reordering the correlation
15160 matrix and displays the significance level on the plot. It also includes a
15161 function for computing a matrix of correlation p-values.")
15162 (license license:gpl2)))
15164 ;; This package includes minified JavaScript files. When upgrading please
15165 ;; check that there are no new minified JavaScript files.
15166 (define-public r-flexdashboard
15168 (name "r-flexdashboard")
15173 (uri (cran-uri "flexdashboard" version))
15176 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
15177 (modules '((guix build utils)))
15180 ;; Delete bundled minified JavaScript files
15181 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15182 (delete-file "inst/www/sly/sly.min.js")
15183 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
15184 (delete-file "inst/www/prism/prism.js")
15186 (build-system r-build-system)
15188 `(#:modules ((guix build utils)
15189 (guix build r-build-system)
15193 (ice-9 textual-ports))
15195 (modify-phases %standard-phases
15196 (add-after 'unpack 'process-javascript
15197 (lambda* (#:key inputs #:allow-other-keys)
15198 (with-directory-excursion "inst"
15199 ;; Concatenate all components of prism.js
15200 (let ((contents (string-join
15201 (map (lambda (name)
15202 (call-with-input-file
15203 (assoc-ref inputs name)
15207 "js-prism-line-numbers"))
15209 (call-with-output-file "prism-src.js"
15210 (cut display contents <>)))
15214 `(("www/stickytableheaders/jquery.stickytableheaders.js"
15215 "www/stickytableheaders/jquery.stickytableheaders.min.js")
15217 "www/sly/sly.min.js")
15219 "www/prism/prism.js")
15220 (,(assoc-ref inputs "js-raphael")
15221 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
15222 (,(assoc-ref inputs "js-featherlight")
15223 "www/featherlight/featherlight.min.js"))))
15224 (lambda (sources targets)
15225 (for-each (lambda (source target)
15226 (format #t "Processing ~a --> ~a~%"
15228 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
15229 (call-with-output-file target
15231 (dump-port minified port)))))
15232 sources targets))))
15235 `(("r-htmltools" ,r-htmltools)
15236 ("r-htmlwidgets" ,r-htmlwidgets)
15237 ("r-jsonlite" ,r-jsonlite)
15238 ("r-knitr" ,r-knitr)
15239 ("r-rmarkdown" ,r-rmarkdown)
15240 ("r-shiny" ,r-shiny)))
15242 `(("uglify-js" ,uglify-js)
15246 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
15249 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
15253 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
15256 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
15260 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
15263 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
15264 ("js-prism-line-numbers"
15267 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
15270 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
15274 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
15277 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
15278 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
15279 (synopsis "R Markdown format for flexible dashboards")
15281 "This package provides an R Markdown format for converting an R Markdown
15282 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
15283 of its components to the containing web page.")
15284 (license license:expat)))
15286 (define-public r-preseqr
15293 (uri (cran-uri "preseqR" version))
15296 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
15297 (properties `((upstream-name . "preseqR")))
15298 (build-system r-build-system)
15300 `(("r-polynom" ,r-polynom)))
15301 (home-page "https://cran.r-project.org/web/packages/preseqR/")
15302 (synopsis "Predicting species accumulation curves")
15304 "This package can be used to predict the r-species accumulation
15305 curve (r-SAC), which is the number of species represented at least r times as
15306 a function of the sampling effort. When r = 1, the curve is known as the
15307 species accumulation curve, or the library complexity curve in high-throughput
15308 genomic sequencing. The package includes both parametric and nonparametric
15309 methods, as described by Deng C, et al. (2018).")
15310 (license license:gpl3)))
15312 (define-public r-mapplots
15314 (name "r-mapplots")
15319 (uri (cran-uri "mapplots" version))
15322 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
15323 (build-system r-build-system)
15324 (home-page "https://cran.r-project.org/web/packages/mapplots/")
15325 (synopsis "Data visualization on maps")
15327 "This package helps you create simple maps; add sub-plots like pie plots
15328 to a map or any other plot; format, plot and export gridded data. The package
15329 was developed for displaying fisheries data but most functions can be used for
15330 more generic data visualisation.")
15331 (license license:gpl2+)))
15333 (define-public r-pmcmr
15340 (uri (cran-uri "PMCMR" version))
15343 "09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
15344 (properties `((upstream-name . "PMCMR")))
15345 (build-system r-build-system)
15346 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
15347 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
15349 "This is a deprecated package for calculating pairwise multiple
15350 comparisons of mean rank sums. This package is superseded by the novel
15351 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
15352 compatibility of dependent packages for some time.")
15353 (license license:gpl3+)))
15355 (define-public r-downloader
15357 (name "r-downloader")
15362 (uri (cran-uri "downloader" version))
15365 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
15366 (build-system r-build-system)
15368 `(("r-digest" ,r-digest)))
15369 (home-page "https://github.com/wch/downloader")
15370 (synopsis "Download files over HTTP and HTTPS")
15372 "This package provides a wrapper for the @code{download.file} function,
15373 making it possible to download files over HTTPS across platforms. The
15374 @code{RCurl} package provides this functionality (and much more) but has
15375 external dependencies. This package has is implemented purely in R.")
15376 (license license:gpl2)))
15378 (define-public r-rex
15385 (uri (cran-uri "rex" version))
15388 "0m7bq8db3m5dhf01rw7xc7xy1ciq3m7dfgsl80p8cy4h8vqr3d06"))))
15389 (build-system r-build-system)
15391 `(("r-lazyeval" ,r-lazyeval)))
15393 `(("r-knitr" ,r-knitr)))
15394 (home-page "https://github.com/kevinushey/rex")
15395 (synopsis "Friendly regular expressions")
15397 "This package provides a friendly interface for the construction of
15398 regular expressions. Regular expressions are a very powerful feature, however
15399 they are often difficult to interpret. Rex allows you to build complex
15400 regular expressions from human readable expressions")
15401 (license license:expat)))
15403 (define-public r-xmlparsedata
15405 (name "r-xmlparsedata")
15410 (uri (cran-uri "xmlparsedata" version))
15413 "0gjr3l5z5dp276lchr2649as1rkj56d2mlvbr66yg393zzw50lsh"))))
15414 (properties `((upstream-name . "xmlparsedata")))
15415 (build-system r-build-system)
15416 (home-page "https://github.com/r-lib/xmlparsedata#readme")
15417 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
15419 "This package provides tools to convert the output of
15420 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
15421 @code{XPath}, and is easier to manipulate in general.")
15422 (license license:expat)))
15424 (define-public r-cyclocomp
15426 (name "r-cyclocomp")
15431 (uri (cran-uri "cyclocomp" version))
15434 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
15435 (properties `((upstream-name . "cyclocomp")))
15436 (build-system r-build-system)
15438 `(("r-callr" ,r-callr)
15439 ("r-crayon" ,r-crayon)
15441 ("r-remotes" ,r-remotes)
15442 ("r-withr" ,r-withr)))
15443 (home-page "https://github.com/MangoTheCat/cyclocomp")
15444 (synopsis "Cyclomatic complexity of R code")
15446 "Cyclomatic complexity is a software metric, used to indicate the
15447 complexity of a program. It is a quantitative measure of the number of
15448 linearly independent paths through a program's source code. This package
15449 provides tools to compute this metric.")
15450 (license license:expat)))
15452 (define-public r-lintr
15459 (uri (cran-uri "lintr" version))
15462 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
15463 (properties `((upstream-name . "lintr")))
15464 (build-system r-build-system)
15466 `(("r-codetools" ,r-codetools)
15467 ("r-crayon" ,r-crayon)
15468 ("r-cyclocomp" ,r-cyclocomp)
15469 ("r-digest" ,r-digest)
15471 ("r-jsonlite" ,r-jsonlite)
15472 ("r-knitr" ,r-knitr)
15474 ("r-rstudioapi" ,r-rstudioapi)
15475 ("r-testthat" ,r-testthat)
15477 ("r-xmlparsedata" ,r-xmlparsedata)))
15478 (home-page "https://github.com/jimhester/lintr")
15479 (synopsis "Linter for R code")
15480 (description "This package checks adherence to a given style, syntax
15481 errors and possible semantic issues. It supports on the fly checking of R
15482 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
15483 (license license:expat)))
15485 (define-public r-sctransform
15487 (name "r-sctransform")
15492 (uri (cran-uri "sctransform" version))
15495 "07v3lzccsrkh1glfxd1q20r8f8gl9ls5az0s1dvxm4vcls0hlhyn"))))
15496 (build-system r-build-system)
15498 `(("r-future-apply" ,r-future-apply)
15499 ("r-ggplot2" ,r-ggplot2)
15500 ("r-gridextra" ,r-gridextra)
15502 ("r-matrix" ,r-matrix)
15504 ("r-rcppeigen" ,r-rcppeigen)
15505 ("r-reshape2" ,r-reshape2)))
15506 (home-page "https://github.com/ChristophH/sctransform")
15507 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
15509 "This package provides a normalization method for single-cell UMI count
15510 data using a variance stabilizing transformation. The transformation is based
15511 on a negative binomial regression model with regularized parameters. As part
15512 of the same regression framework, this package also provides functions for
15513 batch correction, and data correction.")
15514 (license license:gpl3)))
15516 (define-public r-styler
15523 (uri (cran-uri "styler" version))
15526 "1waglhsy2c53qjgd2qhlzda3z0lbzbwx9fkrfhac41y6h91mgkrz"))))
15527 (build-system r-build-system)
15529 `(("r-backports" ,r-backports)
15531 ("r-magrittr" ,r-magrittr)
15532 ("r-purrr" ,r-purrr)
15533 ("r-r-cache" ,r-r-cache)
15534 ("r-rematch2" ,r-rematch2)
15535 ("r-rlang" ,r-rlang)
15536 ("r-rprojroot" ,r-rprojroot)
15537 ("r-tibble" ,r-tibble)
15538 ("r-withr" ,r-withr)
15539 ("r-xfun" ,r-xfun)))
15540 (home-page "https://github.com/r-lib/styler")
15541 (synopsis "Non-invasive pretty printing of R code")
15543 "This is a package for pretty-printing R code without changing the user's
15544 formatting intent.")
15545 (license license:gpl3)))
15547 (define-public r-scrime
15554 (uri (cran-uri "scrime" version))
15557 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
15558 (build-system r-build-system)
15559 (home-page "https://cran.r-project.org/web/packages/scrime/")
15560 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
15562 "This package provides tools for the analysis of high-dimensional data
15563 developed/implemented at the group \"Statistical Complexity Reduction In
15564 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
15565 the functions can also be applied to other types of categorical data.")
15566 (license license:gpl2)))
15568 (define-public r-pbmcapply
15570 (name "r-pbmcapply")
15575 (uri (cran-uri "pbmcapply" version))
15578 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
15579 (build-system r-build-system)
15580 (home-page "https://github.com/kvnkuang/pbmcapply")
15581 (synopsis "Track the progress of apply procedures with a progress bar")
15583 "This light-weight package helps you track and visualize the progress of
15584 parallel versions of vectorized R functions of the @code{mc*apply} family.")
15585 (license license:expat)))
15587 (define-public r-blme
15594 (uri (cran-uri "blme" version))
15597 "1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
15598 (build-system r-build-system)
15599 (propagated-inputs `(("r-lme4" ,r-lme4)))
15600 (home-page "https://github.com/vdorie/blme")
15601 (synopsis "Bayesian linear mixed-effects models")
15603 "This package provides tools for maximum a posteriori estimation for
15604 linear and generalized linear mixed-effects models in a Bayesian setting. It
15605 extends the lme4 package.")
15606 (license license:gpl2+)))
15608 (define-public r-batchtools
15610 (name "r-batchtools")
15615 (uri (cran-uri "batchtools" version))
15618 "02bwfinwgn5nl638997javig61jmr0ci0qybmprz13jnvmam1yns"))))
15619 (build-system r-build-system)
15621 `(("r-backports" ,r-backports)
15622 ("r-base64url" ,r-base64url)
15624 ("r-checkmate" ,r-checkmate)
15625 ("r-data-table" ,r-data-table)
15626 ("r-digest" ,r-digest)
15628 ("r-progress" ,r-progress)
15630 ("r-rappdirs" ,r-rappdirs)
15631 ("r-stringi" ,r-stringi)
15632 ("r-withr" ,r-withr)))
15634 `(("r-knitr" ,r-knitr)))
15635 (home-page "https://github.com/mllg/batchtools")
15636 (synopsis "Tools for computation on batch systems")
15638 "As a successor of the packages BatchJobs and BatchExperiments, this
15639 package provides a parallel implementation of the Map function for high
15640 performance computing systems managed by various schedulers. A multicore and
15641 socket mode allow the parallelization on a local machines, and multiple
15642 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
15643 the package provides an abstraction mechanism to define large-scale computer
15644 experiments in a well-organized and reproducible way.")
15645 (license license:lgpl3)))
15647 (define-public r-clue
15654 (uri (cran-uri "clue" version))
15657 "05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
15658 (build-system r-build-system)
15659 (propagated-inputs `(("r-cluster" ,r-cluster)))
15660 (home-page "https://cran.r-project.org/web/packages/clue/")
15661 (synopsis "Tools for analyzing cluster ensembles")
15662 (description "Cluster ensembles are collections of individual solutions to
15663 a given clustering problem which are useful or necessary to consider in a wide
15664 range of applications. This R package provides an extensible computational
15665 environment for creating and analyzing cluster ensembles, with basic data
15666 structures for representing partitions and hierarchies, and facilities for
15667 computing on them, including methods for measuring proximity and obtaining
15668 consensus and secondary clusterings.")
15669 (license license:gpl2)))
15671 (define-public r-sitmo
15678 (uri (cran-uri "sitmo" version))
15681 "0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
15682 (build-system r-build-system)
15683 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
15684 (home-page "https://github.com/coatless/sitmo/")
15685 (synopsis "Parallel pseudo random number generator header files")
15687 "This package provides two high quality and fast PPRNGs that may be used
15688 in an OpenMP parallel environment. In addition, there is a generator for one
15689 dimensional low-discrepancy sequence.")
15690 (license license:expat)))
15692 (define-public r-dqrng
15699 (uri (cran-uri "dqrng" version))
15702 "0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
15703 (build-system r-build-system)
15707 ("r-sitmo" ,r-sitmo)))
15708 (home-page "https://www.daqana.org/dqrng")
15709 (synopsis "Fast pseudo random number generators")
15711 "Several fast random number generators are provided as C++ header-only
15712 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
15713 Additionally, fast functions for generating random numbers according to a
15714 uniform, normal and exponential distribution are included. The latter two use
15715 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
15716 functions are exported to R and as a C++ interface and are enabled for use
15717 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
15718 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
15719 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
15720 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
15721 ;; whole is distributed under the terms of the AGPL 3.
15722 (license license:agpl3)))
15724 (define-public r-ingredients
15726 (name "r-ingredients")
15731 (uri (cran-uri "ingredients" version))
15734 "1mp1rgi3nnr8mjddpbyi24zvqcbihz0d8np2j13cbjc089n6jci8"))))
15735 (properties `((upstream-name . "ingredients")))
15736 (build-system r-build-system)
15738 `(("r-ggplot2" ,r-ggplot2)
15739 ("r-gridextra" ,r-gridextra)
15740 ("r-scales" ,r-scales)))
15741 (native-inputs `(("r-knitr" ,r-knitr)))
15742 (home-page "https://ModelOriented.github.io/ingredients/")
15743 (synopsis "Effects and importances of model ingredients")
15745 "This is a collection of tools for assessment of feature importance and
15746 feature effects. Key functions are:
15749 @item @code{feature_importance()} for assessment of global level feature
15751 @item @code{ceteris_paribus()} for calculation of the what-if plots,
15752 @item @code{partial_dependence()} for partial dependence plots,
15753 @item @code{conditional_dependence()} for conditional dependence plots,
15754 @item @code{accumulated_dependence()} for accumulated local effects plots,
15755 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
15756 aggregation of ceteris paribus profiles,
15757 @item generic @code{print()} and @code{plot()} for better usability of
15758 selected explainers,
15759 @item generic @code{plotD3()} for interactive, D3 based explanations, and
15760 @item generic @code{describe()} for explanations in natural language.
15762 (license license:gpl3)))
15764 (define-public r-ibreakdown
15766 (name "r-ibreakdown")
15771 (uri (cran-uri "iBreakDown" version))
15774 "0y4zjpyn8j76jrs5phjzs5lfq3lqjspmrwcksqv9wq0rbdgh14vk"))))
15775 (properties `((upstream-name . "iBreakDown")))
15776 (build-system r-build-system)
15777 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
15778 (native-inputs `(("r-knitr" ,r-knitr)))
15779 (home-page "https://ModelOriented.github.io/iBreakDown/")
15780 (synopsis "Model agnostic instance level variable attributions")
15782 "This package provides a model agnostic tool for decomposition of
15783 predictions from black boxes. It supports additive attributions and
15784 attributions with interactions. The Break Down Table shows contributions of
15785 every variable to a final prediction. The Break Down Plot presents variable
15786 contributions in a concise graphical way. This package works for
15787 classification and regression models.")
15788 (license license:gpl3)))
15790 (define-public r-dalex
15797 (uri (cran-uri "DALEX" version))
15800 "0lx8nasm1zgh1ckz8nw3ysp6xjv3dsj39hzhr6k3xhh6i8pm9rxk"))))
15801 (properties `((upstream-name . "DALEX")))
15802 (build-system r-build-system)
15804 `(("r-ggplot2" ,r-ggplot2)
15805 ("r-ibreakdown" ,r-ibreakdown)
15806 ("r-ingredients" ,r-ingredients)))
15807 (home-page "https://pbiecek.github.io/DALEX/")
15808 (synopsis "Descriptive machine learning explanations")
15810 "Machine Learning models are widely used and have various applications in
15811 classification or regression. Models created with boosting, bagging, stacking
15812 or similar techniques are often used due to their high performance, but such
15813 black-box models usually lack interpretability. The DALEX package contains
15814 various explainers that help to understand the link between input variables
15815 and model output.")
15816 ;; Any version of the GPL
15817 (license license:gpl3+)))
15819 (define-public r-enrichr
15826 (uri (cran-uri "enrichR" version))
15829 "0ymhzs9d2wl0s9rvbqc1hqb78mlzwhlc7mmijpfqkm5r720pf6m1"))))
15830 (properties `((upstream-name . "enrichR")))
15831 (build-system r-build-system)
15833 `(("r-httr" ,r-httr)
15834 ("r-rjson" ,r-rjson)))
15835 (home-page "https://cran.r-project.org/web/packages/enrichR/")
15836 (synopsis "R Interface to Enrichr database for analyzing gene sets")
15838 "This package provides an R interface to all Enrichr databases, a
15839 web-based tool for analyzing gene sets and returns any enrichment of common
15840 annotated biological functions.")
15841 (license license:gpl2+)))
15843 (define-public r-plot3d
15850 (uri (cran-uri "plot3D" version))
15853 "1jfzndnlci9a975qbcv66jiy2l46hs3f2049654x4jp3i4kyrr5r"))))
15854 (properties `((upstream-name . "plot3D")))
15855 (build-system r-build-system)
15856 (propagated-inputs `(("r-misc3d" ,r-misc3d)))
15857 (home-page "https://cran.r-project.org/web/packages/plot3D")
15858 (synopsis "Plot multi-dimensional data")
15860 "This package provides functions for viewing 2D and 3D data, including
15861 perspective plots, slice plots, surface plots, scatter plots, etc. It
15862 includes data sets from oceanography.")
15863 (license license:gpl3+)))
15865 (define-public r-ggfortify
15867 (name "r-ggfortify")
15872 (uri (cran-uri "ggfortify" version))
15875 "0wmcwp63h90v3f00ixszvis4z28im621jickvc0wgi6qvjvnayq0"))))
15876 (build-system r-build-system)
15878 `(("r-dplyr" ,r-dplyr)
15879 ("r-ggplot2" ,r-ggplot2)
15880 ("r-gridextra" ,r-gridextra)
15881 ("r-scales" ,r-scales)
15882 ("r-stringr" ,r-stringr)
15883 ("r-tibble" ,r-tibble)
15884 ("r-tidyr" ,r-tidyr)))
15886 `(("r-knitr" ,r-knitr)))
15887 (home-page "https://github.com/sinhrks/ggfortify")
15888 (synopsis "Data visualization tools for statistical analysis results")
15890 "This package provides unified plotting tools for statistics commonly
15891 used, such as GLM, time series, PCA families, clustering and survival
15892 analysis. The package offers a single plotting interface for these analysis
15893 results and plots in a unified style using the @code{ggplot2} package.")
15894 (license license:gpl2)))
15896 (define-public r-refmanager
15898 (name "r-refmanager")
15903 (uri (cran-uri "RefManageR" version))
15906 "1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
15907 (properties `((upstream-name . "RefManageR")))
15908 (build-system r-build-system)
15910 `(("r-bibtex" ,r-bibtex)
15912 ("r-jsonlite" ,r-jsonlite)
15913 ("r-lubridate" ,r-lubridate)
15915 ("r-stringr" ,r-stringr)
15916 ("r-xml2" ,r-xml2)))
15917 (home-page "https://github.com/ropensci/RefManageR/")
15918 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
15920 "This package provides tools for importing and working with bibliographic
15921 references. It greatly enhances the @code{bibentry} class by providing a
15922 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
15923 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
15924 by various formats for name lists (author by last names, translator by full
15925 names, etc.). Entries can be updated, combined, sorted, printed in a number
15926 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
15927 into R and converted to @code{BibEntry} objects.")
15928 ;; Any of these licenses may be picked.
15929 (license (list license:gpl2 license:gpl3 license:bsd-3))))
15931 (define-public r-citr
15938 (uri (cran-uri "citr" version))
15941 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
15942 (build-system r-build-system)
15944 `(("r-assertthat" ,r-assertthat)
15947 ("r-miniui" ,r-miniui)
15948 ("r-refmanager" ,r-refmanager)
15949 ("r-rstudioapi" ,r-rstudioapi)
15950 ("r-shiny" ,r-shiny)
15951 ("r-shinyjs" ,r-shinyjs)
15952 ("r-yaml" ,r-yaml)))
15953 (home-page "https://github.com/crsh/citr")
15954 (synopsis "RStudio add-in to insert Markdown citations")
15956 "This package provides functions and an RStudio add-in that search a
15957 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
15958 the current document.")
15959 (license license:expat)))
15961 (define-public r-xgboost
15964 (version "1.1.1.1")
15968 (uri (cran-uri "xgboost" version))
15971 "13njhcxljhbcs37ni6r5174fk8kx9b5p7rlw1an1ak3w92jn56cq"))))
15972 (build-system r-build-system)
15974 `(("r-data-table" ,r-data-table)
15975 ("r-magrittr" ,r-magrittr)
15976 ("r-matrix" ,r-matrix)
15977 ("r-stringi" ,r-stringi)))
15979 `(("r-knitr" ,r-knitr)))
15980 (home-page "https://github.com/dmlc/xgboost")
15981 (synopsis "Extreme gradient boosting")
15983 "This package provides an R interface to Extreme Gradient Boosting, which
15984 is an efficient implementation of the gradient boosting framework from Chen
15985 and Guestrin (2016). The package includes efficient linear model solver and
15986 tree learning algorithms. The package can automatically do parallel
15987 computation on a single machine. It supports various objective functions,
15988 including regression, classification and ranking. The package is made to be
15989 extensible, so that users are also allowed to define their own objectives
15991 (license license:asl2.0)))
15993 (define-public r-umap
15996 (version "0.2.6.0")
16000 (uri (cran-uri "umap" version))
16003 "0zajn2sk705sckljxl5vz4q2sxpsqim2grmjq2jwwc8ysr1h2s9f"))))
16004 (build-system r-build-system)
16006 `(("r-openssl" ,r-openssl)
16008 ("r-reticulate" ,r-reticulate)
16009 ("r-rspectra" ,r-rspectra)))
16011 `(("r-knitr" ,r-knitr)))
16012 (home-page "https://github.com/tkonopka/umap")
16013 (synopsis "Uniform manifold approximation and projection")
16015 "Uniform manifold approximation and projection is a technique for
16016 dimension reduction. This package provides an interface to the UMAP algorithm
16017 in R, including a translation of the original algorithm into R.")
16018 (license license:expat)))
16020 (define-public r-uwot
16027 (uri (cran-uri "uwot" version))
16030 "1jzh8r1h6f7pw7pb1fr32vn6ai9g10s56ahkq0vi77iznihy1rpd"))))
16031 (build-system r-build-system)
16033 `(("r-dqrng" ,r-dqrng)
16035 ("r-irlba" ,r-irlba)
16036 ("r-matrix" ,r-matrix)
16038 ("r-rcppannoy" ,r-rcppannoy)
16039 ("r-rcppprogress" ,r-rcppprogress)
16040 ("r-rspectra" ,r-rspectra)))
16041 (home-page "https://github.com/jlmelville/uwot")
16042 (synopsis "Uniform manifold approximation and projection")
16044 "This package provides an implementation of the Uniform Manifold
16045 Approximation and Projection dimensionality reduction by McInnes et
16046 al. (2018). It also provides means to transform new data and to carry out
16047 supervised dimensionality reduction. An implementation of the related
16048 LargeVis method of Tang et al. (2016) is also provided.")
16049 (license license:gpl3)))
16051 (define-public r-kableextra
16053 (name "r-kableextra")
16058 (uri (cran-uri "kableExtra" version))
16061 "1nicvw06xsf3a1f5c10mih07b76m2v5s5h165vmz0qx6n1a3492i"))))
16062 (properties `((upstream-name . "kableExtra")))
16063 (build-system r-build-system)
16065 `(("r-digest" ,r-digest)
16067 ("r-htmltools" ,r-htmltools)
16068 ("r-knitr" ,r-knitr)
16069 ("r-magrittr" ,r-magrittr)
16070 ("r-readr" ,r-readr)
16071 ("r-rmarkdown" ,r-rmarkdown)
16072 ("r-rstudioapi" ,r-rstudioapi)
16073 ("r-rvest" ,r-rvest)
16074 ("r-scales" ,r-scales)
16075 ("r-stringr" ,r-stringr)
16076 ("r-viridislite" ,r-viridislite)
16077 ("r-webshot" ,r-webshot)
16078 ("r-xml2" ,r-xml2)))
16079 (home-page "https://haozhu233.github.io/kableExtra/")
16080 (synopsis "Construct complex tables with pipe syntax")
16082 "Build complex HTML or LaTeX tables using @code{kable()} from
16083 @code{knitr} and the piping syntax from @code{magrittr}. The function
16084 @code{kable()} is a light weight table generator coming from @code{knitr}.
