1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
4 ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
5 ;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
6 ;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
7 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
8 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
9 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
10 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
11 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
12 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
13 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
14 ;;; Copyright © 2018, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
15 ;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
16 ;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
17 ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
18 ;;; Copyright © 2018, 2019 Brett Gilio <brettg@gnu.org>
19 ;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
20 ;;; Copyright © 2019, 2020, 2021 Wiktor Żelazny <wzelazny@vurv.cz>
21 ;;; Copyright © 2019 Arne Babenhauserheide <arne_bab@web.de>
22 ;;; Copyright © 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
23 ;;; Copyright © 2020 Todor Kondić <tk.code@protonmail.com>
24 ;;; Copyright © 2020 Danjela Lura <danielaluraa@gmail.com>
25 ;;; Copyright © 2020 Naga Malleswari <nagamalli@riseup.net>
26 ;;; Copyright © 2020 Eric Brown <ecbrown@ericcbrown.com>
27 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
28 ;;; Copyright © 2020 Rafael Luque Leiva <rafael.luque@osoco.es>
29 ;;; Copyright © 2020, 2021 Lars-Dominik Braun <ldb@leibniz-psychology.org>
30 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
31 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
32 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
33 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
34 ;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
35 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
36 ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
37 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
39 ;;; This file is part of GNU Guix.
41 ;;; GNU Guix is free software; you can redistribute it and/or modify it
42 ;;; under the terms of the GNU General Public License as published by
43 ;;; the Free Software Foundation; either version 3 of the License, or (at
44 ;;; your option) any later version.
46 ;;; GNU Guix is distributed in the hope that it will be useful, but
47 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
48 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
49 ;;; GNU General Public License for more details.
51 ;;; You should have received a copy of the GNU General Public License
52 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
54 (define-module (gnu packages cran)
55 #:use-module ((guix licenses) #:prefix license:)
56 #:use-module (guix packages)
57 #:use-module (guix download)
58 #:use-module (guix git-download)
59 #:use-module (guix utils)
60 #:use-module (guix build-system gnu)
61 #:use-module (guix build-system r)
62 #:use-module (gnu packages)
63 #:use-module (gnu packages algebra)
64 #:use-module (gnu packages autotools)
65 #:use-module (gnu packages base)
66 #:use-module (gnu packages bioinformatics)
67 #:use-module (gnu packages c)
68 #:use-module (gnu packages compression)
69 #:use-module (gnu packages crypto)
70 #:use-module (gnu packages curl)
71 #:use-module (gnu packages databases)
72 #:use-module (gnu packages fontutils)
73 #:use-module (gnu packages fribidi)
74 #:use-module (gnu packages gcc)
75 #:use-module (gnu packages geo)
76 #:use-module (gnu packages ghostscript)
77 #:use-module (gnu packages gl)
78 #:use-module (gnu packages gnome)
79 #:use-module (gnu packages graph)
80 #:use-module (gnu packages gtk)
81 #:use-module (gnu packages haskell-xyz)
82 #:use-module (gnu packages icu4c)
83 #:use-module (gnu packages image)
84 #:use-module (gnu packages imagemagick)
85 #:use-module (gnu packages java)
86 #:use-module (gnu packages javascript)
87 #:use-module (gnu packages libevent)
88 #:use-module (gnu packages machine-learning)
89 #:use-module (gnu packages maths)
90 #:use-module (gnu packages mpi)
91 #:use-module (gnu packages multiprecision)
92 #:use-module (gnu packages networking)
93 #:use-module (gnu packages node)
94 #:use-module (gnu packages pcre)
95 #:use-module (gnu packages pdf)
96 #:use-module (gnu packages perl)
97 #:use-module (gnu packages pkg-config)
98 #:use-module (gnu packages pulseaudio) ;libsndfile
99 #:use-module (gnu packages protobuf)
100 #:use-module (gnu packages python)
101 #:use-module (gnu packages python-xyz)
102 #:use-module (gnu packages sqlite)
103 #:use-module (gnu packages statistics)
104 #:use-module (gnu packages tcl)
105 #:use-module (gnu packages textutils)
106 #:use-module (gnu packages tls)
107 #:use-module (gnu packages uglifyjs)
108 #:use-module (gnu packages version-control)
109 #:use-module (gnu packages video)
110 #:use-module (gnu packages web)
111 #:use-module (gnu packages xml)
112 #:use-module (gnu packages xorg))
114 (define-public r-brio
121 (uri (cran-uri "brio" version))
124 "1inwzvlf6zj6gi47gd0byzqv02qajb3l475z8pjvx2b1hm0r1a7a"))))
125 (properties `((upstream-name . "brio")))
126 (build-system r-build-system)
127 (home-page "https://github.com/r-lib/brio")
128 (synopsis "Basic R input output")
130 "This package provides functions to handle basic input output. These
131 functions always read and write UTF-8 (8-bit Unicode Transformation Format)
132 files and provide more explicit control over line endings.")
133 (license license:expat)))
135 (define-public r-cachem
142 (uri (cran-uri "cachem" version))
145 "0r0q5w8lsxak46crnkbi739qzys90hlw7cqqqhv99xzkpkvm554s"))))
146 (properties `((upstream-name . "cachem")))
147 (build-system r-build-system)
149 (list r-fastmap r-rlang))
150 (home-page "https://cachem.r-lib.org/")
151 (synopsis "Cache R objects with automatic pruning")
153 "This package provides key-value stores with automatic pruning. Caches
154 can limit either their total size or the age of the oldest object (or both),
155 automatically pruning objects to maintain the constraints.")
156 (license license:expat)))
158 (define-public r-curry
165 (uri (cran-uri "curry" version))
168 "1ps9hvbnb02m0b8hlw4admwbziyjvswj08ldi2dk3ymnrpawcc29"))))
169 (properties `((upstream-name . "curry")))
170 (build-system r-build-system)
171 (home-page "https://github.com/thomasp85/curry")
172 (synopsis "Partial function application")
174 "Partial application is the process of reducing the arity of a function
175 by fixing one or more arguments, thus creating a new function lacking the
176 fixed arguments. The @code{curry} package provides three different ways of
177 performing partial function application by fixing arguments from either end of
178 the argument list (currying and tail currying) or by fixing multiple named
179 arguments (partial application). This package provides this functionality
180 through the @code{%<%}, @code{%-<%}, and @code{%><%} operators which allows
181 for a programming style comparable to modern functional languages. Compared
182 to other implementations such a @code{purrr::partial()} the operators in
183 @code{curry} composes functions with named arguments, aiding in autocomplete
185 (license license:gpl2+)))
187 (define-public r-datawizard
189 (name "r-datawizard")
194 (uri (cran-uri "datawizard" version))
197 "0hcnwz42zy9hp32brga31jwk34bz063myqjp2wfxsqm4sqrkv2rx"))))
198 (properties `((upstream-name . "datawizard")))
199 (build-system r-build-system)
204 (home-page "https://easystats.github.io/datawizard/")
205 (synopsis "Easy data wrangling")
207 "This package provides a lightweight package to easily manipulate,
208 clean, transform, and prepare your data for analysis. It also forms the data
209 wrangling backend for the packages in the @code{easystats} ecosystem.")
210 (license license:gpl3)))
212 (define-public r-diffobj
219 (uri (cran-uri "diffobj" version))
222 "0q6gwd9pqh41f6j5p9jl92aji4p8kx9inffpha93d7jc3ndsfq6q"))))
223 (properties `((upstream-name . "diffobj")))
224 (build-system r-build-system)
225 (propagated-inputs (list r-crayon))
226 (native-inputs (list r-knitr))
227 (home-page "https://github.com/brodieG/diffobj")
228 (synopsis "Diffs for R objects")
230 "Generate a colorized diff of two R objects for an intuitive
231 visualization of their differences.")
232 (license license:gpl2+)))
234 (define-public r-emdist
241 (uri (cran-uri "emdist" version))
244 "1z14pb9z9nkd0f2c8pln4hzkfqa9dk9n3vg8czc8jiv0ndnqi7rq"))))
245 (properties `((upstream-name . "emdist")))
246 (build-system r-build-system)
247 (home-page "http://www.rforge.net/emd")
248 (synopsis "Earth mover's distance")
250 "This package provides tools to calculate the Earth Mover's
252 (license license:expat)))
254 (define-public r-googledrive
256 (name "r-googledrive")
261 (uri (cran-uri "googledrive" version))
264 "09jsiknzyfgxd0nzdr3wrrjw24allch2x74h96qg8vh8dad4cp30"))))
265 (properties `((upstream-name . "googledrive")))
266 (build-system r-build-system)
284 (home-page "https://googledrive.tidyverse.org")
285 (synopsis "Interface to Google Drive")
286 (description "This package lets you manage Google Drive files from R.")
287 (license license:expat)))
296 (uri (cran-uri "ids" version))
299 "1s6ga94gds5ydr9f8qbjfgfpg2dvbnkcrlybqlb33hk3c0c2l8dn"))))
300 (properties `((upstream-name . "ids")))
301 (build-system r-build-system)
303 (list r-openssl r-uuid))
304 (native-inputs (list r-knitr))
305 (home-page "https://github.com/richfitz/ids")
306 (synopsis "Generate random identifiers")
308 "This package lets you generate random or human readable and
309 pronounceable identifiers.")
310 (license license:expat)))
312 (define-public r-googlesheets4
314 (name "r-googlesheets4")
319 (uri (cran-uri "googlesheets4" version))
322 "0yncqwv9l5knyrv88ys5gwcv44hl1j0mbklpins6v7f9m9v7s40a"))))
323 (properties `((upstream-name . "googlesheets4")))
324 (build-system r-build-system)
340 (home-page "https://github.com/tidyverse/googlesheets4")
341 (synopsis "Access Google Sheets using the Sheets API V4")
343 "This package lets you interact with Google Sheets through the
344 @url{https://developers.google.com/sheets/api,Sheets API v4}. This package
345 can read and write both the metadata and the cell data in a Sheet.")
346 (license license:expat)))
348 (define-public r-waldo
355 (uri (cran-uri "waldo" version))
358 "16q1xjbl9g04l1r1x3nid9hmz1sa35q6j33bigdzh4y4zcd8qb7c"))))
359 (properties `((upstream-name . "waldo")))
360 (build-system r-build-system)
369 (home-page "https://github.com/r-lib/waldo")
370 (synopsis "Find differences between R objects")
372 "Compare complex R objects and reveal the key differences. This package
373 was designed particularly for use in testing packages where being able to
374 quickly isolate key differences makes understanding test failures much
376 (license license:expat)))
378 (define-public r-rticles
385 (uri (cran-uri "rticles" version))
388 "0jgsmqwwqzvsxcbsm9fx0rp724mn3ipi70883bhvm7n9i8mq877m"))))
389 (properties `((upstream-name . "rticles")))
390 (build-system r-build-system)
392 (list r-knitr r-rmarkdown r-tinytex r-xfun r-yaml))
393 (home-page "https://github.com/rstudio/rticles")
394 (synopsis "Article formats for R Markdown")
396 "This package provides a suite of custom R Markdown formats and templates
397 for authoring journal articles and conference submissions.")
398 (license license:gpl3)))
400 (define-public r-benchmarkmedata
402 (name "r-benchmarkmedata")
406 (uri (cran-uri "benchmarkmeData" version))
409 "1n4vjkagqlm6kw2hilf4gjfcdjad0bcg652j9nl2ygbq3kdnh1vf"))))
410 (build-system r-build-system)
412 (list r-dplyr r-tibble))
413 (home-page "https://github.com/csgillespie/benchmarkme-data")
414 (synopsis "Data set for the @code{benchmarkme} package")
415 (description "This package contains the data set for the crowd-sourced
416 benchmarks from running the @code{benchmarkme} package.")
417 (license license:gpl2+)))
419 (define-public r-benchmarkme
421 (name "r-benchmarkme")
425 (uri (cran-uri "benchmarkme" version))
428 "0ymgsxzrvnpyvs0cff09d3lrkl12qyqx5bwammsc4vgl5ng9p69p"))))
429 (build-system r-build-system)
433 (list r-benchmarkmedata
440 (home-page "https://csgillespie.github.io/benchmarkme/")
441 (synopsis "Crowd-sourced system benchmarks")
442 (description "This package provides functionality to benchmark your CPU
443 and compare against other CPUs. Also provides functions for obtaining system
444 specifications, such as RAM, CPU type, and R version.")
445 (license license:gpl2+)))
447 (define-public r-bezier
453 (uri (cran-uri "bezier" version))
456 "1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"))))
457 (build-system r-build-system)
458 (home-page "https://cran.r-project.org/web/packages/bezier/")
459 (synopsis "Bezier curve and spline toolkit")
461 "This package is a toolkit for working with Bezier curves and splines.
462 The package provides functions for point generation, arc length estimation,
463 degree elevation and curve fitting.")
464 (license license:gpl2+)))
466 (define-public r-bwstest
473 (uri (cran-uri "BWStest" version))
475 (base32 "02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"))))
476 (properties `((upstream-name . "BWStest")))
477 (build-system r-build-system)
478 (propagated-inputs (list r-memoise r-rcpp))
479 (home-page "https://github.com/shabbychef/BWStest")
480 (synopsis "Baumgartner Weiss Schindler Test of equal distributions")
482 "This package performs the Baumgartner-Weiss-Schindler two-sample test of
483 equal probability distributions (doi:10.2307/2533862). It also performs
484 similar rank-based tests for equal probability distributions due to Neuhauser
485 (doi:10.1080/10485250108832874) and Murakami
486 (doi:10.1080/00949655.2010.551516).")
487 (license license:lgpl3)))
496 (uri (cran-uri "V8" version))
499 "1j5vknhq12kfzda46y7nwiqdzqipzgympqzjq9d8ckr6f6v4qshl"))))
500 (properties `((upstream-name . "V8")))
501 (build-system r-build-system)
504 (modify-phases %standard-phases
505 (add-after 'unpack 'find-v8
506 (lambda* (#:key inputs #:allow-other-keys)
507 (substitute* "configure"
509 (string-append "PKG_LIBS="
510 (assoc-ref inputs "libnode")
511 "/lib/libnode.so.64\n")))
512 (setenv "INCLUDE_DIR"
514 (assoc-ref inputs "libnode")
518 (assoc-ref inputs "libnode") "/lib")))))))
522 (list r-curl r-jsonlite r-rcpp))
525 (home-page "https://jeroen.cran.dev/V8")
526 (synopsis "Embedded JavaScript and WebAssembly engine for R")
528 "This package provides an R interface to V8: Google's JavaScript and
529 WebAssembly engine.")
530 (license license:expat)))
539 (uri (cran-uri "DOT" version))
542 "0qh5n57cp9c2n5yn59q4wggz82943pwfanp3kx869aba2x3sj30i"))))
543 (properties `((upstream-name . "DOT")))
544 (build-system r-build-system)
547 (home-page "http://haghish.com/dot")
548 (synopsis "Render and Export DOT Graphs in R")
550 "This package provides tools to render DOT diagram markup language in R
551 and also provides the possibility to export the graphs in PostScript and
552 SVG (Scalable Vector Graphics) formats. In addition, it supports literate
553 programming packages such as @code{knitr} and @code{rmarkdown}.")
554 (license license:expat)))
556 (define-public r-clipr
563 (uri (cran-uri "clipr" version))
566 "1ywa4kipwc2d7na6iiz3wzdah99h6aynnh74yxl3nzl40xxlgbgz"))))
567 (build-system r-build-system)
570 (home-page "https://github.com/mdlincoln/clipr")
571 (synopsis "Read and write from the system clipboard")
573 "This package provides simple utility functions to read from and write to
574 the system clipboards.")
575 (license license:gpl3)))
583 (uri (cran-uri "zoo" version))
586 "18vjywalpgzqyk66gajb8x1yp8avdaaf11ykynld9fd8cy82bgmp"))))
587 (build-system r-build-system)
590 (home-page "http://zoo.R-Forge.R-project.org/")
591 (synopsis "S3 infrastructure for regular and irregular time series")
592 (description "This package contains an S3 class with methods for totally
593 ordered indexed observations. It is particularly aimed at irregular time
594 series of numeric vectors/matrices and factors.")
595 (license license:gpl2+)))
597 (define-public r-fontawesome
599 (name "r-fontawesome")
604 (uri (cran-uri "fontawesome" version))
606 (base32 "0r6zb5175cr4ybqj6bl0mbhadwv9xjxaf32yjc0y76rw3d6vcbap"))))
607 (properties `((upstream-name . "fontawesome")))
608 (build-system r-build-system)
610 (list r-htmltools r-rlang))
611 (home-page "https://github.com/rstudio/fontawesome")
612 (synopsis "Easily work with Font Awesome icons")
614 "Easily and flexibly insert Font Awesome icons into R Markdown documents
615 and Shiny apps. These icons can be inserted into HTML content through inline
616 SVG tags or @code{i} tags. There is also a utility function for exporting
617 Font Awesome icons as PNG images for those situations where raster graphics
619 (license license:expat)))
621 (define-public r-fingerprint
623 (name "r-fingerprint")
628 (uri (cran-uri "fingerprint" version))
630 (base32 "04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"))))
631 (properties `((upstream-name . "fingerprint")))
632 (build-system r-build-system)
633 (home-page "https://cran.r-project.org/package=fingerprint")
634 (synopsis "Functions to Operate on Binary Fingerprint Data")
636 "This package provides functions to manipulate binary fingerprints of
637 arbitrary length. A fingerprint is represented by an object of S4 class
638 @code{fingerprint}. The bitwise logical functions in R are overridden so that
639 they can be used directly with @code{fingerprint} objects. A number of
640 distance metrics are also available. Fingerprints can be converted to
641 Euclidean vectors (i.e., points on the unit hypersphere) and can also be
642 folded. Arbitrary fingerprint formats can be handled via line handlers.
643 Currently handlers are provided for CDK, MOE and BCI fingerprint data.")
644 ;; Any version of the GPL
645 (license (list license:gpl2+ license:gpl3+))))
647 (define-public r-fpeek
654 (uri (cran-uri "fpeek" version))
656 (base32 "0kv46g21ndxchg3q8ynq7hjjkh6i2zlc21axn5y1jjzigrw047ii"))))
657 (properties `((upstream-name . "fpeek")))
658 (build-system r-build-system)
659 (propagated-inputs (list r-rcpp))
660 (home-page "https://github.com/davidgohel/fpeek")
661 (synopsis "Check text files content at a glance")
663 "This package provides tools to help working with text files. It can
664 return the number of lines; print the first and last lines; convert encoding.
665 Operations are made without reading the entire file before starting, resulting
666 in good performances with large files.")
667 (license license:expat)))
669 (define-public r-ggalluvial
671 (name "r-ggalluvial")
675 (uri (cran-uri "ggalluvial" version))
678 "0mkan9gxg3yxjism22yxbhvlh2lh7wpbrqpb355za790prcmjbh3"))))
679 (properties `((upstream-name . "ggalluvial")))
680 (build-system r-build-system)
690 (home-page "http://corybrunson.github.io/ggalluvial/")
691 (synopsis "Alluvial plots for ggplot2")
692 (description "This package provides alluvial plots for @code{ggplot2}.
693 Alluvial plots use variable-width ribbons and stacked bar plots to represent
694 multi-dimensional or repeated-measures data with categorical or ordinal
696 (license license:gpl3)))
698 (define-public r-ggpp
705 (uri (cran-uri "ggpp" version))
708 "175mk5zcnhwr8hvs1567x0k0vmq7g2qnq250pnxlwnv1wpmvrqhz"))))
709 (properties `((upstream-name . "ggpp")))
710 (build-system r-build-system)
728 (home-page "https://docs.r4photobiology.info/ggpp/")
729 (synopsis "Grammar extensions to ggplot2")
731 "This package contains extensions to ggplot2.
734 @item Geomas: @code{geom_table}, @code{geom_plot} and @code{geom_grob} add
735 insets to plots using native data coordinates, while @code{geom_table_npc},
736 @code{geom_plot_npc} and @code{geom_grob_npc} do the same using @code{npc}
737 coordinates through new aesthetics @code{npcx} and @code{npcy}.
738 @item Statistics: select observations based on 2D density.
739 @item Positions: radial nudging away from a center point and nudging away from
743 (license license:gpl2+)))
745 (define-public r-lmodel2
752 (uri (cran-uri "lmodel2" version))
754 (base32 "1fiin2nkffbihz1s8ixmw9lgf8mn3j9krr8iiflizk10mdv54hnb"))))
755 (properties `((upstream-name . "lmodel2")))
756 (build-system r-build-system)
757 (home-page "https://cran.r-project.org/package=lmodel2")
758 (synopsis "Model II regression")
760 "This package computes model II simple linear regression using
761 @dfn{ordinary least squares} (OLS), @dfn{major axis} (MA), @dfn{standard major
762 axis} (SMA), and @dfn{ranged major axis} (RMA).")
763 (license license:gpl2)))
765 (define-public r-ggpmisc
771 (uri (cran-uri "ggpmisc" version))
774 "036y3zhl9ndj5wlqy2nkp95vi7pjfpvf63ndsigramzad0fz0c98"))))
775 (build-system r-build-system)
793 (home-page "https://www.r4photobiology.info/")
794 (synopsis "Miscellaneous Extensions to @code{ggplot2}")
795 (description "This package provides extensions to @code{ggplot2},
796 respecting the grammar of its graphics paradigm.")
797 (license license:gpl2+)))
799 (define-public r-gprofiler
806 (uri (cran-uri "gProfileR" version))
809 "1h1v0kgpsn04ald2izznh7fr2riwisj5hcgz4k7h3qc931rf0r4k"))))
810 (properties `((upstream-name . "gProfileR")))
811 (build-system r-build-system)
813 (list r-plyr r-rcurl))
814 (home-page "https://cran.r-project.org/web/packages/gProfileR/")
815 (synopsis "Interface to the g:Profiler toolkit")
817 "This package provides tools for functional enrichment analysis,
818 gene identifier conversion and mapping homologous genes across related
819 organisms via the @code{g:Profiler} toolkit.")
820 (license license:gpl2+)))
822 (define-public r-gprofiler2
824 (name "r-gprofiler2")
829 (uri (cran-uri "gprofiler2" version))
832 "0r0h34b35xzgd9rh55yndn0anxy0z45zdlqa6qfmpn91b6v1bb1g"))))
833 (properties `((upstream-name . "gprofiler2")))
834 (build-system r-build-system)
845 (native-inputs (list r-knitr))
846 (home-page "https://cran.r-project.org/web/packages/gprofiler2/")
847 (synopsis "Interface to the g:Profiler toolset")
849 "This package provides a toolset for functional enrichment analysis and
850 visualization, gene/protein/SNP identifier conversion and mapping orthologous
851 genes across species via @url{https://biit.cs.ut.ee/gprofiler,g:Profiler}.
855 @item @code{g:GOSt}, functional enrichment analysis and visualization of gene
857 @item @code{g:Convert}, gene/protein/transcript identifier conversion across
859 @item @code{g:Orth}, orthology search across species;
860 @item @code{g:SNPense}, mapping SNP rs identifiers to chromosome positions,
861 genes and variant effects.
864 This package is an R interface corresponding to the 2019 update of
865 @code{g:Profiler} and provides access to versions @code{e94_eg41_p11} and
867 (license license:gpl2+)))
869 (define-public r-oenb
876 (uri (cran-uri "oenb" version))
879 "1jgxw7ycx2lcdzglg9nix8k08fs4r6i5jdsjzrd6w1dg6smsinl5"))))
880 (properties `((upstream-name . "oenb")))
881 (build-system r-build-system)
883 (list r-dplyr r-xml))
884 (native-inputs (list r-knitr))
885 (home-page "https://github.com/franzmohr/oenb")
886 (synopsis "Tools for the OeNB Data Web Service")
888 "Tools to access data from the data web service of the
889 @acronym{OeNB, Oesterreichische Nationalbank},
890 @url{https://www.oenb.at/en/Statistics/User-Defined-Tables/webservice.html}.")
891 (license license:gpl2+)))
893 (define-public r-scales
900 (uri (cran-uri "scales" version))
902 (base32 "019ps0njjc0rzrjygqiyn8b9vp0c3c0jd56h1yi19wzi49jvdcj0"))))
903 (build-system r-build-system)
912 (home-page "https://github.com/hadley/scales")
913 (synopsis "Scale functions for visualization")
915 "This package provides graphical scales that map data to aesthetics, and
916 provides methods for automatically determining breaks and labels for axes and
918 (license license:expat)))
920 (define-public r-pacman
926 (uri (cran-uri "pacman" version))
929 "0z7gngd6h83cpjhq1vg75wvzhdjbgjh7gj5d4zvvi9gd2lmagjcy"))))
930 (build-system r-build-system)
933 (home-page "https://github.com/trinker/pacman")
934 (synopsis "Package Management Tool")
935 (description "This package provides tools to more conveniently perform
936 tasks associated with add-on packages. @code{pacman} conveniently wraps
937 library and package related functions and names them in an intuitive and
938 consistent fashion. It seeks to combine functionality from lower level
939 functions which can speed up workflow.")
940 (license license:gpl2)))
942 (define-public r-pheatmap
949 (uri (cran-uri "pheatmap" version))
952 "1hdh74az3vyzz6dqa311rhxdm74n46lyr03p862kn80p0kp9d7ap"))))
953 (build-system r-build-system)
955 (list r-gtable r-rcolorbrewer r-scales))
956 (home-page "https://cran.r-project.org/web/packages/pheatmap")
957 (synopsis "Pretty heatmaps")
959 "This package provides an implementation of heatmaps that offers more
960 control over dimensions and appearance.")
961 (license license:gpl2+)))
963 (define-public r-pnwcolors
970 (uri (cran-uri "PNWColors" version))
973 "1phplnclkficfv8s6wsyrckk4ixzbayiy5iix6dddg40485l9nyj"))))
974 (properties `((upstream-name . "PNWColors")))
975 (build-system r-build-system)
976 (home-page "https://github.com/jakelawlor/PNWColors")
977 (synopsis "Color palettes for data visualizations")
979 "This package provides color palettes. They are checked for colorblind
980 accessibility from hue, saturation, and lightness value scaling using the
981 Chroma.js Color Palette Helper. See @url{https://gka.github.io/palettes}.")
982 (license license:cc0)))
990 (uri (cran-uri "ecp" version))
993 "0n602jssl6rf596nwm6hbl7s9vdlqi20w8mrhxicj373mw5v22m8"))))
994 (build-system r-build-system)
997 (home-page "https://cran.r-project.org/web/packages/ecp/")
998 (synopsis "Multiple change-point analysis of multivariate data")
1000 "This package implements various procedures for finding multiple
1001 change-points. Two methods make use of dynamic programming and pruning, with
1002 no distributional assumptions other than the existence of certain absolute
1003 moments in one method. Hierarchical and exact search methods are included.
1004 All methods return the set of estimated change-points as well as other summary
1006 (license license:gpl2+)))
1008 (define-public r-ellipsis
1015 (uri (cran-uri "ellipsis" version))
1018 "0n0mm9jngklv7j9wa64jdji035z0smmnsp2dfwcz9isrxgjnc0m9"))))
1019 (build-system r-build-system)
1022 (home-page "https://github.com/hadley/ellipsis")
1023 (synopsis "Tools for working with additional arguments")
1025 "In S3 generics, it's useful to take @code{...} so that methods can have
1026 additional arguments. But this flexibility comes at a cost: misspelled
1027 arguments will be silently ignored. The @code{ellipsis} package is an
1028 experiment that allows a generic to warn if any arguments passed in @code{...}
1030 (license license:gpl3)))
1032 (define-public r-grr
1039 (uri (cran-uri "grr" version))
1042 "0arbcgrvhkwb5xk4nry1ffg2qj0v8ivhjghdr505ib4357g0c9i9"))))
1043 (build-system r-build-system)
1044 (home-page "https://cran.r-project.org/web/packages/grr")
1045 (synopsis "Alternative implementations of base R functions")
1047 "This package provides alternative implementations of some base R
1048 functions, including @code{sort}, @code{order}, and @code{match}. The
1049 functions are simplified but can be faster or have other advantages.")
1050 (license license:gpl3)))
1052 (define-public r-matrix-utils
1054 (name "r-matrix-utils")
1059 (uri (cran-uri "Matrix.utils" version))
1062 "0a5fq1scykqk0kc9j051j6fix6j2dqwz5wbgb0amaxsiywz9vigb"))))
1063 (properties `((upstream-name . "Matrix.utils")))
1064 (build-system r-build-system)
1066 (list r-grr r-matrix))
1067 (home-page "https://github.com/cvarrichio/Matrix.utils")
1069 "Data.frame-Like Operations on Sparse and Dense Matrix Objects")
1071 "This package implements data manipulation methods such as @code{cast},
1072 @code{aggregate}, and @code{merge}/@code{join} for Matrix and Matrix-like
1074 (license license:gpl3)))
1076 (define-public r-mboost
1082 (uri (cran-uri "mboost" version))
1085 "0yg07fdd1sbjfhhxn1dqgph2vzqyq7l52cdk5iq2a2zy1vh176yg"))))
1086 (build-system r-build-system)
1095 (home-page "https://github.com/boost-R/mboost")
1096 (synopsis "Model-based boosting")
1098 "This package provides a functional gradient descent algorithm (boosting)
1099 for optimizing general risk functions utilizing component-wise (penalised)
1100 least squares estimates or regression trees as base-learners for fitting
1101 generalized linear, additive and interaction models to potentially
1102 high-dimensional data.")
1103 (license license:gpl2)))
1105 (define-public r-shadowtext
1107 (name "r-shadowtext")
1111 (uri (cran-uri "shadowtext" version))
1114 "01h0w3b02r8snjkx5sxkf2x8xm4gd0r8jm27xqz9cv6hgqfmh1pb"))))
1115 (properties `((upstream-name . "shadowtext")))
1116 (build-system r-build-system)
1118 (list r-ggplot2 r-scales))
1121 (home-page "https://github.com/GuangchuangYu/shadowtext/")
1122 (synopsis "Shadow text grob and layer")
1123 (description "This package implements @code{shadowtextGrob()} for
1124 @code{grid} and @code{geom_shadowtext()} layer for @code{ggplot2}.
1125 These functions draw text grob with background shadow.")
1126 (license license:artistic2.0)))
1128 (define-public r-sys
1135 (uri (cran-uri "sys" version))
1138 "11q4zmx62w44p1j34frwmrsp23mc7l4n354i0zyziw92yax8zy0p"))))
1139 (build-system r-build-system)
1140 (home-page "https://github.com/jeroen/sys")
1141 (synopsis "Powerful and reliable tools for running system commands in R")
1143 "This package provides drop-in replacements for the base @code{system2()}
1144 function with fine control and consistent behavior across platforms. It
1145 supports clean interruption, timeout, background tasks, and streaming STDIN /
1146 STDOUT / STDERR over binary or text connections. The package also provides
1147 functions for evaluating expressions inside a temporary fork. Such
1148 evaluations have no side effects on the main R process, and support reliable
1149 interrupts and timeouts. This provides the basis for a sandboxing
1151 (license license:expat)))
1153 (define-public r-ashr
1159 (uri (cran-uri "ashr" version))
1162 "1rqb5j30ylaf1h4l66x4jxyn5inrvhc42d90qd5mgkxsq0ghdlr4"))))
1163 (properties `((upstream-name . "ashr")))
1164 (build-system r-build-system)
1175 (home-page "https://github.com/stephens999/ashr")
1176 (synopsis "Methods for adaptive shrinkage, using empirical bayes")
1177 (description "This package implements an empirical Bayes approach for
1178 large-scale hypothesis testing and false discovery rate estimation.")
1179 (license license:gpl3+)))
1181 (define-public r-askpass
1188 (uri (cran-uri "askpass" version))
1191 "07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
1192 (build-system r-build-system)
1193 (propagated-inputs (list r-sys))
1194 (home-page "https://github.com/jeroen/askpass")
1195 (synopsis "Safe password entry for R")
1197 "This package provides cross-platform utilities for prompting the user
1198 for credentials or a passphrase, for example to authenticate with a server or
1199 read a protected key.")
1200 (license license:expat)))
1202 (define-public r-astsa
1209 (uri (cran-uri "astsa" version))
1211 (base32 "09zx2q419p0b1c336ybh4i62v5dvn3sp39dxn5kwlrqchjj7f5z6"))))
1212 (properties `((upstream-name . "astsa")))
1213 (build-system r-build-system)
1214 (home-page "https://github.com/nickpoison/astsa/")
1215 (synopsis "Applied statistical time series analysis")
1217 "This package provides data sets and scripts to accompany Time Series
1218 Analysis and Its Applications: With R Examples (4th ed), by R.H. Shumway and
1219 D.S. Stoffer. Springer Texts in Statistics, 2017,
1220 @url{https://doi.org/10.1007/978-3-319-52452-8}, and Time Series: A Data
1221 Analysis Approach Using R. Chapman-Hall, 2019,
1222 @url{https://doi.org/10.1201/9780429273285}.")
1223 (license license:gpl3)))
1225 (define-public r-vegan
1232 (uri (cran-uri "vegan" version))
1235 "0aj6m9l1vkh32sar6fyvq4p8j4h2f2f347w1300qnzgaa5lmhfz6"))))
1236 (build-system r-build-system)
1238 (list r-knitr ; needed for vignettes
1241 (list r-cluster r-lattice r-mass r-mgcv r-permute))
1242 (home-page "https://cran.r-project.org/web/packages/vegan")
1243 (synopsis "Functions for community ecology")
1245 "The vegan package provides tools for descriptive community ecology. It
1246 has most basic functions of diversity analysis, community ordination and
1247 dissimilarity analysis. Most of its multivariate tools can be used for other
1248 data types as well.")
1249 (license license:gpl2+)))
1251 (define-public r-tidyverse
1253 (name "r-tidyverse")
1258 (uri (cran-uri "tidyverse" version))
1261 "0ck6xmsw5p168jmw2fqv79fzfnw5jckfra7mfii261j6kl89bkw3"))))
1262 (build-system r-build-system)
1295 (home-page "https://tidyverse.tidyverse.org")
1296 (synopsis "Install and load packages from the \"Tidyverse\"")
1298 "The @code{tidyverse} is a set of packages that work in harmony because
1299 they share common data representations and API design. This package is
1300 designed to make it easy to install and load multiple tidyverse packages in a
1302 (license license:gpl3)))
1304 (define-public r-rvest
1311 (uri (cran-uri "rvest" version))
1313 (base32 "1905vxgnj3q09l1wf6rwxpbpydznp06nbkrclnc05j2415z4gfw9"))))
1314 (build-system r-build-system)
1325 (home-page "https://github.com/hadley/rvest")
1326 (synopsis "Simple web scraping for R")
1328 "@code{r-rvest} helps you scrape information from web pages. It is
1329 designed to work with @code{magrittr} to make it easy to express common web
1330 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
1331 (license license:gpl3)))
1333 (define-public r-selectr
1340 (uri (cran-uri "selectr" version))
1342 (base32 "09y1n3iy297g49xlpl7xrjpwgnm57pskx5991lyfcpizbz8ax22m"))))
1343 (build-system r-build-system)
1345 (list r-stringr r-r6))
1346 (home-page "https://sjp.co.nz/projects/selectr/")
1347 (synopsis "Translate CSS selectors to XPath expressions")
1349 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
1350 expression. This allows you to use CSS selectors when working with the XML
1351 package as it can only evaluate XPath expressions. Also provided are
1352 convenience functions useful for using CSS selectors on XML nodes. This
1353 package is a port of the Python package @code{cssselect}.")
1354 (license license:bsd-3)))
1356 (define-public r-reprex
1363 (uri (cran-uri "reprex" version))
1366 "09k4rasp7mz6n796dsklcbc5l7prljiznrm7fra16qybr9kqcv8f"))))
1367 (build-system r-build-system)
1381 (home-page "https://github.com/tidyverse/reprex")
1382 (synopsis "Prepare reproducible R code examples for sharing")
1384 "This package provides a convenience wrapper that uses the
1385 @code{rmarkdown} package to render small snippets of code to target formats
1386 that include both code and output. The goal is to encourage the sharing of
1387 small, reproducible, and runnable examples on code-oriented websites or email.
1388 @code{reprex} also extracts clean, runnable R code from various common formats,
1389 such as copy/paste from an R session.")
1390 (license license:expat)))
1392 (define-public r-reordercluster
1394 (name "r-reordercluster")
1398 (uri (cran-uri "ReorderCluster" version))
1401 "0ss750frzvj0bm1w7zblmcsjpszhnbffwlkaw31sm003lbx9hy58"))))
1402 (build-system r-build-system)
1404 (list r-gplots r-rcpp))
1405 (home-page "https://cran.r-project.org/web/packages/ReorderCluster")
1406 (synopsis "Reordering the dendrogram according to the class labels")
1407 (description "This package provides tools for performing the leaf reordering
1408 for the dendrogram that preserves the hierarchical clustering result and at the
1409 same time tries to group instances from the same class together.")
1410 (license license:gpl3+)))
1412 (define-public r-callr
1419 (uri (cran-uri "callr" version))
1422 "02inaf3c7b0hikii7p2zwaphrq5myv4in92d9jxd1ilmhla5awnn"))))
1423 (build-system r-build-system)
1425 (list r-r6 r-processx))
1426 (home-page "https://github.com/r-lib/callr#readme")
1427 (synopsis "Call R from R")
1429 "It is sometimes useful to perform a computation in a separate R process,
1430 without affecting the current R process at all. This package does exactly
1432 (license license:expat)))
1434 (define-public r-depmixs4
1440 (uri (cran-uri "depmixS4" version))
1443 "1pacvhw5m4fsk3ysbal50fdqbvlaz8ywyqp6bn1wh42wipqbb2i8"))))
1445 (list r-nnet r-nlme r-mass r-rsolnp))
1446 (build-system r-build-system)
1447 (home-page "https://cran.r-project.org/web/packages/depmixS4/")
1448 (synopsis "Dependent Mixture Models")
1449 (description "This package fits latent (hidden) Markov models on mixed
1450 categorical and continuous (time series) data, otherwise known as dependent
1452 (license license:gpl2+)))
1454 (define-public r-readxl
1461 (uri (cran-uri "readxl" version))
1464 "15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
1465 (build-system r-build-system)
1467 (list r-cellranger r-progress r-rcpp r-tibble))
1468 (home-page "https://readxl.tidyverse.org")
1469 (synopsis "Read Excel files")
1471 "This package lets you import Excel files into R. It supports
1472 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
1473 the embedded @code{RapidXML} C++ library.")
1474 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
1475 ;; 'rapidxml' which is Boost.
1476 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
1478 (define-public r-model4you
1480 (name "r-model4you")
1484 (uri (cran-uri "model4you" version))
1487 "0pni9v3nradvy8sp2m07903vc7z610xrh426lf19dxss12kgrfi8"))))
1488 (build-system r-build-system)
1496 (home-page "https://cran.r-project.org/web/packages/model4you/")
1497 (synopsis "Stratified and personalised models based on trees and forests")
1499 "This package provides procedures for model-based trees for subgroup
1500 analyses in clinical trials and model-based forests for the estimation and
1501 prediction of personalised treatment effects. Currently partitioning of linear
1502 models, @code{lm()}, generalised linear models, @code{glm()}, and
1503 Weibull models, @code{survreg()}, are supported. Advanced plotting functionality is
1504 supported for the trees and a test for parameter heterogeneity is provided for
1505 the personalised models.")
1506 (license license:gpl2+)))
1508 (define-public r-modelr
1515 (uri (cran-uri "modelr" version))
1518 "1i31nff7bqibk6r4hhd4j1vzwbyaf8493v0bjaagn36njmysfnw2"))))
1519 (build-system r-build-system)
1529 (home-page "https://github.com/tidyverse/modelr")
1530 (synopsis "Helper functions for modelling in pipelines")
1532 "Functions for modelling that help you seamlessly integrate modelling
1533 into a pipeline of data manipulation and visualisation.")
1534 (license license:gpl3)))
1536 (define-public r-hmm
1542 (uri (cran-uri "HMM" version))
1545 "0z0hcqfixx1l2a6d3lpy5hmh0n4gjgs0jnck441akpp3vh37glzw"))))
1546 (properties `((upstream-name . "HMM")))
1547 (build-system r-build-system)
1548 (home-page "https://cran.r-project.org/web/packages/HMM/")
1549 (synopsis "Hidden Markov Models")
1550 (description "This package provides an easy to use library to setup, apply
1551 and make inference with discrete time and discrete space hidden Markov
1553 (license license:gpl2+)))
1555 (define-public r-hiddenmarkov
1557 (name "r-hiddenmarkov")
1561 (uri (cran-uri "HiddenMarkov" version))
1564 "05dm3nl0ffsz2ziw3bz5bivyxk7r5bxs8xhky3hz660qaqzd51ki"))))
1565 (build-system r-build-system)
1568 (home-page "https://cran.r-project.org/web/packages/HiddenMarkov/")
1569 (synopsis "Hidden markov models for R")
1570 (description "This package contains functions for the analysis of Discrete
1571 Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated
1572 Poisson Process. It includes functions for simulation, parameter estimation,
1573 and the Viterbi algorithm. The algorithms are based of those of Walter
1575 (license license:gpl2+)))
1577 (define-public r-httpuv
1583 (uri (cran-uri "httpuv" version))
1586 "0mlilxh2mlrsbbrncla2rg02crr8nnajv649d8whx7ayr8lkdxpm"))
1587 ;; Unvendor bundled libraries. As of 1.5.4 the vendored libuv
1588 ;; only contains fixes for building on Solaris.
1589 (patches (search-patches "r-httpuv-1.5.5-unvendor-libuv.patch"))
1590 (modules '((guix build utils)))
1591 ;; Cannot unbundle http-parser, because it contains local
1594 '(delete-file-recursively "src/libuv"))))
1595 (build-system r-build-system)
1598 (modify-phases %standard-phases
1599 (add-after 'unpack 'unbundle-libuv
1600 (lambda* (#:key outputs #:allow-other-keys)
1601 (substitute* (find-files "src" "\\.cpp$|\\.h$")
1602 (("\"libuv/include/uv\\.h\"")
1604 ;; Fix https://github.com/rstudio/httpuv/issues/282
1605 (substitute* "src/http.cpp"
1606 (("uv_pipe_init\\(pLoop, &pSocket->handle\\.pipe, true\\);")
1607 "uv_pipe_init(pLoop, &pSocket->handle.pipe, 0);")))))))
1611 (list r-later r-promises r-r6 r-rcpp))
1612 (home-page "https://github.com/rstudio/httpuv")
1613 (synopsis "HTTP and WebSocket server library for R")
1615 "The httpuv package provides low-level socket and protocol support for
1616 handling HTTP and WebSocket requests directly from within R. It is primarily
1617 intended as a building block for other packages, rather than making it
1618 particularly easy to create complete web applications using httpuv alone.")
1619 ;; This package includes third-party code that was originally released
1620 ;; under various non-copyleft licenses. Full licensing information can be
1621 ;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
1622 (license license:gpl3+)))
1624 (define-public r-jsonlite
1630 (uri (cran-uri "jsonlite" version))
1633 "0n65x9ifxjssb000g7psgh9pgl374ax2ni1if9kp3sx56rg0n2kj"))))
1634 (build-system r-build-system)
1637 (home-page "https://arxiv.org/abs/1403.2805")
1638 (synopsis "Robust, high performance JSON parser and generator for R")
1640 "The jsonlite package provides a fast JSON parser and generator optimized
1641 for statistical data and the web. It offers flexible, robust, high
1642 performance tools for working with JSON in R and is particularly powerful for
1643 building pipelines and interacting with a web API. In addition to converting
1644 JSON data from/to R objects, jsonlite contains functions to stream, validate,
1645 and prettify JSON data. The unit tests included with the package verify that
1646 all edge cases are encoded and decoded consistently for use with dynamic data
1647 in systems and applications.")
1648 (license license:expat)))
1650 (define-public r-servr
1656 (uri (cran-uri "servr" version))
1659 "11x0857m3xzdbzr4z0vx4fcdk36arfagyf2qgamvprich0qisknr"))))
1660 (build-system r-build-system)
1662 (list r-httpuv r-jsonlite r-mime r-xfun))
1663 (home-page "https://github.com/yihui/servr")
1664 (synopsis "Simple HTTP server to serve static files or dynamic documents")
1666 "Servr provides an HTTP server in R to serve static files, or dynamic
1667 documents that can be converted to HTML files (e.g., R Markdown) under a given
1669 (license license:expat)))
1671 (define-public r-howmany
1677 (uri (cran-uri "howmany" version))
1680 "045ck8qahfg2swbgyf7dpl32ryq1m4sbalhr7m5qdgpm62vz8h7f"))))
1681 (build-system r-build-system)
1682 (home-page "https://cran.r-project.org/web/packages/howmany/")
1683 (synopsis "Lower bound for the number of correct rejections")
1684 (description "When testing multiple hypotheses simultaneously, this package
1685 provides functionality to calculate a lower bound for the number of correct
1686 rejections (as a function of the number of rejected hypotheses), which holds
1687 simultaneously -with high probability- for all possible number of rejections.
1688 As a special case, a lower bound for the total number of false null hypotheses
1689 can be inferred. Dependent test statistics can be handled for multiple tests
1690 of associations. For independent test statistics, it is sufficient to provide
1691 a list of p-values.")
1692 (license license:gpl2+)))
1694 (define-public r-htmltools
1696 (name "r-htmltools")
1700 (uri (cran-uri "htmltools" version))
1703 "1yv74ydyqm28gfhimmr7825sj1iaawpwsnzq05c2ma756q2dbivx"))))
1704 (build-system r-build-system)
1706 (list r-base64enc r-digest r-fastmap r-rlang))
1707 (home-page "https://cran.r-project.org/web/packages/htmltools")
1708 (synopsis "R tools for HTML")
1710 "This package provides tools for HTML generation and output in R.")
1711 (license license:expat)))
1713 (define-public r-htmlwidgets
1715 (name "r-htmlwidgets")
1719 (uri (cran-uri "htmlwidgets" version))
1722 "1hgz8sx8xrvfcdwa4q15k942w4qsqg8lyxbbf7qyfzbi807wcgqs"))))
1723 (build-system r-build-system)
1725 (list r-htmltools r-jsonlite r-yaml))
1728 (home-page "https://github.com/ramnathv/htmlwidgets")
1729 (synopsis "HTML Widgets for R")
1731 "HTML widgets is a framework for creating HTML widgets that render in
1732 various contexts including the R console, R Markdown documents, and Shiny web
1734 (license license:expat)))
1736 (define-public r-htmltable
1738 (name "r-htmltable")
1743 (uri (cran-uri "htmlTable" version))
1745 (base32 "17csp0ry4iy4m5xy271dn5wd81v4p03l79swmvlfxkvpdmhvb8jc"))))
1746 (properties `((upstream-name . "htmlTable")))
1747 (build-system r-build-system)
1758 (home-page "http://gforge.se/packages/")
1759 (synopsis "Advanced tables for Markdown/HTML")
1761 "This package provides functions to build tables with advanced layout
1762 elements such as row spanners, column spanners, table spanners, zebra
1763 striping, and more. While allowing advanced layout, the underlying
1764 CSS-structure is simple in order to maximize compatibility with word
1765 processors such as LibreOffice. The package also contains a few text
1766 formatting functions that help outputting text compatible with HTML or
1768 (license license:gpl3+)))
1770 (define-public r-curl
1776 (uri (cran-uri "curl" version))
1779 "0s55022hy8shjm1pzax1dqzrg20bv4nvlwnjnddk3dp89g5zmcch"))))
1780 (build-system r-build-system)
1783 (modify-phases %standard-phases
1784 ;; The environment variable CURL_CA_BUNDLE is only respected when
1785 ;; running Windows, so we disable the platform checks.
1786 ;; This can be removed once the libcurl has been patched.
1787 (add-after 'unpack 'allow-CURL_CA_BUNDLE
1789 (substitute* "R/onload.R"
1790 (("if \\(!grepl\\(\"mingw\".*")
1792 (substitute* "src/handle.c"
1793 (("/\\* Only set" m)
1795 const char *_ca_bundle = getenv(\"CURL_CA_BUNDLE\");
1796 if(_ca_bundle != NULL) { curl_easy_setopt(handle, CURLOPT_CAINFO, _ca_bundle); }
1801 (list pkg-config r-knitr))
1802 (home-page "https://github.com/jeroenooms/curl")
1803 (synopsis "HTTP client for R")
1805 "The @code{curl()} and @code{curl_download()} functions provide highly
1806 configurable drop-in replacements for base @code{url()} and
1807 @code{download.file()} with better performance, support for encryption, gzip
1808 compression, authentication, and other @code{libcurl} goodies. The core of
1809 the package implements a framework for performing fully customized requests
1810 where data can be processed either in memory, on disk, or streaming via the
1811 callback or connection interfaces.")
1812 (license license:expat)))
1814 (define-public r-hwriter
1821 (uri (cran-uri "hwriter" version))
1824 "0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
1825 (build-system r-build-system)
1826 (home-page "https://cran.r-project.org/web/packages/hwriter")
1827 (synopsis "Output R objects in HTML format")
1829 "This package provides easy-to-use and versatile functions to output R
1830 objects in HTML format.")
1831 (license license:lgpl2.1+)))
1833 (define-public r-rjson
1840 (uri (cran-uri "rjson" version))
1843 "1qm27r1w677zg31gsiln60hcciszbymkw78cnaq7s36cbk9mcawq"))))
1844 (build-system r-build-system)
1845 (home-page "https://cran.r-project.org/web/packages/rjson")
1846 (synopsis "JSON library for R")
1848 "This package provides functions to convert R objects into JSON objects
1850 (license license:gpl2+)))
1852 (define-public r-fastmap
1859 (uri (cran-uri "fastmap" version))
1862 "0aw29hnq3ppn7bsnwg9d9sp84k1cvq30lrmfzqn315n0nhkfa4wi"))))
1863 (properties `((upstream-name . "fastmap")))
1864 (build-system r-build-system)
1865 (home-page "https://r-lib.github.io/fastmap/")
1866 (synopsis "Fast implementation of a key-value store")
1868 "This package provides a fast implementation of a key-value store.
1869 Environments are commonly used as key-value stores, but every time a new key
1870 is used, it is added to R's global symbol table, causing a small amount of
1871 memory leakage. This can be problematic in cases where many different keys
1872 are used. Fastmap avoids this memory leak issue by implementing the map using
1873 data structures in C++.")
1874 (license license:expat)))
1876 (define-public r-fastghquad
1878 (name "r-fastghquad")
1883 (uri (cran-uri "fastGHQuad" version))
1886 "1rjia8wggadr9xwxcmzmal0rc4g6pa3dr5888fbbnb6abl8b2lrj"))))
1887 (properties `((upstream-name . "fastGHQuad")))
1888 (build-system r-build-system)
1891 (home-page "https://github.com/awblocker/fastGHQuad")
1892 (synopsis "Fast Rcpp implementation of Gauss-Hermite Quadrature")
1894 "This package implements numerically-stable Gauss-Hermite quadrature
1895 rules and utility functions for adaptive GH quadrature.")
1896 (license license:expat)))
1898 (define-public r-rstpm2
1905 (uri (cran-uri "rstpm2" version))
1908 "0c6l3z250b2kn6mh2xyb0bd2y5nsbj11n9xfi51dac9s8xq3v7m4"))))
1909 (properties `((upstream-name . "rstpm2")))
1910 (build-system r-build-system)
1922 (home-page "https://github.com/mclements/rstpm2")
1923 (synopsis "Link-based survival models")
1925 "This package provides R implementations of @dfn{generalized survival
1926 models} (GSMs), smooth @dfn{accelerated failure time} (AFT) models and Markov
1927 multi-state models.")
1928 ;; One of these licenses
1929 (license (list license:gpl2 license:gpl3))))
1931 ;; This package includes minified JavaScript files. When upgrading please
1932 ;; check that there are no new minified JavaScript files.
1933 (define-public r-jquerylib
1935 (name "r-jquerylib")
1940 (uri (cran-uri "jquerylib" version))
1943 "04a40v4znpj98j7y6009d74a6g9dchj5rr3p08cgz9p3rlfw3g7h"))
1945 '(for-each delete-file
1946 '("inst/lib/1.12.4/jquery-1.12.4.min.js"
1947 "inst/lib/2.2.4/jquery-2.2.4.min.js"
1948 "inst/lib/3.6.0/jquery-3.6.0.min.js")))))
1949 (properties `((upstream-name . "jquerylib")))
1950 (build-system r-build-system)
1952 `(#:modules ((guix build utils)
1953 (guix build r-build-system)
1956 (modify-phases %standard-phases
1957 (add-after 'unpack 'process-javascript
1958 (lambda* (#:key inputs #:allow-other-keys)
1959 (with-directory-excursion "inst/lib/"
1963 `(("1.12.4/jquery-1.12.4.js"
1964 "1.12.4/jquery-1.12.4.min.js")
1965 ("2.2.4/jquery-2.2.4.js"
1966 "2.2.4/jquery-2.2.4.min.js")
1967 ("3.6.0/jquery-3.6.0.js"
1968 "3.6.0/jquery-3.6.0.min.js"))))
1969 (lambda (sources targets)
1970 (for-each (lambda (source target)
1971 (format #t "Processing ~a --> ~a~%"
1973 (invoke "esbuild" source "--minify"
1974 (string-append "--outfile=" target)))
1975 sources targets)))))))))
1980 (home-page "https://cran.r-project.org/package=jquerylib")
1981 (synopsis "Obtain jQuery as an HTML dependency object")
1983 "Obtain any major version of jQuery and use it in any webpage generated
1984 by htmltools (e.g. shiny, htmlwidgets, and rmarkdown). Most R users don't
1985 need to use this package directly, but other R packages (e.g. shiny,
1986 rmarkdown, etc.) depend on this package to avoid bundling redundant copies of
1988 (license license:expat)))
1990 (define-public r-sass
1997 (uri (cran-uri "sass" version))
2000 "0axw358bbk3vxsqg3wq0bz3xigasa6af8fxvi2ga8hli4cawl1kx"))))
2001 (properties `((upstream-name . "sass")))
2002 (build-system r-build-system)
2004 (list r-fs r-htmltools r-r6 r-rappdirs r-rlang))
2005 (native-inputs (list r-knitr))
2006 (home-page "https://github.com/rstudio/sass")
2007 (synopsis "Syntactically Awesome Style Sheets (SASS)")
2009 "This package provides an SCSS compiler, powered by the libsass library.
2010 With this, R developers can use variables, inheritance, and functions to
2011 generate dynamic style sheets. The package uses the Sass CSS extension
2012 language, which is stable, powerful, and CSS compatible.")
2013 (license license:expat)))
2015 ;; This package includes minified JavaScript files. When upgrading please
2016 ;; check that there are no new minified JavaScript files.
2017 (define-public r-bslib
2024 (uri (cran-uri "bslib" version))
2027 "0jcqklry1nkibz0sydsz5xdsnb4wnrrhvmyr9ji3k45bbipbap2z"))
2029 '(for-each delete-file
2030 '("inst/lib/bs-a11y-p/plugins/js/bootstrap-accessibility.min.js"
2031 "inst/lib/bs-colorpicker/js/bootstrap-colorpicker.min.js"
2032 "inst/lib/bs3/assets/javascripts/bootstrap.min.js"
2033 "inst/lib/bs4/dist/js/bootstrap.bundle.min.js"
2034 "inst/lib/bs5/dist/js/bootstrap.bundle.min.js")))))
2035 (properties `((upstream-name . "bslib")))
2036 (build-system r-build-system)
2038 `(#:modules ((guix build utils)
2039 (guix build r-build-system)
2042 (modify-phases %standard-phases
2043 (add-after 'unpack 'process-javascript
2044 (lambda* (#:key inputs #:allow-other-keys)
2045 (with-directory-excursion "inst/lib/"
2049 `(("bs-a11y-p/plugins/js/bootstrap-accessibility.js"
2050 "bs-a11y-p/plugins/js/bootstrap-accessibility.min.js")
2051 ("bs-colorpicker/js/bootstrap-colorpicker.js"
2052 "bs-colorpicker/js/bootstrap-colorpicker.min.js")
2053 ("bs3/assets/javascripts/bootstrap.js"
2054 "bs3/assets/javascripts/bootstrap.min.js")
2055 (,(assoc-ref inputs "js-bootstrap4-bundle")
2056 "bs4/dist/js/bootstrap.bundle.min.js")
2057 (,(assoc-ref inputs "js-bootstrap5-bundle")
2058 "bs5/dist/js/bootstrap.bundle.min.js"))))
2059 (lambda (sources targets)
2060 (for-each (lambda (source target)
2061 (format #t "Processing ~a --> ~a~%"
2063 (invoke "esbuild" source "--minify"
2064 (string-append "--outfile=" target)))
2065 sources targets)))))))))
2067 (list r-htmltools r-jquerylib r-jsonlite r-rlang r-sass))
2069 `(("esbuild" ,esbuild)
2070 ("js-bootstrap4-bundle"
2073 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v4.6.0/dist/js/bootstrap.bundle.js")
2076 "04abvgp923w36qfqkkl2syim3bl119nwxbgials90z1jyb8jgss1"))))
2077 ("js-bootstrap5-bundle"
2080 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v5.0.2/dist/js/bootstrap.bundle.js")
2083 "06vin94nqw1vzs4zrqcms8z9js9fckbj8gwyx07awm8jkjhnqfhl"))))))
2084 (home-page "https://rstudio.github.io/bslib/")
2085 (synopsis "Custom Bootstrap Sass themes for shiny and rmarkdown")
2087 "This package simplifies custom CSS styling of both shiny and rmarkdown
2088 via Bootstrap Sass. It supports both Bootstrap 3 and 4 as well as their
2089 various Bootswatch themes. An interactive widget is also provided for
2090 previewing themes in real time.")
2091 (license license:expat)))
2093 ;; This package includes minified JavaScript files. When upgrading please
2094 ;; check that there are no new minified JavaScript files.
2095 (define-public r-shiny
2103 (url "https://github.com/rstudio/shiny")
2104 (commit (string-append "v" version))))
2105 (file-name (git-file-name name version))
2108 "0wvc6jlgs41p05wbk8gahnl7sfnc4hpliyh9dbi5w52ngsg6wcr7"))
2110 '(for-each delete-file
2111 '("inst/www/shared/bootstrap/js/bootstrap.min.js"
2112 "inst/www/shared/bootstrap/accessibility/js/bootstrap-accessibility.min.js" ; TODO
2113 "inst/www/shared/datatables/js/jquery.dataTables.min.js"
2114 "inst/www/shared/datepicker/js/bootstrap-datepicker.min.js"
2115 "inst/www/shared/highlight/highlight.pack.js"
2116 "inst/www/shared/ionrangeslider/js/ion.rangeSlider.min.js"
2117 "inst/www/shared/jquery.min.js"
2118 "inst/www/shared/jqueryui/jquery-ui.min.js"
2119 "inst/www/shared/legacy/jquery.min.js"
2120 "inst/www/shared/selectize/accessibility/js/selectize-plugin-a11y.min.js"
2121 "inst/www/shared/selectize/js/selectize.min.js"
2122 "inst/www/shared/shiny.min.js"
2123 "inst/www/shared/showdown/compressed/showdown.js"
2124 "inst/www/shared/strftime/strftime-min.js")))))
2125 (build-system r-build-system)
2127 `(#:modules ((guix build r-build-system)
2128 (guix build minify-build-system)
2131 #:imported-modules (,@%r-build-system-modules
2132 (guix build minify-build-system))
2134 (modify-phases (@ (guix build r-build-system) %standard-phases)
2135 (add-after 'unpack 'replace-bundled-minified-JavaScript
2136 (lambda* (#:key inputs #:allow-other-keys)
2137 (let ((replace-file (lambda (old new)
2138 (format #t "replacing ~a with ~a\n" old new)
2139 (symlink new old))))
2140 ;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
2141 ;; contain just data. They are not minified code, so we don't
2143 (with-directory-excursion "inst/www/shared"
2144 (replace-file "strftime/strftime-min.js"
2145 (search-input-file inputs
2146 "/share/javascript/strftime.min.js"))
2147 (replace-file "highlight/highlight.pack.js"
2148 (search-input-file inputs
2149 "/share/javascript/highlight.min.js"))
2150 (replace-file "datatables/js/jquery.dataTables.min.js"
2151 (search-input-file inputs
2152 "/share/javascript/jquery.dataTables.min.js"))
2153 (replace-file "selectize/js/selectize.min.js"
2154 (search-input-file inputs
2155 "/share/javascript/selectize.min.js"))
2156 (for-each (match-lambda
2158 (minify source #:target target)))
2159 `(("jqueryui/jquery-ui.js" .
2160 "jqueryui/jquery-ui.min.js")
2161 ("datepicker/js/bootstrap-datepicker.js" .
2162 "datepicker/js/bootstrap-datepicker.min.js")
2163 ("ionrangeslider/js/ion.rangeSlider.js" .
2164 "ionrangeslider/js/ion.rangeSlider.min.js")
2165 ("bootstrap/js/bootstrap.js" .
2166 "bootstrap/js/bootstrap.min.js")
2167 (,(assoc-ref inputs "js-bootstrap-accessibility") .
2168 "bootstrap/accessibility/js/bootstrap-accessibility.min.js")
2173 ("legacy/jquery.js" .
2174 "legacy/jquery.min.js")
2175 ("selectize/accessibility/js/selectize-plugin-a11y.js" .
2176 "selectize/accessibility/js/selectize-plugin-a11y.min.js")
2177 ("showdown/src/showdown.js" .
2178 "showdown/compressed/showdown.js"))))))))))
2201 (list js-datatables js-selectize js-strftime js-highlight))
2203 `(("uglifyjs" ,node-uglify-js)
2204 ("gfortran" ,gfortran)
2205 ("js-bootstrap-accessibility"
2208 (uri "https://raw.githubusercontent.com/paypal/bootstrap-accessibility-plugin/\
2209 v1.0.7/_site/plugins/js/bootstrap-accessibility.js")
2212 "1489wyzwrpf86y7vhc13n4v3mszmsfybhd3f75jkpnbvyp5sncm8"))))))
2213 (home-page "https://shiny.rstudio.com")
2214 (synopsis "Easy interactive web applications with R")
2216 "Makes it incredibly easy to build interactive web applications
2217 with R. Automatic \"reactive\" binding between inputs and outputs and
2218 extensive prebuilt widgets make it possible to build beautiful,
2219 responsive, and powerful applications with minimal effort.")
2220 (license license:artistic2.0)))
2222 (define-public r-shinyhelper
2224 (name "r-shinyhelper")
2229 (uri (cran-uri "shinyhelper" version))
2231 (base32 "1c4hvf19j3yyh8r12nx85ldkxs89g98q74csnqs5ml5l79a65vgp"))))
2232 (properties `((upstream-name . "shinyhelper")))
2233 (build-system r-build-system)
2234 (propagated-inputs (list r-markdown r-shiny))
2235 (home-page "https://cran.r-project.org/package=shinyhelper")
2236 (synopsis "Easily add Markdown help files to shiny app elements")
2238 "This package creates a lightweight way to add markdown helpfiles to
2239 Shiny apps, using modal dialog boxes, with no need to observe each help button
2241 (license license:gpl3)))
2243 ;; This package includes minified JavaScript files. When upgrading please
2244 ;; check that there are no new minified JavaScript files.
2245 (define-public r-shinytree
2247 (name "r-shinytree")
2252 (uri (cran-uri "shinyTree" version))
2255 "0jfx2capckv7hf2yx3fn8i4rcmhi222ah91jnmhg497x8wgz31s3"))
2256 (modules '((guix build utils)))
2259 ;; Delete minified JavaScript
2260 (for-each delete-file
2261 '("inst/www/jsTree-3.3.7/libs/require.js"
2262 "inst/www/jsTree-3.3.7/libs/jquery.js"
2263 "inst/www/jsTree-3.3.7/jstree.min.js"))
2265 (properties `((upstream-name . "shinyTree")))
2266 (build-system r-build-system)
2268 `(#:modules ((guix build utils)
2269 (guix build r-build-system)
2273 (modify-phases %standard-phases
2274 (add-after 'unpack 'replace-minified-javascript
2275 (lambda* (#:key inputs #:allow-other-keys)
2276 (with-directory-excursion "inst/www/jsTree-3.3.7/"
2277 (symlink (search-input-file inputs
2278 "/share/javascript/require.min.js")
2283 `((,(assoc-ref inputs "js-jquery")
2287 (lambda (sources targets)
2288 (for-each (lambda (source target)
2289 (format #t "Processing ~a --> ~a~%"
2291 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
2292 (call-with-output-file target
2294 (dump-port minified port)))))
2298 (list r-htmlwidgets r-jsonlite r-promises r-shiny r-stringr))
2300 (list js-requirejs))
2302 `(("uglifyjs" ,node-uglify-js)
2306 (uri "https://code.jquery.com/jquery-3.3.1.js")
2309 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))))
2310 (home-page "https://cran.r-project.org/web/packages/shinyTree/")
2311 (synopsis "jsTree bindings for Shiny")
2313 "This package exposes R bindings to jsTree, a JavaScript library that
2314 supports interactive trees, to enable rich, editable trees in Shiny.")
2315 (license license:expat)))
2317 (define-public r-shinydashboard
2319 (name "r-shinydashboard")
2323 (uri (cran-uri "shinydashboard" version))
2326 "0hrqkwlpb8rnmp5j74p134g4c4cl16icmwc2ip6k1634fa2y8vm5"))))
2327 (build-system r-build-system)
2328 ;; The directory inst/AdminLTE/ contains a minified JavaScript file.
2329 ;; Regenerate it from the included sources.
2332 (modify-phases %standard-phases
2333 (add-after 'unpack 'generate-minified-javascript
2335 (with-directory-excursion "inst/AdminLTE"
2336 (let ((target "app.min.js")
2338 (format #t "Processing ~a --> ~a~%"
2340 (delete-file target)
2341 (invoke "esbuild" source "--minify"
2342 (string-append "--outfile=" target)))))))))
2344 (list r-htmltools r-promises r-shiny))
2347 (home-page "https://rstudio.github.io/shinydashboard/")
2348 (synopsis "Create dashboards with shiny")
2349 (description "This package provides an extension to the Shiny web
2350 application framework for R, making it easy to create attractive dashboards.")
2351 ;; This package includes software that was released under the Expat
2352 ;; license, but the whole package is released under GPL version 2 or
2354 (license license:gpl2+)))
2356 (define-public r-shinyfiles
2358 (name "r-shinyfiles")
2363 (uri (cran-uri "shinyFiles" version))
2365 (base32 "0f8dfdiar376lx0979ccyghgx5rhr08v5z3z60asrrjsxlq4cs85"))))
2366 (properties `((upstream-name . "shinyFiles")))
2367 (build-system r-build-system)
2369 (list r-fs r-htmltools r-jsonlite r-shiny r-tibble))
2370 (home-page "https://github.com/thomasp85/shinyFiles")
2371 (synopsis "Server-side file system viewer for Shiny")
2373 "This package provides functionality for client-side navigation of the
2374 server side file system in shiny apps. In case the app is running locally
2375 this gives the user direct access to the file system without the need to
2376 \"download\" files to a temporary location. Both file and folder selection as
2377 well as file saving is available.")
2378 (license license:gpl2+)))
2380 (define-public r-shinythemes
2382 (name "r-shinythemes")
2387 (uri (cran-uri "shinythemes" version))
2390 "0qr9bfxw8afxns44i2j4msignf6g5qb2nzpay2lpv343rrlqbmip"))))
2391 (properties `((upstream-name . "shinythemes")))
2392 (build-system r-build-system)
2393 (propagated-inputs (list r-shiny))
2394 (home-page "https://rstudio.github.io/shinythemes/")
2395 (synopsis "Themes for Shiny")
2397 "This package provides themes for use with Shiny. It includes several
2398 Bootstrap themes, which are packaged for use with Shiny applications.")
2399 ;; The package is released under version 3 of the GPL, but it includes
2400 ;; source files that are covered by the Expat license. It also includes
2401 ;; fonts under SIL or the ASL.
2402 (license (list license:gpl3 license:expat
2403 license:silofl1.1 license:asl2.0))))
2405 ;; The package sources include minified variants of d3.js and non-minified
2406 ;; source code of d3-jetpack.
2407 (define-public r-d3r
2414 (uri (cran-uri "d3r" version))
2417 "1qijkllfaaw0lb29j8mappm8jz9kg8gkihxq5wqhb4gabsazdwva"))))
2418 (build-system r-build-system)
2420 `(#:modules ((guix build utils)
2421 (guix build r-build-system)
2424 (modify-phases %standard-phases
2425 (add-after 'unpack 'process-javascript
2426 (lambda* (#:key inputs #:allow-other-keys)
2427 (with-directory-excursion "inst/www/d3/"
2431 `((,(assoc-ref inputs "d3.v3.js")
2432 "v3/dist/d3.min.js")
2433 (,(assoc-ref inputs "d3.v4.js")
2434 "v4/dist/d3.min.js")
2435 (,(assoc-ref inputs "d3.v5.js")
2436 "v5/dist/d3.min.js")
2437 (,(assoc-ref inputs "d3.v6.js")
2438 "v6/dist/d3.min.js")
2439 (,(assoc-ref inputs "d3.v7.js")
2440 "v7/dist/d3.min.js"))))
2441 (lambda (sources targets)
2442 (for-each (lambda (source target)
2443 (format #t "Processing ~a --> ~a~%"
2445 (delete-file target)
2446 (invoke "esbuild" source "--minify"
2447 (string-append "--outfile=" target)))
2448 sources targets)))))))))
2450 (list r-dplyr r-htmltools r-rlang r-tidyr))
2452 `(("esbuild" ,esbuild)
2456 (uri "https://d3js.org/d3.v3.js")
2459 "1arr7sr08vy7wh0nvip2mi7dpyjw4576vf3bm45rp4g5lc1k1x41"))))
2463 (uri "https://d3js.org/d3.v4.js")
2466 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))
2470 (uri "https://d3js.org/d3.v5.js")
2473 "0kxvx5pfagxn6nhavdwsdnzyd26g0z5dsfi1pi5dvcmb0c8ipcdn"))))
2477 (uri "https://d3js.org/d3.v6.js")
2480 "1x6432ca7p1pfxhz3airzw943fincn9izzxkclc1wmphcvv2n2p9"))))
2484 (uri "https://d3js.org/d3.v7.js")
2487 "0sd6vavxs8mx5xyb8xahlqghdiczqd284a7d5wravhqnrj0bw097"))))))
2488 (home-page "https://github.com/timelyportfolio/d3r")
2489 (synopsis "d3.js utilities for R")
2491 "This package provides a suite of functions to help ease the use of the
2492 d3.js visualization library in R. These helpers include
2493 @code{htmltools::htmlDependency} functions, hierarchy builders, and conversion
2494 tools for @code{partykit}, @code{igraph}, @code{table}, and @code{data.frame}
2495 R objects into the JSON format that the d3.js library expects.")
2496 (license license:bsd-3)))
2498 ;; We use the latest commit here because the last release was in 2016 while
2499 ;; the latest commit was in 2018.
2500 (define-public r-sankeyd3
2501 (let ((commit "fd50a74e29056e0d67d75b4d04de47afb2f932bc")
2505 (version (git-version "0.3.2" revision commit))
2510 (url "https://github.com/fbreitwieser/sankeyD3")
2512 (file-name (git-file-name name version))
2515 "0jrcnfax321pszbpjdifnkbrgbjr43bjzvlzv1p5a8wskksqwiyx"))))
2516 (build-system r-build-system)
2518 (list r-d3r r-htmlwidgets r-shiny r-magrittr))
2519 (home-page "https://github.com/fbreitwieser/sankeyD3")
2520 (synopsis "Sankey network graphs from R")
2522 "This package provides an R library to generate Sankey network graphs
2523 in R and Shiny via the D3 visualization library.")
2524 ;; The R code is licensed under GPLv3+. It includes the non-minified
2525 ;; JavaScript source code of d3-sankey, which is released under the
2526 ;; 3-clause BSD license.
2527 (license (list license:gpl3+ license:bsd-3)))))
2529 (define-public r-wesanderson
2531 (name "r-wesanderson")
2536 (uri (cran-uri "wesanderson" version))
2539 "09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"))))
2540 (properties `((upstream-name . "wesanderson")))
2541 (build-system r-build-system)
2542 (home-page "https://github.com/karthik/wesanderson")
2543 (synopsis "Wes Anderson color palette generator")
2545 "This package provides color palettes that have been generated mostly
2546 from Wes Anderson movies.")
2547 (license license:expat)))
2549 (define-public r-gg-gap
2556 (uri (cran-uri "gg.gap" version))
2559 "0m66050ryn31xmsmmikjsssllasvjdmp9yjbwfdwfpwdv106zn9h"))))
2560 (properties `((upstream-name . "gg.gap")))
2561 (build-system r-build-system)
2563 (list r-cowplot r-ggplot2))
2564 (home-page "https://github.com/ChrisLou-bioinfo/gg.gap")
2565 (synopsis "Define segments on the y-axis for ggplot2")
2567 "The @code{gg.gap} function enables you to define segments for the y-axis
2568 in a ggplot2 plot.")
2569 (license license:gpl3)))
2571 (define-public r-tablerdash
2573 (name "r-tablerdash")
2578 (uri (cran-uri "tablerDash" version))
2581 "1mnp6lxa7d669r325aynq1n3f35r9sy4v1fvdh4cymbf33s8mkmm"))
2584 ;; Delete minified JavaScript
2585 (for-each delete-file
2586 '("inst/tablerDash-0.1.0/require.min.js"
2587 "inst/bootstrap-4.0.0/bootstrap.bundle.min.js"))
2589 (properties `((upstream-name . "tablerDash")))
2590 (build-system r-build-system)
2592 `(#:modules ((guix build utils)
2593 (guix build r-build-system)
2596 (modify-phases %standard-phases
2597 (add-after 'unpack 'process-javascript
2598 (lambda* (#:key inputs #:allow-other-keys)
2599 (with-directory-excursion "inst"
2603 `((,(assoc-ref inputs "js-requirejs")
2604 "tablerDash-0.1.0/require.min.js")
2605 (,(assoc-ref inputs "js-bootstrap")
2606 "bootstrap-4.0.0/bootstrap.bundle.min.js"))))
2607 (lambda (sources targets)
2608 (for-each (lambda (source target)
2609 (format #t "Processing ~a --> ~a~%"
2611 (invoke "esbuild" source "--minify"
2612 (string-append "--outfile=" target)))
2616 (list r-htmltools r-knitr r-shiny))
2618 `(("esbuild" ,esbuild)
2622 (uri "https://raw.githubusercontent.com/requirejs/requirejs/2.3.5/require.js")
2625 "06w32mwqii9cx409ivda88z58qbkcdb4p6hf6jawchsgagaziyds"))))
2629 (uri "https://raw.githubusercontent.com/twbs/bootstrap/\
2630 v4.0.0/dist/js/bootstrap.bundle.js")
2633 "0cvfqffn45vfbj3fk6wmrhkyndhk4id89vgydssbbzxjkfwprfrj"))))))
2634 (home-page "https://rinterface.github.io/tablerDash/")
2635 (synopsis "Tabler API for Shiny")
2637 "This package provides an R interface to the
2638 @url{https://tabler.io,Tabler} HTML template. tablerDash is a light Bootstrap
2639 4 dashboard template. There are different layouts available such as a one
2640 page dashboard or a multi-page template, where the navigation menu is
2641 contained in the navigation bar.")
2642 (license license:gpl2+)))
2644 (define-public r-spelling
2651 (uri (cran-uri "spelling" version))
2654 "179nj9w1v27qq9q5240ddvggp0795998sxyqjvbqjvq9dmach3bl"))))
2655 (properties `((upstream-name . "spelling")))
2656 (build-system r-build-system)
2658 (list r-commonmark r-hunspell r-knitr r-xml2))
2659 (home-page "https://docs.ropensci.org/spelling/")
2660 (synopsis "Tools for spell checking in R")
2662 "This is an R package for spell checking common document formats
2663 including LaTeX, markdown, manual pages, and DESCRIPTION files. It includes
2664 utilities to automate checking of documentation and vignettes as a unit test
2665 during @code{R CMD check}. Both British and American English are supported
2666 out of the box and other languages can be added. In addition, packages may
2667 define a wordlist to allow custom terminology without having to abuse
2669 (license license:expat)))
2671 (define-public r-crosstalk
2673 (name "r-crosstalk")
2678 (uri (cran-uri "crosstalk" version))
2681 "180y7mhpj17axpadwhh7s0qvrpdnag7g977vk256l96d6nmvlds2"))))
2682 (build-system r-build-system)
2684 (list r-htmltools r-jsonlite r-lazyeval r-r6))
2685 (home-page "https://rstudio.github.io/crosstalk/")
2686 (synopsis "Inter-widget interactivity for HTML widgets")
2688 "This package provides building blocks for allowing HTML widgets to
2689 communicate with each other, with Shiny or without (i.e. static @code{.html}
2690 files). It currently supports linked brushing and filtering.")
2691 (license license:expat)))
2693 (define-public r-rook
2700 (uri (cran-uri "Rook" version))
2703 "00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
2704 (properties `((upstream-name . "Rook")))
2705 (build-system r-build-system)
2706 (propagated-inputs (list r-brew))
2707 (home-page "https://cran.r-project.org/web/packages/Rook")
2708 (synopsis "Web server interface for R")
2710 "This package contains the Rook specification and convenience software
2711 for building and running Rook applications. A Rook application is an R
2712 reference class object that implements a @code{call} method or an R closure
2713 that takes exactly one argument, an environment, and returns a list with three
2714 named elements: the @code{status}, the @code{headers}, and the @code{body}.")
2715 (license license:gpl2)))
2717 (define-public r-miniui
2724 (uri (cran-uri "miniUI" version))
2727 "1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
2728 (properties `((upstream-name . "miniUI")))
2729 (build-system r-build-system)
2731 (list r-htmltools r-shiny))
2732 (home-page "https://cran.r-project.org/web/packages/miniUI/")
2733 (synopsis "Shiny UI widgets for small screens")
2735 "This package provides UI widget and layout functions for writing Shiny apps that
2736 work well on small screens.")
2737 (license license:gpl3)))
2739 (define-public r-feather
2746 (uri (cran-uri "feather" version))
2749 "1gxd0h2m56sjjlzn4dry6s13nddxc4l5i11gsvavaf2dwbahdzsh"))))
2750 (build-system r-build-system)
2752 (list r-hms r-rcpp r-tibble))
2753 (home-page "https://github.com/wesm/feather")
2754 (synopsis "R Bindings to the Feather API")
2755 (description "Read and write feather files, a lightweight binary columnar
2756 data store designed for maximum speed.")
2757 (license license:asl2.0)))
2759 (define-public r-maps
2766 (uri (cran-uri "maps" version))
2769 "0ispkx1szgwxhr0zzhdzgqqwcgc6psg7vry4sj4rb89w76rcq63r"))))
2770 (build-system r-build-system)
2771 (home-page "https://cran.r-project.org/web/packages/maps")
2772 (synopsis "Draw geographical maps")
2773 (description "This package provides an R module for display of maps.
2774 Projection code and larger maps are in separate packages (@code{mapproj} and
2776 (license license:gpl2)))
2778 (define-public r-mapproj
2785 (uri (cran-uri "mapproj" version))
2788 "10bpib827011fpgvzsmlv4j3i41s0r3cv1hvawwdlk753s7i0pw6"))))
2789 (build-system r-build-system)
2790 (propagated-inputs (list r-maps))
2791 (home-page "https://cran.r-project.org/web/packages/mapproj")
2792 (synopsis "Map projection in R")
2793 (description "This package converts latitude/longitude into projected
2795 (license (list license:gpl2 ; The R interface
2796 (license:non-copyleft ; The C code
2797 "https://www.gnu.org/licenses/license-list.en.html#lucent102"
2798 "Lucent Public License Version 1.02")))))
2800 (define-public r-rgooglemaps
2802 (name "r-rgooglemaps")
2807 (uri (cran-uri "RgoogleMaps" version))
2810 "02v8k0bw70q4qwx4lcdy8p25q7n3ql2ll46lfpqllxa1p26svmfi"))))
2811 (properties `((upstream-name . "RgoogleMaps")))
2812 (build-system r-build-system)
2815 (home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
2816 (synopsis "Use Google Maps in R")
2817 (description "This package serves two purposes:
2819 @item Provide a comfortable R interface to query the Google server for static
2821 @item Use the map as a background image to overlay plots within R. This
2822 requires proper coordinate scaling.
2824 (license license:gpl2+)))
2826 (define-public r-geosphere
2828 (name "r-geosphere")
2833 (uri (cran-uri "geosphere" version))
2836 "0bg4vfmrw140j2ax0p6bflvb77w03ir39wa87l96rj473jpa9hzj"))))
2837 (build-system r-build-system)
2838 (propagated-inputs (list r-sp))
2839 (home-page "https://cran.r-project.org/web/packages/geosphere")
2840 (synopsis "Spherical trigonometry")
2841 (description "This package computes spherical trigonometry for geographic
2842 applications. That is, compute distances and related measures for angular
2843 (longitude/latitude) locations.")
2844 (license license:gpl3+)))
2846 (define-public r-jpeg
2853 (uri (cran-uri "jpeg" version))
2856 "0wihj538wdnr71wdldym83qadb4kh68a6rkallwbh2f25r27b881"))))
2857 (build-system r-build-system)
2858 (inputs (list libjpeg-turbo))
2859 (home-page "https://www.rforge.net/jpeg/")
2860 (synopsis "Read and write JPEG images with R")
2861 (description "This package provides a way to read, write and display
2862 bitmap images stored in the JPEG format with R. It can read and write both
2863 files and in-memory raw vectors.")
2864 (license license:gpl2+)))
2866 (define-public r-ggmap
2873 (uri (cran-uri "ggmap" version))
2876 "13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
2877 (build-system r-build-system)
2896 (home-page "https://github.com/dkahle/ggmap")
2897 (synopsis "Spatial visualization with ggplot2")
2898 (description "This package provides a collection of functions to visualize
2899 spatial data and models on top of static maps from various online sources (e.g
2900 Google Maps and Stamen Maps). It includes tools common to those tasks,
2901 including functions for geolocation and routing.")
2902 (license license:gpl2)))
2904 (define-public r-haven
2911 (uri (cran-uri "haven" version))
2914 "0pr9jcdk1r9pi9iz0xm1g5yy5qyjk5r7hh9467abx4kpwx3hzdwm"))
2915 (modules '((guix build utils)))
2917 ;; unvendor readstat
2918 '(delete-file-recursively "src/readstat"))))
2919 (build-system r-build-system)
2922 (modify-phases %standard-phases
2923 (add-after 'unpack 'unbundle-readstat
2925 ;; Not required, since we’re not building readstat.
2926 (substitute* "src/Makevars"
2927 (("-lz") "-lreadstat")))))))
2941 (home-page "https://haven.tidyverse.org")
2942 (synopsis "Import and export SPSS, Stata and SAS files")
2944 "This package lets you import foreign statistical formats into R via the
2945 @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
2946 (license license:expat)))
2948 (define-public r-amap
2954 (uri (cran-uri "amap" version))
2957 "0zpcb73w413na23f6giml9311jh0j0y766w2fh9i40d2h7bbvyvs"))))
2958 (build-system r-build-system)
2961 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
2962 (synopsis "Another multidimensional analysis package")
2963 (description "This package provides tools for clustering and principal
2964 component analysis (with robust methods, and parallelized functions).")
2965 (license license:gpl2+)))
2967 (define-public r-ape
2974 (uri (cran-uri "ape" version))
2977 "1xzpq3a4q5hmksc8nl530c9n31fdkj3nigqm1qhd3vkncl1iwh15"))))
2978 (build-system r-build-system)
2980 (list r-lattice r-nlme r-rcpp))
2981 (home-page "http://ape-package.ird.fr/")
2982 (synopsis "Analyses of phylogenetics and evolution")
2984 "This package provides functions for reading, writing, plotting, and
2985 manipulating phylogenetic trees, analyses of comparative data in a
2986 phylogenetic framework, ancestral character analyses, analyses of
2987 diversification and macroevolution, computing distances from DNA sequences,
2988 and several other tools.")
2989 (license license:gpl2+)))
2991 (define-public r-abbyyr
2998 (uri (cran-uri "abbyyR" version))
3001 "1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
3002 (properties `((upstream-name . "abbyyR")))
3003 (build-system r-build-system)
3011 (home-page "https://github.com/soodoku/abbyyR")
3012 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
3014 "This package provides tools to get text from images of text using Abbyy
3015 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
3016 OCR images, barcodes, forms, documents with machine readable zones, e.g.
3017 passports and get the results in a variety of formats including plain text and
3018 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
3019 (license license:expat)))
3021 (define-public r-colorspace
3023 (name "r-colorspace")
3028 (uri (cran-uri "colorspace" version))
3030 (base32 "0fhq2aykdkxh3r90i8aqjyb37p5api3mjd19ch8mzv99q4pcv4dq"))))
3031 (build-system r-build-system)
3034 (home-page "https://cran.r-project.org/web/packages/colorspace")
3035 (synopsis "Color space manipulation")
3037 "This package carries out a mapping between assorted color spaces
3038 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
3039 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
3040 colors are provided.")
3041 (license license:bsd-3)))
3043 (define-public r-glue
3050 (uri (cran-uri "glue" version))
3053 "1nvqm4fmxyszz9b2y0gjiwbvwssdqj9jflcz00b4487i8jajz31i"))))
3054 (build-system r-build-system)
3055 ;; knitr depends on glue, so we can't add knitr here to build the
3059 `(("r-knitr" ,r-knitr)))
3060 (home-page "https://github.com/tidyverse/glue")
3061 (synopsis "Interpreted string literals")
3063 "This package provides an implementation of interpreted string literals,
3064 inspired by Python's Literal String Interpolation (PEP-0498) and
3065 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
3066 (license license:expat)))
3068 (define-public r-palmerpenguins
3070 (name "r-palmerpenguins")
3075 (uri (cran-uri "palmerpenguins" version))
3078 "0q1k3cdkliq7kwrg1n0vs9b6cjwyfarhlgdijhp9c6riy6y5ik7x"))))
3080 `((upstream-name . "palmerpenguins")))
3081 (build-system r-build-system)
3082 (home-page "https://allisonhorst.github.io/palmerpenguins/")
3083 (synopsis "Palmer Archipelago (Antarctica) penguin data")
3085 "This package includes size measurements, clutch observations, and blood
3086 isotope ratios for adult foraging Adélie, Chinstrap, and Gentoo penguins
3087 observed on islands in the Palmer Archipelago near Palmer Station, Antarctica.
3088 Data were collected and made available by Dr. Kristen Gorman and the Palmer
3089 Station Long Term Ecological Research (LTER) Program.")
3090 (license license:cc0)))
3092 (define-public r-pastecs
3098 (uri (cran-uri "pastecs" version))
3101 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
3102 (build-system r-build-system)
3105 (home-page "https://github.com/phgrosjean/pastecs")
3106 (synopsis "Analysis of space-time ecological series")
3108 "This package provides functions for regulation, decomposition and analysis
3109 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
3110 initiative to bring PASSTEC 2000 functionalities to R.")
3111 (license license:gpl2+)))
3113 (define-public r-partykit
3119 (uri (cran-uri "partykit" version))
3122 "1b73s5l19yicwginqsg5xr7fzb005x372n0wb34kk6jb5x5lbsdj"))))
3123 (build-system r-build-system)
3131 (home-page "http://partykit.R-Forge.R-project.org/partykit")
3132 (synopsis "Toolkit for recursive partytioning")
3134 "This package provides a toolkit with infrastructure for representing,
3135 summarizing, and visualizing tree-structured regression and classification
3137 (license license:gpl2+)))
3139 (define-public r-plogr
3146 (uri (cran-uri "plogr" version))
3149 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
3150 (build-system r-build-system)
3151 (home-page "https://github.com/krlmlr/plogr")
3152 (synopsis "R bindings for the plog C++ logging library")
3154 "This package provides the header files for a stripped-down version of
3155 the plog header-only C++ logging library, and a method to log to R's standard
3157 (license license:expat)))
3159 (define-public r-pls
3166 (uri (cran-uri "pls" version))
3168 (base32 "1gqq8rcq6p0hs2gfzwfj690rz3pwywmnv8qzcv0wsd6aaqkskwzg"))))
3169 (build-system r-build-system)
3170 (home-page "https://mevik.net/work/software/pls.html")
3171 (synopsis "Partial Least Squares and Principal Component Regression")
3173 "The pls package implements multivariate regression methods: Partial Least
3174 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
3175 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
3178 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
3179 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
3180 @item multi-response models (or @dfn{PLS2})
3181 @item flexible cross-validation
3182 @item Jackknife variance estimates of regression coefficients
3183 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
3184 (R)MSEP, R², and correlation loadings
3185 @item formula interface, modelled after @code{lm()}, with methods for predict,
3186 print, summary, plot, update, etc.
3187 @item extraction functions for coefficients, scores, and loadings
3188 @item MSEP, RMSEP, and R² estimates
3189 @item multiplicative scatter correction (@dfn{MSC})
3191 (license license:gpl2)))
3200 (uri (cran-uri "ps" version))
3202 (base32 "0cdzjqgap108whhsilxllg12m2d05pgksryhrz5bq608bvf7vbc9"))))
3203 (build-system r-build-system)
3204 (home-page "https://ps.r-lib.org")
3205 (synopsis "List, query, and manipulate system processes")
3207 "The ps package implements an API to list, query, and manipulate system
3208 processes. Most of its code is based on the @code{psutil} Python package.")
3209 (license license:bsd-3)))
3211 (define-public r-pkgbuild
3218 (uri (cran-uri "pkgbuild" version))
3220 (base32 "0j6v5nbp8kg1m3j999gd1qsbdmqcqm1mf28ngmm177miwv8q4skw"))))
3221 (build-system r-build-system)
3231 (home-page "https://github.com/r-pkgs/pkgbuild")
3232 (synopsis "Find tools needed to build R packages")
3234 "This package provides functions used to build R packages. It locates
3235 compilers needed to build R packages on various platforms and ensures the PATH
3236 is configured appropriately so R can use them.")
3237 (license license:gpl3)))
3239 (define-public r-pkgload
3246 (uri (cran-uri "pkgload" version))
3249 "03yr9mswx9nij27bp21q6c533zx310xwzhwm52dwr7554k42p4fn"))))
3250 (build-system r-build-system)
3259 (home-page "https://github.com/r-lib/pkgload")
3260 (synopsis "Simulate package installation and attach")
3262 "This package simulates the process of installing a package and then
3263 attaching it. This is a key part of the @code{devtools} package as it allows
3264 you to rapidly iterate while developing a package.")
3265 (license license:gpl3)))
3267 (define-public r-pvclust
3273 (uri (cran-uri "pvclust" version))
3276 "0082icm54k2yq60k06qpr92a626k39j2jr0046lva4ylmhxqb4kq"))))
3277 (build-system r-build-system)
3278 (home-page "https://github.com/shimo-lab/pvclust")
3280 "Hierarchical clustering with P-values via multiscale bootstrap resampling")
3281 (description "This package provides an implementation of multiscale bootstrap
3282 resampling for assessing the uncertainty in hierarchical cluster analysis. It
3283 provides an AU (approximately unbiased) P-value as well as a BP (bootstrap probability)
3284 value for each cluster in a dendrogram.")