16085 This package simplifies the way to manipulate the HTML or LaTeX codes
16086 generated by @code{kable()} and allows users to construct complex tables and
16087 customize styles using a readable syntax.")
16088 (license license:expat)))
16090 (define-public r-glasso
16097 (uri (cran-uri "glasso" version))
16099 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
16100 (build-system r-build-system)
16101 (native-inputs `(("gfortran" ,gfortran)))
16102 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
16103 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
16105 "This is a package for estimation of a sparse inverse covariance matrix
16106 using a lasso (L1) penalty. Facilities are provided for estimates along a
16107 path of values for the regularization parameter.")
16108 (license license:gpl2)))
16110 (define-public r-rhpcblasctl
16112 (name "r-rhpcblasctl")
16113 (version "0.20-137")
16117 (uri (cran-uri "RhpcBLASctl" version))
16120 "0vv144sgjhf7fazk633i16fc06g9k43syyxj1g34pi9gsgdcn0nv"))))
16121 (properties `((upstream-name . "RhpcBLASctl")))
16122 (build-system r-build-system)
16123 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
16124 (synopsis "Control the number of threads on BLAS")
16126 "This package allows you to control the number of threads the BLAS
16127 library uses. It is also possible to control the number of threads in
16129 (license license:agpl3+)))
16131 (define-public r-lda
16138 (uri (cran-uri "lda" version))
16141 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
16142 (build-system r-build-system)
16143 (home-page "https://cran.r-project.org/web/packages/lda/")
16144 (synopsis "Collapsed Gibbs sampling methods for topic models")
16146 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
16147 related models. This includes (but is not limited to) sLDA, corrLDA, and the
16148 mixed-membership stochastic blockmodel. Inference for all of these models is
16149 implemented via a fast collapsed Gibbs sampler written in C. Utility
16150 functions for reading/writing data typically used in topic models, as well as
16151 tools for examining posterior distributions are also included.")
16152 ;; Any version of the LGPL
16153 (license license:lgpl3+)))
16155 (define-public r-rann-l1
16162 (uri (cran-uri "RANN.L1" version))
16165 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
16166 (properties `((upstream-name . "RANN.L1")))
16167 (build-system r-build-system)
16168 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
16169 (synopsis "Fast nearest neighbour search using L1 metric")
16171 "This package provides tools to find the k nearest neighbours for every
16172 point in a given dataset in O(N log N) time using Arya and Mount's ANN
16173 library. There is support for approximate as well as exact searches, fixed
16174 radius searches and @code{bd} as well as @code{kd} trees. The distance is
16175 computed using the L1 (Manhattan, taxicab) metric.")
16176 (license license:gpl3+)))
16178 (define-public r-leiden
16185 (uri (cran-uri "leiden" version))
16188 "1hh6bmbz6cpqwl4i94gxylgv9x92zbqdg81r8r4ymfy8c70f3df2"))))
16189 (properties `((upstream-name . "leiden")))
16190 (build-system r-build-system)
16192 `(("r-igraph" ,r-igraph)
16193 ("r-matrix" ,r-matrix)
16194 ("r-reticulate" ,r-reticulate)))
16195 (home-page "https://github.com/TomKellyGenetics/leiden")
16196 (synopsis "R implementation of Leiden clustering algorithm")
16198 "This package implements the Python @code{leidenalg} module to be called
16199 in R. It enables clustering using the Leiden algorithm for partitioning a
16200 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
16201 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
16202 (license license:gpl3)))
16204 (define-public r-patchwork
16206 (name "r-patchwork")
16211 (uri (cran-uri "patchwork" version))
16214 "0wm93a40idrkzn5hpnykhznvh7hdbfqw0dkzzn0zk83qlwyc9g02"))))
16215 (build-system r-build-system)
16217 `(("r-ggplot2" ,r-ggplot2)
16218 ("r-gtable" ,r-gtable)))
16220 `(("r-knitr" ,r-knitr)))
16221 (home-page "https://github.com/thomasp85/patchwork")
16222 (synopsis "Compose ggplot2 plots")
16224 "The @code{ggplot2} package provides a strong API for sequentially
16225 building up a plot, but does not concern itself with composition of multiple
16226 plots. Patchwork is a package that expands the API to allow for arbitrarily
16227 complex composition of plots by providing mathmatical operators for combining
16229 (license license:expat)))
16231 (define-public r-liger
16238 (uri (git-reference
16239 (url "https://github.com/MacoskoLab/liger.git")
16240 (commit (string-append "v" version))))
16241 (file-name (git-file-name name version))
16244 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
16245 (modules '((guix build utils)))
16248 (delete-file "inst/java/ModularityOptimizer.jar")
16250 (build-system r-build-system)
16253 (modify-phases %standard-phases
16254 (add-after 'unpack 'build-java-part
16255 (lambda* (#:key inputs #:allow-other-keys)
16256 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
16257 (for-each (lambda (file) (invoke "javac" file))
16258 (find-files "." "\\.java$"))
16259 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
16260 (find-files "." "\\.class$"))
16263 `(("r-cowplot" ,r-cowplot)
16264 ("r-dosnow" ,r-dosnow)
16265 ("r-dplyr" ,r-dplyr)
16267 ("r-foreach" ,r-foreach)
16268 ("r-ggplot2" ,r-ggplot2)
16269 ("r-ggrepel" ,r-ggrepel)
16270 ("r-hmisc" ,r-hmisc)
16272 ("r-irlba" ,r-irlba)
16273 ("r-matrix" ,r-matrix)
16274 ("r-mclust" ,r-mclust)
16275 ("r-patchwork" ,r-patchwork)
16277 ("r-rann-l1" ,r-rann-l1)
16279 ("r-rcpparmadillo" ,r-rcpparmadillo)
16280 ("r-riverplot" ,r-riverplot)
16281 ("r-rtsne" ,r-rtsne)
16282 ("r-snow" ,r-snow)))
16284 `(("jdk" ,icedtea "jdk")
16285 ;; See https://github.com/MacoskoLab/liger/issues/96
16286 ;; The optimizer is released under the Expat license.
16290 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
16293 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
16295 ("r-knitr" ,r-knitr))) ; for vignettes
16296 (home-page "https://github.com/MacoskoLab/liger")
16297 (synopsis "Integrate and analyze multiple single-cell datasets")
16299 "LIGER is a package for integrating and analyzing multiple single-cell
16300 datasets, developed and maintained by the Macosko lab. It relies on
16301 integrative non-negative matrix factorization to identify shared and
16302 dataset-specific factors.")
16303 (license license:gpl3)))
16305 (define-public r-harmony
16312 (uri (git-reference
16313 (url "https://github.com/immunogenomics/harmony")
16315 (file-name (git-file-name name version))
16318 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
16319 (modules '((guix build utils)))
16322 (for-each delete-file '("config.status" "configure"))
16324 (build-system r-build-system)
16326 `(("r-cowplot" ,r-cowplot)
16327 ("r-dplyr" ,r-dplyr)
16328 ("r-ggplot2" ,r-ggplot2)
16329 ("r-irlba" ,r-irlba)
16330 ("r-matrix" ,r-matrix)
16332 ("r-rcpparmadillo" ,r-rcpparmadillo)
16333 ("r-rcppprogress" ,r-rcppprogress)
16334 ("r-rlang" ,r-rlang)
16335 ("r-tibble" ,r-tibble)
16336 ("r-tidyr" ,r-tidyr)))
16338 `(("autoconf" ,autoconf)))
16339 (home-page "https://github.com/immunogenomics/harmony")
16340 (synopsis "Integration of single cell sequencing data")
16342 "This package provides an implementation of the Harmony algorithm for
16343 single cell integration, described in Korsunsky et al
16344 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
16345 function and interfaces to external frameworks.")
16346 (license license:gpl3)))
16348 (define-public r-covr
16355 (uri (cran-uri "covr" version))
16357 (base32 "1pvr95h7jg9hqq1qq1cccy323pkxldrwafl08151cc410499k4fb"))))
16358 (properties `((upstream-name . "covr")))
16359 (build-system r-build-system)
16361 `(("r-crayon" ,r-crayon)
16362 ("r-digest" ,r-digest)
16364 ("r-jsonlite" ,r-jsonlite)
16366 ("r-withr" ,r-withr)
16367 ("r-yaml" ,r-yaml)))
16369 `(("r-knitr" ,r-knitr))) ; for vignettes
16370 (home-page "https://github.com/r-lib/covr")
16371 (synopsis "Test coverage for R packages")
16373 "Thisp package enables you to track and report code coverage for your
16374 package and (optionally) upload the results to a coverage service. Code
16375 coverage is a measure of the amount of code being exercised by a set of tests.
16376 It is an indirect measure of test quality and completeness. This package is
16377 compatible with any testing methodology or framework and tracks coverage of
16378 both R code and compiled C/C++/FORTRAN code.")
16379 (license license:gpl3)))
16381 (define-public r-systemfonts
16383 (name "r-systemfonts")
16388 (uri (cran-uri "systemfonts" version))
16391 "0wf62mfam5zlrck0wrdbyi4hi7pn5j0739rihgp8sj2cjypm2lnb"))))
16392 (properties `((upstream-name . "systemfonts")))
16393 (build-system r-build-system)
16395 `(("fontconfig" ,fontconfig)
16398 `(("pkg-config" ,pkg-config)
16399 ("r-knitr" ,r-knitr)))
16400 (home-page "https://github.com/r-lib/systemfonts")
16401 (synopsis "System native font finding")
16403 "This package provides system native access to the font catalogue. As
16404 font handling varies between systems it is difficult to correctly locate
16405 installed fonts across different operating systems. The 'systemfonts' package
16406 provides bindings to the native libraries for finding font files that can then
16407 be used further by e.g. graphic devices.")
16408 (license license:expat)))
16410 (define-public r-graphlayouts
16412 (name "r-graphlayouts")
16417 (uri (cran-uri "graphlayouts" version))
16420 "17lc75k8i3c696hfj44zj7j1a5sb0nap8spc5r98v7vd6xh4nii0"))))
16421 (properties `((upstream-name . "graphlayouts")))
16422 (build-system r-build-system)
16424 `(("r-igraph" ,r-igraph)
16426 ("r-rcpparmadillo" ,r-rcpparmadillo)))
16427 (home-page "https://github.com/schochastics/graphlayouts")
16428 (synopsis "Additional layout algorithms for network visualizations")
16430 "This package provides several layout algorithms to visualize networks
16431 which are not part of the igraph library. Most are based on the concept of
16432 stress majorization by Gansner et al. (2004)
16433 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
16434 emphasize hidden group structures in networks or focus on specific nodes.")
16435 (license license:expat)))
16437 (define-public r-tidygraph
16439 (name "r-tidygraph")
16444 (uri (cran-uri "tidygraph" version))
16447 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
16448 (properties `((upstream-name . "tidygraph")))
16449 (build-system r-build-system)
16451 `(("r-dplyr" ,r-dplyr)
16452 ("r-igraph" ,r-igraph)
16453 ("r-magrittr" ,r-magrittr)
16454 ("r-pillar" ,r-pillar)
16457 ("r-rlang" ,r-rlang)
16458 ("r-tibble" ,r-tibble)
16459 ("r-tidyr" ,r-tidyr)))
16460 (home-page "https://github.com/thomasp85/tidygraph")
16461 (synopsis "Tidy API for graph manipulation")
16463 "This package provides a graph implementation that can be thought of as
16464 two tidy data frames describing node and edge data respectively. It provides
16465 an approach to manipulate these two virtual data frames using the API defined
16466 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
16467 common graph algorithms.")
16468 (license license:expat)))
16470 (define-public r-soupx
16471 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
16475 (version (git-version "0.3.1" revision commit))
16479 (uri (git-reference
16480 (url "https://github.com/constantAmateur/SoupX")
16482 (file-name (git-file-name name version))
16485 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
16486 (properties `((upstream-name . "SoupX")))
16487 (build-system r-build-system)
16489 `(("r-ggplot2" ,r-ggplot2)
16490 ("r-matrix" ,r-matrix)
16491 ("r-seurat" ,r-seurat)))
16492 (home-page "https://github.com/constantAmateur/SoupX")
16493 (synopsis "Single cell mRNA Soup eXterminator")
16495 "This package provides a package for quantifying, profiling and
16496 removing cell free mRNA contamination (the \"soup\") from droplet based single
16497 cell RNA-seq experiments.")
16498 (license license:gpl2))))
16500 (define-public r-assertr
16507 (uri (cran-uri "assertr" version))
16510 "1x868pd4dac1c7b1q5390wqh2f6s50km8nqcpim3nxcj2l4qkqdb"))))
16511 (build-system r-build-system)
16513 `(("r-dplyr" ,r-dplyr)
16515 ("r-rlang" ,r-rlang)))
16517 `(("r-knitr" ,r-knitr))) ; needed for vignette
16518 (home-page "https://github.com/ropensci/assertr")
16519 (synopsis "Assertive programming for R analysis pipelines")
16521 "This package provides functionality to assert conditions that have to be
16522 met so that errors in data used in analysis pipelines can fail quickly. It is
16523 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
16525 (license license:expat)))
16527 (define-public r-parameters
16529 (name "r-parameters")
16534 (uri (cran-uri "parameters" version))
16537 "1cmb2hc6f4qdx9aj586zhllckzs6s5sznbqrywvgmhp6a2saaqax"))))
16538 (properties `((upstream-name . "parameters")))
16539 (build-system r-build-system)
16541 `(("r-bayestestr" ,r-bayestestr)
16542 ("r-insight" ,r-insight)))
16544 `(("r-knitr" ,r-knitr)))
16545 (home-page "https://cran.r-project.org/web/packages/parameters")
16546 (synopsis "Processing of model parameters")
16548 "This package provides utilities for processing the parameters of various
16549 statistical models. Beyond computing p values, CIs, and other indices for a
16550 wide variety of models, this package implements features like standardization
16551 or bootstrapping of parameters and models, feature reduction (feature
16552 extraction and variable selection) as well as conversion between indices of
16554 (license license:gpl3)))
16556 (define-public r-rgdal
16563 (uri (cran-uri "rgdal" version))
16565 (base32 "0jvb5ykp539mi0hqs05w4w8wz45blc4nvkhs70aqmzyx27hadfiq"))))
16566 (properties `((upstream-name . "rgdal")))
16567 (build-system r-build-system)
16575 `(("pkg-config" ,pkg-config)
16576 ("r-knitr" ,r-knitr)))
16577 (home-page "http://rgdal.r-forge.r-project.org")
16578 (synopsis "Bindings for the Geospatial Data Abstraction Library")
16580 "This package provides bindings to the Geospatial Data Abstraction
16581 Library (GDAL) and access to projection/transformation operations from the
16583 (license license:gpl2+)))
16585 (define-public r-insol
16592 (uri (cran-uri "insol" version))
16595 "1d2vqmbp94ff80mfkmq4a8y12r6ryym8hh1568ip9qbn7snc64v1"))))
16596 (properties `((upstream-name . "insol")))
16597 (build-system r-build-system)
16599 `(("r-raster" ,r-raster)))
16601 `(("gfortran" ,gfortran)))
16602 (home-page "https://meteoexploration.com/R/insol/index.html")
16603 (synopsis "Tools for calculating solar radiation")
16605 "This package provides functions to compute insolation on tilted
16606 surfaces, computes atmospheric transmittance and related parameters such as:
16607 Earth radius vector, declination, sunset and sunrise, daylength, equation of
16608 time, vector in the direction of the sun, vector normal to surface, and some
16609 atmospheric physics.")
16610 (license license:gpl2+)))
16612 (define-public r-lifecycle
16614 (name "r-lifecycle")
16619 (uri (cran-uri "lifecycle" version))
16622 "0912865c6675fsblrfdk6s568krsj1x8qbk1kipy7m05xs6nwx19"))))
16623 (properties `((upstream-name . "lifecycle")))
16624 (build-system r-build-system)
16626 `(("r-glue" ,r-glue)
16627 ("r-rlang" ,r-rlang)))
16629 `(("r-knitr" ,r-knitr))) ; for vignettes
16630 (home-page "https://github.com/r-lib/lifecycle")
16631 (synopsis "Manage the life cycle of your package functions")
16633 "Manage the life cycle of your exported functions with shared
16634 conventions, documentation badges, and non-invasive deprecation warnings. The
16635 lifecycle package defines four development stages (experimental, maturing,
16636 stable, and questioning) and three deprecation stages (soft-deprecated,
16637 deprecated, and defunct). It makes it easy to insert badges corresponding to
16638 these stages in your documentation. Usage of deprecated functions are
16639 signalled with increasing levels of non-invasive verbosity.")
16640 (license license:gpl3)))
16642 (define-public r-assertable
16644 (name "r-assertable")
16649 (uri (cran-uri "assertable" version))
16652 "1npks9rcrnchmd0silq6qrvqkmdkp9fwjkyyvvp1lqjclyxk6vkk"))))
16653 (build-system r-build-system)
16655 `(("r-data-table" ,r-data-table)))
16656 (home-page "https://cran.r-project.org/web/packages/assertable/")
16657 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
16658 (description "This package provides simple, flexible assertions on
16659 data.frame or data.table objects with verbose output for vetting. While other
16660 assertion packages apply towards more general use-cases, @code{assertable} is
16661 tailored towards tabular data. It includes functions to check variable names
16662 and values, whether the dataset contains all combinations of a given set of
16663 unique identifiers, and whether it is a certain length. In addition,
16664 @code{assertable} includes utility functions to check the existence of target
16665 files and to efficiently import multiple tabular data files into one
16667 (license license:gpl3)))
16669 (define-public r-quadprog
16671 (name "r-quadprog")
16676 (uri (cran-uri "quadprog" version))
16678 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
16679 (build-system r-build-system)
16681 `(("gfortran" ,gfortran)))
16682 (home-page "https://cran.r-project.org/web/packages/quadprog")
16683 (synopsis "Functions to solve quadratic programming problems")
16685 "This package contains routines and documentation for solving quadratic
16686 programming problems.")
16687 (license license:gpl3+)))
16689 (define-public r-desolve
16696 (uri (cran-uri "deSolve" version))
16698 (base32 "0jasvdzig0pzhzspmy20089az19r91xjfb9q6h8gj7c4mr6fymac"))))
16699 (properties `((upstream-name . "deSolve")))
16700 (build-system r-build-system)
16702 `(("gfortran" ,gfortran)))
16703 (home-page "https://desolve.r-forge.r-project.org/")
16704 (synopsis "Solvers for initial value problems of differential equations")
16705 (description "This package provides functions that solve initial value
16706 problems of a system of first-order @dfn{ordinary differential
16707 equations} (ODE), of @dfn{partial differential equations} (PDE), of
16708 @dfn{differential algebraic equations} (DAE), and of delay differential
16709 equations. The functions provide an interface to the FORTRAN functions
16710 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
16711 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
16712 C-implementation of solvers of the Runge-Kutta family with fixed or variable
16713 time steps. The package contains routines designed for solving ODEs resulting
16714 from 1-D, 2-D and 3-D partial differential equations that have been converted
16715 to ODEs by numerical differencing.")
16716 (license license:gpl2+)))
16718 (define-public r-pracma
16724 (uri (cran-uri "pracma" version))
16726 (base32 "07mzhzz73wsjjw1q05l024gcd13hwnzsxf873q9dyhw6x3shzshc"))))
16727 (build-system r-build-system)
16728 (home-page "https://cran.r-project.org/web/packages/pracma/")
16729 (synopsis "Practical numerical math functions")
16730 (description "This package provides functions for numerical analysis and
16731 linear algebra, numerical optimization, differential equations, plus some
16732 special functions. It uses Matlab function names where appropriate to simplify
16734 (license license:gpl3+)))
16736 (define-public r-subplex
16743 (uri (cran-uri "subplex" version))
16746 "1yfbfjvpbhgky7vihw3f4jl41pxpqb39z4nc045d5z7z48bdl18d"))))
16747 (build-system r-build-system)
16749 `(("gfortran" ,gfortran)))
16750 (home-page "https://cran.r-project.org/web/packages/subplex")
16751 (synopsis "Unconstrained optimization using the subplex algorithm")
16753 "This package implements the Subplex optimization algorithm.
16754 It solves unconstrained optimization problems using a simplex method on
16755 subspaces. The method is well suited for optimizing objective functions that
16756 are noisy or are discontinuous at the solution.")
16757 (license license:gpl3+)))
16759 (define-public r-txtplot
16766 (uri (cran-uri "txtplot" version))
16769 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
16770 (build-system r-build-system)
16771 (home-page "https://cran.r-project.org/web/packages/txtplot/")
16772 (synopsis "Text-based plotting")
16773 (description "This package provides functions to produce rudimentary ASCII
16774 graphics directly in the terminal window. This package provides a basic
16775 plotting function (and equivalents of curve, density, acf and barplot) as well
16776 as a boxplot function.")
16777 (license license:lgpl3+)))
16779 (define-public r-bio3d
16786 (uri (cran-uri "bio3d" version))
16789 "07rw6c2d95gb5myxh31727j0jrchd0xisa3x89jjmf4zzs3vv7v7"))))
16790 (properties `((upstream-name . "bio3d")))
16791 (build-system r-build-system)
16792 (inputs `(("zlib" ,zlib)))
16793 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
16794 (home-page "http://thegrantlab.org/bio3d/")
16795 (synopsis "Biological structure analysis")
16797 "This package provides utilities to process, organize and explore protein
16798 structure, sequence and dynamics data. Features include the ability to read
16799 and write structure, sequence and dynamic trajectory data, perform sequence
16800 and structure database searches, data summaries, atom selection, alignment,
16801 superposition, rigid core identification, clustering, torsion analysis,
16802 distance matrix analysis, structure and sequence conservation analysis, normal
16803 mode analysis, principal component analysis of heterogeneous structure data,
16804 and correlation network analysis from normal mode and molecular dynamics data.
16805 In addition, various utility functions are provided to enable the statistical
16806 and graphical power of the R environment to work with biological sequence and
16808 (license license:gpl2+)))
16810 (define-public r-bios2cor
16812 (name "r-bios2cor")
16817 (uri (cran-uri "Bios2cor" version))
16820 "04wk1cjrrxhpv1kdhd67r1qvjv268xxi0z0r105wy912110z9m6x"))))
16821 (properties `((upstream-name . "Bios2cor")))
16822 (build-system r-build-system)
16824 `(("r-bigmemory" ,r-bigmemory)
16825 ("r-bio3d" ,r-bio3d)
16826 ("r-circular" ,r-circular)
16827 ("r-igraph" ,r-igraph)))
16828 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
16829 (synopsis "From biological sequences and simulations to correlation analysis")
16831 "This package provides utilities for computation and analysis of
16832 correlation/covariation in multiple sequence alignments and in side chain
16833 motions during molecular dynamics simulations. Features include the
16834 computation of correlation/covariation scores using a variety of scoring
16835 functions between either sequence positions in alignments or side chain
16836 dihedral angles in molecular dynamics simulations and utilities to analyze the
16837 correlation/covariation matrix through a variety of tools including network
16838 representation and principal components analysis. In addition, several
16839 utility functions are based on the R graphical environment to provide friendly
16840 tools for help in data interpretation.")
16841 (license license:gpl2+)))
16843 ;; This package includes minified JavaScript files. When upgrading please
16844 ;; check that there are no new minified JavaScript files.
16845 (define-public r-networkd3
16847 (name "r-networkd3")
16852 (uri (cran-uri "networkD3" version))
16855 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
16858 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
16860 (properties `((upstream-name . "networkD3")))
16861 (build-system r-build-system)
16863 `(#:modules ((guix build utils)
16864 (guix build r-build-system)
16868 (modify-phases %standard-phases
16869 (add-after 'unpack 'process-javascript
16870 (lambda* (#:key inputs #:allow-other-keys)
16871 (with-directory-excursion "inst/htmlwidgets/lib/"
16875 `((,(assoc-ref inputs "d3.v4.js")
16876 "d3-4.5.0/d3.min.js"))))
16877 (lambda (sources targets)
16878 (for-each (lambda (source target)
16879 (format #t "Processing ~a --> ~a~%"
16881 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
16882 (call-with-output-file target
16884 (dump-port minified port)))))
16885 sources targets))))
16888 `(("uglify-js" ,uglify-js)
16889 ;; NOTE: Make sure that this version of d3 is still valid when
16890 ;; upgrading the package.
16894 (uri "https://d3js.org/d3.v4.js")
16897 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
16899 `(("r-htmlwidgets" ,r-htmlwidgets)
16900 ("r-igraph" ,r-igraph)
16901 ("r-magrittr" ,r-magrittr)))
16902 (home-page "https://cran.r-project.org/package=networkD3")
16903 (synopsis "D3 JavaScript network graphs from R")
16905 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
16907 (license license:gpl3+)))
16909 (define-public r-aasea
16916 (uri (cran-uri "aaSEA" version))
16919 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
16920 (properties `((upstream-name . "aaSEA")))
16921 (build-system r-build-system)
16923 `(("r-bios2cor" ,r-bios2cor)
16925 ("r-hmisc" ,r-hmisc)
16926 ("r-magrittr" ,r-magrittr)
16927 ("r-networkd3" ,r-networkd3)
16928 ("r-plotly" ,r-plotly)
16929 ("r-seqinr" ,r-seqinr)
16930 ("r-shiny" ,r-shiny)
16931 ("r-shinydashboard" ,r-shinydashboard)))
16932 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
16933 (synopsis "Amino acid substitution effect analyzer")
16935 "Given a protein multiple sequence alignment, it is a daunting task to
16936 assess the effects of substitutions along sequence length. The aaSEA package
16937 is intended to help researchers to rapidly analyze property changes caused by
16938 single, multiple and correlated amino acid substitutions in proteins.")