3285 (license license:gpl2+)))
3287 (define-public r-rcpp
3294 (uri (cran-uri "Rcpp" version))
3296 (base32 "1vkqyqly6lzr1h3szaihmayvpjkzscxp4y258vnw8nh4pjb957w7"))))
3297 (build-system r-build-system)
3298 (home-page "http://www.rcpp.org")
3299 (synopsis "Seamless R and C++ integration")
3301 "The Rcpp package provides R functions as well as C++ classes which offer
3302 a seamless integration of R and C++. Many R data types and objects can be
3303 mapped back and forth to C++ equivalents which facilitates both writing of new
3304 code as well as easier integration of third-party libraries. Documentation
3305 about Rcpp is provided by several vignettes included in this package, via the
3306 @code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
3307 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
3308 @code{citation(\"Rcpp\")} for details on these last two.")
3309 (license license:gpl2+)))
3311 (define-public r-rcppthread
3313 (name "r-rcppthread")
3318 (uri (cran-uri "RcppThread" version))
3321 "1hcxdk9mhsnrgg2bp7ls165abwb7b5grgh1gvf2i7sqrf9ggwa09"))))
3322 (properties `((upstream-name . "RcppThread")))
3323 (build-system r-build-system)
3325 "https://github.com/tnagler/RcppThread")
3326 (synopsis "R threading in C++")
3328 "This package provides a C++11-style thread class and thread pool that can
3329 safely be interrupted from R.")
3330 (license license:expat)))
3332 (define-public r-rcppnumerical
3334 (name "r-rcppnumerical")
3338 (uri (cran-uri "RcppNumerical" version))
3341 "1a92fql6mijhnr1kxkcxwivf95pk9lhgmhzkshs51h0ybfv5krik"))))
3342 (build-system r-build-system)
3344 (list r-rcpp r-rcppeigen))
3345 (home-page "https://github.com/yixuan/RcppNumerical")
3346 (synopsis"Numerical computing libraries integration with @code{Rcpp}")
3347 (description "This package provides a collection of libraries for numerical
3348 computing (numerical integration, optimization, etc.) and their integration
3350 (license license:gpl2+)))
3352 (define-public r-bindr
3359 (uri (cran-uri "bindr" version))
3362 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
3363 (build-system r-build-system)
3364 (home-page "https://github.com/krlmlr/bindr")
3365 (synopsis "Parametrized active bindings")
3367 "This package provides a simple interface for creating active bindings
3368 where the bound function accepts additional arguments.")
3369 (license license:expat)))
3371 (define-public r-bindrcpp
3378 (uri (cran-uri "bindrcpp" version))
3381 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
3382 (build-system r-build-system)
3384 (list r-bindr r-plogr r-rcpp))
3385 (home-page "https://github.com/krlmlr/bindrcpp")
3386 (synopsis "Rcpp interface to active bindings")
3388 "This package provides an easy way to fill an environment with active
3389 bindings that call a C++ function.")
3390 (license license:expat)))
3392 (define-public r-auc
3399 (uri (cran-uri "AUC" version))
3402 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
3403 (properties `((upstream-name . "AUC")))
3404 (build-system r-build-system)
3405 (home-page "https://cran.r-project.org/web/packages/AUC")
3406 (synopsis "Compute the area under the curve of selected measures")
3408 "This package includes functions to compute the area under the curve of
3409 selected measures: the area under the sensitivity curve (AUSEC), the area
3410 under the specificity curve (AUSPC), the area under the accuracy
3411 curve (AUACC), and the area under the receiver operating characteristic
3412 curve (AUROC). The curves can also be visualized. Support for partial areas
3414 (license license:gpl2+)))
3416 (define-public r-calibrate
3418 (name "r-calibrate")
3423 (uri (cran-uri "calibrate" version))
3425 (base32 "19kgrnsyq67iqv1biyssqi30a6v2836ql20nabpy2m692ns0jfvi"))))
3426 (build-system r-build-system)
3429 (home-page "https://cran.r-project.org/web/packages/calibrate")
3430 (synopsis "Calibration of scatterplot and biplot axes")
3432 "This is a package for drawing calibrated scales with tick marks
3433 on (non-orthogonal) variable vectors in scatterplots and biplots.")
3434 (license license:gpl2)))
3436 (define-public r-shape
3443 (uri (cran-uri "shape" version))
3446 "0yqbrrx2ywmfl99s6d1n6jblc63k1mxbiqyv8y0kq8jws1g3w45r"))))
3447 (build-system r-build-system)
3448 (home-page "https://cran.r-project.org/web/packages/shape")
3449 (synopsis "Functions for plotting graphical shapes")
3451 "This package provides functions for plotting graphical shapes such as
3452 ellipses, circles, cylinders, arrows, ...")
3453 (license license:gpl3+)))
3455 (define-public r-globaloptions
3457 (name "r-globaloptions")
3462 (uri (cran-uri "GlobalOptions" version))
3464 (base32 "0gkm77w6db9ajyncy1xdcivplap06a51zi99m009kylccschd2a7"))))
3465 (properties `((upstream-name . "GlobalOptions")))
3466 (build-system r-build-system)
3469 (home-page "https://github.com/jokergoo/GlobalOptions")
3470 (synopsis "Generate functions to get or set global options")
3472 "This package provides more controls on the option values such as
3473 validation and filtering on the values, making options invisible or private.")
3474 (license license:gpl2+)))
3476 (define-public r-circlize
3483 (uri (cran-uri "circlize" version))
3486 "16rnqlkgzhnm69y70k9fiz8vvwlm5dyng04hlxqvvaxix3wdpfkc"))))
3487 (build-system r-build-system)
3489 (list r-colorspace r-globaloptions r-shape))
3492 (home-page "https://github.com/jokergoo/circlize")
3493 (synopsis "Circular visualization")
3495 "Circular layout is an efficient way to visualise huge amounts of
3496 information. This package provides an implementation of circular layout
3497 generation in R as well as an enhancement of available software. Its
3498 flexibility is based on the usage of low-level graphics functions such that
3499 self-defined high-level graphics can be easily implemented by users for
3500 specific purposes. Together with the seamless connection between the powerful
3501 computational and visual environment in R, it gives users more convenience and
3502 freedom to design figures for better understanding complex patterns behind
3503 multi-dimensional data.")
3504 (license license:gpl2+)))
3506 (define-public r-powerlaw
3513 (uri (cran-uri "poweRlaw" version))
3515 (base32 "14d1myxllvm1grnfiszzzxaiqpb2jpmsi19wq70r8r2wki293h7g"))))
3516 (properties `((upstream-name . "poweRlaw")))
3517 (build-system r-build-system)
3522 (home-page "https://github.com/csgillespie/poweRlaw")
3523 (synopsis "Tools for the analysis of heavy tailed distributions")
3525 "This package provides an implementation of maximum likelihood estimators
3526 for a variety of heavy tailed distributions, including both the discrete and
3527 continuous power law distributions. Additionally, a goodness-of-fit based
3528 approach is used to estimate the lower cut-off for the scaling region.")
3529 ;; Any of these GPL versions.
3530 (license (list license:gpl2 license:gpl3))))
3532 (define-public r-compare
3539 (uri (cran-uri "compare" version))
3542 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
3543 (build-system r-build-system)
3544 (home-page "https://cran.r-project.org/web/packages/compare")
3545 (synopsis "Comparing objects for differences")
3547 "This package provides functions to compare a model object to a
3548 comparison object. If the objects are not identical, the functions can be
3549 instructed to explore various modifications of the objects (e.g., sorting
3550 rows, dropping names) to see if the modified versions are identical.")
3551 (license license:gpl2+)))
3553 (define-public r-dendextend
3555 (name "r-dendextend")
3560 (uri (cran-uri "dendextend" version))
3563 "06wjs8451hmnimzgngpzbai3yrgy33133vzzapa8jib9crdqi8sb"))))
3564 (build-system r-build-system)
3566 (list r-ggplot2 r-magrittr r-viridis))
3569 (home-page "https://cran.r-project.org/web/packages/dendextend")
3570 (synopsis "Extending 'dendrogram' functionality in R")
3572 "This package offers a set of functions for extending @code{dendrogram}
3573 objects in R, letting you visualize and compare trees of hierarchical
3574 clusterings. You can adjust a tree's graphical parameters (the color, size,
3575 type, etc of its branches, nodes and labels) and visually and statistically
3576 compare different dendrograms to one another.")
3577 ;; Any of these versions
3578 (license (list license:gpl2 license:gpl3))))
3580 (define-public r-getoptlong
3582 (name "r-getoptlong")
3587 (uri (cran-uri "GetoptLong" version))
3590 "00fpm6nd3kqa2ikasxa62jzywi46fvvmx1mdavcp5yrxxn37j8wc"))))
3591 (properties `((upstream-name . "GetoptLong")))
3592 (build-system r-build-system)
3596 (list r-crayon r-globaloptions r-rjson))
3599 (home-page "https://github.com/jokergoo/GetoptLong")
3600 (synopsis "Parsing command-line arguments and variable interpolation")
3602 "This is yet another command-line argument parser which wraps the
3603 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
3604 use in R. It also provides a simple way for variable interpolation in R.")
3605 (license license:gpl2+)))
3607 (define-public r-fastmatch
3609 (name "r-fastmatch")
3614 (uri (cran-uri "fastmatch" version))
3617 "0qcq1gwl9pijgp34giyq5y9rk0ly3d7xza2b7r68xx63ifqa1vqx"))))
3618 (build-system r-build-system)
3619 (home-page "https://www.rforge.net/fastmatch")
3620 (synopsis "Fast match function")
3622 "This package provides a fast @code{match} replacement for cases that
3623 require repeated look-ups. It is slightly faster that R's built-in
3624 @code{match} function on first match against a table, but extremely fast on
3625 any subsequent lookup as it keeps the hash table in memory.")
3626 (license license:gpl2)))
3635 (uri (cran-uri "ff" version))
3638 "0dsh6llfdz04w94xr3yl2b4vkk9g3rwhvfnxcd025v2424krxfls"))))
3639 (build-system r-build-system)
3640 (propagated-inputs (list r-bit))
3641 (home-page "http://ff.r-forge.r-project.org/")
3642 (synopsis "Memory-efficient storage of large data on disk and access functions")
3644 "This package provides data structures that are stored on disk but
3645 behave (almost) as if they were in RAM by transparently mapping only a section
3647 ;; error Architecture not supported.
3648 (supported-systems (delete "aarch64-linux" %supported-systems))
3649 (license license:gpl2)))
3651 (define-public r-ffbase
3658 (uri (cran-uri "ffbase" version))
3661 "1dp6lblfq2j7r1b4b8ls47jlx8j27n88d5vp8w116lb8pa01zxmk"))))
3662 (build-system r-build-system)
3664 (list r-bit r-fastmatch r-ff))
3665 (home-page "https://github.com/edwindj/ffbase")
3666 (synopsis "Basic statistical functions for package 'ff'")
3668 "This package extends the out of memory vectors of @code{ff} with
3669 statistical functions and other utilities to ease their usage.")
3670 (license license:gpl3)))
3672 (define-public r-prettyunits
3674 (name "r-prettyunits")
3679 (uri (cran-uri "prettyunits" version))
3682 "1ibmzgknw5896q2i6r59jz2izblxwgb29ivvjzx50pkd1jl9l6cs"))))
3683 (build-system r-build-system)
3684 (home-page "https://github.com/gaborcsardi/prettyunits")
3685 (synopsis "Pretty, human readable formatting of quantities")
3687 "This package provides tools for pretty, human readable formatting of
3689 (license license:expat)))
3691 (define-public r-princurve
3693 (name "r-princurve")
3697 (uri (cran-uri "princurve" version))
3700 "0wzk329bxljkzz57y220lsfckpsn45w348m6dcxh29zbj0ik65h2"))))
3701 (build-system r-build-system)
3704 (home-page "https://github.com/rcannood/princurve")
3705 (synopsis "Fit a principal curve in arbitrary dimension")
3706 (description "This package provides procedures for fitting a principal
3707 curve to a data matrix in arbitrary dimensions.")
3708 (license license:gpl2)))
3710 (define-public r-reshape
3717 (uri (cran-uri "reshape" version))
3720 "0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
3721 (build-system r-build-system)
3723 (list r-plyr r-rcpp))
3724 (home-page "http://had.co.nz/reshape")
3725 (synopsis "Flexibly reshape data")
3727 "Flexibly restructure and aggregate data using just two functions:
3728 @code{melt} and @code{cast}. This package provides them.")
3729 (license license:expat)))
3731 (define-public r-restrserve
3733 (name "r-restrserve")
3738 (uri (cran-uri "RestRserve" version))
3740 (base32 "1486hrzj5q5w4nbrsbqlv7vv20ly01y90qc2vygl5syzwvyjd422"))))
3741 (build-system r-build-system)
3752 (home-page "https://restrserve.org")
3753 (synopsis "R web API framework")
3755 "RestRserve is an R web API framework for building high-performance AND
3756 robust microservices and app backends. With Rserve backend on UNIX-like
3757 systems it is parallel by design. It will handle incoming requests in
3758 parallel - each request in a separate fork.")
3759 (license license:gpl2+)))
3761 (define-public r-progress
3768 (uri (cran-uri "progress" version))
3771 "0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
3772 (build-system r-build-system)
3774 (list r-crayon r-hms r-prettyunits r-r6))
3775 (home-page "https://github.com/gaborcsardi/progress")
3776 (synopsis "Terminal progress bars")
3778 "This package provides configurable progress bars. They may include
3779 percentage, elapsed time, and/or the estimated completion time. They work in
3780 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
3781 package also provides a C++ API, that works with or without Rcpp.")
3782 (license license:expat)))
3784 (define-public r-ggally
3791 (uri (cran-uri "GGally" version))
3794 "1r98zgh2grn8330cf26r1c20gl131zm778szvn5wj6q6pwv2yd9h"))))
3795 (properties `((upstream-name . "GGally")))
3796 (build-system r-build-system)
3812 (home-page "https://ggobi.github.io/ggally")
3813 (synopsis "Extension to ggplot2")
3815 "The R package ggplot2 is a plotting system based on the grammar of
3816 graphics. GGally extends ggplot2 by adding several functions to reduce the
3817 complexity of combining geometric objects with transformed data. Some of
3818 these functions include a pairwise plot matrix, a two group pairwise plot
3819 matrix, a parallel coordinates plot, a survival plot, and several functions to
3821 (license license:gpl2+)))
3823 (define-public r-proxy
3830 (uri (cran-uri "proxy" version))
3833 "0k8sr24mjfvxp12sf1j9228ah3ngy15nqmm0jw14x5s32f1assv7"))))
3834 (build-system r-build-system)
3835 (home-page "https://cran.r-project.org/web/packages/proxy")
3836 (synopsis "Distance and similarity measures")
3838 "This package provides an extensible framework for the efficient
3839 calculation of auto- and cross-proximities, along with implementations of the
3840 most popular ones.")
3841 (license license:gpl2)))
3850 (uri (cran-uri "sp" version))
3852 (base32 "09m2ddbrbs2aqnq5si42ipa0g1vbd0pxg4zbcx59is2047pv7sws"))))
3853 (build-system r-build-system)
3858 (home-page "https://cran.r-project.org/web/packages/sp")
3859 (synopsis "Classes and methods for spatial data")
3861 "This package provides classes and methods for spatial data; the classes
3862 document where the spatial location information resides, for 2D or 3D data.
3863 Utility functions are provided, e.g. for plotting data as maps, spatial
3864 selection, as well as methods for retrieving coordinates, for subsetting,
3865 print, summary, etc.")
3866 (license license:gpl2+)))
3868 (define-public r-laplacesdemon
3870 (name "r-laplacesdemon")
3875 (uri (cran-uri "LaplacesDemon" version))
3877 (base32 "1dsfp65cg06f25zjzd5ib4qyn1alfhbhpgyvpcw5n6bszn13idap"))))
3878 (properties `((upstream-name . "LaplacesDemon")))
3879 (build-system r-build-system)
3880 (home-page "https://github.com/LaplacesDemonR/LaplacesDemon")
3881 (synopsis "Complete environment for Bayesian inference")
3883 "This package provides a complete environment for Bayesian inference using
3884 a variety of different samplers.")
3885 (license license:expat)))
3887 (define-public r-rmtstat
3894 (uri (cran-uri "RMTstat" version))
3897 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
3898 (properties `((upstream-name . "RMTstat")))
3899 (build-system r-build-system)
3900 (home-page "https://cran.r-project.org/web/packages/RMTstat")
3901 (synopsis "Distributions, statistics and tests derived from random matrix theory")
3903 "This package provides functions for working with the Tracy-Widom laws
3904 and other distributions related to the eigenvalues of large Wishart
3906 (license license:bsd-3)))
3908 (define-public r-rmpi
3914 (uri (cran-uri "Rmpi" version))
3917 "06mxqgrimhfsag5giv810c7ycdbaycqs4qcj41pnfbj0jypw32im"))))
3918 (properties `((upstream-name . "Rmpi")))
3919 (build-system r-build-system)
3921 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
3922 #:phases (modify-phases %standard-phases
3923 (add-before 'install 'mpi-setup
3929 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
3930 (synopsis "R interface to message-passing interface (MPI)")
3932 "This package provides an interface (wrapper) to MPI APIs. It also
3933 provides an interactive R manager and worker environment.")
3934 (license license:gpl2+)))
3936 (define-public r-lmoments
3943 (uri (cran-uri "Lmoments" version))
3946 "0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
3947 (properties `((upstream-name . "Lmoments")))
3948 (build-system r-build-system)
3950 (list r-rcpp r-rcpparmadillo))
3951 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
3952 (synopsis "L-moments and quantile mixtures")
3954 "This package contains functions to estimate L-moments and trimmed
3955 L-moments from the data. It also contains functions to estimate the
3956 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
3957 quantile mixture from L-moments and trimmed L-moments.")
3958 (license license:gpl2)))
3960 (define-public r-distillery
3962 (name "r-distillery")
3967 (uri (cran-uri "distillery" version))
3970 "1ymmxyamkq0zbz2m4gllln1ihks2hcib6gs0mls92as79srz122b"))))
3971 (build-system r-build-system)
3972 (home-page "https://ral.ucar.edu/staff/ericg/")
3973 (synopsis "Functions for confidence intervals and object information")
3975 "This package provides some very simple method functions for confidence
3976 interval calculation and to distill pertinent information from a potentially
3977 complex object; primarily used in common with the packages extRemes and
3979 (license license:gpl2+)))
3981 (define-public r-etrunct
3987 (uri (cran-uri "etrunct" version))
3990 "0ayazgyqlc8jcqr03cwfmfhm4pck6xri1r6vkgqy4arqkrrnrcqr"))))
3991 (properties `((upstream-name . "etrunct")))
3992 (build-system r-build-system)
3993 (home-page "https://cran.r-project.org/web/packages/etrunct")
3994 (synopsis "Computes moments of univariate truncated T distribution")
3995 (description "This package computes moments of univariate truncated
3996 T distribution. There is only one exported function, @code{e_trunct},
3997 which should be seen for details.")
3998 (license license:expat)))
4000 (define-public r-extremes
4007 (uri (cran-uri "extRemes" version))
4010 "00ps7yggp89sx1j0w6c8dk0la3k95rwjv1iz7rdfqy7i46xjf6as"))))
4011 (properties `((upstream-name . "extRemes")))
4012 (build-system r-build-system)
4014 (list r-distillery r-lmoments))
4015 (home-page "https://www.assessment.ucar.edu/toolkit/")
4016 (synopsis "Extreme value analysis")
4018 "ExtRemes is a suite of functions for carrying out analyses on the
4019 extreme values of a process of interest; be they block maxima over long blocks
4020 or excesses over a high threshold.")
4021 (license license:gpl2+)))
4023 (define-public r-lmtest
4030 (uri (cran-uri "lmtest" version))
4033 "126l0y7j2iy6g1w4zii1qkfcjq6wrnc3w2li0bz376smpryddy3i"))))
4034 (build-system r-build-system)
4039 (home-page "https://cran.r-project.org/web/packages/lmtest")
4040 (synopsis "Testing linear regression models")
4042 "This package provides a collection of tests, data sets, and examples for
4043 diagnostic checking in linear regression models. Furthermore, some generic
4044 tools for inference in parametric models are provided.")
4045 ;; Either version is okay
4046 (license (list license:gpl2 license:gpl3))))
4048 (define-public r-idr
4054 (uri (cran-uri "idr" version))
4057 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
4058 (build-system r-build-system)
4059 (home-page "https://cran.r-project.org/web/packages/idr/")
4060 (synopsis "Irreproducible discovery rate")
4062 "This is a package for estimating the copula mixture model and plotting
4063 correspondence curves in \"Measuring reproducibility of high-throughput
4064 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
4065 by Li, Brown, Huang, and Bickel")
4066 (license license:gpl2+)))
4068 (define-public r-inline
4074 (uri (cran-uri "inline" version))
4077 "1mcr9hgq6kkq03n7pkcccxa7vg8jma0q7lfxc5vvkc6snydk1s8f"))))
4078 (build-system r-build-system)
4079 (home-page "https://cran.r-project.org/web/packages/inline")
4080 (synopsis "Functions to inline C, C++, Fortran function calls from R")
4082 "This package provides functionality to dynamically define R functions
4083 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
4084 @code{.Call} calling conventions.")
4085 ;; Any version of the LGPL.
4086 (license license:lgpl3+)))
4088 (define-public r-inum
4094 (uri (cran-uri "inum" version))
4097 "1khkzja8lwn9075864vbyajqina9m588ahf1fsrrajrsqilyzssz"))))
4098 (build-system r-build-system)
4101 (home-page "https://cran.r-project.org/web/packages/inum/")
4102 (synopsis "Interval and enum-type representation of vectors")
4104 "This package provides an enum-type representation of vectors and
4105 representation of intervals, including a method of coercing variables
4107 (license license:gpl2)))
4108 (define-public r-invgamma
4114 (uri (cran-uri "invgamma" version))
4117 "12ga2y4wc9bc5zz6vimvxwgjpsx3ys3209nq63gscbw559ydxa5a"))))
4118 (properties `((upstream-name . "invgamma")))
4119 (build-system r-build-system)
4120 (home-page "https://github.com/dkahle/invgamma")
4121 (synopsis "Inverse gamma distribution")
4122 (description "This package provides a light weight implementation of the
4123 standard distribution functions for the inverse gamma distribution, wrapping
4124 those for the gamma distribution in the @code{stats} package.")
4125 (license license:gpl2)))
4127 (define-public r-bdsmatrix
4129 (name "r-bdsmatrix")
4134 (uri (cran-uri "bdsmatrix" version))
4137 "1sh6pg43rgqvips4fx0k4vmp5i9lmniix0bqwj2yq5m06gs227i5"))))
4138 (properties `((upstream-name . "bdsmatrix")))
4139 (build-system r-build-system)
4140 (home-page "https://cran.r-project.org/web/packages/bdsmatrix/")
4141 (synopsis "Routines for block diagonal symmetric matrices")
4143 "This package provides procedures to work with block diagonal symmetric
4144 matrices, a special case of sparse matrices.")
4145 (license license:lgpl2.0)))
4147 (define-public r-bbmle
4154 (uri (cran-uri "bbmle" version))
4157 "1bck8rmink4wsk8pcbnj4d60svxymp29pxbzwj8p9gzsg42c1v81"))))
4158 (build-system r-build-system)
4168 (home-page "https://cran.r-project.org/web/packages/bbmle")
4169 (synopsis "Tools for General Maximum Likelihood Estimation")
4171 "This package provides methods and functions for fitting maximum
4172 likelihood models in R. This package modifies and extends the @code{mle}
4173 classes in the @code{stats4} package.")
4174 ;; Any version of the GPL
4175 (license license:gpl2+)))
4177 (define-public r-emdbook
4184 (uri (cran-uri "emdbook" version))
4187 "0ls3zxxlwmdv7zn1v9i1y9zc2sn0hbgmyjvsj7zn3ajsw7wwlih6"))))
4188 (build-system r-build-system)
4190 (list r-bbmle r-coda r-lattice r-mass r-plyr))
4191 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
4192 (synopsis "Support functions and data for \"Ecological Models and Data\"")
4194 "This package provides auxiliary functions and data sets for \"Ecological
4195 Models and Data\", a book presenting maximum likelihood estimation and related
4196 topics for ecologists (ISBN 978-0-691-12522-0).")
4198 (license (list license:gpl2 license:gpl3))))
4200 (define-public r-lpsolve
4207 (uri (cran-uri "lpSolve" version))
4210 "1fpkyjyqykwa1dxnhiky01pm09syxg169lm7hpy39bdbg10vw9s6"))))
4211 (properties `((upstream-name . "lpSolve")))
4212 (build-system r-build-system)
4213 (home-page "https://cran.r-project.org/web/packages/lpSolve")
4214 (synopsis "R interface to Lp_solve to solve linear/integer programs")
4216 "Lp_solve is software for solving linear, integer and mixed integer
4217 programs. This implementation supplies a \"wrapper\" function in C and some R
4218 functions that solve general linear/integer problems, assignment problems, and
4219 transportation problems.")
4220 (license license:lgpl2.0)))
4222 (define-public r-limsolve
4229 (uri (cran-uri "limSolve" version))
4232 "1829rd2cnd8qj80z9a7sgc7gx4sf3kvl5g6d2a0lqqw30f9sjzmr"))))
4233 (properties `((upstream-name . "limSolve")))
4234 (build-system r-build-system)
4236 (list r-lpsolve r-mass r-quadprog))
4237 (native-inputs (list gfortran))
4238 (home-page "https://cran.r-project.org/web/packages/limSolve")
4239 (synopsis "Solving linear inverse models")
4241 "This package provides functions that:
4244 @item find the minimum/maximum of a linear or quadratic function,
4245 @item sample an underdetermined or overdetermined system,
4246 @item solve a linear system Ax=B for the unknown x.
4249 It includes banded and tridiagonal linear systems. The package calls Fortran
4250 functions from LINPACK.")
4252 (license (list license:gpl2+ license:gpl3+))))
4254 (define-public r-fitdistrplus
4256 (name "r-fitdistrplus")
4261 (uri (cran-uri "fitdistrplus" version))
4264 "1glnbcm1gghzgvzpxcfsmn7dp2f9jqyx39n3ydwp9fx38409khhp"))))
4265 (build-system r-build-system)
4267 (list r-mass r-survival))
4270 (home-page "http://riskassessment.r-forge.r-project.org")
4271 (synopsis "Fitting a parametric distribution from data")
4273 "This package extends the @code{fitdistr} function of the MASS package
4274 with several functions to help the fit of a parametric distribution to
4275 non-censored or censored data. Censored data may contain left-censored,
4276 right-censored and interval-censored values, with several lower and upper
4277 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
4278 provides moment matching (MME), quantile matching (QME) and maximum
4279 goodness-of-fit estimation (MGE) methods (available only for non-censored
4280 data). Weighted versions of MLE, MME and QME are available.")
4281 (license license:gpl2+)))
4283 (define-public r-energy
4290 (uri (cran-uri "energy" version))
4293 "1ndssfi0hbnsm5jwrns7m63ppxm221hd6gk0b0wa1a7mk7ny1l38"))))
4294 (build-system r-build-system)
4296 (list r-boot r-gsl r-rcpp))
4297 (home-page "https://cran.r-project.org/web/packages/energy")
4298 (synopsis "Multivariate inference via the energy of data")
4300 "This package provides e-statistics (energy) tests and statistics for
4301 multivariate and univariate inference, including distance correlation,
4302 one-sample, two-sample, and multi-sample tests for comparing multivariate
4303 distributions, are implemented. Measuring and testing multivariate
4304 independence based on distance correlation, partial distance correlation,
4305 multivariate goodness-of-fit tests, clustering based on energy distance,
4306 testing for multivariate normality, distance components (disco) for
4307 non-parametric analysis of structured data, and other energy
4308 statistics/methods are implemented.")
4309 (license license:gpl2+)))
4311 (define-public r-suppdists
4313 (name "r-suppdists")
4318 (uri (cran-uri "SuppDists" version))
4321 "025b9nlxz62wk84295csyzbncpn80i3iby3sxdigf3swcgi2fmbb"))))
4322 (properties `((upstream-name . "SuppDists")))
4323 (build-system r-build-system)
4324 (home-page "https://cran.r-project.org/web/packages/SuppDists")
4325 (synopsis "Supplementary distributions")
4327 "This package provides ten distributions supplementing those built into
4328 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
4329 Spearman's rho, maximum F ratio, the Pearson product moment correlation
4330 coefficient, Johnson distributions, normal scores and generalized
4331 hypergeometric distributions. In addition two random number generators of
4332 George Marsaglia are included.")
4333 (license license:gpl2+)))
4335 (define-public r-ksamples
4342 (uri (cran-uri "kSamples" version))
4345 "1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
4346 (properties `((upstream-name . "kSamples")))
4347 (build-system r-build-system)
4350 (home-page "https://cran.r-project.org/web/packages/kSamples")
4351 (synopsis "K-Sample rank tests and their combinations")
4353 "This package provides tools to compares k samples using the
4354 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
4355 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
4356 test. It computes asymptotic, simulated or (limited) exact P-values, all
4357 valid under randomization, with or without ties, or conditionally under random
4358 sampling from populations, given the observed tie pattern. Except for Steel's
4359 test and the JT test it also combines these tests across several blocks of
4361 (license license:gpl2+)))
4363 (define-public r-cvst
4370 (uri (cran-uri "CVST" version))
4373 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
4374 (properties `((upstream-name . "CVST")))
4375 (build-system r-build-system)
4377 (list r-kernlab r-matrix))
4378 (home-page "https://cran.r-project.org/web/packages/CVST")
4379 (synopsis "Fast cross-validation via sequential testing")
4381 "This package implements the fast cross-validation via sequential
4382 testing (CVST) procedure. CVST is an improved cross-validation procedure
4383 which uses non-parametric testing coupled with sequential analysis to
4384 determine the best parameter set on linearly increasing subsets of the data.
4385 Additionally to the CVST the package contains an implementation of the
4386 ordinary k-fold cross-validation with a flexible and powerful set of helper
4387 objects and methods to handle the overall model selection process. The
4388 implementations of the Cochran's Q test with permutations and the sequential
4389 testing framework of Wald are generic and can therefore also be used in other
4391 (license license:gpl2+)))
4393 (define-public r-squarem
4400 (uri (cran-uri "SQUAREM" version))
4403 "0n1s32l9p4vdm3h5q6g43s0qbpzry08difsh0yay80wrla6f3rb6"))))
4404 (properties `((upstream-name . "SQUAREM")))
4405 (build-system r-build-system)
4406 (home-page "https://coah.jhu.edu/people/Faculty_personal_Pages/Varadhan.html")
4407 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
4409 "This package provides algorithms for accelerating the convergence of
4410 slow, monotone sequences from smooth, contraction mapping such as the EM
4411 algorithm. It can be used to accelerate any smooth, linearly convergent
4412 acceleration scheme. A tutorial style introduction to this package is
4413 available in a vignette.")
4414 (license license:gpl2+)))
4416 (define-public r-progressr
4418 (name "r-progressr")
4423 (uri (cran-uri "progressr" version))
4425 (base32 "1p5s35rzh28n2id2lipgyqmh3wzib66m7x0pz9028y8cql8xr5ac"))))
4426 (properties `((upstream-name . "progressr")))
4427 (build-system r-build-system)
4430 (home-page "https://progressr.futureverse.org")
4431 (synopsis "Inclusive, unifying API for progress updates")
4433 "This package provides a minimal, unifying API for scripts and packages
4434 to report progress updates from anywhere including when using parallel
4435 processing. The package is designed such that the developer can to focus on
4436 what progress should be reported on without having to worry about how to
4437 present it. The end user has full control of how, where, and when to render
4438 these progress updates.")
4439 (license license:gpl3+)))
4441 (define-public r-lava
4448 (uri (cran-uri "lava" version))
4451 "0bi3c1aqwlq7jbz4raz6vga4r264w7lldi0i62xjlbl7hnlgi23s"))))
4452 (build-system r-build-system)
4454 (list r-future-apply r-numderiv r-progressr r-squarem r-survival))
4457 (home-page "https://github.com/kkholst/lava")
4458 (synopsis "Latent variable models")
4460 "This package provides tools for the estimation and simulation of latent
4462 (license license:gpl3)))
4464 (define-public r-drr
4471 (uri (cran-uri "DRR" version))
4474 "1y70si1gig4l7jx5jiqsqliyywfsvimkx53x3zh1lc3yj2j6bqwk"))))
4475 (properties `((upstream-name . "DRR")))
4476 (build-system r-build-system)
4478 (list r-cvst r-kernlab r-matrix))
4479 (home-page "https://cran.r-project.org/web/packages/DRR")
4480 (synopsis "Dimensionality reduction via regression")
4482 "This package provides an implementation of dimensionality reduction via
4483 regression using Kernel Ridge Regression.")
4484 (license license:gpl3)))
4486 (define-public r-prodlim
4489 (version "2019.11.13")
4493 (uri (cran-uri "prodlim" version))
4496 "03wvh3kirp1prac5nky6a5whs97rvaf4hc27x0fnh51sa17r42b8"))))
4497 (build-system r-build-system)
4499 (list r-kernsmooth r-lava r-rcpp r-survival))
4500 (home-page "https://cran.r-project.org/web/packages/prodlim")
4501 (synopsis "Product-limit estimation for censored event history analysis")
4503 "This package provides a fast and user-friendly implementation of
4504 nonparametric estimators for censored event history (survival) analysis with
4505 the Kaplan-Meier and Aalen-Johansen methods.")
4506 (license license:gpl2+)))
4508 (define-public r-dimred
4515 (uri (cran-uri "dimRed" version))
4518 "1534axd5gcwma3nbglrn0l2an53n3yyya30fqkgb4d8l124ygb7j"))))
4519 (properties `((upstream-name . "dimRed")))
4520 (build-system r-build-system)
4522 (list r-drr r-magrittr))
4525 (home-page "https://github.com/gdkrmr/dimRed")
4526 (synopsis "Framework for dimensionality reduction")
4528 "This package provides a collection of dimensionality reduction
4529 techniques from R packages and provides a common interface for calling the
4531 (license license:gpl3)))
4533 (define-public r-timedate
4536 (version "3043.102")
4540 (uri (cran-uri "timeDate" version))
4543 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
4544 (properties `((upstream-name . "timeDate")))
4545 (build-system r-build-system)
4546 (home-page "https://www.rmetrics.org")
4547 (synopsis "Chronological and calendar objects")
4549 "This package provides an environment for teaching \"Financial
4550 Engineering and Computational Finance\" and for managing chronological and
4552 (license license:gpl2+)))
4554 (define-public r-magic
4561 (uri (cran-uri "magic" version))
4564 "0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
4565 (build-system r-build-system)
4568 (home-page "https://github.com/RobinHankin/magic.git")
4569 (synopsis "Create and investigate magic squares")
4571 "This package provides a collection of efficient, vectorized algorithms
4572 for the creation and investigation of magic squares and hypercubes, including
4573 a variety of functions for the manipulation and analysis of arbitrarily
4574 dimensioned arrays.")
4575 (license license:gpl2)))
4577 (define-public r-rmysql
4584 (uri (cran-uri "RMySQL" version))
4587 "05aavyggyjv46awa7ggbxlfcy9707vak5kh7kj0ljdx8zga7xb7l"))))
4588 (properties `((upstream-name . "RMySQL")))
4589 (build-system r-build-system)
4591 (list `(,mariadb "dev") zlib))
4594 (home-page "https://github.com/r-dbi/RMySQL")
4595 (synopsis "Database interface and MySQL driver for R")
4597 "This package provides a DBI interface to MySQL / MariaDB. The RMySQL
4598 package contains an old implementation based on legacy code from S-PLUS which
4599 is being phased out. A modern MySQL client based on Rcpp is available from
4600 the RMariaDB package.")
4601 (license license:gpl2)))
4603 (define-public r-rpostgresql
4605 (name "r-rpostgresql")
4610 (uri (cran-uri "RPostgreSQL" version))
4613 "1fbixmnjp1kh6yiv8zhg8zi5ryvdf5j2jxv4agq5gcxf541s3g5x"))))
4614 (properties `((upstream-name . "RPostgreSQL")))
4615 (build-system r-build-system)
4620 (home-page "https://github.com/tomoakin/RPostgreSQL")
4621 (synopsis "R interface to the PostgreSQL database system")
4623 "This package provides a Database Interface (DBI) compliant driver for R
4624 to access PostgreSQL database systems.")
4625 ;; The whole package is released under GPL version 2. It includes code
4626 ;; under the PostgreSQL license.
4627 (license license:gpl2)))
4629 (define-public r-linprog
4636 (uri (cran-uri "linprog" version))
4639 "1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"))))
4640 (build-system r-build-system)
4641 (propagated-inputs (list r-lpsolve))
4642 (home-page "http://linprog.r-forge.r-project.org/")
4643 (synopsis "Linear programming and optimization")
4645 "This package can be used to solve Linear Programming / Linear
4646 Optimization problems by using the simplex algorithm.")
4647 (license license:gpl2+)))
4649 (define-public r-geometry
4656 (uri (cran-uri "geometry" version))
4659 "1n10l8ax3783v3lgaacb15qsn8b3f0wpmhg3k39j31s6ciyd3vcg"))))
4660 (build-system r-build-system)
4662 (list r-magic r-linprog r-lpsolve r-rcpp r-rcppprogress))
4663 (home-page "http://geometry.r-forge.r-project.org/")
4664 (synopsis "Mesh generator and surface tessellator")
4666 "This package makes the qhull library available in R, in a similar manner
4667 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
4668 intersections about a point, Voronoi diagrams, furthest-site Delaunay
4669 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
4670 and higher dimensions. It implements the Quickhull algorithm for computing
4671 the convex hull. Qhull does not support constrained Delaunay triangulations,
4672 or mesh generation of non-convex objects, but the package does include some R
4673 functions that allow for this. Currently the package only gives access to
4674 Delaunay triangulation and convex hull computation.")
4675 ;; The Qhull sources are included and are distributed under a custom
4676 ;; non-copyleft license. The R sources are released under GPL version 2.
4677 (license (list license:gpl2
4678 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
4680 (define-public r-ddalpha
4687 (uri (cran-uri "ddalpha" version))
4690 "1sdnb47r534nh138zk3a6b2mgi74nvshc7p5m304vjs9jlx4l2y3"))))
4691 (build-system r-build-system)
4702 (home-page "https://cran.r-project.org/web/packages/ddalpha")
4703 (synopsis "Depth-Based classification and calculation of data depth")
4705 "This package contains procedures for depth-based supervised learning,
4706 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
4707 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
4708 statistical depth function to a compact low-dimensional space, where the final
4709 classification is done. It also offers an extension to functional data and
4710 routines for calculating certain notions of statistical depth functions. 50
4711 multivariate and 5 functional classification problems are included.")
4712 (license license:gpl2)))
4714 (define-public r-gower
4721 (uri (cran-uri "gower" version))
4724 "0c9n921wn4hhlvjq96r4nkk96s5788376cbldr7y7bwz348200iz"))))
4725 (build-system r-build-system)
4726 (home-page "https://github.com/markvanderloo/gower")
4727 (synopsis "Gower's distance")
4729 "This package provides tools to compute Gower's distance (or similarity)
4730 coefficient between records, and to compute the top-n matches between records.
4731 Core algorithms are executed in parallel on systems supporting OpenMP.")
4732 (license license:gpl3)))
4734 (define-public r-rcpproll
4741 (uri (cran-uri "RcppRoll" version))
4744 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
4745 (properties `((upstream-name . "RcppRoll")))
4746 (build-system r-build-system)
4749 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
4750 (synopsis "Efficient rolling and windowed operations")
4752 "This package provides fast and efficient routines for common rolling /
4753 windowed operations. Routines for the efficient computation of windowed mean,
4754 median, sum, product, minimum, maximum, standard deviation and variance are
4756 (license license:gpl2+)))
4758 (define-public r-ipred
4765 (uri (cran-uri "ipred" version))
4768 "0hsq00382pfd9hzpcgphjxazbxm4zx0k2r6pk6kib56k0ibm7qfn"))))
4769 (build-system r-build-system)
4777 (home-page "https://cran.r-project.org/web/packages/ipred")
4778 (synopsis "Improved predictors")
4780 "This package provides improved predictive models by indirect
4781 classification and bagging for classification, regression and survival
4782 problems as well as resampling based estimators of prediction error.")
4783 (license license:gpl2+)))
4785 (define-public r-psych
4792 (uri (cran-uri "psych" version))
4795 "032h33i2qlwsw2iq82nri5y8hs7d593w40aghcvnibpi2wxf0x8l"))))
4796 (build-system r-build-system)
4798 (list r-lattice r-mnormt r-nlme))
4801 (home-page "https://cran.r-project.org/web/packages/psych/")
4802 (synopsis "Procedures for psychological, psychometric, and personality research")
4804 "This package provides a general purpose toolbox for personality,
4805 psychometric theory and experimental psychology. Functions are primarily for
4806 multivariate analysis and scale construction using factor analysis, principal
4807 component analysis, cluster analysis and reliability analysis, although others
4808 provide basic descriptive statistics. Item Response Theory is done using
4809 factor analysis of tetrachoric and polychoric correlations. Functions for
4810 analyzing data at multiple levels include within and between group statistics,
4811 including correlations and factor analysis. Functions for simulating and
4812 testing particular item and test structures are included. Several functions
4813 serve as a useful front end for structural equation modeling. Graphical
4814 displays of path diagrams, factor analysis and structural equation models are
4815 created using basic graphics.")
4816 (license license:gpl2+)))
4818 (define-public r-generics
4825 (uri (cran-uri "generics" version))
4828 "04hrn6g5m5vi3znrcha3jw2q16lnmm3ygx2jl5aqiahg3azqwix2"))))
4829 (build-system r-build-system)
4830 (home-page "https://github.com/r-lib/generics")
4831 (synopsis "Common S3 generics not provided by base R methods")
4833 "In order to reduce potential package dependencies and conflicts,
4834 generics provides a number of commonly used S3 generics that are not provided
4835 by base R methods related to model fitting.")
4836 (license license:gpl2)))
4838 (define-public r-broom
4845 (uri (cran-uri "broom" version))
4848 "1nbv4a4s8548h2q226xmhyp42higayh95yvllh1rcs264lmw3yh4"))))
4849 (build-system r-build-system)
4864 (home-page "https://github.com/tidyverse/broom")
4865 (synopsis "Convert statistical analysis objects into tidy data frames")
4867 "This package provides tools to convert statistical analysis objects from
4868 R into tidy data frames, so that they can more easily be combined, reshaped
4869 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
4870 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
4871 summarizes a model's statistical findings such as coefficients of a
4872 regression; @code{augment}, which adds columns to the original data such as
4873 predictions, residuals and cluster assignments; and @code{glance}, which
4874 provides a one-row summary of model-level statistics.")
4875 (license license:expat)))
4877 (define-public r-recipes
4884 (uri (cran-uri "recipes" version))
4887 "0gbdc5kvbn14s5zrf4vrdjvkfajs00p7vvb433ii0lqnl07bl87d"))))
4888 (build-system r-build-system)
4910 (home-page "https://github.com/topepo/recipes")
4911 (synopsis "Preprocessing tools to create design matrices")
4913 "Recipes is an extensible framework to create and preprocess design
4914 matrices. Recipes consist of one or more data manipulation and analysis
4915 \"steps\". Statistical parameters for the steps can be estimated from an
4916 initial data set and then applied to other data sets. The resulting design
4917 matrices can then be used as inputs into statistical or machine learning
4919 (license license:gpl2)))
4921 (define-public r-pdist
4928 (uri (cran-uri "pdist" version))
4931 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
4932 (build-system r-build-system)
4933 (home-page "https://github.com/jeffwong/pdist")
4934 (synopsis "Partitioned distance function")
4936 "Pdist computes the euclidean distance between rows of a matrix X and
4937 rows of another matrix Y. Previously, this could be done by binding the two
4938 matrices together and calling @code{dist}, but this creates unnecessary
4939 computation by computing the distances between a row of X and another row of
4940 X, and likewise for Y. Pdist strictly computes distances across the two
4941 matrices, not within the same matrix, making computations significantly faster
4942 for certain use cases.")
4943 (license license:gpl3+)))
4945 (define-public r-ggrepel
4952 (uri (cran-uri "ggrepel" version))
4955 "1z5xyr5f4aryy0v1gzz9m8m4s5fzzwbrf0fxll1nbflr8xnr3yr9"))))
4956 (build-system r-build-system)
4958 (list r-ggplot2 r-rcpp r-rlang r-scales))
4960 (list r-knitr)) ; for vignettes
4961 (home-page "https://github.com/slowkow/ggrepel")
4962 (synopsis "Repulsive text and label geometries for ggplot2")
4964 "This package provides text and label geometries for ggplot2 that help to
4965 avoid overlapping text labels. Labels repel away from each other and away
4966 from the data points.")
4967 (license license:gpl3)))
4969 (define-public r-corrplot
4976 (uri (cran-uri "corrplot" version))
4979 "1g98jk6xsl08z4n6sy5vriif99m31zhbz7j3dh1kfj4w7yb9zh78"))))
4980 (build-system r-build-system)
4983 (home-page "https://github.com/taiyun/corrplot")
4984 (synopsis "Visualization of a correlation matrix")
4986 "This package provides a graphical display of a correlation matrix or
4987 general matrix. It also contains some algorithms to do matrix reordering. In
4988 addition, corrplot is good at details, including choosing color, text labels,
4989 color labels, layout, etc.")
4990 ;; Any version of the GPL
4991 (license license:gpl2+)))
4993 (define-public r-stringdist
4995 (name "r-stringdist")
5000 (uri (cran-uri "stringdist" version))
5002 (base32 "1fv1hbdlm8qwx57b2aj50mw0say5k48awzavx65mfk67qp6ddk7g"))))
5003 (build-system r-build-system)
5004 (home-page "https://github.com/markvanderloo/stringdist")
5005 (synopsis "Approximate string matching and string distance functions")
5007 "This package implements an approximate string matching version of R's
5008 native @code{match} function. It can calculate various string distances based
5009 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment),
5010 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
5011 Jaro-Winkler). An implementation of soundex is provided as well. Distances
5012 can be computed between character vectors while taking proper care of encoding
5013 or between integer vectors representing generic sequences.")
5014 (license license:gpl3+)))
5016 (define-public r-ucminf
5023 (uri (cran-uri "ucminf" version))
5026 "01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
5027 (build-system r-build-system)
5028 (native-inputs (list gfortran))
5029 (home-page "https://cran.r-project.org/web/packages/ucminf/")
5030 (synopsis "General-purpose unconstrained non-linear optimization")
5032 "This package provides an implementation of an algorithm for
5033 general-purpose unconstrained non-linear optimization. The algorithm is of
5034 quasi-Newton type with BFGS updating of the inverse Hessian and soft line
5035 search with a trust region type monitoring of the input to the line search
5036 algorithm. The interface of @code{ucminf} is designed for easy interchange
5037 with the package @code{optim}.")
5038 (license license:gpl2+)))
5040 (define-public r-useful
5046 (uri (cran-uri "useful" version))
5049 "0n50v1q75k518sq23id14jphwla35q4sasahrnrnllwrachl67v1"))))
5050 (properties `((upstream-name . "useful")))
5051 (build-system r-build-system)
5061 (home-page "https://github.com/jaredlander/useful")
5062 (synopsis "Collection of handy, useful functions")
5063 (description "This package provides a set of little functions that have been
5064 found useful to do little odds and ends such as plotting the results of K-means
5065 clustering, substituting special text characters, viewing parts of a
5066 @code{data.frame}, constructing formulas from text and building design and
5067 response matrices.")
5068 (license license:bsd-3)))
5070 (define-public r-ordinal
5073 (version "2019.12-10")
5077 (uri (cran-uri "ordinal" version))
5080 "09bpmjmbf4x82kgf6bm4bkncq2apdv9mk20zj4zgma2jx2vyfhbs"))))
5081 (build-system r-build-system)
5083 (list r-mass r-matrix r-numderiv r-ucminf))
5084 (home-page "https://github.com/runehaubo/ordinal")
5085 (synopsis "Regression models for ordinal data")
5087 "This package provides an implementation of cumulative link (mixed)
5088 models also known as ordered regression models, proportional odds models,
5089 proportional hazards models for grouped survival times and ordered models.
5090 Estimation is via maximum likelihood and mixed models are fitted with the
5091 Laplace approximation and adaptive Gauss-Hermite quadrature.")
5092 (license license:gpl2+)))
5094 (define-public r-jomo
5101 (uri (cran-uri "jomo" version))
5104 "1sbcpacxnxbzwa8rr9x2bq7hh0s3sw6yznr90dkp43n6xk5xaqir"))))
5105 (build-system r-build-system)
5107 (list r-lme4 r-mass r-ordinal r-survival))
5108 (home-page "https://cran.r-project.org/web/packages/jomo/")
5109 (synopsis "Multilevel Joint Modelling Multiple Imputation")
5111 "Similarly to Schafer's package pan, jomo is a package for multilevel
5112 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
5113 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
5114 possibility of handling binary and categorical data through latent normal
5115 variables, the option to use cluster-specific covariance matrices and to
5116 impute compatibly with the substantive model.")
5117 (license license:gpl2)))
5119 (define-public r-pan
5126 (uri (cran-uri "pan" version))
5129 "1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
5130 (build-system r-build-system)
5131 (native-inputs (list gfortran))
5132 (home-page "https://cran.r-project.org/web/packages/pan/")
5133 (synopsis "Multiple imputation for multivariate panel or clustered data")
5135 "This package implements multiple imputation for multivariate panel or
5137 (license license:gpl3)))
5139 (define-public r-mitml
5146 (uri (cran-uri "mitml" version))
5149 "00i18nnvrdrg91crgcp2a431xs71cawaip3xkqk2myv0iav3xga9"))))
5150 (build-system r-build-system)
5152 (list r-haven r-jomo r-pan))
5155 (home-page "https://cran.r-project.org/web/packages/mitml/")
5156 (synopsis "Tools for multiple imputation in multilevel modeling")
5158 "This package provides tools for multiple imputation of missing data in
5159 multilevel modeling. It includes a user-friendly interface to the packages
5160 pan and jomo, and several functions for visualization, data management and the
5161 analysis of multiply imputed data sets.")
5162 (license license:gpl2+)))
5164 (define-public r-mice
5171 (uri (cran-uri "mice" version))
5174 "01fnfrr7adp29s5kic95r9q0rdznkz2pjmziyimnrqzyicyvfyzq"))))
5175 (build-system r-build-system)
5186 (home-page "https://cran.r-project.org/web/packages/mice/")
5187 (synopsis "Multivariate imputation by chained equations")
5189 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
5190 implemented by the MICE algorithm as described in @url{Van Buuren and
5191 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
5192 variable has its own imputation model. Built-in imputation models are
5193 provided for continuous data (predictive mean matching, normal), binary
5194 data (logistic regression), unordered categorical data (polytomous logistic
5195 regression) and ordered categorical data (proportional odds). MICE can also
5196 impute continuous two-level data (normal model, pan, second-level variables).
5197 Passive imputation can be used to maintain consistency between variables.
5198 Various diagnostic plots are available to inspect the quality of the
5200 ;; Any of these two versions.
5201 (license (list license:gpl2 license:gpl3))))
5203 (define-public r-truncnorm
5205 (name "r-truncnorm")
5210 (uri (cran-uri "truncnorm" version))
5213 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
5214 (build-system r-build-system)
5215 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
5216 (synopsis "Truncated normal distribution")
5217 (description "This package provides functions for the truncated normal
5218 distribution with mean equal to @code{mean} and standard deviation equal to
5219 @code{sd}. It includes density, distribution, quantile, and expected value
5220 functions, as well as a random generation function.")
5221 (license license:gpl2)))
5223 (define-public r-rsolnp
5230 (uri (cran-uri "Rsolnp" version))
5233 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
5234 (properties `((upstream-name . "Rsolnp")))
5235 (build-system r-build-system)
5238 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
5239 (synopsis "General non-linear optimization")
5240 (description "The Rsolnp package implements a general non-linear augmented
5241 Lagrange multiplier method solver, a @dfn{sequential quadratic
5242 programming} (SQP) based solver).")
5243 ;; Any version of the GPL.
5244 (license license:gpl2+)))
5246 (define-public r-hardyweinberg
5248 (name "r-hardyweinberg")
5253 (uri (cran-uri "HardyWeinberg" version))
5256 "11y3zg8aqxk5xdzsv7i3bgqkky6a0wgf2n8saa3a4adq75k328ib"))))
5257 (properties `((upstream-name . "HardyWeinberg")))
5258 (build-system r-build-system)
5260 (list r-mice r-nnet r-rcpp r-rsolnp))
5261 (home-page "https://cran.r-project.org/package=HardyWeinberg")
5262 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
5264 "This package contains tools for exploring Hardy-Weinberg equilibrium for
5265 diallelic genetic marker data. All classical tests (chi-square, exact,
5266 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
5267 included in the package, as well as functions for power computation and for
5268 the simulation of marker data under equilibrium and disequilibrium. Routines
5269 for dealing with markers on the X-chromosome are included. Functions for
5270 testing equilibrium in the presence of missing data by using multiple
5271 imputation are also provided. Implements several graphics for exploring the
5272 equilibrium status of a large set of diallelic markers: ternary plots with
5273 acceptance regions, log-ratio plots and Q-Q plots.")
5274 (license license:gpl2+)))
5283 (uri (cran-uri "sm" version))
5286 "03z8igsjqr32x407asxvkrbayvm6yhv9xyfs0n8fkmv8zk5a41r6"))))
5287 (build-system r-build-system)
5288 (native-inputs (list gfortran))
5289 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
5290 (synopsis "Smoothing methods for nonparametric regression and density estimation")
5292 "This is software accompanying the book 'Applied Smoothing Techniques for
5293 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
5294 University Press. It provides smoothing methods for nonparametric regression
5295 and density estimation")
5296 (license license:gpl2+)))
5298 (define-public r-venndiagram
5300 (name "r-venndiagram")
5304 (uri (cran-uri "VennDiagram" version))
5307 "0yw54j9as0vf8ypnq4a3sl2w0lajri6s979f4y11hjzpgmr1m16b"))))
5308 (properties `((upstream-name . "VennDiagram")))
5309 (build-system r-build-system)
5311 (list r-futile-logger))
5312 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
5313 (synopsis "Generate High-Resolution Venn and Euler Plots")
5315 "This package provides a set of functions to generate high-resolution
5316 Venn and Euler plots. It includes handling for several special cases,
5317 including two-case scaling, and extensive customization of plot shape and
5319 (license license:gpl2+)))
5321 (define-public r-vioplot
5328 (uri (cran-uri "vioplot" version))
5331 "1dmdasp3jldc41233z6r08w3j76vyyp9m3jrj7n4ahk48yd5siq6"))))
5332 (build-system r-build-system)
5337 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
5338 (synopsis "Violin plot")
5340 "This package provides a violin plot, which is a combination of a box
5341 plot and a kernel density plot.")
5342 (license license:bsd-3)))
5344 (define-public r-rsofia
5350 ;; This package has been removed from CRAN, so we can
5351 ;; only fetch it from the archives.
5352 (uri (string-append "https://cran.r-project.org/src/"
5353 "contrib/Archive/RSofia/RSofia_"
5357 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
5358 (properties `((upstream-name . "RSofia")))
5359 (build-system r-build-system)
5362 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
5363 (synopsis "Port of sofia-ml to R")
5364 (description "This package is a port of sofia-ml to R. Sofia-ml is a
5365 suite of fast incremental algorithms for machine learning that can be used for
5366 training models for classification or ranking.")
5367 (license license:asl2.0)))
5369 (define-public r-xts
5376 (uri (cran-uri "xts" version))
5379 "0b6a7mpyk9aw6axas7nz01gadczprwwfhii01fz31z26z555i06n"))))
5380 (build-system r-build-system)
5381 (propagated-inputs (list r-zoo))
5382 (home-page "https://github.com/joshuaulrich/xts")
5383 (synopsis "Extensible time series")
5385 "This package provides for uniform handling of R's different time-based
5386 data classes by extending @code{zoo}, maximizing native format information
5387 preservation and allowing for user-level customization and extension, while
5388 simplifying cross-class interoperability.")
5389 (license license:gpl2+)))
5391 (define-public r-performanceanalytics
5393 (name "r-performanceanalytics")
5398 (uri (cran-uri "PerformanceAnalytics" version))
5401 "0ci26hsj4wnw9g0mh4vrn0cg986cpcpx169rvw6v6rbnjxq718bq"))))
5403 `((upstream-name . "PerformanceAnalytics")))
5404 (build-system r-build-system)
5406 (list r-quadprog r-xts r-zoo))
5407 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
5408 (synopsis "Econometric tools for performance and risk analysis")
5409 (description "This is a collection of econometric functions for
5410 performance and risk analysis. This package aims to aid practitioners and
5411 researchers in utilizing the latest research in analysis of non-normal return
5412 streams. In general, it is most tested on return (rather than price) data on
5413 a regular scale, but most functions will work with irregular return data as
5414 well, and increasing numbers of functions will work with P&L or price data
5416 ;; Either version may be picked.
5417 (license (list license:gpl2 license:gpl3))))
5419 (define-public r-laeken
5426 (uri (cran-uri "laeken" version))
5429 "1p3ccbaydlr52p8qmgmm2l6kryvq6jjjx7mqn2vv0gpjaxqhyy92"))))
5430 (build-system r-build-system)
5432 (list r-boot r-mass))
5433 (home-page "https://cran.r-project.org/web/packages/laeken/")
5434 (synopsis "Estimation of indicators on social exclusion and poverty")
5435 (description "This package provides tools for the estimation of indicators
5436 on social exclusion and poverty, as well as an implementation of Pareto tail
5437 modeling for empirical income distributions.")
5438 (license license:gpl2+)))
5440 (define-public r-vcd
5447 (uri (cran-uri "vcd" version))
5450 "13sn77qdcyll9lz7nab0bxzfvpgj8f5rl2cq5ylpz8pibynj1d55"))))
5451 (build-system r-build-system)
5453 (list r-colorspace r-lmtest r-mass))
5454 (home-page "https://cran.r-project.org/web/packages/vcd/")
5455 (synopsis "Visualizing categorical data")
5456 (description "This package provides visualization techniques, data sets,
5457 summary and inference procedures aimed particularly at categorical data.
5458 Special emphasis is given to highly extensible grid graphics. The package was
5459 originally inspired by the book \"Visualizing Categorical Data\" by Michael
5460 Friendly and is now the main support package for a new book, \"Discrete Data
5461 Analysis with R\" by Michael Friendly and David Meyer (2015).")
5462 (license license:gpl2)))
5464 (define-public r-vcfr
5470 (uri (cran-uri "vcfR" version))
5473 "0lhxb3ac4fafwik9q3cds46svzf0hyca8k54chw3dpk50c0zz1yx"))))
5474 (build-system r-build-system)
5490 (home-page "https://github.com/knausb/vcfR")
5491 (synopsis "Manipulate and visualize VCF data")
5492 (description "This package facilitates easy manipulation of variant call
5493 format (VCF) data. Functions are provided to rapidly read from and write to
5494 VCF files. Once VCF data is read into R, a parser function extracts matrices
5495 of data. This information can then be used for quality control or other
5496 purposes. Additional functions provide visualization of genomic data. Once
5497 processing is complete data may be written to a VCF file. It also may be
5498 converted into other popular R objects. This package provides a link between
5499 VCF data and familiar R software.")
5500 (license license:gpl3)))
5502 (define-public r-ica
5509 (uri (cran-uri "ica" version))
5512 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
5513 (build-system r-build-system)
5514 (home-page "https://cran.r-project.org/web/packages/ica/")
5515 (synopsis "Independent component analysis")
5516 (description "This package provides tools for @dfn{Independent Component
5517 Analysis} (ICA) using various algorithms: FastICA,
5518 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
5519 of Eigenmatrices} (JADE).")
5520 (license license:gpl2+)))
5522 (define-public r-dtw
5529 (uri (cran-uri "dtw" version))
5532 "004gm4mzgdzdj807j3bwqsv5lizmnmz5jq514bdjshhkysnzjz6z"))))
5533 (build-system r-build-system)
5534 (propagated-inputs (list r-proxy))
5535 (home-page "http://dtw.r-forge.r-project.org/")
5536 (synopsis "Dynamic Time Warping Algorithms")
5537 (description "This package provides a comprehensive implementation of
5538 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
5539 optimal (least cumulative distance) alignment between points of two time
5540 series. Common DTW variants covered include local (slope) and global (window)
5541 constraints, subsequence matches, arbitrary distance definitions,
5542 normalizations, minimum variance matching, and so on.")
5543 (license license:gpl2+)))
5545 (define-public r-sdmtools
5548 (version "1.1-221.2")
5552 (uri (cran-uri "SDMTools" version))
5555 "1xvcd97ikqsfdpk2fddy3k0z1ajqga7nv9bgac9c1wnjk1gqrpgh"))))
5556 (properties `((upstream-name . "SDMTools")))
5557 (build-system r-build-system)
5558 (propagated-inputs (list r-r-utils))
5559 (home-page "https://www.rforge.net/SDMTools/")
5560 (synopsis "Species distribution modelling tools")
5561 (description "This package provides a set of tools for post processing
5562 the outcomes of species distribution modeling exercises. It includes novel
5563 methods for comparing models and tracking changes in distributions through
5564 time. It further includes methods for visualizing outcomes, selecting
5565 thresholds, calculating measures of accuracy and landscape fragmentation
5567 (license license:gpl3+)))
5569 (define-public r-scatterplot3d
5571 (name "r-scatterplot3d")
5576 (uri (cran-uri "scatterplot3d" version))
5579 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
5580 (build-system r-build-system)
5581 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
5582 (synopsis "3D scatter plot")
5583 (description "This package provides an implementation of scatter plots for
5584 plotting. a three dimensional point cloud.")
5585 (license license:gpl2)))
5587 (define-public r-ggridges
5594 (uri (cran-uri "ggridges" version))
5597 "0bmlqy1p6rac90af97ffpdi6php7dblx66l2hcm8ljidgyqzmspm"))))
5598 (build-system r-build-system)
5600 (list r-ggplot2 r-plyr r-scales r-withr))
5603 (home-page "https://github.com/clauswilke/ggridges")
5604 (synopsis "Ridgeline plots in ggplot2")
5606 "Ridgeline plots provide a convenient way of visualizing changes in
5607 distributions over time or space. This package enables the creation of such
5608 plots in @code{ggplot2}.")
5609 (license license:gpl2)))
5611 (define-public r-ggjoy
5618 (uri (cran-uri "ggjoy" version))
5621 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
5622 (build-system r-build-system)
5624 (list r-ggplot2 r-ggridges))
5625 (home-page "https://github.com/clauswilke/ggjoy")
5626 (synopsis "Joyplots in ggplot2")
5627 (description "Joyplots provide a convenient way of visualizing changes in
5628 distributions over time or space. This package enables the creation of such
5629 plots in @code{ggplot2}.")
5630 (license license:gpl2)))
5632 (define-public r-cli
5639 (uri (cran-uri "cli" version))
5642 "1kslrx22djrs3wnf5xyligwy7h4hzsn5awl946x961fn980ydcy8"))))
5643 (build-system r-build-system)
5646 (home-page "https://github.com/r-lib/cli#readme")
5647 (synopsis "Helpers for developing command line interfaces")
5648 (description "This package provides a suite of tools designed to build
5649 attractive command line interfaces (CLIs). It includes tools for drawing
5650 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
5651 (license license:expat)))
5653 (define-public r-argparser
5655 (name "r-argparser")
5660 (uri (cran-uri "argparser" version))
5663 "0xcl0ivsbc4iw8s7027q4cx68j6s5lihbby0xa9pmlv4wjmcvdr6"))))
5664 (build-system r-build-system)
5665 (home-page "https://bitbucket.org/djhshih/argparser")
5666 (synopsis "Command-line argument parser")
5668 "This package provides a cross-platform command-line argument parser
5669 written purely in R with no external dependencies. It is useful with the
5670 Rscript front-end and facilitates turning an R script into an executable
5672 (license license:gpl3+)))
5674 (define-public r-debugme
5681 (uri (cran-uri "debugme" version))
5684 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
5685 (build-system r-build-system)
5686 (propagated-inputs (list r-crayon))
5687 (home-page "https://github.com/r-lib/debugme#readme")
5688 (synopsis "Debug R packages")
5690 "This package allows the user to specify debug messages as special string
5691 constants, and control debugging of packages via environment variables.")
5692 (license license:expat)))
5694 (define-public r-processx
5701 (uri (cran-uri "processx" version))
5703 (base32 "0azw8sx6nv6pp8m8jrwq01b9na2swrnznn7dwrhn07268w82svzd"))))
5704 (build-system r-build-system)
5707 (home-page "https://github.com/r-lib/processx3")
5708 (synopsis "Execute and control system processes")
5710 "This package provides portable tools to run system processes in the
5711 background. It can check if a background process is running; wait on a
5712 background process to finish; get the exit status of finished processes; kill
5713 background processes and their children; restart processes. It can read the
5714 standard output and error of the processes, using non-blocking connections.
5715 @code{processx} can poll a process for standard output or error, with a
5716 timeout. It can also poll several processes at once.")
5717 (license license:expat)))
5719 (define-public r-tsp
5726 (uri (cran-uri "TSP" version))
5729 "0gdwxbj2gria7jhsswmfvc32r43sdd63z3lyy21gbvmfcakvb8j9"))))
5730 (properties `((upstream-name . "TSP")))
5731 (build-system r-build-system)
5732 (propagated-inputs (list r-foreach))
5733 (home-page "https://cran.r-project.org/web/packages/TSP/")
5734 (synopsis "Traveling salesperson problem (TSP)")
5735 (description "This package provides basic infrastructure and some
5736 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
5737 traveling salesman problem).")
5738 (license license:gpl3)))
5740 (define-public r-qap
5747 (uri (cran-uri "qap" version))
5750 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
5751 (build-system r-build-system)
5752 (native-inputs (list gfortran))
5753 (home-page "https://cran.r-project.org/web/packages/qap/")
5754 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
5755 (description "This package implements heuristics for the @dfn{quadratic
5756 assignment problem} (QAP). Currently only a simulated annealing heuristic is
5758 (license license:gpl3)))
5760 (define-public r-gclus
5767 (uri (cran-uri "gclus" version))
5770 "1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
5771 (build-system r-build-system)
5772 (propagated-inputs (list r-cluster))
5773 (home-page "https://cran.r-project.org/web/packages/gclus/")
5774 (synopsis "Clustering graphics")
5775 (description "This package orders panels in scatterplot matrices and
5776 parallel coordinate displays by some merit index. It contains various indices
5777 of merit, ordering functions, and enhanced versions of @code{pairs} and
5778 @code{parcoord} which color panels according to their merit level.")
5779 (license license:gpl2+)))
5781 (define-public r-webshot
5788 (uri (cran-uri "webshot" version))
5791 "0gq4h8cw51z95yvsnf38kj5l58wgljkm0dalmi8mn1sp06bxr0zi"))))
5792 (build-system r-build-system)
5794 (list r-callr r-jsonlite r-magrittr))
5795 (home-page "https://github.com/wch/webshot/")
5796 (synopsis "Take screenshots of web pages")
5798 "Webshot makes it easy to take screenshots of web pages from within R.
5799 It can also run Shiny applications locally and take screenshots of the
5800 application; and it can render and screenshot static as well as interactive R
5801 Markdown documents.")
5802 (license license:gpl2)))
5804 (define-public r-seriation
5806 (name "r-seriation")
5811 (uri (cran-uri "seriation" version))
5814 "08c37n3xxc4n4vbkw38k3l3hdlmck8drqpl6z274vkgi2sqv8qyf"))))
5815 (build-system r-build-system)
5824 (native-inputs (list gfortran))
5825 (home-page "https://s2.smu.edu/IDA/seriation/")
5826 (synopsis "Infrastructure for ordering objects using seriation")
5828 "This package provides infrastructure for seriation with an
5829 implementation of several seriation/sequencing techniques to reorder matrices,
5830 dissimilarity matrices, and dendrograms. It also provides (optimally)
5831 reordered heatmaps, color images and clustering visualizations like
5832 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
5834 (license license:gpl3)))
5836 (define-public r-xfun
5843 (uri (cran-uri "xfun" version))
5845 (base32 "1x2f49n3ak85nab937wq6q5sqi1mdlfzwbv8603kxl2k8rxvp1dz"))))
5846 (build-system r-build-system)
5847 ;; knitr itself depends on xfun
5850 `(("r-knitr" ,r-knitr)))
5851 (home-page "https://github.com/yihui/xfun")
5852 (synopsis "Miscellaneous functions")
5854 "This package provides miscellaneous functions commonly used in other
5855 packages maintained by Yihui Xie.")
5856 (license license:expat)))
5858 (define-public r-utf8
5865 (uri (cran-uri "utf8" version))
5868 "1x6qg19z4qih9lk3mvnmx0vailm1khp5lylw4hlwz6rssj3yw6m7"))))
5869 (build-system r-build-system)
5871 (list r-knitr r-rmarkdown)) ; for vignettes
5872 (home-page "https://github.com/patperry/r-utf8")
5873 (synopsis "Unicode text processing")
5875 "This package provides tools to process and print UTF-8 encoded
5876 international text (Unicode). Input, validate, normalize, encode, format, and
5878 (license license:asl2.0)))
5880 (define-public r-zeallot
5887 (uri (cran-uri "zeallot" version))
5890 "1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
5891 (build-system r-build-system)
5892 (home-page "https://github.com/nteetor/zeallot")
5893 (synopsis "Multiple, unpacking, and destructuring assignment")
5895 "This package provides a @code{%<-%} operator to perform multiple,
5896 unpacking, and destructuring assignment in R. The operator unpacks the
5897 right-hand side of an assignment into multiple values and assigns these values
5898 to variables on the left-hand side of the assignment.")
5899 (license license:expat)))
5901 (define-public r-vctrs
5908 (uri (cran-uri "vctrs" version))
5911 "1c8v5lmap6iq4jpi7p3w05hsv2dq7rjg057pvnfyc5d1xmsqnkkz"))))
5912 (build-system r-build-system)
5914 (list r-ellipsis r-glue r-rlang))
5917 (home-page "https://github.com/r-lib/vctrs")
5918 (synopsis "Vector helpers")
5920 "There are three main goals to the @code{vctrs} package:
5923 @item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
5924 @code{length()} and @code{class()}. These definitions are paired with a
5925 framework for type-coercion and size-recycling.
5926 @item To define type- and size-stability as desirable function properties, use
5927 them to analyse existing base function, and to propose better alternatives.
5928 This work has been particularly motivated by thinking about the ideal
5929 properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
5930 @item To provide a new @code{vctr} base class that makes it easy to create new
5931 S3 vectors. @code{vctrs} provides methods for many base generics in terms of
5932 a few new @code{vctrs} generics, making implementation considerably simpler
5935 (license license:gpl3)))
5937 (define-public r-pillar
5944 (uri (cran-uri "pillar" version))
5947 "1nqv86zb51jgd6jbhgnyq6j53dzsjx7gwaapndfd3yvp0sxg3yr2"))))
5948 (build-system r-build-system)
5961 (home-page "https://github.com/r-lib/pillar")
5962 (synopsis "Coloured formatting for columns")
5964 "This package provides a @code{pillar} generic designed for formatting
5965 columns of data using the full range of colours provided by modern
5967 (license license:gpl3)))
5969 (define-public r-pinfsc50
5975 (uri (cran-uri "pinfsc50" version))
5978 "1547xyxmfb7zi8h9bsm6k67dcw4hpp129xzvmgwfw7r6p4af47zd"))))
5979 (build-system r-build-system)
5980 (home-page "https://cran.r-project.org/web/packages/pinfsc50/")
5981 (synopsis "Genomic data for the plant pathogen Phytophthora infestans")
5982 (description "This package contains genomic data for the plant pathogen
5983 Phytophthora infestans. It includes a variant file, a sequence file and an
5984 annotation file. This package is intended to be used as example data for
5985 packages that work with genomic data.")
5986 (license license:gpl2+)))
5988 (define-public r-uuid
5995 (uri (cran-uri "uuid" version))
5998 "0il35jnci537r8zkinyiy5jp5q530p85ln6dswpj884zclrlcvj5"))))
5999 (build-system r-build-system)
6000 (home-page "https://www.rforge.net/uuid")
6001 (synopsis "Tools for generating and handling of UUIDs")
6003 "This package provides tools for generating and handling of
6004 @dfn{Universally Unique Identifiers} (UUIDs).")
6005 (license license:expat)))
6007 (define-public r-tinytex
6014 (uri (cran-uri "tinytex" version))
6017 "0y1vfq89yi302cwdcnassm02dk14j9ivk5vf83fp6rb8h6ww3rk5"))))
6018 (build-system r-build-system)
6021 (home-page "https://github.com/yihui/tinytex")
6022 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
6024 "This package provides helper functions to install and maintain the LaTeX
6025 distribution named TinyTeX, a lightweight, cross-platform, portable, and
6026 easy-to-maintain version of TeX Live. This package also contains helper
6027 functions to compile LaTeX documents, and install missing LaTeX packages
6029 (license license:expat)))
6031 (define-public r-tinytest
6038 (uri (cran-uri "tinytest" version))
6041 "1mq31f7bzcz5bkgzl9khm1i80axfzra7gcjqxd2yqb4wrw1m3x4s"))))
6042 (properties `((upstream-name . "tinytest")))
6043 (build-system r-build-system)
6044 (home-page "https://github.com/markvanderloo/tinytest")
6045 (synopsis "Lightweight unit testing framework")
6047 "This package provides a lightweight unit testing framework. Main
6051 @item install tests with the package;
6052 @item test results are treated as data that can be stored and manipulated;
6053 @item test files are R scripts interspersed with test commands, that can be
6055 @item fully automated build-install-test sequence for packages;
6056 @item skip tests when not run locally (e.g. on CRAN);
6057 @item flexible and configurable output printing;
6058 @item compare computed output with output stored with the package;
6059 @item run tests in parallel;
6060 @item extensible by other packages;
6061 @item report side effects.
6064 (license license:gpl3)))
6066 (define-public r-network
6073 (uri (cran-uri "network" version))
6076 "19q563v5xfkbmr0ws9nhqx4wrxkf9jsck51rqc8mm2gq2h03lg7w"))))
6077 (build-system r-build-system)
6079 (list r-magrittr r-statnet-common r-tibble))
6080 (home-page "https://statnet.org/")
6081 (synopsis "Classes for relational data")
6083 "This package provides tools to create and modify network objects. The
6084 @code{network} class can represent a range of relational data types, and
6085 supports arbitrary vertex/edge/graph attributes.")
6086 (license license:gpl2+)))
6088 (define-public r-stabs
6095 (uri (cran-uri "stabs" version))
6098 "1nf1yg14cgxrs4np1yghpzw1nczaslfv3rvf3918wrlzg0vp6l7q"))))
6099 (build-system r-build-system)
6102 (home-page "https://github.com/hofnerb/stabs")
6103 (synopsis "Stability selection with error control")
6105 "This package provides resampling procedures to assess the stability of
6106 selected variables with additional finite sample error control for
6107 high-dimensional variable selection procedures such as Lasso or boosting.
6108 Both, standard stability selection (Meinshausen & Buhlmann, 2010) and
6109 complementary pairs stability selection with improved error bounds
6110 (Shah & Samworth, 2013) are implemented. The package can be combined with
6111 arbitrary user specified variable selection approaches.")
6112 (license license:gpl2)))
6114 (define-public r-rle
6121 (uri (cran-uri "rle" version))
6124 "0sagl0jggg40lihzy7pfq4593rfvc3b3f7g6ggi85s7n18qvwg40"))))
6125 (properties `((upstream-name . "rle")))
6126 (build-system r-build-system)
6127 (home-page "https://cran.r-project.org/web/packages/rle/")
6128 (synopsis "Common functions for run-length encoded vectors")
6130 "This package provides common @code{base} and @code{stats} methods for
6131 @code{rle} objects, aiming to make it possible to treat them transparently as
6133 (license license:gpl3)))
6135 (define-public r-statnet-common
6137 (name "r-statnet-common")
6142 (uri (cran-uri "statnet.common" version))
6145 "0bw8dwnv568i60xrj6d7gv0hnna1x7rvqaayy5i0827khvdj7nrw"))))
6147 `((upstream-name . "statnet.common")))
6148 (build-system r-build-system)
6151 (home-page "https://statnet.org")
6152 (synopsis "R scripts and utilities used by the Statnet software")
6153 (description "This package provides non-statistical utilities used by the
6154 software developed by the Statnet Project.")
6155 (license license:gpl3)))
6157 (define-public r-statcheck
6159 (name "r-statcheck")
6164 (uri (cran-uri "statcheck" version))
6167 "0ivybdcrymlsfv6pg6p5bv70qdvgxf2vgp0kf4r0pf2fcvav1mcp"))))
6168 (build-system r-build-system)
6170 (list r-ggplot2 r-plyr r-rmarkdown))
6171 (home-page "https://cran.r-project.org/web/packages/statcheck/")
6172 (synopsis "Extract statistics from articles and recompute p-values")
6173 (description "This package can automatically extract statistical
6174 null-hypothesis significant testing (NHST) results from articles and recompute
6175 the p-values based on the reported test statistic and degrees of freedom to
6176 detect possible inconsistencies.")
6177 (license license:gpl2)))
6179 (define-public r-sna
6186 (uri (cran-uri "sna" version))
6189 "0ai0v4538d30m4wks5s3lch1yfmx1ml0nnrz7ihs097lv586a09s"))))
6190 (build-system r-build-system)
6192 (list r-network r-statnet-common))
6193 (home-page "https://statnet.org")
6194 (synopsis "Tools for social network analysis")
6196 "This package provides a range of tools for social network analysis,
6197 including node and graph-level indices, structural distance and covariance
6198 methods, structural equivalence detection, network regression, random graph
6199 generation, and 2D/3D network visualization.")
6200 (license license:gpl2+)))
6202 (define-public r-tfisher
6209 (uri (cran-uri "TFisher" version))
6212 "0vz74ww1lf1prfwz74hfsi3a8nzq8ss7aqjr85c1d87vss2796xx"))))
6213 (properties `((upstream-name . "TFisher")))
6214 (build-system r-build-system)
6216 (list r-matrix r-mvtnorm r-sn))
6217 (home-page "https://cran.r-project.org/web/packages/TFisher/")
6218 (synopsis "Optimal thresholding Fisher's p-value combination method")
6220 "This package provides the @dfn{cumulative distribution function} (CDF),
6221 quantile, and statistical power calculator for a collection of thresholding
6222 Fisher's p-value combination methods, including Fisher's p-value combination
6223 method, truncated product method and, in particular, soft-thresholding
6224 Fisher's p-value combination method which is proven to be optimal in some
6225 context of signal detection. The p-value calculator for the omnibus version
6226 of these tests are also included.")
6227 (license license:gpl2)))
6229 (define-public r-ttr
6236 (uri (cran-uri "TTR" version))
6239 "11xsmbvmxq2j119j2z58bx1fkkb2xlhmzc35z5fbwr3nchrfz6jd"))))
6240 (properties `((upstream-name . "TTR")))
6241 (build-system r-build-system)
6243 (list r-curl r-xts r-zoo))
6244 (home-page "https://github.com/joshuaulrich/TTR")
6245 (synopsis "Technical trading rules")
6247 "This package provides functions and data to construct technical trading
6249 (license license:gpl2)))
6251 (define-public r-leaflet-providers
6253 (name "r-leaflet-providers")
6258 (uri (cran-uri "leaflet.providers" version))
6260 (base32 "0yynrwv4xd5cdh49cwvfxm4ranarah9iiry2cd3b4fiihdfcg3wy"))))
6261 (properties `((upstream-name . "leaflet.providers")))
6262 (build-system r-build-system)
6263 (home-page "https://github.com/rstudio/leaflet.providers")
6264 (synopsis "Leaflet map tile providers")
6266 "This package contains third-party map tile provider information from
6267 Leaflet.js, to be used with the @code{leaflet} R package. Additionally,
6268 @code{leaflet.providers} enables users to retrieve up-to-date provider
6269 information between package updates.")
6270 (license license:bsd-2)))
6272 ;; This package contains a lot of minified JavaScript with unclear provenance.
6273 ;; When upgrading please make sure that all minified JavaScript files are
6274 ;; removed in a snippet and that the replacement sources correspond to the
6275 ;; original minified scripts.
6276 (define-public r-leaflet
6283 (uri (cran-uri "leaflet" version))
6285 (base32 "07whi3zkz1lmbqx5ydpiya802ck22ny0s7gskwnx7r8xbwlkiw5h"))
6289 (list "inst/htmlwidgets/lib/leaflet/leaflet.js"
6290 "inst/htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js"
6291 "inst/htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js"
6292 "inst/htmlwidgets/lib/jquery/jquery.min.js"
6293 "inst/htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js"
6294 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js"
6295 "inst/htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js"
6296 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js"
6297 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js"
6298 "inst/htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js"
6299 "inst/legacy/www/leaflet.js")))))
6300 (properties `((upstream-name . "leaflet")))
6301 (build-system r-build-system)
6303 `(#:modules ((guix build utils)
6304 (guix build r-build-system)
6307 (modify-phases %standard-phases
6308 (add-after 'unpack 'process-javascript
6309 (lambda* (#:key inputs #:allow-other-keys)
6310 ;; The inst directory contains some minified JavaScript files.
6311 ;; Regenerate them from sources.
6312 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-leaflet"))
6313 (with-directory-excursion "inst/"
6317 `(("/tmp/leaflet-src.js"
6318 "htmlwidgets/lib/leaflet/leaflet.js")
6319 (,(assoc-ref inputs "js-leaflet-measure")
6320 "htmlwidgets/lib/leaflet-measure/leaflet-measure.min.js")
6321 (,(assoc-ref inputs "js-leaflet-omnivore")
6322 "htmlwidgets/lib/leaflet-omnivore/leaflet-omnivore.min.js")
6323 (,(assoc-ref inputs "js-jquery")
6324 "htmlwidgets/lib/jquery/jquery.min.js")
6325 ("htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.js"
6326 "htmlwidgets/plugins/Leaflet-MiniMap/Control.MiniMap.min.js")
6327 (,(assoc-ref inputs "js-bootstrap3")
6328 "htmlwidgets/plugins/Leaflet.awesome-markers/bootstrap.min.js")
6329 ("htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.js"
6330 "htmlwidgets/plugins/Leaflet.awesome-markers/leaflet.awesome-markers.min.js")
6331 (,(string-append (assoc-ref inputs "js-leaflet-markercluster")
6332 "/dist/leaflet.markercluster-src.js")
6333 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.js")
6334 (,(assoc-ref inputs "js-leaflet-markercluster-freezable")
6335 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.freezable.js")
6336 (,(assoc-ref inputs "js-leaflet-markercluster-layersupport")
6337 "htmlwidgets/plugins/Leaflet.markercluster/leaflet.markercluster.layersupport.js")
6338 (,(assoc-ref inputs "js-proj4leaflet")
6339 "htmlwidgets/plugins/Proj4Leaflet/proj4.min.js")
6340 ("legacy/www/leaflet-src.js"
6341 "legacy/www/leaflet.js"))))
6342 (lambda (sources targets)
6343 (for-each (lambda (source target)
6344 (format #true "Processing ~a --> ~a~%"
6346 (invoke "esbuild" source "--minify"
6347 (string-append "--outfile=" target)))
6348 sources targets)))))))))
6350 `(("esbuild" ,esbuild)
6355 (uri "https://raw.githubusercontent.com/twbs/bootstrap/v3.3.7/dist/js/bootstrap.js")
6358 "1j1qjagwj0m3q322z9wxxnpkd8zbk6g3kl047dsbmqad6gmqvgha"))))
6362 (uri "https://code.jquery.com/jquery-1.12.4.js")
6365 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
6369 (uri "http://cdn.leafletjs.com/leaflet/v1.3.1/leaflet.zip")
6372 "10phzd2vczy3zm1b64whp2nna69cf9hlj2bndc9yq47vf3ddqx8f"))))
6373 ("js-leaflet-omnivore"
6376 (uri (string-append "https://api.tiles.mapbox.com/mapbox.js/plugins/"
6377 "leaflet-omnivore/v0.3.1/leaflet-omnivore.js"))
6380 "1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
6381 ("js-leaflet-markercluster"
6385 (url "https://github.com/Leaflet/Leaflet.markercluster.git")
6387 (file-name (git-file-name "js-leaflet-markercluster" "1.1.0"))
6390 "0ds8c7picqjmc86bm5n6hm8k71fwsa2cpgib19sbdamzr9hm0rs1"))))
6391 ("js-leaflet-markercluster-freezable"
6395 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.Freezable/"
6396 "9db80a3fba7dff4aee940e05d3d4dceaa1fffcf9/src/freezable.js"))
6397 (file-name "leaflet-markercluster-freezable.js")
6400 "1k6sn5n0z2x3an91vwvkzmqq4b8ppswgk5hi5qrr79klas1hbx1k"))))
6401 ("js-leaflet-markercluster-layersupport"
6405 "https://raw.githubusercontent.com/ghybs/Leaflet.MarkerCluster.LayerSupport/"
6406 "87f3848b92e0516d9c98f6d4cd175f7b8a4e3805/src/layersupport.js"))
6407 (file-name "leaflet-markercluster-layersupport.js")
6410 "15qa21xif94y762c65yxxysxykz3mma6y6agw3nxpr3s7wbb75ff"))))
6411 ("js-leaflet-measure"
6414 (uri "https://unpkg.com/leaflet-measure@1.5.2/dist/leaflet-measure.js")
6415 (file-name "js-leaflet-measure-1.5.2.js")
6418 "0ggg3ffmm7pj9ry4gssrh0a17pnad3p6gwi0dg98y819pmpqa7y0"))))
6422 (uri "https://raw.githubusercontent.com/kartena/Proj4Leaflet/1.0.2/lib/proj4.js")
6423 (file-name "js-proj4leaflet-1.0.2.js")
6426 "0vyrbf6gv2lyh4c2bzp5349ivwvvg28gpn87y52a7jdb13rlkpab"))))))
6441 (home-page "https://rstudio.github.io/leaflet/")
6442 (synopsis "Create interactive web maps with the JavaScript Leaflet library")
6444 "Create and customize interactive maps using the Leaflet JavaScript
6445 library and the @code{htmlwidgets} package. These maps can be used directly
6446 from the R console, from RStudio, in Shiny applications and R Markdown
6448 (license license:gpl3)))
6450 (define-public r-leaps
6457 (uri (cran-uri "leaps" version))
6460 "1dn3yl1p03n0iynd1vsdkrr0fhmvgrmfkv37y7n371765h83lz1x"))))
6461 (build-system r-build-system)
6462 (native-inputs (list gfortran))
6463 (home-page "https://cran.r-project.org/web/packages/leaps/")
6464 (synopsis "Regression subset selection")
6466 "This package provides tools for regression subset selection, including
6467 exhaustive search.")
6468 (license license:gpl2+)))
6470 (define-public r-splus2r
6477 (uri (cran-uri "splus2R" version))
6480 "035zd22zcpkh74rik9ws6g8al6vjz7jgrqs5si361bzb5n290p3x"))))
6481 (properties `((upstream-name . "splus2R")))
6482 (build-system r-build-system)
6483 (home-page "https://cran.r-project.org/web/packages/splus2R/")
6484 (synopsis "Supplemental S-PLUS functionality in R")
6486 "Currently there are many functions in S-PLUS that are missing in R. To
6487 facilitate the conversion of S-PLUS packages to R packages, this package
6488 provides some missing S-PLUS functionality in R.")
6489 (license license:gpl2)))
6491 (define-public r-ifultools
6493 (name "r-ifultools")
6498 (uri (cran-uri "ifultools" version))
6501 "16a7rbvlym3bnfm93ikr5kl0l86ppk0s41fva6idvcx765g3fqkk"))))
6502 (build-system r-build-system)
6504 (list r-mass r-splus2r))
6505 (home-page "https://cran.r-project.org/web/packages/ifultools/")
6506 (synopsis "Insightful research tools")
6507 (description "This package provides C code used by the wmtsa, fractal, and
6509 (license license:gpl2)))
6511 (define-public r-sapa
6518 (uri (cran-uri "sapa" version))
6521 "0kj681rd4c2lvqr926lb6f4qwp281x5274dg6vbk8pf5y7s0qlpc"))))
6522 (build-system r-build-system)
6524 (list r-ifultools r-splus2r))
6525 (home-page "https://cran.r-project.org/web/packages/sapa/")
6526 (synopsis "Spectral analysis for physical applications")
6527 (description "This package provides software for the book Spectral
6528 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
6529 Cambridge University Press, 1993.")
6530 (license license:gpl2)))
6532 (define-public r-aggregation
6534 (name "r-aggregation")
6539 (uri (cran-uri "aggregation" version))
6542 "0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
6543 (build-system r-build-system)
6544 (home-page "https://cran.r-project.org/web/packages/aggregation/")
6545 (synopsis "Methods for p-value aggregation")
6547 "This package contains functionality for performing the following methods
6548 of p-value aggregation: Fisher's method, the Lancaster method (weighted
6549 Fisher's method), and Sidak correction.")
6550 (license license:gpl3)))
6552 (define-public r-quantmod
6559 (uri (cran-uri "quantmod" version))
6562 "0dbcrncv06iqcbkky95dd7l32xq0hhbnkb0kj8wwzym1jf748h5a"))))
6563 (build-system r-build-system)
6565 (list r-curl r-ttr r-xts r-zoo))
6566 (home-page "https://cran.r-project.org/web/packages/quantmod/")
6567 (synopsis "Quantitative financial modelling framework")
6568 (description "This package provides a quantitative financial modelling
6569 framework to allow users to specify, build, trade, and analyse quantitative
6570 financial trading strategies.")
6571 (license license:gpl3)))
6573 (define-public r-tseries
6580 (uri (cran-uri "tseries" version))
6583 "1fhldj95d16cwygw8xg0kvr4xk569mpzprdvahlsf4hzykc2dgs5"))))
6584 (build-system r-build-system)
6586 (list r-quadprog r-quantmod r-zoo))
6589 (home-page "https://cran.r-project.org/web/packages/tseries/")
6590 (synopsis "Time series analysis and computational finance")
6592 "This package provides functions relating to time series analysis and
6593 computational finance.")