16939 (license license:gpl3)))
16941 (define-public r-abacus
16948 (uri (cran-uri "ABACUS" version))
16951 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
16952 (properties `((upstream-name . "ABACUS")))
16953 (build-system r-build-system)
16955 `(("r-ggplot2" ,r-ggplot2)
16956 ("r-shiny" ,r-shiny)))
16957 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
16958 (synopsis "Apps-based activities for communicating and understanding statistics")
16960 "This package provides a set of Shiny apps for effective communication
16961 and understanding in statistics. The current version includes properties of
16962 normal distribution, properties of sampling distribution, one-sample z and t
16963 tests, two samples independent (unpaired) t test and analysis of variance.")
16964 (license license:gpl3)))
16966 (define-public r-abc-rap
16973 (uri (cran-uri "ABC.RAP" version))
16976 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
16977 (properties `((upstream-name . "ABC.RAP")))
16978 (build-system r-build-system)
16979 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
16980 (synopsis "Array-based CpG region analysis pipeline")
16982 "This package aims to identify candidate genes that are differentially
16983 methylated between cases and controls. It applies Student's t-test and delta
16984 beta analysis to identify candidate genes containing multiple CpG sites.")
16985 (license license:gpl3)))
16987 (define-public r-abcadm
16994 (uri (cran-uri "abcADM" version))
16997 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
16998 (properties `((upstream-name . "abcADM")))
16999 (build-system r-build-system)
17002 ("r-rcpp" ,r-rcpp)))
17003 (home-page "https://cran.r-project.org/web/packages/abcADM/")
17004 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
17006 "This package provides tools to estimate parameters of accumulated
17007 damage (load duration) models based on failure time data under a Bayesian
17008 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
17009 long-term reliability under stochastic load profiles.")
17010 (license license:gpl3)))
17012 (define-public r-rglpk
17019 (uri (cran-uri "Rglpk" version))
17022 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
17023 (properties `((upstream-name . "Rglpk")))
17024 (build-system r-build-system)
17026 `(("r-slam" ,r-slam)))
17029 (home-page "https://r-forge.r-project.org/projects/rglp/")
17030 (synopsis "R interface to the GNU Linear Programming Kit")
17032 "This package provides an R interface to the GNU Linear Programming Kit,
17033 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
17034 integer linear programming} (MILP) and other related problems.")
17036 (license (list license:gpl2 license:gpl3))))
17038 (define-public r-abcdefba
17040 (name "r-abcdefba")
17045 (uri (cran-uri "abcdeFBA" version))
17048 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
17049 (properties `((upstream-name . "abcdeFBA")))
17050 (build-system r-build-system)
17052 `(("r-corrplot" ,r-corrplot)
17053 ("r-lattice" ,r-lattice)
17055 ("r-rglpk" ,r-rglpk)))
17056 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
17057 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
17059 "This package provides functions for Constraint Based Simulation using
17060 Flux Balance Analysis and informative analysis of the data generated during
17062 (license license:gpl2)))
17064 (define-public r-abcrlda
17071 (uri (cran-uri "abcrlda" version))
17074 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
17075 (properties `((upstream-name . "abcrlda")))
17076 (build-system r-build-system)
17077 (home-page "https://ieeexplore.ieee.org/document/8720003/")
17078 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
17080 "This package offers methods to perform @dfn{asymptotically
17081 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
17082 cost-sensitive binary classification. The bias-correction is an estimate of
17083 the bias term added to regularized discriminant analysis that minimizes the
17085 (license license:gpl3)))
17087 (define-public r-abemus
17094 (uri (cran-uri "abemus" version))
17097 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
17098 (properties `((upstream-name . "abemus")))
17099 (build-system r-build-system)
17101 `(("r-data-table" ,r-data-table)))
17102 (home-page "https://cran.r-project.org/web/packages/abemus/")
17103 (synopsis "Adaptive base error model in ultra-deep sequencing data")
17105 "This package provides an implementation of @dfn{Adaptive Base Error
17106 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
17107 platform-specific genetic knowledge and empirical signal to readily detect and
17108 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
17109 cell free DNA} (cfDNA).")
17110 (license license:gpl3)))
17112 ;; This package includes minified JavaScript files. When upgrading please
17113 ;; check that there are no new minified JavaScript files.
17114 (define-public r-rintrojs
17116 (name "r-rintrojs")
17121 (uri (cran-uri "rintrojs" version))
17124 "0vyqb3pyrh12saddar71ac9csn2vkd2j8ln6ygpqys8ky1lc3427"))))
17125 (properties `((upstream-name . "rintrojs")))
17126 (build-system r-build-system)
17128 `(#:modules ((guix build utils)
17129 (guix build r-build-system)
17133 (modify-phases %standard-phases
17134 (add-after 'unpack 'process-javascript
17135 (lambda* (#:key inputs #:allow-other-keys)
17136 (with-directory-excursion "inst/javascript/introjs/"
17140 `((,(assoc-ref inputs "intro.js")
17142 (lambda (sources targets)
17143 (for-each (lambda (source target)
17144 (format #t "Processing ~a --> ~a~%"
17146 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
17147 (call-with-output-file target
17149 (dump-port minified port)))))
17150 sources targets))))
17153 `(("uglify-js" ,uglify-js)
17157 (uri "https://raw.githubusercontent.com/usablica/intro.js/v2.9.3/intro.js")
17160 "1qf8n1sfy9qkiqqnfgg0xbhmfgh0g3mqsjas8qhz230h3zzlzxj8"))))))
17162 `(("r-jsonlite" ,r-jsonlite)
17163 ("r-shiny" ,r-shiny)))
17164 (home-page "https://github.com/carlganz/rintrojs")
17165 (synopsis "Wrapper for the Intro.js library")
17167 "This package provides a wrapper for the @url{http://www.introjs.com,
17168 Intro.js} library. This package makes it easy to include step-by-step
17169 introductions, and clickable hints in a Shiny application. It supports both
17170 static introductions in the UI, and programmatic introductions from the
17172 (license license:agpl3+)))
17174 (define-public r-sysfonts
17176 (name "r-sysfonts")
17181 (uri (cran-uri "sysfonts" version))
17184 "1xp40hchjfif80a6jj210ghrjcvjjf66vqcssdy7a1j53nl1n994"))))
17185 (properties `((upstream-name . "sysfonts")))
17186 (build-system r-build-system)
17188 `(("freetype" ,freetype)
17192 `(("pkg-config" ,pkg-config)))
17193 (home-page "https://github.com/yixuan/sysfonts")
17194 (synopsis "Loading fonts into R")
17196 "This is a package to simplify loading of system fonts and Google Fonts
17197 into R, in order to support other packages.")
17198 (license license:gpl2)))
17200 (define-public r-showtextdb
17202 (name "r-showtextdb")
17207 (uri (cran-uri "showtextdb" version))
17210 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
17211 (properties `((upstream-name . "showtextdb")))
17212 (build-system r-build-system)
17214 `(("r-sysfonts" ,r-sysfonts)))
17215 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
17216 (synopsis "Font files for the 'showtext' package")
17218 "This package provides font files that can be used by the @code{showtext}
17220 (license license:asl2.0)))
17222 (define-public r-showtext
17224 (name "r-showtext")
17229 (uri (cran-uri "showtext" version))
17232 "1n1cd9f4zrv45k5953akclqh1jh7fy122dqkgmbfi5h122v6p2h0"))))
17233 (properties `((upstream-name . "showtext")))
17234 (build-system r-build-system)
17236 `(("freetype" ,freetype)
17240 `(("r-showtextdb" ,r-showtextdb)
17241 ("r-sysfonts" ,r-sysfonts)))
17243 `(("pkg-config" ,pkg-config)
17244 ("r-knitr" ,r-knitr)))
17245 (home-page "https://github.com/yixuan/showtext")
17246 (synopsis "Using fonts more easily in R graphs")
17248 "This package aims to make it easy to use various types of
17249 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
17250 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
17251 will be converted into polygons or raster images, hence after the plot has
17252 been created, it no longer relies on the font files. No external software
17253 such as Ghostscript is needed to use this package.")
17254 (license license:asl2.0)))
17256 (define-public r-emojifont
17258 (name "r-emojifont")
17263 (uri (cran-uri "emojifont" version))
17266 "1cdrrl3hvrs8rskyy6zgr7q2mmg8yb9k8sld1m64zsp7y009g19k"))))
17267 (properties `((upstream-name . "emojifont")))
17268 (build-system r-build-system)
17270 `(("r-ggplot2" ,r-ggplot2)
17271 ("r-proto" ,r-proto)
17272 ("r-showtext" ,r-showtext)
17273 ("r-sysfonts" ,r-sysfonts)))
17274 (home-page "https://guangchuangyu.github.io/emojifont")
17275 (synopsis "Emoji and Font Awesome in R graphics")
17277 "This package enables the use of emoji and the Font Awesome glyphs in
17278 both base and ggplot2 graphics.")
17279 (license license:artistic2.0)))
17281 (define-public r-abstractr
17283 (name "r-abstractr")
17288 (uri (cran-uri "abstractr" version))
17291 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
17292 (properties `((upstream-name . "abstractr")))
17293 (build-system r-build-system)
17295 `(("r-colourpicker" ,r-colourpicker)
17296 ("r-emojifont" ,r-emojifont)
17297 ("r-ggplot2" ,r-ggplot2)
17298 ("r-gridextra" ,r-gridextra)
17299 ("r-rintrojs" ,r-rintrojs)
17300 ("r-shiny" ,r-shiny)
17301 ("r-shinythemes" ,r-shinythemes)))
17302 (home-page "https://matt-kumar.shinyapps.io/portfolio")
17303 (synopsis "R-Shiny application for creating visual abstracts")
17305 "This package provides an R Shiny application to create visual abstracts
17306 for original research. A variety of user defined options and formatting are
17308 (license license:gpl3)))
17310 (define-public r-qgam
17317 (uri (cran-uri "qgam" version))
17320 "0lks2cj0p7irp1i01756v1l7i26d7alax1fbkc20qd6wpz840fi7"))))
17321 (properties `((upstream-name . "qgam")))
17322 (build-system r-build-system)
17324 `(("r-doparallel" ,r-doparallel)
17327 ("r-shiny" ,r-shiny)))
17328 (native-inputs `(("r-knitr" ,r-knitr)))
17329 (home-page "https://cran.r-project.org/web/packages/qgam/")
17330 (synopsis "Smooth additive quantile regression models")
17332 "This package provides smooth additive quantile regression models, fitted
17333 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
17334 the smoothing parameters are estimated automatically by marginal loss
17335 minimization, while the regression coefficients are estimated using either
17336 PIRLS or Newton algorithm. The learning rate is determined so that the
17337 Bayesian credible intervals of the estimated effects have approximately the
17338 correct coverage. The main function is @code{qgam()} which is similar to
17339 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
17340 regression models.")
17341 (license license:gpl2+)))
17343 (define-public r-abtest
17350 (uri (cran-uri "abtest" version))
17353 "1zfd13d7dplawk24dbdr1ka8cbdp5w6sxb0zlm7k4dhvn6ksi8h0"))))
17354 (properties `((upstream-name . "abtest")))
17355 (build-system r-build-system)
17357 `(("r-matrix" ,r-matrix)
17358 ("r-mvtnorm" ,r-mvtnorm)
17359 ("r-plotrix" ,r-plotrix)
17361 ("r-rcolorbrewer" ,r-rcolorbrewer)
17364 ("r-truncnorm" ,r-truncnorm)))
17365 (home-page "https://cran.r-project.org/web/packages/abtest/")
17366 (synopsis "Bayesian A/B testing")
17368 "This package provides functions for Bayesian A/B testing including prior
17369 elicitation options based on Kass and Vaidyanathan (1992)
17370 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
17371 (license license:gpl2+)))
17373 (define-public r-accept
17380 (uri (cran-uri "accept" version))
17383 "0pn8q0jsi0nb2mm2kv6sjczflflshhy55y7nqqnk70yx9f6wm83y"))))
17384 (properties `((upstream-name . "accept")))
17385 (build-system r-build-system)
17387 `(("r-dplyr" ,r-dplyr)
17388 ("r-extrafont" ,r-extrafont)
17390 ("r-plotly" ,r-plotly)
17391 ("r-stringr" ,r-stringr)
17392 ("r-viridis" ,r-viridis)))
17393 (home-page "https://cran.r-project.org/web/packages/accept/")
17394 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
17396 "This package allows clinicians to predict the rate and severity of
17397 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
17398 Disease} (COPD) patients, based on the clinical prediction model published in
17399 Adibi et al. (2019) @url{doi:10.1101/651901}.")
17400 (license license:gpl3)))
17402 (define-public r-smpracticals
17404 (name "r-smpracticals")
17409 (uri (cran-uri "SMPracticals" version))
17412 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
17413 (properties `((upstream-name . "SMPracticals")))
17414 (build-system r-build-system)
17416 `(("r-ellipse" ,r-ellipse)
17419 ("r-survival" ,r-survival)))
17420 (home-page "http://statwww.epfl.ch/davison/SM/")
17421 (synopsis "Practicals for use with Davison (2003) Statistical Models")
17423 "This package contains the datasets and a few functions for use with the
17424 practicals outlined in Appendix A of the book Statistical Models (Davison,
17425 2003, Cambridge University Press). The practicals themselves can be found at
17426 @url{http://statwww.epfl.ch/davison/SM/}.")
17427 (license license:gpl2+)))
17429 (define-public r-fgui
17436 (uri (cran-uri "fgui" version))
17439 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
17440 (properties `((upstream-name . "fgui")))
17441 (build-system r-build-system)
17443 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
17444 (synopsis "Create GUI for R functions")
17446 "Rapidly create a GUI for a function you created by automatically
17447 creating widgets for arguments of the function. This package automatically
17448 parses help routines for context-sensitive help to these arguments. The
17449 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
17450 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
17451 incorporated into the interface for greater customization for the more
17453 ;; Any version of the GPL.
17454 (license (list license:gpl2+ license:gpl3+))))
17456 (define-public r-tcltk2
17463 (uri (cran-uri "tcltk2" version))
17466 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
17467 (properties `((upstream-name . "tcltk2")))
17468 (build-system r-build-system)
17472 (home-page "https://www.sciviews.org/SciViews-R")
17473 (synopsis "Tcl/Tk additions")
17475 "This package provides a series of additional Tcl commands and Tk widgets
17476 with style and various functions to supplement the tcltk package")
17477 (license license:lgpl3)))
17479 (define-public r-accrual
17486 (uri (cran-uri "accrual" version))
17489 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
17490 (properties `((upstream-name . "accrual")))
17491 (build-system r-build-system)
17493 `(("r-fgui" ,r-fgui)
17494 ("r-smpracticals" ,r-smpracticals)
17495 ("r-tcltk2" ,r-tcltk2)))
17496 (home-page "https://cran.r-project.org/web/packages/accrual/")
17497 (synopsis "Bayesian accrual prediction")
17499 "Subject recruitment for medical research is challenging. Slow patient
17500 accrual leads to delay in research. Accrual monitoring during the process of
17501 recruitment is critical. Researchers need reliable tools to manage the
17502 accrual rate. This package provides an implementation of a Bayesian method
17503 that integrates researcher's experience on previous trials and data from the
17504 current study, providing reliable prediction on accrual rate for clinical
17505 studies. It provides functions for Bayesian accrual prediction which can be
17506 easily used by statisticians and clinical researchers.")
17507 (license license:gpl2)))
17509 (define-public r-accrued
17516 (uri (cran-uri "accrued" version))
17519 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
17520 (properties `((upstream-name . "accrued")))
17521 (build-system r-build-system)
17522 (home-page "https://cran.r-project.org/web/packages/accrued/")
17523 (synopsis "Data quality visualization tools for partially accruing data")
17525 "This is a package for visualizing data quality of partially accruing
17527 (license license:gpl3)))
17529 (define-public r-mda
17536 (uri (cran-uri "mda" version))
17539 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
17540 (properties `((upstream-name . "mda")))
17541 (build-system r-build-system)
17542 (propagated-inputs `(("r-class" ,r-class)))
17543 (native-inputs `(("gfortran" ,gfortran)))
17544 (home-page "https://cran.r-project.org/web/packages/mda/")
17545 (synopsis "Mixture and flexible discriminant analysis")
17547 "This is a package for mixture and flexible discriminant analysis,
17548 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
17549 (license license:gpl2)))
17551 (define-public r-elasticnet
17553 (name "r-elasticnet")
17558 (uri (cran-uri "elasticnet" version))
17561 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
17562 (properties `((upstream-name . "elasticnet")))
17563 (build-system r-build-system)
17565 `(("r-lars" ,r-lars)))
17566 (home-page "http://users.stat.umn.edu/~zouxx019/")
17567 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
17569 "This package provides functions for fitting the entire solution path of
17570 the Elastic-Net and also provides functions for estimating sparse Principal
17571 Components. The Lasso solution paths can be computed by the same function.")
17572 (license license:gpl2+)))
17574 (define-public r-sparselda
17576 (name "r-sparselda")
17581 (uri (cran-uri "sparseLDA" version))
17584 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
17585 (properties `((upstream-name . "sparseLDA")))
17586 (build-system r-build-system)
17588 `(("r-elasticnet" ,r-elasticnet)
17591 (home-page "https://www.imm.dtu.dk/~lkhc/")
17592 (synopsis "Sparse discriminant analysis")
17594 "This package performs sparse linear discriminant analysis for Gaussians
17595 and mixture of Gaussian models.")
17596 (license license:gpl2+)))
17598 (define-public r-accsda
17605 (uri (cran-uri "accSDA" version))
17608 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
17609 (properties `((upstream-name . "accSDA")))
17610 (build-system r-build-system)
17612 `(("r-ggplot2" ,r-ggplot2)
17613 ("r-ggthemes" ,r-ggthemes)
17614 ("r-gridextra" ,r-gridextra)
17616 ("r-rarpack" ,r-rarpack)
17617 ("r-sparselda" ,r-sparselda)))
17618 (home-page "https://github.com/gumeo/accSDA/wiki")
17619 (synopsis "Accelerated sparse discriminant analysis")
17621 "This package provides an implementation of sparse linear discriminant
17622 analysis, which is a supervised classification method for multiple classes.
17623 Various novel optimization approaches to this problem are implemented
17624 including @dfn{alternating direction method of multipliers} (ADMM),
17625 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
17626 Functions for performing cross validation are also supplied along with basic
17627 prediction and plotting functions. @dfn{Sparse zero variance
17628 discriminant} (SZVD) analysis is also included in the package.")
17629 (license license:gpl2+)))
17631 (define-public r-ace2fastq
17633 (name "r-ace2fastq")
17638 (uri (cran-uri "ace2fastq" version))
17641 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
17642 (properties `((upstream-name . "ace2fastq")))
17643 (build-system r-build-system)
17645 `(("r-stringr" ,r-stringr)))
17646 (home-page "https://github.com/c5sire/ace2fastq")
17647 (synopsis "ACE file to FASTQ converter")
17649 "The ACE file format is used in genomics to store contigs from sequencing
17650 machines. This tools converts it into FASTQ format. Both formats contain the
17651 sequence characters and their corresponding quality information. Unlike the
17652 FASTQ file, the ACE file stores the quality values numerically. The
17653 conversion algorithm uses the standard Sanger formula. The package
17654 facilitates insertion into pipelines, and content inspection.")
17655 (license license:gpl3)))
17657 (define-public r-rngwell
17664 (uri (cran-uri "rngWELL" version))
17667 "0pjjcs9pqj7mf0mhb2cwd0aanqpwnm65bm86hk6mi2vw8rgnj2vv"))))
17668 (properties `((upstream-name . "rngWELL")))
17669 (build-system r-build-system)
17670 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
17671 (synopsis "Toolbox for WELL random number generators")
17673 "This is a dedicated package to WELL pseudo random generators, which were
17674 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
17675 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
17676 (license license:bsd-3)))
17678 (define-public r-randtoolbox
17680 (name "r-randtoolbox")
17685 (uri (cran-uri "randtoolbox" version))
17688 "0qg20ar6qns858jdzqhmfq7yji81czhr6cim257958gqpj66sn95"))))
17689 (properties `((upstream-name . "randtoolbox")))
17690 (build-system r-build-system)
17692 `(("r-rngwell" ,r-rngwell)))
17694 `(("gfortran" ,gfortran)))
17695 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
17696 (synopsis "Toolbox for pseudo and quasi random number generation")
17698 "This package provides
17701 @item pseudo random generators, such as general linear
17702 congruential generators, multiple recursive generators and generalized
17703 feedback shift register (SF-Mersenne Twister algorithm and WELL
17706 @item quasi random generators, such as the Torus algorithm, the Sobol
17707 sequence, the Halton sequence (including the Van der Corput sequence), and
17709 @item some generator tests: the gap test, the serial test, the poker test.
17712 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
17713 (license license:bsd-3)))
17715 (define-public r-lhs
17722 (uri (cran-uri "lhs" version))
17725 "0n0i1hr9gmc0hfcs2cvpjvdfgm6k26rhcq3q22r8ic0gfj953572"))))
17726 (properties `((upstream-name . "lhs")))
17727 (build-system r-build-system)
17728 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
17730 `(("r-knitr" ,r-knitr)))
17731 (home-page "https://github.com/bertcarnell/lhs")
17732 (synopsis "Latin Hypercube Samples")
17734 "This package provides a number of methods for creating and augmenting
17735 Latin Hypercube Samples.")
17736 (license license:gpl3)))
17738 (define-public r-acebayes
17740 (name "r-acebayes")
17745 (uri (cran-uri "acebayes" version))
17748 "1imfwm1vpbb24vfmfn1nljhmaz8429mwjihw34892p387s8h7xz2"))))
17749 (properties `((upstream-name . "acebayes")))
17750 (build-system r-build-system)
17752 `(("r-compare" ,r-compare)
17754 ("r-randtoolbox" ,r-randtoolbox)
17756 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17757 (home-page "https://cran.r-project.org/web/packages/acebayes/")
17758 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
17760 "Finding an optimal Bayesian experimental design involves maximizing an
17761 objective function given by the expectation of some appropriately chosen
17762 utility function with respect to the joint distribution of unknown
17763 quantities (including responses). This objective function is usually not
17764 available in closed form and the design space can be continuous and of high
17765 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
17766 to maximise an approximation to the expectation of the utility function.")
17767 (license license:gpl2)))
17769 (define-public r-acet
17776 (uri (cran-uri "ACEt" version))
17779 "0626d6kg485xjya164wagrr5z223jvi93ywbwpdns7fkm03c0dlq"))))
17780 (properties `((upstream-name . "ACEt")))
17781 (build-system r-build-system)
17786 ("r-rcpparmadillo" ,r-rcpparmadillo)))
17787 (home-page "https://cran.r-project.org/web/packages/ACEt/")
17788 (synopsis "Estimating dynamic heritability and twin model comparison")
17790 "This package supports twin models that are able to estimate the dynamic
17791 behaviour of the variance components in the classical twin models with respect
17792 to age using B-splines and P-splines.")
17793 (license license:gpl2+)))
17795 (define-public r-acfmperiod
17797 (name "r-acfmperiod")
17802 (uri (cran-uri "acfMPeriod" version))
17805 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
17806 (properties `((upstream-name . "acfMPeriod")))
17807 (build-system r-build-system)
17809 `(("r-mass" ,r-mass)))
17810 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
17811 (synopsis "Estimation of the ACF from the M-periodogram")
17813 "This package support non-robust and robust computations of the sample
17814 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
17815 univariate and multivariate processes. The methodology consists in reversing
17816 the diagonalization procedure involving the periodogram or the
17817 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
17818 ACOVF or the ACF as discussed in Fuller (1995)
17819 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
17820 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
17821 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
17822 (license license:gpl2+)))
17824 (define-public r-gamlss-data
17826 (name "r-gamlss-data")
17831 (uri (cran-uri "gamlss.data" version))
17834 "1dgfspbmps6ipzcmw681wjdp320nm50dwsxafgrcwxndqgc7fdqd"))))
17835 (properties `((upstream-name . "gamlss.data")))
17836 (build-system r-build-system)
17837 (home-page "http://www.gamlss.org/")
17838 (synopsis "GAMLSS data")
17840 "This package provides data used as examples to demonstrate GAMLSS
17842 ;; Either version of the license
17843 (license (list license:gpl2 license:gpl3))))
17845 (define-public r-gamlss
17852 (uri (cran-uri "gamlss" version))
17855 "16b7ick1khvldbvfmmpw9cjs1vznnrisvifq7717fxzd8c9s5jdr"))))
17856 (properties `((upstream-name . "gamlss")))
17857 (build-system r-build-system)
17859 `(("r-gamlss-data" ,r-gamlss-data)
17860 ("r-gamlss-dist" ,r-gamlss-dist)
17863 ("r-survival" ,r-survival)))
17864 (home-page "http://www.gamlss.org/")
17865 (synopsis "Generalized additive models for location scale and shape")
17867 "This package provides functions for fitting the generalized additive
17868 models for location scale and shape introduced by Rigby and
17869 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
17870 use a distributional regression approach where all the parameters of the
17871 conditional distribution of the response variable are modelled using
17872 explanatory variables.")
17873 ;; Either version of the license
17874 (license (list license:gpl2 license:gpl3))))
17876 (define-public r-acid
17883 (uri (cran-uri "acid" version))
17886 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
17887 (properties `((upstream-name . "acid")))
17888 (build-system r-build-system)
17890 `(("r-gamlss" ,r-gamlss)
17891 ("r-gamlss-dist" ,r-gamlss-dist)
17892 ("r-hmisc" ,r-hmisc)))
17893 (home-page "https://cran.r-project.org/web/packages/acid/")
17894 (synopsis "Analysing conditional income distributions")
17896 "This package provides functions for the analysis of income distributions
17897 for subgroups of the population as defined by a set of variables like age,
17898 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
17899 distribution as well as functions for moments, inequality measures, entropy
17900 measures and polarisation measures of income distributions. This package thus
17901 aides the analysis of income inequality by offering tools for the exploratory
17902 analysis of income distributions at the disaggregated level.")
17903 (license license:gpl3)))
17905 (define-public r-acm4r
17912 (uri (cran-uri "acm4r" version))
17915 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
17916 (properties `((upstream-name . "acm4r")))
17917 (build-system r-build-system)
17918 (propagated-inputs `(("r-mass" ,r-mass)))
17919 (home-page "https://cran.r-project.org/web/packages/acm4r/")
17920 (synopsis "Align-and-count method comparisons of RFLP data")
17922 "This is a package to compare sequence fragment lengths or molecular
17923 weights from pairs of lanes. The number of matching bands in the
17924 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
17925 the align-and-count method.")
17926 ;; Any version of the GPL
17927 (license (list license:gpl2+ license:gpl3+))))
17929 (define-public r-filematrix
17931 (name "r-filematrix")
17936 (uri (cran-uri "filematrix" version))
17939 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
17940 (properties `((upstream-name . "filematrix")))
17941 (build-system r-build-system)
17942 ;; These inputs are needed for vignettes
17944 `(("r-knitr" ,r-knitr)
17945 ("r-rmarkdown" ,r-rmarkdown)
17946 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
17947 (home-page "https://github.com/andreyshabalin/filematrix")
17948 (synopsis "File-backed matrix class with convenient read and write access")
17950 "This package provides an interface for working with large matrices
17951 stored in files, not in computer memory. It supports multiple non-character
17952 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
17953 byte real values). Access to parts of the matrix is done by indexing, exactly
17954 as with usual R matrices. It supports very large matrices; the package has
17955 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
17956 columns, ad allows for quick addition of extra columns to a filematrix.")
17957 (license license:lgpl3)))
17959 (define-public r-acmeeqtl
17961 (name "r-acmeeqtl")
17966 (uri (cran-uri "ACMEeqtl" version))
17969 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
17970 (properties `((upstream-name . "ACMEeqtl")))
17971 (build-system r-build-system)
17973 `(("r-filematrix" ,r-filematrix)))
17974 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
17975 (synopsis "Estimation of interpretable eQTL effect sizes")
17977 "This package provides a non-linear model, termed ACME, that reflects a
17978 parsimonious biological model for allelic contributions of cis-acting eQTLs.
17979 With non-linear least-squares algorithm the maximum likelihood parameters can
17980 be estimated. The ACME model provides interpretable effect size estimates and
17981 p-values with well controlled Type-I error.")
17982 (license license:lgpl3)))
17984 (define-public r-acmer
17991 (uri (cran-uri "acmeR" version))
17994 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
17995 (properties `((upstream-name . "acmeR")))
17996 (build-system r-build-system)
17997 (propagated-inputs `(("r-foreign" ,r-foreign)))
17998 (home-page "https://cran.r-project.org/web/packages/acmeR/")
17999 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
18001 "This package provides an implementation of the ACME estimator, described
18002 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
18003 Mortality at Wind Turbines. Unlike most other models, this estimator supports
18004 decreasing-hazard Weibull model for persistence; decreasing search proficiency
18005 as carcasses age; variable bleed-through at successive searches; and interval
18006 mortality estimates. The package provides, based on search data, functions
18007 for estimating the mortality inflation factor in Frequentist and Bayesian
18009 (license license:expat)))
18011 (define-public r-r-huge
18018 (uri (cran-uri "R.huge" version))
18021 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
18022 (properties `((upstream-name . "R.huge")))
18023 (build-system r-build-system)
18025 `(("r-r-methodss3" ,r-r-methodss3)
18027 ("r-r-utils" ,r-r-utils)))
18028 (home-page "https://github.com/HenrikBengtsson/R.huge")
18029 (synopsis "Methods for accessing huge amounts of data")
18031 "This is a deprecated package for accessing huge amounts of data.
18032 Cross-platform alternatives are the following packages: bigmemory (CRAN),
18033 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
18034 the @code{aroma.affymetrix} package.")
18035 (license license:lgpl2.1+)))
18037 (define-public r-r-filesets
18039 (name "r-r-filesets")
18044 (uri (cran-uri "R.filesets" version))
18047 "124rygq0bl9n4akxcm868nl30cyk3rz0iprb98zlpk62gci9f5fg"))))
18048 (properties `((upstream-name . "R.filesets")))
18049 (build-system r-build-system)
18051 `(("r-digest" ,r-digest)
18052 ("r-r-cache" ,r-r-cache)
18053 ("r-r-methodss3" ,r-r-methodss3)
18055 ("r-r-utils" ,r-r-utils)))
18056 (home-page "https://github.com/HenrikBengtsson/R.filesets")
18057 (synopsis "Easy handling of and access to files")
18059 "This package provides classes and methods to locate, setup, subset,
18060 navigate and iterate file sets, i.e. sets of files located in one or more
18061 directories on the file system. The API is designed such that these classes
18062 can be extended via inheritance to provide a richer API for special file
18063 formats. Moreover, a specific name format is defined such that filenames and
18064 directories can be considered to have full names which consists of a name
18065 followed by comma-separated tags. This adds additional flexibility to
18066 identify file sets and individual files.")
18067 (license license:lgpl2.1+)))
18069 (define-public r-r-devices
18071 (name "r-r-devices")
18076 (uri (cran-uri "R.devices" version))
18079 "15zlnq3g27whq26fbcy5zfl5hiddm256h4rga4frblg6wqlbkvdd"))))
18080 (properties `((upstream-name . "R.devices")))
18081 (build-system r-build-system)
18083 `(("r-base64enc" ,r-base64enc)
18084 ("r-r-methodss3" ,r-r-methodss3)
18086 ("r-r-utils" ,r-r-utils)))
18087 (home-page "https://github.com/HenrikBengtsson/R.devices")
18088 (synopsis "Unified handling of graphics devices")
18090 "This package provides functions for creating plots and image files in a
18091 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
18092 Default device options as well as scales and aspect ratios are controlled in a
18093 uniform way across all device types. Switching output format requires minimal
18094 changes in code. This package is ideal for large-scale batch processing,
18095 because it will never leave open graphics devices or incomplete image files
18096 behind, even on errors or user interrupts.")
18097 (license license:lgpl2.1+)))
18099 (define-public r-acnr
18106 (uri (cran-uri "acnr" version))
18109 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
18110 (properties `((upstream-name . "acnr")))
18111 (build-system r-build-system)
18112 (home-page "https://github.com/mpierrejean/acnr")
18113 (synopsis "Annotated copy-number regions")
18115 "This package provides SNP array data from different types of copy-number
18116 regions. These regions were identified manually by the authors of the package
18117 and may be used to generate realistic data sets with known truth.")
18118 (license license:lgpl2.1+)))
18120 (define-public r-acopula
18127 (uri (cran-uri "acopula" version))
18130 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
18131 (properties `((upstream-name . "acopula")))
18132 (build-system r-build-system)
18133 (home-page "https://cran.r-project.org/web/packages/acopula/")
18134 (synopsis "Modelling dependence with multivariate Archimax copulas")
18136 "Archimax copulas are a mixture of Archimedean and EV copulas. This
18137 package provides definitions of several parametric families of generator and
18138 dependence function, computes CDF and PDF, estimates parameters, tests for
18139 goodness of fit, generates random sample and checks copula properties for
18140 custom constructs. In the 2-dimensional case explicit formulas for density
18141 are used, contrary to higher dimensions when all derivatives are linearly
18142 approximated. Several non-archimax families (normal, FGM, Plackett) are
18143 provided as well.")
18144 (license license:gpl2)))
18146 (define-public r-tuner
18153 (uri (cran-uri "tuneR" version))
18156 "0av978m4h2iqazyfq6n2cgkh4wpllihh7s29lah2nb8ngc0w5hxx"))))
18157 (properties `((upstream-name . "tuneR")))
18158 (build-system r-build-system)
18159 (propagated-inputs `(("r-signal" ,r-signal)))
18160 (home-page "https://cran.r-project.org/web/packages/tuneR/")
18161 (synopsis "Analysis of music and speech")
18163 "This is a package for the analysis of music and speech. Analyze music
18164 and speech, extract features like MFCCs, handle wave files and their
18165 representation in various ways, read MP3, read MIDI, perform steps of a
18166 transcription, ...")
18167 ;; Either of these versions.
18168 (license (list license:gpl2 license:gpl3))))
18170 (define-public r-seewave
18177 (uri (cran-uri "seewave" version))
18180 "123h3q0gps0vy9sikr7gjphnv9m3l4h4mykiydjllmrpaw1s1844"))))
18181 (properties `((upstream-name . "seewave")))
18182 (build-system r-build-system)
18184 `(("libsndfile" ,libsndfile)))
18186 `(("r-tuner" ,r-tuner)))
18187 (home-page "http://rug.mnhn.fr/seewave")
18188 (synopsis "Sound analysis and synthesis")
18190 "This package provides functions for analysing, manipulating, displaying,
18191 editing and synthesizing time waves (particularly sound). This package
18192 processes time analysis (oscillograms and envelopes), spectral content,
18193 resonance quality factor, entropy, cross correlation and autocorrelation,
18194 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
18195 and 3D spectrograms and many other analyses.")
18196 (license license:gpl2+)))
18198 (define-public r-acousticndlcoder
18200 (name "r-acousticndlcoder")
18205 (uri (cran-uri "AcousticNDLCodeR" version))
18208 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
18210 `((upstream-name . "AcousticNDLCodeR")))
18211 (build-system r-build-system)
18213 `(("r-seewave" ,r-seewave)
18214 ("r-tuner" ,r-tuner)
18216 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
18217 (synopsis "Coding sound files for use with NDL")
18219 "Make acoustic cues to use with the R package @code{ndl}.
18220 The package implements functions used in the PLoS ONE paper \"Words from
18221 spontaneous conversational speech can be recognized with human-like accuracy
18222 by an error-driven learning algorithm that discriminates between meanings
18223 straight from smart acoustic features, bypassing the phoneme as recognition
18224 unit.\" @url{doi:10.1371/journal.pone.0174623}")
18225 (license license:gpl2+)))
18227 (define-public r-acp
18234 (uri (cran-uri "acp" version))
18237 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
18238 (properties `((upstream-name . "acp")))
18239 (build-system r-build-system)
18241 `(("r-quantmod" ,r-quantmod)
18242 ("r-tseries" ,r-tseries)))
18243 (home-page "https://cran.r-project.org/web/packages/acp/")
18244 (synopsis "Autoregressive conditional Poisson")
18246 "This package supports the analysis of count data exhibiting
18247 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
18248 model (ACP(p,q)) proposed by Heinen (2003).")
18249 (license license:gpl2)))
18251 (define-public r-ada
18258 (uri (cran-uri "ada" version))
18261 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
18262 (properties `((upstream-name . "ada")))
18263 (build-system r-build-system)
18264 (propagated-inputs `(("r-rpart" ,r-rpart)))
18265 (home-page "https://cran.r-project.org/web/packages/ada/")
18266 (synopsis "Stochastic boosting")
18268 "This package provides a straightforward, well-documented, and broad
18269 boosting routine for classification, ideally suited for small to
18270 moderate-sized data sets. It performs discrete, real, and gentle boost under
18271 both exponential and logistic loss on a given data set.")
18272 ;; Any version of the GPL.
18273 (license (list license:gpl2+ license:gpl3+))))
18275 (define-public r-genalg
18282 (uri (cran-uri "genalg" version))
18285 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
18286 (properties `((upstream-name . "genalg")))
18287 (build-system r-build-system)
18288 (home-page "https://github.com/egonw/genalg")
18289 (synopsis "R based genetic algorithm")
18291 "This package provides an R based genetic algorithm for binary and
18292 floating point chromosomes.")
18293 (license license:gpl2)))
18295 (define-public r-kernelfactory
18297 (name "r-kernelfactory")
18302 (uri (cran-uri "kernelFactory" version))
18305 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
18306 (properties `((upstream-name . "kernelFactory")))
18307 (build-system r-build-system)
18310 ("r-genalg" ,r-genalg)
18311 ("r-kernlab" ,r-kernlab)
18312 ("r-randomforest" ,r-randomforest)))
18313 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
18314 (synopsis "Ensemble of kernel machines")
18316 "Kernel factory is an ensemble method where each base classifier (random
18317 forest) is fit on the kernel matrix of a subset of the training data.")
18318 (license license:gpl2+)))
18320 (define-public r-dummies
18327 (uri (cran-uri "dummies" version))
18330 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
18331 (properties `((upstream-name . "dummies")))
18332 (build-system r-build-system)
18333 (home-page "https://decisionpatterns.com")
18334 (synopsis "Create dummy/indicator variables flexibly and efficiently")
18336 "This package lets you expand factors, characters and other eligible
18337 classes into dummy/indicator variables.")
18338 (license license:gpl2+)))
18340 (define-public r-acrm
18347 (uri (cran-uri "aCRM" version))
18350 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
18351 (properties `((upstream-name . "aCRM")))
18352 (build-system r-build-system)
18355 ("r-dummies" ,r-dummies)
18356 ("r-kernelfactory" ,r-kernelfactory)
18357 ("r-randomforest" ,r-randomforest)))
18358 (home-page "https://cran.r-project.org/web/packages/aCRM/")
18359 (synopsis "Convenience functions for analytical customer relationship management")
18361 "This package provides convenience functions for data preparation and
18362 modeling often used in @dfn{analytical customer relationship
18363 management} (aCRM).")
18364 (license license:gpl2+)))
18366 (define-public r-treeclust
18368 (name "r-treeclust")
18373 (uri (cran-uri "treeClust" version))
18376 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
18377 (properties `((upstream-name . "treeClust")))
18378 (build-system r-build-system)
18380 `(("r-cluster" ,r-cluster)
18381 ("r-rpart" ,r-rpart)))
18382 (home-page "https://cran.r-project.org/web/packages/treeClust/")
18383 (synopsis "Cluster distances through trees")
18385 "This package provides tools to create a measure of inter-point
18386 dissimilarity useful for clustering mixed data, and, optionally, perform the
18388 (license license:gpl2+)))
18390 (define-public r-acrosstic
18392 (name "r-acrosstic")
18397 (uri (cran-uri "AcrossTic" version))
18400 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
18401 (properties `((upstream-name . "AcrossTic")))
18402 (build-system r-build-system)
18404 `(("r-lpsolve" ,r-lpsolve)
18405 ("r-treeclust" ,r-treeclust)))
18406 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
18407 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
18409 "This is a package for constructing minimum-cost regular spanning
18410 subgraph as part of a non-parametric two-sample test for equality of
18412 (license license:gpl2+)))
18414 (define-public r-acrt
18421 (uri (cran-uri "acrt" version))
18424 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
18425 (properties `((upstream-name . "acrt")))
18426 (build-system r-build-system)
18428 `(("r-rcpp" ,r-rcpp)
18429 ("r-rcppeigen" ,r-rcppeigen)
18430 ("r-sandwich" ,r-sandwich)))
18431 (home-page "https://cran.r-project.org/web/packages/acrt/")
18432 (synopsis "Autocorrelation robust testing")
18434 "This package provides functions for testing affine hypotheses on the
18435 regression coefficient vector in regression models with autocorrelated
18437 (license license:gpl2)))
18439 (define-public r-acs
18446 (uri (cran-uri "acs" version))
18449 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
18450 (properties `((upstream-name . "acs")))
18451 (build-system r-build-system)
18453 `(("r-httr" ,r-httr)
18456 ("r-stringr" ,r-stringr)
18458 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
18459 (synopsis "Work with data from the US Census")
18461 "This package provides a general toolkit for downloading, managing,
18462 analyzing, and presenting data from the
18463 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
18464 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
18465 American Community Survey (ACS). Confidence intervals provided with ACS data
18466 are converted to standard errors to be bundled with estimates in complex
18467 @code{acs} objects. The package provides new methods to conduct standard
18468 operations on @code{acs} objects and present/plot data in statistically
18469 appropriate ways.")
18470 (license license:gpl3)))
18472 (define-public r-acss-data
18474 (name "r-acss-data")
18479 (uri (cran-uri "acss.data" version))
18482 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
18483 (properties `((upstream-name . "acss.data")))
18484 (build-system r-build-system)
18485 (home-page "http://complexitycalculator.com/methodology.html")
18486 (synopsis "Data for algorithmic complexity of short strings")
18488 "This is a data only package providing the algorithmic complexity of
18489 short strings, computed using the coding theorem method. For a given set of
18490 symbols in a string, all possible or a large number of random samples of
18491 Turing machines with a given number of states (e.g., 5) and number of symbols
18492 corresponding to the number of symbols in the strings were simulated until
18493 they reached a halting state or failed to end. This package contains data on
18494 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
18495 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
18496 distribution of the halting states.")
18497 (license license:gpl2+)))
18499 (define-public r-acss
18506 (uri (cran-uri "acss" version))
18509 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
18510 (properties `((upstream-name . "acss")))
18511 (build-system r-build-system)
18513 `(("r-acss-data" ,r-acss-data)
18515 (home-page "http://complexitycalculator.com/methodology.html")
18516 (synopsis "Algorithmic complexity for short strings")
18518 "The main purpose of this package is to provide the algorithmic
18519 complexity for short strings, an approximation of the Kolmogorov Complexity of
18520 a short string using the coding theorem method. While the database containing
18521 the complexity is provided in the data only package @code{acss.data}, this
18522 package provides functions accessing the data such as @code{prob_random}
18523 returning the posterior probability that a given string was produced by a
18524 random process. In addition, two traditional (but problematic) measures of
18525 complexity are also provided: entropy and change complexity.")
18526 (license license:gpl2+)))
18528 (define-public r-acswr
18535 (uri (cran-uri "ACSWR" version))
18538 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
18539 (properties `((upstream-name . "ACSWR")))
18540 (build-system r-build-system)
18542 `(("r-mass" ,r-mass)))
18543 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
18544 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
18546 "This is a companion package for the book \"A Course in Statistics with
18547 R\" (ISBN 978-1-119-15272-9.)")
18548 (license license:gpl2)))
18550 (define-public r-alabama
18553 (version "2015.3-1")
18557 (uri (cran-uri "alabama" version))
18560 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
18561 (properties `((upstream-name . "alabama")))
18562 (build-system r-build-system)
18563 (propagated-inputs `(("r-numderiv" ,r-numderiv)))
18564 (home-page "https://cran.r-project.org/web/packages/alabama/")
18565 (synopsis "Constrained nonlinear optimization")
18567 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
18568 Algorithm; it is used for optimizing smooth nonlinear objective functions with
18569 constraints. Linear or nonlinear equality and inequality constraints are
18571 (license license:gpl2+)))
18573 (define-public r-gdina
18580 (uri (cran-uri "GDINA" version))
18583 "0chxnhp37xfd78gafkgwqrmc0jf3pvpdyrkc438kl0l53fb7dld7"))))
18584 (properties `((upstream-name . "GDINA")))
18585 (build-system r-build-system)
18587 `(("r-alabama" ,r-alabama)
18588 ("r-ggplot2" ,r-ggplot2)
18590 ("r-nloptr" ,r-nloptr)
18591 ("r-numderiv" ,r-numderiv)
18593 ("r-rcpparmadillo" ,r-rcpparmadillo)
18594 ("r-rsolnp" ,r-rsolnp)
18595 ("r-shiny" ,r-shiny)
18596 ("r-shinydashboard" ,r-shinydashboard)))
18598 `(("r-knitr" ,r-knitr)))
18599 (home-page "https://github.com/Wenchao-Ma/GDINA")
18600 (synopsis "Generalized DINA model framework")
18602 "This package provides a set of psychometric tools for cognitive
18603 diagnosis modeling based on the generalized deterministic inputs, noisy and
18604 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
18605 and its extensions, including the sequential G-DINA model by Ma and de la
18606 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
18607 polytomous G-DINA model by Chen and de la Torre
18608 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
18609 distribution can be independent, saturated, higher-order, loglinear smoothed
18610 or structured. Q-matrix validation, item and model fit statistics, model
18611 comparison at test and item level and differential item functioning can also
18612 be conducted. A graphical user interface is also provided.")
18613 (license license:gpl3)))
18615 (define-public r-actcd
18622 (uri (cran-uri "ACTCD" version))
18625 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
18626 (properties `((upstream-name . "ACTCD")))
18627 (build-system r-build-system)
18629 `(("r-gdina" ,r-gdina)
18630 ("r-r-methodss3" ,r-r-methodss3)))
18632 `(("gfortran" ,gfortran)))
18633 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
18634 (synopsis "Asymptotic classification theory for cognitive diagnosis")
18636 "This is a package supporting cluster analysis for cognitive diagnosis
18637 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
18638 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
18639 sum-scores, cluster analysis techniques can be used to classify examinees into
18640 latent classes based on their attribute patterns. In addition to the
18641 algorithms used to classify data, three labeling approaches are proposed to
18642 label clusters so that examinees' attribute profiles can be obtained.")
18643 (license license:gpl2+)))
18645 (define-public r-ineq
18652 (uri (cran-uri "ineq" version))
18655 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
18656 (properties `((upstream-name . "ineq")))
18657 (build-system r-build-system)
18658 (home-page "https://cran.r-project.org/web/packages/ineq/")
18659 (synopsis "Measuring inequality, concentration, and poverty")
18661 "This package provides tools for measuring inequality, concentration, and
18662 poverty measures. It provides both empirical and theoretical Lorenz curves.")
18663 ;; Either of these two versions.
18664 (license (list license:gpl2 license:gpl3))))
18666 (define-public r-actfrag
18673 (uri (cran-uri "ActFrag" version))
18676 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
18677 (properties `((upstream-name . "ActFrag")))
18678 (build-system r-build-system)
18680 `(("r-accelerometry" ,r-accelerometry)
18681 ("r-dplyr" ,r-dplyr)
18683 ("r-survival" ,r-survival)
18684 ("r-tidyr" ,r-tidyr)))
18685 (home-page "https://github.com/junruidi/ActFrag")
18686 (synopsis "Activity fragmentation metrics extraction")
18688 "This package provides functions to extract commonly used fragmentation
18689 metrics to quantify time accumulation strategies based on minute level
18690 actigraphy-measured activity counts data.")
18691 (license license:gpl3)))
18693 (define-public r-fda
18700 (uri (cran-uri "fda" version))
18703 "0js4ggl3aiwsqk6npwz72yhcznkb63smddds24ngf6a0p8yp5p2x"))))
18704 (properties `((upstream-name . "fda")))
18705 (build-system r-build-system)
18707 `(("r-matrix" ,r-matrix)))
18708 (home-page "https://www.functionaldata.org")
18709 (synopsis "Functional data analysis")
18711 "These functions were developed to support functional data analysis as
18712 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
18713 Analysis. The package includes data sets and script files working many
18715 (license license:gpl2+)))
18717 (define-public r-actigraphy
18719 (name "r-actigraphy")
18724 (uri (cran-uri "Actigraphy" version))
18727 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
18728 (properties `((upstream-name . "Actigraphy")))
18729 (build-system r-build-system)
18731 `(("r-fda" ,r-fda)))
18732 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
18733 (synopsis "Actigraphy data analysis")
18735 "This package provides tools for functional linear modeling and analysis
18736 of actigraphy data.")
18737 (license license:asl2.0)))
18739 (define-public r-activedriver
18741 (name "r-activedriver")
18746 (uri (cran-uri "ActiveDriver" version))
18749 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
18750 (properties `((upstream-name . "ActiveDriver")))
18751 (build-system r-build-system)
18753 `(("r-mass" ,r-mass)))
18754 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
18755 (synopsis "Tools for finding cancer driver proteins")
18757 "This package provides a mutation analysis tool that discovers cancer
18758 driver genes with frequent mutations in protein signalling sites such as
18759 post-translational modifications (phosphorylation, ubiquitination, etc). The
18760 Poisson generalized linear regression model identifies genes where cancer
18761 mutations in signalling sites are more frequent than expected from the
18762 sequence of the entire gene. Integration of mutations with signalling
18763 information helps find new driver genes and propose candidate mechanisms to
18765 (license license:gpl2+)))
18767 (define-public r-activitycounts
18769 (name "r-activitycounts")
18774 (uri (cran-uri "activityCounts" version))
18777 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
18779 `((upstream-name . "activityCounts")))
18780 (build-system r-build-system)
18782 `(("r-lubridate" ,r-lubridate)
18783 ("r-magrittr" ,r-magrittr)
18784 ("r-seewave" ,r-seewave)
18785 ("r-signal" ,r-signal)
18786 ("r-tibble" ,r-tibble)))
18787 (home-page "https://github.com/walkabillylab/activityCounts")
18788 (synopsis "Generate ActiLife counts")
18790 "ActiLife generates activity counts from data collected by Actigraph
18791 accelerometers. Actigraph is one of the most common research-grade
18792 accelerometers. There is considerable research validating and developing
18793 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
18794 counts are proprietary and difficult to implement if researchers use different
18795 accelerometer brands. The code creates ActiLife counts from raw acceleration
18796 data for different accelerometer brands.")