6594 (license license:gpl2)))
6596 (define-public r-wmtsa
6603 (uri (cran-uri "wmtsa" version))
6606 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
6607 (build-system r-build-system)
6609 (list r-ifultools r-mass r-splus2r))
6610 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
6611 (synopsis "Wavelet methods for time series analysis")
6613 "This package provides software to accompany the book \"Wavelet Methods
6614 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
6615 University Press, 2000.")
6616 (license license:gpl2)))
6618 (define-public r-tsa
6625 (uri (cran-uri "TSA" version))
6628 "1bv5q609lhmrcxnjnvcj497fbjlv89zwa8q918hw4iki5nkvwwdb"))))
6629 (properties `((upstream-name . "TSA")))
6630 (build-system r-build-system)
6632 (list r-leaps r-locfit r-mgcv r-tseries))
6633 (home-page "https://homepage.divms.uiowa.edu/~kchan/TSA.htm")
6634 (synopsis "Time series analysis")
6636 "This package contains R functions and datasets detailed in the book
6637 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
6638 Cryer and Kung-Sik Chan.")
6639 (license license:gpl2+)))
6641 (define-public r-extradistr
6643 (name "r-extradistr")
6648 (uri (cran-uri "extraDistr" version))
6651 "1gypnbvdzczl0mvznvy8r7hzsvc5gvdvi2mmzj21cqdw9n63944r"))))
6652 (properties `((upstream-name . "extraDistr")))
6653 (build-system r-build-system)
6656 (home-page "https://github.com/twolodzko/extraDistr")
6657 (synopsis "Additional univariate and multivariate distributions")
6659 "This package implements density, distribution functions, quantile
6660 functions and random generation functions for a large number of univariate and
6661 multivariate distributions.")
6662 (license license:gpl2)))
6664 (define-public r-fractal
6671 (uri (cran-uri "fractal" version))
6674 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
6675 (build-system r-build-system)
6683 (home-page "https://cran.r-project.org/web/packages/fractal/")
6684 (synopsis "Fractal time series modeling and analysis")
6686 "This package provides tools for stochastic fractal and deterministic
6687 chaotic time series analysis.")
6688 (license license:gpl2)))
6690 (define-public r-urca
6697 (uri (cran-uri "urca" version))
6700 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
6701 (build-system r-build-system)
6702 (propagated-inputs (list r-nlme))
6703 (native-inputs (list gfortran))
6704 (home-page "https://cran.r-project.org/web/packages/urca/")
6705 (synopsis "Unit root and cointegration tests for time series data")
6707 "This package provides unit root and cointegration tests encountered in
6708 applied econometric analysis.")
6709 (license license:gpl2+)))
6711 (define-public r-cubature
6718 (uri (cran-uri "cubature" version))
6721 "0kk9lw3s66h0sayza3in8rdj7bmgqn4v5lfckhslarpvj2fxsnv0"))))
6722 (build-system r-build-system)
6727 (home-page "https://github.com/bnaras/cubature")
6728 (synopsis "Adaptive multivariate integration over hypercubes")
6730 "This package is an R wrapper around the cubature C library for adaptive
6731 multivariate integration over hypercubes. This version provides both
6732 @code{hcubature} and @code{pcubature} routines in addition to a vector
6734 ;; The included cubature C library is released under GPLv2+, but the
6735 ;; wrapper declares the license to be GPLv3+.
6736 (license (list license:gpl2+ license:gpl3+))))
6738 (define-public r-trend
6745 (uri (cran-uri "trend" version))
6748 "1mr5g5gaxiqj6x83ngcbwwh57vhrhcz0x9dh0rmvs9y2ivk29ccs"))))
6749 (build-system r-build-system)
6751 (list r-extradistr))
6754 (home-page "https://cran.r-project.org/web/packages/trend/")
6755 (synopsis "Non-parametric trend tests and change-point detection")
6757 "The analysis of environmental data often requires the detection of
6758 trends and change-points. This package includes tests for trend
6759 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
6760 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
6761 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
6762 correlation trend test), change-point detection (Lanzante's test procedures,
6763 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
6764 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
6765 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
6766 sample Robust Rank-Order Distributional Test.")
6767 (license license:gpl3)))
6769 (define-public r-expm
6776 (uri (cran-uri "expm" version))
6779 "1p5dapwv8ycxaysgi6imnby04i4kh1c5a2czqa4wygz0s8pr2y9c"))))
6780 (build-system r-build-system)
6781 (propagated-inputs (list r-matrix))
6782 (native-inputs (list gfortran))
6783 (home-page "https://r-forge.r-project.org/projects/expm/")
6784 (synopsis "Tools for matrix exponentials and related quantities")
6786 "This package provides tools for the computation of the matrix
6787 exponential, logarithm, square root, and related quantities.")
6788 (license license:gpl2+)))
6790 (define-public r-complexplus
6792 (name "r-complexplus")
6797 (uri (cran-uri "complexplus" version))
6800 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
6801 (build-system r-build-system)
6803 (list r-expm r-matrix))
6804 (home-page "https://cran.r-project.org/web/packages/complexplus/")
6805 (synopsis "Functions of complex or real variables")
6807 "This package extends several functions to the complex domain, including
6808 the matrix exponential and logarithm, and the determinant.")
6809 (license license:gpl2)))
6811 (define-public r-phontools
6813 (name "r-phontools")
6818 (uri (cran-uri "phonTools" version))
6821 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
6822 (properties `((upstream-name . "phonTools")))
6823 (build-system r-build-system)
6824 (home-page "http://www.santiagobarreda.com/rscripts.html")
6825 (synopsis "Tools for phonetic and acoustic analyses")
6827 "This package contains tools for the organization, display, and analysis
6828 of the sorts of data frequently encountered in phonetics research and
6829 experimentation, including the easy creation of IPA vowel plots, and the
6830 creation and manipulation of WAVE audio files.")
6831 (license license:bsd-2)))
6840 (uri (cran-uri "np" version))
6843 "1a9kzn37cddwfdki5zjmzanxp75pccdjnsvqfrh84hhcsy51pcx3"))))
6844 (build-system r-build-system)
6846 (list r-boot r-cubature r-quadprog r-quantreg))
6847 (home-page "https://github.com/JeffreyRacine/R-Package-np")
6848 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
6849 (description "This package provides non-parametric (and semi-parametric)
6850 kernel methods that seamlessly handle a mix of continuous, unordered, and
6851 ordered factor data types.")
6852 ;; Any version of the GPL.
6853 (license license:gpl3+)))
6855 (define-public r-powerplus
6857 (name "r-powerplus")
6862 (uri (cran-uri "powerplus" version))
6865 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
6866 (build-system r-build-system)
6868 (list r-complexplus r-expm r-mass r-matrix r-phontools))
6869 (home-page "https://cran.r-project.org/web/packages/powerplus/")
6870 (synopsis "Exponentiation operations")
6872 "This package provides tools for the computation of matrix and scalar
6874 (license license:gpl2)))
6876 (define-public r-egg
6883 (uri (cran-uri "egg" version))
6886 "1fy7srpiavfn8kyrr1m84an7acgwi6ydzrg71m3b0vk7y9ybmj0m"))))
6887 (properties `((upstream-name . "egg")))
6888 (build-system r-build-system)
6890 (list r-ggplot2 r-gridextra r-gtable))
6891 (home-page "https://cran.r-project.org/web/packages/egg")
6892 (synopsis "Extensions for ggplot2")
6894 "This package provides miscellaneous functions to help customize ggplot2
6895 objects. High-level functions are provided to post-process ggplot2 layouts
6896 and allow alignment between plot panels, as well as setting panel sizes to
6897 fixed values. Other functions include a custom @code{geom}, and helper
6898 functions to enforce symmetric scales or add tags to facetted plots.")
6899 (license license:gpl3)))
6901 (define-public r-heatmap3
6908 (uri (cran-uri "heatmap3" version))
6911 "0sfvizmmwfk1bjhn6zfx5a4qqfgj1ldg8x90b65crqibgfa36k2r"))))
6912 (build-system r-build-system)
6914 (list r-fastcluster))
6917 (home-page "https://cran.r-project.org/web/packages/heatmap3/")
6918 (synopsis "Improved heatmap package")
6920 "This package provides an improved heatmap package. It is completely
6921 compatible with the original R function @code{heatmap}, and provides more
6922 powerful and convenient features.")
6923 (license license:gpl2+)))
6925 (define-public r-heatmaply
6927 (name "r-heatmaply")
6932 (uri (cran-uri "heatmaply" version))
6935 "1w8yyzb68laxd4zxycvgmpqj5wnyidjgv1vbzbxndp9p92f2cp8a"))))
6936 (build-system r-build-system)
6954 (home-page "https://cran.r-project.org/package=heatmaply")
6955 (synopsis "Interactive cluster heat maps using plotly")
6957 "This package enables you to create interactive cluster heatmaps that can
6958 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
6959 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
6960 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
6961 a popular graphical method for visualizing high-dimensional data, in which a
6962 table of numbers is encoded as a grid of colored cells. The rows and columns
6963 of the matrix are ordered to highlight patterns and are often accompanied by
6965 ;; Either version of the license.
6966 (license (list license:gpl2 license:gpl3))))
6975 (uri (cran-uri "h5" version))
6978 "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
6979 (build-system r-build-system)
6986 (home-page "https://github.com/mannau/h5")
6987 (synopsis "Interface to the HDF5 Library")
6989 "This package provides an S4 interface to the HDF5 library supporting
6990 fast storage and retrieval of R-objects like vectors, matrices and arrays to
6991 binary files in a language independent format. The HDF5 format can therefore
6992 be used as an alternative to R's save/load mechanism. Since h5 is able to
6993 access only subsets of stored data it can also handle data sets which do not
6995 (license license:bsd-2)))
6997 (define-public r-cgdsr
7004 (uri (cran-uri "cgdsr" version))
7007 "07yc819hkabpzzh0g0cbqza6bcfy67b2marrzz1lj97f9iba78ja"))))
7008 (build-system r-build-system)
7010 (list r-httr r-r-methodss3 r-r-oo))
7011 (home-page "https://github.com/cBioPortal/cgdsr")
7012 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
7014 "This package provides a basic set of R functions for querying the Cancer
7015 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
7016 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
7017 (license license:lgpl3)))
7019 (define-public r-import
7026 (uri (cran-uri "import" version))
7029 "018s0x224gqnv4cjfh0fwliyfg6ma9vslmwybrlizfsmqcc5wp37"))))
7030 (build-system r-build-system)
7033 (home-page "https://github.com/smbache/import")
7034 (synopsis "Import mechanism for R")
7036 "This is an alternative mechanism for importing objects from packages.
7037 The syntax allows for importing multiple objects from a package with a single
7038 command in an expressive way. The import package bridges some of the gap
7039 between using @code{library} (or @code{require}) and direct (single-object)
7040 imports. Furthermore the imported objects are not placed in the current
7041 environment. It is also possible to import objects from stand-alone @code{.R}
7043 (license license:expat)))
7045 (define-public r-shinyace
7052 (uri (cran-uri "shinyAce" version))
7055 "1m33dfm2kjirvgix7ybv1kbzgjkicdpv411g9c0q3fw6rnyhfxxn"))))
7056 (properties `((upstream-name . "shinyAce")))
7057 (build-system r-build-system)
7059 (list r-shiny r-jsonlite))
7060 (home-page "https://cran.r-project.org/web/packages/shinyAce/")
7061 (synopsis "Ace editor bindings for Shiny")
7063 "This package provides Ace editor bindings to enable a rich text editing
7064 environment within Shiny.")
7065 (license license:expat)))
7067 (define-public r-randomizr
7069 (name "r-randomizr")
7074 (uri (cran-uri "randomizr" version))
7077 "1grm0h3xkb0pdbbv0gd531g1kn6njp0gcy5fh153rrmajxgd8hhw"))))
7078 (properties `((upstream-name . "randomizr")))
7079 (build-system r-build-system)
7082 (home-page "https://declaredesign.org/r/randomizr/")
7083 (synopsis "Tools for common forms of random assignment and sampling")
7085 "This package provides tools for generating random assignments for common
7086 experimental designs and random samples for common sampling designs.")
7087 (license license:expat)))
7089 (define-public r-base64url
7091 (name "r-base64url")
7096 (uri (cran-uri "base64url" version))
7099 "0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
7100 (build-system r-build-system)
7103 (home-page "https://github.com/mllg/base64url")
7104 (synopsis "Fast and URL-safe base64 encoder and decoder")
7106 "This package provides a URL-safe base64 encoder and decoder. In
7107 contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
7108 the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
7109 encoder does not fill the string with trailing @code{=}. The resulting
7110 encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
7111 and thus are safe to use in URLs or for file names. The package also comes
7112 with a simple base32 encoder/decoder suited for case insensitive file
7114 (license license:gpl3)))
7116 (define-public r-radiant-data
7118 (name "r-radiant-data")
7123 (uri (cran-uri "radiant.data" version))
7126 "12x4nz5n6yz1a67ji79pwvznp9flmn50hpp9y9sfhixir7dvwy27"))
7127 (modules '((guix build utils)))
7130 ;; Delete files that are under CC-NC-SA.
7131 (delete-file-recursively "inst/app/tools/help")
7133 (properties `((upstream-name . "radiant.data")))
7134 (build-system r-build-system)
7168 (home-page "https://github.com/radiant-rstats/radiant.data")
7169 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
7171 "The Radiant Data menu includes interfaces for loading, saving, viewing,
7172 visualizing, summarizing, transforming, and combining data. It also contains
7173 functionality to generate reproducible reports of the analyses conducted in
7175 (license license:agpl3)))
7177 (define-public r-algdesign
7179 (name "r-algdesign")
7184 (uri (cran-uri "AlgDesign" version))
7186 (base32 "0ammlg148gk0p24fh700116nd66636np0jb1wwh0axq5jphwk1pz"))))
7187 (properties `((upstream-name . "AlgDesign")))
7188 (build-system r-build-system)
7189 (home-page "https://github.com/jvbraun/AlgDesign")
7190 (synopsis "Algorithmic experimental design")
7192 "This package provides tools to calculate exact and approximate theory
7193 experimental designs for D, A, and I criteria. Very large designs may be
7194 created. Experimental designs may be blocked or blocked designs created from
7195 a candidate list, using several criteria. The blocking can be done when whole
7196 and within plot factors interact.")
7197 (license license:gpl2+)))
7199 (define-public r-alluvial
7206 (uri (cran-uri "alluvial" version))
7208 (base32 "039frwrsxq1lb97s7vf2vbyyadimkigs628ymym06fxka53drdkp"))))
7209 (properties `((upstream-name . "alluvial")))
7210 (build-system r-build-system)
7211 (native-inputs (list r-knitr))
7212 (home-page "https://github.com/mbojan/alluvial")
7213 (synopsis "Create parallel sets plots (Alluvial Diagrams)")
7215 "This package creates alluvial diagrams (also known as parallel sets
7216 plots) for multivariate and time series-like data.")
7217 (license license:expat)))
7219 (define-public r-signal
7226 (uri (cran-uri "signal" version))
7229 "0qaf39vfmhn3d0bdjqd805ayfkaj48dkmf5dqd47bpk7dp21b837"))))
7230 (build-system r-build-system)
7231 (propagated-inputs (list r-mass))
7232 (native-inputs (list gfortran))
7233 (home-page "https://cran.r-project.org/web/packages/signal/")
7234 (synopsis "Signal processing")
7236 "This package provides a set of signal processing functions originally
7237 written for Matlab and GNU Octave. It includes filter generation utilities,
7238 filtering functions, resampling routines, and visualization of filter models.
7239 It also includes interpolation functions.")
7240 (license license:gpl2)))
7242 (define-public r-gsubfn
7249 (uri (cran-uri "gsubfn" version))
7252 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
7253 (build-system r-build-system)
7254 (propagated-inputs (list r-proto))
7255 (home-page "https://code.google.com/archive/p/gsubfn/")
7256 (synopsis "Utilities for strings and function arguments")
7258 "This package provides @code{gsubfn} which is like @code{gsub} but can
7259 take a replacement function or certain other objects instead of the
7260 replacement string. Matches and back references are input to the replacement
7261 function and replaced by the function output. @code{gsubfn} can be used to
7262 split strings based on content rather than delimiters and for quasi-perl-style
7263 string interpolation. The package also has facilities for translating
7264 formulas to functions and allowing such formulas in function calls instead of
7266 (license license:gpl2+)))
7268 (define-public r-sqldf
7275 (uri (cran-uri "sqldf" version))
7278 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
7279 (build-system r-build-system)
7281 (list r-chron r-dbi r-gsubfn r-proto r-rsqlite))
7282 (home-page "https://github.com/ggrothendieck/sqldf")
7283 (synopsis "Manipulate R data frames using SQL")
7285 "The @code{sqldf} function is typically passed a single argument which is
7286 an SQL select statement where the table names are ordinary R data frame names.
7287 @code{sqldf} transparently sets up a database, imports the data frames into
7288 that database, performs the SQL statement and returns the result using a
7289 heuristic to determine which class to assign to each column of the returned
7290 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
7291 used to read filtered files into R even if the original files are larger than
7292 R itself can handle.")
7293 (license license:gpl2)))
7295 (define-public r-abind
7302 (uri (cran-uri "abind" version))
7305 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
7306 (build-system r-build-system)
7307 (home-page "https://cran.r-project.org/web/packages/abind/")
7308 (synopsis "Combine multidimensional arrays")
7310 "This package provides tools to combine multidimensional arrays into a
7311 single array. This is a generalization of @code{cbind} and @code{rbind}. It
7312 works with vectors, matrices, and higher-dimensional arrays. It also provides
7313 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
7314 extracting and replacing data in arrays.")
7315 (license license:lgpl2.0+)))
7317 (define-public r-prroc
7324 (uri (cran-uri "PRROC" version))
7327 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
7328 (properties `((upstream-name . "PRROC")))
7329 (build-system r-build-system)
7330 (home-page "https://cran.r-project.org/web/packages/PRROC/")
7331 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
7333 "This package computes the areas under the @dfn{precision-recall} (PR)
7334 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
7335 contrast to other implementations, the interpolation between points of the PR
7336 curve is done by a non-linear piecewise function. In addition to the areas
7337 under the curves, the curves themselves can also be computed and plotted by a
7338 specific S3-method.")
7339 (license license:gpl3)))
7341 (define-public r-vim
7348 (uri (cran-uri "VIM" version))
7351 "0fbpm6y3hhiw8srnbc38k19b859jcqzsh78ib8yvj86gck5av0bm"))))
7352 (properties `((upstream-name . "VIM")))
7353 (build-system r-build-system)
7370 (home-page "https://github.com/alexkowa/VIM")
7371 (synopsis "Visualization and imputation of missing values")
7373 "This package provides tools for the visualization of missing and/or
7374 imputed values are introduced, which can be used for exploring the data and
7375 the structure of the missing and/or imputed values. Depending on this
7376 structure of the missing values, the corresponding methods may help to
7377 identify the mechanism generating the missing values and explore the
7378 data including missing values. In addition, the quality of imputation can be
7379 visually explored using various univariate, bivariate, multiple and
7380 multivariate plot methods.")
7381 (license license:gpl2+)))
7383 (define-public r-fnn
7390 (uri (cran-uri "FNN" version))
7393 "0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
7394 (properties `((upstream-name . "FNN")))
7395 (build-system r-build-system)
7396 (home-page "https://cran.r-project.org/web/packages/FNN")
7397 (synopsis "Fast nearest neighbor search algorithms and applications")
7399 "This package provides cover-tree and kd-tree fast k-nearest neighbor
7400 search algorithms. Related applications including KNN classification,
7401 regression and information measures are implemented.")
7402 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
7403 ;; later can be used.
7404 (license license:gpl2+)))
7406 (define-public r-smoother
7413 (uri (cran-uri "smoother" version))
7416 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
7417 (build-system r-build-system)
7420 (home-page "https://cran.r-project.org/web/packages/smoother")
7421 (synopsis "Functions relating to the smoothing of numerical data")
7423 "This package provides a collection of methods for smoothing numerical
7424 data, commencing with a port of the Matlab gaussian window smoothing function.
7425 In addition, several functions typically used in smoothing of financial data
7427 (license license:gpl2)))
7429 (define-public r-riverplot
7431 (name "r-riverplot")
7436 (uri (cran-uri "riverplot" version))
7439 "04ap1dsa7fx03l73jhv1ql3adaaaz2100qawdplxa9xmrllgcgbj"))))
7440 (build-system r-build-system)
7442 (list r-rcolorbrewer))
7445 (home-page "https://logfc.wordpress.com")
7446 (synopsis "Sankey or ribbon plots")
7448 "Sankey plots are a type of diagram that is convenient to illustrate how
7449 flow of information, resources etc. separates and joins, much like observing
7450 how rivers split and merge. For example, they can be used to compare
7451 different clusterings. This package provides an implementation of Sankey
7453 (license license:gpl2+)))
7455 (define-public r-dyn
7462 (uri (cran-uri "dyn" version))
7465 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
7466 (build-system r-build-system)
7469 (home-page "https://cran.r-project.org/web/packages/dyn")
7470 (synopsis "Time series regression")
7472 "This package provides the dyn class interfaces @code{ts}, @code{irts},
7473 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
7474 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
7475 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
7476 @code{randomForest::randomForest()} and other regression functions, allowing
7477 those functions to be used with time series including specifications that may
7478 contain lags, diffs and missing values.")
7480 (license license:gpl2+)))
7482 (define-public r-catdap
7489 (uri (cran-uri "catdap" version))
7492 "0fyhl69z2lznymvpzxra9qvcg85ggzkfjy68c6mzdmf1ja44d2k5"))))
7493 (build-system r-build-system)
7496 (home-page "https://cran.r-project.org/web/packages/catdap/")
7497 (synopsis "Tools for categorical data analysis")
7499 "This package provides functions for analyzing multivariate data.
7500 Dependencies of the distribution of the specified variable (response
7501 variable) to other variables (explanatory variables) are derived and
7502 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
7503 (license license:gpl2+)))
7505 (define-public r-arules
7512 (uri (cran-uri "arules" version))
7515 "05g6ik4z87g83nlicmb380331f84sqchvv1vch49zb7rq6v8gw6r"))))
7516 (build-system r-build-system)
7518 (list r-generics r-matrix))
7519 (home-page "https://github.com/mhahsler/arules")
7520 (synopsis "Mining association rules and frequent itemsets")
7522 "This package provides an infrastructure for representing, manipulating
7523 and analyzing transaction data and patterns (frequent itemsets and association rules).
7524 It also provides C implementations of the association mining algorithms Apriori
7526 (license license:gpl3)))
7528 (define-public r-parsedate
7530 (name "r-parsedate")
7535 (uri (cran-uri "parsedate" version))
7538 "05l6f1n3dsm383w7jfg3j38klvmzzfvc7qi9zr5ij13rljj8s1vb"))))
7539 (build-system r-build-system)
7542 (home-page "https://github.com/gaborcsardi/parsedate")
7544 "Recognize and parse dates in various formats")
7546 "This package provides three functions for dealing with dates:
7547 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
7548 time formats, @code{parse_date} parses dates in unspecified formats,
7549 and @code{format_iso_8601} formats a date in ISO 8601 format.")
7550 (license license:gpl2)))
7552 (define-public r-abc-data
7559 (uri (cran-uri "abc.data" version))
7562 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
7563 (properties `((upstream-name . "abc.data")))
7564 (build-system r-build-system)
7565 (home-page "https://cran.r-project.org/web/packages/abc.data/")
7566 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
7568 "This package contains data which are used by functions of the abc
7569 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
7570 algorithms for performing parameter estimation, model selection, and
7572 (license license:gpl3+)))
7574 (define-public r-abc
7581 (uri (cran-uri "abc" version))
7584 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
7585 (build-system r-build-system)
7587 (list r-abc-data r-locfit r-mass r-nnet r-quantreg))
7588 (home-page "https://cran.r-project.org/web/packages/abc/")
7589 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
7591 "This package implements several @dfn{Approximate Bayesian
7592 Computation} (ABC) algorithms for performing parameter estimation, model
7593 selection, and goodness-of-fit. Cross-validation tools are also available for
7594 measuring the accuracy of ABC estimates, and to calculate the
7595 misclassification probabilities of different models.")
7596 (license license:gpl3+)))
7598 (define-public r-zip
7605 (uri (cran-uri "zip" version))
7608 "1n5ryjdj3i16b4mdp29wapgaklz3yzas5k8ffx7q6fa0jry9i5cz"))))
7609 (build-system r-build-system)
7610 (home-page "https://github.com/gaborcsardi/zip")
7611 (synopsis "Cross-platform Zip compression")
7613 "This package provides a cross-platform Zip compression library for R.
7614 It is a replacement for the @code{zip} function, that does not require any
7615 additional external tools on any platform.")
7616 (license license:cc0)))
7618 (define-public r-openxlsx
7625 (uri (cran-uri "openxlsx" version))
7628 "0695b265g7jwiqk5c3vmmfkvagx82bkpwhvqzhqaqmmn34l6vl35"))))
7629 (build-system r-build-system)
7631 (list r-rcpp r-stringi r-zip))
7634 (home-page "https://github.com/awalker89/openxlsx")
7635 (synopsis "Read, write and edit XLSX files")
7637 "This package simplifies the creation of Excel @code{.xlsx} files by
7638 providing a high level interface to writing, styling and editing worksheets.
7639 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
7640 and @code{XLConnect} packages with the added benefit of removing the
7641 dependency on Java.")
7642 (license license:gpl3)))
7644 (define-public r-rio
7651 (uri (cran-uri "rio" version))
7654 "04jlrhyl0791yxwcpp1s8p1hhkljnijlc5iaxpk56h41w63k39lz"))))
7655 (build-system r-build-system)
7666 (home-page "https://github.com/leeper/rio")
7667 (synopsis "Swiss-army knife for data I/O")
7669 "This package provides streamlined data import and export infrastructure
7670 by making assumptions that the user is probably willing to make: @code{import}
7671 and @code{export} determine the data structure from the file extension,
7672 reasonable defaults are used for data import and export (e.g.,
7673 @code{stringsAsFactors=FALSE}), web-based import is natively
7674 supported (including from SSL/HTTPS), compressed files can be read directly
7675 without explicit decompression, and fast import packages are used where
7676 appropriate. An additional convenience function, @code{convert}, provides a
7677 simple method for converting between file types.")
7678 (license license:gpl2)))
7680 (define-public r-maptools
7687 (uri (cran-uri "maptools" version))
7690 "0fa4a43zax8gn3jdp4ngqav61x4g6l33bg9wzqbngkbjhipck59r"))))
7691 (build-system r-build-system)
7693 (list r-foreign r-lattice r-sp))
7694 (home-page "https://r-forge.r-project.org/projects/maptools/")
7695 (synopsis "Tools for reading and handling spatial objects")
7697 "This package provides a set of tools for manipulating and reading
7698 geographic data, in particular ESRI Shapefiles. It includes binary access to
7699 GSHHG shoreline files. The package also provides interface wrappers for
7700 exchanging spatial objects with other R packages.")
7701 ;; The C source files from shapelib are released under the Expat license.
7702 ;; The R code is released under GPL version 2 or later.
7703 (license (list license:gpl2+
7706 (define-public r-later
7713 (uri (cran-uri "later" version))
7716 "0acqg29hcm2iq1418b54np7zb5pnr3xzrwc3ijv2pz9wra10ix88"))))
7717 (build-system r-build-system)
7719 (list r-rcpp r-rlang))
7722 (home-page "https://github.com/r-lib/later")
7723 (synopsis "Utilities for delaying function execution")
7725 "This package provides tools to execute arbitrary R or C functions some
7726 time after the current time, after the R execution stack has emptied.")
7727 (license license:gpl2+)))
7729 (define-public r-promises
7736 (uri (cran-uri "promises" version))
7739 "1dy4cbqw17awh4q8m7cy3anaj0n9iynabfzflb1g94cyj0bq4fld"))))
7740 (build-system r-build-system)
7742 (list r-later r-magrittr r-r6 r-rcpp r-rlang))
7745 (home-page "https://rstudio.github.io/promises")
7746 (synopsis "Abstractions for promise-based asynchronous programming")
7748 "This package provides fundamental abstractions for doing asynchronous
7749 programming in R using promises. Asynchronous programming is useful for
7750 allowing a single R process to orchestrate multiple tasks in the background
7751 while also attending to something else. Semantics are similar to JavaScript
7752 promises, but with a syntax that is idiomatic R.")
7753 (license license:expat)))
7755 (define-public r-dosnow
7762 (uri (cran-uri "doSNOW" version))
7765 "0f07b38cl7s61vwzkyqkzzsic9g4sw9k6ndbxk3g90l4ca0d1ljc"))))
7766 (properties `((upstream-name . "doSNOW")))
7767 (build-system r-build-system)
7769 (list r-foreach r-iterators r-snow))
7770 (home-page "https://cran.r-project.org/web/packages/doSNOW")
7771 (synopsis "Foreach parallel adaptor for the snow package")
7773 "This package provides a parallel backend for the @code{%dopar%} function
7774 using the @code{snow} package.")
7775 (license license:gpl2)))
7777 (define-public r-fst
7784 (uri (cran-uri "fst" version))
7787 "0vwclzxww8mw9nnpyj29bn71mrr8jjg7ka03979h9rbzw6d9bjrr"))))
7788 (properties `((upstream-name . "fst")))
7789 (build-system r-build-system)
7790 (propagated-inputs (list r-rcpp))
7791 (home-page "http://www.fstpackage.org")
7792 (synopsis "Fast serialization of data frames")
7794 "The fst package for R provides a fast, easy and flexible way to
7795 serialize data frames. With access speeds of multiple GB/s, fst is
7796 specifically designed to unlock the potential of high speed solid state disks.
7797 Data frames stored in the fst format have full random access, both in column
7798 and rows. The fst format allows for random access of stored data and
7799 compression with the LZ4 and ZSTD compressors.")
7800 (license license:agpl3)))
7802 (define-public r-snowfall
7805 (version "1.84-6.1")
7808 (uri (cran-uri "snowfall" version))
7810 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
7811 (build-system r-build-system)
7814 (home-page "https://cran.r-project.org/web/packages/snowfall/")
7815 (synopsis "Easier cluster computing")
7816 (description "This package is a usability wrapper around snow for easier
7817 development of parallel R programs. This package offers e.g. extended error
7818 checks, and additional functions. All functions work in sequential mode, too,
7819 if no cluster is present or wished. The package is also designed as connector
7820 to the cluster management tool @code{sfCluster}, but can also used without
7822 (license license:gpl2+)))
7824 (define-public r-rgexf
7831 (uri (cran-uri "rgexf" version))
7834 "00c2zka1n3k7p1l0mlchr063s6x58p9r3fb64d4wgl4rvsq55q3f"))
7835 ;; Delete minified JavaScript files
7837 '(for-each delete-file
7838 '("inst/gexf-js/js/jquery-2.0.2.min.js"
7839 "inst/gexf-js/js/jquery-ui-1.10.3.custom.min.js"
7840 "inst/gexf-js/js/jquery.mousewheel.min.js")))))
7841 (properties `((upstream-name . "rgexf")))
7842 (build-system r-build-system)
7844 `(#:modules ((guix build utils)
7845 (guix build r-build-system)
7849 (modify-phases %standard-phases
7850 (add-after 'unpack 'process-javascript
7851 (lambda* (#:key inputs #:allow-other-keys)
7852 (invoke "unzip" "-d" "/tmp" (assoc-ref inputs "js-jquery-ui"))
7853 (with-directory-excursion "inst/gexf-js/js/"
7857 `((,(assoc-ref inputs "js-jquery")
7858 "jquery-2.0.2.min.js")
7859 ("/tmp/jquery-ui-1.10.3/ui/jquery-ui.js"
7860 "jquery-ui-1.10.3.custom.min.js")
7861 (,(assoc-ref inputs "js-jquery-mousewheel")
7862 "jquery.mousewheel.min.js"))))
7863 (lambda (sources targets)
7864 (for-each (lambda (source target)
7865 (format #true "Processing ~a --> ~a~%"
7867 (invoke "esbuild" source "--minify"
7868 (string-append "--outfile=" target)))
7869 sources targets)))))))))
7871 (list r-igraph r-servr r-xml))
7873 `(("r-knitr" ,r-knitr)
7874 ("esbuild" ,esbuild)
7879 (uri "https://code.jquery.com/jquery-2.0.2.js")
7882 "0v818bxpw48gdk8i95qqqij80r9jcgisi2r4ac6xnxca20h0gvfj"))))
7886 (uri "https://jqueryui.com/resources/download/jquery-ui-1.10.3.zip")
7889 "00xpfy0l69nj2yan4s8k65ldsrlfsjkmyw2dwcg93dc8mv454vxx"))))
7890 ("js-jquery-mousewheel"
7893 (uri "https://raw.githubusercontent.com/jquery/jquery-mousewheel/\
7894 3.0.6/jquery.mousewheel.js")
7897 "19lk5xy2s47bx8hsa7j6bg012f8yw6d770g230bcnm559kf4nc6v"))))))
7898 (home-page "https://gvegayon.github.io/rgexf")
7899 (synopsis "Build, import and export GEXF graph files")
7901 "Create, read and write GEXF (Graph Exchange XML Format) graph
7902 files (used in Gephi and others). It allows the user to easily build/read
7903 graph files including attributes, GEXF visual attributes (such as color, size,
7904 and position), network dynamics (for both edges and nodes) and edge weighting.
7905 Users can build/handle graphs element-by-element or massively through
7906 data-frames, visualize the graph on a web browser through gexf-js (a
7907 JavaScript library) and interact with the igraph package.")
7908 (license license:expat)))
7910 (define-public r-data-tree
7912 (name "r-data-tree")
7917 (uri (cran-uri "data.tree" version))
7920 "0pizmx2312zsym4m42b97q2184bg3hibvbdrblcga05xln84qrs0"))))
7921 (properties `((upstream-name . "data.tree")))
7922 (build-system r-build-system)
7924 (list r-r6 r-stringi))
7927 (home-page "https://github.com/gluc/data.tree")
7928 (synopsis "General purpose hierarchical data structure")
7930 "Create tree structures from hierarchical data, and traverse the tree in
7931 various orders. Aggregate, cumulate, print, plot, convert to and from
7932 data.frame and more. This is useful for decision trees, machine learning,
7933 finance, conversion from and to JSON, and many other applications.")
7934 (license license:gpl2+)))
7936 (define-public r-dtplyr
7943 (uri (cran-uri "dtplyr" version))
7946 "1wyhhn16mvdj55k2xsh7vy489l7xk4mkz7pjrw16z87awk6yjh16"))))
7947 (properties `((upstream-name . "dtplyr")))
7948 (build-system r-build-system)
7962 (home-page "https://github.com/tidyverse/dtplyr")
7963 (synopsis "Data Table back-end for dplyr")
7965 "This package provides a @code{data.table} backend for @code{dplyr}. The
7966 goal of @code{dtplyr} is to allow you to write @code{dplyr} code that is
7967 automatically translated to the equivalent, but usually much faster,
7968 @code{data.table} code.")
7969 (license license:expat)))
7971 (define-public r-collapsibletree
7973 (name "r-collapsibletree")
7978 (uri (cran-uri "collapsibleTree" version))
7981 "0b65pbp1wnpsrayqi630ds4r98jvcvynnlp6wxdqrnnr9nzw5343"))
7984 ;; Delete minified JavaScript file
7985 (delete-file "inst/htmlwidgets/lib/d3-4.10.2/d3.min.js")
7988 `((upstream-name . "collapsibleTree")))
7989 (build-system r-build-system)
7992 (modify-phases %standard-phases
7993 (add-after 'unpack 'process-javascript
7994 (lambda* (#:key inputs #:allow-other-keys)
7995 (with-directory-excursion "inst/htmlwidgets/lib/d3-4.10.2/"
7996 (let ((source (assoc-ref inputs "d3.v4.js"))
7997 (target "d3.min.js"))
7998 (format #t "Processing ~a --> ~a~%"
8000 (invoke "esbuild" source "--minify"
8001 (string-append "--outfile=" target)))))))))
8003 (list r-data-tree r-htmlwidgets))
8005 `(("esbuild" ,esbuild)
8009 (uri "https://d3js.org/d3.v4.js")
8012 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
8013 (home-page "https://github.com/AdeelK93/collapsibleTree")
8014 (synopsis "Interactive collapsible tree diagrams using D3.js")
8016 "This is a package for interactive Reingold-Tilford tree diagrams created
8017 using D3.js, where every node can be expanded and collapsed by clicking on it.
8018 Tooltips and color gradients can be mapped to nodes using a numeric column in
8019 the source data frame.")
8020 (license license:gpl3+)))
8022 (define-public r-rappdirs
8029 (uri (cran-uri "rappdirs" version))
8032 "1161i3jgjvzjv4p8qbz9r976fnggkcrw3mlj4yd1h2svnijrz5a9"))))
8033 (build-system r-build-system)
8034 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
8035 (synopsis "Determine where to save data, caches, and logs")
8037 "This package provides an easy way to determine which directories on the
8038 user's computer should be used to save data, caches and logs. It is a port of
8039 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
8040 (license license:expat)))
8042 (define-public r-rastervis
8044 (name "r-rastervis")
8049 (uri (cran-uri "rasterVis" version))
8052 "0kgg6cm7xjqya2d46w0i1i1wjpkb8f99lyqy7rgwa7l9xmwzj5n1"))))
8053 (properties `((upstream-name . "rasterVis")))
8054 (build-system r-build-system)
8065 (home-page "https://oscarperpinan.github.io/rastervis/")
8066 (synopsis "Visualization methods for raster data")
8068 "This package provides methods for enhanced visualization and interaction
8069 with raster data. It implements visualization methods for quantitative data
8070 and categorical data, both for univariate and multivariate rasters. It also
8071 provides methods to display spatiotemporal rasters, and vector fields.")
8072 (license license:gpl3)))
8074 (define-public r-rentrez
8081 (uri (cran-uri "rentrez" version))
8084 "0x1g2f6hvkqqlb39z8m5qxhcvsizddic5i7rpqw0wy77xfbna9gv"))))
8085 (properties `((upstream-name . "rentrez")))
8086 (build-system r-build-system)
8088 (list r-httr r-jsonlite r-xml))
8091 (home-page "https://docs.ropensci.org/rentrez/")
8092 (synopsis "Entrez in R")
8094 "This package provides an R interface to the NCBI's EUtils API,
8095 allowing users to search databases like GenBank PubMed, process the results of
8096 those searches and pull data into their R sessions.")
8097 (license license:expat)))
8099 (define-public r-renv
8106 (uri (cran-uri "renv" version))
8109 "1nv5hz40cbvdbc2kkr2q2xqnpkgkmp47nlfbr7z57mpn579zyznh"))))
8110 (properties `((upstream-name . "renv")))
8111 (build-system r-build-system)
8114 (home-page "https://rstudio.github.io/renv")
8115 (synopsis "Project environments")
8117 "This package provides a dependency management toolkit for R. Using
8118 renv, you can create and manage project-local R libraries, save the state of
8119 these libraries to a lockfile, and later restore your library as required.
8120 Together, these tools can help make your projects more isolated, portable, and
8122 (license license:expat)))
8124 (define-public r-learnr
8131 (uri (cran-uri "learnr" version))
8134 "08xwmms6x58y3dsfbl9c6d03145hb4ij97nqr1cc9dxxilmr6x31"))))
8135 (build-system r-build-system)
8151 (home-page "https://rstudio.github.io/learnr/")
8152 (synopsis "Interactive tutorials for R")
8154 "This package provides tools to create interactive tutorials using R
8155 Markdown. Use a combination of narrative, figures, videos, exercises, and
8156 quizzes to create self-paced tutorials for learning about R and R packages.")
8157 (license license:asl2.0)))
8159 (define-public r-analytics
8161 (name "r-analytics")
8166 (uri (cran-uri "analytics" version))
8169 "0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
8170 (build-system r-build-system)
8184 (home-page "https://cran.r-project.org/web/packages/analytics/")
8185 (synopsis "Collection of data analysis tools")
8187 "This package is a collection of data analysis tools. It includes tools
8188 for regression outlier detection in a fitted linear model, stationary
8189 bootstrap using a truncated geometric distribution, a comprehensive test for
8190 weak stationarity, column means by group, weighted biplots, and a heuristic to
8191 obtain a better initial configuration in non-metric MDS.")
8192 (license license:gpl2)))
8194 (define-public r-here
8201 (uri (cran-uri "here" version))
8203 (base32 "0srlr8h8qmr0wrmp7gs4g2ry5dni2hx8n947bik3s3a26f091v88"))))
8204 (properties `((upstream-name . "here")))
8205 (build-system r-build-system)
8206 (propagated-inputs (list r-rprojroot))
8207 (native-inputs (list r-knitr))
8208 (home-page "https://here.r-lib.org/")
8209 (synopsis "Simpler way to find files")
8211 "This package lets you construct paths to your project's files. Use the
8212 @code{here} function as a drop-in replacement for @code{file.path}, it will
8213 always locate the files relative to your project root.")
8214 (license license:expat)))
8216 (define-public r-reticulate
8218 (name "r-reticulate")
8223 (uri (cran-uri "reticulate" version))
8226 "1k0nv43fa9lx44pamxpprnvvmsp15adn5z6hg9siyq0n94hca65r"))))
8227 (build-system r-build-system)
8228 (inputs (list python))
8240 (home-page "https://github.com/rstudio/reticulate")
8241 (synopsis "R interface to Python")
8243 "This package provides an interface from R to Python modules, classes,
8244 and functions. When calling into Python, R data types are automatically
8245 converted to their equivalent Python types. When values are returned from
8246 Python to R they are converted back to R types.")
8247 (license license:asl2.0)))
8249 (define-public r-bibtex
8256 (uri (cran-uri "bibtex" version))
8259 "0vdwx6808r73pk15263f33bkqbfmb08d8jkmr4d7h4ml414ikbbv"))))
8260 (build-system r-build-system)
8261 (propagated-inputs (list r-stringr))
8262 (home-page "https://github.com/romainfrancois/bibtex")
8263 (synopsis "Bibtex parser")
8264 (description "This package provides a utility for R to parse a bibtex
8266 (license license:gpl2+)))
8268 (define-public r-ggseqlogo
8270 (name "r-ggseqlogo")
8275 (uri (cran-uri "ggseqlogo" version))
8278 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
8279 (build-system r-build-system)
8280 (propagated-inputs (list r-ggplot2))
8281 (home-page "https://github.com/omarwagih/ggseqlogo")
8282 (synopsis "ggplot2 extension for drawing genetic sequence logos")
8284 "The range of functions provided by this package makes it possible to
8285 draw highly versatile genomic sequence logos. Features include, but are not
8286 limited to, modifying colour schemes and fonts used to draw the logo,
8287 generating multiple logo plots, and aiding the visualisation with annotations.
8288 Sequence logos can easily be combined with other ggplot2 plots.")
8289 ;; Unspecified version of the LGPL.
8290 (license license:lgpl3+)))
8292 (define-public r-ggsci
8299 (uri (cran-uri "ggsci" version))
8302 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
8303 (build-system r-build-system)
8305 (list r-ggplot2 r-scales))
8306 (home-page "https://nanx.me/ggsci/")
8307 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
8309 "This package provides a collection of ggplot2 color palettes inspired by
8310 plots in scientific journals, data visualization libraries, science fiction
8311 movies, and TV shows.")
8312 (license license:gpl3)))
8314 (define-public r-ggsignif
8321 (uri (cran-uri "ggsignif" version))
8324 "1ad774c7s7y4i00xd89lfigr9aybl94q98ch598k3rchanr4b1fa"))))
8325 (build-system r-build-system)
8330 (home-page "https://github.com/const-ae/ggsignif")
8331 (synopsis "Significance brackets for ggplot2")
8333 "Enrich your ggplots with group-wise comparisons. This package provides
8334 an easy way to indicate if two groups are significantly different. Commonly
8335 this is shown by a bracket on top connecting the groups of interest which
8336 itself is annotated with the level of significance. The package provides a
8337 single layer that takes the groups for comparison and the test as arguments
8338 and adds the annotation to the plot.")
8339 (license license:gpl3)))
8341 (define-public r-rstatix
8348 (uri (cran-uri "rstatix" version))
8351 "0330y8iziffqg8j9j5h9zv4qcdyf8ybhmzxrr9fzq9nc6bf1gbm5"))))
8352 (properties `((upstream-name . "rstatix")))
8353 (build-system r-build-system)
8366 (home-page "https://rpkgs.datanovia.com/rstatix/")
8367 (synopsis "Pipe-friendly framework for basic statistical tests")
8369 "This package provides a simple and intuitive pipe-friendly framework,
8370 coherent with the @code{tidyverse} design philosophy, for performing basic
8371 statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and
8372 correlation analyses. The output of each test is automatically transformed
8373 into a tidy data frame to facilitate visualization. Additional functions are
8374 available for reshaping, reordering, manipulating and visualizing correlation
8376 (license license:gpl2)))
8378 (define-public r-ggpubr
8385 (uri (cran-uri "ggpubr" version))
8388 "0x86lmghr25k8w90yrp360dn42dhp5cjvjpdiv2s2gxfn701xcmb"))))
8389 (build-system r-build-system)
8407 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
8408 (synopsis "ggplot2-based publication-ready plots")
8410 "The ggplot2 package is an excellent and flexible package for elegant
8411 data visualization in R. However the default generated plots require some
8412 formatting before we can send them for publication. The ggpubr package
8413 provides some easy-to-use functions for creating and customizing ggplot2-based
8414 publication-ready plots.")
8415 (license license:gpl2)))
8417 (define-public r-ellipse
8424 (uri (cran-uri "ellipse" version))
8427 "1wm5v7zdv2drgdba7z96jwsx74mqhlq80qgrvdb4vb5r02dcw68p"))))
8428 (build-system r-build-system)
8429 (home-page "https://cran.r-project.org/web/packages/ellipse/")
8430 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
8432 "This package contains various routines for drawing ellipses and
8433 ellipse-like confidence regions, implementing the plots described in Murdoch
8434 and Chow (1996), A graphical display of large correlation matrices, The
8435 American Statistician 50, 178-180. There are also routines implementing the
8436 profile plots described in Bates and Watts (1988), Nonlinear Regression
8437 Analysis and its Applications.")
8438 (license license:gpl2+)))
8440 (define-public r-flashclust
8442 (name "r-flashclust")
8447 (uri (cran-uri "flashClust" version))
8450 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
8451 (properties `((upstream-name . "flashClust")))
8452 (build-system r-build-system)
8453 (native-inputs (list gfortran))
8454 (home-page "https://cran.r-project.org/web/packages/flashClust/")
8455 (synopsis "Implementation of optimal hierarchical clustering")
8457 "This package provides a fast implementation of hierarchical
8459 (license license:gpl2+)))
8461 (define-public r-factominer
8463 (name "r-factominer")
8468 (uri (cran-uri "FactoMineR" version))
8471 "0lg8n9fxxk46nchnj4pbpqqf4swxfsq7r9jzr36dmd36kb7avqxr"))))
8472 (properties `((upstream-name . "FactoMineR")))
8473 (build-system r-build-system)
8488 (home-page "http://factominer.free.fr")
8489 (synopsis "Multivariate exploratory data analysis and data mining")
8491 "This package provides exploratory data analysis methods to summarize,
8492 visualize and describe datasets. The main principal component methods are
8493 available, those with the largest potential in terms of applications:
8494 principal component analysis (PCA) when variables are quantitative,
8495 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
8496 variables are categorical, Multiple Factor Analysis when variables are
8497 structured in groups, etc. and hierarchical cluster analysis.")
8498 (license license:gpl2+)))
8500 (define-public r-factoextra
8502 (name "r-factoextra")
8507 (uri (cran-uri "factoextra" version))
8510 "1allvdjhd3pq8xz30b1cymwcik5iaahghrjrlnn54cwkfhfg0kv2"))))
8511 (build-system r-build-system)
8522 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
8523 (synopsis "Extract and visualize the results of multivariate data analyses")
8525 "This package provides some easy-to-use functions to extract and
8526 visualize the output of multivariate data analyses, including
8527 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
8528 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
8529 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
8530 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
8531 packages. It contains also functions for simplifying some clustering analysis
8532 steps and provides ggplot2-based elegant data visualization.")
8533 (license license:gpl2)))
8535 (define-public r-fansi
8542 (uri (cran-uri "fansi" version))
8545 "0mxm06png4lrl5gy5giws5dgig2faryang8y0wcvwfk120pczqni"))))
8546 (build-system r-build-system)
8548 (list r-knitr)) ; for vignettes
8549 (home-page "https://github.com/brodieG/fansi")
8550 (synopsis "ANSI control sequence aware string functions")
8552 "This package provides counterparts to R string manipulation functions
8553 that account for the effects of ANSI text formatting control sequences.")
8554 (license license:gpl2+)))
8556 (define-public r-nbclust
8563 (uri (cran-uri "NbClust" version))
8566 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
8567 (properties `((upstream-name . "NbClust")))
8568 (build-system r-build-system)
8569 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
8570 (synopsis "Determine the best number of clusters in a data set")
8572 "NbClust provides 30 indexes for determining the optimal number of
8573 clusters in a data set and offers the best clustering scheme from different
8574 results to the user.")
8575 (license license:gpl2)))
8577 (define-public r-hdf5r
8584 (uri (cran-uri "hdf5r" version))
8587 "0bv2q4ir73sbk5ra2q4mc8wbcmiwkws8k0mjlnx9ysi2mdrm3dw7"))))
8588 (build-system r-build-system)
8592 (list r-bit64 r-r6))
8595 (home-page "https://hhoeflin.github.io/hdf5r")
8596 (synopsis "Interface to the HDF5 binary data format")
8598 "HDF5 is a data model, library and file format for storing and managing
8599 large amounts of data. This package provides a nearly feature complete,
8600 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
8601 functionality is added so that HDF5 objects behave very similar to their
8602 corresponding R counterparts.")
8603 (license license:asl2.0)))
8605 (define-public r-itertools
8607 (name "r-itertools")
8612 (uri (cran-uri "itertools" version))
8615 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
8616 (build-system r-build-system)
8619 (home-page "https://cran.r-project.org/web/packages/itertools/")
8620 (synopsis "Iterator tools")
8622 "This package provides various tools for creating iterators, many
8623 patterned after functions in the Python @code{itertools} module, and others
8624 patterned after functions in the snow package.")
8625 (license license:gpl2)))
8627 (define-public r-polynom
8634 (uri (cran-uri "polynom" version))
8637 "1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
8638 (build-system r-build-system)
8639 (home-page "https://cran.r-project.org/web/packages/polynom/")
8640 (synopsis "Functions for univariate polynomial manipulations")
8642 "This package provides a collection of functions to implement a class for
8643 univariate polynomial manipulations.")
8644 (license license:gpl2)))
8646 (define-public r-gbrd
8653 (uri (cran-uri "gbRd" version))
8656 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
8657 (properties `((upstream-name . "gbRd")))
8658 (build-system r-build-system)
8659 (home-page "https://cran.r-project.org/web/packages/gbRd/")
8660 (synopsis "Utilities for processing Rd objects and files")
8662 "This package provides utilities for processing Rd objects and files.
8663 Extract argument descriptions and other parts of the help pages of
8665 (license license:gpl2+)))
8667 (define-public r-rjags
8674 (uri (cran-uri "rjags" version))
8677 "041y4zfr50y96g0kl857jcba0a3gpdpk8qfn9fj8zxzbz71k87xr"))))
8678 (build-system r-build-system)
8685 (home-page "http://mcmc-jags.sourceforge.net")
8686 (synopsis "Bayesian graphical models using MCMC")
8688 "This package provides an R interface to the JAGS MCMC library. JAGS is
8689 Just Another Gibbs Sampler. It is a program for analysis of Bayesian
8690 hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
8691 (license license:gpl2)))
8693 (define-public r-rbibutils
8695 (name "r-rbibutils")
8700 (uri (cran-uri "rbibutils" version))
8703 "1iamdbww3hvxy0bbywc307kyhiczx0bvfhw7nngsm33balcng7kw"))))
8704 (properties `((upstream-name . "rbibutils")))
8705 (build-system r-build-system)
8706 (home-page "https://geobosh.github.io/rbibutils/")
8707 (synopsis "Convert between bibliography formats")
8709 "This package converts between a number of bibliography formats,
8710 including BibTeX, BibLaTeX and Bibentry. It includes a port of the bibutils
8711 utilities and supports all bibliography formats and character encodings
8712 implemented in bibutils.")
8713 (license license:gpl2)))
8715 (define-public r-rdpack
8722 (uri (cran-uri "Rdpack" version))
8725 "1f2m9pxm4s4gkrqh58jznkqj2fcw6f29c1l05k5mmkwsdf3ai0c3"))))
8726 (properties `((upstream-name . "Rdpack")))
8727 (build-system r-build-system)
8730 (home-page "https://github.com/GeoBosh/Rdpack")
8731 (synopsis "Update and manipulate Rd documentation objects")
8733 "This package provides functions for manipulation of R documentation
8734 objects, including functions @code{reprompt()} and @code{ereprompt()} for
8735 updating Rd documentation for functions, methods and classes; it also includes
8736 Rd macros for citations and import of references from bibtex files for use in
8737 Rd files and roxygen2 comments, as well as many functions for manipulation of
8738 references and Rd files.")
8739 (license license:gpl2+)))
8741 (define-public r-officer
8748 (uri (cran-uri "officer" version))
8751 "1gfx299zr4q2264q37994pirv5bd5isn1cszccz603ij3q40wajr"))))
8752 (build-system r-build-system)
8754 (list r-r6 r-uuid r-xml2 r-zip))
8757 (home-page "https://davidgohel.github.io/officer")
8758 (synopsis "Manipulation of Word and PowerPoint documents")
8760 "This package provides tools to access and manipulate Word and PowerPoint
8761 documents from R. The package focuses on tabular and graphical reporting from
8762 R; it also provides two functions that let users get document content into
8763 data objects. A set of functions lets add and remove images, tables and
8764 paragraphs of text in new or existing documents. When working with PowerPoint
8765 presentations, slides can be added or removed; shapes inside slides can also
8766 be added or removed. When working with Word documents, a cursor can be used
8767 to help insert or delete content at a specific location in the document.")
8768 (license license:gpl3)))
8770 (define-public r-profilemodel
8772 (name "r-profilemodel")
8777 (uri (cran-uri "profileModel" version))
8780 "01m5nb8cmq0aq555pxk2a99182si65hhmn68yn9nal2j3zl2bp4i"))))
8781 (properties `((upstream-name . "profileModel")))
8782 (build-system r-build-system)
8783 (home-page "https://github.com/ikosmidis/profileModel")
8784 (synopsis "Profiling inference functions for various model classes")
8786 "This package provides tools that can be used to calculate, evaluate,
8787 plot and use for inference the profiles of *arbitrary* inference functions for
8788 arbitrary @code{glm}-like fitted models with linear predictors. More information
8789 on the methods that are implemented can be found in Kosmidis (2008)
8790 @url{https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf}.")
8791 (license license:gpl2+)))
8793 (define-public r-brglm
8800 (uri (cran-uri "brglm" version))
8803 "08shcz0j1npdn7xkhsvlzs3z4rdwq3g4rk6a4xx8wirqw8n8s2an"))))
8804 (properties `((upstream-name . "brglm")))
8805 (build-system r-build-system)
8807 (list r-profilemodel))
8808 (home-page "https://github.com/ikosmidis/brglm")
8809 (synopsis "Bias reduction in binomial-response generalized linear models")
8811 "Fit generalized linear models with binomial responses using either an
8812 adjusted-score approach to bias reduction or maximum penalized likelihood
8813 where penalization is by Jeffreys invariant prior. These procedures return
8814 estimates with improved frequentist properties (bias, mean squared error) that
8815 are always finite even in cases where the maximum likelihood estimates are
8816 infinite (data separation). Fitting takes place by fitting generalized linear
8817 models on iteratively updated pseudo-data. The interface is essentially the
8818 same as @code{glm}. More flexibility is provided by the fact that custom
8819 pseudo-data representations can be specified and used for model fitting.
8820 Functions are provided for the construction of confidence intervals for the
8821 reduced-bias estimates.")
8822 (license license:gpl2+)))
8824 (define-public r-entropy
8831 (uri (cran-uri "entropy" version))
8834 "1f0j8jsn6pzf4gi5g0akixx6x5vc69ci5f4m2vnwp40frvsqjnkg"))))
8835 (properties `((upstream-name . "entropy")))
8836 (build-system r-build-system)
8837 (home-page "https://www.strimmerlab.org/software/entropy/")
8838 (synopsis "Estimation of entropy, mutual information and related quantities")
8840 "This package implements various estimators of entropy, such as the
8841 shrinkage estimator by Hausser and Strimmer, the maximum likelihood and the
8842 Millow-Madow estimator, various Bayesian estimators, and the Chao-Shen
8843 estimator. It also offers an R interface to the NSB estimator. Furthermore,
8844 it provides functions for estimating Kullback-Leibler divergence, chi-squared,
8845 mutual information, and chi-squared statistic of independence. In addition
8846 there are functions for discretizing continuous random variables.")
8847 (license license:gpl3+)))
8849 (define-public r-acd
8856 (uri (cran-uri "ACD" version))
8859 "1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
8860 (properties `((upstream-name . "ACD")))
8861 (build-system r-build-system)
8862 (home-page "https://cran.r-project.org/web/packages/ACD/")
8863 (synopsis "Categorical data analysis with complete or missing responses")
8865 "This package provides tools for categorical data analysis with complete
8866 or missing responses.")
8867 (license license:gpl2+)))
8869 (define-public r-acdm
8876 (uri (cran-uri "ACDm" version))
8879 "0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
8880 (properties `((upstream-name . "ACDm")))
8881 (build-system r-build-system)
8883 (list r-dplyr r-ggplot2 r-plyr r-rsolnp r-zoo))
8884 (home-page "https://cran.r-project.org/web/packages/ACDm/")
8885 (synopsis "Tools for Autoregressive Conditional Duration Models")
8887 "ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
8888 and Russell, 1998) models. It creates trade, price or volume durations from
8889 transactions (tic) data, performs diurnal adjustments, fits various ACD models
8891 (license license:gpl2+)))
8893 (define-public r-overlap
8900 (uri (cran-uri "overlap" version))
8903 "1arxprhz035ab78ks88n6scwnlwmnb97mlac5gsx90ipb6gkgcyk"))))
8904 (build-system r-build-system)
8905 (home-page "https://cran.r-project.org/web/packages/overlap/")
8906 (synopsis "Estimates of coefficient of overlapping for animal activity patterns")
8908 "This package provides functions to fit kernel density functions to data
8909 on temporal activity patterns of animals; estimate coefficients of overlapping
8910 of densities for two species; and calculate bootstrap estimates of confidence
8912 (license license:gpl3+)))
8914 (define-public r-snakecase
8916 (name "r-snakecase")
8921 (uri (cran-uri "snakecase" version))
8924 "1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
8925 (build-system r-build-system)
8927 (list r-stringi r-stringr))
8928 (home-page "https://github.com/Tazinho/snakecase")
8929 (synopsis "Convert strings into any case")
8931 "This package provides a consistent, flexible and easy to use tool to
8932 parse and convert strings into cases like snake or camel among others.")
8933 (license license:gpl3)))
8935 (define-public r-prediction
8937 (name "r-prediction")
8942 (uri (cran-uri "prediction" version))
8945 "0awlq5lxfia6m2b91w73rksp93rbwv5gwqb36wbji4rgq41rzbrx"))))
8946 (build-system r-build-system)
8948 (list r-data-table))
8949 (home-page "https://github.com/leeper/prediction")
8950 (synopsis "Tidy, type-safe prediction methods")
8952 "This package provides the @code{prediction()} function, a type-safe
8953 alternative to @code{predict()} that always returns a data frame. The package
8954 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
8955 from the @code{stats} package, as well as numerous other model classes from
8956 other add-on packages.")
8957 (license license:expat)))
8959 (define-public r-insight
8966 (uri (cran-uri "insight" version))
8969 "1vizx515a24v5x4f5mzbigl0wl4gz75hp5gqw8lkijygw71li8fn"))))
8970 (build-system r-build-system)
8973 (home-page "https://easystats.github.io/insight/")
8974 (synopsis "Easy access to model information for various model objects")
8976 "This package provides a tool to provide an easy, intuitive and
8977 consistent access to information contained in various R models, like model
8978 formulas, model terms, information about random effects, data that was used to
8979 fit the model or data from response variables. The package mainly revolves
8980 around two types of functions: Functions that find (the names of) information,
8981 starting with @code{find_}, and functions that get the underlying data,
8982 starting with @code{get_}. The package has a consistent syntax and works with
8983 many different model objects, where otherwise functions to access these
8984 information are missing.")
8985 (license license:gpl3)))
8987 (define-public r-sjlabelled
8989 (name "r-sjlabelled")
8994 (uri (cran-uri "sjlabelled" version))
8997 "17gskxr43rgbg7syla3b78g2qgksq2kj07iad4139xycqxblxya0"))))
8998 (build-system r-build-system)
9003 (home-page "https://github.com/strengejacke/sjlabelled")
9004 (synopsis "Labelled data utility functions")
9006 "This package provides a collection of functions dealing with labelled
9007 data, like reading and writing data between R and other statistical software
9008 packages. This includes easy ways to get, set or change value and variable
9009 label attributes, to convert labelled vectors into factors or numeric (and
9010 vice versa), or to deal with multiple declared missing values.")
9011 (license license:gpl3)))
9013 (define-public r-sjmisc
9020 (uri (cran-uri "sjmisc" version))
9023 "1gzkq95ckxr0vhrzggflzli9hs7zr8c0yym9zn1wf74yrr0mgc3q"))))
9024 (build-system r-build-system)
9035 (home-page "https://github.com/strengejacke/sjmisc")
9036 (synopsis "Data and variable transformation functions")
9038 "This package is a collection of miscellaneous utility functions,
9039 supporting data transformation tasks like recoding, dichotomizing or grouping
9040 variables, setting and replacing missing values. The data transformation
9041 functions also support labelled data, and all integrate seamlessly into a
9042 tidyverse workflow.")
9043 (license license:gpl3)))
9045 (define-public r-nortest
9052 (uri (cran-uri "nortest" version))
9055 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
9056 (build-system r-build-system)
9057 (home-page "https://cran.r-project.org/web/packages/nortest/")
9058 (synopsis "Tests for normality")
9060 "This package provides five omnibus tests for testing the composite
9061 hypothesis of normality.")
9062 (license license:gpl2+)))
9064 (define-public r-moonbook
9071 (uri (cran-uri "moonBook" version))
9074 "1ml4vvm0mvrprpyi0l50aw38brx18bk2qny4gybmkvlbakalz9bx"))))
9075 (properties `((upstream-name . "moonBook")))
9076 (build-system r-build-system)
9086 (home-page "https://github.com/cardiomoon/moonBook")
9087 (synopsis "Functions and datasets for the book by Keon-Woong Moon")
9089 "This package provides several analysis-related functions for the book
9090 entitled \"R statistics and graph for medical articles\" (written in Korean),
9091 version 1, by Keon-Woong Moon with Korean demographic data with several plot
9093 (license license:gpl2)))
9095 (define-public r-flextable
9097 (name "r-flextable")
9102 (uri (cran-uri "flextable" version))
9105 "01nm0357b0z4dgrplbq9ms63j51n0rgvvxyy068zdsc5p7j3lql2"))))
9106 (build-system r-build-system)
9120 (home-page "https://davidgohel.github.io/flextable")
9121 (synopsis "Functions for tabular reporting")
9123 "This package provides tools to create pretty tables for HTML documents
9124 and other formats. Functions are provided to let users create tables, modify
9125 and format their content. It extends the @code{officer} package and can be
9126 used within R markdown documents when rendering to HTML and to Word
9128 (license license:gpl3)))
9130 (define-public r-writexl
9137 (uri (cran-uri "writexl" version))
9140 "0mfzyn8n5x5x5gf382bqgq61zpw9dymrp5kzdm2sbszplmxf6xry"))))
9141 (build-system r-build-system)
9142 (inputs (list zlib))
9143 (home-page "https://github.com/ropensci/writexl")
9144 (synopsis "Export data frames to xlsx format")
9146 "This package provides a data frame to xlsx exporter based on
9148 (license license:bsd-2)))
9150 (define-public r-biasedurn
9152 (name "r-biasedurn")
9157 (uri (cran-uri "BiasedUrn" version))
9160 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
9161 (properties `((upstream-name . "BiasedUrn")))
9162 (build-system r-build-system)
9163 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
9164 (synopsis "Biased Urn model distributions")
9166 "This package provides statistical models of biased sampling in the form
9167 of univariate and multivariate noncentral hypergeometric distributions,
9168 including Wallenius' noncentral hypergeometric distribution and Fisher's
9169 noncentral hypergeometric distribution (also called extended hypergeometric
9171 (license license:gpl3)))
9173 (define-public r-goplot
9180 (uri (cran-uri "GOplot" version))
9183 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
9184 (properties `((upstream-name . "GOplot")))
9185 (build-system r-build-system)
9187 (list r-ggdendro r-ggplot2 r-gridextra r-rcolorbrewer))
9188 (home-page "https://github.com/wencke/wencke.github.io")
9189 (synopsis "Visualization of functional analysis data")
9191 "This package provides an implementation of multilayered visualizations
9192 for enhanced graphical representation of functional analysis data. It
9193 combines and integrates omics data derived from expression and functional
9194 annotation enrichment analyses. Its plotting functions have been developed
9195 with an hierarchical structure in mind: starting from a general overview to
9196 identify the most enriched categories (modified bar plot, bubble plot) to a
9197 more detailed one displaying different types of relevant information for the
9198 molecules in a given set of categories (circle plot, chord plot, cluster plot,
9199 Venn diagram, heatmap).")
9200 (license license:gpl2)))
9202 (define-public r-getopt
9209 (uri (cran-uri "getopt" version))
9212 "0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
9213 (build-system r-build-system)
9214 (home-page "https://github.com/trevorld/getopt")
9215 (synopsis "Command-line option processor for R")
9217 "This package is designed to be used with Rscript to write shebang
9218 scripts that accept short and long options. Many users will prefer to
9219 use the packages @code{optparse} or @code{argparse} which add extra
9220 features like automatically generated help options and usage texts,
9221 support for default values, positional argument support, etc.")
9222 (license license:gpl2+)))
9224 (define-public r-findpython
9226 (name "r-findpython")
9231 (uri (cran-uri "findpython" version))
9234 "0jf10jpqla90x03kl3k77gnd255zmw9rvr8d724vb17cqawh9yar"))))
9235 (build-system r-build-system)
9236 (home-page "https://github.com/trevorld/findpython")
9237 (synopsis "Functions to find an acceptable Python binary")
9239 "This package was designed to find an acceptable Python binary that
9240 matches version and feature constraints.")
9241 (license license:expat)))
9243 ;; This in not the same as "r-argparser"
9244 (define-public r-argparse
9251 (uri (cran-uri "argparse" version))
9254 "0vm6nrzl6rsq2qw3km3i4s92kq9phs3cbxzv3i8hlyld9ajk3nmf"))))
9255 (build-system r-build-system)
9256 (inputs (list python))
9258 (list r-findpython r-jsonlite r-r6))
9261 (home-page "https://github.com/trevorld/argparse")
9262 (synopsis "Command line optional and positional argument parser")
9264 "This package provides a command line parser to be used with Rscript to
9265 write shebang scripts that gracefully accept positional and optional arguments
9266 and automatically generate usage notices.")
9267 (license license:gpl2+)))
9269 (define-public r-hash
9276 (uri (cran-uri "hash" version))
9279 "0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
9280 (build-system r-build-system)
9281 (home-page "https://cran.r-project.org/web/packages/hash/")
9282 (synopsis "Implementation of hash/associated arrays/dictionaries")
9284 "This package implements a data structure similar to hashes in Perl and
9285 dictionaries in Python but with a purposefully R flavor. For objects of
9286 appreciable size, access using hashes outperforms native named lists and
9288 (license license:gpl2+)))
9290 (define-public r-orddom
9297 (uri (cran-uri "orddom" version))
9300 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
9301 (build-system r-build-system)
9302 (propagated-inputs (list r-psych))
9303 (home-page "https://cran.r-project.org/web/packages/orddom/")
9304 (synopsis "Ordinal dominance statistics")
9306 "This package provides tools to compute ordinal, statistics and effect
9307 sizes as an alternative to mean comparison: Cliff's delta or success rate
9308 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
9309 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
9310 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
9311 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
9312 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
9313 Group (Non-)Overlap considerations.")
9314 (license license:gpl2)))
9316 (define-public r-deriv
9323 (uri (cran-uri "Deriv" version))
9326 "130g3mv0z9sqs6y23a0a94512iiw05yr6fp378vhdxxbignzbnyv"))))
9327 (properties `((upstream-name . "Deriv")))
9328 (build-system r-build-system)
9329 (home-page "https://cran.r-project.org/web/packages/Deriv")
9330 (synopsis "Symbolic differentiation")
9332 "This package provides an R-based solution for symbolic differentiation.
9333 It admits user-defined functions as well as function substitution in arguments
9334 of functions to be differentiated. Some symbolic simplification is part of
9336 (license license:gpl3+)))
9338 (define-public r-doby
9345 (uri (cran-uri "doBy" version))
9348 "1xhjh2d7zfgw8wbcj5yfscvmwbjar1w544ika13da69dydm44j81"))))
9349 (properties `((upstream-name . "doBy")))
9350 (build-system r-build-system)
9365 (home-page "https://people.math.aau.dk/~sorenh/software/doBy/")
9366 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
9368 "This package contains:
9371 @item facilities for working with grouped data: @code{do}
9372 something to data stratified @code{by} some variables.
9373 @item implementations of least-squares means, general linear contrasts, and
9374 @item miscellaneous other utilities.
9376 (license license:gpl2+)))
9378 (define-public r-refgenome
9380 (name "r-refgenome")
9385 (uri (cran-uri "refGenome" version))
9388 "1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
9389 (properties `((upstream-name . "refGenome")))
9390 (build-system r-build-system)
9392 (list r-dbi r-doby r-rsqlite))
9393 (home-page "https://cran.r-project.org/web/packages/refGenome/")
9395 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
9397 "This package contains functionality for importing and managing of
9398 downloaded genome annotation data from the Ensembl genome browser (European
9399 Bioinformatics Institute) and from the UCSC genome browser (University of
9400 California, Santa Cruz) and annotation routines for genomic positions and
9401 splice site positions.")
9402 (license license:gpl2)))
9404 (define-public r-basix
9411 (uri (cran-uri "BASIX" version))
9414 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
9415 (properties `((upstream-name . "BASIX")))
9416 (build-system r-build-system)
9417 (home-page "https://cran.r-project.org/web/packages/BASIX/")
9418 (synopsis "Efficient C/C++ toolset for R")
9420 "BASIX provides some efficient C/C++ implementations of native R
9421 procedures to speed up calculations in R.")
9422 (license license:gpl2)))
9424 (define-public r-blockfest
9426 (name "r-blockfest")
9431 (uri (cran-uri "BlockFeST" version))
9434 "1fcl3yc1cf09znqbj787d3fd2kl5rp63la7pxawsgmap7nxwkp65"))))
9435 (properties `((upstream-name . "BlockFeST")))
9436 (build-system r-build-system)
9437 (propagated-inputs (list r-basix))
9438 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
9439 (synopsis "Bayesian calculation of region-specific fixation index")
9441 "This package provides an R implementation of an extension of the
9442 BayeScan software for codominant markers, adding the option to group
9443 individual SNPs into pre-defined blocks. A typical application of this new
9444 approach is the identification of genomic regions, genes, or gene sets
9445 containing one or more SNPs that evolved under directional selection.")
9446 (license license:gpl2)))
9448 (define-public r-proc
9455 (uri (cran-uri "pROC" version))
9458 "1abvbzdss12n64pp9vlgnn0q3abh0nj4n0a8cinwwvhphjrm9vym"))))
9459 (properties `((upstream-name . "pROC")))
9460 (build-system r-build-system)
9462 (list r-plyr r-rcpp))
9463 (home-page "https://web.expasy.org/pROC/")
9464 (synopsis "Display and analyze ROC curves")
9466 "This package provides tools for visualizing, smoothing and comparing
9467 receiver operating characteristic (ROC curves). The area under the
9468 curve (AUC) can be compared with statistical tests based on U-statistics or
9469 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
9470 (license license:gpl3+)))
9472 (define-public r-rootsolve
9474 (name "r-rootsolve")
9479 (uri (cran-uri "rootSolve" version))
9482 "182bb727sgqi5f3pzmw8jnn328wdjrgj9lfvg49gv8s22rjd3cxm"))))
9483 (properties `((upstream-name . "rootSolve")))
9484 (build-system r-build-system)
9485 (native-inputs (list gfortran))
9486 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
9487 (synopsis "Tools for the analysis of ordinary differential equations")
9489 "This package provides routines to find the root of nonlinear functions,
9490 and to perform steady-state and equilibrium analysis of @dfn{ordinary
9491 differential equations} (ODE). It includes routines that:
9494 @item generate gradient and jacobian matrices (full and banded),
9495 @item find roots of non-linear equations by the Newton-Raphson method,
9496 @item estimate steady-state conditions of a system of (differential) equations
9497 in full, banded or sparse form, using the Newton-Raphson method, or by
9498 dynamically running,
9499 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
9500 and 3-D partial differential equations, that have been converted to ordinary
9501 differential equations by numerical differencing (using the method-of-lines
9504 (license license:gpl2+)))
9506 (define-public r-abcanalysis
9508 (name "r-abcanalysis")
9513 (uri (cran-uri "ABCanalysis" version))
9515 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
9516 (properties `((upstream-name . "ABCanalysis")))
9517 (build-system r-build-system)
9518 (propagated-inputs (list r-plotrix))
9519 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
9520 (synopsis "Computed ABC Analysis")
9522 "Multivariate data sets often differ in several factors or derived statistical
9523 parameters, which have to be selected for a valid interpretation. Basing this
9524 selection on traditional statistical limits leads occasionally to the perception
9525 of losing information from a data set. This package provides tools to calculate
9526 these limits on the basis of the mathematical properties of the distribution of
9527 the analyzed items.")
9528 (license license:gpl3)))
9530 (define-public r-slam
9537 (uri (cran-uri "slam" version))
9539 (base32 "1ggqcf8l1z2hpi7qy4mg0d2ps48bjjb8z1y1xz6fq162cqrbz6bq"))))
9540 (build-system r-build-system)
9541 (home-page "https://cran.r-project.org/web/packages/slam/")
9542 (synopsis "Sparse lightweight arrays and matrices")
9544 "This package contains data structures and algorithms for sparse arrays and matrices,
9545 based on index arrays and simple triplet representations, respectively.")
9546 (license license:gpl2)))
9548 (define-public r-manipulatewidget
9550 (name "r-manipulatewidget")
9555 (uri (cran-uri "manipulateWidget" version))
9557 (base32 "1dpgzmiv08afm57yxr017b014lfn9h3pa4w65prk5k3dgn6p4wsv"))))
9559 `((upstream-name . "manipulateWidget")))
9560 (build-system r-build-system)
9573 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
9574 (synopsis "Add even more interactivity to interactive charts")
9576 "This package lets you create in just a few lines of R code a nice user interface to
9577 modify the data or the graphical parameters of one or multiple interactive
9578 charts. It is useful to quickly explore visually some data or for package
9579 developers to generate user interfaces easy to maintain.")
9580 (license license:gpl2+)))
9589 (uri (cran-uri "A3" version))
9591 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
9592 (properties `((upstream-name . "A3")))
9593 (build-system r-build-system)
9595 (list r-pbapply r-xtable))
9596 (home-page "https://cran.r-project.org/web/packages/A3/")
9597 (synopsis "Error metrics for predictive models")
9599 "This package supplies tools for tabulating and analyzing the results of predictive
9600 models. The methods employed are applicable to virtually any predictive model
9601 and make comparisons between different methodologies straightforward.")
9602 (license license:gpl2+)))
9604 (define-public r-infotheo
9611 (uri (cran-uri "infotheo" version))
9614 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
9615 (build-system r-build-system)
9616 (home-page "http://homepage.meyerp.com/software")
9617 (synopsis "Information-theoretic measures")
9619 "This package implements various measures of information theory based on
9620 several entropy estimators.")
9621 (license license:gpl3+)))
9623 (define-public r-nsprcomp
9630 (uri (cran-uri "nsprcomp" version))
9633 "1zlc1ximx96f235c0l8qfs6vbp1kpnbf943wxsfahnnlnxvwi59f"))))
9634 (properties `((upstream-name . "nsprcomp")))
9635 (build-system r-build-system)
9636 (home-page "https://sigg-iten.ch/research/")
9637 (synopsis "Non-negative and sparse PCA")
9639 "This package implements two methods for performing a constrained
9640 principal component analysis (PCA), where non-negativity and/or sparsity
9641 constraints are enforced on the principal axes (PAs). The function
9642 @code{nsprcomp} computes one principal component (PC) after the other. Each
9643 PA is optimized such that the corresponding PC has maximum additional variance
9644 not explained by the previous components. In contrast, the function
9645 @code{nscumcomp} jointly computes all PCs such that the cumulative variance is
9646 maximal. Both functions have the same interface as the @code{prcomp} function
9647 from the @code{stats} package (plus some extra parameters).")
9648 (license license:gpl2+)))
9650 (define-public r-cmplot
9657 (uri (cran-uri "CMplot" version))
9660 "0xyh75y0c84nnkrv6c8xrvla54w51phgdwn8a69799f2r87z7c81"))))
9661 (properties `((upstream-name . "CMplot")))
9662 (build-system r-build-system)
9663 (home-page "https://github.com/YinLiLin/CMplot")
9664 (synopsis "Circle Manhattan plot")
9666 "Circle Manhattan Plot is an R package that can lay out genome-wide
9667 association study P-value results in both traditional rectangular patterns,
9668 QQ-plot and novel circular ones. United in only one bull's eye style plot,
9669 association results from multiple traits can be compared interactively,
9670 thereby to reveal both similarities and differences between signals.
9671 Additional functions include: highlight signals, a group of SNPs, chromosome
9672 visualization and candidate genes around SNPs.")
9673 (license license:gpl2+)))
9675 (define-public r-precrec
9682 (uri (cran-uri "precrec" version))
9685 "0kwn902z32qcnkffjm6dqnaxagx31xjdcak50clbgrway2pcdjrm"))))
9686 (properties `((upstream-name . "precrec")))
9687 (build-system r-build-system)
9695 (native-inputs (list r-knitr))
9696 (home-page "https://evalclass.github.io/precrec/")
9697 (synopsis "Calculate accurate precision-recall and ROC curves")
9699 "This package provides tools for accurate calculations and visualization
9700 of precision-recall and ROC (Receiver Operator Characteristics) curves.")
9701 (license license:gpl3)))
9703 (define-public r-netrep
9710 (uri (cran-uri "NetRep" version))
9713 "1swlb2k9bc7whvslxbklz864j9ynvna73hvq5rhv61cv5vy05ksd"))))
9714 (properties `((upstream-name . "NetRep")))
9715 (build-system r-build-system)
9725 (native-inputs (list r-knitr))
9726 (home-page "https://cran.r-project.org/package=NetRep")
9727 (synopsis "Permutation testing network module preservation across datasets")
9729 "This package provides functions for assessing the
9730 replication/preservation of a network module's topology across datasets
9731 through permutation testing.")
9732 (license license:gpl2)))
9734 (define-public r-intergraph
9736 (name "r-intergraph")
9741 (uri (cran-uri "intergraph" version))
9744 "18a7xgb2rp0w9jl2rkh8nzyjprrs5w7h2iidvc8c38bzx3qpggkc"))))
9745 (properties `((upstream-name . "intergraph")))
9746 (build-system r-build-system)
9748 (list r-igraph r-network))
9751 (home-page "http://mbojan.github.io/intergraph")
9752 (synopsis "Coercion routines for network data objects")
9754 "Functions implemented in this package allow coercing (i.e. convert)
9755 network data between classes provided by other R packages. Currently
9756 supported classes are those defined in packages @code{network} and
9758 (license license:gpl3)))
9760 (define-public r-abcoptim
9767 (uri (cran-uri "ABCoptim" version))
9769 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
9770 (properties `((upstream-name . "ABCoptim")))
9771 (build-system r-build-system)
9772 (propagated-inputs (list r-rcpp))
9773 (home-page "https://github.com/gvegayon/ABCoptim/")
9774 (synopsis "Optimization of Artificial Bee Colony algorithm")
9776 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
9777 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
9778 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
9779 algorithms, and uses only common control parameters such as colony size and
9780 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
9781 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
9782 This version is a work-in-progress and is written in R code.")
9783 (license license:expat)))
9785 (define-public r-abcp2
9792 (uri (cran-uri "ABCp2" version))
9794 (base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
9795 (properties `((upstream-name . "ABCp2")))
9796 (build-system r-build-system)
9797 (propagated-inputs (list r-mass))
9798 (home-page "https://cran.r-project.org/web/packages/ABCp2/")
9799 (synopsis "Approximate Bayesian Computational Model for Estimating P2")
9801 "This package tests the goodness of fit of a distribution of offspring to the Normal,
9802 Poisson, and Gamma distribution and estimates the proportional paternity of the
9803 second male (P2) based on the best fit distribution.")
9804 (license license:gpl2)))
9806 (define-public r-abcrf
9813 (uri (cran-uri "abcrf" version))
9815 (base32 "1ghbd24yhqy3xhdxas6ccn84nkavqpgldx5ck8kijknc7qjm8k27"))))
9816 (build-system r-build-system)
9827 (home-page "https://cran.r-project.org/web/packages/abcrf/")
9828 (synopsis "Approximate bayesian computation via random forests")
9830 "This package performs approximate bayesian computation (ABC) model choice and
9831 parameter inference via random forests. This machine learning tool named random
9832 forests (RF) can conduct selection among the highly complex models covered by
9834 (license license:gpl2+)))
9836 (define-public r-abctools
9843 (uri (cran-uri "abctools" version))
9845 (base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
9846 (build-system r-build-system)
9848 (list r-abc r-abind r-hmisc r-plyr))
9849 (home-page "https://github.com/dennisprangle/abctools/")
9850 (synopsis "Tools for ABC analyses")
9852 "This @code{r-abctools} package provides tools for approximate Bayesian computation
9853 including summary statistic selection and assessing coverage. This includes
9854 recent dimension reduction algorithms to tune the choice of summary statistics,
9855 and coverage methods to tune the choice of threshold.")
9856 (license license:gpl2+)))
9858 (define-public r-ggstance
9865 (uri (cran-uri "ggstance" version))
9867 (base32 "0jz9vvnmcc6a38n8nzr458r65sna23bgn5r8mxdhzdlyqibihr7d"))))
9868 (build-system r-build-system)
9870 (list r-ggplot2 r-plyr r-rlang r-withr))
9871 (home-page "https://cran.r-project.org/web/packages/ggstance/")
9872 (synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
9874 "This package is a @code{r-ggplot2} extension that provides flipped components:
9876 @item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
9877 @item vertical versions of @code{r-ggplot2} positions.
9879 (license license:gpl3)))
9881 (define-public r-ggnetwork
9883 (name "r-ggnetwork")
9888 (uri (cran-uri "ggnetwork" version))
9891 "0gqdgy5yh700dg0f7xb80hczlnqfisn8l55j7amd1n7fp2x5sr8v"))))
9892 (properties `((upstream-name . "ggnetwork")))
9893 (build-system r-build-system)
9895 (list r-ggplot2 r-ggrepel r-igraph r-network r-sna))
9896 (native-inputs (list r-knitr))
9897 (home-page "https://github.com/briatte/ggnetwork")
9898 (synopsis "Geometries to plot networks with ggplot2")
9900 "This package provides geometries to plot network objects with the
9902 (license license:gpl3)))
9904 (define-public r-cvauc
9911 (uri (cran-uri "cvAUC" version))
9914 "1m2y50a1yapf1c74km9a4r47ds2z2bfp4wwwkqin7swv9v1s7d28"))))
9915 (properties `((upstream-name . "cvAUC")))
9916 (build-system r-build-system)
9918 (list r-data-table r-rocr))
9919 (home-page "https://github.com/ledell/cvAUC")
9920 (synopsis "Cross-validated area under the ROC curve confidence intervals")
9922 "This package contains various tools for working with and evaluating
9923 cross-validated area under the ROC curve (AUC) estimators. The primary
9924 functions of the package are @code{ci.cvAUC} and @code{ci.pooled.cvAUC}, which
9925 report cross-validated AUC and compute confidence intervals for
9926 cross-validated AUC estimates based on influence curves for i.i.d. and pooled
9927 repeated measures data, respectively.")
9928 (license license:asl2.0)))
9930 (define-public r-gam
9937 (uri (cran-uri "gam" version))
9940 "1zhy2fp7pxac8xp3z3hndhprj4s5gx3305b627vc78bal1ml3swi"))))
9941 (properties `((upstream-name . "gam")))
9942 (build-system r-build-system)
9947 (home-page "https://cran.r-project.org/package=gam")
9948 (synopsis "Generalized additive models")
9950 "This package provides functions for fitting and working with generalized
9951 additive models, as described in chapter 7 of \"Statistical Models in
9952 S\" (Chambers and Hastie (eds), 1991), and \"Generalized Additive
9953 Models\" (Hastie and Tibshirani, 1990).")
9954 (license license:gpl2)))
9956 (define-public r-superlearner
9958 (name "r-superlearner")
9963 (uri (cran-uri "SuperLearner" version))
9966 "00any24msgflyagy87nznpfjz5g9v15frqda6c679wa8plx26hjz"))))
9967 (properties `((upstream-name . "SuperLearner")))
9968 (build-system r-build-system)
9970 (list r-cvauc r-gam r-nnls))
9973 (home-page "https://github.com/ecpolley/SuperLearner")
9974 (synopsis "Super learner prediction")
9976 "This package implements the super learner prediction method and contains
9977 a library of prediction algorithms to be used in the super learner.")
9978 (license license:gpl3)))
9980 (define-public r-drtmle
9987 (uri (cran-uri "drtmle" version))
9990 "08a6k0nrg6mqdslwjc71583x52vnax87nbfalk98zczwvrrdwvxa"))))
9991 (properties `((upstream-name . "drtmle")))
9992 (build-system r-build-system)
9994 (list r-future-apply r-np r-superlearner))
9997 (home-page "https://github.com/benkeser/drtmle")
9998 (synopsis "Doubly-robust nonparametric estimation and inference")
10000 "This package implements targeted minimum loss-based estimators of
10001 counterfactual means and causal effects that are doubly-robust with respect
10002 both to consistency and asymptotic normality.")
10003 (license license:expat)))
10005 (define-public r-dofuture
10007 (name "r-dofuture")
10012 (uri (cran-uri "doFuture" version))
10015 "1hqzdlgcrc5l6xjwdylsc9iiysi2wx8k1j1vmw3wryj26057c9y4"))))
10016 (properties `((upstream-name . "doFuture")))
10017 (build-system r-build-system)
10020 (modify-phases %standard-phases
10021 (add-after 'unpack 'set-HOME
10022 (lambda _ (setenv "HOME" "/tmp"))))))
10024 (list r-foreach r-future r-globals r-iterators))
10026 (list r-r-rsp)) ; vignette builder
10027 (home-page "https://github.com/HenrikBengtsson/doFuture")
10028 (synopsis "Foreach parallel adapter using the future API")
10030 "This package provides a @code{%dopar%} adapter such that any type of
10031 futures can be used as backends for the @code{foreach} framework.")
10032 (license license:lgpl2.1+)))
10034 (define-public r-superheat
10036 (name "r-superheat")
10041 (uri (cran-uri "superheat" version))
10044 "01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"))))
10045 (properties `((upstream-name . "superheat")))
10046 (build-system r-build-system)
10055 (home-page "https://cran.r-project.org/package=superheat")
10056 (synopsis "Graphical tool for exploring complex datasets using heatmaps")
10058 "This package provides a system for generating extendable and
10059 customizable heatmaps for exploring complex datasets, including big data and
10060 data with multiple data types.")
10061 (license license:cc0)))
10063 (define-public r-qualv
10070 (uri (cran-uri "qualV" version))
10073 "0rkjzva2h158d5c631jmjjh7qjibbyisl0503san80rk9fgxl45b"))))
10074 (properties `((upstream-name . "qualV")))
10075 (build-system r-build-system)
10077 (list r-kernsmooth))
10078 (home-page "http://qualV.R-Forge.R-Project.org/")
10079 (synopsis "Qualitative Validation Methods")
10081 "This package provides qualitative methods for the validation of dynamic
10082 models. It contains
10085 @item an orthogonal set of deviance measures for absolute, relative and
10087 @item approaches accounting for time shifts.
10090 The first approach transforms time to take time delays and speed differences
10091 into account. The second divides the time series into interval units
10092 according to their main features and finds the @dfn{longest common
10093 subsequence} (LCS) using a dynamic programming algorithm.")
10094 (license license:gpl2+)))
10096 (define-public r-mosaiccore
10098 (name "r-mosaiccore")
10103 (uri (cran-uri "mosaicCore" version))
10105 (base32 "1h3ixzna4xy42rdnd89jj0v9q0riy3fnkd33z6l5c0zaidzm58fz"))))
10106 (properties `((upstream-name . "mosaicCore")))
10107 (build-system r-build-system)
10109 (list r-dplyr r-mass r-rlang r-tidyr))
10110 (home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
10111 (synopsis "Common utilities for mosaic family packages")
10113 "Common utilities used in other Mosaic family packages are collected here.")
10114 (license license:gpl2+)))
10116 (define-public r-labelled
10118 (name "r-labelled")
10123 (uri (cran-uri "labelled" version))
10126 "0ffnhlr239nqcwb35m4hll21abnnhpmyy5wlxnyahrg0kqb0xb1n"))))
10127 (properties `((upstream-name . "labelled")))
10128 (build-system r-build-system)
10139 (home-page "http://larmarange.github.io/labelled/")
10140 (synopsis "Manipulating labelled data")
10142 "This package provides useful functions to deal with the
10143 @code{haven_labelled} and @code{haven_labelled_spss} classes introduced by the
10145 (license license:gpl3)))
10147 (define-public r-ggformula
10149 (name "r-ggformula")
10154 (uri (cran-uri "ggformula" version))
10156 (base32 "1ph5jd8svk8hmshi894vmmpq3zwgdmf4yn3gmdlkad68z8jynhsp"))))
10157 (build-system r-build-system)
10172 (home-page "https://github.com/ProjectMOSAIC/ggformula/")
10173 (synopsis "Formula interface for the @code{r-ggplot2}")
10175 "The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
10176 gf_density(), and so on, bring the formula interface to ggplot(). This captures
10177 and extends the excellent simplicity of the lattice-graphics formula interface,
10178 while providing the intuitive capabilities of @code{r-ggplot2}.")
10179 (license license:expat)))
10181 (define-public r-mosaicdata
10183 (name "r-mosaicdata")
10188 (uri (cran-uri "mosaicData" version))
10190 (base32 "0h3f5fgzkzjfgf3ml0qa5j52921y6wy6jgggxmhs31bs8fd4srg4"))))
10191 (properties `((upstream-name . "mosaicData")))
10192 (build-system r-build-system)
10193 (home-page "https://cran.r-project.org/web/packages/mosaicData/")
10194 (synopsis "Data sets for project Mosaic")
10196 "This package provides data sets from project Mosaic @url{http://mosaic-web.org}
10197 used to teach mathematics, statistics, computation and modeling.")