18797 (license license:gpl3)))
18799 (define-public r-activityindex
18801 (name "r-activityindex")
18806 (uri (cran-uri "ActivityIndex" version))
18809 "14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"))))
18810 (properties `((upstream-name . "ActivityIndex")))
18811 (build-system r-build-system)
18813 `(("r-data-table" ,r-data-table)
18814 ("r-matrixstats" ,r-matrixstats)
18815 ("r-r-utils" ,r-r-utils)))
18816 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
18817 (synopsis "Activity Index calculation using raw accelerometry data")
18819 "This is a package to read raw accelerometry from GT3X+ accelerometry
18820 data and plain table data to calculate the Activity Index from Bai et
18821 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
18822 (license license:gpl3)))
18824 (define-public r-activpal
18826 (name "r-activpal")
18831 (uri (cran-uri "activPAL" version))
18834 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
18835 (properties `((upstream-name . "activPAL")))
18836 (build-system r-build-system)
18838 `(("r-devtools" ,r-devtools)
18839 ("r-dplyr" ,r-dplyr)
18840 ("r-ggplot2" ,r-ggplot2)
18841 ("r-lubridate" ,r-lubridate)
18842 ("r-magrittr" ,r-magrittr)
18843 ("r-tidyr" ,r-tidyr)))
18844 (home-page "https://cran.r-project.org/web/packages/activPAL")
18845 (synopsis "Processing and chart generation from activPAL events files")
18847 "This package contains functions to generate pre-defined summary
18848 statistics from activPAL events files. The package also contains functions to
18849 produce informative graphics that visualize physical activity behaviour and
18850 trends. This includes generating graphs that align physical activity
18851 behaviour with additional time based observations described by other data
18852 sets, such as sleep diaries and continuous glucose monitoring data.")
18853 (license license:gpl3)))
18855 (define-public r-activpalprocessing
18857 (name "r-activpalprocessing")
18862 (uri (cran-uri "activpalProcessing" version))
18865 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
18867 `((upstream-name . "activpalProcessing")))
18868 (build-system r-build-system)
18870 `(("r-chron" ,r-chron)))
18871 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
18872 (synopsis "Process activPAL events files")
18874 "This package performs estimation of physical activity and sedentary
18875 behavior variables from activPAL events files.")
18876 ;; Either version of the GPL.
18877 (license (list license:gpl2 license:gpl3))))
18879 (define-public r-actogrammr
18881 (name "r-actogrammr")
18886 (uri (cran-uri "actogrammr" version))
18889 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
18890 (properties `((upstream-name . "actogrammr")))
18891 (build-system r-build-system)
18893 `(("r-dplyr" ,r-dplyr)
18894 ("r-ggplot2" ,r-ggplot2)
18895 ("r-lubridate" ,r-lubridate)
18896 ("r-readr" ,r-readr)
18897 ("r-tidyr" ,r-tidyr)))
18898 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
18899 (synopsis "Read in activity data and plot actograms")
18901 "Read in activity measurements from standard file formats used by
18902 circadian rhythm researchers, currently only ClockLab format, and process and
18903 plot the data. The central type of plot is the actogram, as first described
18904 in \"Activity and distribution of certain wild mice in relation to biotic
18905 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
18906 (license license:gpl3)))
18908 (define-public r-expint
18915 (uri (cran-uri "expint" version))
18918 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
18919 (properties `((upstream-name . "expint")))
18920 (build-system r-build-system)
18921 (home-page "https://gitlab.com/vigou3/expint")
18922 (synopsis "Exponential integral and incomplete Gamma function")
18924 "This package provides the exponential integrals @code{E_1(x)},
18925 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
18926 function @code{G(a, x)} defined for negative values of its first argument.
18927 The package also gives easy access to the underlying C routines through an
18928 API; see the package vignette for details.")
18929 (license license:gpl2+)))
18931 (define-public r-actuar
18938 (uri (cran-uri "actuar" version))
18941 "0dkp1sczldzy7kj70qvh1q59jhsq1brjybmxdz43jnx63y45llpz"))))
18942 (properties `((upstream-name . "actuar")))
18943 (build-system r-build-system)
18944 (propagated-inputs `(("r-expint" ,r-expint)))
18945 (home-page "https://gitlab.com/vigou3/actuar")
18946 (synopsis "Actuarial functions and heavy tailed distributions")
18948 "This package provides functions and data sets for actuarial science:
18949 modeling of loss distributions; risk theory and ruin theory; simulation of
18950 compound models, discrete mixtures and compound hierarchical models;
18951 credibility theory. It boasts support for many additional probability
18952 distributions to model insurance loss amounts and loss frequency: 19
18953 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
18954 distribution; zero-truncated and zero-modified extensions of the standard
18955 discrete distributions. It also supports phase-type distributions commonly
18956 used to compute ruin probabilities.")
18957 (license license:gpl2+)))
18959 (define-public r-bmp
18966 (uri (cran-uri "bmp" version))
18969 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
18970 (properties `((upstream-name . "bmp")))
18971 (build-system r-build-system)
18972 (home-page "https://cran.r-project.org/web/packages/bmp/")
18973 (synopsis "Read Bitmap (BMP) images")
18975 "This package provides pure R tools to read BMP format images. It is
18976 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
18977 (license license:gpl2+)))
18979 (define-public r-readbitmap
18981 (name "r-readbitmap")
18986 (uri (cran-uri "readbitmap" version))
18989 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
18990 (properties `((upstream-name . "readbitmap")))
18991 (build-system r-build-system)
18993 `(("libjpeg" ,libjpeg-turbo)
18994 ("libpng" ,libpng)))
18999 ("r-tiff" ,r-tiff)))
19000 (home-page "https://github.com/jefferis/readbitmap")
19001 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
19003 "This package provides tools to identify and read BMP, JPEG, PNG, and
19004 TIFF format bitmap images. Identification defaults to the use of the magic
19005 number embedded in the file rather than the file extension.")
19006 (license license:gpl2+)))
19008 (define-public r-imager
19015 (uri (cran-uri "imager" version))
19018 "1wxvbv803222gjrf1ys6a349xlnmmdw3kqgi93piq9gq7lahihvg"))))
19019 (properties `((upstream-name . "imager")))
19020 (build-system r-build-system)
19023 ("libtiff" ,libtiff)
19027 `(("r-downloader" ,r-downloader)
19028 ("r-igraph" ,r-igraph)
19030 ("r-magrittr" ,r-magrittr)
19032 ("r-purrr" ,r-purrr)
19034 ("r-readbitmap" ,r-readbitmap)
19035 ("r-stringr" ,r-stringr)))
19037 `(("pkg-config" ,pkg-config)
19038 ("r-knitr" ,r-knitr)))
19039 (home-page "https://dahtah.github.io/imager/")
19040 (synopsis "Image processing library")
19042 "This is a package for fast image processing for images in up to 4
19043 dimensions (two spatial dimensions, one time/depth dimension, one color
19044 dimension). It provides most traditional image processing tools (filtering,
19045 morphology, transformations, etc.) as well as various functions for easily
19046 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
19047 simple, modern C++ library for image processing.")
19048 (license license:lgpl3)))
19050 (define-public r-acuityview
19052 (name "r-acuityview")
19057 (uri (cran-uri "AcuityView" version))
19060 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
19061 (properties `((upstream-name . "AcuityView")))
19062 (build-system r-build-system)
19064 `(("r-fftwtools" ,r-fftwtools)
19065 ("r-imager" ,r-imager)
19066 ("r-plotrix" ,r-plotrix)))
19067 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
19068 (synopsis "Display scenes as seen by an animal with less acute vision")
19070 "This package provides a simple method for representing a visual scene as
19071 it may be seen by an animal with less acute vision.")
19072 (license license:gpl2+)))
19074 (define-public r-caret
19081 (uri (cran-uri "caret" version))
19084 "0dyflixdw98lvk2x3w136sw24ij0fwx5c7l709dmqr5z7xy1qjns"))))
19085 (build-system r-build-system)
19087 `(("r-foreach" ,r-foreach)
19088 ("r-ggplot2" ,r-ggplot2)
19089 ("r-lattice" ,r-lattice)
19090 ("r-modelmetrics" ,r-modelmetrics)
19094 ("r-recipes" ,r-recipes)
19095 ("r-reshape2" ,r-reshape2)
19096 ("r-withr" ,r-withr)))
19098 `(("r-knitr" ,r-knitr)))
19099 (home-page "https://github.com/topepo/caret")
19100 (synopsis "Classification and regression training")
19102 "This package provides miscellaneous functions for training and plotting
19103 classification and regression models.")
19104 (license license:gpl2+)))
19106 (define-public r-adabag
19113 (uri (cran-uri "adabag" version))
19116 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
19117 (properties `((upstream-name . "adabag")))
19118 (build-system r-build-system)
19120 `(("r-caret" ,r-caret)
19121 ("r-doparallel" ,r-doparallel)
19122 ("r-foreach" ,r-foreach)
19123 ("r-rpart" ,r-rpart)))
19124 (home-page "https://cran.r-project.org/web/packages/adabag/")
19125 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
19127 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
19128 Breiman's Bagging algorithm using classification trees as individual
19129 classifiers. Once these classifiers have been trained, they can be used to
19130 predict on new data. Also, cross validation estimation of the error can be
19132 (license license:gpl2+)))
19134 (define-public r-adagio
19141 (uri (cran-uri "adagio" version))
19144 "1h9l0ddrxq8y35iy9hdkxdvdwsqpnpkzzbkbwwhm4380lq1m7a3k"))))
19145 (properties `((upstream-name . "adagio")))
19146 (build-system r-build-system)
19147 (native-inputs `(("gfortran" ,gfortran)))
19148 (home-page "https://cran.r-project.org/web/packages/adagio/")
19149 (synopsis "Discrete and global optimization routines")
19151 "This package provides methods and algorithms for discrete optimization,
19152 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
19153 Hooke-Jeeves minimization, and some (evolutionary) global optimization
19155 (license license:gpl3+)))
19157 (define-public r-univoutl
19159 (name "r-univoutl")
19164 (uri (cran-uri "univOutl" version))
19167 "0rlc3w7cx2hfxacpjs9kmjzv5p8v9wxnlpxi3rh276wiy5zdr91v"))))
19168 (properties `((upstream-name . "univOutl")))
19169 (build-system r-build-system)
19171 `(("r-hmisc" ,r-hmisc)
19172 ("r-robustbase" ,r-robustbase)))
19173 (home-page "https://github.com/marcellodo/univOutl")
19174 (synopsis "Detection of univariate outliers")
19176 "This package provides well-known outlier detection techniques in the
19177 univariate case. Methods to deal with skewed distribution are included too.
19178 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
19179 historical data is implemented as well. When available, survey weights can be
19180 used in outliers detection.")
19181 (license license:gpl2+)))
19183 (define-public r-tolerance
19185 (name "r-tolerance")
19190 (uri (cran-uri "tolerance" version))
19193 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
19194 (properties `((upstream-name . "tolerance")))
19195 (build-system r-build-system)
19197 `(("r-mass" ,r-mass)
19199 (home-page "https://cran.r-project.org/web/packages/tolerance/")
19200 (synopsis "Statistical tolerance intervals and regions")
19202 "This package provides functions for estimating tolerance
19203 limits (intervals) for various univariate distributions (binomial, Cauchy,
19204 discrete Pareto, exponential, two-parameter exponential, extreme value,
19205 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
19206 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
19207 Bayesian normal tolerance limits, multivariate normal tolerance regions,
19208 nonparametric tolerance intervals, tolerance bands for regression
19209 settings (linear regression, nonlinear regression, nonparametric regression,
19210 and multivariate regression), and analysis of variance tolerance intervals.
19211 Visualizations are also available for most of these settings.")
19212 (license license:gpl2+)))
19214 (define-public r-additivitytests
19216 (name "r-additivitytests")
19221 (uri (cran-uri "additivityTests" version))
19224 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
19226 `((upstream-name . "additivityTests")))
19227 (build-system r-build-system)
19228 (home-page "https://github.com/simecek/additivityTests")
19229 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
19231 "This package provides an implementation of the Tukey, Mandel,
19232 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
19233 (license license:gpl3)))
19235 (define-public r-flexclust
19237 (name "r-flexclust")
19242 (uri (cran-uri "flexclust" version))
19245 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
19246 (properties `((upstream-name . "flexclust")))
19247 (build-system r-build-system)
19249 `(("r-class" ,r-class)
19250 ("r-lattice" ,r-lattice)
19251 ("r-modeltools" ,r-modeltools)))
19252 (home-page "https://cran.r-project.org/web/packages/flexclust/")
19253 (synopsis "Flexible cluster algorithms")
19255 "The main function @code{kcca} implements a general framework for
19256 k-centroids cluster analysis supporting arbitrary distance measures and
19257 centroid computation. Further cluster methods include hard competitive
19258 learning, neural gas, and QT clustering. There are numerous visualization
19259 methods for cluster results (neighborhood graphs, convex cluster hulls,
19260 barcharts of centroids, ...), and bootstrap methods for the analysis of
19261 cluster stability.")
19262 (license license:gpl2)))
19264 (define-public r-biclust
19271 (uri (cran-uri "biclust" version))
19274 "1pk7mvwlg4hkc4cn4w6wr2c192qx03d1xfwlzclk5bw1nmcg483b"))))
19275 (properties `((upstream-name . "biclust")))
19276 (build-system r-build-system)
19278 `(("r-additivitytests" ,r-additivitytests)
19279 ("r-colorspace" ,r-colorspace)
19280 ("r-flexclust" ,r-flexclust)
19281 ("r-ggplot2" ,r-ggplot2)
19282 ("r-lattice" ,r-lattice)
19284 ("r-tidyr" ,r-tidyr)))
19285 (home-page "https://cran.r-project.org/web/packages/biclust/")
19286 (synopsis "BiCluster algorithms")
19288 "The main function @code{biclust()} provides several algorithms to find
19289 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
19290 In addition, the package provides methods for data
19291 preprocessing (normalization and discretization), visualization, and
19292 validation of bicluster solutions.")
19293 (license license:gpl3)))
19295 (define-public r-icge
19302 (uri (cran-uri "ICGE" version))
19305 "0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"))))
19306 (properties `((upstream-name . "ICGE")))
19307 (build-system r-build-system)
19309 `(("r-cluster" ,r-cluster)
19310 ("r-mass" ,r-mass)))
19311 (home-page "https://cran.r-project.org/web/packages/ICGE/")
19312 (synopsis "Cluster estimation and identification of atypical units")
19314 "ICGE is a package that helps to estimate the number of real clusters in
19315 data as well as to identify atypical units. The underlying methods are based
19316 on distances rather than on unit x variables.")
19317 (license license:gpl2+)))
19319 (define-public r-depth
19322 (version "2.1-1.1")
19326 (uri (cran-uri "depth" version))
19329 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
19330 (properties `((upstream-name . "depth")))
19331 (build-system r-build-system)
19333 `(("r-abind" ,r-abind)
19334 ("r-circular" ,r-circular)
19337 `(("gfortran" ,gfortran)))
19338 (home-page "https://cran.r-project.org/web/packages/depth/")
19339 (synopsis "Nonparametric depth functions for multivariate analysis")
19341 "This package provides tools for depth functions methodology applied to
19342 multivariate analysis. Besides allowing calculation of depth values and
19343 depth-based location estimators, the package includes functions or drawing
19344 contour plots and perspective plots of depth functions. Euclidian and
19345 spherical depths are supported.")
19346 (license license:gpl2)))
19348 (define-public r-archetypes
19350 (name "r-archetypes")
19351 (version "2.2-0.1")
19355 (uri (cran-uri "archetypes" version))
19358 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
19359 (properties `((upstream-name . "archetypes")))
19360 (build-system r-build-system)
19362 `(("r-modeltools" ,r-modeltools)
19363 ("r-nnls" ,r-nnls)))
19364 (home-page "https://cran.r-project.org/web/packages/archetypes")
19365 (synopsis "Archetypal analysis")
19367 "The main function @code{archetypes} implements a framework for
19368 archetypal analysis supporting arbitrary problem solving mechanisms for the
19369 different conceptual parts of the algorithm.")
19370 (license license:gpl2+)))
19372 (define-public r-shapes
19379 (uri (cran-uri "shapes" version))
19382 "0gfpdydfysp5mwg7qmkn73s67gvh2szb40mzqrx97h41ijgcgd8s"))))
19383 (properties `((upstream-name . "shapes")))
19384 (build-system r-build-system)
19386 `(("r-mass" ,r-mass)
19387 ("r-minpack-lm" ,r-minpack-lm)
19389 ("r-scatterplot3d" ,r-scatterplot3d)))
19390 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
19391 (synopsis "Statistical shape analysis")
19393 "This package provides routines for the statistical analysis of landmark
19394 shapes, including Procrustes analysis, graphical displays, principal
19395 components analysis, permutation and bootstrap tests, thin-plate spline
19396 transformation grids and comparing covariance matrices. See Dryden, I.L. and
19397 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
19398 Edition), John Wiley and Sons.")
19399 (license license:gpl2)))
19401 (define-public r-anthropometry
19403 (name "r-anthropometry")
19408 (uri (cran-uri "Anthropometry" version))
19411 "0y52g15pcgs4b68sfczn6nnpdqsialsb4mq3wb9a2gba7qdcf76y"))))
19412 (properties `((upstream-name . "Anthropometry")))
19413 (build-system r-build-system)
19415 `(("r-archetypes" ,r-archetypes)
19416 ("r-biclust" ,r-biclust)
19417 ("r-cluster" ,r-cluster)
19418 ("r-depth" ,r-depth)
19423 ("r-shapes" ,r-shapes)))
19425 `(("r-knitr" ,r-knitr)))
19426 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
19427 (synopsis "Statistical methods for anthropometric data")
19429 "This package provides statistical methods especially developed to
19430 analyze anthropometric data. These methods are aimed at providing effective
19431 solutions to some commons problems related to Ergonomics and Anthropometry.
19432 They are based on clustering, the statistical concept of data depth,
19433 statistical shape analysis and archetypal analysis.")
19434 (license license:gpl2+)))
19436 (define-public r-adamethods
19438 (name "r-adamethods")
19443 (uri (cran-uri "adamethods" version))
19446 "0mp73zh5x6h18gv29v981kb9n632kb58lvlcxwr6vcvrx393nrxh"))))
19447 (properties `((upstream-name . "adamethods")))
19448 (build-system r-build-system)
19450 `(("r-anthropometry" ,r-anthropometry)
19451 ("r-archetypes" ,r-archetypes)
19453 ("r-foreach" ,r-foreach)
19455 ("r-tolerance" ,r-tolerance)
19456 ("r-univoutl" ,r-univoutl)))
19457 (home-page "https://cran.r-project.org/web/packages/adamethods/")
19458 (synopsis "Archetypoid algorithms and anomaly detection")
19460 "This package is a collection of several algorithms to obtain
19461 archetypoids with small and large databases and with both classical
19462 multivariate data and functional data (univariate and multivariate). Some of
19463 these algorithms also allow to detect anomalies (outliers).")
19464 (license license:gpl2+)))
19466 (define-public r-idpmisc
19473 (uri (cran-uri "IDPmisc" version))
19476 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
19477 (properties `((upstream-name . "IDPmisc")))
19478 (build-system r-build-system)
19480 `(("r-lattice" ,r-lattice)))
19481 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
19482 (synopsis "Functions for data analyses and visualization")
19484 "This package provides different high-level graphics functions for
19485 displaying large datasets, displaying circular data in a very flexible way,
19486 finding local maxima, brewing color ramps, drawing nice arrows, zooming
19487 2D-plots, creating figures with differently colored margin and plot region.
19488 In addition, the package contains auxiliary functions for data manipulation
19489 like omitting observations with irregular values or selecting data by logical
19490 vectors, which include NAs. Other functions are especially useful in
19491 spectroscopy and analyses of environmental data: robust baseline fitting,
19492 finding peaks in spectra, converting humidity measures.")
19493 (license license:gpl3+)))
19495 (define-public r-qqman
19502 (uri (cran-uri "qqman" version))
19505 "1v9s9ag1hfb47py87wb2nad4mbsfx35832hdmrh5kxrb2f11zl1s"))))
19506 (properties `((upstream-name . "qqman")))
19507 (build-system r-build-system)
19509 `(("r-calibrate" ,r-calibrate)))
19510 (home-page "https://cran.r-project.org/web/packages/qqman/")
19511 (synopsis "Q-Q and Manhattan plots for GWAS data")
19513 "This package allows you to create Q-Q and Manhattan plots for GWAS data
19514 from PLINK results.")
19515 (license license:gpl3)))
19517 (define-public r-ggplot-multistats
19519 (name "r-ggplot-multistats")
19524 (uri (cran-uri "ggplot.multistats" version))
19527 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
19529 `((upstream-name . "ggplot.multistats")))
19530 (build-system r-build-system)
19532 `(("r-ggplot2" ,r-ggplot2)
19533 ("r-hexbin" ,r-hexbin)
19534 ("r-rlang" ,r-rlang)
19535 ("r-scales" ,r-scales)))
19536 (home-page "https://github.com/flying-sheep/ggplot.multistats")
19537 (synopsis "Multiple summary statistics for binned stats/geometries")
19539 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
19540 which functions similar to its singular form, but allows the use of multiple
19541 statistics per bin. Those statistics can be mapped to multiple bin
19543 (license license:gpl3)))
19545 (define-public r-knn-covertree
19547 (name "r-knn-covertree")
19552 (uri (cran-uri "knn.covertree" version))
19555 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
19556 (properties `((upstream-name . "knn.covertree")))
19557 (build-system r-build-system)
19559 `(("r-matrix" ,r-matrix)
19561 ("r-rcppeigen" ,r-rcppeigen)))
19562 (home-page "https://github.com/flying-sheep/knn.covertree")
19563 (synopsis "Accurate kNN Implementation with multiple distance measures")
19565 "Similarly to the FNN package, this package allows calculation of the k
19566 nearest neighbors (kNN) of a data matrix. The implementation is based on
19567 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
19568 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
19569 (license license:agpl3+)))
19571 (define-public r-poibin
19578 (uri (cran-uri "poibin" version))
19581 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
19582 (properties `((upstream-name . "poibin")))
19583 (build-system r-build-system)
19584 (home-page "https://cran.r-project.org/web/packages/poibin/")
19585 (synopsis "Poisson binomial distribution")
19587 "This package provides an implementation of both the exact and
19588 approximation methods for computing the @dfn{cumulative distribution
19589 function} (CDF) of the Poisson binomial distribution. It also provides the
19590 @dfn{probability mass function} (PMF), quantile function, and random number
19591 generation for the Poisson binomial distribution.")
19592 (license license:gpl2)))
19594 (define-public r-diagram
19601 (uri (cran-uri "diagram" version))
19604 "0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"))))
19605 (properties `((upstream-name . "diagram")))
19606 (build-system r-build-system)
19608 `(("r-shape" ,r-shape)))
19609 (home-page "https://cran.r-project.org/web/packages/diagram/")
19610 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
19612 "This package provides tools to visualize simple graphs (networks) based
19613 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
19614 electrical networks, etc. It also includes supporting material for the book
19615 \"A practical guide to ecological modelling - using R as a simulation
19616 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
19617 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
19618 Francesca Mazzia (2012).")
19619 (license license:gpl2+)))
19621 (define-public r-lim
19628 (uri (cran-uri "LIM" version))
19631 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
19632 (properties `((upstream-name . "LIM")))
19633 (build-system r-build-system)
19635 `(("r-diagram" ,r-diagram)
19636 ("r-limsolve" ,r-limsolve)))
19637 (home-page "https://cran.r-project.org/web/packages/LIM/")
19638 (synopsis "Linear inverse model examples and solution methods")
19640 "This package provides functions that read and solve linear inverse
19641 problems (food web problems, linear programming problems).")
19642 (license license:gpl2+)))
19644 (define-public r-shinycssloaders
19646 (name "r-shinycssloaders")
19651 (uri (cran-uri "shinycssloaders" version))
19654 "1gzq1lhcnhqd145ys3ixf0l13l560fiqr2sc3m2nrijwxlgcw54d"))))
19656 `((upstream-name . "shinycssloaders")))
19657 (build-system r-build-system)
19659 `(("r-digest" ,r-digest)
19661 ("r-shiny" ,r-shiny)))
19662 (home-page "https://github.com/andrewsali/shinycssloaders")
19663 (synopsis "Add CSS loading animations to Shiny outputs")
19665 "This package provides tools to create a lightweight Shiny wrapper for
19666 the css-loaders created by Luke Hass
19667 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
19668 automatically show a loader when the output is (re)calculating.")