10198 (license license:gpl2+)))
10200 (define-public r-raster
10207 (uri (cran-uri "raster" version))
10210 "11fnznymwavpph733dayklhcx4phpjgrijfxlaszi122sg2x7ir9"))))
10211 (build-system r-build-system)
10213 (list r-rcpp r-sp r-terra))
10214 (home-page "https://www.rspatial.org/")
10215 (synopsis "Geographic data analysis and modeling")
10217 "The package implements basic and high-level functions for reading,
10218 writing, manipulating, analyzing and modeling of gridded spatial data.
10219 Processing of very large files is supported.")
10220 (license license:gpl3+)))
10222 (define-public r-mosaic
10229 (uri (cran-uri "mosaic" version))
10231 (base32 "1y0isqbva0vi5zlx1xvixbq87n4xp66ljh43qnd0cpzaz0mn21cg"))))
10232 (build-system r-build-system)
10256 (home-page "https://github.com/ProjectMOSAIC/mosaic/")
10257 (synopsis "Mathematics, statistics, and computation teaching utilities")
10259 "This package contain data sets and utilities from
10260 @url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
10261 statistics, computation and modeling. Project MOSAIC is a community of
10262 educators working to tie together aspects of quantitative work that students
10263 in science, technology, engineering and mathematics will need in their
10264 professional lives, but which are usually taught in isolation, if at all.")
10265 (license license:gpl2+)))
10267 (define-public r-abd
10274 (uri (cran-uri "abd" version))
10276 (base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
10277 (build-system r-build-system)
10279 (list r-lattice r-mosaic r-nlme))
10280 (home-page "https://cran.r-project.org/web/packages/abd/")
10281 (synopsis "Analysis of biological data")
10283 "The @code{r-abd} package contains data sets and sample code for the Analysis of
10284 biological data by Michael Whitlock and Dolph Schluter.")
10285 (license license:gpl2)))
10287 (define-public r-svgui
10294 (uri (cran-uri "svGUI" version))
10296 (base32 "0ch5gdfk834xj9w3vxpm3x4770fz3nnlyn8b0jsw9f3n2as7g979"))))
10297 (properties `((upstream-name . "svGUI")))
10298 (build-system r-build-system)
10301 (home-page "https://github.com/SciViews/svGUI/")
10302 (synopsis "Functions for managing GUI clients in R")
10304 "The SciViews @code{svGUI} package eases the management of Graphical User
10305 Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
10306 centralizes info about GUI elements currently used, and it dispatches GUI
10307 calls to the particular toolkits in use in function of the context.")
10308 (license license:gpl2)))
10310 (define-public r-svdialogs
10312 (name "r-svdialogs")
10317 (uri (cran-uri "svDialogs" version))
10319 (base32 "0j00xjvkwv992ir48czhvyj29rb9vpd243vbyyj2binn0q0qa431"))))
10320 (properties `((upstream-name . "svDialogs")))
10321 (build-system r-build-system)
10325 (list r-rstudioapi r-svgui))
10328 (home-page "https://github.com/SciViews/svDialogs/")
10329 (synopsis "Portable dialog boxes")
10331 "This package helps to construct standard dialog boxes for your GUI, including
10332 message boxes, input boxes, list, file or directory selection, and others. In
10333 case R cannot display GUI dialog boxes, a simpler command line version of these
10334 interactive elements is also provided as a fallback solution.")
10335 (license license:gpl2)))
10337 (define-public r-abe
10344 (uri (cran-uri "abe" version))
10347 "1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
10348 (build-system r-build-system)
10349 (home-page "https://cran.r-project.org/web/packages/abe/")
10350 (synopsis "Augmented backward elimination")
10352 "This package performs augmented backward elimination and checks the
10353 stability of the obtained model. Augmented backward elimination combines
10354 significance or information based criteria with the change in estimate to
10355 either select the optimal model for prediction purposes or to serve as a tool
10356 to obtain a practically sound, highly interpretable model.")
10357 (license license:gpl2+)))
10359 (define-public r-abf2
10366 (uri (cran-uri "abf2" version))
10368 (base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
10369 (build-system r-build-system)
10370 (home-page "https://cran.r-project.org/web/packages/abf2/")
10371 (synopsis "Load gap-free axon @code{r-abf2} files")
10373 "This package loads electrophysiology data from ABF2 files, as created by
10374 Axon Instruments/Molecular Devices software. Only files recorded in gap-free
10375 mode are currently supported.")
10376 (license license:artistic2.0)))
10378 (define-public r-abhgenotyper
10380 (name "r-abhgenotyper")
10385 (uri (cran-uri "ABHgenotypeR" version))
10387 (base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
10388 (properties `((upstream-name . "ABHgenotypeR")))
10389 (build-system r-build-system)
10391 (list r-ggplot2 r-reshape2))
10392 (home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
10393 (synopsis "Visualize and manipulate ABH genotypes")
10395 "The @code{r-abhgenotyper} package provides simple imputation,
10396 error-correction and plotting capacities for genotype data. The package is
10397 supposed to serve as an intermediate but independent analysis tool between the
10398 TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
10399 not found in either TASSEL or @code{r-qtl} in addition to visualization of
10400 genotypes as \"graphical genotypes\".")
10401 (license license:gpl3)))
10403 (define-public r-furrr
10410 (uri (cran-uri "furrr" version))
10413 "001p2yhznrpnrjvdcmf2h3wpgdnw01wnqgid7wbq8bhavhi3888a"))))
10414 (build-system r-build-system)
10423 (home-page "https://github.com/DavisVaughan/furrr")
10424 (synopsis "Apply mapping functions in parallel using futures")
10426 "This package provides implementations of the family of @code{map()}
10427 functions from the @code{purrr} package that can be resolved using any
10428 @code{future}-supported backend, e.g. parallel on the local machine or
10429 distributed on a compute cluster.")
10430 (license license:lgpl2.1+)))
10432 (define-public r-abjutils
10434 (name "r-abjutils")
10439 (uri (cran-uri "abjutils" version))
10441 (base32 "18mmlkqsrjfclk8islfjdsp8sbw6dpjj5x45kqilxdiss69gg5zd"))))
10442 (build-system r-build-system)
10452 (home-page "https://github.com/abjur/abjutils/")
10453 (synopsis "Collection of tools for jurimetrical analysis")
10455 "This package implements general purpose tools, such as functions for
10456 sampling and basic manipulation of Brazilian lawsuits identification number.
10457 It also implements functions for text cleaning, such as accentuation
10459 (license license:expat)))
10461 (define-public r-abnormality
10463 (name "r-abnormality")
10468 (uri (cran-uri "abnormality" version))
10470 (base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
10471 (build-system r-build-system)
10473 (list r-mass r-matrix))
10474 (home-page "https://cran.r-project.org/web/packages/abnormality/")
10475 (synopsis "Measure a subject's abnormality with respect to a reference population")
10477 "This package contains functions to implement the methodology and
10478 considerations laid out by Marks et al. in the article \"Measuring abnormality
10479 in high dimensional spaces: applications in biomechanical gait analysis\".
10480 Using high-dimensional datasets to measure a subject's overall level of
10481 abnormality as compared to a reference population is often needed in outcomes
10483 (license license:expat)))
10485 (define-public r-abodoutlier
10487 (name "r-abodoutlier")
10492 (uri (cran-uri "abodOutlier" version))
10494 (base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
10495 (properties `((upstream-name . "abodOutlier")))
10496 (build-system r-build-system)
10499 (home-page "https://cran.r-project.org/web/packages/abodOutlier/")
10500 (synopsis "Angle-based outlier detection")
10502 "This package performs angle-based outlier detection on a given data
10503 frame. It offers three methods to process data:
10505 @item full but slow implementation using all the data that has cubic
10507 @item a fully randomized method;
10508 @item a method using k-nearest neighbours.
10510 These algorithms are well suited for high dimensional data outlier
10512 (license license:expat)))
10514 (define-public r-abps
10521 (uri (cran-uri "ABPS" version))
10523 (base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
10524 (properties `((upstream-name . "ABPS")))
10525 (build-system r-build-system)
10526 (propagated-inputs (list r-kernlab))
10527 (home-page "https://cran.r-project.org/web/packages/ABPS/")
10528 (synopsis "Abnormal blood profile score to detect blood doping")
10530 "This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
10531 The ABPS is a part of the Athlete biological passport program of the World
10532 anti-doping agency, which combines several blood parameters into a single
10533 score in order to detect blood doping. The package also contains functions to
10534 calculate other scores used in anti-doping programs, such as the ratio of
10535 hemoglobin to reticulocytes (OFF-score), as well as example data.")
10536 (license license:gpl2+)))
10538 (define-public r-parmigene
10540 (name "r-parmigene")
10545 (uri (cran-uri "parmigene" version))
10548 "067rqxqyzy1fsjj0s1g7af4527whwdhzjzc5b8a8n7683na59ns4"))))
10549 (build-system r-build-system)
10550 (home-page "https://cran.r-project.org/web/packages/parmigene/")
10551 (synopsis "Mutual information estimation for gene network reconstruction")
10553 "This package provides a parallel estimation of the mutual information
10554 based on entropy estimates from k-nearest neighbors distances and algorithms
10555 for the reconstruction of gene regulatory networks.")
10556 (license license:agpl3+)))
10558 (define-public r-pscl
10565 (uri (cran-uri "pscl" version))
10567 (base32 "0vzf5wazs92bhqhqd66v3vwmbfmnh67gb2466g1xxawim649nk05"))))
10568 (build-system r-build-system)
10571 (home-page "https://github.com/atahk/pscl/")
10572 (synopsis "Political science computational laboratory")
10574 "The @code{pscl} is an R package providing classes and methods for:
10576 @item Bayesian analysis of roll call data (item-response models);
10577 @item elementary Bayesian statistics;
10578 @item maximum likelihood estimation of zero-inflated and hurdle models for count
10580 @item utility functions.
10582 (license license:gpl2)))
10584 (define-public r-accelmissing
10586 (name "r-accelmissing")
10591 (uri (cran-uri "accelmissing" version))
10593 (base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
10594 (build-system r-build-system)
10596 (list r-mice r-pscl))
10597 (home-page "https://cran.r-project.org/web/packages/accelmissing/")
10598 (synopsis "Missing value imputation for accelerometer data")
10600 "This package provides a statistical method to impute the missing values in
10601 accelerometer data. The methodology includes both parametric and
10602 semi-parametric multiple imputations under the zero-inflated Poisson lognormal
10603 model. It also provides multiple functions to preprocess the accelerometer data
10604 previous to the missing data imputation. These include detecting the wearing
10605 and the non-wearing time, selecting valid days and subjects, and creating plots.")
10606 (license license:gpl2+)))
10608 (define-public r-mhsmm
10615 (uri (cran-uri "mhsmm" version))
10617 (base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
10618 (build-system r-build-system)
10619 (propagated-inputs (list r-mvtnorm))
10620 (home-page "https://github.com/jaredo/mhsmm/")
10621 (synopsis "Inference for hidden Markov and semi-Markov models")
10623 "The @code{r-mhsmm} package implements estimation and prediction methods for
10624 hidden Markov and semi-Markov models for multiple observation sequences. Such
10625 techniques are of interest when observed data is thought to be dependent on some
10626 unobserved (or hidden) state. Also, this package is suitable for equidistant
10627 time series data, with multivariate and/or missing data. Allows user defined
10628 emission distributions.")
10629 (license license:gpl2+)))
10631 (define-public r-nleqslv
10638 (uri (cran-uri "nleqslv" version))
10640 (base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
10641 (build-system r-build-system)
10642 (native-inputs (list gfortran))
10643 (home-page "https://cran.r-project.org/web/packages/nleqslv/")
10644 (synopsis "Solve systems of nonlinear equations")
10646 "The @code{r-nleqslv} package solves a system of nonlinear equations using a
10647 Broyden or a Newton method with a choice of global strategies such as line
10648 search and trust region. There are options for using a numerical or user
10649 supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
10650 singular or ill-conditioned Jacobian.")
10651 (license license:gpl2+)))
10653 (define-public r-physicalactivity
10655 (name "r-physicalactivity")
10660 (uri (cran-uri "PhysicalActivity" version))
10662 (base32 "0b27prkv3x6v2afz0y53ccs9scibpc7nj54n0hpd9fgn1wyg4c40"))))
10664 `((upstream-name . "PhysicalActivity")))
10665 (build-system r-build-system)
10666 (home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
10667 (synopsis "Processing accelerometer data for physical activity measurement")
10669 "This @code{r-physicalactivity} package provides a function @code{wearingMarking}
10670 for classification of monitored wear and nonwear time intervals in accelerometer
10671 data collected to assess physical activity. The package also contains functions
10672 for making plots of accelerometer data and obtaining the summary of various
10673 information including daily monitor wear time and the mean monitor wear time
10674 during valid days. The revised package version 0.2-1 improved the functions
10675 regarding speed, robustness and add better support for time zones and daylight
10676 saving. In addition, several functions were added:
10678 @item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
10679 @item the @code{markPAI} can categorize physical activity intensity level based
10680 on user-defined cut-points of accelerometer counts.
10682 It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
10683 @code{queryActigraph} functions.")
10684 (license license:gpl3+)))
10686 (define-public r-acc
10693 (uri (cran-uri "acc" version))
10695 (base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
10696 (build-system r-build-system)
10711 (home-page "https://cran.r-project.org/web/packages/acc/")
10712 (synopsis "Exploring accelerometer data")
10714 "This package processes accelerometer data from uni-axial and tri-axial devices
10715 and generates data summaries. Also, includes functions to plot, analyze, and
10716 simulate accelerometer data.")
10717 (license license:gpl2+)))
10719 (define-public r-rbenchmark
10721 (name "r-rbenchmark")
10726 (uri (cran-uri "rbenchmark" version))
10728 (base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
10729 (build-system r-build-system)
10730 (home-page "https://cran.r-project.org/web/packages/rbenchmark/")
10731 (synopsis "Benchmarking routine for R")
10733 "This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
10734 and is intended to facilitate benchmarking of arbitrary R code. The library
10735 consists of just one function, benchmark, which is a simple wrapper around
10736 system.time. Given a specification of the benchmarking process (counts of
10737 replications, evaluation environment) and an arbitrary number of expressions,
10738 benchmark evaluates each of the expressions in the specified environment,
10739 replicating the evaluation as many times as specified, and returning the results
10740 conveniently wrapped into a data frame.")
10741 (license license:gpl2+)))
10743 (define-public r-mitools
10750 (uri (cran-uri "mitools" version))
10753 "0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
10754 (build-system r-build-system)
10755 (propagated-inputs (list r-dbi))
10756 (home-page "https://cran.r-project.org/web/packages/mitools/")
10757 (synopsis "Tools for multiple imputation of missing data")
10759 "This package provides tools to perform analyses and combine results from
10760 multiple-imputation datasets.")
10761 (license license:gpl2)))
10763 (define-public r-mixsqp
10769 (uri (cran-uri "mixsqp" version))
10772 "1qics04w0swyp216d6g8dmsph8q2kpadpacp66h2qih3521js12q"))))
10773 (properties `((upstream-name . "mixsqp")))
10774 (build-system r-build-system)
10776 (list r-irlba r-rcpp r-rcpparmadillo))
10779 (home-page "https://github.com/stephenslab/mixsqp")
10781 "Sequential quadratic programming for maximum-likelihood estimation")
10783 "This package provides an optimization method based on sequential
10784 quadratic programming for maximum likelihood estimation of the mixture
10785 proportions in a finite mixture model where the component densities are
10786 known. The algorithm is expected to obtain solutions that are at least
10787 as accurate as the state-of-the-art MOSEK interior-point solver, and they
10788 are expected to arrive at solutions more quickly when the number of
10789 samples is large and the number of mixture components is not too large.")
10790 (license license:expat)))
10792 (define-public r-magick
10799 (uri (cran-uri "magick" version))
10802 "0h942bn7wfnzbbgq9hrs75c7igmg5r1c5sad2v0znhza4cp7p1w3"))))
10803 (build-system r-build-system)
10805 (list imagemagick zlib))
10807 (list r-curl r-magrittr r-rcpp))
10809 (list pkg-config r-knitr))
10810 (home-page "https://github.com/ropensci/magick")
10811 (synopsis "Advanced graphics and image-processing in R")
10813 "This package provides bindings to ImageMagick, a comprehensive image
10814 processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
10815 etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
10816 operations are vectorized via the Magick++ STL meaning they operate either on
10817 a single frame or a series of frames for working with layers, collages, or
10818 animation. In RStudio, images are automatically previewed when printed to the
10819 console, resulting in an interactive editing environment.")
10820 (license license:expat)))
10822 (define-public r-survey
10829 (uri (cran-uri "survey" version))
10832 "0ljsszybzri531q6xab04r6zq11vchfs7y0snjzk57m3g0b9ms05"))))
10833 (build-system r-build-system)
10841 (home-page "http://r-survey.r-forge.r-project.org/survey/")
10842 (synopsis "Analysis of complex survey samples")
10844 "This package provides tools for the analysis of complex survey samples.
10845 The provided features include: summary statistics, two-sample tests, rank
10846 tests, generalised linear models, cumulative link models, Cox models,
10847 loglinear models, and general maximum pseudolikelihood estimation for
10848 multistage stratified, cluster-sampled, unequally weighted survey samples;
10849 variances by Taylor series linearisation or replicate weights;
10850 post-stratification, calibration, and raking; two-phase subsampling designs;
10851 graphics; PPS sampling without replacement; principal components, and factor
10853 ;; Either version of the GPL.
10854 (license (list license:gpl2 license:gpl3))))
10856 (define-public r-gee
10859 (version "4.13-20")
10863 (uri (cran-uri "gee" version))
10866 "167pzgnmj4cjc41ykps1mfwi6s7y32zxyycn5z17vn4v0pp4q0ak"))))
10867 (properties `((upstream-name . "gee")))
10868 (build-system r-build-system)
10871 (home-page "https://cran.r-project.org/web/packages/gee/")
10872 (synopsis "Generalized estimation equation solver")
10874 "This package provides a solver for generalized estimation equations.")
10875 (license license:gpl2)))
10877 (define-public r-tab
10884 (uri (cran-uri "tab" version))
10887 "1kg8c1safi9klkx2mdkmsf5dn9piy4jljwd4ma7g4jz2rwl4jzhv"))))
10888 (properties `((upstream-name . "tab")))
10889 (build-system r-build-system)
10891 (list r-dplyr r-kableextra r-knitr r-mass r-survey))
10894 (home-page "https://cran.r-project.org/web/packages/tab/")
10895 (synopsis "Create summary tables for statistical reports")
10897 "This package contains functions for creating various types of summary
10898 tables, e.g. comparing characteristics across levels of a categorical variable
10899 and summarizing fitted generalized linear models, generalized estimating
10900 equations, and Cox proportional hazards models. Functions are available to
10901 handle data from simple random samples as well as complex surveys.")
10902 (license license:gpl3+)))
10904 (define-public r-dvmisc
10911 (uri (cran-uri "dvmisc" version))
10913 (base32 "01v6sixx0f3nrn6ymfifb3pvd2msfrwm21kmdv38laxq29vc4rsi"))))
10914 (build-system r-build-system)
10927 (home-page "https://cran.r-project.org/web/packages/dvmisc/")
10928 (synopsis "Faster computation of common statistics and miscellaneous functions")
10930 "This package implements faster versions of base R functions (e.g. mean, standard
10931 deviation, covariance, weighted mean), mostly written in C++, along with
10932 miscellaneous functions for various purposes (e.g. create the histogram with
10933 fitted probability density function or probability mass function curve, create
10934 the body mass index groups, assess the linearity assumption in logistic
10936 (license license:gpl2)))
10938 (define-public r-accelerometry
10940 (name "r-accelerometry")
10945 (uri (cran-uri "accelerometry" version))
10947 (base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
10948 (build-system r-build-system)
10950 (list r-dvmisc r-rcpp))
10951 (home-page "https://cran.r-project.org/web/packages/accelerometry/")
10952 (synopsis "Functions for processing accelerometer data")
10954 "This package provides a collection of functions that perform operations on
10955 time-series accelerometer data, such as identify the non-wear time, flag minutes
10956 that are part of an activity bout, and find the maximum 10-minute average count
10957 value. The functions are generally very flexible, allowing for a variety of
10958 algorithms to be implemented.")
10959 (license license:gpl3)))
10961 (define-public r-absim
10968 (uri (cran-uri "AbSim" version))
10970 (base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
10971 (properties `((upstream-name . "AbSim")))
10972 (build-system r-build-system)
10974 (list r-ape r-powerlaw))
10975 (home-page "https://cran.r-project.org/web/packages/AbSim/")
10976 (synopsis "Time resolved simulations of antibody repertoires")
10978 "This package provides simulation methods for the evolution of antibody repertoires.
10979 The heavy and light chain variable region of both human and C57BL/6 mice can
10980 be simulated in a time-dependent fashion. Both single lineages using one set of
10981 V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
10982 with an initial V-D-J recombination event, starting the first phylogenetic tree.
10983 Upon completion, the main loop of the algorithm begins, with each iteration
10984 representing one simulated time step. Various mutation events are possible at
10985 each time step, contributing to a diverse final repertoire.")
10986 (license license:gpl2)))
10988 (define-public r-quic
10995 (uri (cran-uri "QUIC" version))
10997 (base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
10998 (properties `((upstream-name . "QUIC")))
10999 (build-system r-build-system)
11000 (home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
11001 (synopsis "Regularized sparse inverse covariance matrix estimation")
11003 "This package implements the regularized Gaussian maximum likelihood
11004 estimation of the inverse of a covariance matrix. It uses Newton's method and
11005 coordinate descent to solve the regularized inverse covariance matrix
11006 estimation problem.")
11007 ;; The project home page states that the release is under GPLv3 or later.
11008 ;; The CRAN page only says GPL-3.
11009 (license license:gpl3+)))
11011 (define-public r-abundant
11013 (name "r-abundant")
11018 (uri (cran-uri "abundant" version))
11020 (base32 "15m3ngj5aipjg961yy5kvdg9xlfcpliw30dq6gchzxabhnfzcipd"))))
11021 (build-system r-build-system)
11024 (home-page "https://cran.r-project.org/web/packages/abundant/")
11025 (synopsis "Abundant regression and high-dimensional principal fitted components")
11027 "This package provides tools to fit and predict with the high-dimensional
11028 principal fitted components model. This model is described by Cook, Forzani,
11029 and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
11030 ;; The DESCRIPTION file states GPL-2, but since it directly depends on a
11031 ;; GPLv3+ package (QUIC) this likely means GPLv2+.
11032 (license license:gpl2+)))
11034 (define-public r-ac3net
11041 (uri (cran-uri "Ac3net" version))
11043 (base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
11044 (properties `((upstream-name . "Ac3net")))
11045 (build-system r-build-system)
11047 (list r-data-table))
11048 (home-page "https://cran.r-project.org/web/packages/Ac3net/")
11049 (synopsis "Inferring directional conservative causal core gene networks")
11050 (description "This package infers directional Conservative causal core
11051 (gene) networks (C3NET). This is a version of the algorithm C3NET with
11052 directional network.")
11053 (license license:gpl3+)))
11055 (define-public r-aca
11062 (uri (cran-uri "ACA" version))
11064 (base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
11065 (properties `((upstream-name . "ACA")))
11066 (build-system r-build-system)
11067 (home-page "https://cran.r-project.org/web/packages/ACA/")
11068 (synopsis "Abrupt change-point or aberration detection in point series")
11070 "This package offers an interactive function for the detection of breakpoints in
11072 ;; Any version of the GPL
11073 (license (list license:gpl2+ license:gpl3+))))
11075 (define-public r-acceptancesampling
11077 (name "r-acceptancesampling")
11082 (uri (cran-uri "AcceptanceSampling" version))
11084 (base32 "13k3zczjycw24n5yp0qmrm233id5j8h6fvra57f1n6js7ljxiiq2"))))
11086 `((upstream-name . "AcceptanceSampling")))
11087 (build-system r-build-system)
11088 (home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
11089 (synopsis "Creation and evaluation of acceptance sampling plans")
11091 "This @code{r-acceptancesampling} provides functionality for creating and evaluating
11092 acceptance sampling plans. Acceptance sampling is a methodology commonly used
11093 in quality control and improvement. International standards of acceptance
11094 sampling provide sampling plans for specific circumstances. The aim of this
11095 package is to provide an easy-to-use interface to visualize single, double or
11096 multiple sampling plans. In addition, methods have been provided to enable the
11097 user to assess sampling plans against pre-specified levels of performance, as
11098 measured by the probability of acceptance for a given level of quality in the
11100 (license license:gpl3+)))
11102 (define-public r-acclma
11109 (uri (cran-uri "ACCLMA" version))
11111 (base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
11112 (properties `((upstream-name . "ACCLMA")))
11113 (build-system r-build-system)
11114 (home-page "https://cran.r-project.org/web/packages/ACCLMA/")
11115 (synopsis "ACC & LMA graph plotting")
11117 "This package contains a function that imports data from a @acronym{CSV,
11118 Comma-Separated Values} file, or uses manually entered data from the format (x,
11119 y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
11120 Curve} vs @acronym{LOI, Line of Independence} graph and
11121 @acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
11122 function is @code{plotLMA} (source file, header) that takes a data set and plots the
11123 appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
11124 string) was passed, a manual data entry window is opened. The header parameter
11125 indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
11126 a header row or not. The dataset should contain only one independent variable
11127 (x) and one dependent variable (y) and can contain a weight for each
11129 (license license:gpl2)))
11131 (define-public r-aspi
11138 (uri (cran-uri "aspi" version))
11140 (base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
11141 (build-system r-build-system)
11143 "https://cran.r-project.org/web/packages/aspi/")
11145 "Analysis of symmetry of parasitic infections")
11147 "This package provides tools for the analysis and visualization of bilateral
11148 asymmetry in parasitic infections.")
11149 (license license:gpl3+)))
11151 (define-public r-sandwich
11153 (name "r-sandwich")
11158 (uri (cran-uri "sandwich" version))
11161 "12aa5083k3sfrfq1jy3l94wffss9h0rga8j71jy3n8pkhiq4nn7n"))))
11162 (build-system r-build-system)
11165 (home-page "https://cran.r-project.org/web/packages/sandwich/")
11166 (synopsis "Robust Covariance Matrix Estimators")
11168 "This package provides model-robust standard error estimators for
11169 cross-sectional, time series, clustered, panel, and longitudinal data.")
11170 ;; Either version of the license.
11171 (license (list license:gpl2 license:gpl3))))
11173 (define-public r-th-data
11180 (uri (cran-uri "TH.data" version))
11183 "0ghihfpk5d8gsdlzf6phw7dwwz3adx64pxk82vlmlqx53ljpxcr1"))))
11184 (properties `((upstream-name . "TH.data")))
11185 (build-system r-build-system)
11187 (list r-mass r-survival))
11190 (home-page "https://cran.r-project.org/web/packages/TH.data/")
11191 (synopsis "Shared data sets")
11193 "This package contains supporting data sets that are used in other
11194 packages maintained by Torsten Hothorn.")
11195 (license license:gpl3)))
11197 (define-public r-multcomp
11199 (name "r-multcomp")
11204 (uri (cran-uri "multcomp" version))
11207 "01i8gjppyxl3xph1dw0kags8qbb7r06j91kk3lkqn5gzrxjmwyhh"))))
11208 (build-system r-build-system)
11210 (list r-codetools r-mvtnorm r-sandwich r-survival r-th-data))
11211 (home-page "https://cran.r-project.org/web/packages/multcomp/")
11212 (synopsis "Simultaneous inference in general parametric models")
11214 "Simultaneous tests and confidence intervals for general linear
11215 hypotheses in parametric models, including linear, generalized linear, linear
11216 mixed effects, and survival models. The package includes demos reproducing
11217 analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
11218 Hothorn, Westfall, 2010, CRC Press).")
11219 (license license:gpl2)))
11221 (define-public r-multcompview
11223 (name "r-multcompview")
11228 (uri (cran-uri "multcompView" version))
11230 (base32 "1rfq9wvvrghq0542ff40wy8vdmsyd8spzz6ihcywcvxdfa8m6g8j"))))
11231 (properties `((upstream-name . "multcompView")))
11232 (build-system r-build-system)
11233 (home-page "https://cran.r-project.org/package=multcompView")
11234 (synopsis "Visualizations of paired comparisons")
11236 "Convert a logical vector or a vector of p-values or a correlation,
11237 difference, or distance matrix into a display identifying the pairs for which
11238 the differences were not significantly different.")
11239 ;; Any version of the GPL.
11240 (license license:gpl3+)))
11242 (define-public r-emmeans
11249 (uri (cran-uri "emmeans" version))
11252 "1g112yvqvxi83x128hwz4qpifwihlm0y5szg82cdsx3c9cm1rrfk"))))
11253 (build-system r-build-system)
11255 (list r-estimability r-mvtnorm r-numderiv r-xtable))
11258 (home-page "https://github.com/rvlenth/emmeans")
11259 (synopsis "Estimated marginal means, aka least-squares means")
11261 "This package provides tools to obtain @dfn{estimated marginal
11262 means} (EMMs) for many linear, generalized linear, and mixed models. It can
11263 be used to compute contrasts or linear functions of EMMs, trends, and
11264 comparisons of slopes.")
11265 ;; Either version of the license.
11266 (license (list license:gpl2 license:gpl3))))
11268 (define-public r-pwr
11275 (uri (cran-uri "pwr" version))
11278 "1kfzy73v3z6ipc3kdfkcjrp4b4p5k54nwk796gqi36srm93hgc2v"))))
11279 (build-system r-build-system)
11282 (home-page "https://github.com/heliosdrm/pwr")
11283 (synopsis "Basic functions for power analysis")
11285 "This package provides power analysis functions along the lines of
11287 (license license:gpl3+)))
11289 (define-public r-libcoin
11296 (uri (cran-uri "libcoin" version))
11298 (base32 "1syrcdj5qg5m3zd3dlxgpfklswbalfg42w058dr09hnzqsvx0z9d"))))
11299 (build-system r-build-system)
11300 (propagated-inputs (list r-mvtnorm))
11301 (home-page "https://cran.r-project.org/web/packages/libcoin")
11302 (synopsis "Linear test statistics for permutation inference")
11304 "This package provides basic infrastructure for linear test statistics
11305 and permutation inference in the framework of Strasser and Weber (1999).")
11306 (license license:gpl2)))
11308 (define-public r-coin
11315 (uri (cran-uri "coin" version))
11318 "1cpv7jx840inzg98bkhrb5yscx0gpag6br237r5qpnc2gbrd2ikm"))))
11319 (build-system r-build-system)
11327 (home-page "http://coin.r-forge.r-project.org")
11328 (synopsis "Conditional inference procedures in a permutation test framework")
11330 "This package provides conditional inference procedures for the general
11331 independence problem including two-sample, K-sample (non-parametric ANOVA),
11332 correlation, censored, ordered and multivariate problems.")
11333 (license license:gpl2)))
11335 (define-public r-bayesplot
11337 (name "r-bayesplot")
11342 (uri (cran-uri "bayesplot" version))
11345 "0aman4273i8hy3z0qay1nrsr7v27m4icm1j6f4w59ylix80l5myq"))))
11346 (build-system r-build-system)
11360 (home-page "https://mc-stan.org/bayesplot")
11361 (synopsis "Plotting for Bayesian models")
11363 "This package provides plotting functions for posterior analysis, model
11364 checking, and MCMC diagnostics. The package is designed not only to provide
11365 convenient functionality for users, but also a common set of functions that
11366 can be easily used by developers working on a variety of R packages for
11367 Bayesian modeling.")
11368 (license license:gpl3+)))
11370 (define-public r-tmb
11377 (uri (cran-uri "TMB" version))
11380 "116k7ffgadhkqq4lckfd4403qvybcls1hcs1ap1b7lkylghjahf2"))))
11381 (properties `((upstream-name . "TMB")))
11382 (build-system r-build-system)
11384 (list r-matrix r-rcppeigen))
11385 (home-page "http://tmb-project.org")
11386 (synopsis "Template model builder: a general random effect tool")
11388 "With this tool, a user should be able to quickly implement complex
11389 random effect models through simple C++ templates. The package combines
11390 @code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
11391 matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
11392 from R) to obtain an efficient implementation of the applied Laplace
11393 approximation with exact derivatives. Key features are: Automatic sparseness
11394 detection, parallelism through BLAS and parallel user templates.")
11395 (license license:gpl2)))
11397 (define-public r-sjstats
11404 (uri (cran-uri "sjstats" version))
11406 (base32 "1cv80yjnyh6qihxf57zivihhia20gibr5f03x8aspy6382wnwlka"))))
11407 (build-system r-build-system)
11426 (home-page "https://github.com/strengejacke/sjstats")
11427 (synopsis "Functions for common statistical computations")
11429 "This package provides a collection of convenient functions for common
11430 statistical computations, which are not directly provided by R's @code{base}
11431 or @code{stats} packages. This package aims at providing, first, shortcuts
11432 for statistical measures, which otherwise could only be calculated with
11433 additional effort. Second, these shortcut functions are generic, and can be
11434 applied not only to vectors, but also to other objects as well. The focus of
11435 most functions lies on summary statistics or fit measures for regression
11436 models, including generalized linear models, mixed effects models and Bayesian
11438 (license license:gpl3)))
11440 (define-public r-glmmtmb
11443 (version "1.1.2.3")
11447 (uri (cran-uri "glmmTMB" version))
11450 "1yfwwz2dhd34vgagg8hi7irkqw8padavbc7337jdiwgk3w01wqsm"))))
11451 (properties `((upstream-name . "glmmTMB")))
11452 (build-system r-build-system)
11461 (list r-knitr)) ; for vignettes
11462 (home-page "https://github.com/glmmTMB")
11463 (synopsis "Generalized linear mixed models")
11465 "Fit linear and generalized linear mixed models with various extensions,
11466 including zero-inflation. The models are fitted using maximum likelihood
11467 estimation via the Template Model Builder. Random effects are assumed to be
11468 Gaussian on the scale of the linear predictor and are integrated out using the
11469 Laplace approximation. Gradients are calculated using automatic
11471 (license license:agpl3+)))
11473 (define-public r-bayestestr
11475 (name "r-bayestestr")
11480 (uri (cran-uri "bayestestR" version))
11483 "0lz8mzacxgmll576p88654mrvlk4pzvhwwghvn5pm7zxisgx0kq0"))))
11484 (properties `((upstream-name . "bayestestR")))
11485 (build-system r-build-system)
11487 (list r-datawizard r-insight))
11490 (home-page "https://github.com/easystats/bayestestR")
11491 (synopsis "Describe Bayesian models and posterior distributions")
11493 "This package provides utilities to understand and describe posterior
11494 distributions and Bayesian models. It includes point-estimates such as
11495 @dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
11496 Density Interval} (HDI), and indices used for null-hypothesis testing (such as
11497 ROPE percentage and pd).")
11498 (license license:gpl3)))
11500 (define-public r-performance
11502 (name "r-performance")
11507 (uri (cran-uri "performance" version))
11510 "1xjjnhqmwfflm5yfgjhycjn0fj0manvsvkk2ppifn0373bajp5n2"))))
11511 (build-system r-build-system)
11513 (list r-bayestestr r-datawizard r-insight))
11514 (home-page "https://easystats.github.io/performance/")
11515 (synopsis "Assessment of regression models performance")
11517 "This package provides utilities for computing measures to assess model
11518 quality, which are not directly provided by R's @code{base} or @code{stats}
11519 packages. These include e.g. measures like r-squared, intraclass correlation
11520 coefficient, root mean squared error or functions to check models for
11521 overdispersion, singularity or zero-inflation and more. Functions apply to a
11522 large variety of regression models, including generalized linear models, mixed
11523 effects models and Bayesian models.")
11524 (license license:gpl3)))
11526 (define-public r-ggeffects
11528 (name "r-ggeffects")
11533 (uri (cran-uri "ggeffects" version))
11536 "0xrb105kblkj3l9zlj9yy52rjlmx5x2aai1wwb5zvjr1f6nlc84l"))))
11537 (build-system r-build-system)
11539 (list r-insight r-mass r-sjlabelled))
11542 (home-page "https://github.com/strengejacke/ggeffects")
11543 (synopsis "Create tidy data frames of marginal effects for ggplot")
11545 "This package provides tools to compute marginal effects from statistical
11546 models and return the result as tidy data frames. These data frames are ready
11547 to use with the @code{ggplot2} package. Marginal effects can be calculated
11548 for many different models. Interaction terms, splines and polynomial terms
11549 are also supported. The two main functions are @code{ggpredict()} and
11550 @code{ggeffect()}. There is a generic @code{plot()} method to plot the
11551 results using @code{ggplot2}.")
11552 (license license:gpl3)))
11554 (define-public r-effectsize
11556 (name "r-effectsize")
11557 (version "0.6.0.1")
11561 (uri (cran-uri "effectsize" version))
11564 "1rhpbhyrv0avinm6dz6v2qw4xxdl9m1wknq1dv2flfxgcz0k9qiz"))))
11565 (properties `((upstream-name . "effectsize")))
11566 (build-system r-build-system)
11568 (list r-bayestestr r-datawizard r-insight r-parameters
11572 (home-page "https://github.com/easystats/effectsize")
11573 (synopsis "Indices of effect size and standardized parameters")
11575 "This package provides utilities to work with indices of effect size and
11576 standardized parameters for a wide variety of models, allowing computation and
11577 conversion of indices such as Cohen's d, r, odds, etc.")
11578 (license license:gpl3)))
11580 (define-public r-sjplot
11587 (uri (cran-uri "sjPlot" version))
11589 (base32 "1rnwhh271xj8xgvvlpqw9ain56mfz37fvl7f6jq9nzx9jxx95bjd"))))
11590 (properties `((upstream-name . "sjPlot")))
11591 (build-system r-build-system)
11613 (home-page "https://strengejacke.github.io/sjPlot/")
11614 (synopsis "Data visualization for statistics in social science")
11616 "This package represents a collection of plotting and table output
11617 functions for data visualization. Results of various statistical
11618 analyses (that are commonly used in social sciences) can be visualized using
11619 this package, including simple and cross tabulated frequencies, histograms,
11620 box plots, (generalized) linear models, mixed effects models, principal
11621 component analysis and correlation matrices, cluster analyses, scatter plots,
11622 stacked scales, effects plots of regression models (including interaction
11623 terms) and much more. This package supports labelled data.")
11624 (license license:gpl3)))
11626 (define-public r-ini
11633 (uri (cran-uri "ini" version))
11636 "04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
11637 (build-system r-build-system)
11638 (home-page "https://github.com/dvdscripter/ini")
11639 (synopsis "Read and write configuration files")
11641 "This package provides tools to parse simple @code{.ini} configuration
11642 files to an structured list. Users can manipulate this resulting list with
11643 @code{lapply()} functions. This same structured list can be used to write
11644 back to file after modifications.")
11645 (license license:gpl3)))
11647 (define-public r-gitcreds
11649 (name "r-gitcreds")
11654 (uri (cran-uri "gitcreds" version))
11657 "1snzn7nxy0rwz0bzjsg6k04c0n811dgn8gn9cmn2v78aj57ayjmi"))))
11658 (properties `((upstream-name . "gitcreds")))
11659 (build-system r-build-system)
11660 (inputs (list git-minimal))
11661 (native-inputs (list r-knitr))
11662 (home-page "https://github.com/r-lib/gitcreds")
11663 (synopsis "Query git credentials from R")
11665 "Query, set, and delete credentials from the git credential store.
11666 Manage GitHub tokens and other git credentials. This package is to be used by
11667 other packages that need to authenticate to GitHub and/or other git
11669 (license license:expat)))
11671 (define-public r-gh
11678 (uri (cran-uri "gh" version))
11681 "077drbxz3rx7idv6w24ipj1p6jnzv86a3iyryab699cc9q2kjh54"))))
11682 (build-system r-build-system)
11684 (list r-cli r-gitcreds r-httr r-ini r-jsonlite))
11687 (home-page "https://github.com/r-lib/gh#readme")
11688 (synopsis "Access the GitHub API via R")
11690 "This package provides a minimal R client to access the GitHub API.")
11691 (license license:expat)))
11693 (define-public r-fs
11700 (uri (cran-uri "fs" version))
11703 "11qr3v0xn65vfhgcxl4l6yv48s4w0w3ldp3anpzc25vd3mwd3jim"))))
11704 (build-system r-build-system)
11707 (home-page "https://fs.r-lib.org")
11708 (synopsis "Cross-platform file system operations based on libuv")
11710 "This package provides a cross-platform interface to file system
11711 operations, built on top of the libuv C library.")
11712 (license license:gpl3)))
11714 (define-public r-clisymbols
11716 (name "r-clisymbols")
11721 (uri (cran-uri "clisymbols" version))
11724 "1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
11725 (build-system r-build-system)
11726 (home-page "https://github.com/gaborcsardi/clisymbols")
11727 (synopsis "Unicode symbols at the R prompt")
11729 "This package provides a small subset of Unicode symbols, that are useful
11730 when building command line applications. They fall back to alternatives on
11731 terminals that do not support Unicode.")
11732 (license license:expat)))
11734 (define-public r-credentials
11736 (name "r-credentials")
11741 (uri (cran-uri "credentials" version))
11744 "1f18j3zrq8c9kah57xwahmmljsjg5qphlgamvx507ynvpq8pryig"))))
11745 (properties `((upstream-name . "credentials")))
11746 (build-system r-build-system)
11749 (modify-phases %standard-phases
11750 (add-after 'unpack 'setenv-HOME
11752 ;; This is necessary because git looks for $HOME/.gitconfig
11753 (setenv "HOME" "/tmp"))))))
11755 (list git-minimal))
11757 (list r-askpass r-curl r-jsonlite r-openssl r-sys))
11760 (home-page "https://docs.ropensci.org/credentials/")
11761 (synopsis "Tools for managing SSH and Git credentials")
11763 "This package assists you in setting up and retrieving of HTTPS and SSH
11764 credentials for use with git and other services. For HTTPS remotes the
11765 package interfaces the @command{git-credential} utility which @command{git}
11766 uses to store HTTP usernames and passwords. For SSH remotes this package
11767 provides convenient functions to find or generate appropriate SSH keys. The
11768 package both helps the user to setup a local git installation, and also
11769 provides a back-end for git/ssh client libraries to authenticate with existing
11770 user credentials.")
11771 (license license:expat)))
11773 (define-public r-gert
11780 (uri (cran-uri "gert" version))
11783 "1bm2fjyh527y6x0dr5cs8h31jgl1fkk09ljzj1h37d0c7f4k1hwz"))))
11784 (properties `((upstream-name . "gert")))
11785 (build-system r-build-system)
11787 (list libgit2 zlib))
11796 (list pkg-config r-knitr))
11797 (home-page "https://docs.ropensci.org/gert/")
11798 (synopsis "Simple Git client for R")
11800 "This package provides a simple git client for R based on libgit2 with
11801 support for SSH and HTTPS remotes. All functions in gert use basic R data
11802 types (such as vectors and data-frames) for their arguments and return values.
11803 User credentials are shared with command line git through the
11804 @code{git-credential} store and SSH keys stored on disk or ssh-agent.")
11805 (license license:expat)))
11807 (define-public r-usethis
11814 (uri (cran-uri "usethis" version))
11817 "0lph2rxv7nq3h022gp8d50wbq5lwicnx85d2l5dx876wxhb9wlvx"))))
11818 (build-system r-build-system)
11839 (home-page "https://github.com/r-lib/usethis")
11840 (synopsis "Automate R package and project setup")
11842 "This package helps you to automate R package and project setup tasks
11843 that are otherwise performed manually. This includes setting up unit testing,
11844 test coverage, continuous integration, Git, GitHub integration, licenses,
11845 Rcpp, RStudio projects, and more.")
11846 (license license:gpl3)))
11848 (define-public r-sessioninfo
11850 (name "r-sessioninfo")
11855 (uri (cran-uri "sessioninfo" version))
11858 "1jy7n37qnrb4fgzmn8s8yf7kv29yw27x8zklwf8qdb2kgj2q6qpm"))))
11859 (build-system r-build-system)
11862 (home-page "https://github.com/r-lib/sessioninfo#readme")
11863 (synopsis "R session information")
11865 "This package provides tools to query and print information about the
11866 current R session. It is similar to @code{utils::sessionInfo()}, but includes
11867 more information about packages, and where they were installed from.")
11868 (license license:gpl2)))
11870 (define-public r-remotes
11877 (uri (cran-uri "remotes" version))
11880 "05m5dgv0nba5vhjbdkd8z5lbhpfxgkw31j58am7vz1d44igqgvzj"))))
11881 (build-system r-build-system)
11884 (home-page "https://github.com/r-lib/remotes#readme")
11885 (synopsis "R package installation from remote repositories")
11887 "Download and install R packages stored in GitHub, BitBucket, or plain
11888 subversion or git repositories. This package is a lightweight replacement of
11889 the @code{install_*} functions in the @code{devtools} package. Indeed most of
11890 the code was copied over from @code{devtools}.")
11891 (license license:gpl2+)))
11893 (define-public r-xopen
11900 (uri (cran-uri "xopen" version))
11903 "1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
11904 (build-system r-build-system)
11907 (home-page "https://github.com/r-lib/xopen#readme")
11908 (synopsis "Open system files, URLs, anything")
11910 "This package provides a cross-platform solution to open files,
11911 directories or URLs with their associated programs.")
11912 (license license:expat)))
11914 (define-public r-rcmdcheck
11916 (name "r-rcmdcheck")
11921 (uri (cran-uri "rcmdcheck" version))
11924 "1l696byn3kjq2xvz4wxybzaj6ink85h4lz3a35v2132ba5yyzm5v"))))
11925 (build-system r-build-system)
11939 (home-page "https://github.com/r-Lib/rcmdcheck#readme")
11940 (synopsis "Run R CMD check from R and capture results")
11942 "Run @code{R CMD check} from R programmatically, and capture the results
11943 of the individual checks.")
11944 (license license:expat)))
11946 (define-public r-rapportools
11948 (name "r-rapportools")
11953 (uri (cran-uri "rapportools" version))
11956 "1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
11957 (build-system r-build-system)
11959 (list r-pander r-plyr r-reshape))
11960 (home-page "https://cran.r-project.org/web/packages/rapportools/")
11961 (synopsis "Miscellaneous helper functions with sane defaults for reporting")
11963 "This package provides helper functions that act as wrappers to more
11964 advanced statistical methods with the advantage of having sane defaults for
11966 (license license:agpl3+)))
11968 (define-public r-pander
11975 (uri (cran-uri "pander" version))
11978 "1knjcr50xxns3w3kh15myjpsizn4d7fdqx071a4yj90imif07qjh"))))
11979 (build-system r-build-system)
11981 (list r-digest r-rcpp))
11984 (home-page "https://rapporter.github.io/pander")
11985 (synopsis "Render R objects into Pandoc's markdown")
11987 "The main aim of the pander R package is to provide a minimal and easy
11988 tool for rendering R objects into Pandoc's markdown. The package is also
11989 capable of exporting/converting complex Pandoc documents (reports) in various
11991 ;; This package is licensed under either the AGPLv3+ or the very rarely
11993 (license license:agpl3+)))
11995 (define-public r-summarytools
11997 (name "r-summarytools")
12002 (uri (cran-uri "summarytools" version))
12005 "04qcysfywljnqkcz2b7kzpy0xv3ykkvvb14vnda63z1wvmadyhkn"))))
12006 (build-system r-build-system)
12022 (home-page "https://github.com/dcomtois/summarytools")
12023 (synopsis "Tools to quickly and neatly summarize data")
12025 "This package provides tools for data frame summaries, cross-tabulations,
12026 weight-enabled frequency tables and common univariate statistics in concise
12027 tables available in a variety of formats (plain ASCII, Markdown and HTML). A
12028 good point-of-entry for exploring data, both for experienced and new R
12030 (license license:gpl2)))
12032 (define-public r-lsei
12039 (uri (cran-uri "lsei" version))
12042 "1dka0rigfw4vj809qma2dkiwjb3nw5635ynnba5cm299cn7hb2b2"))))
12043 (build-system r-build-system)
12046 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
12047 (synopsis "Solve regression problems under equality/inequality constraints")
12049 "It contains functions that solve least squares linear regression
12050 problems under linear equality/inequality constraints. Functions for solving
12051 quadratic programming problems are also available, which transform such
12052 problems into least squares ones first.")
12053 (license license:gpl2+)))
12055 (define-public r-npsurv
12062 (uri (cran-uri "npsurv" version))
12065 "1ihxhb42cga1hssj2jv4ah0f4hlwsky899ij5261fzh1wxvdp1xw"))))
12066 (build-system r-build-system)
12069 (home-page "https://www.stat.auckland.ac.nz/~yongwang")
12070 (synopsis "Nonparametric survival analysis")
12072 "This package contains functions for non-parametric survival analysis of
12073 exact and interval-censored observations.")
12074 (license license:gpl2+)))
12076 (define-public r-clusteval
12078 (name "r-clusteval")
12083 (uri (cran-uri "clusteval" version))
12086 "1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
12087 (build-system r-build-system)
12089 (list r-mvtnorm r-rcpp))
12090 (home-page "https://cran.r-project.org/web/packages/clusteval/")
12091 (synopsis "Evaluation of clustering algorithms")
12093 "This R package provides a suite of tools to evaluate clustering
12094 algorithms, clusterings, and individual clusters.")
12095 (license license:expat)))
12097 (define-public r-tweedie
12104 (uri (cran-uri "tweedie" version))
12107 "1nfhaqblvm62j8gfkyrgba5ai0pb2fsnrxp63637mhys2bawlcm0"))))
12108 (build-system r-build-system)
12109 (native-inputs (list gfortran))
12110 (home-page "https://cran.r-project.org/web/packages/tweedie/")
12111 (synopsis "Evaluation of Tweedie exponential family models")
12113 "Maximum likelihood computations for Tweedie families, including the
12114 series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
12115 the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
12116 and related methods.")
12117 (license license:gpl2+)))
12119 (define-public r-rcppgsl
12126 (uri (cran-uri "RcppGSL" version))
12128 (base32 "0lalz51q31qqy0cr227vc3msi0h47p111lzy4zs93drgl1yhh4l6"))))
12129 (properties `((upstream-name . "RcppGSL")))
12130 (build-system r-build-system)
12133 (home-page "https://cran.r-project.org/web/packages/RcppGSL/")
12134 (synopsis "Rcpp integration for GSL vectors and matrices")
12136 "The GNU Scientific Library (or GSL) is a collection of numerical
12137 routines for scientific computing. It is particularly useful for C and C++
12138 programs as it provides a standard C interface to a wide range of mathematical
12139 routines. There are over 1000 functions in total with an extensive test
12140 suite. The RcppGSL package provides an easy-to-use interface between GSL data
12141 structures and R using concepts from Rcpp which is itself a package that eases
12142 the interfaces between R and C++.")
12143 (license license:gpl2+)))
12145 (define-public r-mvabund
12152 (uri (cran-uri "mvabund" version))
12155 "107pwv2bwird1a98chcnbld2wqj9prkf4pkncyrrp304zpdkkby1"))))
12156 (build-system r-build-system)
12158 (list r-mass r-rcpp r-rcppgsl r-statmod r-tweedie))
12159 (home-page "https://cran.r-project.org/web/packages/mvabund/")
12160 (synopsis "Statistical methods for analysing multivariate abundance data")
12162 "This package provides a set of tools for displaying, modeling and
12163 analysing multivariate abundance data in community ecology.")
12164 (license license:lgpl2.1+)))
12166 (define-public r-afex
12173 (uri (cran-uri "afex" version))
12176 "1k04n6gwk2n8kg0l3yk5j3wrqgkv5f6w04yjpif9y451hx5w7svg"))))
12177 (build-system r-build-system)
12179 (list r-car r-lme4 r-lmertest r-pbkrtest r-reshape2))
12182 (home-page "https://afex.singmann.science/")
12183 (synopsis "Analysis of factorial experiments")
12185 "This package provides convenience functions for analyzing factorial
12186 experiments using ANOVA or mixed models.")
12187 (license license:gpl2+)))
12189 (define-public r-lmertest
12191 (name "r-lmertest")
12196 (uri (cran-uri "lmerTest" version))
12199 "1zd8gqjkazhxgpnnr484xwsq30p62fq8592nzyc171zjyplpbaim"))))
12200 (properties `((upstream-name . "lmerTest")))
12201 (build-system r-build-system)
12203 (list r-ggplot2 r-lme4 r-mass r-numderiv))
12204 (home-page "https://github.com/runehaubo/lmerTestR")
12205 (synopsis "Tests in linear mixed effects models")
12207 "This package provides p-values in type I, II or III anova and summary
12208 tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
12209 method. A Kenward-Roger method is also available via the @code{pbkrtest}
12210 package. Model selection methods include step, drop1 and anova-like tables
12211 for random effects (ranova). Methods for Least-Square means (LS-means) and
12212 tests of linear contrasts of fixed effects are also available.")
12213 (license license:gpl2+)))
12215 (define-public r-r2glmm
12222 (uri (cran-uri "r2glmm" version))
12225 "0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
12226 (build-system r-build-system)
12238 (home-page "https://github.com/bcjaeger/r2glmm")
12239 (synopsis "Compute R squared for mixed (multilevel) models")
12241 "This package computes model and semi partial R squared with confidence
12242 limits for the linear and generalized linear mixed model (LMM and GLMM). The
12243 R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
12244 using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
12246 (license license:gpl2)))
12248 (define-public r-cmdfun
12255 (uri (cran-uri "cmdfun" version))
12258 "1pbcq7hi2lcmqnghmy3q2fsk0c9fy5m0637acyzmc096fxbx723j"))))
12259 (properties `((upstream-name . "cmdfun")))
12260 (build-system r-build-system)
12270 (home-page "https://snystrom.github.io/cmdfun/")
12271 (synopsis "Framework for building interfaces to shell commands")
12273 "Writing interfaces to command line software is cumbersome. The cmdfun
12274 package provides a framework for building function calls to seamlessly
12275 interface with shell commands by allowing lazy evaluation of command line
12276 arguments. It also provides methods for handling user-specific paths to tool
12277 installs or secrets like API keys. Its focus is to equally serve package
12278 builders who wish to wrap command line software, and to help analysts stay
12279 inside R when they might usually leave to execute non-R software.")
12280 (license license:expat)))
12282 (define-public r-rslurm
12289 (uri (cran-uri "rslurm" version))
12292 "19451icfh7snjbbmpzpr1hrdf52q8ijv0ag1di3y55r2la3jxxcf"))))
12293 (properties `((upstream-name . "rslurm")))
12294 (build-system r-build-system)
12295 (propagated-inputs (list r-whisker))
12296 (native-inputs (list r-knitr))
12297 (home-page "http://cyberhelp.sesync.org/rslurm/")
12298 (synopsis "Submit R calculations to a Slurm cluster")
12300 "This package provides functions that simplify submitting R scripts to a
12301 Slurm workload manager, in part by automating the division of embarrassingly
12302 parallel calculations across cluster nodes.")
12303 (license license:gpl3)))
12305 (define-public r-chk
12312 (uri (cran-uri "chk" version))
12315 "1fxsxgvd08lkb6amjgs4x48dhqr046mmjngjfgy2ya9cl2shd7ls"))))
12316 (properties `((upstream-name . "chk")))
12317 (build-system r-build-system)
12319 (list r-lifecycle r-rlang))
12320 (native-inputs (list r-knitr))
12321 (home-page "https://github.com/poissonconsulting/chk")
12322 (synopsis "Check user-supplied function arguments")
12324 "This is a package for developers to check user-supplied function
12325 arguments. It is designed to be simple, fast and customizable. Error
12326 messages follow the tidyverse style guide.")
12327 (license license:expat)))
12329 (define-public r-weights
12336 (uri (cran-uri "weights" version))
12339 "1fnchf7f0hyl514bk8sc3l884kg25kb5xm4mc2l28n6hm7l6bgpg"))))
12340 (build-system r-build-system)
12342 (list r-gdata r-hmisc r-lme4 r-mice))
12343 (home-page "https://cran.r-project.org/web/packages/weights/")
12344 (synopsis "Weighting and weighted statistics")
12345 (description "This package Provides a variety of functions for producing
12346 simple weighted statistics, such as weighted Pearson's correlations, partial
12347 correlations, Chi-Squared statistics, histograms, and t-tests. Also now
12348 includes some software for quickly recoding survey data and plotting point
12349 estimates from interaction terms in regressions (and multiply imputed
12350 regressions). NOTE: Weighted partial correlation calculations pulled to
12352 (license license:gpl2+)))
12354 (define-public r-rcppannoy
12356 (name "r-rcppannoy")
12361 (uri (cran-uri "RcppAnnoy" version))
12364 "12k8ny981dmky5js8yl6bih5r5mq3w43f2f9admhkwqn0n80kcl9"))))
12365 (properties `((upstream-name . "RcppAnnoy")))
12366 (build-system r-build-system)
12369 (home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
12370 (synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
12372 "Annoy is a small C++ library for Approximate Nearest Neighbors written
12373 for efficient memory usage as well an ability to load from and save to disk.
12374 This package provides an R interface.")
12375 ;; Annoy is released under ASL 2.0, but this wrapper is released under
12377 (license (list license:gpl2+ license:asl2.0))))
12379 (define-public r-rcpphnsw
12381 (name "r-rcpphnsw")
12386 (uri (cran-uri "RcppHNSW" version))
12389 "01z0plf1i6dyibw4ica8shmijyk1grpqb886hcga72z2cpm4xsx0"))))
12390 (properties `((upstream-name . "RcppHNSW")))
12391 (build-system r-build-system)
12392 (propagated-inputs (list r-rcpp))
12393 (home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
12394 (synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
12396 "Hnswlib is a C++ library for approximate nearest neighbors. This
12397 package provides a minimal R interface by relying on the Rcpp package.")
12398 ;; hnswlib is released under Version 2.0 of the Apache License.
12399 (license (list license:gpl3 license:asl2.0))))
12401 (define-public r-rcppparallel
12403 (name "r-rcppparallel")
12408 (uri (cran-uri "RcppParallel" version))
12411 "1sn211ajlb1p12sglxqns175rg078yvww268m8cp0vvd7cmk55k3"))))
12412 (properties `((upstream-name . "RcppParallel")))
12413 (build-system r-build-system)
12414 (home-page "https://rcppcore.github.io/RcppParallel/")
12415 (synopsis "Parallel programming tools for Rcpp")
12417 "This package provides high level functions for parallel programming with
12418 Rcpp. For example, the @code{parallelFor()} function can be used to convert
12419 the work of a standard serial @code{for} loop into a parallel one and the
12420 @code{parallelReduce()} function can be used for accumulating aggregates or
12422 (license license:gpl2)))
12424 (define-public r-ncdf4
12431 (uri (cran-uri "ncdf4" version))
12434 "0qzvin2fjzcb7h2knlnw14s6043pwi1nm7yf6p27ax7w269173fb"))))
12435 (build-system r-build-system)
12437 (list netcdf zlib))
12438 (home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
12439 (synopsis "R interface to Unidata netCDF format data files")
12441 "This package provides a high-level R interface to data files written
12442 using Unidata's netCDF library (version 4 or earlier), which are binary data
12443 files that are portable across platforms and include metadata information in
12444 addition to the data sets. Using this package, netCDF files can be opened and
12445 data sets read in easily. It is also easy to create new netCDF dimensions,
12446 variables, and files, in either version 3 or 4 format, and manipulate existing
12448 (license license:gpl3+)))
12450 (define-public r-biocmanager
12452 (name "r-biocmanager")
12453 (version "1.30.16")
12457 (uri (cran-uri "BiocManager" version))
12459 (base32 "0m9qxwqajg8lp0z06blbpgk3zw0z73aly1cvmjk6mvwja6jm99vm"))))
12460 (properties `((upstream-name . "BiocManager")))
12461 (build-system r-build-system)
12464 (home-page "https://cran.r-project.org/web/packages/BiocManager/")
12465 (synopsis "Access the Bioconductor project package repository")
12467 "This package provides a convenient tool to install and update
12468 Bioconductor packages.")
12469 (license license:artistic2.0)))
12471 (define-public r-rgl
12474 (version "0.108.3")
12478 (uri (cran-uri "rgl" version))
12481 "0fqkx079z9y5b1gdg6qfz2wpw2j8q3ddflfkd9wwrkyacas6xyc9"))))
12482 (build-system r-build-system)
12484 (list pkg-config r-knitr))
12499 (home-page "https://r-forge.r-project.org/projects/rgl/")
12500 (synopsis "3D visualization using OpenGL")
12502 "This package provides medium to high level functions for 3D interactive graphics,
12503 including functions modelled on base graphics (@code{plot3d()}, etc.) as well
12504 as functions for constructing representations of geometric
12505 objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
12506 various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
12507 image formats, including PNG, Postscript, SVG, PGF.")
12508 ;; Any version of the GPL.
12509 (license (list license:gpl2+ license:gpl3+))))
12511 (define-public r-multicool
12513 (name "r-multicool")
12518 (uri (cran-uri "multicool" version))
12521 "0djacq0irfqz4nlnx238kja73yvr1n5qybbfyl6bw1n6qgcjhza8"))))
12522 (build-system r-build-system)
12523 (propagated-inputs (list r-rcpp))
12524 (home-page "https://cran.r-project.org/web/packages/multicool/")
12525 (synopsis "Permutations of multisets in cool-lex order")
12527 "This package provides a set of tools to permute multisets without loops
12528 or hash tables and to generate integer partitions. Cool-lex order is similar
12529 to colexicographical order.")
12530 (license license:gpl2)))
12532 (define-public r-misc3d
12539 (uri (cran-uri "misc3d" version))
12542 "0r9x57s63kx9f6dgam2nhbziq8nrs9wd8pk7g76hds2kw46vnyx0"))))
12543 (build-system r-build-system)
12544 (home-page "https://cran.r-project.org/web/packages/misc3d/")
12545 (synopsis "Miscellaneous 3D Plots")
12547 "This package provides a collection of miscellaneous 3d plots, including
12549 ;; Any version of the GPL.
12550 (license (list license:gpl2+ license:gpl3+))))
12552 (define-public r-ks
12559 (uri (cran-uri "ks" version))
12561 (base32 "0wyfdmhr753vpizns9kl7h7pfnnb16c7m7w9a4bpz62xcvgq1yyy"))))
12562 (build-system r-build-system)
12574 (home-page "https://www.mvstat.net/tduong/")
12575 (synopsis "Kernel smoothing")
12577 "This package provides kernel smoothers for univariate and multivariate
12578 data, including density functions, density derivatives, cumulative
12579 distributions, modal clustering, discriminant analysis, and two-sample
12580 hypothesis testing.")
12581 ;; Either version of the GPL.
12582 (license (list license:gpl2 license:gpl3))))
12584 (define-public r-feature
12591 (uri (cran-uri "feature" version))
12594 "0yzn1w1sasilcp8v0pcjnxjv9l6lspkskqi412i6h040gqmjjf6y"))))
12595 (build-system r-build-system)
12597 (list r-ks r-plot3d))
12600 (home-page "https://www.mvstat.net/tduong/")
12601 (synopsis "Inferential feature significance for kernel density estimation")
12603 "The feature package contains functions to display and compute kernel
12604 density estimates, significant gradient and significant curvature regions.
12605 Significant gradient and/or curvature regions often correspond to significant
12606 features (e.g. local modes).")
12607 ;; Either version of the GPL.
12608 (license (list license:gpl2 license:gpl3))))
12610 (define-public r-arm
12617 (uri (cran-uri "arm" version))
12620 "0pagrc1vkaz460d0lvrgb4xj6gcd920f4mrc8zpzw07c3v1s2sw1"))))
12621 (build-system r-build-system)
12629 (home-page "https://cran.r-project.org/web/packages/arm/")
12630 (synopsis "Data analysis using regression and multilevel/hierarchical models")
12632 "This package provides functions to accompany A. Gelman and J. Hill,
12633 Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
12634 University Press, 2007.")
12635 (license license:gpl3+)))
12637 (define-public r-circular
12639 (name "r-circular")
12644 (uri (cran-uri "circular" version))
12647 "0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
12648 (build-system r-build-system)
12650 (list r-boot r-mvtnorm))
12653 (home-page "https://cran.r-project.org/web/packages/circular/")
12654 (synopsis "Circular statistics")
12656 "This package provides tools for circular statistics, from \"Topics in
12657 circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
12659 (license license:gpl2+)))
12661 (define-public r-activity
12663 (name "r-activity")
12668 (uri (cran-uri "activity" version))
12671 "1wn2a0hx7wfr2jyj1b772w5fgl6bcqkkw8cybais2s1wyjx8kjr5"))))
12672 (build-system r-build-system)
12674 (list r-circular r-insol r-pbapply))
12675 (home-page "https://cran.r-project.org/web/packages/activity/")
12676 (synopsis "Animal activity statistics")
12678 "This package provides functions to fit kernel density functions to
12679 animal activity time data; plot activity distributions; quantify overall
12680 levels of activity; statistically compare activity metrics through
12681 bootstrapping; and evaluate variation in linear variables with time (or other
12682 circular variables).")
12683 (license license:gpl3)))
12685 (define-public r-ouch
12692 (uri (cran-uri "ouch" version))
12695 "1a7r24j59xz3lxa5wc694j6b80j8m5l86zd1sw9pvs66l8gd98kf"))))
12696 (build-system r-build-system)
12697 (propagated-inputs (list r-subplex))
12698 (home-page "https://kingaa.github.io/ouch/")
12699 (synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
12701 "This package provides tools to fit and compare Ornstein-Uhlenbeck models
12702 for evolution along a phylogenetic tree.")
12703 (license license:gpl2+)))
12705 (define-public r-fmsb
12712 (uri (cran-uri "fmsb" version))
12715 "1ylwj4385wg7rymx0m3kayyvrbil89wxb7phdl0fvi0xq2krkzhb"))))
12716 (build-system r-build-system)
12717 (home-page "http://minato.sip21c.org/msb/")
12718 (synopsis "Functions for medical statistics book with demographic data")
12720 "This package provides several utility functions for the book entitled
12721 \"Practices of Medical and Health Data Analysis using R\" (Pearson Education
12722 Japan, 2007) with Japanese demographic data and some demographic analysis
12723 related functions.")
12724 (license license:gpl2+)))
12726 (define-public r-stabledist
12728 (name "r-stabledist")
12733 (uri (cran-uri "stabledist" version))
12736 "0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
12737 (build-system r-build-system)
12738 (home-page "https://www.rmetrics.org")
12739 (synopsis "Stable distribution functions")
12741 "This package provides density, probability and quantile functions, and
12742 random number generation for (skew) stable distributions, using the
12743 parametrizations of Nolan.")
12744 (license license:gpl2+)))
12746 (define-public r-gsl
12749 (version "2.1-7.1")
12753 (uri (cran-uri "gsl" version))
12756 "118rj9kjx9rzlynvhrly19qz3yxg8jzws35971ssgzrp5lwd367f"))))
12757 (build-system r-build-system)
12760 (home-page "https://cran.r-project.org/web/packages/gsl")
12761 (synopsis "Wrapper for the GNU Scientific Library")
12763 "This package provides an R wrapper for the special functions and quasi
12764 random number generators of the GNU Scientific Library.")
12765 (license license:gpl2+)))
12767 (define-public r-adgoftest
12769 (name "r-adgoftest")
12774 (uri (cran-uri "ADGofTest" version))
12777 "0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
12778 (properties `((upstream-name . "ADGofTest")))
12779 (build-system r-build-system)
12780 (home-page "https://cran.r-project.org/web/packages/ADGofTest")
12781 (synopsis "Anderson-Darling GoF test")
12783 "This package provides an implementation of the Anderson-Darling GoF test
12784 with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
12785 Anderson-Darling Distribution\".")
12786 ;; Any version of the GPL.
12787 (license license:gpl3+)))
12789 (define-public r-admisc
12796 (uri (cran-uri "admisc" version))
12798 (base32 "0md0sygwdglyw7ss0dw6h235n70vpf25npp1q5b5nmb4db0fq80c"))))
12799 (properties `((upstream-name . "admisc")))
12800 (build-system r-build-system)
12801 (home-page "https://github.com/dusadrian/admisc")
12802 (synopsis "Adrian Dusa's miscellaneous")
12804 "This package contains miscellaneous functions used to interpret and
12805 translate, factorize and negate Sum of Products expressions, for both binary
12806 and multi-value crisp sets, and to extract information (set names, set values)
12807 from those expressions. Other functions perform various other checks if
12808 possibly numeric (even if all numbers reside in a character vector) and coerce
12809 to numeric, or check if the numbers are whole. It also offers, among many
12810 others, a highly flexible recoding routine and a more flexible alternative to
12811 the base function @code{with()}.")
12812 (license license:gpl3+)))
12814 (define-public r-sodium
12821 (uri (cran-uri "sodium" version))
12824 "0x4jb3cf1nv1spz1jc9xp8hly2b4a7nj48xr4s33jnfcpdjkmn5q"))))
12825 (properties `((upstream-name . "sodium")))
12826 (build-system r-build-system)
12830 (list pkg-config r-knitr))
12831 (home-page "https://github.com/jeroen/sodium")
12832 (synopsis "R bindings to the libsodium crypto library")
12834 "This package provides bindings to libsodium: a library for encryption,
12835 decryption, signatures, password hashing and more. Sodium uses curve25519, a
12836 Diffie-Hellman function by Daniel Bernstein, which has become very popular
12837 after it was discovered that the NSA had backdoored Dual EC DRBG.")
12838 (license license:expat)))
12840 (define-public r-softimpute
12842 (name "r-softimpute")
12847 (uri (cran-uri "softImpute" version))
12850 "1v2a4d688ij5zcvkzpra9yx40xckdfnllnfnyq2450zf3n1kjk7a"))))
12851 (properties `((upstream-name . "softImpute")))
12852 (build-system r-build-system)
12856 (list gfortran r-knitr))
12857 (home-page "https://cran.r-project.org/web/packages/softImpute")
12858 (synopsis "Matrix completion via iterative soft-thresholded SVD")
12860 "This package provides iterative methods for matrix completion that use
12861 nuclear-norm regularization. The package includes procedures for centering
12862 and scaling rows, columns or both, and for computing low-rank @dfn{single
12863 value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
12865 (license license:gpl2)))
12867 (define-public r-fftwtools
12869 (name "r-fftwtools")
12874 (uri (cran-uri "fftwtools" version))
12877 "0zrchp4l0jdbir2gibjf00x225y9giqk80zvqmr2yyvc12lwkw7i"))))
12878 (build-system r-build-system)
12879 (inputs (list fftw))
12882 (home-page "https://github.com/krahim/fftwtools")
12883 (synopsis "Wrapper for FFTW3")
12885 "This package provides a wrapper for several FFTW functions. It provides
12886 access to the two-dimensional FFT, the multivariate FFT, and the
12887 one-dimensional real to complex FFT using the FFTW3 library. The package
12888 includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
12889 mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
12890 The FFT functions have a parameter that allows them to not return the
12891 redundant complex conjugate when the input is real data.")
12892 (license license:gpl2+)))
12894 (define-public r-tiff
12901 (uri (cran-uri "tiff" version))
12904 "0xgc7vyndxxahfhc2qqzmwi56bnfyl0pn72l820jz5sd24aymhxq"))))
12905 (build-system r-build-system)
12907 (list libtiff libjpeg-turbo zlib))
12910 (home-page "https://www.rforge.net/tiff/")
12911 (synopsis "Read and write TIFF images")
12913 "This package provides an easy and simple way to read, write and display
12914 bitmap images stored in the TIFF format. It can read and write both files and
12915 in-memory raw vectors.")
12916 ;; Either of these two license versions.
12917 (license (list license:gpl2 license:gpl3))))
12919 (define-public r-nlp
12926 (uri (cran-uri "NLP" version))
12929 "1dpj04fmld2lnhg072ahgjbhmciqqy9h1lrz0wf32mr7mm9s9sh5"))))
12930 (properties `((upstream-name . "NLP")))
12931 (build-system r-build-system)
12932 (home-page "https://cran.r-project.org/web/packages/NLP/")
12933 (synopsis "Natural language processing infrastructure")
12935 "This package provides basic classes and methods for Natural Language
12937 (license license:gpl3)))
12939 (define-public r-tm
12946 (uri (cran-uri "tm" version))
12949 "0mk2lsplynms15nw92vbdgsafg4bw1m0ik31gch1mnsnv61idsxi"))))
12950 (properties `((upstream-name . "tm")))
12951 (build-system r-build-system)
12953 (list r-bh r-nlp r-rcpp r-slam r-xml2))
12954 (home-page "http://tm.r-forge.r-project.org/")
12955 (synopsis "Text mining package")
12957 "This package provides a framework for text mining applications within R.")
12958 (license license:gpl3)))
12960 (define-public r-waveslim
12962 (name "r-waveslim")
12967 (uri (cran-uri "waveslim" version))
12970 "0ibivnhz0l06sss5rrrcvyiwg3qpbyk3qn4vx4pp90kj09x4yg0k"))))
12971 (build-system r-build-system)
12974 (home-page "http://waveslim.blogspot.com")
12975 (synopsis "Basic wavelet routines for signal processing")
12977 "This package provides basic wavelet routines for time series (1D),
12978 image (2D) and array (3D) analysis. The code provided here is based on
12979 wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
12980 and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
12981 Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
12982 pairs (Selesnick 2001, 2002).")
12983 (license license:bsd-3)))
12985 (define-public r-wordcloud
12987 (name "r-wordcloud")
12992 (uri (cran-uri "wordcloud" version))
12995 "0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
12996 (build-system r-build-system)
12998 (list r-rcolorbrewer r-rcpp
12999 ;; The "tm" package is only "suggested" according to CRAN, but the
13000 ;; wordcloud package cannot be loaded without it.
13002 (home-page "https://cran.r-project.org/web/packages/wordcloud")
13003 (synopsis "Word clouds")
13005 "This package provides functionality to create pretty word clouds,
13006 visualize differences and similarity between documents, and avoid
13007 over-plotting in scatter plots with text.")
13008 (license license:lgpl2.1)))
13010 (define-public r-colorramps
13012 (name "r-colorramps")
13017 (uri (cran-uri "colorRamps" version))
13020 "0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
13021 (properties `((upstream-name . "colorRamps")))
13022 (build-system r-build-system)
13023 (home-page "https://cran.r-project.org/web/packages/colorRamps")
13024 (synopsis "Build color tables")
13025 (description "This package provides features to build gradient color
13027 ;; Any version of the GPL
13028 (license license:gpl3+)))
13030 (define-public r-tidytree
13032 (name "r-tidytree")
13037 (uri (cran-uri "tidytree" version))
13039 (base32 "1wp411lf3syf0g1czhx3ksb4mx5d6vaw6ppipv0s0k69ivag45kq"))))
13040 (build-system r-build-system)
13053 (home-page "https://github.com/GuangchuangYu/tidytree")
13054 (synopsis "Tidy tool for phylogenetic tree data manipulation")
13056 "Phylogenetic trees generally contain multiple components including nodes,
13057 edges, branches and associated data. This package provides an approach to
13058 convert tree objects to tidy data frames. It also provides tidy interfaces to
13059 manipulate tree data.")
13060 (license license:artistic2.0)))
13062 (define-public r-rvcheck
13069 (uri (cran-uri "rvcheck" version))
13071 (base32 "09khjklvzbafd7r55496by01a9g3y291d87hpy43w44dmz9fzn9a"))))
13072 (build-system r-build-system)
13074 (list r-biocmanager r-yulab-utils))
13075 (home-page "https://cran.r-project.org/web/packages/rvcheck")
13076 (synopsis "R package version check")
13078 "This package provides tools to check the latest release version of R and
13079 R packages (on CRAN, Bioconductor or Github).")
13080 (license license:artistic2.0)))
13082 (define-public r-docopt
13089 (uri (cran-uri "docopt" version))
13092 "1zxhwizs916qm5by7nfslqnarl2q5202xc2azlhrnzk0wj3khiwz"))))
13093 (build-system r-build-system)
13094 (home-page "https://github.com/docopt/docopt.R")
13095 (synopsis "Command-line interface specification language")
13097 "This package enables you to define a command-line interface by just
13098 giving it a description in the specific format.")
13099 (license license:expat)))
13101 (define-public r-sparsesvd
13103 (name "r-sparsesvd")
13108 (uri (cran-uri "sparsesvd" version))
13111 "1xm969fjq3fv1p2sqza2apz8picibj4s2agpwf1sx9nwn3b587qs"))))
13112 (build-system r-build-system)
13113 (propagated-inputs (list r-matrix))
13114 (home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
13115 (synopsis "Sparse truncated singular value decomposition")
13117 "This package provides a Wrapper around the SVDLIBC library
13118 for (truncated) singular value decomposition of a sparse matrix. Currently,
13119 only sparse real matrices in Matrix package format are supported.")
13120 ;; SVDLIBC is released under BSD-2. The R interface is released under
13122 (license (list license:bsd-3 license:bsd-2))))
13124 (define-public r-speedglm
13126 (name "r-speedglm")
13131 (uri (cran-uri "speedglm" version))
13134 "0f37w4lj8dpcg1sfkd7cv6qpdkanmb97mnd8zih2fxzv8bpd0rfh"))))
13135 (build-system r-build-system)
13137 (list r-mass r-matrix))
13138 (home-page "https://cran.r-project.org/web/packages/speedglm")
13139 (synopsis "Fit linear and generalized linear models to large data sets")
13141 "This package provides tools for fitting linear models and generalized
13142 linear models to large data sets by updating algorithms.")
13143 ;; Any version of the GPL
13144 (license license:gpl2+)))
13146 (define-public r-densityclust
13148 (name "r-densityclust")
13153 (uri (cran-uri "densityClust" version))
13156 "1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
13157 (properties `((upstream-name . "densityClust")))
13158 (build-system r-build-system)
13167 (home-page "https://cran.r-project.org/web/packages/densityClust")
13168 (synopsis "Clustering by fast search and find of density peaks")
13170 "This package provides an improved implementation (based on k-nearest
13171 neighbors) of the density peak clustering algorithm, originally described by
13172 Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
13173 large datasets (> 100,000 samples) very efficiently.")
13174 (license license:gpl2+)))
13176 (define-public r-combinat
13178 (name "r-combinat")
13183 (uri (cran-uri "combinat" version))
13186 "1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
13187 (build-system r-build-system)
13188 (home-page "https://cran.r-project.org/web/packages/combinat")
13189 (synopsis "Combinatorics utilities")
13190 (description "This package provides assorted routines for combinatorics.")
13191 (license license:gpl2)))
13193 (define-public r-qlcmatrix
13195 (name "r-qlcmatrix")
13200 (uri (cran-uri "qlcMatrix" version))
13203 "0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
13204 (properties `((upstream-name . "qlcMatrix")))
13205 (build-system r-build-system)
13207 (list r-docopt r-matrix r-slam r-sparsesvd))
13208 (home-page "https://cran.r-project.org/web/packages/qlcMatrix")
13209 (synopsis "Sparse matrix functions for quantitative language comparison")
13211 "This package provides an extension of the functionality of the Matrix
13212 package for using sparse matrices. Some of the functions are very general,
13213 while other are highly specific for the special data format used for
13214 @dfn{quantitative language comparison} (QLC).")
13215 (license license:gpl3)))
13217 (define-public r-ddrtree
13224 (uri (cran-uri "DDRTree" version))
13227 "16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
13228 (properties `((upstream-name . "DDRTree")))
13229 (build-system r-build-system)
13231 (list r-bh r-irlba r-rcpp r-rcppeigen))
13232 (home-page "https://cran.r-project.org/web/packages/DDRTree")
13233 (synopsis "Learning principal graphs with DDRTree")
13235 "This package provides an implementation of the framework of
13236 @dfn{reversed graph embedding} (RGE) which projects data into a reduced
13237 dimensional space while constructs a principal tree which passes through the
13238 middle of the data simultaneously. DDRTree shows superiority to
13239 alternatives (Wishbone, DPT) for inferring the ordering as well as the
13240 intrinsic structure of single cell genomics data. In general, it could be
13241 used to reconstruct the temporal progression as well as the bifurcation
13242 structure of any data type.")
13243 (license license:asl2.0)))
13245 (define-public r-corpcor
13252 (uri (cran-uri "corpcor" version))
13255 "028fw61n61i79fhnaqx7gmdifdpbvp3yiaq9vvfrbv4k7i84r83i"))))
13256 (build-system r-build-system)
13257 (home-page "http://strimmerlab.org/software/corpcor/")
13258 (synopsis "Efficient estimation of covariance and (partial) correlation")
13260 "This package implements a James-Stein-type shrinkage estimator for the
13261 covariance matrix, with separate shrinkage for variances and correlations.
13262 Furthermore, functions are available for fast singular value decomposition,
13263 for computing the pseudoinverse, and for checking the rank and positive
13264 definiteness of a matrix.")
13265 (license license:gpl3+)))
13267 (define-public r-rspectra
13269 (name "r-rspectra")
13274 (uri (cran-uri "RSpectra" version))
13277 "1ab45as2ysjrvkhvmx7y3nbhd0y1w4j9k2a789lcd973zz4wzwda"))))
13278 (properties `((upstream-name . "RSpectra")))
13279 (build-system r-build-system)
13281 (list r-matrix r-rcpp r-rcppeigen))
13282 (home-page "https://github.com/yixuan/RSpectra")
13283 (synopsis "Solvers for large-scale Eigenvalue and SVD problems")
13285 "This package provides an R interface to the Spectra library for
13286 large-scale eigenvalue and SVD problems. It is typically used to compute a
13287 few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
13288 which is usually more efficient than @code{eigen()} if k << n.")
13290 (license license:mpl2.0)))
13292 (define-public r-vbsr
13299 (uri (cran-uri "vbsr" version))
13302 "1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
13303 (build-system r-build-system)
13304 (home-page "https://cran.r-project.org/web/packages/vbsr")
13305 (synopsis "Variational Bayes spike regression regularized linear models")
13307 "This package provides an efficient algorithm for solving ultra-sparse
13308 regularized regression models using a variational Bayes algorithm with a spike
13309 prior. The algorithm is solved on a path, with coordinate updates, and is
13310 capable of generating very sparse models. Very general model
13311 diagnostics for controlling type-1 errors are also provided.")
13312 (license license:gpl2)))
13314 (define-public r-flare
13321 (uri (cran-uri "flare" version))
13324 "0f992dmgnr6s8g3386i9bjfyf08q8srgw7sjz2yx7snj8znq7251"))))
13325 (build-system r-build-system)
13327 (list r-igraph r-lattice r-mass r-matrix))
13328 (home-page "https://cran.r-project.org/web/packages/flare")
13329 (synopsis "Family of Lasso regression implementations")
13331 "This package provides implementations of a family of Lasso variants
13332 including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
13333 high dimensional sparse linear models.")
13334 (license license:gpl2)))
13336 (define-public r-lassopv
13343 (uri (cran-uri "lassopv" version))
13346 "0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
13347 (build-system r-build-system)
13348 (propagated-inputs (list r-lars))
13349 (home-page "https://github.com/lingfeiwang/lassopv")
13350 (synopsis "Non-parametric p-value estimation for predictors in Lasso")
13352 "This package enables you to estimate the p-values for predictors x
13353 against target variable y in Lasso regression, using the regularization
13354 strength when each predictor enters the active set of regularization path for
13355 the first time as the statistic.")
13356 (license license:gpl3)))
13358 (define-public r-splitstackshape
13360 (name "r-splitstackshape")
13365 (uri (cran-uri "splitstackshape" version))
13368 "0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
13369 (build-system r-build-system)
13371 (list r-data-table))
13372 (home-page "https://github.com/mrdwab/splitstackshape")
13373 (synopsis "Stack and reshape datasets after splitting concatenated values")
13375 "Online data collection tools like Google Forms often export
13376 multiple-response questions with data concatenated in cells. The
13377 @code{concat.split} (cSplit) family of functions provided by this package
13378 splits such data into separate cells. This package also includes functions to
13379 stack groups of columns and to reshape wide data, even when the data are
13380 \"unbalanced\"---something which @code{reshape} (from base R) does not handle,
13381 and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
13383 (license license:gpl3)))
13385 (define-public r-tfmpvalue
13387 (name "r-tfmpvalue")
13392 (uri (cran-uri "TFMPvalue" version))
13395 "0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
13396 (properties `((upstream-name . "TFMPvalue")))
13397 (build-system r-build-system)
13398 (propagated-inputs (list r-rcpp))
13399 (home-page "https://github.com/ge11232002/TFMPvalue")
13400 (synopsis "P-value computation for position weight matrices")
13402 "In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
13403 identification from sequence/alignments, we are interested in the significance
13404 of certain match scores. TFMPvalue provides the accurate calculation of a
13405 p-value with a score threshold for position weight matrices, or the score with
13406 a given p-value. It is an interface to code originally made available by
13407 Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
13408 Touzet and Varre (2007).")
13409 (license license:gpl2)))
13411 (define-public r-rncl
13417 (uri (cran-uri "rncl" version))
13420 "0ss9jqrvv7bhvl5j74cjrp8r866d9dlavrbbfscwz3mhkgfx06bb"))))
13421 (build-system r-build-system)
13423 (list r-progress r-rcpp))
13424 (home-page "https://github.com/fmichonneau/rncl")
13425 (synopsis "Interface to the Nexus class library")
13426 (description "This package provides an interface to the Nexus class
13427 library which allows parsing of NEXUS, Newick and other phylogenetic tree
13428 file formats. It provides elements of the file that can be used to build
13429 phylogenetic objects such as @code{ape}'s @code{phylo} or @code{phylobase}'s
13430 @code{phylo4(d)}. This functionality is demonstrated with
13431 @code{read_newick_phylo()} and @code{read_nexus_phylo()}.")
13432 (license license:bsd-2)))
13434 (define-public r-phylobase
13436 (name "r-phylobase")
13440 (uri (cran-uri "phylobase" version))
13443 "0jzr1gdvmi4l640hwwzh9bxqmpja69bn3ygnaqx37awvyh7khi2s"))))
13444 (build-system r-build-system)
13446 (list r-ade4 r-ape r-rcpp r-rncl r-rnexml))
13449 (home-page "https://github.com/fmichonneau/phylobase")
13450 (synopsis "Base package for phylogenetic structures and comparative data")
13451 (description "This package provides a base @code{S4} class for comparative
13452 methods, incorporating one or more trees and trait data.")
13453 (license license:gpl2+)))
13455 (define-public r-rnexml
13461 (uri (cran-uri "RNeXML" version))
13464 "1wsl4xq9w5bp3wk69dw57bg0qcw1vs6ajwya4p0w1r00ck5pwrib"))))
13465 (build-system r-build-system)
13481 (home-page "https://docs.ropensci.org/RNeXML/")
13482 (synopsis "Semantically rich I/O for the NeXML Format")
13483 (description "This package provides access to phyloinformatic data in
13484 NeXML format. The package should add new functionality to R such as the
13485 possibility to manipulate NeXML objects in more various and refined way
13486 and compatibility with @code{ape} objects.")
13487 (license license:bsd-3)))
13489 (define-public r-rnifti
13496 (uri (cran-uri "RNifti" version))
13499 "0bz10ar6hrgkvlzh9j2im24kwi3s2nnax668z40a2wj6s5xghqlr"))))
13500 (properties `((upstream-name . "RNifti")))
13501 (build-system r-build-system)
13502 (propagated-inputs (list r-rcpp))
13503 (home-page "https://github.com/jonclayden/RNifti")
13504 (synopsis "Fast R and C++ access to NIfTI images")
13506 "This package provides very fast read and write access to images stored
13507 in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
13508 compiled C and interpreted R code. It also provides a C/C++ API that can be
13509 used by other packages.")
13510 (license license:gpl2)))
13512 (define-public r-shades
13519 (uri (cran-uri "shades" version))
13522 "1zg95sjhrfvbdlfc387g9p0vnb8nb6agdk1mb3wq3kwkm2da0bqj"))))
13523 (build-system r-build-system)
13524 (home-page "https://github.com/jonclayden/shades")
13525 (synopsis "Simple color manipulation")
13527 "This package provides functions for easily manipulating colors,
13528 creating color scales and calculating color distances.")
13529 (license license:bsd-3)))
13531 (define-public r-ore
13534 (version "1.7.1.1")
13538 (uri (cran-uri "ore" version))
13540 (base32 "0rs5r5h11x4l4nsbl4xqzbl4ahajd5374fq05abcmfjnjr9j64w5"))))
13541 (build-system r-build-system)
13542 (home-page "https://github.com/jonclayden/ore")
13543 (synopsis "R interface to the Onigmo regular expression library")
13545 "This package provides an alternative to R's built-in functionality for
13546 handling regular expressions, based on the Onigmo library. It offers
13547 first-class compiled regex objects, partial matching and function-based
13548 substitutions, amongst other features.")
13549 (license license:bsd-3)))
13551 (define-public r-reportr
13558 (uri (cran-uri "reportr" version))
13561 "0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
13562 (build-system r-build-system)
13563 (propagated-inputs (list r-ore))
13564 (home-page "https://github.com/jonclayden/reportr")
13565 (synopsis "General message and error reporting system")
13567 "This package provides a system for reporting messages, which offers
13568 certain useful features over the standard R system, such as the incorporation
13569 of output consolidation, message filtering, assertions, expression
13570 substitution, automatic generation of stack traces for debugging, and
13571 conditional reporting based on the current \"output level\".")
13572 (license license:gpl2)))
13574 (define-public r-tractor-base
13576 (name "r-tractor-base")
13577 (version "3.3.3.1")
13581 (uri (cran-uri "tractor.base" version))
13584 "0w5jw7pf77npkgig7667yikpbwv4dfk1dcq63qm88l409ga2f95p"))))
13585 (properties `((upstream-name . "tractor.base")))
13586 (build-system r-build-system)
13588 (list r-ore r-reportr r-rnifti r-shades))
13589 (home-page "https://www.tractor-mri.org.uk")
13590 (synopsis "Read, manipulate and visualize magnetic resonance images")
13592 "This package provides functions for working with magnetic resonance
13593 images. It supports reading and writing of popular file formats (DICOM,
13594 Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
13595 visualization; flexible image manipulation; metadata and sparse image
13597 (license license:gpl2)))
13599 (define-public r-grimport
13601 (name "r-grimport")
13606 (uri (cran-uri "grImport" version))
13609 "0pbzc45wgp0cpycnw0bzn65ckdszzay0zrp7c7ssxdkifp8bai3a"))))
13610 (properties `((upstream-name . "grImport")))
13611 (build-system r-build-system)
13613 (list ghostscript))
13616 (home-page "https://cran.r-project.org/web/packages/grImport")
13617 (synopsis "Convert, import, and draw PostScript pictures")
13619 "This package provides functions for converting, importing, and drawing
13620 PostScript pictures in R plots.")
13621 (license license:gpl2+)))
13623 (define-public r-grimport2
13625 (name "r-grimport2")
13630 (uri (cran-uri "grImport2" version))
13633 "19q0dd8fpp1g4xf6sg5f8dxybwxjfw553ra6wgjd8b74fzca40m1"))))
13634 (properties `((upstream-name . "grImport2")))
13635 (build-system r-build-system)
13637 (list r-base64enc r-jpeg r-png r-xml))
13638 (home-page "https://cran.r-project.org/web/packages/grImport2/")
13639 (synopsis "Import SVG graphics")
13641 "This package provides functions for importing external vector images and
13642 drawing them as part of R plots. This package is different from the
13643 @code{grImport} package because, where that package imports PostScript format
13644 images, this package imports SVG format images. Furthermore, this package
13645 imports a specific subset of SVG, so external images must be preprocessed
13646 using a package like @code{rsvg} to produce SVG that this package can import.
13647 SVG features that are not supported by R graphics, such as gradient fills, can
13648 be imported and then exported via the @code{gridSVG} package.")
13649 (license license:gpl2+)))
13651 (define-public r-kohonen
13658 (uri (cran-uri "kohonen" version))
13661 "1ck7j13x701g67bx81x7plszz804jfhl1yg42krcj9x88vm5cscr"))))
13662 (build-system r-build-system)
13665 (home-page "https://cran.r-project.org/web/packages/kohonen")
13666 (synopsis "Supervised and unsupervised self-organising maps")
13668 "This package provides functions to train @dfn{self-organising
13669 maps} (SOMs). Also interrogation of the maps and prediction using trained
13670 maps are supported. The name of the package refers to Teuvo Kohonen, the
13671 inventor of the SOM.")
13672 (license license:gpl2+)))
13674 (define-public r-nnls
13681 (uri (cran-uri "nnls" version))
13684 "07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
13685 (build-system r-build-system)
13686 (native-inputs (list gfortran))
13687 (home-page "https://cran.r-project.org/web/packages/nnls")
13688 (synopsis "Lawson-Hanson algorithm for non-negative least squares")
13690 "This package provides an R interface to the Lawson-Hanson implementation
13691 of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
13692 the combination of non-negative and non-positive constraints.")
13693 (license license:gpl2+)))
13695 (define-public r-iso
13698 (version "0.0-18.1")
13702 (uri (cran-uri "Iso" version))
13705 "0vy6jdyvp751430sf2f690yhasjr70cpk3p3lnaaxjq3fs5gg99g"))))
13706 (properties `((upstream-name . "Iso")))
13707 (build-system r-build-system)
13708 (native-inputs (list gfortran))
13709 (home-page "https://www.stat.auckland.ac.nz/~rolf/")
13710 (synopsis "Functions to perform isotonic regression")
13712 "This package provides support for linear order and unimodal
13713 order (univariate) isotonic regression and bivariate isotonic regression with
13714 linear order on both variables.")
13715 (license license:gpl2+)))
13717 (define-public r-chemometricswithr
13719 (name "r-chemometricswithr")
13724 (uri (cran-uri "ChemometricsWithR" version))
13727 "166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
13729 `((upstream-name . "ChemometricsWithR")))
13730 (build-system r-build-system)
13732 (list r-devtools r-kohonen r-mass r-pls))
13733 (home-page "https://github.com/rwehrens/CWR")
13734 (synopsis "Chemometrics with R")
13736 "This package provides functions and scripts used in the book
13737 \"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
13738 Life Sciences\" by Ron Wehrens, Springer (2011).")
13739 (license license:gpl2+)))
13741 (define-public r-als
13748 (uri (cran-uri "ALS" version))
13751 "1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
13752 (properties `((upstream-name . "ALS")))
13753 (build-system r-build-system)
13755 (list r-iso r-nnls))
13756 (home-page "https://cran.r-project.org/web/packages/ALS")
13757 (synopsis "Multivariate curve resolution alternating least squares")
13759 "Alternating least squares is often used to resolve components
13760 contributing to data with a bilinear structure; the basic technique may be
13761 extended to alternating constrained least squares. This package provides an
13762 implementation of @dfn{multivariate curve resolution alternating least
13763 squares} (MCR-ALS).
13765 Commonly applied constraints include unimodality, non-negativity, and
13766 normalization of components. Several data matrices may be decomposed
13767 simultaneously by assuming that one of the two matrices in the bilinear
13768 decomposition is shared between datasets.")
13769 (license license:gpl2+)))
13771 (define-public r-strucchange
13773 (name "r-strucchange")
13778 (uri (cran-uri "strucchange" version))
13781 "1y022363a4pp0mnji91sjh1qiyspkh09sybqwj03r9pmwrd7q93x"))))
13782 (build-system r-build-system)
13784 (list r-sandwich r-zoo))
13785 (home-page "https://cran.r-project.org/web/packages/strucchange")
13786 (synopsis "Testing, monitoring, and dating structural changes")
13788 "This package provides tools for testing, monitoring and dating
13789 structural changes in (linear) regression models. It features tests/methods
13790 from the generalized fluctuation test framework as well as from the F
13791 test (Chow test) framework. This includes methods to fit, plot and test
13792 fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
13793 statistics, respectively. It is possible to monitor incoming data online
13794 using fluctuation processes. Finally, the breakpoints in regression models
13795 with structural changes can be estimated together with confidence intervals.
13796 Emphasis is always given to methods for visualizing the data.")
13797 ;; Either of these two GPL versions
13798 (license (list license:gpl2 license:gpl3))))
13800 (define-public r-pixmap
13807 (uri (cran-uri "pixmap" version))
13810 "1v1a1adsgh5jlvvi98j4nhb1h681s97ip76zdrga12rlsjaahfw9"))))
13811 (build-system r-build-system)
13812 (home-page "https://cran.r-project.org/web/packages/pixmap")
13813 (synopsis "Tools for bitmap images")
13815 "This package provides functions for importing, exporting, plotting and
13816 other manipulations of bitmapped images.")
13817 (license license:gpl2)))
13819 (define-public r-rapidjsonr
13821 (name "r-rapidjsonr")
13826 (uri (cran-uri "rapidjsonr" version))
13829 "07zdirhbzmvq3cp4xn8ngk1lgxbbabzays315zxbs3sxrz6lzjb2"))))
13830 (build-system r-build-system)
13831 (home-page "https://cran.r-project.org/web/packages/rapidjsonr")
13832 (synopsis "JSON parser")
13834 "This package provides JSON parsing capability through the Rapidjson
13836 (license license:expat)))
13838 (define-public r-ontologyindex
13840 (name "r-ontologyindex")
13845 (uri (cran-uri "ontologyIndex" version))
13848 "0j3h1spqwjhh1wbmwivmqcyi042yy7d565c3kxgn70xrmy693x1k"))))
13849 (properties `((upstream-name . "ontologyIndex")))
13850 (build-system r-build-system)
13853 (home-page "https://cran.r-project.org/web/packages/ontologyIndex")
13854 (synopsis "Functions for processing ontologies in R")
13856 "This package provides functions for reading ontologies into R as lists
13857 and manipulating sets of ontological terms.")
13858 (license license:gpl2+)))
13860 (define-public r-gargle
13867 (uri (cran-uri "gargle" version))
13870 "0fypj70c1fjmvs57birik76wfx8a2fs4gzicbb52k57i6clwlijd"))))
13871 (build-system r-build-system)
13884 (home-page "https://gargle.r-lib.org")
13885 (synopsis "Utilities for working with Google APIs")
13887 "This package provides utilities for working with Google APIs. This
13888 includes functions and classes for handling common credential types and for
13889 preparing, executing, and processing HTTP requests.")
13890 (license license:expat)))
13892 (define-public r-bigrquery
13894 (name "r-bigrquery")
13899 (uri (cran-uri "bigrquery" version))
13902 "02msq61l7vamzpvbhvalh3qil1aa7pr68pwpsivbb6pvz6p4zyns"))))
13903 (build-system r-build-system)
13920 (home-page "https://github.com/rstats-db/bigrquery")
13921 (synopsis "R interface to Google's BigQuery API")
13923 "This package provides an R interface to Google's BigQuery database.")
13924 (license license:gpl3)))
13926 (define-public r-gmp
13929 (version "0.6-2.1")
13933 (uri (cran-uri "gmp" version))
13936 "1mj7hy6riaxl9n4q2cnyyjazwad90xbjszk25si968618rih4n64"))))
13937 (build-system r-build-system)
13940 (modify-phases %standard-phases
13941 (add-after 'unpack 'set-CC
13942 (lambda _ (setenv "CC" "gcc") #t)))))
13943 (inputs (list gmp))
13944 (home-page "https://cran.r-project.org/web/packages/gmp")
13945 (synopsis "Multiple precision arithmetic")
13947 "This package supports multiple precision arithmetic (big integers and
13948 rationals, prime number tests, matrix computation), \"arithmetic without
13949 limitations\" using the GNU Multiple Precision library.")
13950 ;; Any version of the GPL.
13951 (license license:gpl3+)))
13953 (define-public r-rmpfr
13960 (uri (cran-uri "Rmpfr" version))
13963 "1ljpbxvm4agbxnab5dfffbpw5k964hy3gw57dzydq1gpbxwdphlk"))))
13964 (properties `((upstream-name . "Rmpfr")))
13965 (build-system r-build-system)
13972 (home-page "http://rmpfr.r-forge.r-project.org/")
13973 (synopsis "R bindings to the MPFR library")
13975 "This package supports arithmetic (via S4 classes and methods) for
13976 arbitrary precision floating point numbers, including transcendental
13977 functions. To this end, the package interfaces with the @dfn{Multiple
13978 Precision Floating-Point Reliable} (MPFR) library.")
13979 (license license:gpl2+)))
13981 (define-public r-assertive-base
13983 (name "r-assertive-base")
13988 (uri (cran-uri "assertive.base" version))
13991 "07m0ddz092bgbl2fn1yk932h0iajdcqkri632477wl5a1q5r3w2b"))))
13993 `((upstream-name . "assertive.base")))
13994 (build-system r-build-system)
13995 (home-page "https://bitbucket.org/richierocks/assertive.base")
13996 (synopsis "Core of the assertive package")
13998 "This package provides a minimal set of predicates and assertions used by
13999 the assertive package. This is mainly for use by other package developers who
14000 want to include run-time testing features in their own packages.")
14001 (license license:gpl3+)))
14003 (define-public r-assertive-properties
14005 (name "r-assertive-properties")
14010 (uri (cran-uri "assertive.properties" version))
14013 "0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
14015 `((upstream-name . "assertive.properties")))
14016 (build-system r-build-system)
14018 (list r-assertive-base))
14019 (home-page "https://bitbucket.org/richierocks/assertive.properties")
14020 (synopsis "Assertions to check properties of variables")
14022 "This package provides a set of predicates and assertions for checking
14023 the properties of variables, such as length, names and attributes. This is
14024 mainly for use by other package developers who want to include run-time
14025 testing features in their own packages.")
14026 (license license:gpl3+)))
14028 (define-public r-assertive-numbers
14030 (name "r-assertive-numbers")
14035 (uri (cran-uri "assertive.numbers" version))
14038 "0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
14040 `((upstream-name . "assertive.numbers")))
14041 (build-system r-build-system)
14043 (list r-assertive-base))
14044 (home-page "https://bitbucket.org/richierocks/assertive.numbers")
14045 (synopsis "Assertions to check properties of numbers")
14047 "This package provides a set of predicates and assertions for checking
14048 the properties of numbers. This is mainly for use by other package developers
14049 who want to include run-time testing features in their own packages.")
14050 (license license:gpl3+)))
14052 (define-public r-assertive-sets
14054 (name "r-assertive-sets")
14059 (uri (cran-uri "assertive.sets" version))
14062 "1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
14064 `((upstream-name . "assertive.sets")))
14065 (build-system r-build-system)
14067 (list r-assertive-base))
14068 (home-page "https://bitbucket.org/richierocks/assertive.sets")
14069 (synopsis "Assertions to check properties of sets")
14071 "This package provides a set of predicates and assertions for checking
14072 the properties of sets. This is mainly for use by other package developers
14073 who want to include run-time testing features in their own packages.")
14074 (license license:gpl3+)))
14076 (define-public r-assertive-matrices
14078 (name "r-assertive-matrices")
14083 (uri (cran-uri "assertive.matrices" version))
14086 "16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
14088 `((upstream-name . "assertive.matrices")))
14089 (build-system r-build-system)
14091 (list r-assertive-base))
14092 (home-page "https://bitbucket.org/richierocks/assertive.matrices")
14093 (synopsis "Assertions to check properties of matrices")
14095 "This package provides a set of predicates and assertions for checking
14096 the properties of matrices. This is mainly for use by other package
14097 developers who want to include run-time testing features in their own
14099 (license license:gpl3+)))
14101 (define-public r-assertive-models
14103 (name "r-assertive-models")
14108 (uri (cran-uri "assertive.models" version))
14111 "0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
14113 `((upstream-name . "assertive.models")))
14114 (build-system r-build-system)
14116 (list r-assertive-base))
14117 (home-page "https://bitbucket.org/richierocks/assertive.models")
14118 (synopsis "Assertions to check properties of models")
14120 "This package provides a set of predicates and assertions for checking
14121 the properties of models. This is mainly for use by other package developers
14122 who want to include run-time testing features in their own packages.")
14123 (license license:gpl3+)))
14125 (define-public r-assertive-reflection
14127 (name "r-assertive-reflection")
14132 (uri (cran-uri "assertive.reflection" version))
14135 "1g9lpwzy6r2xmyi2mlbcccnfgyzhzbmx5bsicf3vkffxrlkrpjn2"))))
14137 `((upstream-name . "assertive.reflection")))
14138 (build-system r-build-system)
14140 (list r-assertive-base))
14141 (home-page "https://bitbucket.org/richierocks/assertive.reflection")
14142 (synopsis "Assertions for checking the state of R")
14144 "This package provides a set of predicates and assertions for checking
14145 the state and capabilities of R, the operating system it is running on, and
14146 the IDE being used. This is mainly for use by other package developers who
14147 want to include run-time testing features in their own packages.")
14148 (license license:gpl3+)))
14150 (define-public r-assertive-types
14152 (name "r-assertive-types")
14157 (uri (cran-uri "assertive.types" version))
14160 "0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
14162 `((upstream-name . "assertive.types")))
14163 (build-system r-build-system)
14165 (list r-assertive-base r-assertive-properties r-codetools))
14166 (home-page "https://bitbucket.org/richierocks/assertive.types")
14167 (synopsis "Assertions to check types of variables")
14169 "This package provides a set of predicates and assertions for checking
14170 the types of variables. This is mainly for use by other package developers
14171 who want to include run-time testing features in their own packages.")
14172 (license license:gpl3+)))
14174 (define-public r-assertive-files
14176 (name "r-assertive-files")
14181 (uri (cran-uri "assertive.files" version))
14184 "02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
14186 `((upstream-name . "assertive.files")))
14187 (build-system r-build-system)
14189 (list r-assertive-base r-assertive-numbers))
14190 (home-page "https://bitbucket.org/richierocks/assertive.files")
14191 (synopsis "Assertions to check properties of files")
14193 "This package provides a set of predicates and assertions for checking
14194 the properties of files and connections. This is mainly for use by other
14195 package developers who want to include run-time testing features in their own
14197 (license license:gpl3+)))
14199 (define-public r-assertive-code
14201 (name "r-assertive-code")
14206 (uri (cran-uri "assertive.code" version))
14209 "1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
14211 `((upstream-name . "assertive.code")))
14212 (build-system r-build-system)
14214 (list r-assertive-base r-assertive-properties r-assertive-types))
14215 (home-page "https://bitbucket.org/richierocks/assertive.code")
14216 (synopsis "Assertions to check properties of code")
14218 "This package provides a set of predicates and assertions for checking
14219 the properties of code. This is mainly for use by other package developers
14220 who want to include run-time testing features in their own packages.")
14221 (license license:gpl3+)))
14223 (define-public r-assertive-datetimes
14225 (name "r-assertive-datetimes")
14230 (uri (cran-uri "assertive.datetimes" version))
14233 "151d05z8n6dpl44pqsa1jfi0ijbigr3zfc43xlw53nd8ymi22kh1"))))
14235 `((upstream-name . "assertive.datetimes")))
14236 (build-system r-build-system)
14238 (list r-assertive-base r-assertive-types))
14239 (home-page "https://bitbucket.org/richierocks/assertive.datetimes")
14240 (synopsis "Assertions to check properties of dates and times")
14242 "This package provides a set of predicates and assertions for checking
14243 the properties of dates and times. This is mainly for use by other package
14244 developers who want to include run-time testing features in their own
14246 (license license:gpl3+)))
14248 (define-public r-assertive-strings
14250 (name "r-assertive-strings")
14255 (uri (cran-uri "assertive.strings" version))
14258 "0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
14260 `((upstream-name . "assertive.strings")))
14261 (build-system r-build-system)
14263 (list r-assertive-base r-assertive-types r-stringi))
14264 (home-page "https://bitbucket.org/richierocks/assertive.strings")
14265 (synopsis "Assertions to check properties of strings")
14267 "This package provides a set of predicates and assertions for checking
14268 the properties of strings. This is mainly for use by other package developers
14269 who want to include run-time testing features in their own packages.")
14270 (license license:gpl3+)))
14272 (define-public r-assertive-data-us
14274 (name "r-assertive-data-us")
14279 (uri (cran-uri "assertive.data.us" version))
14282 "1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
14284 `((upstream-name . "assertive.data.us")))
14285 (build-system r-build-system)
14287 (list r-assertive-base r-assertive-strings))
14288 (home-page "https://bitbucket.org/richierocks/assertive.data.us")
14289 (synopsis "Assertions to check properties of strings")
14291 "This package provides a set of predicates and assertions for checking
14292 the properties of US-specific complex data types. This is mainly for use by
14293 other package developers who want to include run-time testing features in
14294 their own packages.")
14295 (license license:gpl3+)))
14297 (define-public r-assertive-data-uk
14299 (name "r-assertive-data-uk")
14304 (uri (cran-uri "assertive.data.uk" version))
14307 "1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
14309 `((upstream-name . "assertive.data.uk")))
14310 (build-system r-build-system)
14312 (list r-assertive-base r-assertive-strings))
14313 (home-page "https://bitbucket.org/richierocks/assertive.data.uk")
14314 (synopsis "Assertions to check properties of strings")
14316 "This package provides a set of predicates and assertions for checking
14317 the properties of UK-specific complex data types. This is mainly for use by
14318 other package developers who want to include run-time testing features in
14319 their own packages.")
14320 (license license:gpl3+)))
14322 (define-public r-assertive-data
14324 (name "r-assertive-data")
14329 (uri (cran-uri "assertive.data" version))
14332 "00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
14334 `((upstream-name . "assertive.data")))
14335 (build-system r-build-system)
14337 (list r-assertive-base r-assertive-strings))
14338 (home-page "https://bitbucket.org/richierocks/assertive.data")
14339 (synopsis "Assertions to check properties of data")
14341 "This package provides a set of predicates and assertions for checking
14342 the properties of (country independent) complex data types. This is mainly
14343 for use by other package developers who want to include run-time testing
14344 features in their own packages.")
14345 (license license:gpl3+)))
14347 (define-public r-assertive
14349 (name "r-assertive")
14354 (uri (cran-uri "assertive" version))
14357 "02palil82idqhhshcdjsfsja9qkqnd0dczqzj5gbccy4hfg1c0y4"))))
14358 (build-system r-build-system)
14360 (list r-assertive-base
14363 r-assertive-data-uk
14364 r-assertive-data-us
14365 r-assertive-datetimes
14367 r-assertive-matrices
14369 r-assertive-numbers
14370 r-assertive-properties
14371 r-assertive-reflection
14373 r-assertive-strings
14378 (home-page "https://bitbucket.org/richierocks/assertive")
14379 (synopsis "Readable check functions to ensure code integrity")
14381 "This package provides lots of predicates (@code{is_*} functions) to
14382 check the state of your variables, and assertions (@code{assert_*} functions)
14383 to throw errors if they aren't in the right form.")
14384 (license license:gpl3+)))
14386 (define-public r-dotcall64
14388 (name "r-dotcall64")
14393 (uri (cran-uri "dotCall64" version))
14396 "1im5k8jbviwj2i42mq1kmjskh80isa7jr9w8i0fknidrzzy2h2zi"))))
14397 (properties `((upstream-name . "dotCall64")))
14398 (build-system r-build-system)
14399 (native-inputs (list gfortran))
14400 (home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
14401 (synopsis "Enhanced foreign function interface supporting long vectors")
14403 "This package provides @code{.C64()}, an enhanced version of @code{.C()}
14404 and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
14405 supports long vectors, arguments of type 64-bit integer, and provides a
14406 mechanism to avoid unnecessary copies of read-only and write-only arguments.
14407 This makes it a convenient and fast interface to C/C++ and Fortran code.")
14408 (license license:gpl2+)))
14410 (define-public r-spam
14417 (uri (cran-uri "spam" version))
14419 (base32 "1ann2a2ifr3z983fcg1c0pkgmbxz6a0ym5q1dmq1r382bd1pg0fr"))))
14420 (build-system r-build-system)
14422 (list r-dotcall64))
14424 (list gfortran r-knitr))
14425 (home-page "https://www.math.uzh.ch/pages/spam/")
14426 (synopsis "Sparse matrix algebra")
14428 "This package provides a set of functions for sparse matrix algebra.
14429 Differences with other sparse matrix packages are:
14432 @item it only supports (essentially) one sparse matrix format;
14433 @item it is based on transparent and simple structure(s);
14434 @item it is tailored for MCMC calculations within G(M)RF;
14435 @item and it is fast and scalable (with the extension package @code{spam64}).
14437 ;; Either of these licenses
14438 (license (list license:bsd-3 license:lgpl2.0))))
14440 (define-public r-fields
14447 (uri (cran-uri "fields" version))
14449 (base32 "1hs4k5a9hh0r5fsrnpnvs6wvf78xpjzj8a2j6643dsz73a5q6ln6"))))
14450 (build-system r-build-system)
14452 (list r-maps r-spam r-viridis))
14455 (home-page "https://www.image.ucar.edu/fields")
14456 (synopsis "Tools for spatial data")
14458 "This is a package for curve, surface and function fitting with an
14459 emphasis on splines, spatial data and spatial statistics. The major methods
14460 include cubic, and thin plate splines, Kriging, and compactly supported
14461 covariance functions for large data sets.")
14462 (license license:gpl2+)))
14464 (define-public r-spatialextremes
14466 (name "r-spatialextremes")
14471 (uri (cran-uri "SpatialExtremes" version))
14474 "1mhn1c8n3bmgf0fjyac3wji4790zswzkqliqcv3n8kv9806crb0y"))))
14476 `((upstream-name . "SpatialExtremes")))
14477 (build-system r-build-system)
14479 (list r-fields r-maps))
14480 (home-page "http://spatialextremes.r-forge.r-project.org/")
14481 (synopsis "Modelling spatial extremes")
14483 "This package provides tools for the statistical modelling of spatial
14484 extremes using max-stable processes, copula or Bayesian hierarchical models.
14485 More precisely, this package allows (conditional) simulations from various
14486 parametric max-stable models, analysis of the extremal spatial dependence, the
14487 fitting of such processes using composite likelihoods or least square (simple
14488 max-stable processes only), model checking and selection and prediction.")
14489 (license license:gpl2+)))
14491 (define-public r-drc
14498 (uri (cran-uri "drc" version))
14501 "0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
14502 (build-system r-build-system)
14510 (home-page "https://cran.r-project.org/web/packages/drc")
14511 (synopsis "Analysis of dose-response curves")
14513 "This package provides a suite of flexible and versatile model fitting
14514 and after-fitting functions for the analysis of dose-response data.")
14515 (license license:gpl2+)))
14517 (define-public r-rmeta
14524 (uri (cran-uri "rmeta" version))
14527 "0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
14528 (build-system r-build-system)
14529 (home-page "https://cran.r-project.org/web/packages/rmeta")
14530 (synopsis "Tools for meta-analysis")
14532 "This package provides functions for simple fixed and random effects
14533 meta-analysis for two-sample comparisons and cumulative meta-analyses. It
14534 draws standard summary plots, funnel plots, and computes summaries and tests
14535 for association and heterogeneity.")
14536 (license license:gpl2)))
14538 (define-public r-bootstrap
14540 (name "r-bootstrap")
14545 (uri (cran-uri "bootstrap" version))
14548 "1546jqhhw5h177ii8jkdikyd26rv6gwkav816np1zks4p7zgsljj"))))
14549 (build-system r-build-system)
14550 (native-inputs (list gfortran))
14551 (home-page "https://cran.r-project.org/web/packages/bootstrap")
14552 (synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
14554 "This package provides software and data for the book \"An Introduction
14555 to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
14556 This package is primarily provided for projects already based on it, and for
14557 support of the book. New projects should preferentially use the recommended
14558 package \"boot\".")
14559 (license license:bsd-3)))
14561 (define-public r-survivalroc
14563 (name "r-survivalroc")
14568 (uri (cran-uri "survivalROC" version))
14571 "0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
14572 (properties `((upstream-name . "survivalROC")))
14573 (build-system r-build-system)
14574 (home-page "https://cran.r-project.org/web/packages/survivalROC")
14575 (synopsis "Time-dependent ROC curve estimation from censored survival data")
14577 "Compute time-dependent ROC curve from censored survival data using
14578 Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
14579 Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
14580 (license license:gpl2+)))
14582 (define-public r-locfdr
14588 (uri (cran-uri "locfdr" version))
14591 "1falkbp2xz07am8jlhwlvyqvxnli4nwl188kd0g58vdfjcjy3mj2"))))
14592 (build-system r-build-system)
14593 (home-page "https://cran.r-project.org/web/packages/locfdr/")
14594 (synopsis "Computes local false discovery rates")
14595 (description "This package can be used to compute local false
14597 (license license:gpl2)))
14599 (define-public r-longitudinal
14601 (name "r-longitudinal")
14606 (uri (cran-uri "longitudinal" version))
14609 "046w3xbr535c5jyd68adv42a7limxp1mv57b5w6w673w707lmw2p"))))
14610 (build-system r-build-system)
14611 (propagated-inputs (list r-corpcor))
14612 (home-page "http://strimmerlab.org/software/longitudinal/")
14613 (synopsis "Analysis of multiple time course data")
14615 "This package contains general data structures and functions for
14616 longitudinal data with multiple variables, repeated measurements, and
14617 irregularly spaced time points. It also implements a shrinkage estimator of
14618 dynamical correlation and dynamical covariance.")
14619 (license license:gpl3+)))
14621 (define-public r-genenet
14628 (uri (cran-uri "GeneNet" version))
14631 "1r1khga3nxxjghs4vnbymzp0cwb1q17zw2v3a94qz8fsrirq1sf1"))))
14632 (properties `((upstream-name . "GeneNet")))
14633 (build-system r-build-system)
14635 (list r-corpcor r-fdrtool r-longitudinal))
14636 (home-page "http://strimmerlab.org/software/genenet/")
14637 (synopsis "Modeling and inferring gene networks")
14639 "This package analyzes gene expression (time series) data with focus on
14640 the inference of gene networks. In particular, GeneNet implements the methods
14641 of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
14642 for learning large-scale gene association networks (including assignment of
14643 putative directions).")
14644 (license license:gpl3+)))
14646 (define-public r-rbamtools
14648 (name "r-rbamtools")
14649 (version "2.16.17")
14653 (uri (cran-uri "rbamtools" version))
14656 "0qj37ljdva3v29s01dkrbg31mcfzy3bl145cp40d54v4h9xhcghc"))))
14657 (build-system r-build-system)
14658 (inputs (list zlib))
14660 (list r-refgenome))
14661 (home-page "https://cran.r-project.org/web/packages/rbamtools")
14662 (synopsis "Read and write BAM (binary alignment) files")
14664 "This package provides an R interface to functions of the SAMtools
14666 (license license:artistic2.0)))
14668 (define-public r-protviz
14675 (uri (cran-uri "protViz" version))
14678 "0l1pmfr9kmc90rl5s9b0141451rxrjmiiasp3lsvl2x3ps0smqaj"))))
14679 (properties `((upstream-name . "protViz")))
14680 (build-system r-build-system)
14681 (propagated-inputs (list r-rcpp))
14682 (home-page "https://github.com/protViz/protViz/")
14683 (synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
14685 "This package helps with quality checks, visualizations and analysis of
14686 mass spectrometry data, coming from proteomics experiments. The package is
14687 developed, tested and used at the Functional Genomics Center Zurich, where it
14688 is used mainly for prototyping, teaching, and having fun with proteomics data.
14689 But it can also be used to do data analysis for small scale data sets.")
14690 (license license:gpl3)))
14692 (define-public r-cmprsk
14699 (uri (cran-uri "cmprsk" version))
14701 (base32 "050f24l5ab1ds9824c7yjahimf6pg8ih2k83jzpzfb0n5k5jfh44"))))
14702 (build-system r-build-system)
14707 (home-page "https://cran.r-project.org/web/packages/cmprsk")
14708 (synopsis "Subdistribution analysis of competing risks")
14710 "This package provides tool for estimation, testing and regression
14711 modeling of subdistribution functions in competing risks, as described in
14712 Gray (1988), A class of K-sample tests for comparing the cumulative incidence
14713 of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
14714 A proportional hazards model for the subdistribution of a competing risk,
14715 JASA, 94:496-509.")
14716 (license license:gpl2+)))
14718 (define-public r-etm
14725 (uri (cran-uri "etm" version))
14728 "1hvrplmdpjjpjji663rw0vjbbrzj2nvr04d1nkc8bf46p4ixyxgy"))))
14729 (build-system r-build-system)
14731 (list r-data-table r-lattice r-rcpp r-rcpparmadillo r-survival))
14732 (home-page "https://cran.r-project.org/web/packages/etm")
14733 (synopsis "Empirical transition matrix")
14735 "The @dfn{empirical transition matrix} (etm) package estimates
14736 the matrix of transition probabilities for any time-inhomogeneous multistate
14737 model with finite state space using the Aalen-Johansen estimator.")
14738 (license license:expat)))
14740 (define-public r-epi
14747 (uri (cran-uri "Epi" version))
14750 "1wcxr1f7irgfdwzz4vf67114yhxrhxxxnhy4hfaww0zy91vzxx10"))))
14751 (properties `((upstream-name . "Epi")))
14752 (build-system r-build-system)
14766 (home-page "https://BendixCarstensen.com/Epi/")
14767 (synopsis "Statistical analysis in epidemiology")
14769 "This package provides functions for demographic and epidemiological
14770 analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
14771 particular representation, manipulation and simulation of multistate data -
14772 the Lexis suite of functions, which includes interfaces to the @code{mstate},
14773 @code{etm} and @code{cmprsk} packages. It also contains functions for
14774 Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
14775 data and some useful functions for tabulation and plotting, as well as a
14776 number of epidemiological data sets.")
14777 (license license:gpl2)))
14779 (define-public r-ppls
14782 (version "1.6-1.1")
14786 (uri (cran-uri "ppls" version))
14789 "1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
14790 (build-system r-build-system)
14791 (propagated-inputs (list r-mass))
14792 (home-page "https://cran.r-project.org/web/packages/ppls")
14793 (synopsis "Penalized partial least squares")
14795 "This package contains linear and nonlinear regression methods based on
14796 partial least squares and penalization techniques. Model parameters are
14797 selected via cross-validation, and confidence intervals ans tests for the
14798 regression coefficients can be conducted via jackknifing.")
14799 (license license:gpl2+)))
14801 (define-public r-huge
14808 (uri (cran-uri "huge" version))
14810 (base32 "1sl457a1lndrx98y2j9a2smanawx2iqlhl82iand0g3p5xp8ch4j"))))
14811 (build-system r-build-system)
14813 (list r-igraph r-mass r-matrix r-rcpp r-rcppeigen))
14814 (home-page "https://cran.r-project.org/web/packages/huge")
14815 (synopsis "High-dimensional undirected graph estimation")
14817 "This package provides a general framework for high-dimensional
14818 undirected graph estimation. It integrates data preprocessing, neighborhood
14819 screening, graph estimation, and model selection techniques into a pipeline.")
14820 (license license:gpl2)))
14822 (define-public r-parcor
14829 (uri (cran-uri "parcor" version))
14832 "0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
14833 (build-system r-build-system)
14835 (list r-epi r-genenet r-glmnet r-mass r-ppls))
14836 (home-page "https://cran.r-project.org/web/packages/parcor")
14837 (synopsis "Regularized estimation of partial correlation matrices")
14839 "This package estimates the matrix of partial correlations based on
14840 different regularized regression methods: lasso, adaptive lasso, PLS, and
14841 Ridge Regression. In addition, the package provides model selection for
14842 lasso, adaptive lasso and Ridge regression based on cross-validation.")
14843 (license license:gpl2+)))
14845 (define-public r-mcmc
14852 (uri (cran-uri "mcmc" version))
14855 "0q42m8ab7b6bxhns494ksjdss5f3c5m2jjfdlfj6fk1nz7ax7i5p"))))
14856 (build-system r-build-system)
14857 (home-page "https://www.stat.umn.edu/geyer/mcmc/")
14858 (synopsis "Markov chain Monte Carlo")
14860 "This package simulates continuous distributions of random vectors using
14861 @dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
14862 function that evaluates the log unnormalized density. Algorithms are random
14863 walk Metropolis algorithm (function @code{metrop}), simulated
14864 tempering (function @code{temper}), and morphometric random walk
14865 Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
14866 by change of variable.")
14867 (license license:expat)))
14869 (define-public r-listenv
14876 (uri (cran-uri "listenv" version))
14879 "0ps8bk7zlhbviawrw7vw25skjq81hkk3ijyi6g74dmfqy8zsyapx"))))
14880 (build-system r-build-system)
14883 (modify-phases %standard-phases
14884 (add-after 'unpack 'set-HOME
14885 (lambda _ (setenv "HOME" "/tmp"))))))
14887 (list r-r-rsp)) ; vignette builder
14888 (home-page "https://github.com/HenrikBengtsson/listenv")
14889 (synopsis "Environments behaving (almost) as lists")
14891 "This package implements list environments. List environments are
14892 environments that have list-like properties. For instance, the elements of a
14893 list environment are ordered and can be accessed and iterated over using index
14895 (license license:lgpl2.1+)))
14897 (define-public r-globals
14904 (uri (cran-uri "globals" version))
14907 "1wrjiiif6rpc268zz79pvpw33si6n6ffgxdnxmmcracwhb5vqg90"))))
14908 (build-system r-build-system)
14910 (list r-codetools))
14911 (home-page "https://github.com/HenrikBengtsson/globals")
14912 (synopsis "Identify global objects in R expressions")
14914 "This package provides tools to identify global (\"unknown\" or \"free\")
14915 objects in R expressions by code inspection using various strategies, e.g.
14916 conservative or liberal. The objective of this package is to make it as
14917 simple as possible to identify global objects for the purpose of exporting
14918 them in distributed compute environments.")
14919 (license license:lgpl2.1+)))
14921 (define-public r-parallelly
14923 (name "r-parallelly")
14928 (uri (cran-uri "parallelly" version))
14931 "0fwzkzw9vjblwk5rg56yl8qfn7irnbpm70405lmj7awvf35q1c5a"))))
14932 (properties `((upstream-name . "parallelly")))
14933 (build-system r-build-system)
14934 (home-page "https://github.com/HenrikBengtsson/parallelly")
14935 (synopsis "Enhancements of the parallel package")
14937 "This package provides utility functions that enhance the @code{parallel}
14938 package and support the built-in parallel backends of the @code{future}
14939 package. For example, @code{availableCores} gives the number of CPU cores
14940 available to your R process as given by R options and environment variables,
14941 including those set by job schedulers on high-performance compute clusters.
14942 If none is set, it will fall back to @code{parallel::detectCores}. Another
14943 example is @code{makeClusterPSOCK}, which is backward compatible with
14944 @code{parallel::makePSOCKcluster} while doing a better job in setting up
14945 remote cluster workers without the need for configuring the firewall to do
14946 port-forwarding to your local computer.")
14947 (license license:lgpl2.1+)))
14949 (define-public r-future
14956 (uri (cran-uri "future" version))
14959 "1y5qzpsg0r2dccynyybbb2ngxbl1y3phs1dq2jj3f2bwhc7chsfq"))))
14960 (build-system r-build-system)
14963 (modify-phases %standard-phases
14964 (add-after 'unpack 'set-HOME
14965 (lambda _ (setenv "HOME" "/tmp"))))))
14967 (list r-digest r-globals r-listenv r-parallelly))
14969 (list r-r-rsp)) ; vignette builder
14970 (home-page "https://github.com/HenrikBengtsson/future")
14971 (synopsis "Unified parallel and distributed processing in R")
14973 "The purpose of this package is to provide a lightweight and unified
14974 Future API for sequential and parallel processing of R expression via futures.
14975 This package implements sequential, multicore, multisession, and cluster
14976 futures. With these, R expressions can be evaluated on the local machine, in
14977 parallel a set of local machines, or distributed on a mix of local and remote
14978 machines. Extensions to this package implement additional backends for
14979 processing futures via compute cluster schedulers etc. Because of its unified
14980 API, there is no need to modify any code in order to switch from sequential on
14981 the local machine to, say, distributed processing on a remote compute cluster.")
14982 (license license:lgpl2.1+)))
14984 (define-public r-future-apply
14986 (name "r-future-apply")
14991 (uri (cran-uri "future.apply" version))
14994 "1ix61bfbk43pwnjb0wk8lkfgdsy5zi8svk74gar5nrl90b5w6nqd"))))
14995 (properties `((upstream-name . "future.apply")))
14996 (build-system r-build-system)
14999 (modify-phases %standard-phases
15000 (add-after 'unpack 'set-HOME
15001 (lambda _ (setenv "HOME" "/tmp"))))))
15003 (list r-future r-globals))
15005 (list r-r-rsp)) ; vignette builder
15006 (home-page "https://github.com/HenrikBengtsson/future.apply")
15007 (synopsis "Apply function to elements in parallel using futures")
15009 "This package provides implementations of @code{apply()},
15010 @code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
15011 @code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
15012 can be resolved using any future-supported backend, e.g. parallel on the local
15013 machine or distributed on a compute cluster.")
15014 (license license:gpl2+)))
15016 (define-public r-rsvd
15023 (uri (cran-uri "rsvd" version))
15026 "07p2hjmpcwcsang8z9sjkpy94rydcin7m3hyvcgzgm5cd6w8c1p4"))))
15027 (build-system r-build-system)
15030 (home-page "https://github.com/erichson/rSVD")
15031 (synopsis "Randomized singular value decomposition")
15033 "Low-rank matrix decompositions are fundamental tools and widely used for
15034 data analysis, dimension reduction, and data compression. Classically, highly
15035 accurate deterministic matrix algorithms are used for this task. However, the
15036 emergence of large-scale data has severely challenged our computational
15037 ability to analyze big data. The concept of randomness has been demonstrated
15038 as an effective strategy to quickly produce approximate answers to familiar
15039 problems such as the @dfn{singular value decomposition} (SVD). This package
15040 provides several randomized matrix algorithms such as the randomized singular
15041 value decomposition (@code{rsvd}), randomized principal component
15042 analysis (@code{rpca}), randomized robust principal component
15043 analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
15044 and the randomized CUR decomposition (@code{rcur}). In addition several plot
15045 functions are provided.")
15046 (license license:gpl3+)))
15048 (define-public r-sloop
15055 (uri (cran-uri "sloop" version))
15058 "00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
15059 (build-system r-build-system)
15061 (list r-codetools r-crayon r-purrr r-rlang r-tibble))
15062 (home-page "https://github.com/r-lib/sloop")
15063 (synopsis "Helpers for object-oriented programming in R")
15065 "This package provides a collection of helper functions designed to
15066 help you to better understand object oriented programming in R, particularly
15068 (license license:gpl3)))
15070 (define-public r-capushe
15077 (uri (cran-uri "capushe" version))
15080 "1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
15081 (build-system r-build-system)
15082 (propagated-inputs (list r-mass))
15083 (home-page "https://cran.r-project.org/web/packages/capushe/index.html")
15084 (synopsis "Calibrating penalties using slope heuristics")
15086 "This package provides tools for the calibration of penalized criteria
15087 for model selection. The calibration methods available are based on the slope
15089 (license license:gpl2+)))
15091 (define-public r-dorng
15098 (uri (cran-uri "doRNG" version))
15101 "1jff27zzrvd1fd61x2m9468h8xn3s1c9f6wibviy5zdhj5dx9s9k"))))
15102 (properties `((upstream-name . "doRNG")))
15103 (build-system r-build-system)
15105 (list r-foreach r-iterators r-rngtools))
15106 (home-page "https://renozao.github.io/doRNG/")
15107 (synopsis "Generic reproducible parallel backend for foreach loops")
15109 "This package provides functions to perform reproducible parallel
15110 @code{foreach} loops, using independent random streams as generated by
15111 L'Ecuyer's combined multiple-recursive generator. It enables to easily
15112 convert standard @code{%dopar%} loops into fully reproducible loops,
15113 independently of the number of workers, the task scheduling strategy, or the
15114 chosen parallel environment and associated foreach backend.")
15115 (license license:gpl2+)))
15117 (define-public r-blockmodeling
15119 (name "r-blockmodeling")
15124 (uri (cran-uri "blockmodeling" version))
15127 "1vc8gy4slsywcwxq532373i0dq73fhs5cac9mr6zz2pjaaxjghhq"))))
15128 (build-system r-build-system)
15131 (native-inputs (list gfortran))
15132 (home-page "https://cran.r-project.org/web/packages/blockmodeling")
15133 (synopsis "Generalized and classical blockmodeling of valued networks")
15135 "This package is primarily meant as an implementation of generalized
15136 blockmodeling for valued networks. In addition, measures of similarity or
15137 dissimilarity based on structural equivalence and regular equivalence (REGE
15138 algorithms) can be computed and partitioned matrices can be plotted.")
15139 (license license:gpl2+)))
15141 (define-public r-upsetr
15148 (uri (cran-uri "UpSetR" version))
15151 "007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
15152 (properties `((upstream-name . "UpSetR")))
15153 (build-system r-build-system)
15155 (list r-ggplot2 r-gridextra r-plyr r-scales))
15156 (home-page "https://github.com/hms-dbmi/UpSetR")
15157 (synopsis "Visualize intersecting sets")
15159 "This package provides a more scalable alternative to Venn and Euler
15160 diagrams for visualizing intersecting sets. Create visualizations of
15161 intersecting sets using a novel matrix design, along with visualizations of
15162 several common set, element and attribute related tasks.")
15163 (license license:expat)))
15165 ;; This package includes a JavaScript file, which is not minified. When
15166 ;; upgrading please check that there are no new minified JavaScript files.
15167 (define-public r-shinybs
15174 (uri (cran-uri "shinyBS" version))
15177 "0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
15178 (properties `((upstream-name . "shinyBS")))
15179 (build-system r-build-system)
15180 ;; The tests spawn Shiny browser apps. They cannot be run
15181 ;; non-interactively.
15182 (arguments '(#:tests? #f))
15184 (list r-htmltools r-shiny))
15185 (home-page "https://ebailey78.github.io/shinyBS/")
15186 (synopsis "Twitter Bootstrap components for Shiny")
15188 "This package adds additional Twitter Bootstrap components to Shiny.")
15189 (license license:gpl3)))
15191 (define-public r-shinyjqui
15193 (name "r-shinyjqui")
15198 (uri (cran-uri "shinyjqui" version))
15201 "0ins0pmfis34jr0rimsp1k1aw856r3xjdnsvv8lkwqhvp58nzqah"))
15204 (delete-file "inst/www/shinyjqui.min.js")))))
15205 (properties `((upstream-name . "shinyjqui")))
15206 (build-system r-build-system)
15209 (modify-phases %standard-phases
15210 (add-after 'unpack 'process-javascript
15211 (lambda* (#:key inputs #:allow-other-keys)
15212 (with-directory-excursion "inst/www/"
15213 (let ((source "shinyjqui.js")
15214 (target "shinyjqui.min.js"))
15215 (format #true "Processing ~a --> ~a~%"
15217 (invoke "esbuild" source "--minify"
15218 (string-append "--outfile=" target)))))))))
15220 (list r-htmltools r-htmlwidgets r-jsonlite r-shiny))
15222 (list r-knitr esbuild))
15223 (home-page "https://github.com/yang-tang/shinyjqui")
15224 (synopsis "jQuery UI interactions and effects for Shiny")
15226 "This is an extension to Shiny that brings interactions and animation
15227 effects from the jQuery UI library.")
15228 (license license:expat)))
15230 (define-public r-outliers
15232 (name "r-outliers")
15237 (uri (cran-uri "outliers" version))
15240 "0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
15241 (build-system r-build-system)
15242 (home-page "https://cran.r-project.org/web/packages/outliers/index.html")
15243 (synopsis "Tests for outliers")
15245 "This package provides a collection of some tests commonly used for
15246 identifying outliers.")
15247 (license license:gpl2+)))
15249 (define-public r-bayesm
15256 (uri (cran-uri "bayesm" version))
15258 (base32 "154glks7rsjkza0sfi1kj7wj727py9sl1ba6sswflwmwc9n226q6"))))
15259 (build-system r-build-system)
15261 (list r-rcpp r-rcpparmadillo))
15262 (home-page "http://www.perossi.org/home/bsm-1")
15263 (synopsis "Bayesian inference for marketing/micro-econometrics")
15265 "This package covers many important models used in marketing and
15266 micro-econometrics applications, including Bayes Regression (univariate or
15267 multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
15268 Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
15269 Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
15270 Mixtures of Normals (including clustering), Dirichlet Process Prior Density
15271 Estimation with normal base, Hierarchical Linear Models with normal prior and
15272 covariates, Hierarchical Linear Models with a mixture of normals prior and
15273 covariates, Hierarchical Multinomial Logits with a mixture of normals prior
15274 and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
15275 and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
15276 analysis of choice-based conjoint data, Bayesian treatment of linear
15277 instrumental variables models, Analysis of Multivariate Ordinal survey data
15278 with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
15279 Coefficient Logit Models.")
15280 (license license:gpl2+)))
15282 (define-public r-tensora
15289 (uri (cran-uri "tensorA" version))
15292 "19wwh654qlja4z1n7afjpzsrrm53p8ddysa2vra5mdnkddb4g2cf"))))
15293 (properties `((upstream-name . "tensorA")))
15294 (build-system r-build-system)
15295 (home-page "http://www.stat.boogaart.de/tensorA")
15296 (synopsis "Advanced tensor arithmetic with named indices")
15298 "This package provides convenience functions for advanced linear algebra
15299 with tensors and computation with datasets of tensors on a higher level
15300 abstraction. It includes Einstein and Riemann summing conventions, dragging,
15301 co- and contravariate indices, and parallel computations on sequences of
15303 (license license:gpl2+)))
15305 (define-public r-rarpack
15312 (uri (cran-uri "rARPACK" version))
15315 "12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
15316 (properties `((upstream-name . "rARPACK")))
15317 (build-system r-build-system)
15318 (propagated-inputs (list r-rspectra))
15319 (home-page "https://github.com/yixuan/rARPACK")
15320 (synopsis "Solvers for large scale eigenvalue and SVD problems")
15322 "This package was previously an R wrapper of the ARPACK library, and now
15323 a shell of the R package RSpectra, an R interface to the Spectra library for
15324 solving large scale eigenvalue/vector problems. The current version of
15325 rARPACK simply imports and exports the functions provided by RSpectra. New
15326 users of rARPACK are advised to switch to the RSpectra package.")
15327 (license license:bsd-3)))
15329 (define-public r-compositions
15331 (name "r-compositions")
15336 (uri (cran-uri "compositions" version))
15339 "1bqg0qqzsf92q0jb7hdjycr54bwv8rk7ajhvxgch5yslyqxpm73v"))))
15340 (build-system r-build-system)
15342 (list r-bayesm r-mass r-robustbase r-tensora))
15345 (home-page "http://www.stat.boogaart.de/compositions")
15346 (synopsis "Compositional data analysis")
15348 "This package provides functions for the consistent analysis of
15349 compositional data (e.g. portions of substances) and positive
15350 numbers (e.g. concentrations).")
15351 (license license:gpl2+)))
15353 (define-public r-cobs
15360 (uri (cran-uri "cobs" version))
15363 "0hiw5smk6kgk0gb9840kcqkhkybl7n30s77xhjc395x09izbgix1"))))
15364 (build-system r-build-system)
15366 (list r-quantreg r-sparsem))
15367 (home-page "https://cran.r-project.org/web/packages/cobs")
15368 (synopsis "Constrained B-Splines (sparse matrix based)")
15370 "This package provides qualitatively constrained (regression) smoothing
15371 splines via linear programming and sparse matrices.")
15372 (license license:gpl2+)))
15374 (define-public r-drimpute
15376 (name "r-drimpute")
15381 (uri (cran-uri "DrImpute" version))
15384 "1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
15385 (properties `((upstream-name . "DrImpute")))
15386 (build-system r-build-system)
15388 (list r-rcpp r-rcpparmadillo))
15389 (home-page "https://github.com/ikwak2/DrImpute")
15390 (synopsis "Imputing dropout events in single-cell RNA-Seq data")
15392 "This is an R package for imputing dropout events. Many statistical
15393 methods in cell type identification, visualization and lineage reconstruction
15394 do not account for dropout events. DrImpute can improve the performance of
15395 such software by imputing dropout events.")
15396 (license license:gpl3)))
15398 (define-public r-gamlss-dist
15400 (name "r-gamlss-dist")
15405 (uri (cran-uri "gamlss.dist" version))
15407 (base32 "0m41n7zf7m0mh1w9ql70wqnzsf2f013ql699im7zmp6fdggb8qxm"))))
15408 (properties `((upstream-name . "gamlss.dist")))
15409 (build-system r-build-system)
15410 (propagated-inputs (list r-mass))
15411 (home-page "http://www.gamlss.org/")
15412 (synopsis "Distributions for Generalized Additive Models for location scale and shape")
15414 "This package provides a set of distributions which can be used for
15415 modelling the response variables in Generalized Additive Models for Location
15416 Scale and Shape. The distributions can be continuous, discrete or mixed
15417 distributions. Extra distributions can be created, by transforming, any
15418 continuous distribution defined on the real line, to a distribution defined on
15419 ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
15420 transformation, respectively.")
15421 ;; Either version of the GPL.
15422 (license (list license:gpl2 license:gpl3))))
15424 ;; This package includes JavaScript files, which are not minified. When
15425 ;; upgrading please check that there are no new minified JavaScript files.
15426 (define-public r-shinyjs
15433 (uri (cran-uri "shinyjs" version))
15436 "1id9gsrkr28xl80a8794in17rxmmz06zqvd5hlns7mqz3fzhrhky"))))
15437 (build-system r-build-system)
15439 (list r-digest r-jsonlite r-shiny))
15442 (home-page "https://deanattali.com/shinyjs")
15443 (synopsis "Improve the user experience of your Shiny apps")
15445 "Perform common useful JavaScript operations in Shiny apps that will
15446 greatly improve your apps without having to know any JavaScript. Examples
15447 include: hiding an element, disabling an input, resetting an input back to its
15448 original value, delaying code execution by a few seconds, and many more useful
15449 functions for both the end user and the developer. Shinyjs can also be used
15450 to easily call your own custom JavaScript functions from R.")
15451 (license license:agpl3+)))
15453 ;; This package includes minified JavaScript files. When upgrading please
15454 ;; check that there are no new minified JavaScript files.
15455 (define-public r-colourpicker
15457 (name "r-colourpicker")
15462 (uri (cran-uri "colourpicker" version))
15465 "1q1wi3g403fbzp4ys3gsjbwdc86x770cx323qgi47ca8n219kl50"))))
15466 (build-system r-build-system)
15469 (modify-phases %standard-phases
15470 (add-after 'unpack 'process-javascript
15471 (lambda* (#:key inputs #:allow-other-keys)
15472 (with-directory-excursion "inst"
15474 `((,(assoc-ref inputs "js-salvattore")
15475 . "examples/colourInput/www/salvattore.min.js")
15476 (,(assoc-ref inputs "js-jquery")
15477 . "htmlwidgets/lib/jquery/jquery.min.js")
15478 ("www/shared/colourpicker/js/colourpicker.js"
15479 . "www/shared/colourpicker/js/colourpicker.min.js"))))
15480 (for-each (lambda (source target)
15481 (format #true "Processing ~a --> ~a~%"
15483 (delete-file target)
15484 (invoke "esbuild" source "--minify"
15485 (string-append "--outfile=" target)))
15487 (map cdr mapping)))))))))
15497 `(("esbuild" ,esbuild)
15501 (uri "https://code.jquery.com/jquery-1.11.3.js")
15504 "1v956yf5spw0156rni5z77hzqwmby7ajwdcd6mkhb6zvl36awr90"))))
15508 (uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
15511 "0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
15512 (home-page "https://github.com/daattali/colourpicker")
15513 (synopsis "Color picker tool for Shiny and for selecting colors in plots")
15515 "This package provides a color picker that can be used as an input in
15516 Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
15517 custom color palettes, and many more options. A plot color helper tool is
15518 available as an RStudio Addin, which helps you pick colors to use in your
15519 plots. A more generic color picker RStudio Addin is also provided to let you
15520 select colors to use in your R code.")
15521 (license license:expat)))
15523 (define-public r-ggextra
15530 (uri (cran-uri "ggExtra" version))
15533 "18mbi6gblqmrsciad1d2c9ngllk6mayaqj43k40hjq9ydqnvjbgj"))))
15534 (properties `((upstream-name . "ggExtra")))
15535 (build-system r-build-system)
15537 (list r-colourpicker
15547 (home-page "https://github.com/daattali/ggExtra")
15548 (synopsis "Marginal histograms for ggplot2 and other enhancements")
15550 "This package is a collection of functions and layers to enhance ggplot2.
15551 The flagship function is @code{ggMarginal()}, which can be used to add
15552 marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
15553 (license license:expat)))
15555 (define-public r-minpack-lm
15557 (name "r-minpack-lm")
15562 (uri (cran-uri "minpack.lm" version))
15565 "18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
15566 (properties `((upstream-name . "minpack.lm")))
15567 (build-system r-build-system)
15568 (native-inputs (list gfortran))
15569 (home-page "https://cran.r-project.org/web/packages/minpack.lm")
15570 (synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
15572 "The @code{nls.lm} function provides an R interface to @code{lmder} and
15573 @code{lmdif} from the MINPACK library, for solving nonlinear least-squares
15574 problems by a modification of the Levenberg-Marquardt algorithm, with support
15575 for lower and upper parameter bounds. The implementation can be used via
15576 @code{nls}-like calls using the @code{nlsLM} function.")
15577 (license license:gpl3)))
15579 (define-public r-moments
15586 (uri (cran-uri "moments" version))
15589 "0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
15590 (build-system r-build-system)
15591 (home-page "https://cran.r-project.org/web/packages/moments")
15592 (synopsis "Moments, cumulants, skewness, kurtosis and related tests")
15594 "This package provides functions to calculate: moments, Pearson's
15595 kurtosis, Geary's kurtosis and skewness; it also includes tests related to
15596 them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
15597 (license license:gpl2+)))
15599 (define-public r-msir
15606 (uri (cran-uri "msir" version))
15609 "1wm83m3cqd6llxb9p2jwim0wb81v84pgdmgcznygzaaq6kbn3n84"))))
15610 (build-system r-build-system)
15615 (home-page "https://cran.r-project.org/web/packages/msir")
15616 (synopsis "Model-based sliced inverse regression")
15618 "This is an R package for dimension reduction based on finite Gaussian
15619 mixture modeling of inverse regression.")
15620 (license license:gpl2+)))
15622 (define-public r-pbivnorm
15624 (name "r-pbivnorm")
15629 (uri (cran-uri "pbivnorm" version))
15632 "05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
15633 (build-system r-build-system)
15634 (native-inputs (list gfortran))
15635 (home-page "https://github.com/brentonk/pbivnorm")
15636 (synopsis "Vectorized bivariate normal CDF")
15638 "This package provides a vectorized R function for calculating
15639 probabilities from a standard bivariate normal CDF.")
15640 (license license:gpl2+)))
15642 (define-public r-lavaan
15649 (uri (cran-uri "lavaan" version))
15652 "0dwc8rgrzyrrb0ivx297ln2qbrsxbpn6mdf7laiffhspdpml8sad"))))
15653 (build-system r-build-system)
15655 (list r-mass r-mnormt r-numderiv r-pbivnorm))
15656 (home-page "https://lavaan.ugent.be")
15657 (synopsis "Latent variable analysis")
15659 "This package provides tools to fit a variety of latent variable models,
15660 including confirmatory factor analysis, structural equation modeling and
15661 latent growth curve models.")
15662 (license license:gpl2+)))
15664 (define-public r-nonnest2
15666 (name "r-nonnest2")
15671 (uri (cran-uri "nonnest2" version))
15674 "1ddaqwx8i3ygwvxf11mc8xhgk4nkvnail99nr5szq8i168752zq2"))))
15675 (build-system r-build-system)
15677 (list r-compquadform r-lavaan r-mvtnorm r-sandwich))
15680 (home-page "https://cran.r-project.org/web/packages/nonnest2/")
15681 (synopsis "Tests of non-nested models")
15683 "This package allows for testing of non-nested models. It includes tests
15684 of model distinguishability and of model fit that can be applied to both
15685 nested and non-nested models. The package also includes functionality to
15686 obtain confidence intervals associated with AIC and BIC.")
15687 ;; Either version of the GPL.
15688 (license (list license:gpl2 license:gpl3))))
15690 (define-public r-penalized
15692 (name "r-penalized")
15697 (uri (cran-uri "penalized" version))
15700 "1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
15701 (build-system r-build-system)
15703 (list r-rcpp r-rcpparmadillo r-survival))
15704 (home-page "https://cran.r-project.org/web/packages/penalized/")
15705 (synopsis "Penalized estimation in GLMs and in the Cox model")
15707 "This package provides tools for fitting possibly high dimensional
15708 penalized regression models. The penalty structure can be any combination of
15709 an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
15710 constraint on the regression coefficients. The supported regression models
15711 are linear, logistic and Poisson regression and the Cox Proportional Hazards
15712 model. Cross-validation routines allow optimization of the tuning
15714 (license license:gpl2+)))
15716 (define-public r-zim
15723 (uri (cran-uri "ZIM" version))
15726 "0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
15727 (properties `((upstream-name . "ZIM")))
15728 (build-system r-build-system)
15729 (propagated-inputs (list r-mass))
15730 (home-page "https://github.com/biostatstudio/ZIM")
15731 (synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
15733 "Analyze count time series with excess zeros. Two types of statistical
15734 models are supported: Markov regression and state-space models. They are also
15735 known as observation-driven and parameter-driven models respectively in the
15736 time series literature. The functions used for Markov regression or
15737 observation-driven models can also be used to fit ordinary regression models
15738 with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
15739 negative binomial (ZINB) assumption. The package also contains miscellaneous
15740 functions to compute density, distribution, quantile, and generate random
15741 numbers from ZIP and ZINB distributions.")
15742 (license license:gpl3)))
15744 (define-public r-nor1mix
15751 (uri (cran-uri "nor1mix" version))
15754 "1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
15755 (build-system r-build-system)
15756 (home-page "https://cran.r-project.org/web/packages/nor1mix/")
15757 (synopsis "Normal (1-d) mixture models")
15759 "This package provides S3 classes and methods for one-dimensional normal
15760 mixture models, for, e.g., density estimation or clustering algorithms
15761 research and teaching; it provides the widely used Marron-Wand densities. It
15762 also provides tools for efficient random number generation and graphics.")
15763 (license license:gpl2+)))
15765 (define-public r-beanplot
15767 (name "r-beanplot")
15772 (uri (cran-uri "beanplot" version))
15775 "0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
15776 (build-system r-build-system)
15777 (home-page "https://cran.r-project.org/web/packages/beanplot/")
15778 (synopsis "Visualization via beanplots")
15780 "This package provides beanplots, an alternative to
15781 boxplot/stripchart/violin plots. It can be used to plot univariate comparison
15783 (license license:gpl2)))
15785 (define-public r-pbdzmq
15792 (uri (cran-uri "pbdZMQ" version))
15795 "0yy3x3l04vx13jbjbvkvsc8jdbf0abndjfknszdx3bi18b2chi4r"))))
15796 (properties `((upstream-name . "pbdZMQ")))
15797 (build-system r-build-system)
15799 (list zeromq zlib))
15802 (home-page "https://pbdr.org/")
15803 (synopsis "R interface to ZeroMQ")
15805 "ZeroMQ is a well-known library for high-performance asynchronous
15806 messaging in scalable, distributed applications. This package provides high
15807 level R wrapper functions to easily utilize ZeroMQ. The main focus is on
15808 interactive client/server programming frameworks. A few wrapper functions
15809 compatible with @code{rzmq} are also provided.")
15810 (license license:gpl3)))
15812 (define-public r-repr
15819 (uri (cran-uri "repr" version))
15822 "0h3h14ybamcbwmm31ib66fx13v75vkzn4bn2v26n2h097sl9qybg"))))
15823 (build-system r-build-system)
15825 (list r-base64enc r-htmltools r-jsonlite r-pillar))
15826 (home-page "https://cran.r-project.org/web/packages/repr/")
15827 (synopsis "Serializable representations")
15829 "This package provides string and binary representations of objects for
15830 several formats and MIME types.")
15831 (license license:gpl3)))
15833 (define-public r-irdisplay
15835 (name "r-irdisplay")
15840 (uri (cran-uri "IRdisplay" version))
15843 "0awdiv4rr93y8jb1d64sm1iy37ywyniqm7w98yv6qm0zz47h7sw3"))))
15844 (properties `((upstream-name . "IRdisplay")))
15845 (build-system r-build-system)
15848 (home-page "https://cran.r-project.org/web/packages/IRdisplay/")
15849 (synopsis "Jupyter display machinery")
15851 "This package provides an interface to the rich display capabilities of
15852 Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
15853 running IRkernel session.")
15854 (license license:expat)))
15856 (define-public r-irkernel
15858 (name "r-irkernel")
15863 (uri (cran-uri "IRkernel" version))
15866 "00qrmsywpzw2hfp88020zjaijma7q4hqm9h2cz53rywdjzywnzss"))))
15867 (properties `((upstream-name . "IRkernel")))
15868 (build-system r-build-system)
15871 (modify-phases %standard-phases
15872 (add-after 'install 'install-kernelspec
15873 (lambda* (#:key outputs #:allow-other-keys)
15874 (let ((out (assoc-ref outputs "out")))
15875 (setenv "HOME" "/tmp")
15876 (invoke "jupyter" "kernelspec" "install"
15879 (string-append out "/site-library/IRkernel/kernelspec"))
15880 ;; Record the absolute file name of the 'R' executable in
15882 (substitute* (string-append out "/share/jupyter"
15883 "/kernels/ir/kernel.json")
15885 (string-append "[\"" (which "R") "\",")))
15895 ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
15900 (home-page "https://cran.r-project.org/web/packages/IRkernel/")
15901 (synopsis "Native R kernel for Jupyter")
15903 "The R kernel for the Jupyter environment executes R code which the
15904 front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
15906 (license license:expat)))
15908 (define-public r-gmodels
15915 (uri (cran-uri "gmodels" version))
15918 "0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
15919 (build-system r-build-system)
15921 (list r-gdata r-mass))
15922 (home-page "https://cran.r-project.org/web/packages/gmodels/")
15923 (synopsis "Various R programming tools for model fitting")
15925 "This package provides various R programming tools for model fitting.")
15926 (license license:gpl2)))
15928 (define-public r-apcluster
15930 (name "r-apcluster")
15935 (uri (cran-uri "apcluster" version))
15938 "0wnbb3kj9m7rfq63xr43jjf6n8jxm1r2wvvx6g0qkss0wvipbb1s"))))
15939 (build-system r-build-system)
15941 (list r-matrix r-rcpp))
15942 (native-inputs (list r-knitr))
15943 (home-page "https://cran.r-project.org/web/packages/apcluster/")
15944 (synopsis "Affinity propagation clustering")
15946 "This package implements affinity propagation clustering introduced by
15947 Frey and Dueck (2007). The package further provides leveraged affinity
15948 propagation and an algorithm for exemplar-based agglomerative clustering that
15949 can also be used to join clusters obtained from affinity propagation. Various
15950 plotting functions are available for analyzing clustering results.")
15951 (license license:gpl2+)))
15953 (define-public r-rematch2
15955 (name "r-rematch2")
15960 (uri (cran-uri "rematch2" version))
15963 "1fzpz8vhghw8ygwg6rsvfy3783pqk7ch029i5851lwypkplvz77y"))))
15964 (build-system r-build-system)
15967 (home-page "https://github.com/r-lib/rematch2")
15968 (synopsis "Tidy output from regular expression matching")
15970 "This package provides wrappers on @code{regexpr} and @code{gregexpr} to
15971 return the match results in tidy data frames.")
15972 (license license:expat)))
15974 (define-public r-picante
15981 (uri (cran-uri "picante" version))
15984 "19savjzj44b7ifdxcp02ynj22z4n4ikq2aipc74ljzy3yykmqmjn"))))
15985 (build-system r-build-system)
15987 (list r-ape r-nlme r-vegan))
15988 (home-page "https://cran.r-project.org/web/packages/picante/")
15989 (synopsis "Integrating phylogenies and ecology")
15991 "This package provides functions for phylocom integration, community
15992 analyses, null-models, traits and evolution. It implements numerous
15993 ecophylogenetic approaches including measures of community phylogenetic and
15994 trait diversity, phylogenetic signal, estimation of trait values for
15995 unobserved taxa, null models for community and phylogeny randomizations, and
15996 utility functions for data input/output and phylogeny plotting. A full
15997 description of package functionality and methods are provided by Kembel et
15999 (license license:gpl2)))
16001 (define-public r-reinforcelearn
16003 (name "r-reinforcelearn")
16008 (uri (cran-uri "reinforcelearn" version))
16011 "176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
16012 (build-system r-build-system)
16014 (list r-checkmate r-nnet r-purrr r-r6))
16015 (home-page "https://markusdumke.github.io/reinforcelearn")
16016 (synopsis "Reinforcement learning")
16018 "This package implements reinforcement learning environments and
16019 algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
16020 can be used with function approximation, eligibility traces (Singh & Sutton,
16021 1996) and experience replay (Mnih et al., 2013).")
16022 (license license:expat)))
16024 (define-public r-lemon
16031 (uri (cran-uri "lemon" version))
16034 "1y3ljidhqdakxlya2npj2w0az820g8kw6gl1cfm4f0cxvzgd1ly4"))))
16035 (build-system r-build-system)
16047 (home-page "https://github.com/stefanedwards/lemon")
16048 (synopsis "Freshen up your ggplot2 plots")
16050 "This package provides functions for working with legends and axis lines
16051 of ggplot2, facets that repeat axis lines on all panels, and some knitr
16053 (license license:gpl3)))
16055 (define-public r-wgaim
16062 (uri (cran-uri "wgaim" version))
16064 (base32 "1qiyfkpsbzjr9xsq5kqq6rlqpndngkn2irdfh3gyi45h6hn118j4"))))
16065 (build-system r-build-system)
16067 (list r-ggplot2 r-qtl))
16068 (home-page "https://cran.r-project.org/web/packages/wgaim")
16069 (synopsis "Whole genome average interval mapping for QTL detection")
16071 "This package integrates sophisticated mixed modelling methods with a
16072 whole genome approach to detecting significant QTL in linkage maps.")
16073 (license license:gpl2+)))
16075 (define-public r-bedr
16082 (uri (cran-uri "bedr" version))
16085 "0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
16086 (build-system r-build-system)
16095 htslib)) ; for tabix
16097 (list r-knitr)) ; for vignettes
16098 (home-page "https://cran.r-project.org/web/packages/bedr")
16099 (synopsis "Genomic region processing")
16101 "This package is for genomic regions processing using command line tools
16102 such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
16103 utilities to perform genome arithmetic e.g indexing, formatting and merging.
16104 The bedr package's API enhances access to these tools as well as offers
16105 additional utilities for genomic regions processing.")
16106 (license license:gpl2)))
16108 (define-public r-sets
16115 (uri (cran-uri "sets" version))
16118 "1mkmqi3n1lh01k47yvkr0dlf4imqdi6d6bglx9bvrjmg816p4jr3"))))
16119 (properties `((upstream-name . "sets")))
16120 (build-system r-build-system)
16121 (home-page "https://cran.r-project.org/web/packages/sets")
16122 (synopsis "Sets, generalized sets, customizable sets and intervals")
16124 "This package provides data structures and basic operations for ordinary
16125 sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets,
16126 customizable sets, and intervals.")
16127 (license license:gpl2)))
16129 (define-public r-partitions
16131 (name "r-partitions")
16136 (uri (cran-uri "partitions" version))
16139 "1qqy4df28wy4q0g572azrj171jlhvrnzbh7x0wr2g7v6gr20y0ns"))))
16140 (build-system r-build-system)
16142 (list r-gmp r-polynom r-sets))
16143 (home-page "https://cran.r-project.org/web/packages/partitions")
16144 (synopsis "Additive partitions of integers")
16146 "This package provides tools to enumerates the partitions, unequal
16147 partitions, and restricted partitions of an integer; the three corresponding
16148 partition functions are also given.")
16149 ;; Any version of the GPL
16150 (license license:gpl2+)))
16152 (define-public r-brobdingnag
16154 (name "r-brobdingnag")
16159 (uri (cran-uri "Brobdingnag" version))
16162 "1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
16163 (properties `((upstream-name . "Brobdingnag")))
16164 (build-system r-build-system)
16165 (home-page "https://github.com/RobinHankin/Brobdingnag.git")
16166 (synopsis "Very large numbers in R")
16168 "This package handles very large numbers in R. Real numbers are held
16169 using their natural logarithms, plus a logical flag indicating sign. The
16170 package includes a vignette that gives a step-by-step introduction to using S4
16172 ;; Any version of the GPL
16173 (license license:gpl2+)))
16175 (define-public r-untb
16182 (uri (cran-uri "untb" version))
16185 "1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
16186 (build-system r-build-system)
16188 (list r-brobdingnag r-partitions r-polynom))
16189 (home-page "https://github.com/RobinHankin/untb.git")
16190 (synopsis "Ecological drift under the UNTB")
16192 "This package provides numerical simulations, and visualizations, of
16193 Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
16194 (license license:gpl2+)))
16196 (define-public r-stepwise
16198 (name "r-stepwise")
16203 (uri (cran-uri "stepwise" version))
16206 "1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
16207 (build-system r-build-system)
16208 (home-page "https://stat.sfu.ca/statgen/research/stepwise.html")
16209 (synopsis "Stepwise detection of recombination breakpoints")
16211 "This package provides a stepwise approach to identifying recombination
16212 breakpoints in a genomic sequence alignment.")
16213 (license license:gpl2+)))
16215 (define-public r-snpmaxsel
16217 (name "r-snpmaxsel")
16222 (uri (cran-uri "SNPmaxsel" version))
16225 "0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
16226 (properties `((upstream-name . "SNPmaxsel")))
16227 (build-system r-build-system)
16229 (list r-combinat r-mvtnorm))
16230 (home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
16231 (synopsis "Maximally selected statistics for SNP data")
16233 "This package implements asymptotic methods related to maximally selected
16234 statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
16236 (license license:gpl2+)))
16238 (define-public r-acsnminer
16240 (name "r-acsnminer")
16241 (version "0.16.8.25")
16244 (uri (cran-uri "ACSNMineR" version))
16247 "0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
16248 (properties `((upstream-name . "ACSNMineR")))
16249 (build-system r-build-system)
16251 (list r-ggplot2 r-gridextra))
16252 (home-page "https://cran.r-project.org/web/packages/ACSNMineR")
16253 (synopsis "Gene enrichment analysis")
16255 "This package provides tools to compute and represent gene set enrichment
16256 or depletion from your data based on pre-saved maps from the @dfn{Atlas of
16257 Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
16258 enrichment can be run with hypergeometric test or Fisher exact test, and can
16259 use multiple corrections. Visualization of data can be done either by
16260 barplots or heatmaps.")
16261 (license license:gpl2+)))
16263 (define-public r-seqinr
16270 (uri (cran-uri "seqinr" version))
16273 "1xz9spln6s9mcwpgcv1m4jymn4gnl1bb6vh90bphqcn0vvlk8jsq"))))
16274 (build-system r-build-system)
16276 (list r-ade4 r-segmented))
16279 (home-page "http://seqinr.r-forge.r-project.org/")
16280 (synopsis "Biological sequences retrieval and analysis")
16282 "This package provides tools for exploratory data analysis and data
16283 visualization of biological sequence (DNA and protein) data. It also includes
16284 utilities for sequence data management under the ACNUC system.")
16285 (license license:gpl2+)))
16287 (define-public r-units
16294 (uri (cran-uri "units" version))
16297 "1ss0f15h4yqzk488ilsa5d2ibrj3wzwplx4160mn600i8ciy02xr"))))
16298 (build-system r-build-system)
16305 (home-page "https://github.com/r-quantities/units/")
16306 (synopsis "Measurement Units for R Vectors")
16308 "This package provides support for measurement units in R vectors,
16309 matrices and arrays: automatic propagation, conversion, derivation and
16310 simplification of units; raising errors in case of unit incompatibility. It
16311 is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
16313 (license license:gpl2)))
16315 (define-public r-udunits2
16317 (name "r-udunits2")
16322 (uri (cran-uri "udunits2" version))
16325 "0sarkw5ciafiaq1haam8d8w0cmai63wrw2m4rcbjfa5k0648j07f"))))
16326 (properties `((upstream-name . "udunits2")))
16327 (build-system r-build-system)
16330 (home-page "https://cran.r-project.org/package=udunits2")
16331 (synopsis "Udunits-2 bindings for R")
16333 "This package provides simple bindings to Unidata's udunits library.")
16334 (license license:gpl2)))
16336 (define-public r-classint
16338 (name "r-classint")
16343 (uri (cran-uri "classInt" version))
16346 "1b1lqhpzxm6b8pza8l3s0cxy74mm9y45lcd3354i2v3bg8m7mply"))))
16347 (properties `((upstream-name . "classInt")))
16348 (build-system r-build-system)
16350 (list r-class r-e1071 r-kernsmooth))
16352 (list gfortran r-knitr))
16353 (home-page "https://github.com/r-spatial/classInt/")
16354 (synopsis "Choose univariate class intervals")
16356 "This package provides selected commonly used methods for choosing
16357 univariate class intervals for mapping or other graphics purposes.")
16358 (license license:gpl2+)))
16360 (define-public r-spdata
16367 (uri (cran-uri "spData" version))
16370 "1z4hp5ivwzyvl8mkp98j2ng1cl1xksqbjxv85vdlqfqjwpia6df6"))))
16371 (properties `((upstream-name . "spData")))
16372 (build-system r-build-system)
16374 (list r-raster r-sp))
16375 (home-page "https://github.com/Nowosad/spData")
16376 (synopsis "Datasets for spatial analysis")
16378 "This a package containing diverse spatial datasets for demonstrating,
16379 benchmarking and teaching spatial data analysis. It includes R data of class
16380 @code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
16381 range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
16382 of the datasets are designed to illustrate specific analysis techniques.
16383 @code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
16384 illustrate point pattern analysis techniques.")
16385 (license license:cc0)))
16387 (define-public r-learnbayes
16389 (name "r-learnbayes")
16394 (uri (cran-uri "LearnBayes" version))
16397 "0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
16398 (properties `((upstream-name . "LearnBayes")))
16399 (build-system r-build-system)
16400 (home-page "https://cran.r-project.org/web/packages/LearnBayes")
16401 (synopsis "Functions for learning Bayesian inference")
16403 "This package provides a collection of functions helpful in learning the
16404 basic tenets of Bayesian statistical inference. It contains functions for
16405 summarizing basic one and two parameter posterior distributions and predictive
16406 distributions. It contains MCMC algorithms for summarizing posterior
16407 distributions defined by the user. It also contains functions for regression
16408 models, hierarchical models, Bayesian tests, and illustrations of Gibbs
16410 (license license:gpl2+)))
16412 (define-public r-deldir
16419 (uri (cran-uri "deldir" version))
16422 "1igq0l2knsbhizncgydcsidgkvvlwwlkrifbcdyhnzk0bhrdixkd"))))
16423 (build-system r-build-system)
16424 (native-inputs (list gfortran))
16425 (home-page "https://cran.r-project.org/web/packages/deldir")
16426 (synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
16428 "This package provides tools for calculating the Delaunay triangulation
16429 and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
16430 of a planar point set. It plots triangulations and tessellations in various
16431 ways, clips tessellations to sub-windows, calculates perimeters of
16432 tessellations, and summarizes information about the tiles of the
16434 (license license:gpl2+)))
16436 (define-public r-wk
16443 (uri (cran-uri "wk" version))
16446 "1xga4rrqsr190g55by39az4nimnn06bf5b6mcjgwqvba0lvjhb5g"))))
16447 (properties `((upstream-name . "wk")))
16448 (build-system r-build-system)
16449 (home-page "https://paleolimbot.github.io/wk/")
16450 (synopsis "Lightweight well-known geometry parsing")
16452 "This package provides a minimal R and C++ API for parsing well-known
16453 binary and well-known text representation of geometries to and from R-native
16454 formats. Well-known binary is compact and fast to parse; well-known text is
16455 human-readable and is useful for writing tests. These formats are only useful
16456 in R if the information they contain can be accessed in R, for which
16457 high-performance functions are provided here.")
16458 (license license:expat)))
16460 (define-public r-s2
16467 (uri (cran-uri "s2" version))
16470 "0gwydn6wdl675ydkcckrci6ylcx30qn8nfhmrp4qx4r9mv3c2410"))))
16471 (properties `((upstream-name . "s2")))
16472 (build-system r-build-system)
16474 (list r-rcpp r-wk))
16479 (home-page "https://r-spatial.github.io/s2/")
16480 (synopsis "Spherical geometry operators using the S2 geometry library")
16482 "This package provides R bindings for Google's s2 library for geometric
16483 calculations on the sphere. High-performance constructors and exporters
16484 provide high compatibility with existing spatial packages, transformers
16485 construct new geometries from existing geometries, predicates provide a means
16486 to select geometries based on spatial relationships, and accessors extract
16487 information about geometries.")
16488 (license license:asl2.0)))
16490 (define-public r-sf
16497 (uri (cran-uri "sf" version))
16500 "1i0s9839m9zffad2aq6zgcpz0d61g68caqh9wxaxaxx7bvx2h319"))))
16501 (build-system r-build-system)
16503 (list gdal geos proj sqlite zlib))
16512 (list pkg-config r-knitr))
16513 (home-page "https://github.com/r-spatial/sf/")
16514 (synopsis "Simple features for R")
16516 "This package provides support for simple features, a standardized way to
16517 encode spatial vector data. It binds to GDAL for reading and writing data, to
16518 GEOS for geometrical operations, and to PROJ for projection conversions and
16519 datum transformations.")
16520 ;; Either of these licenses
16521 (license (list license:gpl2 license:expat))))
16523 (define-public r-spdep
16529 (uri (cran-uri "spdep" version))
16532 "08sya6vy7s87h337g2fanncw6xx9y9z8nxpqalbdxv9vpsc6zx4l"))
16534 '(for-each delete-file '("inst/doc/CO69.html"
16538 "inst/doc/nb_sf.html"
16540 "inst/doc/nb_sf.Rmd"
16541 "inst/doc/sids.html"
16542 "inst/doc/sids.R")))))
16543 (build-system r-build-system)
16555 (home-page "https://github.com/r-spatial/spdep/")
16556 (synopsis "Spatial dependence: weighting schemes, statistics and models")
16558 "This package provides a collection of functions to create spatial
16559 weights matrix objects from polygon contiguities, from point patterns by
16560 distance and tessellations, for summarizing these objects, and for permitting
16561 their use in spatial data analysis, including regional aggregation by minimum
16563 (license license:gpl2+)))
16565 (define-public r-adegenet
16567 (name "r-adegenet")
16572 (uri (cran-uri "adegenet" version))
16575 "1wjp31634n6z6wglf4z3ydrhhn5jmpwwckmp3n2b0v5f3p2fivp4"))))
16576 (build-system r-build-system)
16589 (home-page "https://github.com/thibautjombart/adegenet")
16590 (synopsis "Exploratory analysis of genetic and genomic data")
16592 "This package provides a toolset for the exploration of genetic and
16593 genomic data. Adegenet provides formal (S4) classes for storing and handling
16594 various genetic data, including genetic markers with varying ploidy and
16595 hierarchical population structure (@code{genind} class), alleles counts by
16596 populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
16597 also implements original multivariate methods (DAPC, sPCA), graphics,
16598 statistical tests, simulation tools, distance and similarity measures, and
16599 several spatial methods. A range of both empirical and simulated datasets is
16600 also provided to illustrate various methods.")
16601 (license license:gpl2+)))
16603 (define-public r-pegas
16610 (uri (cran-uri "pegas" version))
16612 (base32 "0ngd0laqbs139ji9hm9kwsm9rm56agw2yyfcplxgqva936l93fl7"))))
16613 (build-system r-build-system)
16616 (home-page "http://ape-package.ird.fr/pegas.html")
16617 (synopsis "Population and evolutionary genetics analysis system")
16619 "This package provides functions for reading, writing, plotting,
16620 analysing, and manipulating allelic and haplotypic data, including from VCF
16621 files, and for the analysis of population nucleotide sequences and
16622 micro-satellites including coalescent analyses, linkage disequilibrium,
16623 population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
16624 minimum spanning tree and network, and median-joining networks.")
16625 (license license:gpl2+)))
16627 (define-public r-rmetasim
16629 (name "r-rmetasim")
16634 (uri (cran-uri "rmetasim" version))
16637 "0rdkhfgyr97r2d1kd9g8ipb2pn563qxm1y4m9z678q0kqan2ddl0"))))
16638 (build-system r-build-system)
16640 (list r-ade4 r-adegenet r-gtools r-pegas))
16641 (home-page "https://cran.r-project.org/web/packages/rmetasim")
16642 (synopsis "Individual-based population genetic simulation environment")
16644 "This package provides an interface between R and the metasim simulation
16645 engine. The simulation environment is documented in: Strand, A.(2002),
16646 Metasim 1.0: an individual-based environment for simulating population
16647 genetics of complex population dynamics.")
16649 (license license:gpl2+)))
16651 (define-public r-genetics
16653 (name "r-genetics")
16654 (version "1.3.8.1.3")
16658 (uri (cran-uri "genetics" version))
16661 "0lljxvz7nc6y2z303icphar2niir0i407w5cyhy2pwspd9gwkwpy"))))
16662 (build-system r-build-system)
16664 (list r-combinat r-gdata r-gtools r-mass r-mvtnorm))
16665 (home-page "https://cran.r-project.org/web/packages/genetics/")
16666 (synopsis "Population genetics")
16668 "This package provides classes and methods for handling genetic data.
16669 It includes classes to represent genotypes and haplotypes at single markers up
16670 to multiple markers on multiple chromosomes. Function include allele
16671 frequencies, flagging homo/heterozygotes, flagging carriers of certain
16672 alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
16673 and testing for linkage disequilibrium, ...")
16674 ;; Any GPL version.
16675 (license license:gpl2+)))
16677 (define-public r-snp-plotter
16679 (name "r-snp-plotter")
16684 (uri (cran-uri "snp.plotter" version))
16687 "16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
16688 (properties `((upstream-name . "snp.plotter")))
16689 (build-system r-build-system)
16690 (propagated-inputs (list r-genetics))
16691 (home-page "https://cran.r-project.org/web/packages/snp.plotter/")
16692 (synopsis "Plot p-values using single SNP and/or haplotype data")
16694 "This package helps you create plots of p-values using single SNP and/or
16695 haplotype data. Main features of the package include options to display a
16696 @dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
16697 datasets simultaneously. Plots can be created using global and/or individual
16698 haplotype p-values along with single SNP p-values. Images are created as
16699 either PDF/EPS files.")
16700 (license license:gpl2+)))
16702 (define-public r-polspline
16704 (name "r-polspline")
16709 (uri (cran-uri "polspline" version))
16711 (base32 "0rhzf735hmbqfn2xbgcln4sqx7m9far72g5gq9mghgkw016kqglm"))))
16712 (build-system r-build-system)
16713 (native-inputs (list gfortran))
16714 (home-page "https://cran.r-project.org/web/packages/polspline/")
16715 (synopsis "Polynomial spline routines")
16717 "This package provides routines for the polynomial spline fitting
16718 routines hazard regression, hazard estimation with flexible tails, logspline,
16719 lspec, polyclass, and polymars.")
16720 (license license:gpl2+)))
16722 (define-public r-rms
16729 (uri (cran-uri "rms" version))
16731 (base32 "1di4xvsx0rwkr77nfqiysbg4qf699199xqil70i39d4zwfzqrm8h"))))
16732 (build-system r-build-system)
16749 (native-inputs (list gfortran))
16750 (home-page "http://biostat.mc.vanderbilt.edu/rms")
16751 (synopsis "Regression modeling strategies")
16753 "This is a package for regression modeling, testing, estimation,
16754 validation, graphics, prediction, and typesetting by storing enhanced model
16755 design attributes in the fit. The rms package is a collection of functions
16756 that assist with and streamline modeling. It also contains functions for
16757 binary and ordinal logistic regression models, ordinal models for continuous Y
16758 with a variety of distribution families, and the Buckley-James multiple
16759 regression model for right-censored responses, and implements penalized
16760 maximum likelihood estimation for logistic and ordinary linear models. The
16761 package works with almost any regression model, but it was especially written
16762 to work with binary or ordinal regression models, Cox regression, accelerated
16763 failure time models, ordinary linear models, the Buckley-James model,
16764 generalized least squares for serially or spatially correlated observations,
16765 generalized linear models, and quantile regression.")
16766 (license license:gpl2+)))
16768 (define-public r-arsenal
16775 (uri (cran-uri "arsenal" version))
16778 "0qvs3ld28djnjnggdhqjwq8sbv8zz322qahlvf7dnx35yqf6xkms"))))
16779 (properties `((upstream-name . "arsenal")))
16780 (build-system r-build-system)
16781 (propagated-inputs (list r-knitr))
16782 (native-inputs (list r-knitr))
16783 (home-page "https://github.com/mayoverse/arsenal")
16784 (synopsis "Functions for large-scale statistical summaries")
16786 "This package provides an arsenal of R functions for large-scale
16787 statistical summaries, which are streamlined to work within the latest
16788 reporting tools in R and RStudio and which use formulas and versatile
16789 summary statistics for summary tables and models. The primary functions
16793 @item @code{tableby}, a Table-1-like summary of multiple variable types by the
16794 levels of one or more categorical variables;
16795 @item @code{paired}, a Table-1-like summary of multiple variable types paired
16796 across two time points;
16797 @item @code{modelsum}, which performs simple model fits on one or more
16798 endpoints for many variables (univariate or adjusted for covariates);
16799 @item @code{freqlist}, a powerful frequency table across many categorical
16801 @item @code{comparedf}, a function for comparing @code{data.frames}; and
16802 @item @code{write2}, a function to output tables to a document.
16805 (license license:gpl2+)))
16807 (define-public r-haplo-stats
16809 (name "r-haplo-stats")
16814 (uri (cran-uri "haplo.stats" version))
16817 "1q2zn72j92bwhcdswk4qqfgzch56p9pcy2xhkd3safvqp3l9rzpw"))))
16818 (properties `((upstream-name . "haplo.stats")))
16819 (build-system r-build-system)
16821 (list r-arsenal r-rms))
16823 (list r-r-rsp)) ; for vignettes
16824 (home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
16825 (synopsis "Analysis of haplotypes when linkage phase is ambiguous")
16827 "This package provides routines for the analysis of indirectly measured
16828 haplotypes. The statistical methods assume that all subjects are unrelated
16829 and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
16830 markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
16831 @code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
16832 examples in the vignette.")
16833 (license license:gpl2+)))
16835 (define-public r-bqtl
16842 (uri (cran-uri "bqtl" version))
16845 "1sbzpi9z94f010lw2y1gmifjrvpmiqs4m26za7vr1xz72azrqvs9"))))
16846 (build-system r-build-system)
16847 (native-inputs (list gfortran))
16848 (home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
16849 (synopsis "Bayesian QTL mapping toolkit")
16851 "This is a QTL mapping toolkit for inbred crosses and recombinant inbred
16852 lines. It includes maximum likelihood and Bayesian tools.")
16853 (license license:gpl2+)))
16855 (define-public r-ibdreg
16862 (uri (cran-uri "ibdreg" version))
16865 "1x8z0vr2cmdks12hxfm0wwxskb0cr669w5j5rpa2ln8q704yy41g"))))
16866 (build-system r-build-system)
16867 (home-page "https://www.mayo.edu/research/labs/\
16868 statistical-genetics-genetic-epidemiology/software")
16869 (synopsis "Regression methods for IBD linkage with covariates")
16871 "This package provides a method to test genetic linkage with covariates
16872 by regression methods with response IBD sharing for relative pairs. Account
16873 for correlations of IBD statistics and covariates for relative pairs within
16874 the same pedigree.")
16875 (license license:gpl2+)))
16877 (define-public r-dlmap
16884 (uri (cran-uri "dlmap" version))
16887 "0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
16888 (build-system r-build-system)
16890 (list r-ibdreg r-mgcv r-nlme r-qtl r-wgaim))
16891 (home-page "https://cran.r-project.org/web/packages/dlmap/")
16892 (synopsis "Detection localization mapping for QTL")
16894 "This is package for QTL mapping in a mixed model framework with separate
16895 detection and localization stages. The first stage detects the number of QTL
16896 on each chromosome based on the genetic variation due to grouped markers on
16897 the chromosome; the second stage uses this information to determine the most
16898 likely QTL positions. The mixed model can accommodate general fixed and
16899 random effects, including spatial effects in field trials and pedigree
16900 effects. It is applicable to backcrosses, doubled haploids, recombinant
16901 inbred lines, F2 intercrosses, and association mapping populations.")
16902 (license license:gpl2)))
16904 (define-public r-hwde
16911 (uri (cran-uri "hwde" version))
16914 "0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
16915 (build-system r-build-system)
16916 (home-page "https://cran.r-project.org/web/packages/hwde/")
16917 (synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
16919 "This package fits models for genotypic disequilibria, as described in
16920 Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
16921 terms are available that account for first order interactions between loci.
16922 It also implements, for a single locus in a single population, a conditional
16923 exact test for Hardy-Weinberg equilibrium.")
16924 (license license:gpl2+)))
16926 (define-public r-tdthap
16933 (uri (cran-uri "tdthap" version))
16936 "15qlj2bivvz3pizd8dq34wczbkbxhzqh3cqp1ixkdkprlyvcxj5k"))))
16937 (build-system r-build-system)
16938 (home-page "https://cran.r-project.org/web/packages/tdthap/")
16939 (synopsis "TDT tests for extended haplotypes")
16941 "Functions and examples are provided for transmission/disequilibrium
16942 tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
16943 \"Transmission/disequilibrium tests for extended marker haplotypes\".")