19669 (license license:gpl3)))
19671 (define-public r-rsvg
19678 (uri (cran-uri "rsvg" version))
19681 "0bxnwa9sbzx6jlxrzh3ymjq81vkxil2qx7kk7wp13a0cql7dhxcn"))))
19682 (properties `((upstream-name . "rsvg")))
19683 (build-system r-build-system)
19685 `(("librsvg" ,librsvg)
19688 `(("pkg-config" ,pkg-config)
19689 ("r-knitr" ,r-knitr)))
19690 (home-page "https://github.com/jeroen/rsvg#readme")
19691 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
19693 "This package allows you to render vector-based SVG images into
19694 high-quality custom-size bitmap arrays using the librsvg2 library. The
19695 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
19696 addition, the package can convert images directly to various formats such as
19697 PDF or PostScript.")
19698 (license license:expat)))
19700 (define-public r-influencer
19702 (name "r-influencer")
19707 (uri (cran-uri "influenceR" version))
19710 "12p9362hkndlnz1rd8j2rykg57kbm6l7ks60by3rd25xg50k5jag"))))
19711 (properties `((upstream-name . "influenceR")))
19712 (build-system r-build-system)
19714 `(("r-igraph" ,r-igraph)
19715 ("r-matrix" ,r-matrix)))
19716 (home-page "https://github.com/rcc-uchicago/influenceR")
19717 (synopsis "Tools to quantify structural importance of nodes in a network")
19719 "This package provides functionality to compute various node centrality
19720 measures on networks. Included are functions to compute betweenness
19721 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
19722 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
19723 algorithm to identify key players, and Valente's bridging metric. The
19724 betweenness, Key Players, and bridging implementations are parallelized with
19726 (license license:gpl2)))
19728 (define-public r-emplik
19735 (uri (cran-uri "emplik" version))
19738 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
19739 (properties `((upstream-name . "emplik")))
19740 (build-system r-build-system)
19742 `(("r-quantreg" ,r-quantreg)))
19743 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
19744 (synopsis "Empirical likelihood ratio for censored/truncated data")
19746 "This package provides empirical likelihood ratio tests for
19747 means/quantiles/hazards from possibly censored and/or truncated data. It also
19749 (license license:gpl2+)))
19751 (define-public r-imputeyn
19753 (name "r-imputeyn")
19758 (uri (cran-uri "imputeYn" version))
19761 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
19762 (properties `((upstream-name . "imputeYn")))
19763 (build-system r-build-system)
19765 `(("r-boot" ,r-boot)
19766 ("r-emplik" ,r-emplik)
19767 ("r-mvtnorm" ,r-mvtnorm)
19768 ("r-quadprog" ,r-quadprog)
19769 ("r-survival" ,r-survival)))
19770 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
19771 (synopsis "Impute last largest censored observation under weighted least squares")
19773 "This package allows for the imputation of the last largest censored
19774 observantions. This method brings less bias and more efficient estimates for
19776 (license license:gpl2)))
19778 (define-public r-adapenetclass
19780 (name "r-adapenetclass")
19785 (uri (cran-uri "AdapEnetClass" version))
19788 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
19789 (properties `((upstream-name . "AdapEnetClass")))
19790 (build-system r-build-system)
19792 `(("r-glmnet" ,r-glmnet)
19793 ("r-imputeyn" ,r-imputeyn)
19795 ("r-quadprog" ,r-quadprog)))
19796 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
19797 (synopsis "Class of adaptive elastic net methods for censored data")
19799 "This package provides methods for variable selection for AFT models.")
19800 (license license:gpl2)))
19802 (define-public r-flock
19809 (uri (cran-uri "flock" version))
19812 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
19813 (properties `((upstream-name . "flock")))
19814 (build-system r-build-system)
19815 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
19816 (home-page "https://cran.r-project.org/web/packages/flock/")
19817 (synopsis "Process synchronization using file locks")
19819 "This package implements synchronization between R processes (spawned by
19820 using the @code{parallel} package for instance) using file locks. It supports
19821 both exclusive and shared locking.")
19822 (license license:asl2.0)))
19824 (define-public r-archivist
19826 (name "r-archivist")
19831 (uri (cran-uri "archivist" version))
19834 "1i11hrcq1910jgd6diw6h3sxx624v57zjianm49pqvb2dvd0b8y7"))))
19835 (properties `((upstream-name . "archivist")))
19836 (build-system r-build-system)
19839 ("r-digest" ,r-digest)
19840 ("r-flock" ,r-flock)
19842 ("r-lubridate" ,r-lubridate)
19843 ("r-magrittr" ,r-magrittr)
19844 ("r-rcurl" ,r-rcurl)
19845 ("r-rsqlite" ,r-rsqlite)))
19846 (home-page "https://pbiecek.github.io/archivist/")
19847 (synopsis "Tools for storing, restoring and searching for R objects")
19849 "Data exploration and modelling is a process in which a lot of data
19850 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
19851 statistical models, different versions of data sets and different versions of
19852 results. Archivist helps to store and manage artifacts created in R. It
19853 allows you to store selected artifacts as binary files together with their
19854 metadata and relations. Archivist allows sharing artifacts with others. It
19855 can look for already created artifacts by using its class, name, date of the
19856 creation or other properties. It also makes it easy to restore such
19858 (license license:gpl2)))
19860 (define-public r-versions
19862 (name "r-versions")
19867 (uri (cran-uri "versions" version))
19870 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
19871 (properties `((upstream-name . "versions")))
19872 (build-system r-build-system)
19873 (home-page "https://cran.r-project.org/web/packages/versions/")
19874 (synopsis "Query and install specific versions of CRAN packages")
19876 "This package allows you to install specified versions of R packages
19877 hosted on CRAN and provides functions to list available versions and the
19878 versions of currently installed packages.")
19879 (license license:bsd-3)))
19881 (define-public r-adapr
19888 (uri (cran-uri "adapr" version))
19891 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
19892 (properties `((upstream-name . "adapr")))
19893 (build-system r-build-system)
19895 `(("r-archivist" ,r-archivist)
19896 ("r-devtools" ,r-devtools)
19897 ("r-digest" ,r-digest)
19898 ("r-doparallel" ,r-doparallel)
19899 ("r-gdata" ,r-gdata)
19900 ("r-ggplot2" ,r-ggplot2)
19901 ("r-git2r" ,r-git2r)
19902 ("r-igraph" ,r-igraph)
19903 ("r-knitr" ,r-knitr)
19904 ("r-plotly" ,r-plotly)
19906 ("r-rmarkdown" ,r-rmarkdown)
19907 ("r-shiny" ,r-shiny)
19908 ("r-shinydashboard" ,r-shinydashboard)
19909 ("r-versions" ,r-versions)))
19910 (home-page "https://cran.r-project.org/web/packages/adapr/")
19911 (synopsis "Implementation of an accountable data analysis process")
19913 "This package tracks reading and writing within R scripts that are
19914 organized into a directed acyclic graph. It contains an interactive Shiny
19915 application @code{adaprApp()}. It uses Git and file hashes to track version
19916 histories of inputs and outputs.")
19917 (license license:lgpl2.0)))
19919 (define-public r-adapsamp
19921 (name "r-adapsamp")
19926 (uri (cran-uri "AdapSamp" version))
19929 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
19930 (properties `((upstream-name . "AdapSamp")))
19931 (build-system r-build-system)
19932 (propagated-inputs `(("r-pracma" ,r-pracma)))
19933 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
19934 (synopsis "Adaptive sampling algorithms")
19936 "For distributions whose probability density functions are log-concave,
19937 the adaptive rejection sampling algorithm can be used to build envelope
19938 functions for sampling. For others, the modified adaptive rejection sampling
19939 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
19940 adaptive slice sampling algorithm can be used. This R package mainly includes
19941 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
19942 @code{rASS()}. These functions can realize sampling based on the algorithms
19944 (license license:gpl2)))
19946 (define-public r-adaptalint
19948 (name "r-adaptalint")
19953 (uri (cran-uri "adaptalint" version))
19956 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
19957 (properties `((upstream-name . "adaptalint")))
19958 (build-system r-build-system)
19960 `(("r-dplyr" ,r-dplyr)
19961 ("r-lintr" ,r-lintr)
19962 ("r-purrr" ,r-purrr)))
19963 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
19964 (synopsis "Check R code style")
19966 "This package provides tools to infer the code style (which style rules
19967 are followed and which ones are not) from one package and use it to check
19968 another. This makes it easier to find and correct the most important problems
19970 (license license:gpl3)))
19972 (define-public r-fracdiff
19974 (name "r-fracdiff")
19979 (uri (cran-uri "fracdiff" version))
19982 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
19983 (properties `((upstream-name . "fracdiff")))
19984 (build-system r-build-system)
19985 (home-page "https://github.com/mmaechler/fracdiff")
19987 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
19989 "This package provides tools for the maximum likelihood estimation of the
19990 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
19991 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
19992 (license license:gpl2+)))
19994 (define-public r-forecast
19996 (name "r-forecast")
20001 (uri (cran-uri "forecast" version))
20004 "1ycj5z4wd5a16nlcjy07dqm8jkih240xa02cn4wvysnnhkapyq7b"))))
20005 (properties `((upstream-name . "forecast")))
20006 (build-system r-build-system)
20008 `(("r-colorspace" ,r-colorspace)
20009 ("r-fracdiff" ,r-fracdiff)
20010 ("r-ggplot2" ,r-ggplot2)
20011 ("r-lmtest" ,r-lmtest)
20012 ("r-magrittr" ,r-magrittr)
20015 ("r-rcpparmadillo" ,r-rcpparmadillo)
20016 ("r-timedate" ,r-timedate)
20017 ("r-tseries" ,r-tseries)
20021 `(("r-knitr" ,r-knitr))) ; needed for vignettes
20022 (home-page "https://pkg.robjhyndman.com/forecast/")
20023 (synopsis "Forecasting functions for time series and linear models")
20025 "This package provides methods and tools for displaying and analysing
20026 univariate time series forecasts including exponential smoothing via state
20027 space models and automatic ARIMA modelling.")
20028 (license license:gpl3)))
20030 (define-public r-xmisc
20037 (uri (cran-uri "Xmisc" version))
20040 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
20041 (properties `((upstream-name . "Xmisc")))
20042 (build-system r-build-system)
20043 (home-page "https://cran.r-project.org/package=Xmisc")
20045 "Xiaobei's miscellaneous classes and functions")
20047 "This package provides Xiaobei's miscellaneous classes and functions,
20048 which are useful when developing R packages for @dfn{object oriented
20049 programming} (OOP) using R Reference Class.")
20050 (license license:gpl2+)))
20052 (define-public r-proxyc
20059 (uri (cran-uri "proxyC" version))
20062 "159bc42x4shm6n3rh9fc8ziv3ivq0ipmpbasrh279hhn1prc8gg6"))))
20063 (properties `((upstream-name . "proxyC")))
20064 (build-system r-build-system)
20066 `(("r-matrix" ,r-matrix)
20068 ("r-rcpparmadillo" ,r-rcpparmadillo)
20069 ("r-rcppparallel" ,r-rcppparallel)))
20070 (home-page "https://cran.r-project.org/package=proxyC")
20071 (synopsis "Compute proximity in large sparse matrices")
20073 "This package provides efficient tools to compute the proximity between
20074 rows or columns of large matrices. Functions are optimised for large sparse
20075 matrices using the Armadillo and Intel TBB libraries. Among several built-in
20076 similarity/distance measures, computation of correlation, cosine similarity
20077 and Euclidean distance is particularly fast.")
20078 (license license:gpl3)))
20080 (define-public r-isocodes
20082 (name "r-isocodes")
20083 (version "2020.03.16")
20087 (uri (cran-uri "ISOcodes" version))
20090 "1hz1sj57qkkkrgn8slsz2n4jv1fkyp40503j9rg30lxy4gmb83hn"))))
20091 (properties `((upstream-name . "ISOcodes")))
20092 (build-system r-build-system)
20093 (home-page "https://cran.r-project.org/package=ISOcodes")
20094 (synopsis "Selected ISO codes")
20096 "This package provides ISO language, territory, currency, script and
20097 character codes. It provides ISO 639 language codes, ISO 3166 territory
20098 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
20099 character codes as well as the UN M.49 area codes.")
20100 (license license:gpl2)))
20102 (define-public r-stopwords
20104 (name "r-stopwords")
20109 (uri (cran-uri "stopwords" version))
20112 "155g00ansyqfpp1mzd2q6mn0k214xinf78nww2368h24kz761jjw"))))
20113 (properties `((upstream-name . "stopwords")))
20114 (build-system r-build-system)
20116 `(("r-desc" ,r-desc)
20117 ("r-isocodes" ,r-isocodes)
20118 ("r-usethis" ,r-usethis)))
20119 (home-page "https://github.com/quanteda/stopwords")
20120 (synopsis "Multilingual stopword lists")
20122 "This package provides multiple sources of stopwords, for use in text
20123 analysis and natural language processing.")
20124 (license license:expat)))
20126 (define-public r-spacyr
20133 (uri (cran-uri "spacyr" version))
20136 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
20137 (properties `((upstream-name . "spacyr")))
20138 (build-system r-build-system)
20140 `(("r-data-table" ,r-data-table)
20141 ("r-reticulate" ,r-reticulate)))
20142 (home-page "https://spacyr.quanteda.io")
20143 (synopsis "R wrapper for the spaCy NLP library")
20145 "This package provides an R wrapper to the Python @dfn{natural language
20146 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
20147 (license license:gpl3)))
20149 (define-public r-snowballc
20151 (name "r-snowballc")
20156 (uri (cran-uri "SnowballC" version))
20159 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
20160 (properties `((upstream-name . "SnowballC")))
20161 (build-system r-build-system)
20162 (home-page "https://r-forge.r-project.org/projects/r-temis/")
20163 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
20165 "This package provides an R interface to the C @code{libstemmer} library
20166 that implements Porter's word stemming algorithm for collapsing words to a
20167 common root to aid comparison of vocabulary. Currently supported languages
20168 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
20169 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
20170 (license license:bsd-3)))
20172 (define-public r-quanteda
20174 (name "r-quanteda")
20179 (uri (cran-uri "quanteda" version))
20182 "0pym6vdzqbkyj87m3pla229092xvvx4j830x67qflxzzdmc9dzhz"))))
20183 (properties `((upstream-name . "quanteda")))
20184 (build-system r-build-system)
20186 `(("r-data-table" ,r-data-table)
20187 ("r-extrafont" ,r-extrafont)
20188 ("r-fastmatch" ,r-fastmatch)
20189 ("r-ggplot2" ,r-ggplot2)
20190 ("r-ggrepel" ,r-ggrepel)
20191 ("r-jsonlite" ,r-jsonlite)
20192 ("r-magrittr" ,r-magrittr)
20193 ("r-matrix" ,r-matrix)
20194 ("r-network" ,r-network)
20195 ("r-proxyc" ,r-proxyc)
20197 ("r-rcpparmadillo" ,r-rcpparmadillo)
20198 ("r-rcppparallel" ,r-rcppparallel)
20200 ("r-snowballc" ,r-snowballc)
20201 ("r-stopwords" ,r-stopwords)
20202 ("r-stringi" ,r-stringi)
20204 ("r-yaml" ,r-yaml)))
20206 `(("r-knitr" ,r-knitr)))
20207 (home-page "https://quanteda.io")
20208 (synopsis "Quantitative analysis of textual data")
20210 "This package provides a fast, flexible, and comprehensive framework for
20211 quantitative text analysis in R. It provides functionality for corpus
20212 management, creating and manipulating tokens and ngrams, exploring keywords in
20213 context, forming and manipulating sparse matrices of documents by features and
20214 feature co-occurrences, analyzing keywords, computing feature similarities and
20215 distances, applying content dictionaries, applying supervised and unsupervised
20216 machine learning, visually representing text and text analyses, and more.")
20217 (license license:gpl3)))
20219 (define-public r-topicmodels
20221 (name "r-topicmodels")
20226 (uri (cran-uri "topicmodels" version))
20229 "0jmp6wva99y0w40cfw7b0faylndhjam097x36ilc4vmyczcv89lw"))))
20230 (properties `((upstream-name . "topicmodels")))
20231 (build-system r-build-system)
20235 `(("r-modeltools" ,r-modeltools)
20238 (home-page "https://cran.r-project.org/package=topicmodels")
20239 (synopsis "Topic models")
20241 "This package provides an interface to the C code for @dfn{Latent
20242 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
20243 David M. Blei and co-authors and the C++ code for fitting LDA models using
20244 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
20245 (license license:gpl2)))
20247 (define-public r-stm
20254 (uri (cran-uri "stm" version))
20257 "1yyfxaxqc6yq0yq68zhdnhpwpvsyp71dlmivn7zxixfmp932s6cn"))))
20258 (properties `((upstream-name . "stm")))
20259 (build-system r-build-system)
20261 `(("r-data-table" ,r-data-table)
20262 ("r-glmnet" ,r-glmnet)
20264 ("r-matrix" ,r-matrix)
20265 ("r-matrixstats" ,r-matrixstats)
20266 ("r-quadprog" ,r-quadprog)
20267 ("r-quanteda" ,r-quanteda)
20269 ("r-rcpparmadillo" ,r-rcpparmadillo)
20271 ("r-stringr" ,r-stringr)))
20272 (home-page "http://www.structuraltopicmodel.com/")
20273 (synopsis "Estimation of the Structural Topic Model")
20275 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
20276 topic models with document-level covariates. The package also includes tools
20277 for model selection, visualization, and estimation of topic-covariate
20279 (license license:expat)))
20281 (define-public r-polycor
20288 (uri (cran-uri "polycor" version))
20291 "0wzwzklflbhi8sv9m7ijwr16v9zmkk0j0v4pbcpf32f8lbn3psna"))))
20292 (properties `((upstream-name . "polycor")))
20293 (build-system r-build-system)
20295 `(("r-matrix" ,r-matrix)
20296 ("r-mvtnorm" ,r-mvtnorm)))
20297 (home-page "https://r-forge.r-project.org/projects/polycor/")
20298 (synopsis "Polychoric and polyserial correlations")
20300 "This package provides tools to compute polychoric and polyserial
20301 correlations by quick \"two-step\" methods or ML, optionally with standard
20302 errors; tetrachoric and biserial correlations are special cases.")
20303 (license license:gpl2+)))
20305 (define-public r-msm
20312 (uri (cran-uri "msm" version))
20315 "1d32y8f0vb2dfv3999liigpns788j145nrvd1xpxb9i2lsg8mwgk"))))
20316 (properties `((upstream-name . "msm")))
20317 (build-system r-build-system)
20319 `(("r-expm" ,r-expm)
20320 ("r-mvtnorm" ,r-mvtnorm)
20321 ("r-survival" ,r-survival)))
20322 (home-page "https://github.com/chjackson/msm")
20323 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
20325 "This package provides functions for fitting continuous-time Markov and
20326 hidden Markov multi-state models to longitudinal data. It was designed for
20327 processes observed at arbitrary times in continuous time (panel data) but some
20328 other observation schemes are supported. Both Markov transition rates and the
20329 hidden Markov output process can be modelled in terms of covariates, which may
20330 be constant or piecewise-constant in time.")
20331 (license license:gpl2+)))
20333 (define-public r-ltm
20340 (uri (cran-uri "ltm" version))
20343 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
20344 (properties `((upstream-name . "ltm")))
20345 (build-system r-build-system)
20347 `(("r-mass" ,r-mass)
20349 ("r-polycor" ,r-polycor)))
20350 (home-page "https://github.com/drizopoulos/ltm")
20351 (synopsis "Latent trait models under IRT")
20353 "This is a package supporting the analysis of multivariate dichotomous
20354 and polytomous data using latent trait models under the Item Response Theory
20355 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
20356 Three-Parameter, the Graded Response, and the Generalized Partial Credit
20358 (license license:gpl2+)))
20360 (define-public r-mi
20367 (uri (cran-uri "mi" version))
20370 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
20371 (properties `((upstream-name . "mi")))
20372 (build-system r-build-system)
20375 ("r-matrix" ,r-matrix)))
20376 (home-page "http://www.stat.columbia.edu/~gelman/")
20377 (synopsis "Missing data imputation and model checking")
20379 "This package provides functions for data manipulation, imputing missing
20380 values in an approximate Bayesian framework, diagnostics of the models used to
20381 generate the imputations, confidence-building mechanisms to validate some of
20382 the assumptions of the imputation algorithm, and functions to analyze multiply
20383 imputed data sets with the appropriate degree of sampling uncertainty.")
20384 (license license:gpl2+)))
20386 (define-public r-matrixcalc
20388 (name "r-matrixcalc")
20393 (uri (cran-uri "matrixcalc" version))
20396 "1c4w9dhi5w98qj1wwh9bbpnfk39rhiwjbanalr8bi5nmxkpcmrhp"))))
20397 (properties `((upstream-name . "matrixcalc")))
20398 (build-system r-build-system)
20399 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
20400 (synopsis "Collection of functions for matrix calculations")
20402 "This package provides a collection of functions to support matrix
20403 calculations for probability, econometric and numerical analysis. There are
20404 additional functions that are comparable to APL functions which are useful for
20405 actuarial models such as pension mathematics.")
20406 (license license:gpl2+)))
20408 (define-public r-sem
20415 (uri (cran-uri "sem" version))
20418 "03j3ig6fy34pi6nwfq9w8f5m555lilw5skr1vn6ay4yvjmvavc9k"))))
20419 (properties `((upstream-name . "sem")))
20420 (build-system r-build-system)
20422 `(("r-boot" ,r-boot)
20424 ("r-matrixcalc" ,r-matrixcalc)
20426 (home-page "https://cran.r-project.org/package=sem")
20427 (synopsis "Structural equation models")
20429 "This package provides functions for fitting general linear structural
20430 equation models (with observed and latent variables) using the RAM approach,
20431 and for fitting structural equations in observed-variable models by two-stage
20433 (license license:gpl2+)))
20435 (define-public r-semtools
20437 (name "r-semtools")
20442 (uri (cran-uri "semTools" version))
20445 "0k3w10fnq0l89inhxvnypyrfhlrm921mfn0kwyyfpndvbqizky1d"))))
20446 (properties `((upstream-name . "semTools")))
20447 (build-system r-build-system)
20449 `(("r-lavaan" ,r-lavaan)))
20450 (home-page "https://github.com/simsem/semTools/wiki")
20451 (synopsis "Useful tools for structural equation modeling")
20453 "This package provides useful tools for structural equation modeling.")
20454 (license license:gpl2+)))
20456 (define-public r-regsem
20463 (uri (cran-uri "regsem" version))
20466 "0ch057010xfsw0nqcsarzakdbiplvxaldyqlbbacspqs65ax1yk7"))))
20467 (properties `((upstream-name . "regsem")))
20468 (build-system r-build-system)
20470 `(("r-lavaan" ,r-lavaan)
20472 ("r-rcpparmadillo" ,r-rcpparmadillo)
20473 ("r-rsolnp" ,r-rsolnp)))
20474 (home-page "https://cran.r-project.org/package=regsem")
20475 (synopsis "Regularized structural equation modeling")
20477 "This package uses both ridge and lasso penalties (and extensions) to
20478 penalize specific parameters in structural equation models. The package
20479 offers additional cost functions, cross validation, and other extensions
20480 beyond traditional structural equation models. It also contains a function to
20481 perform @dfn{exploratory mediation} (XMed).")
20482 (license license:gpl2+)))
20484 (define-public r-stanheaders
20486 (name "r-stanheaders")
20487 (version "2.21.0-5")
20491 (uri (cran-uri "StanHeaders" version))
20494 "1zyph2x47x9a5baj5d79a1lzj7gajirisajvkrcngrjvw8bq7810"))))
20495 (properties `((upstream-name . "StanHeaders")))
20496 (build-system r-build-system)
20497 (inputs `(("pandoc" ,ghc-pandoc)))
20499 `(("r-rcppeigen" ,r-rcppeigen)
20500 ("r-rcppparallel" ,r-rcppparallel)))
20502 `(("gfortran" ,gfortran)
20503 ("r-knitr" ,r-knitr))) ; for vignettes
20504 (home-page "https://mc-stan.org/")
20505 (synopsis "C++ header files for Stan")
20507 "The C++ header files of the Stan project are provided by this package.
20508 There is a shared object containing part of the @code{CVODES} library, but it
20509 is not accessible from R. @code{r-stanheaders} is only useful for developers
20510 who want to utilize the @code{LinkingTo} directive of their package's
20511 DESCRIPTION file to build on the Stan library without incurring unnecessary
20514 The Stan project develops a probabilistic programming language that implements
20515 full or approximate Bayesian statistical inference via Markov Chain Monte
20516 Carlo or variational methods and implements (optionally penalized) maximum
20517 likelihood estimation via optimization. The Stan library includes an advanced
20518 automatic differentiation scheme, templated statistical and linear algebra
20519 functions that can handle the automatically differentiable scalar types (and
20520 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
20521 package provides user-facing R functions to parse, compile, test, estimate,
20522 and analyze Stan models.")
20523 (license license:bsd-3)))
20525 (define-public r-rpf
20532 (uri (cran-uri "rpf" version))
20535 "17crcgsbcsh0c00n7bgdqfnd7n1vzz7drfxjs7d18253yl5x44pl"))))
20536 (properties `((upstream-name . "rpf")))
20537 (build-system r-build-system)
20539 `(("r-lifecycle" ,r-lifecycle)
20540 ("r-mvtnorm" ,r-mvtnorm)
20542 ("r-rcppeigen" ,r-rcppeigen)))
20544 `(("r-knitr" ,r-knitr)))
20545 (home-page "https://github.com/jpritikin/rpf")
20546 (synopsis "Response probability functions")
20548 "The purpose of this package is to factor out logic and math common to
20549 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
20550 core support code suitable for more specialized IRT packages to build upon.
20551 Complete access to optimized C functions is made available with
20552 @code{R_RegisterCCallable()}.")
20553 (license license:gpl3+)))
20555 (define-public r-openmx
20562 (uri (cran-uri "OpenMx" version))
20565 "07y4w7xdb63p5kkrj6sdx1kabbsgbbj7nw9hc690jy84r15aryal"))))
20566 (properties `((upstream-name . "OpenMx")))
20567 (build-system r-build-system)
20570 ("r-digest" ,r-digest)
20572 ("r-matrix" ,r-matrix)
20574 ("r-rcppeigen" ,r-rcppeigen)
20576 ("r-stanheaders" ,r-stanheaders)))
20577 (native-inputs `(("gfortran" ,gfortran)))
20578 (home-page "http://openmx.ssri.psu.edu")
20579 (synopsis "Extended structural equation modelling")
20581 "This package allows for the estimation of a wide variety of advanced
20582 multivariate statistical models. It consists of a library of functions and
20583 optimizers that allow you to quickly and flexibly define an SEM model and
20584 estimate parameters given observed data.")
20585 (license license:asl2.0)))
20587 (define-public r-kutils
20594 (uri (cran-uri "kutils" version))
20597 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
20598 (properties `((upstream-name . "kutils")))
20599 (build-system r-build-system)
20601 `(("r-foreign" ,r-foreign)
20602 ("r-openxlsx" ,r-openxlsx)
20604 ("r-runit" ,r-runit)
20605 ("r-xtable" ,r-xtable)))
20606 (home-page "https://cran.r-project.org/package=kutils")
20607 (synopsis "Project management tools")
20609 "This package provides tools for data importation, recoding, and
20610 inspection. There are functions to create new project folders, R code
20611 templates, create uniquely named output directories, and to quickly obtain a
20612 visual summary for each variable in a data frame. The main feature here is
20613 the systematic implementation of the \"variable key\" framework for data
20614 importation and recoding.")