16944 (license license:artistic2.0)))
16946 (define-public r-sparql
16952 (uri (cran-uri "SPARQL" version))
16955 "0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
16956 (properties `((upstream-name . "SPARQL")))
16957 (build-system r-build-system)
16959 (list r-rcurl r-xml))
16960 (home-page "https://cran.r-project.org/web/packages/SPARQL")
16961 (synopsis "SPARQL client for R")
16962 (description "This package provides an interface to use SPARQL to pose
16963 SELECT or UPDATE queries to an end-point.")
16964 ;; The only license indication is found in the DESCRIPTION file,
16965 ;; which states GPL-3. So we cannot assume GPLv3+.
16966 (license license:gpl3)))
16968 (define-public r-bookdown
16970 (name "r-bookdown")
16974 (uri (cran-uri "bookdown" version))
16977 "1qqvvfbpbd6sin8vpvr3zzlhlyx1i6b98yp77xj5zl220nid5slb"))))
16978 (build-system r-build-system)
16988 ;; We cannot add knitr because this package depends on xfun, which is an
16992 `(("r-knitr" ,r-knitr)))
16993 (home-page "https://github.com/rstudio/bookdown")
16994 (synopsis "Authoring books and technical documents with R markdown")
16995 (description "This package provides output formats and utilities for
16996 authoring books and technical documents with R Markdown.")
16997 (license license:gpl3)))
16999 (define-public r-optparse
17001 (name "r-optparse")
17006 (uri (cran-uri "optparse" version))
17009 "1rqz0y4r94y3mwbb9kyz97cjqpnprka96qbncvbnbmgg2d630kij"))))
17010 (build-system r-build-system)
17015 (home-page "https://github.com/trevorld/optparse")
17016 (synopsis "Command line option parser")
17018 "This package provides a command line parser inspired by Python's
17019 @code{optparse} library to be used with Rscript to write shebang scripts
17020 that accept short and long options.")
17021 (license license:gpl2+)))
17023 (define-public r-kernlab
17030 (uri (cran-uri "kernlab" version))
17032 (base32 "0vqhndl4zm7pvkfvq0f6i9cbrm7pij6kmdp7d7w39pa100x6knn3"))))
17033 (build-system r-build-system)
17034 (home-page "https://cran.r-project.org/web/packages/kernlab")
17035 (synopsis "Kernel-based machine learning tools")
17037 "This package provides kernel-based machine learning methods for
17038 classification, regression, clustering, novelty detection, quantile regression
17039 and dimensionality reduction. Among other methods @code{kernlab} includes
17040 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
17042 (license license:gpl2)))
17044 (define-public r-hierfstat
17046 (name "r-hierfstat")
17051 (uri (cran-uri "hierfstat" version))
17054 "1p4vlna185sa3b5xjbysiqxcj9aa5s7dmxy41hg79vlqdivf874r"))))
17055 (build-system r-build-system)
17057 (list r-ade4 r-adegenet r-gaston r-gtools))
17060 (home-page "https://cran.r-project.org/web/packages/hierfstat/")
17061 (synopsis "Estimation and tests of hierarchical F-statistics")
17063 "This package allows the estimation of hierarchical F-statistics from
17064 haploid or diploid genetic data with any numbers of levels in the hierarchy,
17065 following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
17066 are also given to test via randomisations the significance of each F and
17067 variance components, using the likelihood-ratio statistics G.")
17068 (license license:gpl2+)))
17070 (define-public r-hapassoc
17072 (name "r-hapassoc")
17077 (uri (cran-uri "hapassoc" version))
17080 "0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
17081 (build-system r-build-system)
17082 (home-page "https://stat.sfu.ca/statgen/research/hapassoc.html")
17083 (synopsis "Inference of trait associations with SNP haplotypes")
17085 "Hapassoc performs likelihood inference of trait associations with
17086 haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
17087 functions are developed primarily for data collected in cohort or
17088 cross-sectional studies. They can accommodate uncertain haplotype phase and
17089 handle missing genotypes at some SNPs.")
17090 (license license:gpl2)))
17092 (define-public r-sampling
17094 (name "r-sampling")
17099 (uri (cran-uri "sampling" version))
17102 "11xis4vzn2ga8ml9xrgfgqzccvwbnabq35aidzdvpnvciybsanvz"))))
17103 (build-system r-build-system)
17105 (list r-lpsolve r-mass))
17106 (home-page "https://cran.r-project.org/web/packages/sampling/")
17107 (synopsis "Survey sampling")
17109 "This package provides functions for drawing and calibrating samples.")
17110 (license license:gpl2+)))
17112 (define-public r-r2html
17119 (uri (cran-uri "R2HTML" version))
17122 "00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
17123 (properties `((upstream-name . "R2HTML")))
17124 (build-system r-build-system)
17125 (home-page "https://github.com/nalimilan/R2HTML")
17126 (synopsis "HTML export for R objects")
17128 "This package includes HTML functions and methods to write in an HTML
17129 file. Thus, making HTML reports is easy. It includes a function that allows
17130 redirection on the fly, which appears to be very useful for teaching purposes,
17131 as the student can keep a copy of the produced output to keep all that they
17132 did during the course. The package comes with a vignette describing how to
17133 write HTML reports for statistical analysis. Finally, a driver for Sweave
17134 parses HTML flat files containing R code and to automatically write
17135 the corresponding outputs (tables and graphs).")
17136 (license license:gpl2+)))
17138 (define-public r-rjava
17145 (uri (cran-uri "rJava" version))
17148 "1ijqhvnb8ab38cp9pwdf7zq7xqqlm6x94gkrab2dd98p6d4x1472"))))
17149 (properties `((upstream-name . "rJava")))
17150 (build-system r-build-system)
17152 `(#:modules ((guix build utils)
17153 (guix build r-build-system)
17156 (modify-phases %standard-phases
17157 (add-after 'unpack 'set-JAVA_HOME
17158 (lambda* (#:key inputs #:allow-other-keys)
17159 (let ((jdk (assoc-ref inputs "jdk")))
17160 (setenv "JAVA_HOME" jdk)
17161 (setenv "JAVA" (which "java"))
17162 (setenv "JAR" (which "jar"))
17163 (setenv "JAVAC" (which "javac"))
17164 (setenv "JAVAH" (which "javah"))
17165 (setenv "JAVA_CPPFLAGS"
17166 (string-append "-I" jdk "/include "
17167 "-I" jdk "/include/linux"))
17168 (match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
17169 ((lib) (setenv "JAVA_LIBS" lib))
17170 (_ (error "Could not find libjvm.so"))))
17174 ("jdk" ,icedtea-8 "jdk")
17176 (home-page "https://www.rforge.net/rJava/")
17177 (synopsis "Low-Level R to Java interface")
17179 "This package provides a low-level interface to the Java VM very much
17180 like .C/.Call and friends. It allows the creation of objects, calling methods
17181 and accessing fields.")
17182 (license license:gpl2)))
17184 (define-public r-svmisc
17191 (uri (cran-uri "svMisc" version))
17194 "1r3kih5bnr4plnzdn5f2gg3xl3krgyl7gkdlf58a2l8vk13j3m9d"))))
17195 (properties `((upstream-name . "svMisc")))
17196 (build-system r-build-system)
17199 (home-page "https://github.com/SciViews/svMisc")
17200 (synopsis "Miscellaneous functions for SciViews")
17202 "This package provides miscellaneous functions for SciViews or general
17203 use, including tools to manage a temporary environment attached to the search
17204 path for temporary variables you do not want to @code{save()} or
17205 @code{load()}; test the current platform; showing progress bars, etc.")
17206 (license license:gpl2)))
17208 (define-public r-xyz
17215 (uri (cran-uri "xyz" version))
17218 "13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
17219 (build-system r-build-system)
17222 (home-page "https://cran.r-project.org/web/packages/xyz/")
17223 (synopsis "Algorithm for fast interaction search in high-dimensional data")
17225 "High dimensional interaction search by brute force requires a quadratic
17226 computational cost in the number of variables. The xyz algorithm provably
17227 finds strong interactions in almost linear time. For details of the algorithm
17228 see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
17229 interaction search in high-dimensional data.")
17230 ;; Any version of the GPL.
17231 (license license:gpl2+)))
17233 (define-public r-rttf2pt1
17235 (name "r-rttf2pt1")
17240 (uri (cran-uri "Rttf2pt1" version))
17243 "0w9ybqvr4bvpa2dyfkrscg4in0x2dkzmxdn1n6003j1rss7f8rw6"))))
17244 (properties `((upstream-name . "Rttf2pt1")))
17245 (build-system r-build-system)
17246 (home-page "https://github.com/wch/Rttf2pt1")
17247 (synopsis "Font conversion utility")
17249 "This package contains the program @code{ttf2pt1}, for use with the
17250 @code{extrafont} package.")
17251 ;; Most of the files are covered under the Expat license. Some files are
17252 ;; covered under BSD-3. Deviations for individual files are recorded in
17253 ;; the LICENSE file.
17254 (license (list license:bsd-3 license:expat
17255 (license:non-copyleft "file://LICENSE")))))
17257 (define-public r-extrafontdb
17259 (name "r-extrafontdb")
17264 (uri (cran-uri "extrafontdb" version))
17267 "115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
17268 (build-system r-build-system)
17269 (home-page "https://github.com/wch/extrafontdb")
17270 (synopsis "Database for the extrafont package")
17272 "This package holds the database for the @code{extrafont} package.")
17273 (license license:gpl2)))
17275 (define-public r-extrafont
17277 (name "r-extrafont")
17282 (uri (cran-uri "extrafont" version))
17285 "0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
17286 (build-system r-build-system)
17288 (list r-extrafontdb r-rttf2pt1))
17289 (home-page "https://github.com/wch/extrafont")
17290 (synopsis "Tools for using fonts in R")
17292 "The extrafont package makes it easier to use fonts other than the basic
17293 PostScript fonts that R uses. Fonts that are imported into extrafont can be
17294 used with PDF or PostScript output files. There are two hurdles for using
17295 fonts in PDF (or Postscript) output files:
17298 @item Making R aware of the font and the dimensions of the characters.
17299 @item Embedding the fonts in the PDF file so that the PDF can be displayed
17300 properly on a device that doesn't have the font. This is usually needed if
17301 you want to print the PDF file or share it with others.
17304 The extrafont package makes both of these things easier.")
17305 (license license:gpl2)))
17307 (define-public r-xkcd
17314 (uri (cran-uri "xkcd" version))
17317 "1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
17318 (build-system r-build-system)
17320 (list r-extrafont r-ggplot2 r-hmisc))
17321 (home-page "https://cran.r-project.org/web/packages/xkcd/")
17322 (synopsis "Plot ggplot2 graphics in the XKCD style")
17324 "This package provides the means to plot ggplot2 graphs in the style of
17325 the XKCD web comic.")
17326 (license license:gpl3)))
17328 (define-public r-babelgene
17330 (name "r-babelgene")
17335 (uri (cran-uri "babelgene" version))
17338 "1gk5pm3b3shr1id66a11ywc1b823gbj8yckg24szzfhj8g4ixyf0"))))
17339 (properties `((upstream-name . "babelgene")))
17340 (build-system r-build-system)
17342 (list r-dplyr r-rlang))
17346 "https://igordot.github.io/babelgene/")
17347 (synopsis "Gene orthologs for model organisms in a Tidy data format")
17349 "Genomic analysis of model organisms often requires the use of databases
17350 based on human data or making comparisons to patient-derived resources. This
17351 requires converting genes between human and non-human analogues. The
17352 babelgene R package provides predicted gene orthologs/homologs for frequently
17353 studied model organisms in an R-friendly tidy/long format. The package
17354 integrates orthology assertion predictions sourced from multiple databases as
17355 compiled by the HGNC Comparison of Orthology Predictions (HCOP).")
17356 (license license:expat)))
17358 (define-public r-msigdbr
17365 (uri (cran-uri "msigdbr" version))
17368 "103m52av68pkjfh8f81qh6j3cs1mj1lg831ciwybr34cax767jr1"))))
17369 (build-system r-build-system)
17379 (home-page "https://github.com/igordot/msigdbr")
17380 (synopsis "MSigDB gene sets for multiple organisms")
17382 "This package provides the @dfn{Molecular Signatures Database} (MSigDB)
17383 gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
17384 software in a standard R data frame with key-value pairs. Included are the
17385 original human gene symbols and Entrez IDs as well as the equivalents for
17386 various frequently studied model organisms such as mouse, rat, pig, fly, and
17388 ;; The package is covered under the Expat license, but the upstream MSigDB
17389 ;; files are made available under the Creative Commons Attribution 4.0
17390 ;; International license.
17391 (license (list license:expat license:cc-by4.0))))
17393 (define-public r-gridgraphics
17395 (name "r-gridgraphics")
17400 (uri (cran-uri "gridGraphics" version))
17403 "12yswy02j3h5wir7m5jnkhpjmb0sa4snn61vjd68i49qwsa6w219"))))
17404 (properties `((upstream-name . "gridGraphics")))
17405 (build-system r-build-system)
17406 (home-page "https://github.com/pmur002/gridgraphics")
17407 (synopsis "Redraw base graphics using @code{grid} graphics")
17409 "This package provides functions to convert a page of plots drawn with
17410 the @code{graphics} package into identical output drawn with the @code{grid}
17411 package. The result looks like the original @code{graphics}-based plot, but
17412 consists of @code{grid} grobs and viewports that can then be manipulated with
17413 @code{grid} functions (e.g., edit grobs and revisit viewports).")
17414 (license license:gpl2+)))
17416 (define-public r-farver
17423 (uri (cran-uri "farver" version))
17426 "1x6ffwxqbrwlylnk995jz2a6nz2y9z59jaq0ncpni7q40w367j75"))))
17427 (build-system r-build-system)
17428 (home-page "https://github.com/thomasp85/farver")
17429 (synopsis "Vectorized color conversion and comparison")
17431 "The encoding of color can be handled in many different ways, using
17432 different color spaces. As different color spaces have different uses,
17433 efficient conversion between these representations are important. This
17434 package provides a set of functions that gives access to very fast color space
17435 conversion and comparisons implemented in C++, and offers 100-fold speed
17436 improvements over the @code{convertColor} function in the @code{grDevices}
17438 (license license:expat)))
17440 (define-public r-yulab-utils
17442 (name "r-yulab-utils")
17447 (uri (cran-uri "yulab.utils" version))
17450 "1bj93gnj7j4b7dgkbr5v22rsbwfcw5dvipl5irmidaakvrihd19q"))))
17451 (properties `((upstream-name . "yulab.utils")))
17452 (build-system r-build-system)
17453 (home-page "https://cran.r-project.org/package=yulab.utils")
17454 (synopsis "Supporting functions for packages maintained by YuLab-SMU")
17456 "Miscellaneous functions commonly used by YuLab-SMU, such as
17457 @code{install_zip_gh} to install R packages from Github ZIP files.")
17458 (license license:artistic2.0)))
17460 (define-public r-ggplotify
17462 (name "r-ggplotify")
17467 (uri (cran-uri "ggplotify" version))
17470 "12mk3fa8fdjxj7xxz21jkr7h91w5wdgwjqhszcz1qffwsgb773qp"))))
17471 (build-system r-build-system)
17473 (list r-ggplot2 r-gridgraphics r-yulab-utils))
17476 (home-page "https://github.com/GuangchuangYu/ggplotify")
17477 (synopsis "Convert plots to @code{grob} or @code{ggplot} object")
17479 "This package provides tools to convert plot function calls (using
17480 expression or formula) to @code{grob} or @code{ggplot} objects that are
17481 compatible with the @code{grid} and @code{ggplot2} environment. With this
17482 package, we are able to e.g. use @code{cowplot} to align plots produced by
17483 @code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
17484 converting them to @code{ggplot} objects.")
17485 (license license:artistic2.0)))
17487 (define-public r-triebeard
17489 (name "r-triebeard")
17494 (uri (cran-uri "triebeard" version))
17497 "1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
17498 (build-system r-build-system)
17499 (propagated-inputs (list r-rcpp))
17500 (home-page "https://github.com/Ironholds/triebeard/")
17501 (synopsis "Radix trees in Rcpp")
17503 "Radix trees, or tries, are key-value data structures optimized for
17504 efficient lookups, similar in purpose to hash tables. This package provides
17505 an implementation of radix trees for use in R programming and in developing
17506 packages with Rcpp.")
17507 (license license:expat)))
17509 (define-public r-tweenr
17516 (uri (cran-uri "tweenr" version))
17519 "17znizh4yabh2zs9mzyr0sl6p0pw49961i61br7cl1b7v9sza18q"))))
17520 (build-system r-build-system)
17522 (list r-farver r-magrittr r-rcpp r-rlang))
17523 (home-page "https://github.com/thomasp85/tweenr")
17524 (synopsis "Interpolate data for smooth animations")
17526 "In order to create smooth animation between states of data, tweening is
17527 necessary. This package provides a range of functions for creating tweened
17528 data that can be used as basis for animation. Furthermore it adds a number of
17529 vectorized interpolaters for common R data types such as numeric, date and
17531 (license license:expat)))
17533 (define-public r-polyclip
17535 (name "r-polyclip")
17540 (uri (cran-uri "polyclip" version))
17543 "0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
17544 (build-system r-build-system)
17545 (native-inputs (list pkg-config))
17546 (home-page "http://www.angusj.com/delphi/clipper.php")
17547 (synopsis "Polygon clipping")
17549 "This package provides an R port of the library Clipper. It performs
17550 polygon clipping operations (intersection, union, set minus, set difference)
17551 for polygonal regions of arbitrary complexity, including holes. It computes
17552 offset polygons (spatial buffer zones, morphological dilations, Minkowski
17553 dilations) for polygonal regions and polygonal lines. It computes the
17554 Minkowski Sum of general polygons. There is a function for removing
17555 self-intersections from polygon data.")
17556 (license license:boost1.0)))
17558 (define-public r-urltools
17560 (name "r-urltools")
17565 (uri (cran-uri "urltools" version))
17568 "04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
17569 (build-system r-build-system)
17571 (list r-rcpp r-triebeard))
17572 (home-page "https://github.com/Ironholds/urltools/")
17573 (synopsis "Vectorized tools for URL handling and parsing")
17575 "This package provides a toolkit for all URL-handling needs, including
17576 encoding and decoding, parsing, parameter extraction and modification. All
17577 functions are designed to be both fast and entirely vectorized. It is
17578 intended to be useful for people dealing with web-related datasets, such as
17579 server-side logs, although may be useful for other situations involving large
17581 (license license:expat)))
17583 (define-public r-ggforce
17590 (uri (cran-uri "ggforce" version))
17593 "0bwzjbjl678xvc2ihm80dwn9pidwafqjdab3k299csys16s3na1a"))))
17594 (build-system r-build-system)
17607 (home-page "https://ggforce.data-imaginist.com")
17608 (synopsis "Accelerating ggplot2")
17610 "The aim of the ggplot2 package is to aid in visual data investigations.
17611 This focus has led to a lack of facilities for composing specialized plots.
17612 This package aims to be a collection of mainly new statistics and geometries
17613 that fills this gap.")
17614 (license license:expat)))
17616 (define-public r-europepmc
17618 (name "r-europepmc")
17623 (uri (cran-uri "europepmc" version))
17626 "16japbndid34shqg8n0bmjrxn84xmhrylvz832zclcllm6i93fn1"))))
17627 (build-system r-build-system)
17642 (home-page "https://github.com/ropensci/europepmc/")
17643 (synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
17645 "This package provides an R Client for the
17646 @url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
17647 Service}. It gives access to both metadata on life science literature and
17648 open access full texts. Europe PMC indexes all PubMed content and other
17649 literature sources including Agricola, a bibliographic database of citations
17650 to the agricultural literature, or Biological Patents. In addition to
17651 bibliographic metadata, the client allows users to fetch citations and
17652 reference lists. Links between life-science literature and other EBI
17653 databases, including ENA, PDB or ChEMBL are also accessible.")
17654 (license license:gpl3)))
17656 (define-public r-ggraph
17663 (uri (cran-uri "ggraph" version))
17666 "0m4n8iw2b9jk8hcy5blg5w59zsqcpsbv27wbw598dvljpafx8sp3"))))
17667 (build-system r-build-system)
17686 (home-page "https://cran.r-project.org/web/packages/ggraph/")
17687 (synopsis "Implementation of grammar of graphics for graphs and networks")
17689 "The grammar of graphics as implemented in ggplot2 is a poor fit for
17690 graph and network visualizations due to its reliance on tabular data input.
17691 The ggraph package is an extension of the ggplot2 API tailored to graph
17692 visualizations and provides the same flexible approach to building up plots
17694 (license license:gpl3)))
17696 (define-public r-gkmsvm
17703 (uri (cran-uri "gkmSVM" version))
17706 "119g5rhc7ffyviz04r04aj5z1g6abnj3ddd01g7db505sdr6lapj"))))
17707 (properties `((upstream-name . "gkmSVM")))
17708 (build-system r-build-system)
17710 (list r-kernlab r-rcpp r-rocr r-seqinr))
17711 (home-page "https://cran.r-project.org/web/packages/gkmSVM")
17712 (synopsis "Gapped-kmer support vector machine")
17714 "This R package provides tools for training gapped-kmer SVM classifiers
17715 for DNA and protein sequences. This package supports several sequence
17716 kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
17717 (license license:gpl2+)))
17719 (define-public r-varselrf
17721 (name "r-varselrf")
17726 (uri (cran-uri "varSelRF" version))
17729 "0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
17730 (properties `((upstream-name . "varSelRF")))
17731 (build-system r-build-system)
17733 (list r-randomforest))
17734 (home-page "https://www.ligarto.org/rdiaz/software/software")
17735 (synopsis "Variable selection using random forests")
17737 "This package provides tools for the variable selection from random
17738 forests using both backwards variable elimination (for the selection of small
17739 sets of non-redundant variables) and selection based on the importance
17740 spectrum (somewhat similar to scree plots; for the selection of large,
17741 potentially highly-correlated variables). The main applications are in
17742 high-dimensional data (e.g., microarray data, and other genomics and
17743 proteomics applications).")
17744 (license license:gpl2+)))
17746 (define-public r-pamr
17753 (uri (cran-uri "pamr" version))
17756 "0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
17757 (build-system r-build-system)
17759 (list r-cluster r-survival))
17760 (native-inputs (list gfortran))
17761 (home-page "https://cran.r-project.org/web/packages/pamr/")
17762 (synopsis "Prediction Analysis for Microarrays")
17764 "This package provides some functions for sample classification in
17766 (license license:gpl2)))
17768 (define-public r-rda
17771 (version "1.0.2-2.1")
17775 (uri (cran-uri "rda" version))
17778 "1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
17779 (build-system r-build-system)
17780 (home-page "https://cran.r-project.org/web/packages/rda/")
17781 (synopsis "Shrunken centroids regularized discriminant analysis")
17783 "This package provides tools for shrunken centroids regularized
17784 discriminant analysis for the purpose of classifying high dimensional data.")
17785 (license license:gpl2+)))
17787 (define-public r-ggvis
17794 (uri (cran-uri "ggvis" version))
17797 "1qv512pd4x5vmx15y9nvqmabbbw14h75fmi1sjbcg5yl25z0cswy"))))
17798 (build-system r-build-system)
17807 (home-page "https://ggvis.rstudio.com/")
17808 (synopsis "Interactive grammar of graphics")
17810 "This package is a data visualization package for R providing an
17811 implementation of an interactive grammar of graphics, taking the best parts of
17812 ggplot2, combining them with the reactive framework of Shiny and drawing web
17813 graphics using Vega.")
17814 (license license:gpl2)))
17816 (define-public r-gbm
17823 (uri (cran-uri "gbm" version))
17826 "1h9f4ww9yc3nsvghgr2q7jjrlz29ibabxjbax1sk5wmqh2wy6pbx"))))
17827 (build-system r-build-system)
17829 (list r-lattice r-survival))
17832 (home-page "https://github.com/gbm-developers/gbm")
17833 (synopsis "Generalized boosted regression models")
17835 "This package is an implementation of extensions to Freund and Schapire's
17836 AdaBoost algorithm and Friedman's gradient boosting machine. It includes
17837 regression methods for least squares, absolute loss, t-distribution loss,
17838 quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
17839 hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
17840 and Learning to Rank measures (LambdaMart).")
17841 (license license:gpl2+)))
17843 (define-public r-threejs
17850 (uri (cran-uri "threejs" version))
17853 "1711h351nzxfkbbdwvfzyhciyvi9c6wx3jq1g97lzcqgnb45kivn"))))
17854 (build-system r-build-system)
17856 `(#:modules ((guix build utils)
17857 (guix build r-build-system)
17861 (modify-phases %standard-phases
17862 (add-after 'unpack 'process-javascript
17863 (lambda* (#:key inputs #:allow-other-keys)
17864 (with-directory-excursion "inst"
17868 `((,(assoc-ref inputs "js-jquery")
17869 "htmlwidgets/lib/jquery/jquery.min.js")
17870 (,(assoc-ref inputs "js-threejs-111")
17871 "htmlwidgets/lib/threejs-111/three.min.js"))))
17872 (lambda (sources targets)
17873 (for-each (lambda (source target)
17874 (format #t "Processing ~a --> ~a~%"
17876 (delete-file target)
17877 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
17878 (call-with-output-file target
17880 (dump-port minified port)))))
17881 sources targets))))
17884 (list r-base64enc r-crosstalk r-htmlwidgets r-igraph))
17886 `(("uglifyjs" ,node-uglify-js)
17890 (uri "https://code.jquery.com/jquery-1.12.4.js")
17893 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
17897 (uri "https://raw.githubusercontent.com/mrdoob/three.js/r111/build/three.js")
17900 "1cxdkw3plmlw1xvhbx5dm39gqczgzxip2dm887v6whhsxqxl9cky"))))))
17901 (home-page "https://bwlewis.github.io/rthreejs")
17902 (synopsis "Interactive 3D scatter plots, networks and globes")
17904 "Create interactive 3D scatter plots, network plots, and globes in R
17905 using the three.js visualization library.")
17906 (license license:expat)))
17908 (define-public r-mlbench
17915 (uri (cran-uri "mlbench" version))
17918 "157iqsld0wj8g8cbs7nh6p2x6kasmkhs3078hsmqac946gk2pydi"))))
17919 (build-system r-build-system)
17920 (home-page "https://cran.r-project.org/web/packages/mlbench/")
17921 (synopsis "Machine learning benchmark problems")
17923 "This package provides a collection of artificial and real-world machine
17924 learning benchmark problems, including, e.g., several data sets from the UCI
17926 (license license:gpl2)))
17928 (define-public r-mpm
17935 (uri (cran-uri "mpm" version))
17938 "0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
17939 (build-system r-build-system)
17941 (list r-kernsmooth r-mass))
17942 (home-page "http://mpm.r-forge.r-project.org")
17943 (synopsis "Multivariate projection methods")
17945 "This is a package for exploratory graphical analysis of multivariate
17946 data, specifically gene expression data with different projection methods:
17947 principal component analysis, correspondence analysis, spectral map
17949 (license license:gpl2+)))
17951 (define-public r-png
17957 (uri (cran-uri "png" version))
17960 "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
17961 (build-system r-build-system)
17963 (list libpng zlib))
17964 (home-page "https://www.rforge.net/png/")
17965 (synopsis "Read and write PNG images")
17967 "This package provides an easy and simple way to read, write and display
17968 bitmap images stored in the PNG format. It can read and write both files and
17969 in-memory raw vectors.")
17970 ;; Any of these GPL versions.
17971 (license (list license:gpl2 license:gpl3))))
17973 (define-public r-ggcorrplot
17975 (name "r-ggcorrplot")
17980 (uri (cran-uri "ggcorrplot" version))
17983 "0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
17984 (build-system r-build-system)
17986 (list r-ggplot2 r-reshape2))
17987 (home-page "http://www.sthda.com/english/wiki/ggcorrplot")
17988 (synopsis "Visualization of a correlation matrix using ggplot2")
17990 "The ggcorrplot package can be used to visualize easily a correlation
17991 matrix using ggplot2. It provides a solution for reordering the correlation
17992 matrix and displays the significance level on the plot. It also includes a
17993 function for computing a matrix of correlation p-values.")
17994 (license license:gpl2)))
17996 (define-public r-ggfun
18003 (uri (cran-uri "ggfun" version))
18006 "10spayf5jzmizhs6aassjplrjr9mr6bcww30pyxzyb1djfl41qxi"))))
18007 (properties `((upstream-name . "ggfun")))
18008 (build-system r-build-system)
18010 (list r-ggplot2 r-rlang))
18011 (native-inputs (list r-knitr))
18012 (home-page "https://cran.r-project.org/package=ggfun")
18013 (synopsis "Miscellaneous functions for ggplot2")
18015 "This package provides useful functions to edit ggplot object (e.g.,
18016 setting fonts for theme and layers, adding rounded rectangle as background for
18017 each of the legends).")
18018 (license license:artistic2.0)))
18020 (define-public r-gridtext
18022 (name "r-gridtext")
18027 (uri (cran-uri "gridtext" version))
18030 "131kw7nkfwksviwfifd2kk7lyvhxzzzv1nnj8rahkr3dik3akk61"))))
18031 (properties `((upstream-name . "gridtext")))
18032 (build-system r-build-system)
18042 (home-page "https://wilkelab.org/gridtext/")
18043 (synopsis "Improved text rendering support for Grid graphics")
18045 "This package provides support for rendering of formatted text using Grid
18046 graphics. Text can be formatted via a minimal subset of Markdown, HTML, and
18047 inline CSS directives, and it can be rendered both with and without word
18049 (license license:expat)))
18051 (define-public r-ggtext
18058 (uri (cran-uri "ggtext" version))
18061 "0n19dlcys8v7myfyckr6dnq0kx79k3sbh8nwx1jsx8pgzfbi8a2b"))))
18062 (properties `((upstream-name . "ggtext")))
18063 (build-system r-build-system)
18065 (list r-ggplot2 r-gridtext r-rlang r-scales))
18066 (native-inputs (list r-knitr))
18067 (home-page "https://wilkelab.org/ggtext/")
18068 (synopsis "Improved text rendering support for ggplot2")
18070 "This package provides a ggplot2 extension that enables the rendering of
18071 complex formatted plot labels (titles, subtitles, facet labels, axis labels,
18072 etc.). Text boxes with automatic word wrap are also supported.")
18073 (license license:gpl2)))
18075 ;; This package includes minified JavaScript files. When upgrading please
18076 ;; check that there are no new minified JavaScript files.
18077 (define-public r-flexdashboard
18079 (name "r-flexdashboard")
18084 (uri (cran-uri "flexdashboard" version))
18087 "1bh759llp15fxrx2rwvxd8p3w84vjmkid32ism7zg49a127fjib4"))
18088 (modules '((guix build utils)))
18091 ;; Delete bundled minified JavaScript files
18092 (delete-file "inst/htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
18093 (delete-file "inst/www/sly/sly.min.js")
18094 (delete-file "inst/www/stickytableheaders/jquery.stickytableheaders.min.js")
18095 (delete-file "inst/www/prism/prism.js")
18097 (build-system r-build-system)
18099 `(#:modules ((guix build utils)
18100 (guix build r-build-system)
18104 (ice-9 textual-ports))
18106 (modify-phases %standard-phases
18107 (add-after 'unpack 'process-javascript
18108 (lambda* (#:key inputs #:allow-other-keys)
18109 (with-directory-excursion "inst"
18110 ;; Concatenate all components of prism.js
18111 (let ((contents (string-join
18112 (map (lambda (name)
18113 (call-with-input-file
18114 (assoc-ref inputs name)
18118 "js-prism-line-numbers"))
18120 (call-with-output-file "prism-src.js"
18121 (cut display contents <>)))
18125 `(("www/stickytableheaders/jquery.stickytableheaders.js"
18126 "www/stickytableheaders/jquery.stickytableheaders.min.js")
18128 "www/sly/sly.min.js")
18130 "www/prism/prism.js")
18131 (,(assoc-ref inputs "js-raphael")
18132 "htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
18133 (,(assoc-ref inputs "js-featherlight")
18134 "www/featherlight/featherlight.min.js"))))
18135 (lambda (sources targets)
18136 (for-each (lambda (source target)
18137 (format #t "Processing ~a --> ~a~%"
18139 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
18140 (call-with-output-file target
18142 (dump-port minified port)))))
18143 sources targets))))
18153 `(("uglifyjs" ,node-uglify-js)
18157 (uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
18160 "1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
18164 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
18167 "0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
18171 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
18174 "1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
18175 ("js-prism-line-numbers"
18178 (uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
18181 "1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
18185 (uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
18188 "14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
18189 (home-page "https://rmarkdown.rstudio.com/flexdashboard")
18190 (synopsis "R Markdown format for flexible dashboards")
18192 "This package provides an R Markdown format for converting an R Markdown
18193 document to a grid-oriented dashboard. The dashboard flexibly adapts the size
18194 of its components to the containing web page.")
18195 (license license:expat)))
18197 (define-public r-preseqr
18204 (uri (cran-uri "preseqR" version))
18207 "1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
18208 (properties `((upstream-name . "preseqR")))
18209 (build-system r-build-system)
18212 (home-page "https://cran.r-project.org/web/packages/preseqR/")
18213 (synopsis "Predicting species accumulation curves")
18215 "This package can be used to predict the r-species accumulation
18216 curve (r-SAC), which is the number of species represented at least r times as
18217 a function of the sampling effort. When r = 1, the curve is known as the
18218 species accumulation curve, or the library complexity curve in high-throughput
18219 genomic sequencing. The package includes both parametric and nonparametric
18220 methods, as described by Deng C, et al. (2018).")
18221 (license license:gpl3)))
18223 (define-public r-mapplots
18225 (name "r-mapplots")
18230 (uri (cran-uri "mapplots" version))
18233 "18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
18234 (build-system r-build-system)
18235 (home-page "https://cran.r-project.org/web/packages/mapplots/")
18236 (synopsis "Data visualization on maps")
18238 "This package helps you create simple maps; add sub-plots like pie plots
18239 to a map or any other plot; format, plot and export gridded data. The package
18240 was developed for displaying fisheries data but most functions can be used for
18241 more generic data visualisation.")
18242 (license license:gpl2+)))
18244 (define-public r-pmcmr
18251 (uri (cran-uri "PMCMR" version))
18254 "05n13pp5yff6pzk4ry07crddfaj3jlglrd1vkcnacyd8jpaxkd77"))))
18255 (properties `((upstream-name . "PMCMR")))
18256 (build-system r-build-system)
18257 (home-page "https://cran.r-project.org/web/packages/PMCMR/")
18258 (synopsis "Calculate pairwise multiple comparisons of mean rank sums")
18260 "This is a deprecated package for calculating pairwise multiple
18261 comparisons of mean rank sums. This package is superseded by the novel
18262 PMCMRplus package. The PMCMR package is no longer maintained, but kept for
18263 compatibility of dependent packages for some time.")
18264 (license license:gpl3+)))
18266 (define-public r-downloader
18268 (name "r-downloader")
18273 (uri (cran-uri "downloader" version))
18276 "1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
18277 (build-system r-build-system)
18280 (home-page "https://github.com/wch/downloader")
18281 (synopsis "Download files over HTTP and HTTPS")
18283 "This package provides a wrapper for the @code{download.file} function,
18284 making it possible to download files over HTTPS across platforms. The
18285 @code{RCurl} package provides this functionality (and much more) but has
18286 external dependencies. This package has is implemented purely in R.")
18287 (license license:gpl2)))
18289 (define-public r-aplot
18296 (uri (cran-uri "aplot" version))
18299 "1w09flb6a4fxibfrm1z24pg672r80b7phgc0m7mv3vfw3l84v749"))))
18300 (properties `((upstream-name . "aplot")))
18301 (build-system r-build-system)
18309 (home-page "https://github.com/YuLab-SMU/aplot")
18310 (synopsis "Decorate a ggplot with associated information")
18312 "Users may want to align plots with associated information that requires
18313 axes to be exactly matched in subplots, e.g. hierarchical clustering with a
18314 heatmap. This package provides utilities to align associated subplots to a
18315 main plot at different sides (left, right, top and bottom) with axes exactly
18317 (license license:artistic2.0)))
18319 (define-public r-ggnewscale
18321 (name "r-ggnewscale")
18326 (uri (cran-uri "ggnewscale" version))
18329 "1hjysfagd2lqy8yivqq9q7l6hbvyq8kasw3zqh5fk9xn18ikc702"))))
18330 (properties `((upstream-name . "ggnewscale")))
18331 (build-system r-build-system)
18334 (home-page "https://cran.r-project.org/package=ggnewscale")
18335 (synopsis "Multiple fill and color scales in ggplot2")
18337 "This package lets you use multiple fill and color scales in ggplot2.")
18338 (license license:gpl3)))
18340 (define-public r-ggpointdensity
18342 (name "r-ggpointdensity")
18347 (uri (cran-uri "ggpointdensity" version))
18350 "0c9a14j3b0hvamqylhzldw2hjdxmfbllwahjkf3gg2rw337ld9iy"))))
18352 `((upstream-name . "ggpointdensity")))
18353 (build-system r-build-system)
18356 (home-page "https://github.com/LKremer/ggpointdensity")
18357 (synopsis "Cross between a 2D density plot and a scatter plot")
18359 "This package provides a cross between a 2D density plot and a scatter
18360 plot, implemented as a ggplot2 @code{geom}. Points in the scatter plot are
18361 colored by the number of neighboring points. This is useful to visualize the
18362 2D-distribution of points in case of overplotting.")
18363 (license license:gpl3)))
18365 (define-public r-arrow
18372 (uri (cran-uri "arrow" version))
18375 "14fghz9xijcrck0c65crvfidgyhgzy9b2apwmg7qrgn2sy09xm0p"))))
18376 (properties `((upstream-name . "arrow")))
18377 (build-system r-build-system)
18379 (list `(,apache-arrow "lib") zlib))
18389 (list pkg-config r-knitr))
18390 (home-page "https://github.com/apache/arrow/")
18391 (synopsis "R integration to Apache Arrow")
18393 "Apache Arrow is a cross-language development platform for in-memory
18394 data. It specifies a standardized language-independent columnar memory format
18395 for flat and hierarchical data, organized for efficient analytic operations on
18396 modern hardware. This package provides an R interface to the Arrow C++
18398 (license license:asl2.0)))
18400 (define-public r-rex
18407 (uri (cran-uri "rex" version))
18410 "1mmzlc3j7xa0rbjxa369f4sr0iw3gq58g8fmjjxbsjvfq14ychmg"))))
18411 (build-system r-build-system)
18416 (home-page "https://github.com/kevinushey/rex")
18417 (synopsis "Friendly regular expressions")
18419 "This package provides a friendly interface for the construction of
18420 regular expressions. Regular expressions are a very powerful feature, however
18421 they are often difficult to interpret. Rex allows you to build complex
18422 regular expressions from human readable expressions")
18423 (license license:expat)))
18425 (define-public r-mlapi
18432 (uri (cran-uri "mlapi" version))
18435 "023vk5bp8cjcq88sapkl87kdxr92bay1dyxl6xirnyj699pyj51k"))))
18436 (properties `((upstream-name . "mlapi")))
18437 (build-system r-build-system)
18439 (list r-matrix r-r6))
18442 (home-page "https://cran.r-project.org/package=mlapi")
18443 (synopsis "Abstract classes for building scikit-learn like API")
18445 "This package provides R6 abstract classes for building machine learning
18446 models with a scikit-learn like API. Scikit-learn is a popular module for the
18447 Python programming language whose design became a de facto standard in
18448 industry for machine learning tasks.")
18449 (license license:expat)))
18451 (define-public r-float
18458 (uri (cran-uri "float" version))
18461 "1bx5yxkb123001v31jjk7h7f0qissmjydvbil5cj3jvmqkayq1a1"))))
18462 (properties `((upstream-name . "float")))
18463 (build-system r-build-system)
18466 (home-page "https://github.com/wrathematics/float")
18467 (synopsis "32-bit floats")
18469 "R comes with a suite of utilities for linear algebra with
18470 \"numeric\" (double precision) vectors/matrices. However, sometimes single
18471 precision (or less!) is more than enough for a particular task. This package
18472 extends R's linear algebra facilities to include 32-bit float (single
18473 precision) data. Float vectors/matrices have half the precision of their
18474 \"numeric\"-type counterparts but are generally faster to numerically operate
18475 on, for a performance vs accuracy trade-off.")
18476 (license license:bsd-2)))
18478 (define-public r-rsparse
18485 (uri (cran-uri "rsparse" version))
18488 "0d05h47j29zipyxbkv9cwzv2dzj894z6hh9dqfhwswwjbv6ciwpq"))))
18489 (properties `((upstream-name . "rsparse")))
18490 (build-system r-build-system)
18500 (home-page "https://github.com/rexyai/rsparse")
18501 (synopsis "Statistical learning on sparse matrices")
18503 "This package implements many algorithms for statistical learning on
18504 sparse matrices: matrix factorizations, matrix completion, elastic net
18505 regressions, factorization machines. The rsparse package also enhances the
18506 Matrix package by providing methods for multithreaded <sparse, dense> matrix
18507 products and native slicing of the sparse matrices in @dfn{Compressed Sparse
18508 Row} (CSR) format.")
18509 (license license:gpl2+)))
18511 (define-public r-text2vec
18513 (name "r-text2vec")
18518 (uri (cran-uri "text2vec" version))
18521 "0r75cv77x2zm1z66s95hic71dpbqmybz39n48q6mz7gfd3m7312y"))))
18522 (properties `((upstream-name . "text2vec")))
18523 (build-system r-build-system)
18536 (home-page "http://text2vec.org")
18537 (synopsis "Text mining framework for R")
18539 "This package provides fast and memory-friendly tools for text
18540 vectorization, topic modeling (LDA, LSA), word embeddings (GloVe),
18541 similarities. It provides a source-agnostic streaming API, which allows
18542 researchers to perform analysis of collections of documents which are larger
18543 than available RAM. All core functions are parallelized to benefit from
18544 multicore machines.")
18545 (license license:gpl2+)))
18547 (define-public r-mcmcpack
18549 (name "r-mcmcpack")
18554 (uri (cran-uri "MCMCpack" version))
18557 "16zjx8yz29ii75wfxj3p562l657bng8jnwzp2b54s7fiaws4kfdm"))))
18558 (properties `((upstream-name . "MCMCpack")))
18559 (build-system r-build-system)
18561 (list r-coda r-lattice r-mass r-mcmc r-quantreg))
18562 (home-page "https://cran.r-project.org/package=MCMCpack")
18563 (synopsis "Markov Chain Monte Carlo (MCMC) package")
18565 "This package contains functions to perform Bayesian inference using
18566 posterior simulation for a number of statistical models. Most simulation is
18567 done in compiled C++ written in the Scythe Statistical Library. All models
18568 return @code{coda} @code{mcmc} objects that can then be summarized using the
18569 @code{coda} package. Some useful utility functions such as density functions,
18570 pseudo-random number generators for statistical distributions, a general
18571 purpose Metropolis sampling algorithm, and tools for visualization are
18573 (license license:gpl3)))
18575 (define-public r-xmlparsedata
18577 (name "r-xmlparsedata")
18582 (uri (cran-uri "xmlparsedata" version))
18585 "1c6bnz3ng1qw7sfip8wq3a4dn36a4d6rbja0sadn0a4pbsmk8q3n"))))
18586 (properties `((upstream-name . "xmlparsedata")))
18587 (build-system r-build-system)
18588 (home-page "https://github.com/r-lib/xmlparsedata#readme")
18589 (synopsis "Parse data of @code{R} code as an @code{XML} tree")
18591 "This package provides tools to convert the output of
18592 @code{utils::getParseData()} to an @code{XML} tree, that one can search via
18593 @code{XPath}, and is easier to manipulate in general.")
18594 (license license:expat)))
18596 (define-public r-cyclocomp
18598 (name "r-cyclocomp")
18603 (uri (cran-uri "cyclocomp" version))
18606 "0gky3svk02wiajw7nfjh30684h3qxili4bvsab0m7b6cggw6bgyd"))))
18607 (properties `((upstream-name . "cyclocomp")))
18608 (build-system r-build-system)
18610 (list r-callr r-crayon r-desc r-remotes r-withr))
18611 (home-page "https://github.com/MangoTheCat/cyclocomp")
18612 (synopsis "Cyclomatic complexity of R code")
18614 "Cyclomatic complexity is a software metric, used to indicate the
18615 complexity of a program. It is a quantitative measure of the number of
18616 linearly independent paths through a program's source code. This package
18617 provides tools to compute this metric.")
18618 (license license:expat)))
18620 (define-public r-lintr
18627 (uri (cran-uri "lintr" version))
18630 "14yfh641afg6griaadbdciyr3k94fl55s055qwzghgk5gdsj61zy"))))
18631 (properties `((upstream-name . "lintr")))
18632 (build-system r-build-system)
18646 (home-page "https://github.com/jimhester/lintr")
18647 (synopsis "Linter for R code")
18648 (description "This package checks adherence to a given style, syntax
18649 errors and possible semantic issues. It supports on the fly checking of R
18650 code edited with @code{RStudio IDE}, @code{Emacs} and @code{Vim}.")
18651 (license license:expat)))
18653 (define-public r-sctransform
18655 (name "r-sctransform")
18660 (uri (cran-uri "sctransform" version))
18663 "0aqbcarsvvzkh5h4i65f08y4b8dfcs3zi62hmvfy24gj81f15bw3"))))
18664 (build-system r-build-system)
18679 (home-page "https://github.com/ChristophH/sctransform")
18680 (synopsis "Variance stabilizing transformations for Single Cell UMI Data")
18682 "This package provides a normalization method for single-cell UMI count
18683 data using a variance stabilizing transformation. The transformation is based
18684 on a negative binomial regression model with regularized parameters. As part
18685 of the same regression framework, this package also provides functions for
18686 batch correction, and data correction.")
18687 (license license:gpl3)))
18689 (define-public r-styler
18696 (uri (cran-uri "styler" version))
18699 "0p7p2mh4f469drfn5z4wc4xrg06mpnm9wkw76fghclf8m9vcqbx6"))))
18700 (build-system r-build-system)
18703 (modify-phases %standard-phases
18704 (add-after 'unpack 'set-HOME
18705 (lambda _ (setenv "HOME" "/tmp"))))))
18721 (home-page "https://github.com/r-lib/styler")
18722 (synopsis "Non-invasive pretty printing of R code")
18724 "This is a package for pretty-printing R code without changing the user's
18725 formatting intent.")
18726 (license license:gpl3)))
18728 (define-public r-scrime
18735 (uri (cran-uri "scrime" version))
18738 "0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
18739 (build-system r-build-system)
18740 (home-page "https://cran.r-project.org/web/packages/scrime/")
18741 (synopsis "Analysis of high-dimensional categorical data such as SNP data")
18743 "This package provides tools for the analysis of high-dimensional data
18744 developed/implemented at the group \"Statistical Complexity Reduction In
18745 Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
18746 the functions can also be applied to other types of categorical data.")
18747 (license license:gpl2)))
18749 (define-public r-pbmcapply
18751 (name "r-pbmcapply")
18756 (uri (cran-uri "pbmcapply" version))
18759 "0i58gcqpnbyvc448qfgm45b7rpbmrnagsvk1h1hsqchbbicfslnz"))))
18760 (build-system r-build-system)
18761 (home-page "https://github.com/kvnkuang/pbmcapply")
18762 (synopsis "Track the progress of apply procedures with a progress bar")
18764 "This light-weight package helps you track and visualize the progress of
18765 parallel versions of vectorized R functions of the @code{mc*apply} family.")
18766 (license license:expat)))
18768 (define-public r-blme
18775 (uri (cran-uri "blme" version))
18778 "0413j7gwr5yj14jamkizj55q7xii1a0kgazzj0ilqn2ascclz6k7"))))
18779 (build-system r-build-system)
18780 (propagated-inputs (list r-lme4))
18781 (home-page "https://github.com/vdorie/blme")
18782 (synopsis "Bayesian linear mixed-effects models")
18784 "This package provides tools for maximum a posteriori estimation for
18785 linear and generalized linear mixed-effects models in a Bayesian setting. It
18786 extends the lme4 package.")
18787 (license license:gpl2+)))
18789 (define-public r-batchtools
18791 (name "r-batchtools")
18796 (uri (cran-uri "batchtools" version))
18799 "0d2xy77hkzhcnyz8zxcv98i80fx6ripjw4rvyx4ww1d0vjjgqf52"))))
18800 (build-system r-build-system)
18816 (home-page "https://github.com/mllg/batchtools")
18817 (synopsis "Tools for computation on batch systems")
18819 "As a successor of the packages BatchJobs and BatchExperiments, this
18820 package provides a parallel implementation of the Map function for high
18821 performance computing systems managed by various schedulers. A multicore and
18822 socket mode allow the parallelization on a local machines, and multiple
18823 machines can be hooked up via SSH to create a makeshift cluster. Moreover,
18824 the package provides an abstraction mechanism to define large-scale computer
18825 experiments in a well-organized and reproducible way.")
18826 (license license:lgpl3)))
18828 (define-public r-clue
18835 (uri (cran-uri "clue" version))
18838 "0apgpdnn74mqg2bnr8yjyxgyvdl411h0r2b1r2xd67k21pyxs8bd"))))
18839 (build-system r-build-system)
18840 (propagated-inputs (list r-cluster))
18841 (home-page "https://cran.r-project.org/web/packages/clue/")
18842 (synopsis "Tools for analyzing cluster ensembles")
18843 (description "Cluster ensembles are collections of individual solutions to
18844 a given clustering problem which are useful or necessary to consider in a wide
18845 range of applications. This R package provides an extensible computational
18846 environment for creating and analyzing cluster ensembles, with basic data
18847 structures for representing partitions and hierarchies, and facilities for
18848 computing on them, including methods for measuring proximity and obtaining
18849 consensus and secondary clusterings.")
18850 (license license:gpl2)))
18852 (define-public r-sitmo
18859 (uri (cran-uri "sitmo" version))
18862 "1hm89zi38ldgbskyx1cn7gm87yqy7zrxli8q05a36y1ndvazi3j4"))))
18863 (build-system r-build-system)
18864 (propagated-inputs (list r-rcpp))
18867 (home-page "https://github.com/coatless/sitmo/")
18868 (synopsis "Parallel pseudo random number generator header files")
18870 "This package provides two high quality and fast PPRNGs that may be used
18871 in an OpenMP parallel environment. In addition, there is a generator for one
18872 dimensional low-discrepancy sequence.")
18873 (license license:expat)))
18875 (define-public r-dqrng
18882 (uri (cran-uri "dqrng" version))
18885 "1fwsldqcri2lccna4icbmmlqic3w4xyjm7rn0xmikrsw4kzapvjb"))))
18886 (build-system r-build-system)
18888 (list r-bh r-rcpp r-sitmo))
18891 (home-page "https://www.daqana.org/dqrng")
18892 (synopsis "Fast pseudo random number generators")
18894 "Several fast random number generators are provided as C++ header-only
18895 libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
18896 Additionally, fast functions for generating random numbers according to a
18897 uniform, normal and exponential distribution are included. The latter two use
18898 the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
18899 functions are exported to R and as a C++ interface and are enabled for use
18900 with the default 64 bit generator from the PCG family, Xoroshiro128+ and
18901 Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
18902 engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
18903 ;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
18904 ;; whole is distributed under the terms of the AGPL 3.
18905 (license license:agpl3)))
18907 (define-public r-ingredients
18909 (name "r-ingredients")
18914 (uri (cran-uri "ingredients" version))
18917 "11bv4l4fn9kr7y2nfzrwnaya8fi9w3nwcm9vzlqb7dva83rkqbsc"))))
18918 (properties `((upstream-name . "ingredients")))
18919 (build-system r-build-system)
18921 (list r-ggplot2 r-gridextra r-scales))
18922 (native-inputs (list r-knitr))
18923 (home-page "https://ModelOriented.github.io/ingredients/")
18924 (synopsis "Effects and importances of model ingredients")
18926 "This is a collection of tools for assessment of feature importance and
18927 feature effects. Key functions are:
18930 @item @code{feature_importance()} for assessment of global level feature
18932 @item @code{ceteris_paribus()} for calculation of the what-if plots,
18933 @item @code{partial_dependence()} for partial dependence plots,
18934 @item @code{conditional_dependence()} for conditional dependence plots,
18935 @item @code{accumulated_dependence()} for accumulated local effects plots,
18936 @item @code{aggregate_profiles()} and @code{cluster_profiles()} for
18937 aggregation of ceteris paribus profiles,
18938 @item generic @code{print()} and @code{plot()} for better usability of
18939 selected explainers,
18940 @item generic @code{plotD3()} for interactive, D3 based explanations, and
18941 @item generic @code{describe()} for explanations in natural language.
18943 (license license:gpl3)))
18945 (define-public r-ibreakdown
18947 (name "r-ibreakdown")
18952 (uri (cran-uri "iBreakDown" version))
18955 "00jzrndb3ahsv6ihp2pvs732n9cc944m83vdinrl9v1pxd82prkh"))))
18956 (properties `((upstream-name . "iBreakDown")))
18957 (build-system r-build-system)
18958 (propagated-inputs (list r-ggplot2))
18959 (native-inputs (list r-knitr))
18960 (home-page "https://ModelOriented.github.io/iBreakDown/")
18961 (synopsis "Model agnostic instance level variable attributions")
18963 "This package provides a model agnostic tool for decomposition of
18964 predictions from black boxes. It supports additive attributions and
18965 attributions with interactions. The Break Down Table shows contributions of
18966 every variable to a final prediction. The Break Down Plot presents variable
18967 contributions in a concise graphical way. This package works for
18968 classification and regression models.")
18969 (license license:gpl3)))
18971 (define-public r-dae
18978 (uri (cran-uri "dae" version))
18981 "0mq94ah21p1glvsbvdmi2p7nlgz1bvq7w3rz2z3mdqq18kz6nkjw"))))
18982 (build-system r-build-system)
18984 (list r-ggplot2 r-plyr))
18986 (list r-r-rsp)) ; vignette builder
18987 (home-page "http://chris.brien.name")
18988 (synopsis "Functions useful in the design and ANOVA of experiments")
18990 "This package provides functions useful in the design and ANOVA of
18991 experiments. The content falls into the following groupings:
18995 @item factor manipulation functions,
18996 @item design functions,
18997 @item ANOVA functions,
18998 @item matrix functions,
18999 @item projector and canonical efficiency functions, and
19000 @item miscellaneous functions.
19003 There is a vignette called @code{DesignNotes} describing how to use the design
19004 functions for randomizing and assessing designs. The ANOVA functions
19005 facilitate the extraction of information when the @code{Error} function has
19006 been used in the call to @code{aov}.")
19007 (license license:gpl2)))
19009 (define-public r-dalex
19016 (uri (cran-uri "DALEX" version))
19019 "0x8rcl3p1h1dpzgsfnalfjhvv345gg5v0z8dxqwrk6i32xk5wmzb"))))
19020 (properties `((upstream-name . "DALEX")))
19021 (build-system r-build-system)
19023 (list r-ggplot2 r-ibreakdown r-ingredients))
19024 (home-page "https://pbiecek.github.io/DALEX/")
19025 (synopsis "Descriptive machine learning explanations")
19027 "Machine Learning models are widely used and have various applications in
19028 classification or regression. Models created with boosting, bagging, stacking
19029 or similar techniques are often used due to their high performance, but such
19030 black-box models usually lack interpretability. The DALEX package contains
19031 various explainers that help to understand the link between input variables
19032 and model output.")
19033 ;; Any version of the GPL
19034 (license license:gpl3+)))
19036 (define-public r-enrichr
19043 (uri (cran-uri "enrichR" version))
19046 "0i3kfq4fkmx47n61zj5f87iv8ci6gbgy90a7s8dy9zbndzvbgya3"))))
19047 (properties `((upstream-name . "enrichR")))
19048 (build-system r-build-system)
19050 (list r-ggplot2 r-httr r-rjson))
19053 (home-page "https://cran.r-project.org/web/packages/enrichR/")
19054 (synopsis "R Interface to Enrichr database for analyzing gene sets")
19056 "This package provides an R interface to all Enrichr databases, a
19057 web-based tool for analyzing gene sets and returns any enrichment of common
19058 annotated biological functions.")
19059 (license license:gpl2+)))
19061 (define-public r-plot3d
19068 (uri (cran-uri "plot3D" version))
19071 "1h59zlsyzbjylaziwavppl9bjmnba4iiq34772y3dys6fqclajnh"))))
19072 (properties `((upstream-name . "plot3D")))
19073 (build-system r-build-system)
19074 (propagated-inputs (list r-misc3d))
19075 (home-page "https://cran.r-project.org/web/packages/plot3D")
19076 (synopsis "Plot multi-dimensional data")
19078 "This package provides functions for viewing 2D and 3D data, including
19079 perspective plots, slice plots, surface plots, scatter plots, etc. It
19080 includes data sets from oceanography.")
19081 (license license:gpl3+)))
19083 (define-public r-ggfortify
19085 (name "r-ggfortify")
19090 (uri (cran-uri "ggfortify" version))
19093 "038m74azpy43869ax1yi6wxbl1kr59iaxl8raiikjg749vcx6njw"))))
19094 (build-system r-build-system)
19105 (home-page "https://github.com/sinhrks/ggfortify")
19106 (synopsis "Data visualization tools for statistical analysis results")
19108 "This package provides unified plotting tools for statistics commonly
19109 used, such as GLM, time series, PCA families, clustering and survival
19110 analysis. The package offers a single plotting interface for these analysis
19111 results and plots in a unified style using the @code{ggplot2} package.")
19112 (license license:gpl2)))
19114 (define-public r-refmanager
19116 (name "r-refmanager")
19121 (uri (cran-uri "RefManageR" version))
19124 "1spzdp5ni52dybcaxqnhwdphh27wjyrsfy4hsxsplpg9rqwfqfps"))))
19125 (properties `((upstream-name . "RefManageR")))
19126 (build-system r-build-system)
19136 (home-page "https://github.com/ropensci/RefManageR/")
19137 (synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
19139 "This package provides tools for importing and working with bibliographic
19140 references. It greatly enhances the @code{bibentry} class by providing a
19141 class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
19142 UTF-8 encoding, and can be easily searched by any field, by date ranges, and
19143 by various formats for name lists (author by last names, translator by full
19144 names, etc.). Entries can be updated, combined, sorted, printed in a number
19145 of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
19146 into R and converted to @code{BibEntry} objects.")
19147 ;; Any of these licenses may be picked.
19148 (license (list license:gpl2 license:gpl3 license:bsd-3))))
19150 (define-public r-citr
19157 (uri (cran-uri "citr" version))
19160 "1qbarvafjb8jgkrnrhh6jw7mcglmjwf7dpdiibxf39jkmlhf7las"))))
19161 (build-system r-build-system)
19172 (home-page "https://github.com/crsh/citr")
19173 (synopsis "RStudio add-in to insert Markdown citations")
19175 "This package provides functions and an RStudio add-in that search a
19176 BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
19177 the current document.")
19178 (license license:expat)))
19180 (define-public r-xgboost
19183 (version "1.5.0.2")
19187 (uri (cran-uri "xgboost" version))
19190 "04xbgrrb3aq067hrivslq5f2rd1v95yfv7lkj596ijyqi6ibjl27"))))
19191 (build-system r-build-system)
19193 (list r-data-table r-jsonlite r-matrix))
19196 (home-page "https://github.com/dmlc/xgboost")
19197 (synopsis "Extreme gradient boosting")
19199 "This package provides an R interface to Extreme Gradient Boosting, which
19200 is an efficient implementation of the gradient boosting framework from Chen
19201 and Guestrin (2016). The package includes efficient linear model solver and
19202 tree learning algorithms. The package can automatically do parallel
19203 computation on a single machine. It supports various objective functions,
19204 including regression, classification and ranking. The package is made to be
19205 extensible, so that users are also allowed to define their own objectives
19207 (license license:asl2.0)))
19209 (define-public r-umap
19212 (version "0.2.7.0")
19216 (uri (cran-uri "umap" version))
19219 "191vpy84s0bar06y9z1qx43x2kc4qp7lmrcmd0cvz2pnzq722jab"))))
19220 (build-system r-build-system)
19222 (list r-openssl r-rcpp r-reticulate r-rspectra))
19225 (home-page "https://github.com/tkonopka/umap")
19226 (synopsis "Uniform manifold approximation and projection")
19228 "Uniform manifold approximation and projection is a technique for
19229 dimension reduction. This package provides an interface to the UMAP algorithm
19230 in R, including a translation of the original algorithm into R.")
19231 (license license:expat)))
19233 (define-public r-uwot
19240 (uri (cran-uri "uwot" version))
19243 "06ylzxmdh8jipbrzgqaiivd2lnqmbcva41cyvc0iyals6vqr1ksg"))))
19244 (build-system r-build-system)
19254 (home-page "https://github.com/jlmelville/uwot")
19255 (synopsis "Uniform manifold approximation and projection")
19257 "This package provides an implementation of the Uniform Manifold
19258 Approximation and Projection dimensionality reduction by McInnes et
19259 al. (2018). It also provides means to transform new data and to carry out
19260 supervised dimensionality reduction. An implementation of the related
19261 LargeVis method of Tang et al. (2016) is also provided.")
19262 (license license:gpl3)))
19264 (define-public r-kableextra
19266 (name "r-kableextra")
19271 (uri (cran-uri "kableExtra" version))
19274 "1c5vzy95cbz36jwyssr927qicrayifinv861rvnmg4nghb1gl7q9"))))
19275 (properties `((upstream-name . "kableExtra")))
19276 (build-system r-build-system)
19294 (home-page "https://haozhu233.github.io/kableExtra/")
19295 (synopsis "Construct complex tables with pipe syntax")
19297 "Build complex HTML or LaTeX tables using @code{kable()} from
19298 @code{knitr} and the piping syntax from @code{magrittr}. The function
19299 @code{kable()} is a light weight table generator coming from @code{knitr}.
19300 This package simplifies the way to manipulate the HTML or LaTeX codes
19301 generated by @code{kable()} and allows users to construct complex tables and
19302 customize styles using a readable syntax.")
19303 (license license:expat)))
19305 (define-public r-glasso
19312 (uri (cran-uri "glasso" version))
19314 (base32 "02p3612rpydk195n2qr77lp1j2w8zsw1ckkk98c8angm4r5q8dsc"))))
19315 (build-system r-build-system)
19316 (native-inputs (list gfortran))
19317 (home-page "https://statweb.stanford.edu/~tibs/glasso/")
19318 (synopsis "Graphical Lasso: estimation of Gaussian graphical models")
19320 "This is a package for estimation of a sparse inverse covariance matrix
19321 using a lasso (L1) penalty. Facilities are provided for estimates along a
19322 path of values for the regularization parameter.")
19323 (license license:gpl2)))
19325 (define-public r-rhpcblasctl
19327 (name "r-rhpcblasctl")
19328 (version "0.21-247.1")
19332 (uri (cran-uri "RhpcBLASctl" version))
19335 "0scpr6jq25xx7wmqyc380ann4h536ll0g7wblikk25yqvpamzrav"))))
19336 (properties `((upstream-name . "RhpcBLASctl")))
19337 (build-system r-build-system)
19338 (home-page "https://prs.ism.ac.jp/~nakama/Rhpc/")
19339 (synopsis "Control the number of threads on BLAS")
19341 "This package allows you to control the number of threads the BLAS
19342 library uses. It is also possible to control the number of threads in
19344 (license license:agpl3+)))
19346 (define-public r-lda
19353 (uri (cran-uri "lda" version))
19356 "03r4h5kgr8mfy44p66mfj5bp4k00g8zh4a1mhn46jw14pkhs21jn"))))
19357 (build-system r-build-system)
19358 (home-page "https://cran.r-project.org/web/packages/lda/")
19359 (synopsis "Collapsed Gibbs sampling methods for topic models")
19361 "This package implements @dfn{latent Dirichlet allocation} (LDA) and
19362 related models. This includes (but is not limited to) sLDA, corrLDA, and the
19363 mixed-membership stochastic blockmodel. Inference for all of these models is
19364 implemented via a fast collapsed Gibbs sampler written in C. Utility
19365 functions for reading/writing data typically used in topic models, as well as
19366 tools for examining posterior distributions are also included.")
19367 ;; Any version of the LGPL
19368 (license license:lgpl3+)))
19370 (define-public r-rann-l1
19377 (uri (cran-uri "RANN.L1" version))
19380 "1hanh3my84mdr5wy6b89fawqzfc184vff1y65wy4l5ld9qza1n44"))))
19381 (properties `((upstream-name . "RANN.L1")))
19382 (build-system r-build-system)
19383 (home-page "https://github.com/jefferis/RANN/tree/master-L1")
19384 (synopsis "Fast nearest neighbour search using L1 metric")
19386 "This package provides tools to find the k nearest neighbours for every
19387 point in a given dataset in O(N log N) time using Arya and Mount's ANN
19388 library. There is support for approximate as well as exact searches, fixed
19389 radius searches and @code{bd} as well as @code{kd} trees. The distance is
19390 computed using the L1 (Manhattan, taxicab) metric.")
19391 (license license:gpl3+)))
19393 (define-public r-leiden
19400 (uri (cran-uri "leiden" version))
19403 "03gaxpcab3a1av5lk8r5ll1s858gvyx5ndknci1sia96w1v44xc1"))))
19404 (properties `((upstream-name . "leiden")))
19405 (build-system r-build-system)
19407 (list r-igraph r-matrix r-reticulate))
19410 (home-page "https://github.com/TomKellyGenetics/leiden")
19411 (synopsis "R implementation of Leiden clustering algorithm")
19413 "This package implements the Python @code{leidenalg} module to be called
19414 in R. It enables clustering using the Leiden algorithm for partitioning a
19415 graph into communities. See also Traag et al (2018) \"From Louvain to Leiden:
19416 guaranteeing well-connected communities.\" <arXiv:1810.08473>.")
19417 (license license:gpl3)))
19419 (define-public r-patchwork
19421 (name "r-patchwork")
19426 (uri (cran-uri "patchwork" version))
19429 "10glgkf58lcykcwda1hj6xdps02m3i247qynk6s2jmwljagps3fg"))))
19430 (build-system r-build-system)
19432 (list r-ggplot2 r-gtable))
19435 (home-page "https://github.com/thomasp85/patchwork")
19436 (synopsis "Compose ggplot2 plots")
19438 "The @code{ggplot2} package provides a strong API for sequentially
19439 building up a plot, but does not concern itself with composition of multiple
19440 plots. Patchwork is a package that expands the API to allow for arbitrarily
19441 complex composition of plots by providing mathematical operators for combining
19443 (license license:expat)))
19445 (define-public r-liger
19452 (uri (git-reference
19453 (url "https://github.com/MacoskoLab/liger")
19454 (commit (string-append "v" version))))
19455 (file-name (git-file-name name version))
19458 "16dzwwcpw6n78pxlc5w3kraigki35ix7zhd2cbx5f3y60bbkhlmx"))
19459 (modules '((guix build utils)))
19462 (delete-file "inst/java/ModularityOptimizer.jar")
19464 (build-system r-build-system)
19467 (modify-phases %standard-phases
19468 (add-after 'unpack 'build-java-part
19469 (lambda* (#:key inputs #:allow-other-keys)
19470 (invoke "unzip" (assoc-ref inputs "optimizer-src"))
19471 (for-each (lambda (file) (invoke "javac" file))
19472 (find-files "." "\\.java$"))
19473 (apply invoke "jar" "cf" "inst/java/ModularityOptimizer.jar"
19474 (find-files "." "\\.class$"))
19498 `(("jdk" ,icedtea "jdk")
19499 ;; See https://github.com/MacoskoLab/liger/issues/96
19500 ;; The optimizer is released under the Expat license.
19504 (uri "http://www.ludowaltman.nl/slm/modularity_optimizer_source.zip")
19507 "01hmm6sapcmldvayknqx2w4cav3qv71mwwkdkwj4qgq6dss09g18"))))
19509 ("r-knitr" ,r-knitr))) ; for vignettes
19510 (home-page "https://github.com/MacoskoLab/liger")
19511 (synopsis "Integrate and analyze multiple single-cell datasets")
19513 "LIGER is a package for integrating and analyzing multiple single-cell
19514 datasets, developed and maintained by the Macosko lab. It relies on
19515 integrative non-negative matrix factorization to identify shared and
19516 dataset-specific factors.")
19517 (license license:gpl3)))
19519 (define-public r-harmony
19526 (uri (git-reference
19527 (url "https://github.com/immunogenomics/harmony")
19529 (file-name (git-file-name name version))
19532 "05r401q09rbr6fqhb9mbd95082cjdi3nag1cv6zn96xkr0f6imq9"))
19533 (modules '((guix build utils)))
19536 (for-each delete-file '("config.status" "configure"))
19538 (build-system r-build-system)
19553 (home-page "https://github.com/immunogenomics/harmony")
19554 (synopsis "Integration of single cell sequencing data")
19556 "This package provides an implementation of the Harmony algorithm for
19557 single cell integration, described in Korsunsky et al
19558 @url{doi.org/10.1101/461954}. The package includes a standalone Harmony
19559 function and interfaces to external frameworks.")
19560 (license license:gpl3)))
19562 (define-public r-covr
19569 (uri (cran-uri "covr" version))
19571 (base32 "0v5cv3cw2kpdr6wxmkbd3wclavr17zipypdcb10hhmpa4cvgqk55"))))
19572 (properties `((upstream-name . "covr")))
19573 (build-system r-build-system)
19583 (list r-knitr)) ; for vignettes
19584 (home-page "https://github.com/r-lib/covr")
19585 (synopsis "Test coverage for R packages")
19587 "Thisp package enables you to track and report code coverage for your
19588 package and (optionally) upload the results to a coverage service. Code
19589 coverage is a measure of the amount of code being exercised by a set of tests.
19590 It is an indirect measure of test quality and completeness. This package is
19591 compatible with any testing methodology or framework and tracks coverage of
19592 both R code and compiled C/C++/FORTRAN code.")
19593 (license license:gpl3)))
19595 (define-public r-systemfonts
19597 (name "r-systemfonts")
19602 (uri (cran-uri "systemfonts" version))
19605 "1fmv1ni77ncz6rrm4iv8a7l6pbqnk2ri0yzad2bs943gxbarjz34"))))
19606 (properties `((upstream-name . "systemfonts")))
19607 (build-system r-build-system)
19611 (list fontconfig zlib))
19613 (list pkg-config r-knitr))
19614 (home-page "https://github.com/r-lib/systemfonts")
19615 (synopsis "System native font finding")
19617 "This package provides system native access to the font catalogue. As
19618 font handling varies between systems it is difficult to correctly locate
19619 installed fonts across different operating systems. The 'systemfonts' package
19620 provides bindings to the native libraries for finding font files that can then
19621 be used further by e.g. graphic devices.")
19622 (license license:expat)))
19624 (define-public r-graphlayouts
19626 (name "r-graphlayouts")
19631 (uri (cran-uri "graphlayouts" version))
19634 "1l7gkn0r1ijllv3w7cbwcbi0jggs7wlkq9b2lykprng4g1kjc96p"))))
19635 (properties `((upstream-name . "graphlayouts")))
19636 (build-system r-build-system)
19638 (list r-igraph r-rcpp r-rcpparmadillo))
19639 (home-page "https://github.com/schochastics/graphlayouts")
19640 (synopsis "Additional layout algorithms for network visualizations")
19642 "This package provides several layout algorithms to visualize networks
19643 which are not part of the igraph library. Most are based on the concept of
19644 stress majorization by Gansner et al. (2004)
19645 <doi:10.1007/978-3-540-31843-9_25>. Some more specific algorithms
19646 emphasize hidden group structures in networks or focus on specific nodes.")
19647 (license license:expat)))
19649 (define-public r-terra
19656 (uri (cran-uri "terra" version))
19659 "1rz6dd78i3aq82vl9q4fw17y5cxj2pcmra5mlhb0ca1df78mgb77"))))
19660 (properties `((upstream-name . "terra")))
19661 (build-system r-build-system)
19666 sqlite ; needed for proj
19672 (home-page "https://rspatial.org/terra")
19673 (synopsis "Spatial data analysis")
19675 "This package provides methods for spatial data analysis, especially
19676 raster data. The included methods allow for low-level data manipulation as
19677 well as high-level global, local, zonal, and focal computation. The predict
19678 and interpolate methods facilitate the use of regression type (interpolation,
19679 machine learning) models for spatial prediction. Processing of very large
19680 files is supported.")
19681 (license license:gpl3+)))
19683 (define-public r-tidygraph
19685 (name "r-tidygraph")
19690 (uri (cran-uri "tidygraph" version))
19693 "17qjns33zcj82jcsl7bn7i4zxcm7ric50zyf7agi0i01zi16qz85"))))
19694 (properties `((upstream-name . "tidygraph")))
19695 (build-system r-build-system)
19706 (home-page "https://github.com/thomasp85/tidygraph")
19707 (synopsis "Tidy API for graph manipulation")
19709 "This package provides a graph implementation that can be thought of as
19710 two tidy data frames describing node and edge data respectively. It provides
19711 an approach to manipulate these two virtual data frames using the API defined
19712 in the @code{dplyr} package, and it also provides tidy interfaces to a lot of
19713 common graph algorithms.")
19714 (license license:expat)))
19716 (define-public r-soupx
19717 (let ((commit "a3354be76fb52fd795be6ddf163cf056c05c6cb8")
19721 (version (git-version "0.3.1" revision commit))
19725 (uri (git-reference
19726 (url "https://github.com/constantAmateur/SoupX")
19728 (file-name (git-file-name name version))
19731 "1zmlyzrl0fz6l79gn2wswid670p88mm3y292is89sa5p3h7frr99"))))
19732 (properties `((upstream-name . "SoupX")))
19733 (build-system r-build-system)
19735 (list r-ggplot2 r-matrix r-seurat))
19736 (home-page "https://github.com/constantAmateur/SoupX")
19737 (synopsis "Single cell mRNA Soup eXterminator")
19739 "This package provides a package for quantifying, profiling and
19740 removing cell free mRNA contamination (the \"soup\") from droplet based single
19741 cell RNA-seq experiments.")
19742 (license license:gpl2))))
19744 (define-public r-assertr
19751 (uri (cran-uri "assertr" version))
19754 "00764vv86r3bn4r85in4w637harffyw605fgq0dj6mrbrwcfb650"))))
19755 (build-system r-build-system)
19757 (list r-dplyr r-mass r-rlang))
19759 (list r-knitr)) ; needed for vignette
19760 (home-page "https://github.com/ropensci/assertr")
19761 (synopsis "Assertive programming for R analysis pipelines")
19763 "This package provides functionality to assert conditions that have to be
19764 met so that errors in data used in analysis pipelines can fail quickly. It is
19765 similar to @code{stopifnot()} but more powerful, friendly, and easier for use
19767 (license license:expat)))
19769 (define-public r-parameters
19771 (name "r-parameters")
19776 (uri (cran-uri "parameters" version))
19779 "1i295d5nqjr3pvp9vz59wiasrxy9n78q518phcd15sxcjzcj0l27"))))
19780 (properties `((upstream-name . "parameters")))
19781 (build-system r-build-system)
19783 (list r-bayestestr r-datawizard r-insight))
19786 (home-page "https://cran.r-project.org/web/packages/parameters")
19787 (synopsis "Processing of model parameters")
19789 "This package provides utilities for processing the parameters of various
19790 statistical models. Beyond computing p values, CIs, and other indices for a
19791 wide variety of models, this package implements features like standardization
19792 or bootstrapping of parameters and models, feature reduction (feature
19793 extraction and variable selection) as well as conversion between indices of
19795 (license license:gpl3)))
19797 (define-public r-rgdal
19804 (uri (cran-uri "rgdal" version))
19806 (base32 "18k1w8cb77h4mw1m5b21r0fng40arb1md24fyriv83ccz8n46m3z"))))
19807 (properties `((upstream-name . "rgdal")))
19808 (build-system r-build-system)
19810 (list gdal proj zlib))
19814 (list pkg-config r-knitr))
19815 (home-page "http://rgdal.r-forge.r-project.org")
19816 (synopsis "Bindings for the Geospatial Data Abstraction Library")
19818 "This package provides bindings to the Geospatial Data Abstraction
19819 Library (GDAL) and access to projection/transformation operations from the
19821 (license license:gpl2+)))
19823 (define-public r-insol
19830 (uri (cran-uri "insol" version))
19833 "166kgxgzbh55y2qqya6c2si22x0v7asi70im054g6xxwc5187kh3"))))
19834 (properties `((upstream-name . "insol")))
19835 (build-system r-build-system)
19840 (home-page "https://meteoexploration.com/R/insol/index.html")
19841 (synopsis "Tools for calculating solar radiation")
19843 "This package provides functions to compute insolation on tilted
19844 surfaces, computes atmospheric transmittance and related parameters such as:
19845 Earth radius vector, declination, sunset and sunrise, daylength, equation of
19846 time, vector in the direction of the sun, vector normal to surface, and some
19847 atmospheric physics.")
19848 (license license:gpl2+)))
19850 (define-public r-lifecycle
19852 (name "r-lifecycle")
19857 (uri (cran-uri "lifecycle" version))
19860 "183v1z1h037pvsgrj6vakpwhnhsr29hsw8p16k59dgpi00f6x9qx"))))
19861 (properties `((upstream-name . "lifecycle")))
19862 (build-system r-build-system)
19864 (list r-glue r-rlang))
19866 (list r-knitr)) ; for vignettes
19867 (home-page "https://github.com/r-lib/lifecycle")
19868 (synopsis "Manage the life cycle of your package functions")
19870 "Manage the life cycle of your exported functions with shared
19871 conventions, documentation badges, and non-invasive deprecation warnings. The
19872 lifecycle package defines four development stages (experimental, maturing,
19873 stable, and questioning) and three deprecation stages (soft-deprecated,
19874 deprecated, and defunct). It makes it easy to insert badges corresponding to
19875 these stages in your documentation. Usage of deprecated functions are
19876 signalled with increasing levels of non-invasive verbosity.")
19877 (license license:gpl3)))
19879 (define-public r-assertable
19881 (name "r-assertable")
19886 (uri (cran-uri "assertable" version))
19889 "1cciil1nzxd8gbj49w99jiv077lbpb59vx7bmb4p218aj2h5hqq4"))))
19890 (build-system r-build-system)
19892 (list r-data-table))
19895 (home-page "https://cran.r-project.org/web/packages/assertable/")
19896 (synopsis "Verbose assertions for tabular data (data.frames and data.tables)")
19897 (description "This package provides simple, flexible assertions on
19898 data.frame or data.table objects with verbose output for vetting. While other
19899 assertion packages apply towards more general use-cases, @code{assertable} is
19900 tailored towards tabular data. It includes functions to check variable names
19901 and values, whether the dataset contains all combinations of a given set of
19902 unique identifiers, and whether it is a certain length. In addition,
19903 @code{assertable} includes utility functions to check the existence of target
19904 files and to efficiently import multiple tabular data files into one
19906 (license license:gpl3)))
19908 (define-public r-quadprog
19910 (name "r-quadprog")
19915 (uri (cran-uri "quadprog" version))
19917 (base32 "1ka9g8zak8sg4y2xbz93dfrldznlk9qpd4pq9z21cdcdn3b8s4i2"))))
19918 (build-system r-build-system)
19921 (home-page "https://cran.r-project.org/web/packages/quadprog")
19922 (synopsis "Functions to solve quadratic programming problems")
19924 "This package contains routines and documentation for solving quadratic
19925 programming problems.")
19926 (license license:gpl3+)))
19928 (define-public r-desolve
19935 (uri (cran-uri "deSolve" version))
19937 (base32 "0j7mmg1mimdpql8f4i9dn920ciyyq80a5qnc4fq5xn5lyrx5vxir"))))
19938 (properties `((upstream-name . "deSolve")))
19939 (build-system r-build-system)
19942 (home-page "https://desolve.r-forge.r-project.org/")
19943 (synopsis "Solvers for initial value problems of differential equations")
19944 (description "This package provides functions that solve initial value
19945 problems of a system of first-order @dfn{ordinary differential
19946 equations} (ODE), of @dfn{partial differential equations} (PDE), of
19947 @dfn{differential algebraic equations} (DAE), and of delay differential
19948 equations. The functions provide an interface to the FORTRAN functions
19949 @code{lsoda}, @code{lsodar}, @code{lsode}, @code{lsodes} of the ODEPACK
19950 collection, to the FORTRAN functions @code{dvode} and @code{daspk} and a
19951 C-implementation of solvers of the Runge-Kutta family with fixed or variable
19952 time steps. The package contains routines designed for solving ODEs resulting
19953 from 1-D, 2-D and 3-D partial differential equations that have been converted
19954 to ODEs by numerical differencing.")
19955 (license license:gpl2+)))
19957 (define-public r-pmcmrplus
19959 (name "r-pmcmrplus")
19964 (uri (cran-uri "PMCMRplus" version))
19966 (base32 "00sgk4c7vpmbfifrsbqd5gh7hwdpm8kymlpnnrdzlhvkymhbmfkn"))))
19967 (properties `((upstream-name . "PMCMRplus")))
19968 (build-system r-build-system)
19969 (inputs (list gmp))
19979 (native-inputs (list gfortran r-knitr))
19980 (home-page "https://cran.r-project.org/package=PMCMRplus")
19981 (synopsis "Calculate pairwise multiple comparisons of mean rank sums extended")
19983 "This package provides multiple pairwise tests.")
19984 (license license:gpl3+)))
19986 (define-public r-pracma
19992 (uri (cran-uri "pracma" version))
19994 (base32 "1pmqk7b6c600v6pn0s047p3msl13azwk611zvh05w5f993yq7b0p"))))
19995 (build-system r-build-system)
19996 (home-page "https://cran.r-project.org/web/packages/pracma/")
19997 (synopsis "Practical numerical math functions")
19998 (description "This package provides functions for numerical analysis and
19999 linear algebra, numerical optimization, differential equations, plus some
20000 special functions. It uses Matlab function names where appropriate to simplify
20002 (license license:gpl3+)))
20004 (define-public r-subplex
20011 (uri (cran-uri "subplex" version))
20014 "11zqzydbj6ivgvlw1gv1r2yxra7misbc622g575p2vckhjjg9v6m"))))
20015 (build-system r-build-system)
20018 (home-page "https://cran.r-project.org/web/packages/subplex")
20019 (synopsis "Unconstrained optimization using the subplex algorithm")
20021 "This package implements the Subplex optimization algorithm.
20022 It solves unconstrained optimization problems using a simplex method on
20023 subspaces. The method is well suited for optimizing objective functions that
20024 are noisy or are discontinuous at the solution.")
20025 (license license:gpl3+)))
20027 (define-public r-txtplot
20034 (uri (cran-uri "txtplot" version))
20037 "00sriml48y70j18jz235dsfm5x3a81bnzskfp3hnv6cbjwwsmca4"))))
20038 (build-system r-build-system)
20039 (home-page "https://cran.r-project.org/web/packages/txtplot/")
20040 (synopsis "Text-based plotting")
20041 (description "This package provides functions to produce rudimentary ASCII
20042 graphics directly in the terminal window. This package provides a basic
20043 plotting function (and equivalents of curve, density, acf and barplot) as well
20044 as a boxplot function.")
20045 (license license:lgpl3+)))
20047 (define-public r-bio3d
20054 (uri (cran-uri "bio3d" version))
20057 "1jvcmpzi9knhxq5jsbhg8slm8hnlx2y8smmwwrbnbyd0rmk5fhci"))))
20058 (properties `((upstream-name . "bio3d")))
20059 (build-system r-build-system)
20060 (inputs (list zlib))
20061 (propagated-inputs (list r-rcpp))
20064 (home-page "http://thegrantlab.org/bio3d/")
20065 (synopsis "Biological structure analysis")
20067 "This package provides utilities to process, organize and explore protein
20068 structure, sequence and dynamics data. Features include the ability to read
20069 and write structure, sequence and dynamic trajectory data, perform sequence
20070 and structure database searches, data summaries, atom selection, alignment,
20071 superposition, rigid core identification, clustering, torsion analysis,
20072 distance matrix analysis, structure and sequence conservation analysis, normal
20073 mode analysis, principal component analysis of heterogeneous structure data,
20074 and correlation network analysis from normal mode and molecular dynamics data.
20075 In addition, various utility functions are provided to enable the statistical
20076 and graphical power of the R environment to work with biological sequence and
20078 (license license:gpl2+)))
20080 (define-public r-bios2cor
20082 (name "r-bios2cor")
20087 (uri (cran-uri "Bios2cor" version))
20090 "1wkj9vr33m9jilidil9jpw5rzr3pf7gkimxdvch22ks4bgkx7l1w"))))
20091 (properties `((upstream-name . "Bios2cor")))
20092 (build-system r-build-system)
20094 (list r-bigmemory r-bio3d r-circular r-igraph))
20095 (home-page "https://cran.r-project.org/web/packages/Bios2cor/")
20096 (synopsis "From biological sequences and simulations to correlation analysis")
20098 "This package provides utilities for computation and analysis of
20099 correlation/covariation in multiple sequence alignments and in side chain
20100 motions during molecular dynamics simulations. Features include the
20101 computation of correlation/covariation scores using a variety of scoring
20102 functions between either sequence positions in alignments or side chain
20103 dihedral angles in molecular dynamics simulations and utilities to analyze the
20104 correlation/covariation matrix through a variety of tools including network
20105 representation and principal components analysis. In addition, several
20106 utility functions are based on the R graphical environment to provide friendly
20107 tools for help in data interpretation.")
20108 (license license:gpl2+)))
20110 ;; This package includes minified JavaScript files. When upgrading please
20111 ;; check that there are no new minified JavaScript files.
20112 (define-public r-networkd3
20114 (name "r-networkd3")
20119 (uri (cran-uri "networkD3" version))
20122 "02wxki67drppgfka1is1ykg1f2rxf0x0657c0crj7ipfy62jbf1k"))
20125 (delete-file "inst/htmlwidgets/lib/d3-4.5.0/d3.min.js")
20127 (properties `((upstream-name . "networkD3")))
20128 (build-system r-build-system)
20130 `(#:modules ((guix build utils)
20131 (guix build r-build-system)
20135 (modify-phases %standard-phases
20136 (add-after 'unpack 'process-javascript
20137 (lambda* (#:key inputs #:allow-other-keys)
20138 (with-directory-excursion "inst/htmlwidgets/lib/"
20142 `((,(assoc-ref inputs "d3.v4.js")
20143 "d3-4.5.0/d3.min.js"))))
20144 (lambda (sources targets)
20145 (for-each (lambda (source target)
20146 (format #t "Processing ~a --> ~a~%"
20148 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
20149 (call-with-output-file target
20151 (dump-port minified port)))))
20152 sources targets))))
20155 `(("uglifyjs" ,node-uglify-js)
20156 ;; NOTE: Make sure that this version of d3 is still valid when
20157 ;; upgrading the package.
20161 (uri "https://d3js.org/d3.v4.js")
20164 "0y7byf6kcinfz9ac59jxc4v6kppdazmnyqfav0dm4h550fzfqqlg"))))))
20166 (list r-htmlwidgets r-igraph r-magrittr))
20167 (home-page "https://cran.r-project.org/package=networkD3")
20168 (synopsis "D3 JavaScript network graphs from R")
20170 "This package creates D3 JavaScript network, tree, dendrogram, and Sankey
20172 (license license:gpl3+)))
20174 (define-public r-aasea
20181 (uri (cran-uri "aaSEA" version))
20184 "0him4r8qyp0xssgrmdxjs45yn4d28h5anv4jyxxbbs9phb0m6j3h"))))
20185 (properties `((upstream-name . "aaSEA")))
20186 (build-system r-build-system)
20197 (home-page "https://cran.r-project.org/web/packages/aaSEA/")
20198 (synopsis "Amino acid substitution effect analyzer")
20200 "Given a protein multiple sequence alignment, it is a daunting task to
20201 assess the effects of substitutions along sequence length. The aaSEA package
20202 is intended to help researchers to rapidly analyze property changes caused by
20203 single, multiple and correlated amino acid substitutions in proteins.")
20204 (license license:gpl3)))
20206 (define-public r-abacus
20213 (uri (cran-uri "ABACUS" version))
20216 "0m1dnkwjr1522l9ddbzzx7ayxvli17sbmk6s28adpmzzjwh2kd1i"))))
20217 (properties `((upstream-name . "ABACUS")))
20218 (build-system r-build-system)
20220 (list r-ggplot2 r-shiny))
20221 (home-page "https://shiny.abdn.ac.uk/Stats/apps/")
20222 (synopsis "Apps-based activities for communicating and understanding statistics")
20224 "This package provides a set of Shiny apps for effective communication
20225 and understanding in statistics. The current version includes properties of
20226 normal distribution, properties of sampling distribution, one-sample z and t
20227 tests, two samples independent (unpaired) t test and analysis of variance.")
20228 (license license:gpl3)))
20230 (define-public r-abc-rap
20237 (uri (cran-uri "ABC.RAP" version))
20240 "1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"))))
20241 (properties `((upstream-name . "ABC.RAP")))
20242 (build-system r-build-system)
20243 (home-page "https://cran.r-project.org/web/packages/ABC.RAP/")
20244 (synopsis "Array-based CpG region analysis pipeline")
20246 "This package aims to identify candidate genes that are differentially
20247 methylated between cases and controls. It applies Student's t-test and delta
20248 beta analysis to identify candidate genes containing multiple CpG sites.")
20249 (license license:gpl3)))
20251 (define-public r-abcadm
20258 (uri (cran-uri "abcADM" version))
20261 "0vcabnnnwc0psv9v3rda5aap9s8cq1pjh02zva3ki64hlavf2a10"))))
20262 (properties `((upstream-name . "abcADM")))
20263 (build-system r-build-system)
20265 (list r-bh r-rcpp))
20266 (home-page "https://cran.r-project.org/web/packages/abcADM/")
20267 (synopsis "Fit accumulated damage models and estimate reliability using ABC")
20269 "This package provides tools to estimate parameters of accumulated
20270 damage (load duration) models based on failure time data under a Bayesian
20271 framework, using @dfn{Approximate Bayesian Computation} (ABC), and to assess
20272 long-term reliability under stochastic load profiles.")
20273 (license license:gpl3)))
20275 (define-public r-rglpk
20282 (uri (cran-uri "Rglpk" version))
20285 "19mzpyimzq9zqnbi05j79b2di3nzaln8swggs9p8sqdr60qvr3d2"))))
20286 (properties `((upstream-name . "Rglpk")))
20287 (build-system r-build-system)
20292 (home-page "https://r-forge.r-project.org/projects/rglp/")
20293 (synopsis "R interface to the GNU Linear Programming Kit")
20295 "This package provides an R interface to the GNU Linear Programming Kit,
20296 software for solving large-scale @dfn{linear programming} (LP), @dfn{mixed
20297 integer linear programming} (MILP) and other related problems.")
20299 (license (list license:gpl2 license:gpl3))))
20301 (define-public r-abcdefba
20303 (name "r-abcdefba")
20308 (uri (cran-uri "abcdeFBA" version))
20311 "1rxjripy8v6bxi25vdfjnbk24zkmf752qbl73cin6nvnqflwxkx4"))))
20312 (properties `((upstream-name . "abcdeFBA")))
20313 (build-system r-build-system)
20315 (list r-corrplot r-lattice r-rgl r-rglpk))
20316 (home-page "https://cran.r-project.org/web/packages/abcdeFBA/")
20317 (synopsis "A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package")
20319 "This package provides functions for Constraint Based Simulation using
20320 Flux Balance Analysis and informative analysis of the data generated during
20322 (license license:gpl2)))
20324 (define-public r-abcrlda
20331 (uri (cran-uri "abcrlda" version))
20334 "04pcdnk2szfpc2ylcw5ds7y895ivy03bycal03kxw7cwylzxasks"))))
20335 (properties `((upstream-name . "abcrlda")))
20336 (build-system r-build-system)
20337 (home-page "https://ieeexplore.ieee.org/document/8720003/")
20338 (synopsis "Asymptotically bias-corrected regularized linear discriminant analysis")
20340 "This package offers methods to perform @dfn{asymptotically
20341 bias-corrected regularized linear discriminant analysis} (ABC_RLDA) for
20342 cost-sensitive binary classification. The bias-correction is an estimate of
20343 the bias term added to regularized discriminant analysis that minimizes the
20345 (license license:gpl3)))
20347 (define-public r-abemus
20354 (uri (cran-uri "abemus" version))
20357 "1dhllb184byp1yl15rg2w02zgw3iajag7cxshirg47mnmm7n70bb"))))
20358 (properties `((upstream-name . "abemus")))
20359 (build-system r-build-system)
20361 (list r-data-table))
20362 (home-page "https://cran.r-project.org/web/packages/abemus/")
20363 (synopsis "Adaptive base error model in ultra-deep sequencing data")
20365 "This package provides an implementation of @dfn{Adaptive Base Error
20366 Model in Ultra-deep Sequencing data} (ABEMUS), which combines
20367 platform-specific genetic knowledge and empirical signal to readily detect and
20368 quantify somatic @dfn{single nucleotide variants} (SNVs) in @dfn{circulating
20369 cell free DNA} (cfDNA).")
20370 (license license:gpl3)))
20372 ;; This package includes minified JavaScript files. When upgrading please
20373 ;; check that there are no new minified JavaScript files.
20374 (define-public r-rintrojs
20376 (name "r-rintrojs")
20381 (uri (cran-uri "rintrojs" version))
20384 "00l5mk80gj3xkbf3m1kip566ic98bhd88lh0bg69ybkpk4gifpyw"))
20386 '(delete-file "inst/javascript/introjs/intro.min.js"))))
20387 (properties `((upstream-name . "rintrojs")))
20388 (build-system r-build-system)
20391 (modify-phases %standard-phases
20392 (add-after 'unpack 'process-javascript
20393 (lambda* (#:key inputs #:allow-other-keys)
20394 (with-directory-excursion "inst/javascript/introjs/"
20395 (let ((source (assoc-ref inputs "intro.js"))
20396 (target "intro.min.js"))
20397 (format #true "Processing ~a --> ~a~%"
20399 (invoke "esbuild" source "--minify"
20400 (string-append "--outfile=" target)))))))))
20402 `(("esbuild" ,esbuild)
20406 (uri "https://cdn.jsdelivr.net/npm/intro.js@3.2.1/intro.js")
20409 "0vh5n7hqqyx2pdvlqq6xadfqibcn78h5961rwhpf817kpxfzv8v7"))))))
20411 (list r-jsonlite r-shiny))
20412 (home-page "https://github.com/carlganz/rintrojs")
20413 (synopsis "Wrapper for the Intro.js library")
20415 "This package provides a wrapper for the @url{http://www.introjs.com,
20416 Intro.js} library. This package makes it easy to include step-by-step
20417 introductions, and clickable hints in a Shiny application. It supports both
20418 static introductions in the UI, and programmatic introductions from the
20420 ;; The intro.js library is licensed under Expat.
20421 (license (list license:agpl3+ license:expat))))
20423 (define-public r-sysfonts
20425 (name "r-sysfonts")
20430 (uri (cran-uri "sysfonts" version))
20433 "1fhf0x5sqx3mv72j9d0clkq1qzqiqxbxn1h808f7ccf0mb04v43y"))))
20434 (properties `((upstream-name . "sysfonts")))
20435 (build-system r-build-system)
20437 (list freetype libpng zlib))
20440 (home-page "https://github.com/yixuan/sysfonts")
20441 (synopsis "Loading fonts into R")
20443 "This is a package to simplify loading of system fonts and Google Fonts
20444 into R, in order to support other packages.")
20445 (license license:gpl2)))
20447 (define-public r-showtextdb
20449 (name "r-showtextdb")
20454 (uri (cran-uri "showtextdb" version))
20457 "0hlnc3fhgrdkd46n7hb6id0gg1v0bf8s4679nrr7rchyp455szq2"))))
20458 (properties `((upstream-name . "showtextdb")))
20459 (build-system r-build-system)
20462 (home-page "https://cran.r-project.org/web/packages/showtextdb/")
20463 (synopsis "Font files for the 'showtext' package")
20465 "This package provides font files that can be used by the @code{showtext}
20467 (license license:asl2.0)))
20469 (define-public r-showtext
20471 (name "r-showtext")
20476 (uri (cran-uri "showtext" version))
20479 "1gvj32wrs5q31bmg5dy6n85d0igm3jhkldhdv8kscw0pfrk89y36"))))
20480 (properties `((upstream-name . "showtext")))
20481 (build-system r-build-system)
20483 (list freetype libpng zlib))
20485 (list r-showtextdb r-sysfonts))
20487 (list pkg-config r-knitr))
20488 (home-page "https://github.com/yixuan/showtext")
20489 (synopsis "Using fonts more easily in R graphs")
20491 "This package aims to make it easy to use various types of
20492 fonts (TrueType, OpenType, Type 1, web fonts, etc.) in R graphs, and supports
20493 most output formats of R graphics including PNG, PDF and SVG. Text glyphs
20494 will be converted into polygons or raster images, hence after the plot has
20495 been created, it no longer relies on the font files. No external software
20496 such as Ghostscript is needed to use this package.")
20497 (license license:asl2.0)))
20499 (define-public r-emojifont
20501 (name "r-emojifont")
20506 (uri (cran-uri "emojifont" version))
20509 "1hhrwilv36hd9gs1kcl2zsi6519md0h9aixjrm6lfclxvz8r6k1i"))))
20510 (properties `((upstream-name . "emojifont")))
20511 (build-system r-build-system)
20513 (list r-ggplot2 r-proto r-showtext r-sysfonts))
20516 (home-page "https://guangchuangyu.github.io/emojifont")
20517 (synopsis "Emoji and Font Awesome in R graphics")
20519 "This package enables the use of emoji and the Font Awesome glyphs in
20520 both base and ggplot2 graphics.")
20521 (license license:artistic2.0)))
20523 (define-public r-abstractr
20525 (name "r-abstractr")
20530 (uri (cran-uri "abstractr" version))
20533 "1ymwp7syrynwd4i8aj2x5n8jdi9d96fjzl6jb09n0bnr5fgl7vig"))))
20534 (properties `((upstream-name . "abstractr")))
20535 (build-system r-build-system)
20537 (list r-colourpicker
20544 (home-page "https://matt-kumar.shinyapps.io/portfolio")
20545 (synopsis "R-Shiny application for creating visual abstracts")
20547 "This package provides an R Shiny application to create visual abstracts
20548 for original research. A variety of user defined options and formatting are
20550 (license license:gpl3)))
20552 (define-public r-qgam
20559 (uri (cran-uri "qgam" version))
20562 "1jyamamdffaks89rspyhmg18b4iik0nb1j0vgqzvfnm890514cvn"))))
20563 (properties `((upstream-name . "qgam")))
20564 (build-system r-build-system)
20566 (list r-doparallel r-mgcv r-plyr r-shiny))
20567 (native-inputs (list r-knitr))
20568 (home-page "https://cran.r-project.org/web/packages/qgam/")
20569 (synopsis "Smooth additive quantile regression models")
20571 "This package provides smooth additive quantile regression models, fitted
20572 using the methods of Fasiolo et al. (2017). Differently from @code{quantreg},
20573 the smoothing parameters are estimated automatically by marginal loss
20574 minimization, while the regression coefficients are estimated using either
20575 PIRLS or Newton algorithm. The learning rate is determined so that the
20576 Bayesian credible intervals of the estimated effects have approximately the
20577 correct coverage. The main function is @code{qgam()} which is similar to
20578 @code{gam()} in the @code{mgcv} package, but fits non-parametric quantile
20579 regression models.")
20580 (license license:gpl2+)))
20582 (define-public r-abtest
20589 (uri (cran-uri "abtest" version))
20592 "0jz2ry5364p8h8xlk5a5sycn8xlpxd1iasfg99bcr4jqzd92jfqg"))))
20593 (properties `((upstream-name . "abtest")))
20594 (build-system r-build-system)
20604 (home-page "https://cran.r-project.org/web/packages/abtest/")
20605 (synopsis "Bayesian A/B testing")
20607 "This package provides functions for Bayesian A/B testing including prior
20608 elicitation options based on Kass and Vaidyanathan (1992)
20609 @url{doi:10.1111/j.2517-6161.1992.tb01868.x}.")
20610 (license license:gpl2+)))
20612 (define-public r-reldist
20619 (uri (cran-uri "reldist" version))
20622 "0i04d6w3r6fzm4bykz6lnnh6dngmd61v5wlpli70r3fzdzhi7fji"))))
20623 (properties `((upstream-name . "reldist")))
20624 (build-system r-build-system)
20626 (list r-densestbayes r-hmisc r-mgcv))
20627 (home-page "http://www.stat.ucla.edu/~handcock/RelDist")
20628 (synopsis "Relative distribution methods")
20630 "This package provides tools for the comparison of distributions. This
20631 includes nonparametric estimation of the relative distribution PDF and CDF and
20632 numerical summaries as described in \"Relative Distribution Methods in the
20633 Social Sciences\" by Mark S. Handcock and Martina Morris, Springer-Verlag,
20634 1999, Springer-Verlag, ISBN 0387987789.")
20635 ;; See also https://cran.r-project.org/web/packages/reldist/LICENSE for
20636 ;; attribution requirements.
20637 (license license:gpl3)))
20639 (define-public r-accept
20646 (uri (cran-uri "accept" version))
20649 "0qn4lm6bk0z2iijwsfbymx1c9y39988fw124ncgmlrgw5kv80b7x"))))
20650 (properties `((upstream-name . "accept")))
20651 (build-system r-build-system)
20653 (list r-dplyr r-reldist))
20654 (home-page "https://cran.r-project.org/web/packages/accept/")
20655 (synopsis "Acute COPD Exacerbation Prediction Tool (ACCEPT)")
20657 "This package allows clinicians to predict the rate and severity of
20658 future acute exacerbation in @dfn{Chronic Obstructive Pulmonary
20659 Disease} (COPD) patients, based on the clinical prediction model published in
20660 Adibi et al. (2019) @url{doi:10.1101/651901}.")
20661 (license license:gpl3)))
20663 (define-public r-smpracticals
20665 (name "r-smpracticals")
20670 (uri (cran-uri "SMPracticals" version))
20673 "0zxq84f9i3b86xx6msb25b61gyj9k09iab2b7wg4d93yas9qzayf"))))
20674 (properties `((upstream-name . "SMPracticals")))
20675 (build-system r-build-system)
20677 (list r-ellipse r-mass r-nlme r-survival))
20678 (home-page "http://statwww.epfl.ch/davison/SM/")
20679 (synopsis "Practicals for use with Davison (2003) Statistical Models")
20681 "This package contains the datasets and a few functions for use with the
20682 practicals outlined in Appendix A of the book Statistical Models (Davison,
20683 2003, Cambridge University Press). The practicals themselves can be found at
20684 @url{http://statwww.epfl.ch/davison/SM/}.")
20685 (license license:gpl2+)))
20687 (define-public r-fgui
20694 (uri (cran-uri "fgui" version))
20697 "024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"))))
20698 (properties `((upstream-name . "fgui")))
20699 (build-system r-build-system)
20701 "https://sites.google.com/site/thomashoffmannproject/software/fgui")
20702 (synopsis "Create GUI for R functions")
20704 "Rapidly create a GUI for a function you created by automatically
20705 creating widgets for arguments of the function. This package automatically
20706 parses help routines for context-sensitive help to these arguments. The
20707 interface is essentially a wrapper to some Tcl/Tk routines to both simplify
20708 and facilitate GUI creation. More advanced Tcl/Tk routines/GUI objects can be
20709 incorporated into the interface for greater customization for the more
20711 ;; Any version of the GPL.
20712 (license (list license:gpl2+ license:gpl3+))))
20714 (define-public r-tcltk2
20721 (uri (cran-uri "tcltk2" version))
20724 "1ibxld379600xx7kiqq3fck083s8psry12859980218rnzikl65d"))))
20725 (properties `((upstream-name . "tcltk2")))
20726 (build-system r-build-system)
20729 (home-page "https://www.sciviews.org/SciViews-R")
20730 (synopsis "Tcl/Tk additions")
20732 "This package provides a series of additional Tcl commands and Tk widgets
20733 with style and various functions to supplement the tcltk package")
20734 (license license:lgpl3)))
20736 (define-public r-accrual
20743 (uri (cran-uri "accrual" version))
20746 "11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"))))
20747 (properties `((upstream-name . "accrual")))
20748 (build-system r-build-system)
20750 (list r-fgui r-smpracticals r-tcltk2))
20751 (home-page "https://cran.r-project.org/web/packages/accrual/")
20752 (synopsis "Bayesian accrual prediction")
20754 "Subject recruitment for medical research is challenging. Slow patient
20755 accrual leads to delay in research. Accrual monitoring during the process of
20756 recruitment is critical. Researchers need reliable tools to manage the
20757 accrual rate. This package provides an implementation of a Bayesian method
20758 that integrates researcher's experience on previous trials and data from the
20759 current study, providing reliable prediction on accrual rate for clinical
20760 studies. It provides functions for Bayesian accrual prediction which can be
20761 easily used by statisticians and clinical researchers.")
20762 (license license:gpl2)))
20764 (define-public r-accrued
20771 (uri (cran-uri "accrued" version))
20774 "05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"))))
20775 (properties `((upstream-name . "accrued")))
20776 (build-system r-build-system)
20777 (home-page "https://cran.r-project.org/web/packages/accrued/")
20778 (synopsis "Data quality visualization tools for partially accruing data")
20780 "This is a package for visualizing data quality of partially accruing
20782 (license license:gpl3)))
20784 (define-public r-mda
20791 (uri (cran-uri "mda" version))
20794 "1hq0zhhz9klmp4zcr1w8hyn7s1h9kfg57d2l2mfm7psx459j0krl"))))
20795 (properties `((upstream-name . "mda")))
20796 (build-system r-build-system)
20797 (propagated-inputs (list r-class))
20798 (native-inputs (list gfortran))
20799 (home-page "https://cran.r-project.org/web/packages/mda/")
20800 (synopsis "Mixture and flexible discriminant analysis")
20802 "This is a package for mixture and flexible discriminant analysis,
20803 @dfn{multivariate adaptive regression splines} (MARS), BRUTO, and so on.")
20804 (license license:gpl2)))
20806 (define-public r-elasticnet
20808 (name "r-elasticnet")
20813 (uri (cran-uri "elasticnet" version))
20816 "0nxcw06d0cp2mbqzg2fm9yys5xm6xx7bfcfvr0avcs8afkvz29j8"))))
20817 (properties `((upstream-name . "elasticnet")))
20818 (build-system r-build-system)
20821 (home-page "http://users.stat.umn.edu/~zouxx019/")
20822 (synopsis "Elastic-Net for sparse estimation and sparse PCA")
20824 "This package provides functions for fitting the entire solution path of
20825 the Elastic-Net and also provides functions for estimating sparse Principal
20826 Components. The Lasso solution paths can be computed by the same function.")
20827 (license license:gpl2+)))
20829 (define-public r-sparselda
20831 (name "r-sparselda")
20836 (uri (cran-uri "sparseLDA" version))
20839 "1k3sw9kc40yxnfss4vrsx34qxmv8ssddyhbfjhxrdldvblhbwchb"))))
20840 (properties `((upstream-name . "sparseLDA")))
20841 (build-system r-build-system)
20843 (list r-elasticnet r-mass r-mda))
20844 (home-page "https://www.imm.dtu.dk/~lkhc/")
20845 (synopsis "Sparse discriminant analysis")
20847 "This package performs sparse linear discriminant analysis for Gaussians
20848 and mixture of Gaussian models.")
20849 (license license:gpl2+)))
20851 (define-public r-accsda
20858 (uri (cran-uri "accSDA" version))
20861 "0sgxy5y8kkc1n35657kifwfjsba7y5m1vbr7rkk5lmbpkzahqm61"))))
20862 (properties `((upstream-name . "accSDA")))
20863 (build-system r-build-system)
20871 (home-page "https://github.com/gumeo/accSDA/wiki")
20872 (synopsis "Accelerated sparse discriminant analysis")
20874 "This package provides an implementation of sparse linear discriminant
20875 analysis, which is a supervised classification method for multiple classes.
20876 Various novel optimization approaches to this problem are implemented
20877 including @dfn{alternating direction method of multipliers} (ADMM),
20878 @dfn{proximal gradient} (PG) and @dfn{accelerated proximal gradient} (APG).
20879 Functions for performing cross validation are also supplied along with basic
20880 prediction and plotting functions. @dfn{Sparse zero variance
20881 discriminant} (SZVD) analysis is also included in the package.")
20882 (license license:gpl2+)))
20884 (define-public r-ace2fastq
20886 (name "r-ace2fastq")
20891 (uri (cran-uri "ace2fastq" version))
20894 "09kk3yyqnr2xp820g0p3aai9a21figigjr9lxkr3zjq2d8gzwfic"))))
20895 (properties `((upstream-name . "ace2fastq")))
20896 (build-system r-build-system)
20899 (home-page "https://github.com/c5sire/ace2fastq")
20900 (synopsis "ACE file to FASTQ converter")
20902 "The ACE file format is used in genomics to store contigs from sequencing
20903 machines. This tools converts it into FASTQ format. Both formats contain the
20904 sequence characters and their corresponding quality information. Unlike the
20905 FASTQ file, the ACE file stores the quality values numerically. The
20906 conversion algorithm uses the standard Sanger formula. The package
20907 facilitates insertion into pipelines, and content inspection.")
20908 (license license:gpl3)))
20910 (define-public r-rngwell
20917 (uri (cran-uri "rngWELL" version))
20920 "0f1dxxaimfb0fww8ym9ciqf6q760ai46wxldl37m5mfpd57ca00c"))))
20921 (properties `((upstream-name . "rngWELL")))
20922 (build-system r-build-system)
20923 (home-page "https://cran.r-project.org/web/packages/rngWELL/")
20924 (synopsis "Toolbox for WELL random number generators")
20926 "This is a dedicated package to WELL pseudo random generators, which were
20927 introduced in Panneton et al. (2006), ``Improved Long-Period Generators Based
20928 on Linear Recurrences Modulo 2'', ACM Transactions on Mathematical Software.")
20929 (license license:bsd-3)))
20931 (define-public r-rnmf
20937 (uri (cran-uri "rNMF" version))
20940 "1nz6h0j5ywdh48m0swmhp34hbkycd7n13rclrxaw85qi9wc42597"))))
20941 (build-system r-build-system)
20943 (list r-knitr r-nnls))
20944 (home-page "https://cran.r-project.org/web/packages/rNMF/")
20945 (synopsis "Robust nonnegative matrix factorization")
20947 "This package provides an implementation of robust nonnegative matrix
20948 factorization (rNMF). The rNMF algorithm decomposes a nonnegative high
20949 dimension data matrix into the product of two low rank nonnegative matrices,
20950 while detecting and trimming outliers. The main function is @code{rnmf()}.
20951 The package also includes a visualization tool, @code{see()}, that arranges
20952 and prints vectorized images.")
20953 (license license:gpl2+)))
20955 (define-public r-randtoolbox
20957 (name "r-randtoolbox")
20962 (uri (cran-uri "randtoolbox" version))
20965 "1b9vjzqg014hxp1vfb62m01d7xim5vmpbyxzlbll49bqas0jx69h"))))
20966 (properties `((upstream-name . "randtoolbox")))
20967 (build-system r-build-system)
20972 (home-page "https://cran.r-project.org/web/packages/randtoolbox/")
20973 (synopsis "Toolbox for pseudo and quasi random number generation")
20975 "This package provides
20978 @item pseudo random generators, such as general linear
20979 congruential generators, multiple recursive generators and generalized
20980 feedback shift register (SF-Mersenne Twister algorithm and WELL
20983 @item quasi random generators, such as the Torus algorithm, the Sobol
20984 sequence, the Halton sequence (including the Van der Corput sequence), and
20986 @item some generator tests: the gap test, the serial test, the poker test.
20989 See e.g. Gentle (2003) @url{doi:10.1007/b97336}.")
20990 (license license:bsd-3)))
20992 (define-public r-lhs
20999 (uri (cran-uri "lhs" version))
21002 "1l861h76q5w0nbnbybhgg7hiw7fks677jakyd49n1whwvd48sfz4"))))
21003 (properties `((upstream-name . "lhs")))
21004 (build-system r-build-system)
21005 (propagated-inputs (list r-rcpp))
21008 (home-page "https://github.com/bertcarnell/lhs")
21009 (synopsis "Latin Hypercube Samples")
21011 "This package provides a number of methods for creating and augmenting
21012 Latin Hypercube Samples.")
21013 (license license:gpl3)))
21015 (define-public r-acebayes
21017 (name "r-acebayes")
21022 (uri (cran-uri "acebayes" version))
21025 "11bffz430gdfdaxjx3simig66vhynmx6l1ylac4q2shcmj52nx73"))))
21026 (properties `((upstream-name . "acebayes")))
21027 (build-system r-build-system)
21029 (list r-compare r-lhs r-randtoolbox r-rcpp r-rcpparmadillo))
21030 (home-page "https://cran.r-project.org/web/packages/acebayes/")
21031 (synopsis "Optimal Bayesian experimental design using the ACE algorithm")
21033 "Finding an optimal Bayesian experimental design involves maximizing an
21034 objective function given by the expectation of some appropriately chosen
21035 utility function with respect to the joint distribution of unknown
21036 quantities (including responses). This objective function is usually not
21037 available in closed form and the design space can be continuous and of high
21038 dimensionality. This package uses @dfn{Approximate Coordinate Exchange} (ACE)
21039 to maximise an approximation to the expectation of the utility function.")
21040 (license license:gpl2)))
21042 (define-public r-acet
21049 (uri (cran-uri "ACEt" version))
21052 "0b5lfpnppyk0237phr2aybhx29nhm8ngwk2qa1y4lshrvsw97wg4"))))
21053 (properties `((upstream-name . "ACEt")))
21054 (build-system r-build-system)
21056 (list r-bh r-mass r-rcpp r-rcpparmadillo))
21057 (home-page "https://cran.r-project.org/web/packages/ACEt/")
21058 (synopsis "Estimating dynamic heritability and twin model comparison")
21060 "This package supports twin models that are able to estimate the dynamic
21061 behaviour of the variance components in the classical twin models with respect
21062 to age using B-splines and P-splines.")
21063 (license license:gpl2+)))
21065 (define-public r-acfmperiod
21067 (name "r-acfmperiod")
21072 (uri (cran-uri "acfMPeriod" version))
21075 "1yww8isfrbs2v9s94hx7p2imyszcgadwafdgpj438n2ik0q6p9d5"))))
21076 (properties `((upstream-name . "acfMPeriod")))
21077 (build-system r-build-system)
21080 (home-page "https://cran.r-project.org/web/packages/acfMPeriod/")
21081 (synopsis "Estimation of the ACF from the M-periodogram")
21083 "This package support non-robust and robust computations of the sample
21084 autocovariance (ACOVF) and sample autocorrelation functions (ACF) of
21085 univariate and multivariate processes. The methodology consists in reversing
21086 the diagonalization procedure involving the periodogram or the
21087 cross-periodogram and the Fourier transform vectors, and, thus, obtaining the
21088 ACOVF or the ACF as discussed in Fuller (1995)
21089 @url{doi:10.1002/9780470316917}. The robust version is obtained by fitting
21090 robust M-regressors to obtain the M-periodogram or M-cross-periodogram as
21091 discussed in Reisen et al. (2017) @url{doi:10.1016/j.jspi.2017.02.008}.")
21092 (license license:gpl2+)))
21094 (define-public r-gamlss-data
21096 (name "r-gamlss-data")
21101 (uri (cran-uri "gamlss.data" version))
21104 "07mpdl4h9rwmnpl9jmsn6ig8ji11an6pyjfsvg62h2alapwbdcyv"))))
21105 (properties `((upstream-name . "gamlss.data")))
21106 (build-system r-build-system)
21107 (home-page "http://www.gamlss.org/")
21108 (synopsis "GAMLSS data")
21110 "This package provides data used as examples to demonstrate GAMLSS
21112 ;; Either version of the license
21113 (license (list license:gpl2 license:gpl3))))
21115 (define-public r-gamlss
21122 (uri (cran-uri "gamlss" version))
21125 "06mh00jjxnqwknbv777hawjk0zm81ixrp35fg59mrlqz8y3p2w3j"))))
21126 (properties `((upstream-name . "gamlss")))
21127 (build-system r-build-system)
21129 (list r-gamlss-data r-gamlss-dist r-mass r-nlme r-survival))
21130 (home-page "http://www.gamlss.org/")
21131 (synopsis "Generalized additive models for location scale and shape")
21133 "This package provides functions for fitting the generalized additive
21134 models for location scale and shape introduced by Rigby and
21135 Stasinopoulos (2005), @url{doi:10.1111/j.1467-9876.2005.00510.x}. The models
21136 use a distributional regression approach where all the parameters of the
21137 conditional distribution of the response variable are modelled using
21138 explanatory variables.")
21139 ;; Either version of the license
21140 (license (list license:gpl2 license:gpl3))))
21142 (define-public r-acid
21149 (uri (cran-uri "acid" version))
21152 "030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"))))
21153 (properties `((upstream-name . "acid")))
21154 (build-system r-build-system)
21156 (list r-gamlss r-gamlss-dist r-hmisc))
21157 (home-page "https://cran.r-project.org/web/packages/acid/")
21158 (synopsis "Analysing conditional income distributions")
21160 "This package provides functions for the analysis of income distributions
21161 for subgroups of the population as defined by a set of variables like age,
21162 gender, region, etc. This entails a Kolmogorov-Smirnov test for a mixture
21163 distribution as well as functions for moments, inequality measures, entropy
21164 measures and polarisation measures of income distributions. This package thus
21165 aides the analysis of income inequality by offering tools for the exploratory
21166 analysis of income distributions at the disaggregated level.")
21167 (license license:gpl3)))
21169 (define-public r-acm4r
21176 (uri (cran-uri "acm4r" version))
21179 "1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"))))
21180 (properties `((upstream-name . "acm4r")))
21181 (build-system r-build-system)
21182 (propagated-inputs (list r-mass))
21183 (home-page "https://cran.r-project.org/web/packages/acm4r/")
21184 (synopsis "Align-and-count method comparisons of RFLP data")
21186 "This is a package to compare sequence fragment lengths or molecular
21187 weights from pairs of lanes. The number of matching bands in the
21188 @dfn{Restriction Fragment Length Polymorphism} (RFLP) data is calculated using
21189 the align-and-count method.")
21190 ;; Any version of the GPL
21191 (license (list license:gpl2+ license:gpl3+))))
21193 (define-public r-filelock
21195 (name "r-filelock")
21200 (uri (cran-uri "filelock" version))
21203 "00ql5fw1hidpfnm0szaavf43ahmsnvdbi8i5lr1nrcc90yaiaadc"))))
21204 (properties `((upstream-name . "filelock")))
21205 (build-system r-build-system)
21206 (home-page "https://github.com/r-lib/filelock")
21207 (synopsis "Portable file locking")
21209 "This library lets you place an exclusive or shared lock on a file using
21210 the appropriate system call provided by the underlying operating system.")
21211 (license license:expat)))
21213 (define-public r-filematrix
21215 (name "r-filematrix")
21220 (uri (cran-uri "filematrix" version))
21223 "1v3aj1ng742msb0sfdnjsbqb508mqjf8jlq2v33vxldhradw5w0b"))))
21224 (properties `((upstream-name . "filematrix")))
21225 (build-system r-build-system)
21226 ;; These inputs are needed for vignettes
21228 (list r-knitr r-rmarkdown))
21229 (home-page "https://github.com/andreyshabalin/filematrix")
21230 (synopsis "File-backed matrix class with convenient read and write access")
21232 "This package provides an interface for working with large matrices
21233 stored in files, not in computer memory. It supports multiple non-character
21234 data types (double, integer, logical and raw) of various sizes (e.g. 8 and 4
21235 byte real values). Access to parts of the matrix is done by indexing, exactly
21236 as with usual R matrices. It supports very large matrices; the package has
21237 been tested on multi-terabyte matrices. It allows for more than 2^32 rows or
21238 columns, ad allows for quick addition of extra columns to a filematrix.")
21239 (license license:lgpl3)))
21241 (define-public r-acmeeqtl
21243 (name "r-acmeeqtl")
21248 (uri (cran-uri "ACMEeqtl" version))
21251 "049xjv2ym35bbn43zwi68cq27fwdh404vp0r2ca5gxgmmx8kj1cz"))))
21252 (properties `((upstream-name . "ACMEeqtl")))
21253 (build-system r-build-system)
21255 (list r-filematrix))
21256 (home-page "https://github.com/andreyshabalin/ACMEeqtl")
21257 (synopsis "Estimation of interpretable eQTL effect sizes")
21259 "This package provides a non-linear model, termed ACME, that reflects a
21260 parsimonious biological model for allelic contributions of cis-acting eQTLs.
21261 With non-linear least-squares algorithm the maximum likelihood parameters can
21262 be estimated. The ACME model provides interpretable effect size estimates and
21263 p-values with well controlled Type-I error.")
21264 (license license:lgpl3)))
21266 (define-public r-acmer
21273 (uri (cran-uri "acmeR" version))
21276 "000b2hqlhj93958nddw0fqb15ahigs08najv2miivym046x04mf7"))))
21277 (properties `((upstream-name . "acmeR")))
21278 (build-system r-build-system)
21279 (propagated-inputs (list r-foreign))
21280 (home-page "https://cran.r-project.org/web/packages/acmeR/")
21281 (synopsis "ACME estimator of bird and bat mortality by wind turbines")
21283 "This package provides an implementation of the ACME estimator, described
21284 in Wolpert (2015), ACME: A Partially Periodic Estimator of Avian & Chiropteran
21285 Mortality at Wind Turbines. Unlike most other models, this estimator supports
21286 decreasing-hazard Weibull model for persistence; decreasing search proficiency
21287 as carcasses age; variable bleed-through at successive searches; and interval
21288 mortality estimates. The package provides, based on search data, functions
21289 for estimating the mortality inflation factor in Frequentist and Bayesian
21291 (license license:expat)))
21293 (define-public r-r-huge
21300 (uri (cran-uri "R.huge" version))
21303 "13p558qalv60pgr24nsm6mi92ryj65rsbqa6pgdwy0snjqx12bgi"))))
21304 (properties `((upstream-name . "R.huge")))
21305 (build-system r-build-system)
21307 (list r-r-methodss3 r-r-oo r-r-utils))
21308 (home-page "https://github.com/HenrikBengtsson/R.huge")
21309 (synopsis "Methods for accessing huge amounts of data")
21311 "This is a deprecated package for accessing huge amounts of data.
21312 Cross-platform alternatives are the following packages: bigmemory (CRAN),
21313 ff (CRAN), or BufferedMatrix (Bioconductor). The main usage of it was inside
21314 the @code{aroma.affymetrix} package.")
21315 (license license:lgpl2.1+)))
21317 (define-public r-r-filesets
21319 (name "r-r-filesets")
21324 (uri (cran-uri "R.filesets" version))
21327 "08xv8b3c81nf54viyr3w912al18483k5gfnjpg7bxbdfk70dfzbh"))))
21328 (properties `((upstream-name . "R.filesets")))
21329 (build-system r-build-system)
21332 (modify-phases %standard-phases
21333 (add-after 'unpack 'set-HOME
21334 (lambda _ (setenv "HOME" "/tmp"))))))
21336 (list r-digest r-r-cache r-r-methodss3 r-r-oo r-r-utils))
21337 (home-page "https://github.com/HenrikBengtsson/R.filesets")
21338 (synopsis "Easy handling of and access to files")
21340 "This package provides classes and methods to locate, setup, subset,
21341 navigate and iterate file sets, i.e. sets of files located in one or more
21342 directories on the file system. The API is designed such that these classes
21343 can be extended via inheritance to provide a richer API for special file
21344 formats. Moreover, a specific name format is defined such that filenames and
21345 directories can be considered to have full names which consists of a name
21346 followed by comma-separated tags. This adds additional flexibility to
21347 identify file sets and individual files.")
21348 (license license:lgpl2.1+)))
21350 (define-public r-r-devices
21352 (name "r-r-devices")
21357 (uri (cran-uri "R.devices" version))
21360 "1djz6vm1b7sjvx1q319dl47gbnz9kvipaxcz9i0spyp094lv3m62"))))
21361 (properties `((upstream-name . "R.devices")))
21362 (build-system r-build-system)
21364 (list r-base64enc r-r-methodss3 r-r-oo r-r-utils))
21365 (home-page "https://github.com/HenrikBengtsson/R.devices")
21366 (synopsis "Unified handling of graphics devices")
21368 "This package provides functions for creating plots and image files in a
21369 unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.).
21370 Default device options as well as scales and aspect ratios are controlled in a
21371 uniform way across all device types. Switching output format requires minimal
21372 changes in code. This package is ideal for large-scale batch processing,
21373 because it will never leave open graphics devices or incomplete image files
21374 behind, even on errors or user interrupts.")
21375 (license license:lgpl2.1+)))
21377 (define-public r-acnr
21384 (uri (cran-uri "acnr" version))
21387 "087hq4i7jp67ba2finzsqjfnqbiprl33na6ryjv9zqzsdawj9cym"))))
21388 (properties `((upstream-name . "acnr")))
21389 (build-system r-build-system)
21390 (home-page "https://github.com/mpierrejean/acnr")
21391 (synopsis "Annotated copy-number regions")
21393 "This package provides SNP array data from different types of copy-number
21394 regions. These regions were identified manually by the authors of the package
21395 and may be used to generate realistic data sets with known truth.")
21396 (license license:lgpl2.1+)))
21398 (define-public r-acopula
21405 (uri (cran-uri "acopula" version))
21408 "0vvbbw8pfs9jwfz5c57lw48pr0qj661r0ys007q6zf9jmlrhx1ln"))))
21409 (properties `((upstream-name . "acopula")))
21410 (build-system r-build-system)
21411 (home-page "https://cran.r-project.org/web/packages/acopula/")
21412 (synopsis "Modelling dependence with multivariate Archimax copulas")
21414 "Archimax copulas are a mixture of Archimedean and EV copulas. This
21415 package provides definitions of several parametric families of generator and
21416 dependence function, computes CDF and PDF, estimates parameters, tests for
21417 goodness of fit, generates random sample and checks copula properties for
21418 custom constructs. In the 2-dimensional case explicit formulas for density
21419 are used, contrary to higher dimensions when all derivatives are linearly
21420 approximated. Several non-archimax families (normal, FGM, Plackett) are
21421 provided as well.")
21422 (license license:gpl2)))
21424 (define-public r-tuner
21427 (version "1.3.3.1")
21431 (uri (cran-uri "tuneR" version))
21434 "12nixpqrc5gp7p2clr7ia6jwb0jq2i3brlxiwlp00ixmnm5g1jyd"))))
21435 (properties `((upstream-name . "tuneR")))
21436 (build-system r-build-system)
21437 (propagated-inputs (list r-signal))
21438 (home-page "https://cran.r-project.org/web/packages/tuneR/")
21439 (synopsis "Analysis of music and speech")
21441 "This is a package for the analysis of music and speech. Analyze music
21442 and speech, extract features like MFCCs, handle wave files and their
21443 representation in various ways, read MP3, read MIDI, perform steps of a
21444 transcription, ...")
21445 ;; Either of these versions.
21446 (license (list license:gpl2 license:gpl3))))
21448 (define-public r-seewave
21455 (uri (cran-uri "seewave" version))
21458 "1szcvryvl4kb3av2pcvl14bz6whl7xrq4wb1ck6w7lfc4mrlirhh"))))
21459 (properties `((upstream-name . "seewave")))
21460 (build-system r-build-system)
21465 (home-page "http://rug.mnhn.fr/seewave")
21466 (synopsis "Sound analysis and synthesis")
21468 "This package provides functions for analysing, manipulating, displaying,
21469 editing and synthesizing time waves (particularly sound). This package
21470 processes time analysis (oscillograms and envelopes), spectral content,
21471 resonance quality factor, entropy, cross correlation and autocorrelation,
21472 zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D
21473 and 3D spectrograms and many other analyses.")
21474 (license license:gpl2+)))
21476 (define-public r-acousticndlcoder
21478 (name "r-acousticndlcoder")
21483 (uri (cran-uri "AcousticNDLCodeR" version))
21486 "1fgzgwanpv2pzy74xdk3hamc44p8qch467wh163dxby8jr9ik0sb"))))
21488 `((upstream-name . "AcousticNDLCodeR")))
21489 (build-system r-build-system)
21491 (list r-seewave r-tuner r-zoo))
21492 (home-page "https://cran.r-project.org/web/packages/AcousticNDLCodeR/")
21493 (synopsis "Coding sound files for use with NDL")
21495 "Make acoustic cues to use with the R package @code{ndl}.
21496 The package implements functions used in the PLoS ONE paper \"Words from
21497 spontaneous conversational speech can be recognized with human-like accuracy
21498 by an error-driven learning algorithm that discriminates between meanings
21499 straight from smart acoustic features, bypassing the phoneme as recognition
21500 unit.\" @url{doi:10.1371/journal.pone.0174623}")
21501 (license license:gpl2+)))
21503 (define-public r-acp
21510 (uri (cran-uri "acp" version))
21513 "0lcwbjcyyr32m6qjmjqh25qjwrbyqj1n092xhgbhxzd8fslppnmn"))))
21514 (properties `((upstream-name . "acp")))
21515 (build-system r-build-system)
21517 (list r-quantmod r-tseries))
21518 (home-page "https://cran.r-project.org/web/packages/acp/")
21519 (synopsis "Autoregressive conditional Poisson")
21521 "This package supports the analysis of count data exhibiting
21522 autoregressive properties, using the @dfn{Autoregressive Conditional Poisson}
21523 model (ACP(p,q)) proposed by Heinen (2003).")
21524 (license license:gpl2)))
21526 (define-public r-ada
21533 (uri (cran-uri "ada" version))
21536 "1h3a07czp0w3hrhjcg1fz721y8vsfclzqi3rq8qfzgpfb4h1f06r"))))
21537 (properties `((upstream-name . "ada")))
21538 (build-system r-build-system)
21539 (propagated-inputs (list r-rpart))
21540 (home-page "https://cran.r-project.org/web/packages/ada/")
21541 (synopsis "Stochastic boosting")
21543 "This package provides a straightforward, well-documented, and broad
21544 boosting routine for classification, ideally suited for small to
21545 moderate-sized data sets. It performs discrete, real, and gentle boost under
21546 both exponential and logistic loss on a given data set.")
21547 ;; Any version of the GPL.
21548 (license (list license:gpl2+ license:gpl3+))))
21550 (define-public r-genalg
21557 (uri (cran-uri "genalg" version))
21560 "1wzfamq8k5yhwbdx0wy1w5bks93brj0p890xxc4yqrja4w38ja3s"))))
21561 (properties `((upstream-name . "genalg")))
21562 (build-system r-build-system)
21563 (home-page "https://github.com/egonw/genalg")
21564 (synopsis "R based genetic algorithm")
21566 "This package provides an R based genetic algorithm for binary and
21567 floating point chromosomes.")
21568 (license license:gpl2)))
21570 (define-public r-kernelfactory
21572 (name "r-kernelfactory")
21577 (uri (cran-uri "kernelFactory" version))
21580 "001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"))))
21581 (properties `((upstream-name . "kernelFactory")))
21582 (build-system r-build-system)
21584 (list r-auc r-genalg r-kernlab r-randomforest))
21585 (home-page "https://cran.r-project.org/web/packages/kernelFactory/")
21586 (synopsis "Ensemble of kernel machines")
21588 "Kernel factory is an ensemble method where each base classifier (random
21589 forest) is fit on the kernel matrix of a subset of the training data.")
21590 (license license:gpl2+)))
21592 (define-public r-dummies
21599 (uri (cran-uri "dummies" version))
21602 "01f84crqx17xd6xy55qxlvsj3knm8lhw7jl26p2rh2w3y0nvqlbm"))))
21603 (properties `((upstream-name . "dummies")))
21604 (build-system r-build-system)
21605 (home-page "https://decisionpatterns.com")
21606 (synopsis "Create dummy/indicator variables flexibly and efficiently")
21608 "This package lets you expand factors, characters and other eligible
21609 classes into dummy/indicator variables.")
21610 (license license:gpl2+)))
21612 (define-public r-acrm
21619 (uri (cran-uri "aCRM" version))
21622 "0kzp568hd9c9a9qgniia5s5gv0q5f89xfvvwpzb197gqhs3x092v"))))
21623 (properties `((upstream-name . "aCRM")))
21624 (build-system r-build-system)
21626 (list r-ada r-dummies r-kernelfactory r-randomforest))
21627 (home-page "https://cran.r-project.org/web/packages/aCRM/")
21628 (synopsis "Convenience functions for analytical customer relationship management")
21630 "This package provides convenience functions for data preparation and
21631 modeling often used in @dfn{analytical customer relationship
21632 management} (aCRM).")
21633 (license license:gpl2+)))
21635 (define-public r-tree
21641 (uri (cran-uri "tree" version))
21644 "13jwdxx3na16mly176n01zdkaqn4a8x9fc43rq5xx5vx31drkkr1"))))
21645 (build-system r-build-system)
21646 (home-page "https://cran.r-project.org/web/packages/tree/")
21647 (synopsis "Classification and regression trees")
21648 (description "This package provides procedures to work with classification
21649 and regression trees.")
21650 (license license:gpl2+)))
21652 (define-public r-treeclust
21654 (name "r-treeclust")
21659 (uri (cran-uri "treeClust" version))
21662 "1s7kh6q0bkixsygrip95zf1bi10ihddsa5lq9dfxd68yh8rsby6z"))))
21663 (properties `((upstream-name . "treeClust")))
21664 (build-system r-build-system)
21666 (list r-cluster r-rpart))
21667 (home-page "https://cran.r-project.org/web/packages/treeClust/")
21668 (synopsis "Cluster distances through trees")
21670 "This package provides tools to create a measure of inter-point
21671 dissimilarity useful for clustering mixed data, and, optionally, perform the
21673 (license license:gpl2+)))
21675 (define-public r-acrosstic
21677 (name "r-acrosstic")
21682 (uri (cran-uri "AcrossTic" version))
21685 "03180h79jhjd66ibrnsfp3yyp2jlfysp7cymw46phzj2palghsc0"))))
21686 (properties `((upstream-name . "AcrossTic")))
21687 (build-system r-build-system)
21689 (list r-lpsolve r-treeclust))
21690 (home-page "https://cran.r-project.org/web/packages/AcrossTic/")
21691 (synopsis "Cost-minimal regular spanning subgraph with TreeClust")
21693 "This is a package for constructing minimum-cost regular spanning
21694 subgraph as part of a non-parametric two-sample test for equality of
21696 (license license:gpl2+)))
21698 (define-public r-acrt
21705 (uri (cran-uri "acrt" version))
21708 "0y9ndcq8ffpfrv7w9rikm4zn68jpsj6baqisq9kp2433xrwzdb6s"))))
21709 (properties `((upstream-name . "acrt")))
21710 (build-system r-build-system)
21712 (list r-rcpp r-rcppeigen r-sandwich))
21713 (home-page "https://cran.r-project.org/web/packages/acrt/")
21714 (synopsis "Autocorrelation robust testing")
21716 "This package provides functions for testing affine hypotheses on the
21717 regression coefficient vector in regression models with autocorrelated
21719 (license license:gpl2)))
21721 (define-public r-acs
21728 (uri (cran-uri "acs" version))
21731 "0ajw9rf8l8akcvgqvbxjvryc6wjx74521xyxswz2b0bky3m6kah5"))))
21732 (properties `((upstream-name . "acs")))
21733 (build-system r-build-system)
21735 (list r-httr r-plyr r-rcpp r-stringr r-xml))
21736 (home-page "https://dusp.mit.edu/faculty/ezra-haber-glenn")
21737 (synopsis "Work with data from the US Census")
21739 "This package provides a general toolkit for downloading, managing,
21740 analyzing, and presenting data from the
21741 @url{https://www.census.gov/data/developers/data-sets.html, U.S. Census},
21742 including SF1 (Decennial short-form), SF3 (Decennial long-form), and the
21743 American Community Survey (ACS). Confidence intervals provided with ACS data
21744 are converted to standard errors to be bundled with estimates in complex
21745 @code{acs} objects. The package provides new methods to conduct standard
21746 operations on @code{acs} objects and present/plot data in statistically
21747 appropriate ways.")
21748 (license license:gpl3)))
21750 (define-public r-acss-data
21752 (name "r-acss-data")
21757 (uri (cran-uri "acss.data" version))
21760 "09kl4179ipr8bq19g89xcdi1xxs397zcx5cvgp6viy8gn687ilgv"))))
21761 (properties `((upstream-name . "acss.data")))
21762 (build-system r-build-system)
21763 (home-page "http://complexitycalculator.com/methodology.html")
21764 (synopsis "Data for algorithmic complexity of short strings")
21766 "This is a data only package providing the algorithmic complexity of
21767 short strings, computed using the coding theorem method. For a given set of
21768 symbols in a string, all possible or a large number of random samples of
21769 Turing machines with a given number of states (e.g., 5) and number of symbols
21770 corresponding to the number of symbols in the strings were simulated until
21771 they reached a halting state or failed to end. This package contains data on
21772 4.5 million strings from length 1 to 12 simulated on Turing machines with 2,
21773 4, 5, 6, and 9 symbols. The complexity of the string corresponds to the
21774 distribution of the halting states.")
21775 (license license:gpl2+)))
21777 (define-public r-acss
21784 (uri (cran-uri "acss" version))
21787 "0cqa60544f58l5qd7h6xmsir40b9hqnq6pqgd5hfx2j2l5n7qhmk"))))
21788 (properties `((upstream-name . "acss")))
21789 (build-system r-build-system)
21791 (list r-acss-data r-zoo))
21792 (home-page "http://complexitycalculator.com/methodology.html")
21793 (synopsis "Algorithmic complexity for short strings")
21795 "The main purpose of this package is to provide the algorithmic
21796 complexity for short strings, an approximation of the Kolmogorov Complexity of
21797 a short string using the coding theorem method. While the database containing
21798 the complexity is provided in the data only package @code{acss.data}, this
21799 package provides functions accessing the data such as @code{prob_random}
21800 returning the posterior probability that a given string was produced by a
21801 random process. In addition, two traditional (but problematic) measures of
21802 complexity are also provided: entropy and change complexity.")
21803 (license license:gpl2+)))
21805 (define-public r-acswr
21812 (uri (cran-uri "ACSWR" version))
21815 "195vjrkang5cl7gwsna0aq4p0h4jym9xg9yh94bnf8vq6wf8j83n"))))
21816 (properties `((upstream-name . "ACSWR")))
21817 (build-system r-build-system)
21820 (home-page "https://cran.r-project.org/web/packages/ACSWR/")
21821 (synopsis "Companion package for the book \"A Course in Statistics with R\"")
21823 "This is a companion package for the book \"A Course in Statistics with
21824 R\" (ISBN 978-1-119-15272-9.)")
21825 (license license:gpl2)))
21827 (define-public r-alabama
21830 (version "2015.3-1")
21834 (uri (cran-uri "alabama" version))
21837 "0mlgk929gdismikwx4k2ndqq57nnqj7mlgvd3479b214hksgq036"))))
21838 (properties `((upstream-name . "alabama")))
21839 (build-system r-build-system)
21840 (propagated-inputs (list r-numderiv))
21841 (home-page "https://cran.r-project.org/web/packages/alabama/")
21842 (synopsis "Constrained nonlinear optimization")
21844 "Alabama stands for Augmented Lagrangian Adaptive Barrier Minimization
21845 Algorithm; it is used for optimizing smooth nonlinear objective functions with
21846 constraints. Linear or nonlinear equality and inequality constraints are
21848 (license license:gpl2+)))
21850 (define-public r-gdina
21857 (uri (cran-uri "GDINA" version))
21860 "1slq1npsq8s8aghnrpm6vvc6kxj4svz0kr2x0akblndrcr25wxjr"))))
21861 (properties `((upstream-name . "GDINA")))
21862 (build-system r-build-system)
21875 (home-page "https://github.com/Wenchao-Ma/GDINA")
21876 (synopsis "Generalized DINA model framework")
21878 "This package provides a set of psychometric tools for cognitive
21879 diagnosis modeling based on the generalized deterministic inputs, noisy and
21880 gate (G-DINA) model by de la Torre (2011) @url{doi:10.1007/s11336-011-9207-7}
21881 and its extensions, including the sequential G-DINA model by Ma and de la
21882 Torre (2016) @url{doi:10.1111/bmsp.12070} for polytomous responses, and the
21883 polytomous G-DINA model by Chen and de la Torre
21884 @url{doi:10.1177/0146621613479818} for polytomous attributes. Joint attribute
21885 distribution can be independent, saturated, higher-order, loglinear smoothed
21886 or structured. Q-matrix validation, item and model fit statistics, model
21887 comparison at test and item level and differential item functioning can also
21888 be conducted. A graphical user interface is also provided.")
21889 (license license:gpl3)))
21891 (define-public r-actcd
21898 (uri (cran-uri "ACTCD" version))
21901 "0mzjxxr2zfdidw8ibh6w8mvpkw3q3nvngqi05g9ind26ckvk053p"))))
21902 (properties `((upstream-name . "ACTCD")))
21903 (build-system r-build-system)
21905 (list r-gdina r-r-methodss3))
21908 (home-page "https://cran.r-project.org/web/packages/ACTCD/")
21909 (synopsis "Asymptotic classification theory for cognitive diagnosis")
21911 "This is a package supporting cluster analysis for cognitive diagnosis
21912 based on the Asymptotic Classification Theory (Chiu, Douglas & Li, 2009;
21913 @url{doi:10.1007/s11336-009-9125-0}). Given the sample statistic of
21914 sum-scores, cluster analysis techniques can be used to classify examinees into
21915 latent classes based on their attribute patterns. In addition to the
21916 algorithms used to classify data, three labeling approaches are proposed to
21917 label clusters so that examinees' attribute profiles can be obtained.")
21918 (license license:gpl2+)))
21920 (define-public r-ineq
21927 (uri (cran-uri "ineq" version))
21930 "09fsxyrh0j7mwmb5hkhmrzgcy7kf85jxkh7zlwpgqgcsyl1n91z0"))))
21931 (properties `((upstream-name . "ineq")))
21932 (build-system r-build-system)
21933 (home-page "https://cran.r-project.org/web/packages/ineq/")
21934 (synopsis "Measuring inequality, concentration, and poverty")
21936 "This package provides tools for measuring inequality, concentration, and
21937 poverty measures. It provides both empirical and theoretical Lorenz curves.")
21938 ;; Either of these two versions.
21939 (license (list license:gpl2 license:gpl3))))
21941 (define-public r-actfrag
21948 (uri (cran-uri "ActFrag" version))
21951 "08r3gwjz4fkyy85dxqix0ffm5xyq45032qv3snnzxnlqxslxbqn1"))))
21952 (properties `((upstream-name . "ActFrag")))
21953 (build-system r-build-system)
21955 (list r-accelerometry r-dplyr r-ineq r-survival r-tidyr))
21956 (home-page "https://github.com/junruidi/ActFrag")
21957 (synopsis "Activity fragmentation metrics extraction")
21959 "This package provides functions to extract commonly used fragmentation
21960 metrics to quantify time accumulation strategies based on minute level
21961 actigraphy-measured activity counts data.")
21962 (license license:gpl3)))
21964 (define-public r-ash
21971 (uri (cran-uri "ash" version))
21974 "1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"))))
21975 (properties `((upstream-name . "ash")))
21976 (build-system r-build-system)
21977 (native-inputs (list gfortran))
21978 (home-page "https://cran.r-project.org/web/packages/ash/")
21979 (synopsis "David Scott's ASH routines")
21981 "This package provides David Scott's ASH routines ported from S-PLUS to
21983 (license license:gpl2+)))
21985 (define-public r-hdrcde
21992 (uri (cran-uri "hdrcde" version))
21995 "16qlk44cjvn2s0vzaf915df65ksdx20dbxhy7fpdqins46hccha3"))))
21996 (properties `((upstream-name . "hdrcde")))
21997 (build-system r-build-system)
22005 (native-inputs (list gfortran))
22006 (home-page "http://pkg.robjhyndman.com/hdrcde")
22007 (synopsis "Highest density regions and conditional density estimation")
22009 "This is a package for the computation of highest density regions in one
22010 and two dimensions, kernel estimation of univariate density functions
22011 conditional on one covariate, and multimodal regression.")
22012 (license license:gpl3)))
22014 (define-public r-rainbow
22021 (uri (cran-uri "rainbow" version))
22024 "11vfcck17d2xjc049ci5i8l1nqv345anmd110gdz7654i1pj9lb3"))))
22025 (properties `((upstream-name . "rainbow")))
22026 (build-system r-build-system)
22034 (home-page "https://cran.r-project.org/web/packages/rainbow/")
22035 (synopsis "Bagplots, boxplots and rainbow plots for functional data")
22037 "This is a package for visualizing functional data and identifying
22038 functional outliers with bagplots, boxplots and rainbow plots.")
22039 (license license:gpl3)))
22041 (define-public r-fds
22048 (uri (cran-uri "fds" version))
22051 "1284vncixrzrz9x6b52gslrbrbia07sd0xac7nwdqhp5f5v5wfi0"))))
22052 (properties `((upstream-name . "fds")))
22053 (build-system r-build-system)
22055 (list r-rainbow r-rcurl))
22056 (home-page "https://cran.r-project.org/web/packages/fds/")
22057 (synopsis "Functional data sets")
22058 (description "This package contains a list of functional time series,
22059 sliced functional time series, and functional data sets. Functional time
22060 series is a special type of functional data observed over time. Sliced
22061 functional time series is a special type of functional time series with a time
22062 variable observed over time.")
22063 (license license:gpl2+)))
22065 (define-public r-fda
22072 (uri (cran-uri "fda" version))
22075 "0fm2vswc8fdi2p1axby0hjwh8m6lc1zrdikrpiamilr6w9m2zanw"))))
22076 (properties `((upstream-name . "fda")))
22077 (build-system r-build-system)
22079 (list r-desolve r-fds r-matrix))
22080 (home-page "https://www.functionaldata.org")
22081 (synopsis "Functional data analysis")
22083 "These functions were developed to support functional data analysis as
22084 described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data
22085 Analysis. The package includes data sets and script files working many
22087 (license license:gpl2+)))
22089 (define-public r-actigraphy
22091 (name "r-actigraphy")
22096 (uri (cran-uri "Actigraphy" version))
22099 "0bpmvszzv5fm72nar3wgnmfl5am7znqfajmlbv38ihkbi7jbwk20"))))
22100 (properties `((upstream-name . "Actigraphy")))
22101 (build-system r-build-system)
22104 (home-page "https://cran.r-project.org/web/packages/Actigraphy/")
22105 (synopsis "Actigraphy data analysis")
22107 "This package provides tools for functional linear modeling and analysis
22108 of actigraphy data.")
22109 (license license:asl2.0)))
22111 (define-public r-activedriver
22113 (name "r-activedriver")
22118 (uri (cran-uri "ActiveDriver" version))
22121 "10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"))))
22122 (properties `((upstream-name . "ActiveDriver")))
22123 (build-system r-build-system)
22126 (home-page "https://cran.r-project.org/web/packages/ActiveDriver/")
22127 (synopsis "Tools for finding cancer driver proteins")
22129 "This package provides a mutation analysis tool that discovers cancer
22130 driver genes with frequent mutations in protein signalling sites such as
22131 post-translational modifications (phosphorylation, ubiquitination, etc). The
22132 Poisson generalized linear regression model identifies genes where cancer
22133 mutations in signalling sites are more frequent than expected from the
22134 sequence of the entire gene. Integration of mutations with signalling
22135 information helps find new driver genes and propose candidate mechanisms to
22137 (license license:gpl2+)))
22139 (define-public r-activitycounts
22141 (name "r-activitycounts")
22146 (uri (cran-uri "activityCounts" version))
22149 "0zgxr2sk3a8kmygfxx1p5hnrfwdkxx7php6jlrhm8wv6052ck8jz"))))
22151 `((upstream-name . "activityCounts")))
22152 (build-system r-build-system)
22154 (list r-lubridate r-magrittr r-seewave r-signal r-tibble))
22155 (home-page "https://github.com/walkabillylab/activityCounts")
22156 (synopsis "Generate ActiLife counts")
22158 "ActiLife generates activity counts from data collected by Actigraph
22159 accelerometers. Actigraph is one of the most common research-grade
22160 accelerometers. There is considerable research validating and developing
22161 algorithms for human activity using ActiLife counts. Unfortunately, ActiLife
22162 counts are proprietary and difficult to implement if researchers use different
22163 accelerometer brands. The code creates ActiLife counts from raw acceleration
22164 data for different accelerometer brands.")
22165 (license license:gpl3)))
22167 (define-public r-activityindex
22169 (name "r-activityindex")
22174 (uri (cran-uri "ActivityIndex" version))
22177 "1zj2b6x31a1kxl80rarmkrlm7ack4154mrkbqs3fpi48zpmjbgd5"))))
22178 (properties `((upstream-name . "ActivityIndex")))
22179 (build-system r-build-system)
22181 (list r-data-table r-matrixstats r-r-utils))
22184 (home-page "https://cran.r-project.org/web/packages/ActivityIndex/")
22185 (synopsis "Activity Index calculation using raw accelerometry data")
22187 "This is a package to read raw accelerometry from GT3X+ accelerometry
22188 data and plain table data to calculate the Activity Index from Bai et
22189 al. (2016) @url{doi:10.1371/journal.pone.0160644}.")
22190 (license license:gpl3)))
22192 (define-public r-activpal
22194 (name "r-activpal")
22199 (uri (cran-uri "activPAL" version))
22202 "1h6hp5z89ji73gdzxy1dgbfwjysiy5lvcqh90xagpb7sa7ahs3na"))))
22203 (properties `((upstream-name . "activPAL")))
22204 (build-system r-build-system)
22212 (home-page "https://cran.r-project.org/web/packages/activPAL")
22213 (synopsis "Processing and chart generation from activPAL events files")
22215 "This package contains functions to generate pre-defined summary
22216 statistics from activPAL events files. The package also contains functions to
22217 produce informative graphics that visualize physical activity behaviour and
22218 trends. This includes generating graphs that align physical activity
22219 behaviour with additional time based observations described by other data
22220 sets, such as sleep diaries and continuous glucose monitoring data.")
22221 (license license:gpl3)))
22223 (define-public r-activpalprocessing
22225 (name "r-activpalprocessing")
22230 (uri (cran-uri "activpalProcessing" version))
22233 "1y0bjx2qx53iy930y9iww4q1yzjj8y16cwgixk1mq3w4g1f116d1"))))
22235 `((upstream-name . "activpalProcessing")))
22236 (build-system r-build-system)
22239 (home-page "https://cran.r-project.org/web/packages/activpalProcessing/")
22240 (synopsis "Process activPAL events files")
22242 "This package performs estimation of physical activity and sedentary
22243 behavior variables from activPAL events files.")
22244 ;; Either version of the GPL.
22245 (license (list license:gpl2 license:gpl3))))
22247 (define-public r-actogrammr
22249 (name "r-actogrammr")
22254 (uri (cran-uri "actogrammr" version))
22257 "1jzvarmd41yqlrkagzlc8m19n5mn0w0b36fy50lyvgrfsafjfbqa"))))
22258 (properties `((upstream-name . "actogrammr")))
22259 (build-system r-build-system)
22261 (list r-dplyr r-ggplot2 r-lubridate r-readr r-tidyr))
22262 (home-page "https://cran.r-project.org/web/packages/actogrammr/")
22263 (synopsis "Read in activity data and plot actograms")
22265 "Read in activity measurements from standard file formats used by
22266 circadian rhythm researchers, currently only ClockLab format, and process and
22267 plot the data. The central type of plot is the actogram, as first described
22268 in \"Activity and distribution of certain wild mice in relation to biotic
22269 communities\" by MS Johnson (1926) @url{doi:10.2307/1373575}.")
22270 (license license:gpl3)))
22272 (define-public r-expint
22279 (uri (cran-uri "expint" version))
22282 "0iai25cglcdnf44d2d1fz1xpw4q600my4zq4493fk4cs5673mlf7"))))
22283 (properties `((upstream-name . "expint")))
22284 (build-system r-build-system)
22285 (home-page "https://gitlab.com/vigou3/expint")
22286 (synopsis "Exponential integral and incomplete Gamma function")
22288 "This package provides the exponential integrals @code{E_1(x)},
22289 @code{E_2(x)}, @code{E_n(x)} and @code{Ei(x)}, and the incomplete gamma
22290 function @code{G(a, x)} defined for negative values of its first argument.
22291 The package also gives easy access to the underlying C routines through an
22292 API; see the package vignette for details.")
22293 (license license:gpl2+)))
22295 (define-public r-actuar
22302 (uri (cran-uri "actuar" version))
22305 "1avqgkls4xvwgfr6j7g2f7p474rlpi82q5aksw8nzf8wcyp7592f"))))
22306 (properties `((upstream-name . "actuar")))
22307 (build-system r-build-system)
22308 (propagated-inputs (list r-expint))
22309 (home-page "https://gitlab.com/vigou3/actuar")
22310 (synopsis "Actuarial functions and heavy tailed distributions")
22312 "This package provides functions and data sets for actuarial science:
22313 modeling of loss distributions; risk theory and ruin theory; simulation of
22314 compound models, discrete mixtures and compound hierarchical models;
22315 credibility theory. It boasts support for many additional probability
22316 distributions to model insurance loss amounts and loss frequency: 19
22317 continuous heavy tailed distributions; the Poisson-inverse Gaussian discrete
22318 distribution; zero-truncated and zero-modified extensions of the standard
22319 discrete distributions. It also supports phase-type distributions commonly
22320 used to compute ruin probabilities.")
22321 (license license:gpl2+)))
22323 (define-public r-bmp
22330 (uri (cran-uri "bmp" version))
22333 "0jd67r11bn98hjwgyr6gas423787xy7ji2hq7ay80blkkcj91xxx"))))
22334 (properties `((upstream-name . "bmp")))
22335 (build-system r-build-system)
22336 (home-page "https://cran.r-project.org/web/packages/bmp/")
22337 (synopsis "Read Bitmap (BMP) images")
22339 "This package provides pure R tools to read BMP format images. It is
22340 currently limited to 8 bit greyscale images and 24, 32 bit (A)RGB images.")
22341 (license license:gpl2+)))
22343 (define-public r-readbitmap
22345 (name "r-readbitmap")
22350 (uri (cran-uri "readbitmap" version))
22353 "14825906l326w59g6apy00j55jg3h5kx2r6s031f4gdkbrc7szbk"))))
22354 (properties `((upstream-name . "readbitmap")))
22355 (build-system r-build-system)
22357 (list libjpeg-turbo libpng))
22359 (list r-bmp r-jpeg r-png r-tiff))
22360 (home-page "https://github.com/jefferis/readbitmap")
22361 (synopsis "Unified interface to read bitmap images (BMP, JPEG, PNG, TIFF)")
22363 "This package provides tools to identify and read BMP, JPEG, PNG, and
22364 TIFF format bitmap images. Identification defaults to the use of the magic
22365 number embedded in the file rather than the file extension.")
22366 (license license:gpl2+)))
22368 (define-public r-imager
22371 (version "0.42.11")
22375 (uri (cran-uri "imager" version))
22378 "1a1jhmgrpv1d0fk14axj88qvxgb25bqnj65d60g1k985ipzvgy27"))))
22379 (properties `((upstream-name . "imager")))
22380 (build-system r-build-system)
22382 (list fftw libtiff libx11 zlib))
22394 (list pkg-config r-knitr))
22395 (home-page "https://dahtah.github.io/imager/")
22396 (synopsis "Image processing library")
22398 "This is a package for fast image processing for images in up to 4
22399 dimensions (two spatial dimensions, one time/depth dimension, one color
22400 dimension). It provides most traditional image processing tools (filtering,
22401 morphology, transformations, etc.) as well as various functions for easily
22402 analyzing image data using R. The package wraps @url{http://cimg.eu, CImg}, a
22403 simple, modern C++ library for image processing.")
22404 (license license:lgpl3)))
22406 (define-public r-acuityview
22408 (name "r-acuityview")
22413 (uri (cran-uri "AcuityView" version))
22416 "0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"))))
22417 (properties `((upstream-name . "AcuityView")))
22418 (build-system r-build-system)
22420 (list r-fftwtools r-imager r-plotrix))
22421 (home-page "https://cran.r-project.org/web/packages/AcuityView/")
22422 (synopsis "Display scenes as seen by an animal with less acute vision")
22424 "This package provides a simple method for representing a visual scene as
22425 it may be seen by an animal with less acute vision.")
22426 (license license:gpl2+)))
22428 (define-public r-caret
22435 (uri (cran-uri "caret" version))
22438 "1g36m06hp2fxxwv155bwbqlf97xhcia1lmg3axg6d74kgpns8lg8"))))
22439 (build-system r-build-system)
22454 (home-page "https://github.com/topepo/caret")
22455 (synopsis "Classification and regression training")
22457 "This package provides miscellaneous functions for training and plotting
22458 classification and regression models.")
22459 (license license:gpl2+)))
22461 (define-public r-adabag
22468 (uri (cran-uri "adabag" version))
22471 "109wrl1pwvmyv2l909hrvk7dg4aa9pv449mvdycp50zwrsw9w0a7"))))
22472 (properties `((upstream-name . "adabag")))
22473 (build-system r-build-system)
22475 (list r-caret r-doparallel r-foreach r-rpart))
22476 (home-page "https://cran.r-project.org/web/packages/adabag/")
22477 (synopsis "Multiclass AdaBoost.M1, SAMME and Bagging")
22479 "This package implements Freund and Schapire's Adaboost.M1 algorithm and
22480 Breiman's Bagging algorithm using classification trees as individual
22481 classifiers. Once these classifiers have been trained, they can be used to
22482 predict on new data. Also, cross validation estimation of the error can be
22484 (license license:gpl2+)))
22486 (define-public r-adagio
22493 (uri (cran-uri "adagio" version))
22496 "0ihv05402iq003m0338f85pnqnlnrmx0pf1mg8cz9sgi5h98mbnl"))))
22497 (properties `((upstream-name . "adagio")))
22498 (build-system r-build-system)
22501 (home-page "https://cran.r-project.org/web/packages/adagio/")
22502 (synopsis "Discrete and global optimization routines")
22504 "This package provides methods and algorithms for discrete optimization,
22505 e.g. knapsack and subset sum procedures, derivative-free Nelder-Mead and
22506 Hooke-Jeeves minimization, and some (evolutionary) global optimization
22508 (license license:gpl3+)))
22510 (define-public r-univoutl
22512 (name "r-univoutl")
22517 (uri (cran-uri "univOutl" version))
22520 "1hhpxrpmp2wbrynx9xjndnp2sccirgky2x6ksd6yk6phmk0rbzjp"))))
22521 (properties `((upstream-name . "univOutl")))
22522 (build-system r-build-system)
22524 (list r-hmisc r-robustbase))
22525 (home-page "https://github.com/marcellodo/univOutl")
22526 (synopsis "Detection of univariate outliers")
22528 "This package provides well-known outlier detection techniques in the
22529 univariate case. Methods to deal with skewed distribution are included too.
22530 The Hidiroglou-Berthelot (1986) method to search for outliers in ratios of
22531 historical data is implemented as well. When available, survey weights can be
22532 used in outliers detection.")
22533 (license license:gpl2+)))
22535 (define-public r-tolerance
22537 (name "r-tolerance")
22542 (uri (cran-uri "tolerance" version))
22545 "001snzr2ipag3zprynydlbi9prkjzrllc054qh7m0qwkb3r19jjd"))))
22546 (properties `((upstream-name . "tolerance")))
22547 (build-system r-build-system)
22549 (list r-mass r-rgl))
22550 (home-page "https://cran.r-project.org/web/packages/tolerance/")
22551 (synopsis "Statistical tolerance intervals and regions")
22553 "This package provides functions for estimating tolerance
22554 limits (intervals) for various univariate distributions (binomial, Cauchy,
22555 discrete Pareto, exponential, two-parameter exponential, extreme value,
22556 hypergeometric, Laplace, logistic, negative binomial, negative hypergeometric,
22557 normal, Pareto, Poisson-Lindley, Poisson, uniform, and Zipf-Mandelbrot),
22558 Bayesian normal tolerance limits, multivariate normal tolerance regions,
22559 nonparametric tolerance intervals, tolerance bands for regression
22560 settings (linear regression, nonlinear regression, nonparametric regression,
22561 and multivariate regression), and analysis of variance tolerance intervals.
22562 Visualizations are also available for most of these settings.")
22563 (license license:gpl2+)))
22565 (define-public r-additivitytests
22567 (name "r-additivitytests")
22572 (uri (cran-uri "additivityTests" version))
22575 "048ds90wqjdjy1nyhna3m06asdklbh8sx1n556kss2j1r1pma1sw"))))
22577 `((upstream-name . "additivityTests")))
22578 (build-system r-build-system)
22579 (home-page "https://github.com/simecek/additivityTests")
22580 (synopsis "Additivity tests in the two way Anova with single sub-class numbers")
22582 "This package provides an implementation of the Tukey, Mandel,
22583 Johnson-Graybill, LBI, Tusell and modified Tukey non-additivity tests.")
22584 (license license:gpl3)))
22586 (define-public r-flexclust
22588 (name "r-flexclust")
22593 (uri (cran-uri "flexclust" version))
22596 "0x7wxk8y46ndyz6fdacym0rd6p9wh3pcfr28chjcg5d7fm849zl2"))))
22597 (properties `((upstream-name . "flexclust")))
22598 (build-system r-build-system)
22600 (list r-class r-lattice r-modeltools))
22601 (home-page "https://cran.r-project.org/web/packages/flexclust/")
22602 (synopsis "Flexible cluster algorithms")
22604 "The main function @code{kcca} implements a general framework for
22605 k-centroids cluster analysis supporting arbitrary distance measures and
22606 centroid computation. Further cluster methods include hard competitive
22607 learning, neural gas, and QT clustering. There are numerous visualization
22608 methods for cluster results (neighborhood graphs, convex cluster hulls,
22609 barcharts of centroids, ...), and bootstrap methods for the analysis of
22610 cluster stability.")
22611 (license license:gpl2)))
22613 (define-public r-biclust
22620 (uri (cran-uri "biclust" version))
22623 "0lgyc2f04dhr65cwga78pradxsdzgjrpp8vphchqn60ab1z95dlp"))))
22624 (properties `((upstream-name . "biclust")))
22625 (build-system r-build-system)
22627 (list r-additivitytests
22634 (home-page "https://cran.r-project.org/web/packages/biclust/")
22635 (synopsis "BiCluster algorithms")
22637 "The main function @code{biclust()} provides several algorithms to find
22638 biclusters in two-dimensional data, spectral, plaid model, xmotifs, and bimax.
22639 In addition, the package provides methods for data
22640 preprocessing (normalization and discretization), visualization, and
22641 validation of bicluster solutions.")
22642 (license license:gpl3)))
22644 (define-public r-icge
22651 (uri (cran-uri "ICGE" version))
22654 "0w6hbi3h98q6gsxqbb43p95v6xykgrasxcjivwm8hw9fly4avxyi"))))
22655 (properties `((upstream-name . "ICGE")))
22656 (build-system r-build-system)
22658 (list r-cluster r-fastcluster r-mass))
22659 (home-page "https://cran.r-project.org/web/packages/ICGE/")
22660 (synopsis "Cluster estimation and identification of atypical units")
22662 "ICGE is a package that helps to estimate the number of real clusters in
22663 data as well as to identify atypical units. The underlying methods are based
22664 on distances rather than on unit x variables.")
22665 (license license:gpl2+)))
22667 (define-public r-depth
22670 (version "2.1-1.1")
22674 (uri (cran-uri "depth" version))
22677 "0szy0027nh4ps1z919i740i50app5q7cfyg1fj7pdyl45nbl8k6m"))))
22678 (properties `((upstream-name . "depth")))
22679 (build-system r-build-system)
22681 (list r-abind r-circular r-rgl))
22684 (home-page "https://cran.r-project.org/web/packages/depth/")
22685 (synopsis "Nonparametric depth functions for multivariate analysis")
22687 "This package provides tools for depth functions methodology applied to
22688 multivariate analysis. Besides allowing calculation of depth values and
22689 depth-based location estimators, the package includes functions or drawing
22690 contour plots and perspective plots of depth functions. Euclidean and
22691 spherical depths are supported.")
22692 (license license:gpl2)))
22694 (define-public r-archetypes
22696 (name "r-archetypes")
22697 (version "2.2-0.1")
22701 (uri (cran-uri "archetypes" version))
22704 "0ibxsr173ib77gjhid91m85s8gjii4mi2w3d52q5301igv20p7r0"))))
22705 (properties `((upstream-name . "archetypes")))
22706 (build-system r-build-system)
22708 (list r-modeltools r-nnls))
22709 (home-page "https://cran.r-project.org/web/packages/archetypes")
22710 (synopsis "Archetypal analysis")
22712 "The main function @code{archetypes} implements a framework for
22713 archetypal analysis supporting arbitrary problem solving mechanisms for the
22714 different conceptual parts of the algorithm.")
22715 (license license:gpl2+)))
22717 (define-public r-shapes
22724 (uri (cran-uri "shapes" version))
22727 "1p9fr95zk3q2v277c5ksb0nh26mcpzwjzjb2lmag51z6hck8cb66"))))
22728 (properties `((upstream-name . "shapes")))
22729 (build-system r-build-system)
22731 (list r-mass r-minpack-lm r-rgl r-scatterplot3d))
22732 (home-page "http://www.maths.nottingham.ac.uk/~ild/shapes")
22733 (synopsis "Statistical shape analysis")
22735 "This package provides routines for the statistical analysis of landmark
22736 shapes, including Procrustes analysis, graphical displays, principal
22737 components analysis, permutation and bootstrap tests, thin-plate spline
22738 transformation grids and comparing covariance matrices. See Dryden, I.L. and
22739 Mardia, K.V. (2016). Statistical shape analysis, with Applications in R (2nd
22740 Edition), John Wiley and Sons.")
22741 (license license:gpl2)))
22743 (define-public r-anthropometry
22745 (name "r-anthropometry")
22750 (uri (cran-uri "Anthropometry" version))
22753 "0vxjlzxv16bygw8n57f25msq5bd1dydg41my92ximah0nzzvbg41"))))
22754 (properties `((upstream-name . "Anthropometry")))
22755 (build-system r-build-system)
22768 (home-page "https://cran.r-project.org/web/packages/Anthropometry/")
22769 (synopsis "Statistical methods for anthropometric data")
22771 "This package provides statistical methods especially developed to
22772 analyze anthropometric data. These methods are aimed at providing effective
22773 solutions to some commons problems related to Ergonomics and Anthropometry.
22774 They are based on clustering, the statistical concept of data depth,
22775 statistical shape analysis and archetypal analysis.")
22776 (license license:gpl2+)))
22778 (define-public r-anndata
22781 (version "0.7.5.3")
22785 (uri (cran-uri "anndata" version))
22787 (base32 "115v7gdilayd18hd519vzkixp2s6rvvrd1inc1i6amn7d0spy8r1"))))
22788 (properties `((upstream-name . "anndata")))
22789 (build-system r-build-system)
22790 (propagated-inputs (list r-assertthat r-matrix r-r6 r-reticulate))
22791 (native-inputs (list r-knitr))
22792 (home-page "https://anndata.dynverse.org")
22793 (synopsis "Anndata for R")
22795 "This package provides a reticulate wrapper for the Python package
22796 @code{anndata}. It provides a scalable way of keeping track of data and
22797 learned annotations. It is used to read from and write to the h5ad file
22799 (license license:expat)))
22801 (define-public r-adamethods
22803 (name "r-adamethods")
22808 (uri (cran-uri "adamethods" version))
22811 "150awbd3skb1mqca18bqjykhyycqw8crviw66s6qrcnmcsbk77pj"))))
22812 (properties `((upstream-name . "adamethods")))
22813 (build-system r-build-system)
22815 (list r-anthropometry
22822 (home-page "https://cran.r-project.org/web/packages/adamethods/")
22823 (synopsis "Archetypoid algorithms and anomaly detection")
22825 "This package is a collection of several algorithms to obtain
22826 archetypoids with small and large databases and with both classical
22827 multivariate data and functional data (univariate and multivariate). Some of
22828 these algorithms also detect anomalies (outliers).")
22829 (license license:gpl2+)))
22831 (define-public r-idpmisc
22838 (uri (cran-uri "IDPmisc" version))
22841 "0zy6mxqa8arq0vvhsdcifzm3085c23rnwa1n36fhircph1xwvfdw"))))
22842 (properties `((upstream-name . "IDPmisc")))
22843 (build-system r-build-system)
22846 (home-page "https://cran.r-project.org/web/packages/IDPmisc/")
22847 (synopsis "Functions for data analyses and visualization")
22849 "This package provides different high-level graphics functions for
22850 displaying large datasets, displaying circular data in a very flexible way,
22851 finding local maxima, brewing color ramps, drawing nice arrows, zooming
22852 2D-plots, creating figures with differently colored margin and plot region.
22853 In addition, the package contains auxiliary functions for data manipulation
22854 like omitting observations with irregular values or selecting data by logical
22855 vectors, which include NAs. Other functions are especially useful in
22856 spectroscopy and analyses of environmental data: robust baseline fitting,
22857 finding peaks in spectra, converting humidity measures.")
22858 (license license:gpl3+)))
22860 (define-public r-qqman
22867 (uri (cran-uri "qqman" version))
22870 "1a6qp5wv9bvwjchfw8x4jh48hkynlnfr21a8vqgnswldvwbq7njq"))))
22871 (properties `((upstream-name . "qqman")))
22872 (build-system r-build-system)
22874 (list r-calibrate))
22877 (home-page "https://cran.r-project.org/web/packages/qqman/")
22878 (synopsis "Q-Q and Manhattan plots for GWAS data")
22880 "This package allows you to create Q-Q and Manhattan plots for GWAS data
22881 from PLINK results.")
22882 (license license:gpl3)))
22884 (define-public r-ggplot-multistats
22886 (name "r-ggplot-multistats")
22891 (uri (cran-uri "ggplot.multistats" version))
22894 "1afzfa86vc484bcwpg7m1ky03jpax584rigzgai8w06pifkmz0il"))))
22896 `((upstream-name . "ggplot.multistats")))
22897 (build-system r-build-system)
22899 (list r-ggplot2 r-hexbin r-rlang r-scales))
22900 (home-page "https://github.com/flying-sheep/ggplot.multistats")
22901 (synopsis "Multiple summary statistics for binned stats/geometries")
22903 "This package provides the ggplot binning layer @code{stat_summaries_hex()},
22904 which functions similar to its singular form, but allows the use of multiple
22905 statistics per bin. Those statistics can be mapped to multiple bin
22907 (license license:gpl3)))
22909 (define-public r-knn-covertree
22911 (name "r-knn-covertree")
22916 (uri (cran-uri "knn.covertree" version))
22919 "0msfcmwydws7q7m5jdb0dxab0nkbl7mq5llg6v3r4qrnlvrdggvz"))))
22920 (properties `((upstream-name . "knn.covertree")))
22921 (build-system r-build-system)
22923 (list r-matrix r-rcpp r-rcppeigen))
22924 (home-page "https://github.com/flying-sheep/knn.covertree")
22925 (synopsis "Accurate kNN Implementation with multiple distance measures")
22927 "Similarly to the FNN package, this package allows calculation of the k
22928 nearest neighbors (kNN) of a data matrix. The implementation is based on
22929 cover trees introduced by Alina Beygelzimer, Sham Kakade, and John
22930 Langford (2006) @url{doi:10.1145/1143844.1143857}.")
22931 (license license:agpl3+)))
22933 (define-public r-poibin
22940 (uri (cran-uri "poibin" version))
22943 "1sxryvwwz6ldsnkzdy56p8c895s5yvpcai9ndyjv1x5q3l05wf9v"))))
22944 (properties `((upstream-name . "poibin")))
22945 (build-system r-build-system)
22946 (home-page "https://cran.r-project.org/web/packages/poibin/")
22947 (synopsis "Poisson binomial distribution")
22949 "This package provides an implementation of both the exact and
22950 approximation methods for computing the @dfn{cumulative distribution
22951 function} (CDF) of the Poisson binomial distribution. It also provides the
22952 @dfn{probability mass function} (PMF), quantile function, and random number
22953 generation for the Poisson binomial distribution.")
22954 (license license:gpl2)))
22956 (define-public r-diagram
22963 (uri (cran-uri "diagram" version))
22966 "1r3lyl0h7mk9cfg8smr3jydfkjdawaphnxibkxfjqa7029vkxh79"))))
22967 (properties `((upstream-name . "diagram")))
22968 (build-system r-build-system)
22971 (home-page "https://cran.r-project.org/web/packages/diagram/")
22972 (synopsis "Visualize simple graphs (networks) and plot flow diagrams")
22974 "This package provides tools to visualize simple graphs (networks) based
22975 on a transition matrix, utilities to plot flow diagrams, visualizing webs,
22976 electrical networks, etc. It also includes supporting material for the book
22977 \"A practical guide to ecological modelling - using R as a simulation
22978 platform\" by Karline Soetaert and Peter M.J. Herman (2009) and the book
22979 \"Solving Differential Equations in R\" by Karline Soetaert, Jeff Cash and
22980 Francesca Mazzia (2012).")
22981 (license license:gpl2+)))
22983 (define-public r-lim
22990 (uri (cran-uri "LIM" version))
22993 "03x1gnm06bw1wrzc01110bjzd2mvjdzbc2mbrazh22jrmb32w5d8"))))
22994 (properties `((upstream-name . "LIM")))
22995 (build-system r-build-system)
22997 (list r-diagram r-limsolve))
22998 (home-page "https://cran.r-project.org/web/packages/LIM/")
22999 (synopsis "Linear inverse model examples and solution methods")
23001 "This package provides functions that read and solve linear inverse
23002 problems (food web problems, linear programming problems).")
23003 (license license:gpl2+)))
23005 (define-public r-shinycssloaders
23007 (name "r-shinycssloaders")
23012 (uri (cran-uri "shinycssloaders" version))
23015 "0r3xm273lhdhzbs2mkgw1m2kwb7z1dh1pzya8yxy5vacda1l2ikl"))))
23017 `((upstream-name . "shinycssloaders")))
23018 (build-system r-build-system)
23020 (list r-digest r-glue r-shiny))
23021 (home-page "https://github.com/andrewsali/shinycssloaders")
23022 (synopsis "Add CSS loading animations to Shiny outputs")
23024 "This package provides tools to create a lightweight Shiny wrapper for
23025 the css-loaders created by Luke Hass
23026 @url{https://github.com/lukehaas/css-loaders}. Wrapping a Shiny output will
23027 automatically show a loader when the output is (re)calculating.")
23028 (license license:gpl3)))
23030 (define-public r-rsvg
23037 (uri (cran-uri "rsvg" version))
23040 "10p6aps2rsvhf4xgngl9x20cf2wqbzhlpjds8biyihvj58c1q8nn"))))
23041 (properties `((upstream-name . "rsvg")))
23042 (build-system r-build-system)
23044 (list librsvg zlib))
23046 (list pkg-config r-knitr))
23047 (home-page "https://github.com/jeroen/rsvg#readme")
23048 (synopsis "Render SVG images into PDF, PNG, PostScript, or Bitmap arrays")
23050 "This package allows you to render vector-based SVG images into
23051 high-quality custom-size bitmap arrays using the librsvg2 library. The
23052 resulting bitmap can be written to e.g. PNG, JPEG or WEBP format. In
23053 addition, the package can convert images directly to various formats such as
23054 PDF or PostScript.")
23055 (license license:expat)))
23057 (define-public r-influencer
23059 (name "r-influencer")
23060 (version "0.1.0.1")
23064 (uri (cran-uri "influenceR" version))
23067 "0rj7rm236vn3v8302nwl12s0kvpv6xpdbm3q3gxk7vgwfl8nzi33"))))
23068 (properties `((upstream-name . "influenceR")))
23069 (build-system r-build-system)
23071 (list r-igraph r-matrix))
23072 (home-page "https://github.com/rcc-uchicago/influenceR")
23073 (synopsis "Tools to quantify structural importance of nodes in a network")
23075 "This package provides functionality to compute various node centrality
23076 measures on networks. Included are functions to compute betweenness
23077 centrality (by utilizing Madduri and Bader's SNAP library), implementations of
23078 Burt's constraint and @dfn{effective network size} (ENS) metrics, Borgatti's
23079 algorithm to identify key players, and Valente's bridging metric. The
23080 betweenness, Key Players, and bridging implementations are parallelized with
23082 (license license:gpl2)))
23084 (define-public r-emplik
23091 (uri (cran-uri "emplik" version))
23094 "1kw8g8j075bsicdvgkjf4870rfv5c30gvmw6qkkaz3ki22x74w77"))))
23095 (properties `((upstream-name . "emplik")))
23096 (build-system r-build-system)
23099 (home-page "https://www.ms.uky.edu/~mai/EmpLik.html")
23100 (synopsis "Empirical likelihood ratio for censored/truncated data")
23102 "This package provides empirical likelihood ratio tests for
23103 means/quantiles/hazards from possibly censored and/or truncated data. It also
23105 (license license:gpl2+)))
23107 (define-public r-imputeyn
23109 (name "r-imputeyn")
23114 (uri (cran-uri "imputeYn" version))
23117 "1b21w1aa5f7yiq8k0wa86wvbg4ij7f6ldwn6asfqwb0b90rvsgvs"))))
23118 (properties `((upstream-name . "imputeYn")))
23119 (build-system r-build-system)
23121 (list r-boot r-emplik r-mvtnorm r-quadprog r-survival))
23122 (home-page "https://cran.r-project.org/web/packages/imputeYn/")
23123 (synopsis "Impute last largest censored observation under weighted least squares")
23125 "This package allows for the imputation of the last largest censored
23126 observantions. This method brings less bias and more efficient estimates for
23128 (license license:gpl2)))
23130 (define-public r-adapenetclass
23132 (name "r-adapenetclass")
23137 (uri (cran-uri "AdapEnetClass" version))
23140 "01k3mj4g1ckbng7wkzzn9h0k9yf01cpnnkly0sjda574c5jhj0rc"))))
23141 (properties `((upstream-name . "AdapEnetClass")))
23142 (build-system r-build-system)
23144 (list r-glmnet r-imputeyn r-lars r-quadprog))
23145 (home-page "https://cran.r-project.org/web/packages/AdapEnetClass/")
23146 (synopsis "Class of adaptive elastic net methods for censored data")
23148 "This package provides methods for variable selection for AFT models.")
23149 (license license:gpl2)))
23151 (define-public r-flock
23158 (uri (cran-uri "flock" version))
23161 "1zg93p74icj4bhxnmnssj2xp6vw4yaksyavq03497v33xfpdxss7"))))
23162 (properties `((upstream-name . "flock")))
23163 (build-system r-build-system)
23164 (propagated-inputs (list r-rcpp))
23165 (home-page "https://cran.r-project.org/web/packages/flock/")
23166 (synopsis "Process synchronization using file locks")
23168 "This package implements synchronization between R processes (spawned by
23169 using the @code{parallel} package for instance) using file locks. It supports
23170 both exclusive and shared locking.")
23171 (license license:asl2.0)))
23173 (define-public r-archivist
23175 (name "r-archivist")
23180 (uri (cran-uri "archivist" version))
23183 "0q1qysack30xzxdbvvi56rk7r85hsj4ghls9r70ki7bl3rqwr4c9"))))
23184 (properties `((upstream-name . "archivist")))
23185 (build-system r-build-system)
23197 (home-page "https://pbiecek.github.io/archivist/")
23198 (synopsis "Tools for storing, restoring and searching for R objects")
23200 "Data exploration and modelling is a process in which a lot of data
23201 artifacts are produced. Artifacts like: subsets, data aggregates, plots,
23202 statistical models, different versions of data sets and different versions of
23203 results. Archivist helps to store and manage artifacts created in R. It
23204 allows you to store selected artifacts as binary files together with their
23205 metadata and relations. Archivist allows sharing artifacts with others. It
23206 can look for already created artifacts by using its class, name, date of the
23207 creation or other properties. It also makes it easy to restore such
23209 (license license:gpl2)))
23211 (define-public r-versions
23213 (name "r-versions")
23218 (uri (cran-uri "versions" version))
23221 "0zm49j785dgv7fyr1yl9q5f0dsk8hhpim5q5bpkgrkzv7pwjribd"))))
23222 (properties `((upstream-name . "versions")))
23223 (build-system r-build-system)
23224 (home-page "https://cran.r-project.org/web/packages/versions/")
23225 (synopsis "Query and install specific versions of CRAN packages")
23227 "This package allows you to install specified versions of R packages
23228 hosted on CRAN and provides functions to list available versions and the
23229 versions of currently installed packages.")
23230 (license license:bsd-3)))
23232 (define-public r-adapr
23239 (uri (cran-uri "adapr" version))
23242 "1s57jdbi5pik56xjz1d4438ax6cywg2yq2s47h5g6wrwvpgr1qfw"))))
23243 (properties `((upstream-name . "adapr")))
23244 (build-system r-build-system)
23261 (home-page "https://cran.r-project.org/web/packages/adapr/")
23262 (synopsis "Implementation of an accountable data analysis process")
23264 "This package tracks reading and writing within R scripts that are
23265 organized into a directed acyclic graph. It contains an interactive Shiny
23266 application @code{adaprApp()}. It uses Git and file hashes to track version
23267 histories of inputs and outputs.")