20615 (license license:gpl2)))
20617 (define-public r-rockchalk
20619 (name "r-rockchalk")
20620 (version "1.8.144")
20624 (uri (cran-uri "rockchalk" version))
20627 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
20628 (properties `((upstream-name . "rockchalk")))
20629 (build-system r-build-system)
20631 `(("r-cardata" ,r-cardata)
20632 ("r-kutils" ,r-kutils)
20634 ("r-mass" ,r-mass)))
20635 (home-page "https://cran.r-project.org/package=rockchalk")
20636 (synopsis "Regression estimation and presentation")
20638 "This package provides a collection of functions for interpretation and
20639 presentation of regression analysis. These functions are used to produce the
20640 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
20641 includes regression diagnostics, regression tables, and plots of interactions
20642 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
20643 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
20644 fairly comprehensive overview.")
20645 (license license:gpl3+)))
20647 (define-public r-lisreltor
20649 (name "r-lisreltor")
20654 (uri (cran-uri "lisrelToR" version))
20657 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
20658 (properties `((upstream-name . "lisrelToR")))
20659 (build-system r-build-system)
20660 (home-page "https://cran.r-project.org/package=lisrelToR")
20661 (synopsis "Import output from LISREL into R")
20663 "This is an unofficial package aimed at automating the import of LISREL
20665 (license license:gpl2)))
20667 (define-public r-bdgraph
20674 (uri (cran-uri "BDgraph" version))
20677 "1b1vfar940swvn3pcil848qsp8ji50fjjll8jjzp6y2adx0f8pby"))))
20678 (properties `((upstream-name . "BDgraph")))
20679 (build-system r-build-system)
20681 `(("r-igraph" ,r-igraph)))
20682 (home-page "https://www.uva.nl/profile/a.mohammadi")
20683 (synopsis "Bayesian structure learning in graphical models")
20685 "This package provides statistical tools for Bayesian structure learning
20686 in undirected graphical models for continuous, discrete, and mixed data. It
20687 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
20688 on a continuous-time birth-death process.")
20689 (license license:gpl2+)))
20691 (define-public r-d3network
20693 (name "r-d3network")
20694 (version "0.5.2.1")
20698 (uri (cran-uri "d3Network" version))
20701 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
20702 (properties `((upstream-name . "d3Network")))
20703 (build-system r-build-system)
20705 `(("r-plyr" ,r-plyr)
20706 ("r-rjson" ,r-rjson)
20707 ("r-whisker" ,r-whisker)))
20708 (home-page "http://christophergandrud.github.io/d3Network/")
20709 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
20711 "This package is intended to make it easy to create D3 JavaScript
20712 network, tree, dendrogram, and Sankey graphs from R using data frames.")
20713 (license license:gpl3+)))
20715 (define-public r-qgraph
20722 (uri (cran-uri "qgraph" version))
20725 "0pwys9irxvp0ap158drplyypkplbmwqinv0fmlsblk7q875cr592"))))
20726 (properties `((upstream-name . "qgraph")))
20727 (build-system r-build-system)
20729 `(("r-abind" ,r-abind)
20730 ("r-bdgraph" ,r-bdgraph)
20731 ("r-colorspace" ,r-colorspace)
20732 ("r-corpcor" ,r-corpcor)
20733 ("r-d3network" ,r-d3network)
20734 ("r-dplyr" ,r-dplyr)
20735 ("r-fdrtool" ,r-fdrtool)
20736 ("r-ggplot2" ,r-ggplot2)
20737 ("r-ggraph" ,r-ggraph)
20738 ("r-glasso" ,r-glasso)
20739 ("r-gtools" ,r-gtools)
20740 ("r-hmisc" ,r-hmisc)
20742 ("r-igraph" ,r-igraph)
20744 ("r-lavaan" ,r-lavaan)
20745 ("r-matrix" ,r-matrix)
20746 ("r-pbapply" ,r-pbapply)
20749 ("r-psych" ,r-psych)
20751 ("r-reshape2" ,r-reshape2)
20752 ("r-tidygraph" ,r-tidygraph)))
20753 (home-page "http://sachaepskamp.com/qgraph/")
20754 (synopsis "Weighted network visualization and analysis")
20756 "This package implements tools for weighted network visualization and
20757 analysis, as well as Gaussian graphical model computation. It contains graph
20758 plotting methods, and tools for psychometric data visualization and graphical
20759 model estimation. See Epskamp et al. (2012)
20760 @url{doi:10.18637/jss.v048.i04}.")
20761 (license license:gpl2)))
20763 (define-public r-semplot
20770 (uri (cran-uri "semPlot" version))
20773 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
20774 (properties `((upstream-name . "semPlot")))
20775 (build-system r-build-system)
20777 `(("r-colorspace" ,r-colorspace)
20778 ("r-corpcor" ,r-corpcor)
20779 ("r-igraph" ,r-igraph)
20780 ("r-lavaan" ,r-lavaan)
20781 ("r-lisreltor" ,r-lisreltor)
20782 ("r-openmx" ,r-openmx)
20784 ("r-qgraph" ,r-qgraph)
20785 ("r-regsem" ,r-regsem)
20786 ("r-rockchalk" ,r-rockchalk)
20789 (home-page "https://github.com/SachaEpskamp/semPlot")
20790 (synopsis "Unified visualizations of structural equation models")
20792 "Structural equation modeling (SEM) has a long history of representing
20793 models graphically as path diagrams. The semPlot package for R fills the gap
20794 between advanced, but time-consuming, graphical software and the limited
20795 graphics produced automatically by SEM software. In addition, semPlot offers
20796 more functionality than drawing path diagrams: it can act as a common ground
20797 for importing SEM results into R. Any result usable as input to semPlot can
20798 also be represented in any of the three popular SEM frame-works, as well as
20799 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
20800 (license license:gpl2)))
20802 (define-public r-cdm
20809 (uri (cran-uri "CDM" version))
20812 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
20813 (properties `((upstream-name . "CDM")))
20814 (build-system r-build-system)
20816 `(("r-mvtnorm" ,r-mvtnorm)
20817 ("r-polycor" ,r-polycor)
20819 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20821 "https://github.com/alexanderrobitzsch/CDM")
20822 (synopsis "Cognitive diagnosis modeling")
20824 "This package provides functions for cognitive diagnosis modeling and
20825 multidimensional item response modeling for dichotomous and polytomous item
20826 responses. It enables the estimation of the DINA and DINO model, the multiple
20827 group (polytomous) GDINA model, the multiple choice DINA model, the general
20828 diagnostic model (GDM), the structured latent class model (SLCA), and
20829 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
20830 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
20831 estimation and the package structure. For tutorials on how to use the CDM
20832 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
20833 well as Ravand and Robitzsch (2015).")
20834 (license license:gpl2+)))
20836 (define-public r-tam
20843 (uri (cran-uri "TAM" version))
20846 "1x1pdy0hrk4c3x5l4gcslpvyb0sv2zgly4n3a7y8j6yrzajx0sg7"))))
20847 (properties `((upstream-name . "TAM")))
20848 (build-system r-build-system)
20852 ("r-rcpparmadillo" ,r-rcpparmadillo)))
20853 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
20854 (synopsis "Test analysis modules")
20856 "This package includes tools for marginal maximum likelihood estimation
20857 and joint maximum likelihood estimation for unidimensional and
20858 multidimensional item response models. The package functionality covers the
20859 Rasch model, 2PL model, 3PL model, generalized partial credit model,
20860 multi-faceted Rasch model, nominal item response model, structured latent
20861 class model, mixture distribution IRT models, and located latent class models.
20862 Latent regression models and plausible value imputation are also supported.")
20863 (license license:gpl2+)))
20865 (define-public r-erm
20872 (uri (cran-uri "eRm" version))
20875 "0njqzznnhnkvalmhiq5yq1w7gwp2myki5cv61w42ydvd27hdyyg9"))))
20876 (properties `((upstream-name . "eRm")))
20877 (build-system r-build-system)
20879 `(("r-colorspace" ,r-colorspace)
20880 ("r-lattice" ,r-lattice)
20882 ("r-matrix" ,r-matrix)
20883 ("r-psych" ,r-psych)))
20884 (native-inputs `(("gfortran" ,gfortran)))
20885 (home-page "https://cran.r-project.org/package=eRm")
20886 (synopsis "Extended Rasch modeling")
20888 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
20889 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
20890 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
20891 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
20892 data matrix. Additional features are the ML estimation of the person
20893 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
20894 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
20895 infit and outfit measures, ICC and other plots, automated stepwise item
20896 elimination, and a simulation module for various binary data matrices.")
20897 (license license:gpl3)))
20899 (define-public r-irtoys
20906 (uri (cran-uri "irtoys" version))
20909 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
20910 (properties `((upstream-name . "irtoys")))
20911 (build-system r-build-system)
20915 (home-page "https://cran.r-project.org/package=irtoys")
20916 (synopsis "Collection of functions related to Item Response Theory (IRT)")
20918 "This package provides a collection of functions useful in learning and
20919 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
20920 programs. It provides basic CTT analysis, a simple common interface to the
20921 estimation of item parameters in IRT models for binary responses with three
20922 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
20923 EAP, WLE, plausible values), item and person fit statistics, scaling
20924 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
20925 array of parametric and non-parametric (kernel) plots. It estimates and plots
20926 Haberman's interaction model when all items are dichotomously scored.")
20927 (license license:gpl2+)))
20929 (define-public r-iheatmapr
20931 (name "r-iheatmapr")
20936 (uri (cran-uri "iheatmapr" version))
20939 "0s479j9l35xiss599vablxgvg6i2j9zq9sxphsq4vdk3bafg84bw"))))
20940 (properties `((upstream-name . "iheatmapr")))
20941 (build-system r-build-system)
20943 `(("r-fastcluster" ,r-fastcluster)
20944 ("r-ggdendro" ,r-ggdendro)
20945 ("r-htmlwidgets" ,r-htmlwidgets)
20946 ("r-jsonlite" ,r-jsonlite)
20947 ("r-knitr" ,r-knitr)
20948 ("r-magrittr" ,r-magrittr)
20950 ("r-rcolorbrewer" ,r-rcolorbrewer)
20951 ("r-s4vectors" ,r-s4vectors)
20952 ("r-scales" ,r-scales)))
20953 (home-page "https://docs.ropensci.org/iheatmapr")
20954 (synopsis "Interactive, Complex Heatmaps")
20956 "iheatmapr is an R package for building complex, interactive heatmaps
20957 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
20958 subplots along the rows or columns of the main heatmap add more information
20959 about each row or column. For example, a one column additional heatmap may
20960 indicate what group a particular row or column belongs to. Complex heatmaps
20961 may also include multiple side by side heatmaps which show different types of
20962 data for the same conditions. Interactivity can improve complex heatmaps by
20963 providing tooltips with information about each cell and enabling zooming into
20964 interesting features. iheatmapr uses the plotly library for interactivity.")
20965 (license license:expat)))
20967 (define-public r-packrat
20974 (uri (cran-uri "packrat" version))
20977 "1xy5dd2hrpqa07jfl4s7dsrya05mf36ms74j833scdz0zf89586n"))))
20978 (properties `((upstream-name . "packrat")))
20979 (build-system r-build-system)
20980 (home-page "https://github.com/rstudio/packrat/")
20981 (synopsis "Dependency management R projects")
20983 "This package provides a dependency manager for R projects that allows
20984 you to manage the R packages your project depends on in an isolated, portable,
20985 and reproducible way.")
20986 (license license:gpl2)))
20988 (define-public r-rsconnect
20990 (name "r-rsconnect")
20995 (uri (cran-uri "rsconnect" version))
20998 "05ii0p0p7xpf8z0c1594s5q7wpwcs7lmlddrd67s5p2ka5m8qwiz"))))
20999 (properties `((upstream-name . "rsconnect")))
21000 (build-system r-build-system)
21002 `(("r-curl" ,r-curl)
21003 ("r-digest" ,r-digest)
21004 ("r-jsonlite" ,r-jsonlite)
21005 ("r-openssl" ,r-openssl)
21006 ("r-packrat" ,r-packrat)
21007 ("r-rstudioapi" ,r-rstudioapi)
21008 ("r-yaml" ,r-yaml)))
21009 (home-page "https://github.com/rstudio/rsconnect")
21010 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
21012 "This package provides a programmatic deployment interface for RPubs,
21013 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
21014 documents, Shiny applications, Plumber APIs, plots, and static web content.")
21015 (license license:gpl2)))
21017 ;; This package includes minified JavaScript files. When upgrading please
21018 ;; check that there are no new minified JavaScript files.
21019 (define-public r-dygraphs
21021 (name "r-dygraphs")
21022 (version "1.1.1.6")
21026 (uri (cran-uri "dygraphs" version))
21029 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
21030 (properties `((upstream-name . "dygraphs")))
21031 (build-system r-build-system)
21033 `(#:modules ((guix build utils)
21034 (guix build r-build-system)
21038 (modify-phases %standard-phases
21039 (add-after 'unpack 'process-javascript
21040 (lambda* (#:key inputs #:allow-other-keys)
21041 (with-directory-excursion "inst/htmlwidgets/lib/"
21045 `(("dygraphs/dygraph-combined-dev.js"
21046 "dygraph-combined.js")
21047 (,(assoc-ref inputs "js-jquery")
21048 "jquery/jquery.min.js")
21049 (,(assoc-ref inputs "js-fquarter")
21050 "fquarter/moment-fquarter.min.js"))))
21051 (lambda (sources targets)
21052 (for-each (lambda (source target)
21053 (format #t "Processing ~a --> ~a~%"
21055 (let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
21056 (call-with-output-file target
21058 (dump-port minified port)))))
21059 sources targets))))
21062 `(("uglify-js" ,uglify-js)
21063 ;; They actually use version 1.11.1, but this more recent version
21064 ;; should be just fine.
21068 (uri "https://code.jquery.com/jquery-1.12.4.js")
21071 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
21075 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
21076 "moment-fquarter/1.0.1/moment-fquarter.js"))
21079 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
21081 `(("r-htmltools" ,r-htmltools)
21082 ("r-htmlwidgets" ,r-htmlwidgets)
21083 ("r-magrittr" ,r-magrittr)
21086 (home-page "https://github.com/rstudio/dygraphs")
21087 (synopsis "Interface to Dygraphs interactive time series charting library")
21089 "This package provides an R interface to the dygraphs JavaScript charting
21090 library (a copy of which is included in the package). It provides rich
21091 facilities for charting time-series data in R, including highly configurable
21092 series- and axis-display and interactive features like zoom/pan and
21093 series/point highlighting.")
21094 (license license:expat)))
21096 (define-public r-shinystan
21098 (name "r-shinystan")
21103 (uri (cran-uri "shinystan" version))
21106 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
21107 (properties `((upstream-name . "shinystan")))
21108 (build-system r-build-system)
21110 `(("r-bayesplot" ,r-bayesplot)
21111 ("r-colourpicker" ,r-colourpicker)
21113 ("r-dygraphs" ,r-dygraphs)
21114 ("r-ggplot2" ,r-ggplot2)
21115 ("r-gridextra" ,r-gridextra)
21116 ("r-gtools" ,r-gtools)
21117 ("r-markdown" ,r-markdown)
21118 ("r-reshape2" ,r-reshape2)
21119 ("r-rsconnect" ,r-rsconnect)
21120 ("r-rstan" ,r-rstan)
21121 ("r-shiny" ,r-shiny)
21122 ("r-shinyjs" ,r-shinyjs)
21123 ("r-shinythemes" ,r-shinythemes)
21124 ("r-threejs" ,r-threejs)
21125 ("r-xtable" ,r-xtable)
21127 (home-page "https://mc-stan.org/")
21128 (synopsis "Interactive visual and numerical analysis for Bayesian models")
21130 "This package provides a graphical user interface for interactive
21131 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
21132 for analyzing a posterior sample. The interface is powered by the Shiny web
21133 application framework and works with the output of MCMC programs written in
21134 any programming language (and has extended functionality for Stan models fit
21135 using the @code{rstan} and @code{rstanarm} packages).")
21136 (license license:gpl3+)))
21138 (define-public r-rstantools
21140 (name "r-rstantools")
21145 (uri (cran-uri "rstantools" version))
21148 "1il0pn4ksbdkska5fmhvgaicvwnnc6cs08g6ags9fj1xkjiqmrsa"))))
21149 (properties `((upstream-name . "rstantools")))
21150 (build-system r-build-system)
21151 (inputs `(("pandoc" ,ghc-pandoc)))
21153 `(("r-desc" ,r-desc)
21154 ("r-rcpp" ,r-rcpp)))
21155 (home-page "https://mc-stan.org/rstantools/")
21156 (synopsis "Tools for developing R packages interfacing with Stan")
21158 "This package provides various tools for developers of R packages
21159 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
21160 up the required package structure, S3 generics and default methods to unify
21161 function naming across Stan-based R packages, and vignettes with
21162 recommendations for developers.")
21163 (license license:gpl3+)))
21165 (define-public r-loo
21172 (uri (cran-uri "loo" version))
21175 "1hq1zcj76x55z9kic6cwf7mfq9pzqfbr341jbc9wp7x8ac4zcva6"))))
21176 (properties `((upstream-name . "loo")))
21177 (build-system r-build-system)
21179 `(("pandoc" ,ghc-pandoc)
21180 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21182 `(("r-checkmate" ,r-checkmate)
21183 ("r-matrixstats" ,r-matrixstats)))
21184 (home-page "https://mc-stan.org/loo/")
21185 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
21187 "This package provides an implementation of efficient approximate
21188 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
21189 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
21190 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
21191 procedure for regularizing importance weights. As a byproduct of the
21192 calculations, we also obtain approximate standard errors for estimated
21193 predictive errors and for the comparison of predictive errors between models.
21194 The package also provides methods for using stacking and other model weighting
21195 techniques to average Bayesian predictive distributions.")
21196 (license license:gpl3+)))
21198 (define-public r-rstan
21205 (uri (cran-uri "rstan" version))
21208 "128ndwjrhf8b1qvvqz4bl13qlm8718z9qs5ryc6gsdr3vk65s0np"))))
21209 (properties `((upstream-name . "rstan")))
21210 (build-system r-build-system)
21213 (modify-phases %standard-phases
21214 (add-before 'install 'set-timezone
21215 ;; This package is picky about timezones.
21216 (lambda* (#:key inputs #:allow-other-keys)
21217 (setenv "TZ" "UTC+1")
21219 (string-append (assoc-ref inputs "tzdata")
21220 "/share/zoneinfo"))
21223 `(("tzdata" ,tzdata-for-tests)
21224 ("pandoc" ,ghc-pandoc)))
21227 ("r-ggplot2" ,r-ggplot2)
21228 ("r-gridextra" ,r-gridextra)
21229 ("r-inline" ,r-inline)
21231 ("r-pkgbuild" ,r-pkgbuild)
21233 ("r-rcppeigen" ,r-rcppeigen)
21234 ("r-stanheaders" ,r-stanheaders)))
21235 (home-page "https://discourse.mc-stan.org/")
21236 (synopsis "R interface to Stan")
21238 "User-facing R functions are provided to parse, compile, test, estimate,
21239 and analyze Stan models by accessing the header-only Stan library provided by
21240 the StanHeaders package. The Stan project develops a probabilistic
21241 programming language that implements full Bayesian statistical inference via
21242 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
21243 approximation, and (optionally penalized) maximum likelihood estimation via
21244 optimization. In all three cases, automatic differentiation is used to
21245 quickly and accurately evaluate gradients without burdening the user with the
21246 need to derive the partial derivatives.")
21247 (license license:gpl3+)))
21249 (define-public r-rstanarm
21251 (name "r-rstanarm")
21256 (uri (cran-uri "rstanarm" version))
21259 "0gxjq8bdlvdd8kn3dhp12xlymdab036r7n12lzmd3xlkl4cnxq3s"))))
21260 (properties `((upstream-name . "rstanarm")))
21261 (build-system r-build-system)
21263 `(("pandoc" ,ghc-pandoc)
21264 ("pandoc-citeproc" ,ghc-pandoc-citeproc)))
21266 `(("r-bayesplot" ,r-bayesplot)
21268 ("r-ggplot2" ,r-ggplot2)
21271 ("r-matrix" ,r-matrix)
21274 ("r-rcppeigen" ,r-rcppeigen)
21275 ("r-rcppparallel" ,r-rcppparallel)
21276 ("r-rstan" ,r-rstan)
21277 ("r-rstantools" ,r-rstantools)
21278 ("r-shinystan" ,r-shinystan)
21279 ("r-stanheaders" ,r-stanheaders)
21280 ("r-survival" ,r-survival)))
21281 (home-page "https://mc-stan.org/rstanarm/")
21282 (synopsis "Bayesian applied regression modeling via Stan")
21284 "This package estimates previously compiled regression models using the
21285 @code{rstan} package, which provides the R interface to the Stan C++ library
21286 for Bayesian estimation. Users specify models via the customary R syntax with
21287 a formula and @code{data.frame} plus some additional arguments for priors.")
21288 (license license:gpl3+)))
21290 (define-public r-kendall
21297 (uri (cran-uri "Kendall" version))
21300 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
21301 (properties `((upstream-name . "Kendall")))
21302 (build-system r-build-system)
21304 `(("r-boot" ,r-boot)))
21306 `(("gfortran" ,gfortran)))
21307 (home-page "https://cran.r-project.org/web/packages/Kendall/")
21308 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
21310 "This package computes the Kendall rank correlation and Mann-Kendall
21312 (license license:gpl2+)))
21314 (define-public r-zyp
21317 (version "0.10-1.1")
21321 (uri (cran-uri "zyp" version))
21324 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
21325 (properties `((upstream-name . "zyp")))
21326 (build-system r-build-system)
21328 `(("r-kendall" ,r-kendall)))
21329 (home-page "https://cran.r-project.org/web/packages/zyp/")
21330 (synopsis "Zhang + Yue-Pilon Trends Package")
21332 "This package contains an efficient implementation of Sen's slope
21333 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
21334 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
21336 (license license:lgpl2.1)))
21338 (define-public r-rlinsolve
21340 (name "r-rlinsolve")
21345 (uri (cran-uri "Rlinsolve" version))
21348 "1x02xxbkchcwwfa2123n9yqfzinfi0zba8zxhp977czzwysy75cc"))))
21349 (properties `((upstream-name . "Rlinsolve")))
21350 (build-system r-build-system)
21352 `(("r-matrix" ,r-matrix)
21354 ("r-rcpparmadillo" ,r-rcpparmadillo)
21355 ("r-rdpack" ,r-rdpack)))
21356 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
21357 (synopsis "Iterative solvers for (sparse) linear system of equations")
21359 "Solving a system of linear equations is one of the most fundamental
21360 computational problems for many fields of mathematical studies, such as
21361 regression problems from statistics or numerical partial differential
21362 equations. This package provides basic stationary iterative solvers such as
21363 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
21364 Nonstationary, also known as Krylov subspace methods are also provided.
21365 Sparse matrix computation is also supported in that solving large and sparse
21366 linear systems can be manageable using the @code{Matrix} package along with
21367 @code{RcppArmadillo}.")
21368 (license license:gpl3+)))
21370 (define-public r-zvcv
21377 (uri (cran-uri "ZVCV" version))
21380 "0np6h6x74kz1x13wmbkkm1wq43d8bnn2khzjc80prqdi6n0m9v8r"))))
21381 (properties `((upstream-name . "ZVCV")))
21382 (build-system r-build-system)
21384 `(("r-abind" ,r-abind)
21386 ("r-dplyr" ,r-dplyr)
21387 ("r-glmnet" ,r-glmnet)
21388 ("r-magrittr" ,r-magrittr)
21389 ("r-mvtnorm" ,r-mvtnorm)
21391 ("r-rcpparmadillo" ,r-rcpparmadillo)
21392 ("r-rlinsolve" ,r-rlinsolve)))
21393 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
21394 (synopsis "Zero-Variance Control Variates")
21396 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
21397 to reduce the variance of Monte Carlo estimators of expectations using the
21398 derivatives of the log target. Once the derivatives are available, the only
21399 additional computational effort is in solving a linear regression problem.
21400 This method has been extended to higher dimensions using regularisation. This
21401 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
21402 samples, derivatives and function evaluations are available. Additional
21403 functions for applying ZV-CV to two estimators for the normalising constant of
21404 the posterior distribution in Bayesian statistics are also supplied.")
21405 (license license:gpl2+)))
21407 (define-public r-ztype
21414 (uri (cran-uri "ztype" version))
21417 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
21418 (properties `((upstream-name . "ztype")))
21419 (build-system r-build-system)
21421 `(("r-assertthat" ,r-assertthat)
21422 ("r-dplyr" ,r-dplyr)
21423 ("r-ggplot2" ,r-ggplot2)
21424 ("r-lubridate" ,r-lubridate)
21425 ("r-magrittr" ,r-magrittr)
21426 ("r-rvest" ,r-rvest)
21427 ("r-stringr" ,r-stringr)))
21428 (home-page "https://cran.r-project.org/web/packages/ztype/")
21429 (synopsis "Run a Ztype game loaded with R functions")
21431 "How fast can you type R functions on your keyboard? Find out by running
21432 a @code{zty.pe} game: export R functions as instructions to type to destroy
21433 opponents' vessels.")
21434 (license license:gpl3)))
21436 (define-public r-zseq
21443 (uri (cran-uri "Zseq" version))
21446 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
21447 (properties `((upstream-name . "Zseq")))
21448 (build-system r-build-system)
21450 `(("r-gmp" ,r-gmp)))
21451 (home-page "https://cran.r-project.org/web/packages/Zseq/")
21452 (synopsis "Integer sequence generator")
21454 "This package generates well-known integer sequences. The @code{gmp}
21455 package is adopted for computing with arbitrarily large numbers. Every
21456 function has a hyperlink to its corresponding item in the @dfn{On-Line
21457 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
21458 (license license:gpl3+)))
21460 (define-public r-isoband
21467 (uri (cran-uri "isoband" version))
21470 "044fg014gb6v6v11gm7ivfipz45iqw9cpahjhaacw6kyahyb66zx"))))
21471 (properties `((upstream-name . "isoband")))
21472 (build-system r-build-system)
21474 `(("r-testthat" ,r-testthat)))
21476 `(("r-knitr" ,r-knitr)))
21477 (home-page "https://github.com/wilkelab/isoband")
21478 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
21480 "This package provides a fast C++ implementation to generate contour
21481 lines (isolines) and contour polygons (isobands) from regularly spaced grids
21482 containing elevation data.")
21483 (license license:expat)))
21485 (define-public r-ppcor
21492 (uri (cran-uri "ppcor" version))
21495 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
21496 (properties `((upstream-name . "ppcor")))
21497 (build-system r-build-system)
21499 `(("r-mass" ,r-mass)))
21500 (home-page "https://cran.r-project.org/web/packages/ppcor/")
21501 (synopsis "Partial and semi-partial correlation")
21503 "This package provides users not only with a function to readily
21504 calculate the higher-order partial and semi-partial correlations but also with
21505 statistics and p-values of the correlation coefficients.")
21506 (license license:gpl2)))
21508 (define-public r-hrbrthemes
21510 (name "r-hrbrthemes")
21515 (uri (cran-uri "hrbrthemes" version))
21517 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
21518 (properties `((upstream-name . "hrbrthemes")))
21519 (build-system r-build-system)
21521 `(("r-extrafont" ,r-extrafont)
21522 ("r-gdtools" ,r-gdtools)
21523 ("r-ggplot2" ,r-ggplot2)
21524 ("r-htmltools" ,r-htmltools)
21525 ("r-knitr" ,r-knitr)
21526 ("r-magrittr" ,r-magrittr)
21527 ("r-rmarkdown" ,r-rmarkdown)
21528 ("r-scales" ,r-scales)))
21530 `(("r-knitr" ,r-knitr)))
21531 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
21532 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
21534 "This package provides a compilation of extra @code{ggplot2} themes,
21535 scales and utilities, including a spell check function for plot label fields
21536 and an overall emphasis on typography.")
21537 (license license:expat)))
21539 (define-public r-crochet
21546 (uri (cran-uri "crochet" version))
21549 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
21550 (build-system r-build-system)
21552 `(("r-knitr" ,r-knitr)))
21553 (home-page "https://github.com/agrueneberg/crochet")
21554 (synopsis "Implementation Helper for Matrix-Like Types")
21556 "Functions to help implement the extraction / subsetting / indexing
21557 function @code{[} and replacement function @code{[<-} of custom matrix-like
21558 types (based on S3, S4, etc.), modeled as closely to the base matrix class
21559 as possible (with tests to prove it).")
21560 (license license:expat)))
21562 (define-public r-boa
21565 (version "1.1.8-2")
21569 (uri (cran-uri "boa" version))
21572 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
21573 (properties `((upstream-name . "boa")))
21574 (build-system r-build-system)
21575 (home-page "http://www.jstatsoft.org/v21/i11")
21576 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
21578 "This package provides a menu-driven program and library of functions for
21579 carrying out convergence diagnostics and statistical and graphical analysis of
21580 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
21581 (license license:gpl2+)))
21583 (define-public r-httpcode
21585 (name "r-httpcode")
21589 (uri (cran-uri "httpcode" version))
21592 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
21593 (build-system r-build-system)
21594 (home-page "https://github.com/sckott/httpcode")
21595 (synopsis "HTTP status code helper")
21596 (description "@code{httpcode} provides functionality for finding and
21597 explaining the meaning of @code{HTTP} status codes. Functions are included for
21598 searching for codes by full or partial number, by message, and to get
21599 appropriate dog and cat images for many status codes.")
21600 (license license:expat)))
21602 (define-public r-latex2exp
21604 (name "r-latex2exp")
21608 (uri (cran-uri "latex2exp" version))
21611 "12nbcgfmv13k6sc6m326ras9bcvy380b7rxcxphn06r3cfkby0zw"))))
21612 (build-system r-build-system)
21614 `(("r-stringr" ,r-stringr)
21615 ("r-magrittr", r-magrittr)))
21616 (home-page "https://github.com/stefano-meschiari/latex2exp/")
21617 (synopsis "Use LaTeX expressions in plots")
21618 (description "@code{latex2exp} parses and converts LaTeX math formulas to
21619 R's plotmath expressions, used to enter mathematical formulas and symbols to be
21620 rendered as text, axis labels, etc. throughout R's plotting system.")
21621 (license license:expat)))
21623 (define-public r-oai
21629 (uri (cran-uri "oai" version))
21632 "1ipw9bq3ra66d1ddj1rylyyd20mlcb2i7phzhywra53s1fdifq1g"))))
21633 (build-system r-build-system)
21635 `(("r-xml2" ,r-xml2)
21638 ("r-stringr" ,r-stringr)
21639 ("r-tibble" ,r-tibble)))
21640 (home-page "https://github.com/ropensci/oai/")
21641 (synopsis "General purpose OAI-PMH services client")
21642 (description "@code{oai} provides a general purpose client to work with
21643 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
21644 service. Functions are provided to work with the OAI-PMH verbs:
21645 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
21646 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
21647 (license license:expat)))
21649 (define-public r-argon2
21656 (uri (cran-uri "argon2" version))
21659 "0kqn06rpb39jlzizjlnc5c44mfic8llrshxn7ljgmyj35lbqwxqh"))))
21660 (properties `((upstream-name . "argon2")))
21661 (build-system r-build-system)
21662 (home-page "https://github.com/wrathematics/argon2")
21663 (synopsis "Secure password hashing based on the argon2 algorithm")
21665 "This package provides utilities for secure password hashing via the
21666 argon2 algorithm.")
21667 (license license:bsd-2)))
21669 (define-public r-getpass
21676 (uri (cran-uri "getPass" version))
21679 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
21680 (properties `((upstream-name . "getPass")))
21681 (build-system r-build-system)
21683 `(("r-rstudioapi" ,r-rstudioapi)))
21684 (home-page "https://github.com/wrathematics/getPass")
21685 (synopsis "Masked user input")
21687 "This package provides a micro-package for reading \"passwords\", i.e.
21688 reading user input with masking, so that the input is not displayed as it is
21689 typed. Currently, RStudio, the command line (every OS), and any platform
21690 where tcltk is present are supported.")
21691 (license license:bsd-2)))
21693 (define-public r-remoter
21700 (uri (cran-uri "remoter" version))
21703 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
21704 (properties `((upstream-name . "remoter")))
21705 (build-system r-build-system)
21707 `(("r-argon2" ,r-argon2)
21708 ("r-getpass" ,r-getpass)
21709 ("r-pbdzmq" ,r-pbdzmq)
21711 (home-page "https://github.com/RBigData/remoter")
21712 (synopsis "Control a remote R session from a local one")
21714 "This package provides a set of utilities for client/server computing
21715 with R, controlling a remote R session (the server) from a local one (the
21717 (license license:bsd-2)))
21719 (define-public r-asd
21726 (uri (cran-uri "asd" version))
21729 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
21730 (properties `((upstream-name . "asd")))
21731 (build-system r-build-system)
21733 `(("r-mvtnorm" ,r-mvtnorm)))
21734 (home-page "https://cran.r-project.org/web/packages/asd")
21735 (synopsis "Simulations for Adaptive Seamless Designs")
21737 "This package provdes means to run simulations for adaptive seamless
21738 designs with and without early outcomes for treatment selection and
21739 subpopulation type designs.")
21740 (license license:gpl3)))
21742 (define-public r-nbconvertr
21744 (name "r-nbconvertr")
21749 (uri (cran-uri "nbconvertR" version))
21752 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
21753 (properties `((upstream-name . "nbconvertR")))
21754 (build-system r-build-system)
21756 `(("jupyter" ,python-nbconvert)
21757 ("pandoc" ,ghc-pandoc)))
21758 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
21759 (synopsis "Vignette engine wrapping Jupyter notebooks")
21761 "This package calls the Jupyter script @code{nbconvert} to create
21762 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
21763 containing rich text, code, and its output. Code cells can be edited and
21764 evaluated interactively.")
21765 (license license:gpl3)))
21767 (define-public r-bridgesampling
21769 (name "r-bridgesampling")
21774 (uri (cran-uri "bridgesampling" version))
21777 "1awhvv0v42w2q6llqi1wqpaiv5zx74cqzigdsvphy2jfp8ajw64y"))))
21779 `((upstream-name . "bridgesampling")))
21780 (build-system r-build-system)
21782 `(("r-brobdingnag" ,r-brobdingnag)
21784 ("r-matrix" ,r-matrix)
21785 ("r-mvtnorm" ,r-mvtnorm)
21786 ("r-scales" ,r-scales)
21787 ("r-stringr" ,r-stringr)))
21789 `(("r-knitr" ,r-knitr)))
21790 (home-page "https://github.com/quentingronau/bridgesampling")
21791 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
21793 "This package provides functions for estimating marginal likelihoods,
21794 Bayes factors, posterior model probabilities, and normalizing constants in
21795 general, via different versions of bridge sampling.")
21796 (license license:gpl2+)))
21798 (define-public r-tea
21805 (uri (cran-uri "tea" version))
21808 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
21810 `((upstream-name . "tea")))
21811 (build-system r-build-system)
21813 `(("r-matrix" ,r-matrix)))
21814 (home-page "https://cran.r-project.org/web/packages/tea/")
21815 (synopsis "Threshold estimation approaches")
21817 "This package provides different approaches for selecting the threshold
21818 in generalized Pareto distributions. Most of them are based on minimizing the
21819 AMSE-criterion or atleast by reducing the bias of the assumed GPD-model.
21820 Others are heuristically motivated by searching for stable sample paths, i.e.
21821 a nearly constant region of the tail index estimator with respect to k, which
21822 is the number of data in the tail. The third class is motivated by graphical
21823 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
21824 is also implemented here.")
21825 (license license:gpl3)))
21827 (define-public r-awsmethods
21829 (name "r-awsmethods")
21834 (uri (cran-uri "awsMethods" version))
21837 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
21839 `((upstream-name . "awsMethods")))
21840 (build-system r-build-system)
21841 (home-page "http://www.wias-berlin.de/software/imaging/")
21842 (synopsis "Class and methods definitions")
21844 "This package defines the generic method @code{extract} and provides
21845 @code{openMP} support as needed in several packages like
21846 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
21847 (license license:gpl2+)))
21849 (define-public r-aws
21856 (uri (cran-uri "aws" version))
21859 "1czlsy64nx6j7h1smgb561yyv3f98pwqwglk77yla4mx3fp14bvq"))))
21861 `((upstream-name . "aws")))
21862 (build-system r-build-system)
21864 `(("r-awsmethods" ,r-awsmethods)
21867 `(("gfortran" ,gfortran)))
21868 (home-page "https://cran.r-project.org/web/packages/aws/")
21869 (synopsis "Adaptive weights smoothing")
21871 "This package provides a collection of R-functions implementing adaptive
21872 smoothing procedures in 1D, 2D and 3D. This includes the
21873 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
21874 Confidence Intervals} (ICI), variational approaches, and a non-local means
21876 (license license:gpl2+)))
21878 (define-public r-sgloptim
21880 (name "r-sgloptim")
21885 (uri (cran-uri "sglOptim" version))
21888 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
21890 `((upstream-name . "sglOptim")))
21891 (build-system r-build-system)
21894 ("r-doparallel" ,r-doparallel)
21895 ("r-foreach" ,r-foreach)
21896 ("r-matrix" ,r-matrix)
21898 ("r-rcpparmadillo" ,r-rcpparmadillo)
21899 ("r-rcppprogress" ,r-rcppprogress)))
21901 `(("r-knitr" ,r-knitr)))
21902 (home-page "https://github.com/nielsrhansen/sglOptim")
21903 (synopsis "Generic sparse group Lasso solver")
21905 "This package provides a fast generic solver for sparse group lasso
21906 optimization problems. The loss (objective) function must be defined in a C++
21907 module. The optimization problem is solved using a coordinate gradient
21908 descent algorithm. Convergence of the algorithm is established and the
21909 algorithm is applicable to a broad class of loss functions. Use of parallel
21910 computing for cross validation and subsampling is supported through the
21911 @code{foreach} and @code{doParallel} packages.")
21912 (license license:gpl2+)))
21914 (define-public r-grouped
21921 (uri (cran-uri "grouped" version))
21924 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
21926 `((upstream-name . "grouped")))
21927 (build-system r-build-system)
21929 `(("r-mass" ,r-mass)))
21930 (home-page "https://cran.r-project.org/web/packages/grouped/")
21931 (synopsis "Regression analysis of grouped and coarse data")
21933 "This package provides regression models for grouped and coarse data,
21934 under the coarsened at random assumption.")
21935 (license license:gpl2+)))
21937 (define-public r-stam
21944 (uri (cran-uri "stam" version))
21947 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
21949 `((upstream-name . "stam")))
21950 (build-system r-build-system)
21954 (home-page "https://cran.r-project.org/web/packages/stam")
21955 (synopsis "Spatio-temporal analysis and modelling")
21957 "This package provides various methods to conduct Spatio-Temporal
21958 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
21959 Inferred Spatio-Temporal Modelling.")
21960 (license license:gpl2+)))
21962 (define-public r-dcv
21969 (uri (cran-uri "dcv" version))
21972 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
21974 `((upstream-name . "dcv")))
21975 (build-system r-build-system)
21977 `(("r-lmtest" ,r-lmtest)))
21978 (home-page "https://cran.r-project.org/web/packages/dcv/")
21979 (synopsis "Conventional cross-validation statistics for climate-growth model")
21981 "This package performs several conventional cross-validation statistical
21982 methods for climate-growth model in the climate reconstruction from tree
21983 rings, including Sign Test statistic, Reduction of Error statistic, Product
21984 Mean Test, Durbin-Watson statistic etc.")
21985 (license license:gpl2)))
21987 (define-public r-rcdd
21994 (uri (cran-uri "rcdd" version))
21997 "0pzpbqnlgzr240iici70278py5wnbbxkzlgn112f9wv5ga3riric"))))
21999 `((upstream-name . "rcdd")))
22000 (build-system r-build-system)
22003 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
22004 (synopsis "Computational geometry")
22006 "This package converts back and forth between two representations of a
22007 convex polytope: as solution of a set of linear equalities and inequalities
22008 and as convex hull of set of points and rays. Also does linear programming
22009 and redundant generator elimination. All functions can use exact
22010 infinite-precision rational arithmetic.")
22011 (license license:gpl2)))
22013 (define-public r-rxnat
22020 (uri (cran-uri "Rxnat" version))
22023 "12xcs2l6vn50bwzfmv60j1qahjw2npfm1a3yjhffcxzh6p8chwbg"))))
22025 `((upstream-name . "Rxnat")))
22026 (build-system r-build-system)
22028 `(("r-httr" ,r-httr)
22029 ("r-rcurl" ,r-rcurl)))
22031 `(("r-knitr" ,r-knitr)))
22032 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
22033 (synopsis "Queries and extracts images from neuroimaging datasets")
22035 "This package allows communication with the Extensible Neuroimaging
22036 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
22038 (license license:gpl2)))
22040 (define-public r-rserve
22047 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
22048 version ".tar.gz"))
22051 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
22052 (build-system r-build-system)
22054 `(("r-checkmate" ,r-checkmate)
22056 ("r-jsonlite" ,r-jsonlite)
22057 ("r-knitr" ,r-knitr)
22060 ("r-uuid" ,r-uuid)))
22062 `(("openssl" ,openssl)
22064 (home-page "https://github.com/s-u/Rserve")
22066 "Server providing access to R from many languages and systems")
22068 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
22069 binary requests to be sent to R. Every connection has a separate workspace
22070 and working directory. Client-side implementations are available for popular
22071 languages such as C/C++ and Java, allowing any application to use facilities
22072 of R without the need of linking to R code. Rserve supports remote
22073 connection, user authentication and file transfer. A simple R client is
22074 included in this package as well.")
22075 (license license:gpl2)))
22077 (define-public r-brms
22084 (uri (cran-uri "brms" version))
22087 "0vdncdawxawi16f326qrgy9jjjipmqdjxh741y9p7xdzd4fwaxx3"))))
22088 (properties `((upstream-name . "brms")))
22089 (build-system r-build-system)
22091 `(("r-abind" ,r-abind)
22092 ("r-backports" ,r-backports)
22093 ("r-bayesplot" ,r-bayesplot)
22094 ("r-bridgesampling" ,r-bridgesampling)
22096 ("r-future" ,r-future)
22097 ("r-ggplot2" ,r-ggplot2)
22100 ("r-matrix" ,r-matrix)
22101 ("r-matrixstats" ,r-matrixstats)
22103 ("r-nleqslv" ,r-nleqslv)
22106 ("r-rstan" ,r-rstan)
22107 ("r-rstantools" ,r-rstantools)
22108 ("r-shinystan" ,r-shinystan)))
22109 (native-inputs `(("r-knitr" ,r-knitr)))
22111 "https://github.com/paul-buerkner/brms")
22113 "Bayesian Regression Models using 'Stan'")
22115 "Fit Bayesian generalized (non-)linear multivariate multilevel models
22116 using 'Stan' for full Bayesian inference. A wide range of distributions and
22117 link functions are supported, allowing users to fit -- among others -- linear,
22118 robust linear, count data, survival, response times, ordinal, zero-inflated,
22119 hurdle, and even self-defined mixture models all in a multilevel context.
22120 Further modeling options include non-linear and smooth terms, auto-correlation
22121 structures, censored data, meta-analytic standard errors, and quite a few
22122 more. In addition, all parameters of the response distribution can be
22123 predicted in order to perform distributional regression. Prior specifications
22124 are flexible and explicitly encourage users to apply prior distributions that
22125 actually reflect their beliefs. Model fit can easily be assessed and compared
22126 with posterior predictive checks and leave-one-out cross-validation.")
22127 (license license:gpl2)))
22129 (define-public r-mstate
22136 (uri (cran-uri "mstate" version))
22139 "0qnhivbibzss8yfsg44cvbf73n4jj4i28rbdysl88g14ig5sabgv"))))
22140 (properties `((upstream-name . "mstate")))
22141 (build-system r-build-system)
22143 `(("r-rcolorbrewer" ,r-rcolorbrewer)
22144 ("r-survival" ,r-survival)))
22146 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
22148 "Data Preparation, Estimation and Prediction in Multi-State Models")
22150 "Contains functions for data preparation, descriptives, hazard estimation
22151 and prediction with Aalen-Johansen or simulation in competing risks and
22152 multi-state models.")
22153 (license license:gpl2+)))
22155 (define-public r-scatterpie
22157 (name "r-scatterpie")
22162 (uri (cran-uri "scatterpie" version))
22165 "0g5sn0iv6c1q7y51j4gbbbnil5089dgk1w4q94c7h5y3x7wfrzqb"))))
22166 (properties `((upstream-name . "scatterpie")))
22167 (build-system r-build-system)
22169 `(("r-ggforce" ,r-ggforce)
22170 ("r-ggplot2" ,r-ggplot2)
22171 ("r-rlang" ,r-rlang)
22172 ("r-rvcheck" ,r-rvcheck)
22173 ("r-tidyr" ,r-tidyr)))
22175 `(("r-knitr" ,r-knitr)))
22176 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
22177 (synopsis "Scatter pie plot")
22179 "This package creates scatterpie plots, especially useful for plotting
22181 (license license:artistic2.0)))
22183 (define-public r-boruta
22190 (uri (cran-uri "Boruta" version))
22193 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
22194 (properties `((upstream-name . "Boruta")))
22195 (build-system r-build-system)
22196 (propagated-inputs `(("r-ranger" ,r-ranger)))
22197 (home-page "https://gitlab.com/mbq/Boruta/")
22198 (synopsis "Wrapper algorithm for all relevant feature selection")
22200 "This package provides an all relevant feature selection wrapper
22201 algorithm. It finds relevant features by comparing original attributes'
22202 importance with importance achievable at random, estimated using their
22203 permuted copies (shadows).")
22204 (license license:gpl2+)))
22206 (define-public r-directlabels
22208 (name "r-directlabels")
22209 (version "2020.6.17")
22213 (uri (cran-uri "directlabels" version))
22216 "1b6v206kizz5rjw03chjvn40a7cqihjpk80h1h79z2x27hp1qi3f"))))
22217 (build-system r-build-system)
22219 `(("r-quadprog" ,r-quadprog)))
22221 `(("r-knitr" ,r-knitr)))
22222 (home-page "http://directlabels.r-forge.r-project.org/")
22223 (synopsis "Direct labels for multicolor plots")
22225 "This package provides an extensible framework for automatically placing
22226 direct labels onto multicolor plots. Label positions are described using
22227 positioning methods that can be re-used across several different plots. There
22228 are heuristics for examining @code{trellis} and @code{ggplot} objects and
22229 inferring an appropriate positioning method.")
22230 (license license:gpl3)))
22232 (define-public r-lsd
22239 (uri (cran-uri "LSD" version))
22241 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
22242 (properties `((upstream-name . "LSD")))
22243 (build-system r-build-system)
22244 (home-page "https://cran.r-project.org/web/packages/LSD/")
22245 (synopsis "Lots of superior depictions tool creates colorful plots")
22247 "This package creates lots of colorful plots in a multitude of variations.
22248 Try a demo of the LSD by running @code{demotour()}.")
22250 (license (list license:gpl2 license:gpl3))))
22252 (define-public r-fourcseq
22254 (name "r-fourcseq")
22259 (uri (bioconductor-uri "FourCSeq" version))
22261 (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x"))))
22262 (properties `((upstream-name . "FourCSeq")))
22263 (build-system r-build-system)
22265 `(("r-biobase" ,r-biobase)
22266 ("r-biostrings" ,r-biostrings)
22267 ("r-deseq2" ,r-deseq2)
22269 ("r-genomicalignments" ,r-genomicalignments)
22270 ("r-genomicranges" ,r-genomicranges)
22271 ("r-ggbio" ,r-ggbio)
22272 ("r-ggplot2" ,r-ggplot2)
22273 ("r-gtools" ,r-gtools)
22275 ("r-matrix" ,r-matrix)
22276 ("r-reshape2" ,r-reshape2)
22277 ("r-rsamtools" ,r-rsamtools)
22278 ("r-rtracklayer" ,r-rtracklayer)
22279 ("r-summarizedexperiment" ,r-summarizedexperiment)))
22281 `(("r-knitr" ,r-knitr)))
22283 "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
22284 (synopsis "Analysis of multiplexed 4C sequencing data")
22286 "This package is an R package dedicated to the analysis of (multiplexed)
22287 4C sequencing data. @code{r-fourcseq} provides a pipeline to detect specific
22288 interactions between DNA elements and identify differential interactions
22289 between conditions. The statistical analysis in R starts with individual bam
22290 files for each sample as inputs. To obtain these files, the package contains
22291 a Python script to demultiplex libraries and trim off primer sequences. With
22292 a standard alignment software the required bam files can be then be
22294 (license license:gpl3+)))
22296 (define-public r-phylogram
22298 (name "r-phylogram")
22303 (uri (cran-uri "phylogram" version))
22305 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
22306 (properties `((upstream-name . "phylogram")))
22307 (build-system r-build-system)
22308 (propagated-inputs `(("r-ape" ,r-ape)))
22309 (home-page "https://github.com/ropensci/phylogram/")
22310 (synopsis "Dendrograms for evolutionary analysis")
22312 "The @code{r-phylogram} package is a tool for for developing phylogenetic
22313 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
22314 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
22315 as well as several tools for command-line tree manipulation and import/export
22316 via Newick parenthetic text. This improves accessibility to the comprehensive
22317 range of object-specific analytical and tree-visualization functions found
22318 across a wide array of bioinformatic R packages.")
22319 (license license:gpl3)))
22321 (define-public r-kmer
22328 (uri (cran-uri "kmer" version))
22330 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
22331 (properties `((upstream-name . "kmer")))
22332 (build-system r-build-system)
22334 `(("r-openssl" ,r-openssl)
22335 ("r-phylogram" ,r-phylogram)
22336 ("r-rcpp" ,r-rcpp)))
22337 (home-page "https://github.com/shaunpwilkinson/kmer/")
22338 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
22340 "@code{r-kmer} is an R package for rapidly computing distance matrices
22341 and clustering large sequence datasets using fast alignment-free k-mer
22342 counting and recursive k-means partitioning.")
22343 (license license:gpl3)))
22345 (define-public r-shapforxgboost
22347 (name "r-shapforxgboost")
22352 (uri (cran-uri "SHAPforxgboost" version))
22355 "0k6bg27wqnkzv82bcahbapmqhiz6rvnx81m23zbjw58c7lwshgnq"))))
22357 `((upstream-name . "SHAPforxgboost")))
22358 (build-system r-build-system)
22360 `(("r-bbmisc" ,r-bbmisc)
22361 ("r-data-table" ,r-data-table)
22362 ("r-ggextra" ,r-ggextra)
22363 ("r-ggforce" ,r-ggforce)
22364 ("r-ggplot2" ,r-ggplot2)
22365 ("r-ggpubr" ,r-ggpubr)
22366 ("r-rcolorbrewer" ,r-rcolorbrewer)
22367 ("r-xgboost" ,r-xgboost)))
22368 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
22369 (synopsis "SHAP Plots for XGBoost")
22371 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
22372 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
22373 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
22374 and force plot. It relies on the @code{XGBoost} package to produce SHAP
22376 (license license:expat)))