23268 (license license:lgpl2.0)))
23270 (define-public r-adapsamp
23272 (name "r-adapsamp")
23277 (uri (cran-uri "AdapSamp" version))
23280 "1jayjrsiib2ij4rxxj59g71r3xhzl5yqh0lhi8k6cfy03i7dkvis"))))
23281 (properties `((upstream-name . "AdapSamp")))
23282 (build-system r-build-system)
23283 (propagated-inputs (list r-pracma))
23284 (home-page "https://cran.r-project.org/web/packages/AdapSamp/")
23285 (synopsis "Adaptive sampling algorithms")
23287 "For distributions whose probability density functions are log-concave,
23288 the adaptive rejection sampling algorithm can be used to build envelope
23289 functions for sampling. For others, the modified adaptive rejection sampling
23290 algorithm, the concave-convex adaptive rejection sampling algorithm, and the
23291 adaptive slice sampling algorithm can be used. This R package mainly includes
23292 these four functions: @code{rARS()}, @code{rMARS()}, @code{rCCARS()}, and
23293 @code{rASS()}. These functions can realize sampling based on the algorithms
23295 (license license:gpl2)))
23297 (define-public r-adaptalint
23299 (name "r-adaptalint")
23304 (uri (cran-uri "adaptalint" version))
23307 "15qdcvnnbgcps8j5k79354wsc9alswijv8lcafg2i3lghaw536yf"))))
23308 (properties `((upstream-name . "adaptalint")))
23309 (build-system r-build-system)
23311 (list r-dplyr r-lintr r-purrr))
23312 (home-page "https://cran.r-project.org/web/packages/adaptalint/")
23313 (synopsis "Check R code style")
23315 "This package provides tools to infer the code style (which style rules
23316 are followed and which ones are not) from one package and use it to check
23317 another. This makes it easier to find and correct the most important problems
23319 (license license:gpl3)))
23321 (define-public r-fracdiff
23323 (name "r-fracdiff")
23328 (uri (cran-uri "fracdiff" version))
23331 "1dhfjlhr9sb38qgpsx0sm73l9lgc13d0fk32l7fmjfnalhr3n45q"))))
23332 (properties `((upstream-name . "fracdiff")))
23333 (build-system r-build-system)
23334 (home-page "https://github.com/mmaechler/fracdiff")
23336 "Fractionally differenced ARIMA aka ARFIMA(P,d,q) models")
23338 "This package provides tools for the maximum likelihood estimation of the
23339 parameters of a fractionally differenced ARIMA(p,d,q) model (Haslett and
23340 Raftery, Appl.Statistics, 1989); it includes inference and basic methods.")
23341 (license license:gpl2+)))
23343 (define-public r-forecast
23345 (name "r-forecast")
23350 (uri (cran-uri "forecast" version))
23353 "0zvn44k7npxai8kj0hgxaaqv1hgd8rxicnvj4cg7wfl8ba4yn0cz"))))
23354 (properties `((upstream-name . "forecast")))
23355 (build-system r-build-system)
23370 (list r-knitr)) ; needed for vignettes
23371 (home-page "https://pkg.robjhyndman.com/forecast/")
23372 (synopsis "Forecasting functions for time series and linear models")
23374 "This package provides methods and tools for displaying and analysing
23375 univariate time series forecasts including exponential smoothing via state
23376 space models and automatic ARIMA modelling.")
23377 (license license:gpl3)))
23379 (define-public r-formattable
23381 (name "r-formattable")
23386 (uri (cran-uri "formattable" version))
23388 (base32 "1vdxi0xmg019qyzjrp8bkjxciz245jcxsrkhfzd44ynqcwi4s3ag"))))
23389 (properties `((upstream-name . "formattable")))
23390 (build-system r-build-system)
23392 (list r-htmltools r-htmlwidgets r-lifecycle r-rmarkdown))
23395 (home-page "https://github.com/renkun-ken/formattable")
23396 (synopsis "Print vectors and data frames with text fromatting")
23398 "This R package provides functions to create formattable vectors and data
23399 frames. @emph{Formattable} vectors are printed with text formatting, and
23400 formattable data frames are printed with multiple types of formatting in HTML
23401 to improve the readability of data presented in tabular form rendered in web
23403 (license license:expat)))
23405 (define-public r-xmisc
23412 (uri (cran-uri "Xmisc" version))
23415 "11gwlcyxhz1p50m68cnqrxmisdk99v8vrsbvyr7k67f0kvsznzs1"))))
23416 (properties `((upstream-name . "Xmisc")))
23417 (build-system r-build-system)
23418 (home-page "https://cran.r-project.org/package=Xmisc")
23420 "Xiaobei's miscellaneous classes and functions")
23422 "This package provides Xiaobei's miscellaneous classes and functions,
23423 which are useful when developing R packages for @dfn{object oriented
23424 programming} (OOP) using R Reference Class.")
23425 (license license:gpl2+)))
23427 (define-public r-proxyc
23434 (uri (cran-uri "proxyC" version))
23437 "1mcimswrx1cjjm7wsgkzfrgh3jpf4sncwfvdvg2f14fzfzy7afd6"))))
23438 (properties `((upstream-name . "proxyC")))
23439 (build-system r-build-system)
23441 (list r-matrix r-rcpp r-rcpparmadillo r-rcppparallel))
23442 (home-page "https://cran.r-project.org/package=proxyC")
23443 (synopsis "Compute proximity in large sparse matrices")
23445 "This package provides efficient tools to compute the proximity between
23446 rows or columns of large matrices. Functions are optimised for large sparse
23447 matrices using the Armadillo and Intel TBB libraries. Among several built-in
23448 similarity/distance measures, computation of correlation, cosine similarity
23449 and Euclidean distance is particularly fast.")
23450 (license license:gpl3)))
23452 (define-public r-isocodes
23454 (name "r-isocodes")
23455 (version "2022.01.10")
23459 (uri (cran-uri "ISOcodes" version))
23462 "0gy7n5bgxnl4rawry0pg078bkks9lzsbsrwjq8q5cvxl4k3dwpdj"))))
23463 (properties `((upstream-name . "ISOcodes")))
23464 (build-system r-build-system)
23465 (home-page "https://cran.r-project.org/package=ISOcodes")
23466 (synopsis "Selected ISO codes")
23468 "This package provides ISO language, territory, currency, script and
23469 character codes. It provides ISO 639 language codes, ISO 3166 territory
23470 codes, ISO 4217 currency codes, ISO 15924 script codes, and the ISO 8859
23471 character codes as well as the UN M.49 area codes.")
23472 (license license:gpl2)))
23474 (define-public r-stopwords
23476 (name "r-stopwords")
23481 (uri (cran-uri "stopwords" version))
23484 "1ci1cgxrcvlhhplximsfv0plvjdbcd5kv0nphxnpildsn5m1rv65"))))
23485 (properties `((upstream-name . "stopwords")))
23486 (build-system r-build-system)
23489 (home-page "https://github.com/quanteda/stopwords")
23490 (synopsis "Multilingual stopword lists")
23492 "This package provides multiple sources of stopwords, for use in text
23493 analysis and natural language processing.")
23494 (license license:expat)))
23496 (define-public r-spacyr
23503 (uri (cran-uri "spacyr" version))
23506 "1b2ccgwsiqkvp7w37x8k7699c676q16vfrybkrfvyczyhki4s6nw"))))
23507 (properties `((upstream-name . "spacyr")))
23508 (build-system r-build-system)
23510 (list r-data-table r-reticulate))
23511 (home-page "https://spacyr.quanteda.io")
23512 (synopsis "R wrapper for the spaCy NLP library")
23514 "This package provides an R wrapper to the Python @dfn{natural language
23515 processing} (NLP) library @code{spaCy}, from @url{http://spacy.io}.")
23516 (license license:gpl3)))
23518 (define-public r-snowballc
23520 (name "r-snowballc")
23525 (uri (cran-uri "SnowballC" version))
23528 "1wwm71mp4b2mjb5985x782p6xj519dfrpd40qli7lmig6afyw3xi"))))
23529 (properties `((upstream-name . "SnowballC")))
23530 (build-system r-build-system)
23531 (home-page "https://r-forge.r-project.org/projects/r-temis/")
23532 (synopsis "Snowball stemmers based on the C libstemmer UTF-8 library")
23534 "This package provides an R interface to the C @code{libstemmer} library
23535 that implements Porter's word stemming algorithm for collapsing words to a
23536 common root to aid comparison of vocabulary. Currently supported languages
23537 are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian,
23538 Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.")
23539 (license license:bsd-3)))
23541 (define-public r-quanteda
23543 (name "r-quanteda")
23548 (uri (cran-uri "quanteda" version))
23551 "0q72jsc6zalnl35qq02z9niissnyax4zxzqzpfpjsmgmxpd797mw"))))
23552 (properties `((upstream-name . "quanteda")))
23553 (build-system r-build-system)
23568 (home-page "https://quanteda.io")
23569 (synopsis "Quantitative analysis of textual data")
23571 "This package provides a fast, flexible, and comprehensive framework for
23572 quantitative text analysis in R. It provides functionality for corpus
23573 management, creating and manipulating tokens and ngrams, exploring keywords in
23574 context, forming and manipulating sparse matrices of documents by features and
23575 feature co-occurrences, analyzing keywords, computing feature similarities and
23576 distances, applying content dictionaries, applying supervised and unsupervised
23577 machine learning, visually representing text and text analyses, and more.")
23578 (license license:gpl3)))
23580 (define-public r-topicmodels
23582 (name "r-topicmodels")
23587 (uri (cran-uri "topicmodels" version))
23590 "1d6iizmn042b59q2y6qc82z19wq3xm0zvgkf8iqf8fdzh51kmn5g"))))
23591 (properties `((upstream-name . "topicmodels")))
23592 (build-system r-build-system)
23596 (list r-modeltools r-slam r-tm))
23597 (home-page "https://cran.r-project.org/package=topicmodels")
23598 (synopsis "Topic models")
23600 "This package provides an interface to the C code for @dfn{Latent
23601 Dirichlet Allocation} (LDA) models and @dfn{Correlated Topics Models} (CTM) by
23602 David M. Blei and co-authors and the C++ code for fitting LDA models using
23603 Gibbs sampling by Xuan-Hieu Phan and co-authors.")
23604 (license license:gpl2)))
23606 (define-public r-stm
23613 (uri (cran-uri "stm" version))
23616 "0qwq4nin2n9fjd06852r8k7arvcgh46kcfb3lm21swgx6j8bgrhb"))))
23617 (properties `((upstream-name . "stm")))
23618 (build-system r-build-system)
23631 (home-page "http://www.structuraltopicmodel.com/")
23632 (synopsis "Estimation of the Structural Topic Model")
23634 "The @dfn{Structural Topic Model} (STM) allows researchers to estimate
23635 topic models with document-level covariates. The package also includes tools
23636 for model selection, visualization, and estimation of topic-covariate
23638 (license license:expat)))
23640 (define-public r-polycor
23647 (uri (cran-uri "polycor" version))
23650 "0285rvx8238qp8dix0jq0cqq7ks8h6cjwsscbc7dx4n9nph56pzh"))))
23651 (properties `((upstream-name . "polycor")))
23652 (build-system r-build-system)
23654 (list r-admisc r-matrix r-mvtnorm))
23655 (home-page "https://r-forge.r-project.org/projects/polycor/")
23656 (synopsis "Polychoric and polyserial correlations")
23658 "This package provides tools to compute polychoric and polyserial
23659 correlations by quick \"two-step\" methods or ML, optionally with standard
23660 errors; tetrachoric and biserial correlations are special cases.")
23661 (license license:gpl2+)))
23663 (define-public r-msm
23670 (uri (cran-uri "msm" version))
23673 "08vhazswyxr3y1zb9y60mbg3bappzlizxml8s08p65mh82xxkz5f"))))
23674 (properties `((upstream-name . "msm")))
23675 (build-system r-build-system)
23677 (list r-expm r-mvtnorm r-survival))
23678 (home-page "https://github.com/chjackson/msm")
23679 (synopsis "Multi-state Markov and hidden Markov models in continuous time")
23681 "This package provides functions for fitting continuous-time Markov and
23682 hidden Markov multi-state models to longitudinal data. It was designed for
23683 processes observed at arbitrary times in continuous time (panel data) but some
23684 other observation schemes are supported. Both Markov transition rates and the
23685 hidden Markov output process can be modelled in terms of covariates, which may
23686 be constant or piecewise-constant in time.")
23687 (license license:gpl2+)))
23689 (define-public r-ltm
23696 (uri (cran-uri "ltm" version))
23699 "1qrgzwx5l58qf5rfp1knxc84r0g943q5sdr3ky74zzwpnmrf2vf7"))))
23700 (properties `((upstream-name . "ltm")))
23701 (build-system r-build-system)
23703 (list r-mass r-msm r-polycor))
23704 (home-page "https://github.com/drizopoulos/ltm")
23705 (synopsis "Latent trait models under IRT")
23707 "This is a package supporting the analysis of multivariate dichotomous
23708 and polytomous data using latent trait models under the Item Response Theory
23709 approach. It includes the Rasch, the Two-Parameter Logistic, the Birnbaum's
23710 Three-Parameter, the Graded Response, and the Generalized Partial Credit
23712 (license license:gpl2+)))
23714 (define-public r-mi
23721 (uri (cran-uri "mi" version))
23724 "1h47k5mpbvhid83277dvvj2di493bgzz9iarpyv3r30y219l7x1l"))))
23725 (properties `((upstream-name . "mi")))
23726 (build-system r-build-system)
23728 (list r-arm r-matrix))
23729 (home-page "http://www.stat.columbia.edu/~gelman/")
23730 (synopsis "Missing data imputation and model checking")
23732 "This package provides functions for data manipulation, imputing missing
23733 values in an approximate Bayesian framework, diagnostics of the models used to
23734 generate the imputations, confidence-building mechanisms to validate some of
23735 the assumptions of the imputation algorithm, and functions to analyze multiply
23736 imputed data sets with the appropriate degree of sampling uncertainty.")
23737 (license license:gpl2+)))
23739 (define-public r-matrixcalc
23741 (name "r-matrixcalc")
23746 (uri (cran-uri "matrixcalc" version))
23749 "1jkgl1v1q7cqpl1rf49qahdr9y0f33f0ldsbgby8xhfv0vpy21jr"))))
23750 (properties `((upstream-name . "matrixcalc")))
23751 (build-system r-build-system)
23752 (home-page "https://cran.r-project.org/web/packages/matrixcalc/")
23753 (synopsis "Collection of functions for matrix calculations")
23755 "This package provides a collection of functions to support matrix
23756 calculations for probability, econometric and numerical analysis. There are
23757 additional functions that are comparable to APL functions which are useful for
23758 actuarial models such as pension mathematics.")
23759 (license license:gpl2+)))
23761 (define-public r-matrixextra
23763 (name "r-matrixextra")
23764 (version "0.1.9-1")
23768 (uri (cran-uri "MatrixExtra" version))
23770 (base32 "098apgqlncgxspa8mi4bx2nk5fbk3880whqiwkvydsfsqrbv1sj0"))))
23771 (properties `((upstream-name . "MatrixExtra")))
23772 (build-system r-build-system)
23774 (list r-float r-matrix r-rcpp r-rhpcblasctl))
23777 (home-page "https://github.com/david-cortes/MatrixExtra")
23778 (synopsis "Extra methods for sparse matrices")
23780 "This package extends sparse matrix and vector classes from the Matrix
23781 package by providing:
23784 @item Methods and operators that work natively on CSR formats (compressed
23785 sparse row, a.k.a. @code{RsparseMatrix}) such as slicing/sub-setting,
23786 assignment, @code{rbind()}, mathematical operators for CSR and COO such as
23787 addition or @code{sqrt()}, and methods such as @code{diag()};
23788 @item Multi-threaded matrix multiplication and cross-product for many
23789 @code{<sparse, dense>} types, including the @code{float32} type from
23791 @item Coercion methods between pairs of classes which are not present in
23792 @code{Matrix}, such as from @code{dgCMatrix} to @code{ngRMatrix}, as well as
23793 convenience conversion functions;
23794 @item Utility functions for sparse matrices such as sorting the indices or
23795 removing zero-valued entries;
23796 @item Fast transposes that work by outputting in the opposite storage format;
23797 @item Faster replacements for many @code{Matrix} methods for all sparse types,
23798 such as slicing and elementwise multiplication.
23799 @item Convenience functions for sparse objects, such as @code{mapSparse} or a
23800 shorter @code{show} method.
23803 (license license:gpl2+)))
23805 (define-public r-sem
23812 (uri (cran-uri "sem" version))
23815 "0r9g4j0w6q4qy9jl9gkjkihml4109ymg3y6zmhyg806q19qryx07"))))
23816 (properties `((upstream-name . "sem")))
23817 (build-system r-build-system)
23819 (list r-boot r-mass r-mi))
23820 (home-page "https://cran.r-project.org/package=sem")
23821 (synopsis "Structural equation models")
23823 "This package provides functions for fitting general linear structural
23824 equation models (with observed and latent variables) using the RAM approach,
23825 and for fitting structural equations in observed-variable models by two-stage
23827 (license license:gpl2+)))
23829 (define-public r-semtools
23831 (name "r-semtools")
23836 (uri (cran-uri "semTools" version))
23839 "1dpsn43ifvfy5v8w2fqdy54yclmy0d3qlzix67lflr2r7isq7y6x"))))
23840 (properties `((upstream-name . "semTools")))
23841 (build-system r-build-system)
23843 (list r-lavaan r-pbivnorm))
23844 (home-page "https://github.com/simsem/semTools/wiki")
23845 (synopsis "Useful tools for structural equation modeling")
23847 "This package provides useful tools for structural equation modeling.")
23848 (license license:gpl2+)))
23850 (define-public r-regsem
23857 (uri (cran-uri "regsem" version))
23860 "1v33wkrsawcvaa06cijp8ybwi82a0x34y59hdknwdbywplnirzr8"))))
23861 (properties `((upstream-name . "regsem")))
23862 (build-system r-build-system)
23864 (list r-lavaan r-rcpp r-rcpparmadillo r-rsolnp))
23867 (home-page "https://cran.r-project.org/package=regsem")
23868 (synopsis "Regularized structural equation modeling")
23870 "This package uses both ridge and lasso penalties (and extensions) to
23871 penalize specific parameters in structural equation models. The package
23872 offers additional cost functions, cross validation, and other extensions
23873 beyond traditional structural equation models. It also contains a function to
23874 perform @dfn{exploratory mediation} (XMed).")
23875 (license license:gpl2+)))
23877 (define-public r-stanheaders
23879 (name "r-stanheaders")
23880 (version "2.21.0-7")
23884 (uri (cran-uri "StanHeaders" version))
23887 "0srkyawyiykn3p5lw1z3zf18s4ax4iasv1ci3l1px40f9w36wm17"))))
23888 (properties `((upstream-name . "StanHeaders")))
23889 (build-system r-build-system)
23890 (inputs (list pandoc))
23892 (list r-rcppeigen r-rcppparallel))
23894 (list gfortran r-knitr)) ; for vignettes
23895 (home-page "https://mc-stan.org/")
23896 (synopsis "C++ header files for Stan")
23898 "The C++ header files of the Stan project are provided by this package.
23899 There is a shared object containing part of the @code{CVODES} library, but it
23900 is not accessible from R. @code{r-stanheaders} is only useful for developers
23901 who want to utilize the @code{LinkingTo} directive of their package's
23902 DESCRIPTION file to build on the Stan library without incurring unnecessary
23905 The Stan project develops a probabilistic programming language that implements
23906 full or approximate Bayesian statistical inference via Markov Chain Monte
23907 Carlo or variational methods and implements (optionally penalized) maximum
23908 likelihood estimation via optimization. The Stan library includes an advanced
23909 automatic differentiation scheme, templated statistical and linear algebra
23910 functions that can handle the automatically differentiable scalar types (and
23911 doubles, ints, etc.), and a parser for the Stan language. The @code{r-rstan}
23912 package provides user-facing R functions to parse, compile, test, estimate,
23913 and analyze Stan models.")
23914 (license license:bsd-3)))
23916 (define-public r-rpf
23923 (uri (cran-uri "rpf" version))
23926 "1yr1i7kswq57mcxv05lh7bvbicz1djqxcl6f13dlgsf3ww56gzg1"))))
23927 (properties `((upstream-name . "rpf")))
23928 (build-system r-build-system)
23930 (list r-lifecycle r-mvtnorm r-rcpp r-rcppeigen))
23933 (home-page "https://github.com/jpritikin/rpf")
23934 (synopsis "Response probability functions")
23936 "The purpose of this package is to factor out logic and math common to
23937 Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as
23938 core support code suitable for more specialized IRT packages to build upon.
23939 Complete access to optimized C functions is made available with
23940 @code{R_RegisterCCallable()}.")
23941 (license license:gpl3+)))
23943 (define-public r-openmx
23950 (uri (cran-uri "OpenMx" version))
23953 "1flkm5nsvdnqhjayzajv80lsvjbh21v4zbm7ak09051x0giv3shj"))))
23954 (properties `((upstream-name . "OpenMx")))
23955 (build-system r-build-system)
23967 (native-inputs (list r-knitr gfortran))
23968 (home-page "http://openmx.ssri.psu.edu")
23969 (synopsis "Extended structural equation modelling")
23971 "This package allows for the estimation of a wide variety of advanced
23972 multivariate statistical models. It consists of a library of functions and
23973 optimizers that allow you to quickly and flexibly define an SEM model and
23974 estimate parameters given observed data.")
23975 (license license:asl2.0)))
23977 (define-public r-kutils
23984 (uri (cran-uri "kutils" version))
23987 "06jk66wbq3jmdf2jdhqns6r3yk36l2x7c907x977zv80sqxa1l37"))))
23988 (properties `((upstream-name . "kutils")))
23989 (build-system r-build-system)
23991 (list r-foreign r-openxlsx r-plyr r-runit r-xtable))
23992 (home-page "https://cran.r-project.org/package=kutils")
23993 (synopsis "Project management tools")
23995 "This package provides tools for data importation, recoding, and
23996 inspection. There are functions to create new project folders, R code
23997 templates, create uniquely named output directories, and to quickly obtain a
23998 visual summary for each variable in a data frame. The main feature here is
23999 the systematic implementation of the \"variable key\" framework for data
24000 importation and recoding.")
24001 (license license:gpl2)))
24003 (define-public r-rockchalk
24005 (name "r-rockchalk")
24006 (version "1.8.144")
24010 (uri (cran-uri "rockchalk" version))
24013 "07dp1n155b9gfvk8l30h6bhjbhbylsjxfzns08mryn4mxj3nqpnb"))))
24014 (properties `((upstream-name . "rockchalk")))
24015 (build-system r-build-system)
24017 (list r-cardata r-kutils r-lme4 r-mass))
24018 (home-page "https://cran.r-project.org/package=rockchalk")
24019 (synopsis "Regression estimation and presentation")
24021 "This package provides a collection of functions for interpretation and
24022 presentation of regression analysis. These functions are used to produce the
24023 statistics lectures in @url{http://pj.freefaculty.org/guides}. The package
24024 includes regression diagnostics, regression tables, and plots of interactions
24025 and \"moderator\" variables. The emphasis is on \"mean-centered\" and
24026 \"residual-centered\" predictors. The vignette @code{rockchalk} offers a
24027 fairly comprehensive overview.")
24028 (license license:gpl3+)))
24030 (define-public r-lisreltor
24032 (name "r-lisreltor")
24037 (uri (cran-uri "lisrelToR" version))
24040 "0zicq0z3hhixan1p1apybnf3v5s6v6ysll4pcz8ivygwr2swv3p5"))))
24041 (properties `((upstream-name . "lisrelToR")))
24042 (build-system r-build-system)
24043 (home-page "https://cran.r-project.org/package=lisrelToR")
24044 (synopsis "Import output from LISREL into R")
24046 "This is an unofficial package aimed at automating the import of LISREL
24048 (license license:gpl2)))
24050 (define-public r-bdgraph
24057 (uri (cran-uri "BDgraph" version))
24060 "0pnzbw09c7amsvj8l4p1jnmss4rkbr1dsmagiygh8lj5fbrklgr4"))))
24061 (properties `((upstream-name . "BDgraph")))
24062 (build-system r-build-system)
24065 (home-page "https://www.uva.nl/profile/a.mohammadi")
24066 (synopsis "Bayesian structure learning in graphical models")
24068 "This package provides statistical tools for Bayesian structure learning
24069 in undirected graphical models for continuous, discrete, and mixed data. It
24070 uses a trans-dimensional @dfn{Markov Chain Monte Carlo} (MCMC) approach based
24071 on a continuous-time birth-death process.")
24072 (license license:gpl2+)))
24074 (define-public r-d3network
24076 (name "r-d3network")
24077 (version "0.5.2.1")
24081 (uri (cran-uri "d3Network" version))
24084 "1gh979z9wksyxxxdzlfzibn0ysvf6h1ij7vwpd55fvbwr308syaw"))))
24085 (properties `((upstream-name . "d3Network")))
24086 (build-system r-build-system)
24088 (list r-plyr r-rjson r-whisker))
24089 (home-page "http://christophergandrud.github.io/d3Network/")
24090 (synopsis "Create D3 JavaScript network, tree, dendrogram, and Sankey graphs")
24092 "This package is intended to make it easy to create D3 JavaScript
24093 network, tree, dendrogram, and Sankey graphs from R using data frames.")
24094 (license license:gpl3+)))
24096 (define-public r-qgraph
24103 (uri (cran-uri "qgraph" version))
24106 "1ahhzp64jdgki5p2wga5mn8a2n1x2zldgpilrpf7hy5l9nf4imz1"))))
24107 (properties `((upstream-name . "qgraph")))
24108 (build-system r-build-system)
24128 (home-page "http://sachaepskamp.com/qgraph/")
24129 (synopsis "Weighted network visualization and analysis")
24131 "This package implements tools for weighted network visualization and
24132 analysis, as well as Gaussian graphical model computation. It contains graph
24133 plotting methods, and tools for psychometric data visualization and graphical
24134 model estimation. See Epskamp et al. (2012)
24135 @url{doi:10.18637/jss.v048.i04}.")
24136 (license license:gpl2)))
24138 (define-public r-semplot
24145 (uri (cran-uri "semPlot" version))
24148 "0l1v9yi1pv59iwfknw4dh9qskk5y8r347jq1vq13gnfd3bmd71xr"))))
24149 (properties `((upstream-name . "semPlot")))
24150 (build-system r-build-system)
24164 (home-page "https://github.com/SachaEpskamp/semPlot")
24165 (synopsis "Unified visualizations of structural equation models")
24167 "Structural equation modeling (SEM) has a long history of representing
24168 models graphically as path diagrams. The semPlot package for R fills the gap
24169 between advanced, but time-consuming, graphical software and the limited
24170 graphics produced automatically by SEM software. In addition, semPlot offers
24171 more functionality than drawing path diagrams: it can act as a common ground
24172 for importing SEM results into R. Any result usable as input to semPlot can
24173 also be represented in any of the three popular SEM frame-works, as well as
24174 translated to input syntax for the R packages @code{sem} and @code{lavaan}.")
24175 (license license:gpl2)))
24177 (define-public r-cdm
24184 (uri (cran-uri "CDM" version))
24187 "159ny2dz0rf1r3k1mqlfwambffc8rx425sggf5bn51nybpzanq3l"))))
24188 (properties `((upstream-name . "CDM")))
24189 (build-system r-build-system)
24191 (list r-mvtnorm r-polycor r-rcpp r-rcpparmadillo))
24193 "https://github.com/alexanderrobitzsch/CDM")
24194 (synopsis "Cognitive diagnosis modeling")
24196 "This package provides functions for cognitive diagnosis modeling and
24197 multidimensional item response modeling for dichotomous and polytomous item
24198 responses. It enables the estimation of the DINA and DINO model, the multiple
24199 group (polytomous) GDINA model, the multiple choice DINA model, the general
24200 diagnostic model (GDM), the structured latent class model (SLCA), and
24201 regularized latent class analysis. See George, Robitzsch, Kiefer, Gross, and
24202 Uenlue (2017) @url{doi:10.18637/jss.v074.i02} for further details on
24203 estimation and the package structure. For tutorials on how to use the CDM
24204 package see George and Robitzsch (2015, @url{doi:10.20982/tqmp.11.3.p189}) as
24205 well as Ravand and Robitzsch (2015).")
24206 (license license:gpl2+)))
24208 (define-public r-tam
24215 (uri (cran-uri "TAM" version))
24218 "1969xm1f7s183h0xnd4g1bxhjp80rl7kad29zwcig0fmw6bs2mpd"))))
24219 (properties `((upstream-name . "TAM")))
24220 (build-system r-build-system)
24222 (list r-cdm r-rcpp r-rcpparmadillo))
24223 (home-page "http://www.edmeasurementsurveys.com/TAM/Tutorials/")
24224 (synopsis "Test analysis modules")
24226 "This package includes tools for marginal maximum likelihood estimation
24227 and joint maximum likelihood estimation for unidimensional and
24228 multidimensional item response models. The package functionality covers the
24229 Rasch model, 2PL model, 3PL model, generalized partial credit model,
24230 multi-faceted Rasch model, nominal item response model, structured latent
24231 class model, mixture distribution IRT models, and located latent class models.
24232 Latent regression models and plausible value imputation are also supported.")
24233 (license license:gpl2+)))
24235 (define-public r-erm
24242 (uri (cran-uri "eRm" version))
24245 "0smym010kswc5vx90qr3x1vl16xj1x1i54rvrj006dc4agc1vmlk"))))
24246 (properties `((upstream-name . "eRm")))
24247 (build-system r-build-system)
24249 (list r-colorspace r-lattice r-mass r-matrix r-psych))
24250 (native-inputs (list gfortran))
24251 (home-page "https://cran.r-project.org/package=eRm")
24252 (synopsis "Extended Rasch modeling")
24254 "This package provides tools to fit @dfn{Rasch models} (RM), @dfn{linear
24255 logistic test models} (LLTM), @dfn{rating scale model} (RSM), @dfn{linear
24256 rating scale models} (LRSM), @dfn{partial credit models} (PCM), and
24257 @dfn{linear partial credit models} (LPCM). Missing values are allowed in the
24258 data matrix. Additional features are the ML estimation of the person
24259 parameters, Andersen's LR-test, item-specific Wald test, Martin-Loef-Test,
24260 nonparametric Monte-Carlo Tests, itemfit and personfit statistics including
24261 infit and outfit measures, ICC and other plots, automated stepwise item
24262 elimination, and a simulation module for various binary data matrices.")
24263 (license license:gpl3)))
24265 (define-public r-irtoys
24272 (uri (cran-uri "irtoys" version))
24275 "0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"))))
24276 (properties `((upstream-name . "irtoys")))
24277 (build-system r-build-system)
24280 (home-page "https://cran.r-project.org/package=irtoys")
24281 (synopsis "Collection of functions related to Item Response Theory (IRT)")
24283 "This package provides a collection of functions useful in learning and
24284 practicing @dfn{Item Response Theory} (IRT), which can be combined into larger
24285 programs. It provides basic CTT analysis, a simple common interface to the
24286 estimation of item parameters in IRT models for binary responses with three
24287 different programs (ICL, BILOG-MG, and ltm), ability estimation (MLE, BME,
24288 EAP, WLE, plausible values), item and person fit statistics, scaling
24289 methods (MM, MS, Stocking-Lord, and the complete Hebaera method), and a rich
24290 array of parametric and non-parametric (kernel) plots. It estimates and plots
24291 Haberman's interaction model when all items are dichotomously scored.")
24292 (license license:gpl2+)))
24294 (define-public r-iheatmapr
24296 (name "r-iheatmapr")
24301 (uri (cran-uri "iheatmapr" version))
24304 "1pwkwh7ljlpr6zyz6j8knpz3iw60xzkw8amc98x4pc2mw148jvzx"))))
24305 (properties `((upstream-name . "iheatmapr")))
24306 (build-system r-build-system)
24308 (list r-fastcluster
24318 (home-page "https://docs.ropensci.org/iheatmapr")
24319 (synopsis "Interactive, Complex Heatmaps")
24321 "iheatmapr is an R package for building complex, interactive heatmaps
24322 using modular building blocks. \"Complex\" heatmaps are heatmaps in which
24323 subplots along the rows or columns of the main heatmap add more information
24324 about each row or column. For example, a one column additional heatmap may
24325 indicate what group a particular row or column belongs to. Complex heatmaps
24326 may also include multiple side by side heatmaps which show different types of
24327 data for the same conditions. Interactivity can improve complex heatmaps by
24328 providing tooltips with information about each cell and enabling zooming into
24329 interesting features. iheatmapr uses the plotly library for interactivity.")
24330 (license license:expat)))
24332 (define-public r-packrat
24339 (uri (cran-uri "packrat" version))
24342 "1hnwhdgqljqs3m7c4rjlyndyc0k85jpa4rbfymxkm3zjg3yy3g78"))))
24343 (properties `((upstream-name . "packrat")))
24344 (build-system r-build-system)
24345 (home-page "https://github.com/rstudio/packrat/")
24346 (synopsis "Dependency management R projects")
24348 "This package provides a dependency manager for R projects that allows
24349 you to manage the R packages your project depends on in an isolated, portable,
24350 and reproducible way.")
24351 (license license:gpl2)))
24353 (define-public r-rsconnect
24355 (name "r-rsconnect")
24360 (uri (cran-uri "rsconnect" version))
24363 "1kyr4v7vds2yw3xmkk2yr56ylz1h95944brylwvwmwj5yxvm419w"))))
24364 (properties `((upstream-name . "rsconnect")))
24365 (build-system r-build-system)
24374 (home-page "https://github.com/rstudio/rsconnect")
24375 (synopsis "Deployment interface for R Markdown documents and Shiny applications")
24377 "This package provides a programmatic deployment interface for RPubs,
24378 shinyapps.io, and RStudio Connect. Supported content types include R Markdown
24379 documents, Shiny applications, Plumber APIs, plots, and static web content.")
24380 (license license:gpl2)))
24382 ;; This package includes minified JavaScript files. When upgrading please
24383 ;; check that there are no new minified JavaScript files.
24384 (define-public r-dygraphs
24386 (name "r-dygraphs")
24387 (version "1.1.1.6")
24391 (uri (cran-uri "dygraphs" version))
24394 "022j007mzfa9k2n31yg4aizcsf571vv3jip092h23rqj03rk3ly3"))))
24395 (properties `((upstream-name . "dygraphs")))
24396 (build-system r-build-system)
24398 `(#:modules ((guix build utils)
24399 (guix build r-build-system)
24403 (modify-phases %standard-phases
24404 (add-after 'unpack 'process-javascript
24405 (lambda* (#:key inputs #:allow-other-keys)
24406 (with-directory-excursion "inst/htmlwidgets/lib/"
24410 `(("dygraphs/dygraph-combined-dev.js"
24411 "dygraph-combined.js")
24412 (,(assoc-ref inputs "js-jquery")
24413 "jquery/jquery.min.js")
24414 (,(assoc-ref inputs "js-fquarter")
24415 "fquarter/moment-fquarter.min.js"))))
24416 (lambda (sources targets)
24417 (for-each (lambda (source target)
24418 (format #t "Processing ~a --> ~a~%"
24420 (let ((minified (open-pipe* OPEN_READ "uglifyjs" source)))
24421 (call-with-output-file target
24423 (dump-port minified port)))))
24424 sources targets))))
24427 `(("uglifyjs" ,node-uglify-js)
24428 ;; They actually use version 1.11.1, but this more recent version
24429 ;; should be just fine.
24433 (uri "https://code.jquery.com/jquery-1.12.4.js")
24436 "0x9mrc1668icvhpwzvgafm8xm11x9lfai9nwr66aw6pjnpwkc3s3"))))
24440 (uri (string-append "https://raw.githubusercontent.com/robgallen/"
24441 "moment-fquarter/1.0.1/moment-fquarter.js"))
24444 "01mdnsaibm9jy2f1qpbn692hpv309lhj5si9nagib4dawmrkffij"))))))
24446 (list r-htmltools r-htmlwidgets r-magrittr r-xts r-zoo))
24447 (home-page "https://github.com/rstudio/dygraphs")
24448 (synopsis "Interface to Dygraphs interactive time series charting library")
24450 "This package provides an R interface to the dygraphs JavaScript charting
24451 library (a copy of which is included in the package). It provides rich
24452 facilities for charting time-series data in R, including highly configurable
24453 series- and axis-display and interactive features like zoom/pan and
24454 series/point highlighting.")
24455 (license license:expat)))
24457 (define-public r-shinystan
24459 (name "r-shinystan")
24464 (uri (cran-uri "shinystan" version))
24467 "18alf5kiqw7y2l6m5nxxizwc2znsf9frxfsqhvgcad8hld9cbya5"))))
24468 (properties `((upstream-name . "shinystan")))
24469 (build-system r-build-system)
24488 (home-page "https://mc-stan.org/")
24489 (synopsis "Interactive visual and numerical analysis for Bayesian models")
24491 "This package provides a graphical user interface for interactive
24492 @dfn{Markov chain Monte Carlo} (MCMC) diagnostics and plots and tables helpful
24493 for analyzing a posterior sample. The interface is powered by the Shiny web
24494 application framework and works with the output of MCMC programs written in
24495 any programming language (and has extended functionality for Stan models fit
24496 using the @code{rstan} and @code{rstanarm} packages).")
24497 (license license:gpl3+)))
24499 (define-public r-rstantools
24501 (name "r-rstantools")
24506 (uri (cran-uri "rstantools" version))
24509 "0b9x8rzj3dr4m7yjx476nn42z22xd1xnw85m9frfwxy5ivg1any9"))))
24510 (properties `((upstream-name . "rstantools")))
24511 (build-system r-build-system)
24512 (inputs (list pandoc))
24514 (list r-desc r-rcpp r-rcppparallel))
24517 (home-page "https://mc-stan.org/rstantools/")
24518 (synopsis "Tools for developing R packages interfacing with Stan")
24520 "This package provides various tools for developers of R packages
24521 interfacing with @url{https://mc-stan.org, Stan}, including functions to set
24522 up the required package structure, S3 generics and default methods to unify
24523 function naming across Stan-based R packages, and vignettes with
24524 recommendations for developers.")
24525 (license license:gpl3+)))
24527 (define-public r-loo
24534 (uri (cran-uri "loo" version))
24536 (base32 "0l2v8zpashqbnck3qx5lp1gqjcfphzky8mxyw5gfk9wk99mzn8dw"))))
24537 (properties `((upstream-name . "loo")))
24538 (build-system r-build-system)
24542 (list r-checkmate r-matrixstats))
24545 (home-page "https://mc-stan.org/loo/")
24546 (synopsis "Leave-One-Out cross-validation and WAIC for Bayesian models")
24548 "This package provides an implementation of efficient approximate
24549 @dfn{leave-one-out} (LOO) cross-validation for Bayesian models fit using
24550 Markov chain Monte Carlo, as described in @url{doi:10.1007/s11222-016-9696-4}.
24551 The approximation uses @dfn{Pareto smoothed importance sampling} (PSIS), a new
24552 procedure for regularizing importance weights. As a byproduct of the
24553 calculations, we also obtain approximate standard errors for estimated
24554 predictive errors and for the comparison of predictive errors between models.
24555 The package also provides methods for using stacking and other model weighting
24556 techniques to average Bayesian predictive distributions.")
24557 (license license:gpl3+)))
24559 (define-public r-rstan
24566 (uri (cran-uri "rstan" version))
24569 "1ccjdwh0xspna2c0m5p8as8y2b0lnhdyk9hfd3jh58j6n8fbzg3n"))))
24570 (properties `((upstream-name . "rstan")))
24571 (build-system r-build-system)
24574 (modify-phases %standard-phases
24575 (add-before 'install 'set-timezone
24576 ;; This package is picky about timezones.
24577 (lambda* (#:key inputs #:allow-other-keys)
24578 (setenv "TZ" "UTC+1")
24580 (search-input-directory inputs
24581 "share/zoneinfo")))))))
24583 (list tzdata-for-tests pandoc r-knitr))
24595 (home-page "https://discourse.mc-stan.org/")
24596 (synopsis "R interface to Stan")
24598 "User-facing R functions are provided to parse, compile, test, estimate,
24599 and analyze Stan models by accessing the header-only Stan library provided by
24600 the StanHeaders package. The Stan project develops a probabilistic
24601 programming language that implements full Bayesian statistical inference via
24602 Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
24603 approximation, and (optionally penalized) maximum likelihood estimation via
24604 optimization. In all three cases, automatic differentiation is used to
24605 quickly and accurately evaluate gradients without burdening the user with the
24606 need to derive the partial derivatives.")
24607 (license license:gpl3+)))
24609 (define-public r-rstanarm
24611 (name "r-rstanarm")
24616 (uri (cran-uri "rstanarm" version))
24619 "04ggzak3f7jaxza3dxyrmxp5b48qcgyspy22ykbhr03g4hzp7jk8"))))
24620 (properties `((upstream-name . "rstanarm")))
24621 (build-system r-build-system)
24642 (home-page "https://mc-stan.org/rstanarm/")
24643 (synopsis "Bayesian applied regression modeling via Stan")
24645 "This package estimates previously compiled regression models using the
24646 @code{rstan} package, which provides the R interface to the Stan C++ library
24647 for Bayesian estimation. Users specify models via the customary R syntax with
24648 a formula and @code{data.frame} plus some additional arguments for priors.")
24649 (license license:gpl3+)))
24651 (define-public r-kendall
24658 (uri (cran-uri "Kendall" version))
24661 "0z2yr3x2nvdm81w2imb61hxwcbmg14kfb2bxgh3wmkmv3wfjwkwn"))))
24662 (properties `((upstream-name . "Kendall")))
24663 (build-system r-build-system)
24668 (home-page "https://cran.r-project.org/web/packages/Kendall/")
24669 (synopsis "Kendall rank correlation and Mann-Kendall trend test")
24671 "This package computes the Kendall rank correlation and Mann-Kendall
24673 (license license:gpl2+)))
24675 (define-public r-keyring
24682 (uri (cran-uri "keyring" version))
24685 "1j8l6nmh4dr70kwybiais8yh687fdwrj134xynq68igw1b1rm8ga"))))
24686 (properties `((upstream-name . "keyring")))
24687 (build-system r-build-system)
24697 (native-inputs (list pkg-config))
24698 (home-page "https://github.com/r-lib/keyring")
24699 (synopsis "Access the system credential store from R")
24701 "This package provides a platform-independent API to access the operating
24702 system's credential store. It currently supports Keychain on macOS,
24703 Credential Store on Windows, the Secret Service API on GNU/Linux, and a
24704 simple, platform independent store implemented with environment variables.
24705 Additional storage back-ends can be added easily.")
24706 (license license:expat)))
24708 (define-public r-zyp
24711 (version "0.10-1.1")
24715 (uri (cran-uri "zyp" version))
24718 "03cxpkfbhrx1fy8l0dl9a13ghz93cqq6877wa8rig09ksdiivaw9"))))
24719 (properties `((upstream-name . "zyp")))
24720 (build-system r-build-system)
24723 (home-page "https://cran.r-project.org/web/packages/zyp/")
24724 (synopsis "Zhang + Yue-Pilon Trends Package")
24726 "This package contains an efficient implementation of Sen's slope
24727 method (Sen, 1968) plus implementation of Xuebin Zhang's (Zhang, 1999) and
24728 Yue-Pilon's (Yue, 2002) pre-whitening approaches to determining trends in
24730 (license license:lgpl2.1)))
24732 (define-public r-rlinsolve
24734 (name "r-rlinsolve")
24739 (uri (cran-uri "Rlinsolve" version))
24742 "1xv500n1480qyakw0isanw1s5ywykhc207hqja4804s5s2m8zfjw"))))
24743 (properties `((upstream-name . "Rlinsolve")))
24744 (build-system r-build-system)
24746 (list r-matrix r-rcpp r-rcpparmadillo r-rdpack))
24747 (home-page "https://cran.r-project.org/web/packages/Rlinsolve/")
24748 (synopsis "Iterative solvers for (sparse) linear system of equations")
24750 "Solving a system of linear equations is one of the most fundamental
24751 computational problems for many fields of mathematical studies, such as
24752 regression problems from statistics or numerical partial differential
24753 equations. This package provides basic stationary iterative solvers such as
24754 Jacobi, Gauss-Seidel, Successive Over-Relaxation and SSOR methods.
24755 Nonstationary, also known as Krylov subspace methods are also provided.
24756 Sparse matrix computation is also supported in that solving large and sparse
24757 linear systems can be manageable using the @code{Matrix} package along with
24758 @code{RcppArmadillo}.")
24759 (license license:gpl3+)))
24761 (define-public r-zvcv
24768 (uri (cran-uri "ZVCV" version))
24771 "0gc76j9i8fkm2v638nyzzb1qxl4zmapbspkkaffb8gi5qyjja448"))))
24772 (properties `((upstream-name . "ZVCV")))
24773 (build-system r-build-system)
24784 (home-page "https://cran.r-project.org/web/packages/ZVCV/")
24785 (synopsis "Zero-Variance Control Variates")
24787 "@dfn{Zero-variance control variates} (ZV-CV) is a post-processing method
24788 to reduce the variance of Monte Carlo estimators of expectations using the
24789 derivatives of the log target. Once the derivatives are available, the only
24790 additional computational effort is in solving a linear regression problem.
24791 This method has been extended to higher dimensions using regularisation. This
24792 package can be used to easily perform ZV-CV or regularised ZV-CV when a set of
24793 samples, derivatives and function evaluations are available. Additional
24794 functions for applying ZV-CV to two estimators for the normalising constant of
24795 the posterior distribution in Bayesian statistics are also supplied.")
24796 (license license:gpl2+)))
24798 (define-public r-ztype
24805 (uri (cran-uri "ztype" version))
24808 "0brbq2rgkl4mhjbb70kkfv47lzs66k9ppfs2klavcbripirxn5fx"))))
24809 (properties `((upstream-name . "ztype")))
24810 (build-system r-build-system)
24819 (home-page "https://cran.r-project.org/web/packages/ztype/")
24820 (synopsis "Run a Ztype game loaded with R functions")
24822 "How fast can you type R functions on your keyboard? Find out by running
24823 a @code{zty.pe} game: export R functions as instructions to type to destroy
24824 opponents' vessels.")
24825 (license license:gpl3)))
24827 (define-public r-zseq
24834 (uri (cran-uri "Zseq" version))
24837 "06dndi2b1q79bmxax11bv0l5ifcz1mhpvbn90y6a6xymrgcq0ivi"))))
24838 (properties `((upstream-name . "Zseq")))
24839 (build-system r-build-system)
24842 (home-page "https://cran.r-project.org/web/packages/Zseq/")
24843 (synopsis "Integer sequence generator")
24845 "This package generates well-known integer sequences. The @code{gmp}
24846 package is adopted for computing with arbitrarily large numbers. Every
24847 function has a hyperlink to its corresponding item in the @dfn{On-Line
24848 Encyclopedia of Integer Sequences} (OEIS) in the function help page.")
24849 (license license:gpl3+)))
24851 (define-public r-isoband
24858 (uri (cran-uri "isoband" version))
24861 "19bbi0n0kz33xdgmdprcmc6raphd1hcm1w1brc16z5phcsh3zxa6"))))
24862 (properties `((upstream-name . "isoband")))
24863 (build-system r-build-system)
24866 (home-page "https://github.com/wilkelab/isoband")
24867 (synopsis "Generate isolines and isobands from regularly spaced elevation grids")
24869 "This package provides a fast C++ implementation to generate contour
24870 lines (isolines) and contour polygons (isobands) from regularly spaced grids
24871 containing elevation data.")
24872 (license license:expat)))
24874 (define-public r-ppcor
24881 (uri (cran-uri "ppcor" version))
24884 "1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"))))
24885 (properties `((upstream-name . "ppcor")))
24886 (build-system r-build-system)
24889 (home-page "https://cran.r-project.org/web/packages/ppcor/")
24890 (synopsis "Partial and semi-partial correlation")
24892 "This package provides users not only with a function to readily
24893 calculate the higher-order partial and semi-partial correlations but also with
24894 statistics and p-values of the correlation coefficients.")
24895 (license license:gpl2)))
24897 (define-public r-hrbrthemes
24899 (name "r-hrbrthemes")
24904 (uri (cran-uri "hrbrthemes" version))
24906 (base32 "057h60b5p53dcyjyfwlgjc1ry968s9s64dw78p443w8717zk7zpc"))))
24907 (properties `((upstream-name . "hrbrthemes")))
24908 (build-system r-build-system)
24920 (home-page "https://github.com/hrbrmstr/hrbrthemes/")
24921 (synopsis "Additional themes, theme components and utilities for @code{ggplot2}")
24923 "This package provides a compilation of extra @code{ggplot2} themes,
24924 scales and utilities, including a spell check function for plot label fields
24925 and an overall emphasis on typography.")
24926 (license license:expat)))
24928 (define-public r-crochet
24935 (uri (cran-uri "crochet" version))
24938 "0zvjaf6cv0nrjb4l4llkr0mmgha7ig31p4ri2rlnqyjlxi5l8hyq"))))
24939 (build-system r-build-system)
24942 (home-page "https://github.com/agrueneberg/crochet")
24943 (synopsis "Implementation Helper for Matrix-Like Types")
24945 "Functions to help implement the extraction / subsetting / indexing
24946 function @code{[} and replacement function @code{[<-} of custom matrix-like
24947 types (based on S3, S4, etc.), modeled as closely to the base matrix class
24948 as possible (with tests to prove it).")
24949 (license license:expat)))
24951 (define-public r-boa
24954 (version "1.1.8-2")
24958 (uri (cran-uri "boa" version))
24961 "04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"))))
24962 (properties `((upstream-name . "boa")))
24963 (build-system r-build-system)
24964 (home-page "https://www.jstatsoft.org/v21/i11")
24965 (synopsis "Library for @dfn{Bayesian Output Analysis Program} (BOA) for MCMC")
24967 "This package provides a menu-driven program and library of functions for
24968 carrying out convergence diagnostics and statistical and graphical analysis of
24969 @dfn{Markov chain Monte Carlo} (MCMC) sampling output.")
24970 (license license:gpl2+)))
24972 (define-public r-httpcode
24974 (name "r-httpcode")
24978 (uri (cran-uri "httpcode" version))
24981 "0xig0rvc81hg7mw0iq9s0an1nw24fg0kfs2p2n6dzhwl9w506fjr"))))
24982 (build-system r-build-system)
24983 (home-page "https://github.com/sckott/httpcode")
24984 (synopsis "HTTP status code helper")
24985 (description "@code{httpcode} provides functionality for finding and
24986 explaining the meaning of @code{HTTP} status codes. Functions are included for
24987 searching for codes by full or partial number, by message, and to get
24988 appropriate dog and cat images for many status codes.")
24989 (license license:expat)))
24991 (define-public r-latex2exp
24993 (name "r-latex2exp")
24997 (uri (cran-uri "latex2exp" version))
25000 "0hfixybyds1jxhyiy3p6256z0fxzc65r654jhc62q9cd3v86a5z6"))))
25001 (build-system r-build-system)
25003 (list r-stringr r-magrittr))
25006 (home-page "https://github.com/stefano-meschiari/latex2exp/")
25007 (synopsis "Use LaTeX expressions in plots")
25008 (description "@code{latex2exp} parses and converts LaTeX math formulas to
25009 R's plotmath expressions, used to enter mathematical formulas and symbols to be
25010 rendered as text, axis labels, etc. throughout R's plotting system.")
25011 (license license:expat)))
25013 (define-public r-oai
25019 (uri (cran-uri "oai" version))
25022 "1zcbcxhw692s0y6izvwazyzhgx0iwsxsbcan2nk0mb7n11p7bypb"))))
25023 (build-system r-build-system)
25025 (list r-xml2 r-httr r-plyr r-stringr r-tibble))
25028 (home-page "https://github.com/ropensci/oai/")
25029 (synopsis "General purpose OAI-PMH services client")
25030 (description "@code{oai} provides a general purpose client to work with
25031 any @dfn{Open Archives Initiative Protocol for 'Metadata' Harvesting} (OAI-PMH)
25032 service. Functions are provided to work with the OAI-PMH verbs:
25033 @code{GetRecord}, @code{Identify}, @code{ListIdentifiers},
25034 @code{ListMetadataFormats}, @code{ListRecords}, and @code{ListSets}.")
25035 (license license:expat)))
25037 (define-public r-argon2
25044 (uri (cran-uri "argon2" version))
25047 "09hzl0wz0lw2v7g64rdv0lij2hq36zl37a6rmxwvinmjdzijcsyw"))))
25048 (properties `((upstream-name . "argon2")))
25049 (build-system r-build-system)
25050 (home-page "https://github.com/wrathematics/argon2")
25051 (synopsis "Secure password hashing based on the argon2 algorithm")
25053 "This package provides utilities for secure password hashing via the
25054 argon2 algorithm.")
25055 (license license:bsd-2)))
25057 (define-public r-getpass
25064 (uri (cran-uri "getPass" version))
25067 "03ydafhh0sk3rcnpr3paajyji64x2ddp6p814p9mvbmyrblcgzcc"))))
25068 (properties `((upstream-name . "getPass")))
25069 (build-system r-build-system)
25071 (list r-rstudioapi))
25072 (home-page "https://github.com/wrathematics/getPass")
25073 (synopsis "Masked user input")
25075 "This package provides a micro-package for reading \"passwords\", i.e.
25076 reading user input with masking, so that the input is not displayed as it is
25077 typed. Currently, RStudio, the command line (every OS), and any platform
25078 where tcltk is present are supported.")
25079 (license license:bsd-2)))
25081 (define-public r-remoter
25088 (uri (cran-uri "remoter" version))
25091 "1a7m63l8phv5jnazvdqdrqkaqjwqzaac5y4jm2jn0ypy4n8jvkfl"))))
25092 (properties `((upstream-name . "remoter")))
25093 (build-system r-build-system)
25095 (list r-argon2 r-getpass r-pbdzmq r-png))
25096 (home-page "https://github.com/RBigData/remoter")
25097 (synopsis "Control a remote R session from a local one")
25099 "This package provides a set of utilities for client/server computing
25100 with R, controlling a remote R session (the server) from a local one (the
25102 (license license:bsd-2)))
25104 (define-public r-asd
25111 (uri (cran-uri "asd" version))
25114 "0p3r4qjam3sl3rpcilb0pgx4xx3ly71xqnvkv31vzjs885lgxz4l"))))
25115 (properties `((upstream-name . "asd")))
25116 (build-system r-build-system)
25119 (home-page "https://cran.r-project.org/web/packages/asd")
25120 (synopsis "Simulations for Adaptive Seamless Designs")
25122 "This package provdes means to run simulations for adaptive seamless
25123 designs with and without early outcomes for treatment selection and
25124 subpopulation type designs.")
25125 (license license:gpl3)))
25127 (define-public r-nbconvertr
25129 (name "r-nbconvertr")
25134 (uri (cran-uri "nbconvertR" version))
25137 "0yhmz177r1miain65vspclahhz8cg7638ldbpsw8ylgf7a60l0sg"))))
25138 (properties `((upstream-name . "nbconvertR")))
25139 (build-system r-build-system)
25141 (list python-nbconvert pandoc))
25142 (home-page "https://cran.r-project.org/web/packages/nbconvertR/")
25143 (synopsis "Vignette engine wrapping Jupyter notebooks")
25145 "This package calls the Jupyter script @code{nbconvert} to create
25146 vignettes from notebooks. Those notebooks (@code{.ipynb} files) are files
25147 containing rich text, code, and its output. Code cells can be edited and
25148 evaluated interactively.")
25149 (license license:gpl3)))
25151 (define-public r-bridgesampling
25153 (name "r-bridgesampling")
25158 (uri (cran-uri "bridgesampling" version))
25161 "0sry1xwiv4y52k44hq6z8y2kysp5kxgl4dix3m94svg3ladd7v2l"))))
25163 `((upstream-name . "bridgesampling")))
25164 (build-system r-build-system)
25166 (list r-brobdingnag
25174 (home-page "https://github.com/quentingronau/bridgesampling")
25175 (synopsis "Bridge sampling for marginal likelihoods and Bayes factors")
25177 "This package provides functions for estimating marginal likelihoods,
25178 Bayes factors, posterior model probabilities, and normalizing constants in
25179 general, via different versions of bridge sampling.")
25180 (license license:gpl2+)))
25182 (define-public r-tea
25189 (uri (cran-uri "tea" version))
25192 "0ql7lrxk0ihm49kqsvz79ig8i54rwiy9nxav4v9hy72j9kj5bgjn"))))
25194 `((upstream-name . "tea")))
25195 (build-system r-build-system)
25198 (home-page "https://cran.r-project.org/web/packages/tea/")
25199 (synopsis "Threshold estimation approaches")
25201 "This package provides different approaches for selecting the threshold
25202 in generalized Pareto distributions. Most of them are based on minimizing the
25203 AMSE-criterion or at least by reducing the bias of the assumed GPD-model.
25204 Others are heuristically motivated by searching for stable sample paths, i.e.
25205 a nearly constant region of the tail index estimator with respect to k, which
25206 is the number of data in the tail. The third class is motivated by graphical
25207 inspection. In addition, a sequential testing procedure for GPD-GoF-tests
25208 is also implemented here.")
25209 (license license:gpl3)))
25211 (define-public r-awsmethods
25213 (name "r-awsmethods")
25218 (uri (cran-uri "awsMethods" version))
25221 "0hbmrcpdyg15zg4rysscsmxpxlpy0dkxx2aa63qibq7l1k14v4sh"))))
25223 `((upstream-name . "awsMethods")))
25224 (build-system r-build-system)
25225 (home-page "http://www.wias-berlin.de/software/imaging/")
25226 (synopsis "Class and methods definitions")
25228 "This package defines the generic method @code{extract} and provides
25229 @code{openMP} support as needed in several packages like
25230 @code{aws}, @code{adimpro}, @code{fmri}, and @code{dwi}.")
25231 (license license:gpl2+)))
25233 (define-public r-aws
25240 (uri (cran-uri "aws" version))
25243 "1fhm87iax6bkvd4vszvjbcqw3b2drs11rjxr7zf2w4sgc72svaz8"))))
25245 `((upstream-name . "aws")))
25246 (build-system r-build-system)
25248 (list r-awsmethods r-gsl))
25251 (home-page "https://cran.r-project.org/web/packages/aws/")
25252 (synopsis "Adaptive weights smoothing")
25254 "This package provides a collection of R-functions implementing adaptive
25255 smoothing procedures in 1D, 2D and 3D. This includes the
25256 Propagation-Separation approach to adaptive smoothing, the @dfn{Intersecting
25257 Confidence Intervals} (ICI), variational approaches, and a non-local means
25259 (license license:gpl2+)))
25261 (define-public r-sgloptim
25263 (name "r-sgloptim")
25268 (uri (cran-uri "sglOptim" version))
25271 "15bkkvgp9v9vsp65wps48g3c2fa0fj1025hbrziywq14j7wayyjr"))))
25273 `((upstream-name . "sglOptim")))
25274 (build-system r-build-system)
25285 (home-page "https://github.com/nielsrhansen/sglOptim")
25286 (synopsis "Generic sparse group Lasso solver")
25288 "This package provides a fast generic solver for sparse group lasso
25289 optimization problems. The loss (objective) function must be defined in a C++
25290 module. The optimization problem is solved using a coordinate gradient
25291 descent algorithm. Convergence of the algorithm is established and the
25292 algorithm is applicable to a broad class of loss functions. Use of parallel
25293 computing for cross validation and subsampling is supported through the
25294 @code{foreach} and @code{doParallel} packages.")
25295 (license license:gpl2+)))
25297 (define-public r-grouped
25304 (uri (cran-uri "grouped" version))
25307 "1glxgacpwk7yjbkwg5ci6bmb2il6hf5zhydwi5bbq6hc032m9976"))))
25309 `((upstream-name . "grouped")))
25310 (build-system r-build-system)
25313 (home-page "https://cran.r-project.org/web/packages/grouped/")
25314 (synopsis "Regression analysis of grouped and coarse data")
25316 "This package provides regression models for grouped and coarse data,
25317 under the coarsened at random assumption.")
25318 (license license:gpl2+)))
25320 (define-public r-stam
25327 (uri (cran-uri "stam" version))
25330 "1x1j45fir64kffny0nssb2hwn4rcp8gd2cjv6fw4yy0l4d0xi5iv"))))
25332 `((upstream-name . "stam")))
25333 (build-system r-build-system)
25336 (home-page "https://cran.r-project.org/web/packages/stam")
25337 (synopsis "Spatio-temporal analysis and modelling")
25339 "This package provides various methods to conduct Spatio-Temporal
25340 Analysis and Modelling, including Exploratory Spatio-Temporal Analysis and
25341 Inferred Spatio-Temporal Modelling.")
25342 (license license:gpl2+)))
25344 (define-public r-dcv
25351 (uri (cran-uri "dcv" version))
25354 "12c716x8dnxnqksibpmyysqp2axggvy9dpd55s9bhnsvqvi6dshj"))))
25356 `((upstream-name . "dcv")))
25357 (build-system r-build-system)
25360 (home-page "https://cran.r-project.org/web/packages/dcv/")
25361 (synopsis "Conventional cross-validation statistics for climate-growth model")
25363 "This package performs several conventional cross-validation statistical
25364 methods for climate-growth model in the climate reconstruction from tree
25365 rings, including Sign Test statistic, Reduction of Error statistic, Product
25366 Mean Test, Durbin-Watson statistic etc.")
25367 (license license:gpl2)))
25369 (define-public r-rcdd
25376 (uri (cran-uri "rcdd" version))
25379 "0zxx0qvv26ba30jkm8mvca4h59rqklay4jwazpcw7h9dzp4189jr"))))
25381 `((upstream-name . "rcdd")))
25382 (build-system r-build-system)
25385 (home-page "https://www.stat.umn.edu/geyer/rcdd/")
25386 (synopsis "Computational geometry")
25388 "This package converts back and forth between two representations of a
25389 convex polytope: as solution of a set of linear equalities and inequalities
25390 and as convex hull of set of points and rays. Also does linear programming
25391 and redundant generator elimination. All functions can use exact
25392 infinite-precision rational arithmetic.")
25393 (license license:gpl2)))
25395 (define-public r-rxnat
25402 (uri (cran-uri "Rxnat" version))
25405 "0siylypjd8cgcmr2c443w8krg8sgr5gz4zapbinanp8vsfzivdv2"))))
25407 `((upstream-name . "Rxnat")))
25408 (build-system r-build-system)
25410 (list r-httr r-rcurl r-tibble))
25413 (home-page "https://cran.r-project.org/web/packages/Rxnat/")
25414 (synopsis "Queries and extracts images from neuroimaging datasets")
25416 "This package allows communication with the Extensible Neuroimaging
25417 Archive Toolkit. Rxnat uses the XNAT REST API to perform data queries and
25419 (license license:gpl2)))
25421 (define-public r-rserve
25428 (uri (string-append "http://www.rforge.net/Rserve/snapshot/Rserve_"
25429 version ".tar.gz"))
25432 "017kkzv9lxlz9qhg3gprrf1wcyflxrif6wjk27x9b4bdzylw6bsx"))))
25433 (build-system r-build-system)
25436 (modify-phases %standard-phases
25437 (add-before 'install 'install-server-binary
25438 ;; Makevars tries to install to R's store directory.
25439 (lambda* (#:key outputs #:allow-other-keys)
25440 (let* ((out (assoc-ref outputs "out"))
25441 (bin (string-append out "/bin")))
25442 (substitute* "src/Makevars.in"
25443 (("\\$\\(R_HOME\\)") out))
25444 (mkdir-p bin)))))))
25454 (list openssl zlib))
25455 (home-page "https://github.com/s-u/Rserve")
25457 "Server providing access to R from many languages and systems")
25459 "Rserve acts as a socket server (TCP/IP or local sockets) which allows
25460 binary requests to be sent to R. Every connection has a separate workspace
25461 and working directory. Client-side implementations are available for popular
25462 languages such as C/C++ and Java, allowing any application to use facilities
25463 of R without the need of linking to R code. Rserve supports remote
25464 connection, user authentication and file transfer. A simple R client is
25465 included in this package as well.")
25466 (license license:gpl2)))
25468 (define-public r-gamm4
25475 (uri (cran-uri "gamm4" version))
25478 "128c725y9s07c1m9cvd9hgi9hldrymcs5divd8pw7bdjh9jvdiap"))))
25479 (properties `((upstream-name . "gamm4")))
25480 (build-system r-build-system)
25482 (list r-lme4 r-matrix r-mgcv))
25483 (home-page "https://cran.r-project.org/web/packages/gamm4/")
25484 (synopsis "Generalized additive mixed models using mgcv and lme4")
25486 "Estimate generalized additive mixed models via a version of function
25487 @code{gamm} from the @code{mgcv} package, using the @code{lme4} packagefor
25489 (license license:gpl2+)))
25491 (define-public r-optimx
25494 (version "2021-10.12")
25498 (uri (cran-uri "optimx" version))
25501 "0hvrpfya767vp3anmb8ih516v4zz1sv4h193rn93kyjydf2lqf1r"))))
25502 (properties `((upstream-name . "optimx")))
25503 (build-system r-build-system)
25504 (propagated-inputs (list r-numderiv))
25505 (native-inputs (list r-knitr))
25506 (home-page "https://cran.r-project.org/web/packages/optimx/")
25507 (synopsis "Expanded replacement and extension of the optim function")
25509 "This package provides a replacement and extension of the @code{optim}
25510 function to call to several function minimization codes in R in a single
25511 statement. These methods handle smooth, possibly box constrained functions of
25512 several or many parameters. Note that the function @code{optimr} was prepared
25513 to simplify the incorporation of minimization codes going forward. This
25514 package also implements some utility codes and some extra solvers, including
25515 safeguarded Newton methods. Many methods previously separate are now included
25517 (license license:gpl2)))
25519 (define-public r-projpred
25521 (name "r-projpred")
25526 (uri (cran-uri "projpred" version))
25529 "0nx514mrfh3gv854pr71w5x3zgdnn0kinf5nh7z90q3h7ysry2mg"))))
25530 (properties `((upstream-name . "projpred")))
25531 (build-system r-build-system)
25547 (native-inputs (list r-knitr))
25548 (home-page "https://mc-stan.org/projpred/")
25549 (synopsis "Projection predictive feature selection")
25551 "This package performs projection predictive feature selection for
25552 generalized linear models and generalized linear and additive multilevel
25553 models. The package is compatible with the @code{rstanarm} and @code{brms}
25554 packages, but other reference models can also be used. See the package
25555 vignette for more information and examples.")
25556 (license license:gpl3)))
25558 (define-public r-distributional
25560 (name "r-distributional")
25565 (uri (cran-uri "distributional" version))
25568 "1mji8xlhwrw8msih5wdpbzwv4g59kly0xkdklhn8yzb18rrnrczs"))))
25570 `((upstream-name . "distributional")))
25571 (build-system r-build-system)
25583 (home-page "https://pkg.mitchelloharawild.com/distributional/")
25584 (synopsis "Vectorized probability distributions")
25586 "This package provides vectorized distribution objects with tools for
25587 manipulating, visualizing, and using probability distributions. It was
25588 designed to allow model prediction outputs to return distributions rather than
25589 their parameters, allowing users to directly interact with predictive
25590 distributions in a data-oriented workflow. In addition to providing generic
25591 replacements for p/d/q/r functions, other useful statistics can be computed
25592 including means, variances, intervals, and highest density regions.")
25593 (license license:gpl3)))
25595 (define-public r-posterior
25597 (name "r-posterior")
25602 (uri (cran-uri "posterior" version))
25605 "11j3jgk8mykicqi77a6frn0gck7fx0i6sl6g774sqj44m48ig81b"))))
25606 (properties `((upstream-name . "posterior")))
25607 (build-system r-build-system)
25620 (home-page "https://mc-stan.org/posterior/")
25621 (synopsis "Tools for working with posterior distributions")
25623 "This package provides useful tools for both users and developers of
25624 packages for fitting Bayesian models or working with output from Bayesian
25625 models. The primary goals of the package are to:
25628 @item Efficiently convert between many different useful formats of
25629 draws (samples) from posterior or prior distributions.
25631 @item Provide consistent methods for operations commonly performed on draws,
25632 for example, subsetting, binding, or mutating draws.
25634 @item Provide various summaries of draws in convenient formats.
25636 @item Provide lightweight implementations of state of the art posterior
25637 inference diagnostics.
25640 (license license:bsd-3)))
25642 (define-public r-brms
25649 (uri (cran-uri "brms" version))
25652 "1q93z4cf3iy4rs6pgvph6z7hc8q05iwif76hcg8p4kr6nl82nc38"))))
25653 (properties `((upstream-name . "brms")))
25654 (build-system r-build-system)
25675 (native-inputs (list r-knitr))
25677 "https://github.com/paul-buerkner/brms")
25679 "Bayesian Regression Models using 'Stan'")
25681 "Fit Bayesian generalized (non-)linear multivariate multilevel models
25682 using 'Stan' for full Bayesian inference. A wide range of distributions and
25683 link functions are supported, allowing users to fit -- among others -- linear,
25684 robust linear, count data, survival, response times, ordinal, zero-inflated,
25685 hurdle, and even self-defined mixture models all in a multilevel context.
25686 Further modeling options include non-linear and smooth terms, auto-correlation
25687 structures, censored data, meta-analytic standard errors, and quite a few
25688 more. In addition, all parameters of the response distribution can be
25689 predicted in order to perform distributional regression. Prior specifications
25690 are flexible and explicitly encourage users to apply prior distributions that
25691 actually reflect their beliefs. Model fit can easily be assessed and compared
25692 with posterior predictive checks and leave-one-out cross-validation.")
25693 (license license:gpl2)))
25695 (define-public r-mstate
25702 (uri (cran-uri "mstate" version))
25705 "054dzrd5b0xjjjl7862q3aq1jwgrxbkqz7zpvbdirqsld3zksirw"))))
25706 (properties `((upstream-name . "mstate")))
25707 (build-system r-build-system)
25718 "https://www.lumc.nl/org/bds/research/medische-statistiek/survival-analysis/")
25720 "Data Preparation, Estimation and Prediction in Multi-State Models")
25722 "Contains functions for data preparation, descriptives, hazard estimation
25723 and prediction with Aalen-Johansen or simulation in competing risks and
25724 multi-state models.")
25725 (license license:gpl2+)))
25727 (define-public r-scatterpie
25729 (name "r-scatterpie")
25734 (uri (cran-uri "scatterpie" version))
25737 "1pmspv8a7k20zyd5xvmav2k9mnjrkfhdij3rr9k504zyki8hfy1z"))))
25738 (properties `((upstream-name . "scatterpie")))
25739 (build-system r-build-system)
25741 (list r-ggforce r-ggfun r-ggplot2 r-rlang r-tidyr))
25744 (home-page "https://cran.r-project.org/web/packages/scatterpie/")
25745 (synopsis "Scatter pie plot")
25747 "This package creates scatterpie plots, especially useful for plotting
25749 (license license:artistic2.0)))
25751 (define-public r-scrypt
25758 (uri (cran-uri "scrypt" version))
25761 "14iblgbp9v2by8fjbrpsd59iknp5babcz7j3yv1yxxzcwyb6wrrm"))))
25762 (properties `((upstream-name . "scrypt")))
25763 (build-system r-build-system)
25766 (home-page "https://github.com/rstudio/rscrypt")
25767 (synopsis "Key derivation functions for R based on Scrypt")
25769 "This package provides functions for working with the scrypt key
25770 derivation functions. Scrypt is a password-based key derivation function
25771 created by Colin Percival. The algorithm was specifically designed to make it
25772 costly to perform large-scale custom hardware attacks by requiring large
25773 amounts of memory.")
25774 (license license:bsd-2)))
25776 (define-public r-boruta
25783 (uri (cran-uri "Boruta" version))
25786 "0y2w4wb45kfnzrxcrdsiwgal9fsnlr3wad1sqdc70qv8gp921xbg"))))
25787 (properties `((upstream-name . "Boruta")))
25788 (build-system r-build-system)
25789 (propagated-inputs (list r-ranger))
25790 (home-page "https://gitlab.com/mbq/Boruta/")
25791 (synopsis "Wrapper algorithm for all relevant feature selection")
25793 "This package provides an all relevant feature selection wrapper
25794 algorithm. It finds relevant features by comparing original attributes'
25795 importance with importance achievable at random, estimated using their
25796 permuted copies (shadows).")
25797 (license license:gpl2+)))
25799 (define-public r-directlabels
25801 (name "r-directlabels")
25802 (version "2021.1.13")
25806 (uri (cran-uri "directlabels" version))
25809 "0415kh9k2qzdwi8zb32fh2icl5wf5335kyj11cyfdmfxji39zv2w"))))
25810 (build-system r-build-system)
25815 (home-page "http://directlabels.r-forge.r-project.org/")
25816 (synopsis "Direct labels for multicolor plots")
25818 "This package provides an extensible framework for automatically placing
25819 direct labels onto multicolor plots. Label positions are described using
25820 positioning methods that can be re-used across several different plots. There
25821 are heuristics for examining @code{trellis} and @code{ggplot} objects and
25822 inferring an appropriate positioning method.")
25823 (license license:gpl3)))
25825 (define-public r-lsd
25832 (uri (cran-uri "LSD" version))
25834 (base32 "17pbdlcbhzf3v7l42mjikln1ga5xjp5r78gjg6a88iahk0lwwlvm"))))
25835 (properties `((upstream-name . "LSD")))
25836 (build-system r-build-system)
25837 (home-page "https://cran.r-project.org/web/packages/LSD/")
25838 (synopsis "Lots of superior depictions tool creates colorful plots")
25840 "This package creates lots of colorful plots in a multitude of variations.
25841 Try a demo of the LSD by running @code{demotour()}.")
25843 (license (list license:gpl2 license:gpl3))))
25845 (define-public r-phylogram
25847 (name "r-phylogram")
25852 (uri (cran-uri "phylogram" version))
25854 (base32 "1p4h5pirc0m5pzc18q0jk3mcmb5n48gdf9abz03vml3a209xxl2v"))))
25855 (properties `((upstream-name . "phylogram")))
25856 (build-system r-build-system)
25857 (propagated-inputs (list r-ape))
25858 (home-page "https://github.com/ropensci/phylogram/")
25859 (synopsis "Dendrograms for evolutionary analysis")
25861 "The @code{r-phylogram} package is a tool for for developing phylogenetic
25862 trees as deeply-nested lists known as \"dendrogram\" objects. It provides
25863 functions for conversion between \"dendrogram\" and \"phylo\" class objects,
25864 as well as several tools for command-line tree manipulation and import/export
25865 via Newick parenthetic text. This improves accessibility to the comprehensive
25866 range of object-specific analytical and tree-visualization functions found
25867 across a wide array of bioinformatic R packages.")
25868 (license license:gpl3)))
25870 (define-public r-kmer
25877 (uri (cran-uri "kmer" version))
25879 (base32 "0jimn9r0abglwxdl1zqz0lxa99cmj6haydkxjzqfbpx9by80wnww"))))
25880 (properties `((upstream-name . "kmer")))
25881 (build-system r-build-system)
25883 (list r-openssl r-phylogram r-rcpp))
25884 (home-page "https://github.com/shaunpwilkinson/kmer/")
25885 (synopsis "Fast K-Mer counting and clustering for biological sequence analysis")
25887 "@code{r-kmer} is an R package for rapidly computing distance matrices
25888 and clustering large sequence datasets using fast alignment-free k-mer
25889 counting and recursive k-means partitioning.")
25890 (license license:gpl3)))
25892 (define-public r-hardhat
25899 (uri (cran-uri "hardhat" version))
25902 "07mx8c24gy0xfmip9hb5w29gp10sfnpnilzc1pi0hjadnrqz8mks"))))
25903 (properties `((upstream-name . "hardhat")))
25904 (build-system r-build-system)
25906 (list r-glue r-rlang r-tibble r-vctrs))
25909 (home-page "https://github.com/tidymodels/hardhat")
25910 (synopsis "Construct modeling packages")
25912 "Building modeling packages is hard. A large amount of effort generally
25913 goes into providing an implementation for a new method that is efficient,
25914 fast, and correct, but often less emphasis is put on the user interface. A
25915 good interface requires specialized knowledge about S3 methods and formulas,
25916 which the average package developer might not have. The goal of
25917 @code{hardhat} is to reduce the burden around building new modeling packages
25918 by providing functionality for preprocessing, predicting, and validating
25920 (license license:expat)))
25922 (define-public r-lightgbm
25924 (name "r-lightgbm")
25929 (uri (cran-uri "lightgbm" version))
25932 "12hbvm1va6sb5yny564jvhhzrkcq4j33rcdhqhwxaac2m08cpi8s"))))
25933 (properties `((upstream-name . "lightgbm")))
25934 (build-system r-build-system)
25936 (list r-data-table r-jsonlite r-matrix r-r6))
25937 (home-page "https://github.com/Microsoft/LightGBM")
25938 (synopsis "Light gradient boosting machine")
25940 "Tree based algorithms can be improved by introducing boosting
25941 frameworks. LightGBM is one such framework, based on Ke, Guolin et
25942 al. (2017). This package offers an R interface to work with it. It is
25943 designed to be distributed and efficient with the following goals:
25946 @item Faster training speed and higher efficiency;
25947 @item lower memory usage;
25948 @item better accuracy;
25949 @item parallel learning supported; and
25950 @item capable of handling large-scale data.
25953 (license license:expat)))
25955 (define-public r-shapforxgboost
25957 (name "r-shapforxgboost")
25962 (uri (cran-uri "SHAPforxgboost" version))
25965 "106nsf02b1w3yshb55lwnyw1rl1a60162v2wk8znjz3b4ln3mqj5"))))
25967 `((upstream-name . "SHAPforxgboost")))
25968 (build-system r-build-system)
25980 (home-page "https://github.com/liuyanguu/SHAPforxgboost")
25981 (synopsis "SHAP Plots for XGBoost")
25983 "The aim of @code{SHAPforxgboost} is to aid in visual data investigations
25984 using @dfn{SHAP} (Shapley additive explanation) visualization plots for
25985 @code{XGBoost}. It provides summary plot, dependence plot, interaction plot,
25986 and force plot. It relies on the @code{XGBoost} package to produce SHAP
25988 (license license:expat)))
25990 (define-public r-rismed
25997 (uri (cran-uri "RISmed" version))
26000 "0vpi88gzi9r85v6nhjz9jbw671zkrmyazwna2z881346wfyr3l8b"))))
26001 (properties `((upstream-name . "RISmed")))
26002 (build-system r-build-system)
26004 (list r-httr r-xml2))
26005 (home-page "https://cran.r-project.org/web/packages/RISmed")
26006 (synopsis "Download content from NCBI databases")
26008 "This package provides a set of tools to extract bibliographic
26009 content from the National Center for Biotechnology Information (NCBI)
26010 databases, including PubMed. The name RISmed is a portmanteau of
26011 RIS (for Research Information Systems, a common tag format for
26012 bibliographic data) and PubMed.")
26013 (license license:gpl2+)))
26015 (define-public r-semver
26022 (uri (cran-uri "semver" version))
26025 "10wpkyms2cix3bsin2q0qhkbl445pwwpa5gm2s4jjw1989namkxy"))))
26026 (properties `((upstream-name . "semver")))
26027 (build-system r-build-system)
26029 (list r-assertthat r-rcpp))
26030 (native-inputs (list r-knitr))
26031 (home-page "https://github.com/johndharrison/semver")
26032 (synopsis "Parser for Semantic Versioning 2.0.0")
26034 "This package provides tools and functions for parsing, rendering and
26035 operating on semantic version strings. Semantic versioning is a simple set of
26036 rules and requirements that dictate how version numbers are assigned and
26037 incremented as outlined at @url{http://semver.org}.")
26038 (license license:expat)))
26040 (define-public r-binman
26047 (uri (cran-uri "binman" version))
26050 "00l7m98h41r67gf0qxqis3vx63j7wylnk9vlgcyk41szkrz8ikkc"))))
26051 (properties `((upstream-name . "binman")))
26052 (build-system r-build-system)
26061 (native-inputs (list r-knitr))
26062 (home-page "https://github.com/ropensci/binman")
26063 (synopsis "Binary download manager")
26065 "This package provides tools and functions for managing the download of
26066 binary files. Binary repositories are defined in the YAML format. Defining
26067 new pre-download, download and post-download templates allow additional
26068 repositories to be added.")
26069 (license license:expat)))
26071 (define-public r-wdman
26078 (uri (cran-uri "wdman" version))
26081 "1yf41lsrr9dbf5n4f5hv9mlmzl736fhnp9gxkm2g9apws6gsig02"))))
26082 (properties `((upstream-name . "wdman")))
26083 (build-system r-build-system)
26085 (list r-assertthat r-binman r-processx r-semver r-yaml))
26086 (native-inputs (list r-knitr))
26087 (home-page "https://docs.ropensci.org/wdman/")
26088 (synopsis "Webdriver/Selenium binary manager")
26090 "There are a number of binary files associated with the
26091 Webdriver/Selenium project (see @url{http://www.seleniumhq.org/download/},
26092 @url{https://sites.google.com/a/chromium.org/chromedriver/},
26093 @url{https://github.com/mozilla/geckodriver},
26094 @url{http://phantomjs.org/download.html}, and
26095 @url{https://github.com/SeleniumHQ/selenium/wiki/InternetExplorerDriver} for
26096 more information). This package provides functions to download these binaries
26097 and to manage processes involving them.")
26098 (license license:expat)))
26100 (define-public r-rselenium
26102 (name "r-rselenium")
26107 (uri (cran-uri "RSelenium" version))
26110 "1xn5fdbzmq7b1f5fc9ls23g177bmnd8bn4p4d8aafr6z3jwkmfir"))))
26111 (properties `((upstream-name . "RSelenium")))
26112 (build-system r-build-system)
26120 (native-inputs (list r-knitr))
26121 (home-page "https://docs.ropensci.org/RSelenium/")
26122 (synopsis "R bindings for Selenium WebDriver")
26124 "This package provides a set of R bindings for the Selenium 2.0
26125 WebDriver (see @url{https://selenium.dev/documentation/en/} for more
26126 information) using the @code{JsonWireProtocol} (see
26127 @url{https://github.com/SeleniumHQ/selenium/wiki/JsonWireProtocol} for more
26128 information). Selenium 2.0 WebDriver allows driving a web browser natively as
26129 a user would either locally or on a remote machine using the Selenium server
26130 it marks a leap forward in terms of web browser automation. Selenium
26131 automates web browsers (commonly referred to as browsers). Using RSelenium
26132 you can automate browsers locally or remotely.")
26133 (license license:agpl3+)))
26135 (define-public r-conquer
26142 (uri (cran-uri "conquer" version))
26145 "0i9g27f52zl2kb2392g0y614drf6s87dqz12aphj889ajq7zjm0k"))))
26146 (properties `((upstream-name . "conquer")))
26147 (build-system r-build-system)
26149 (list r-caret r-matrix r-matrixstats r-rcpp r-rcpparmadillo))
26150 (home-page "https://github.com/XiaoouPan/conquer")
26151 (synopsis "Convolution-type smoothed quantile regression")
26153 "This package provides fast and accurate convolution-type smoothed
26154 quantile regression, implemented using Barzilai-Borwein gradient descent with
26155 a Huber regression warm start. Confidence intervals for regression
26156 coefficients are constructed using multiplier bootstrap.")
26157 (license license:gpl3)))
26159 (define-public r-fastshap
26161 (name "r-fastshap")
26166 (uri (cran-uri "fastshap" version))
26169 "0gxch67i3bj6m8nb94m5hswq058w6n1q9war4dy2qnimlv7cmhdv"))))
26170 (properties `((upstream-name . "fastshap")))
26171 (build-system r-build-system)
26181 (home-page "https://github.com/bgreenwell/fastshap")
26182 (synopsis "Fast approximate Shapley values")
26184 "This package computes fast (relative to other implementations)
26185 approximate Shapley values for any supervised learning model. Shapley values
26186 help to explain the predictions from any black box model using ideas from game
26187 theory; see @url{Strumbel and Kononenko (2014),
26188 doi.org/10.1007/s10115-013-0679-x} for details.")
26189 (license license:gpl2+)))
26191 (define-public r-memuse
26197 (uri (cran-uri "memuse" version))
26200 "1wvwnjaaiv2647561z2b55dss35033ildx4kk8hzxfzgsjmdpsgm"))))
26201 (properties `((upstream-name . "memuse")))
26202 (build-system r-build-system)
26203 (home-page "https://github.com/shinra-dev/memuse")
26204 (synopsis "Memory Estimation Utilities")
26206 "This package provides procedures to answer the following questions:
26207 How much ram do you need to store a 100,000 by 100,000 matrix? How much ram is
26208 your current R session using? How much ram do you even have?")
26209 (license license:bsd-2)))
26211 (define-public r-metrics
26218 (uri (cran-uri "Metrics" version))
26221 "0fh8qbjlwzagh272lgwr4bxcqcjb1qpz53mgs8rzlvncax6nk5bk"))))
26222 (properties `((upstream-name . "Metrics")))
26223 (build-system r-build-system)
26224 (home-page "https://github.com/mfrasco/Metrics")
26225 (synopsis "Evaluation metrics for machine learning")
26227 "This package provides an implementation of evaluation metrics in R that
26228 are commonly used in supervised machine learning. It implements metrics for
26229 regression, time series, binary classification, classification, and
26230 information retrieval problems. It has zero dependencies and a consistent,
26231 simple interface for all functions.")
26232 (license license:bsd-3)))
26234 (define-public r-iml
26241 (uri (cran-uri "iml" version))
26244 "1wz6xqhvqkzj723nw7qrlwb1171wvvpxhv3pa8cq7vcbkiflq37r"))))
26245 (properties `((upstream-name . "iml")))
26246 (build-system r-build-system)
26258 (native-inputs (list r-knitr))
26259 (home-page "https://github.com/christophM/iml")
26260 (synopsis "Interpretable machine learning")
26262 "This package provides interpretability methods to analyze the behavior
26263 and predictions of any machine learning model. Implemented methods are:
26266 @item Feature importance described by Fisher et al. (2018),
26267 @item accumulated local effects plots described by Apley (2018),
26268 @item partial dependence plots described by Friedman (2001),
26269 @item individual conditional expectation ('ice') plots described by Goldstein
26270 et al. (2013) @url{https://doi.org/10.1080/10618600.2014.907095},
26271 @item local models (variant of 'lime') described by Ribeiro et. al (2016),
26272 @item the Shapley Value described by Strumbelj et. al (2014)
26273 @url{https://doi.org/10.1007/s10115-013-0679-x},
26274 @item feature interactions described by Friedman et. al
26275 @url{https://doi.org/10.1214/07-AOAS148} and tree surrogate models.
26278 (license license:expat)))
26280 (define-public r-goftest
26287 (uri (cran-uri "goftest" version))
26290 "06bz6k7smr4jbvzmb73qc5fkf4my59w5gbl18wlmpkkymsv78prs"))))
26291 (properties `((upstream-name . "goftest")))
26292 (build-system r-build-system)
26293 (home-page "https://github.com/baddstats/goftest")
26294 (synopsis "Classical Goodness-of-Fit tests for univariate distributions")
26296 "This package provides Cramer-Von Mises and Anderson-Darling tests of
26297 goodness-of-fit for continuous univariate distributions, using efficient
26299 (license license:gpl2+)))
26301 (define-public r-tensor
26308 (uri (cran-uri "tensor" version))
26311 "19mfsgr6vz4lgwidm80i4yw0y1dr3n8i6qz7g4n2xa0k74zc5pp1"))))
26312 (properties `((upstream-name . "tensor")))
26313 (build-system r-build-system)
26314 (home-page "https://cran.r-project.org/web/packages/tensor/")
26315 (synopsis "Tensor product of arrays")
26317 "The tensor product of two arrays is notionally an outer product of the
26318 arrays collapsed in specific extents by summing along the appropriate
26319 diagonals. This package allows you to compute the tensor product of arrays.")
26320 (license license:gpl2+)))
26322 (define-public r-spatstat-utils
26324 (name "r-spatstat-utils")
26329 (uri (cran-uri "spatstat.utils" version))
26332 "06nvn2ffyrskhzaavsy6lmdp0m8askkrp1fnwrhjsj01lbjnq2az"))))
26334 `((upstream-name . "spatstat.utils")))
26335 (build-system r-build-system)
26336 (home-page "http://www.spatstat.org")
26337 (synopsis "Utility functions for spatstat")
26339 "This package contains utility functions for the @code{spatstat} package
26340 which may also be useful for other purposes.")
26341 (license license:gpl2+)))
26343 (define-public r-spatstat-sparse
26345 (name "r-spatstat-sparse")
26350 (uri (cran-uri "spatstat.sparse" version))
26353 "148fxbxss569w73xaqpzwpz9rfjdgznh2ngf06gvm33631222680"))))
26355 `((upstream-name . "spatstat.sparse")))
26356 (build-system r-build-system)
26358 (list r-abind r-matrix r-spatstat-utils r-tensor))
26359 (home-page "http://spatstat.org/")
26360 (synopsis "Sparse three-dimensional arrays and linear algebra utilities")
26362 "This package defines sparse three-dimensional arrays and supports
26363 standard operations on them. The package also includes utility functions for
26364 matrix calculations that are common in statistics, such as quadratic forms.")
26365 (license license:gpl2+)))
26367 (define-public r-spatstat-data
26369 (name "r-spatstat-data")
26374 (uri (cran-uri "spatstat.data" version))
26377 "1r8s4xl25xr71h4g5qqi5y370h2ik3kz5fb4qyml2b6dwsl1ildv"))))
26378 (properties `((upstream-name . "spatstat.data")))
26379 (build-system r-build-system)
26381 (list r-matrix r-spatstat-utils))
26382 (home-page "http://www.spatstat.org")
26383 (synopsis "Datasets for spatstat")
26385 "This package contains all the datasets for the @code{spatstat}
26387 (license license:gpl2+)))
26389 (define-public r-spatstat-geom
26391 (name "r-spatstat-geom")
26396 (uri (cran-uri "spatstat.geom" version))
26399 "1h3ja45in7hnar2gwqp18jkz4rcqi99gllar6jqzlsvdbb85hgpj"))))
26400 (properties `((upstream-name . "spatstat.geom")))
26401 (build-system r-build-system)
26403 (list r-deldir r-polyclip r-spatstat-data r-spatstat-utils))
26404 (home-page "http://spatstat.org/")
26405 (synopsis "Geometrical functionality of the spatstat package")
26407 "This is a subset of the original spatstat package, containing the
26408 user-level code from spatstat which performs geometrical operations, except
26409 for the geometry of linear networks.")
26410 (license license:gpl2+)))
26412 (define-public r-spatstat-core
26414 (name "r-spatstat-core")
26419 (uri (cran-uri "spatstat.core" version))
26422 "0g7nj8nf9ywhdbc5irxlry6kzq6bwwbkk9cp22kyv1wigycnskbz"))))
26423 (properties `((upstream-name . "spatstat.core")))
26424 (build-system r-build-system)
26437 (home-page "http://spatstat.org/")
26438 (synopsis "Core functionality of the spatstat package")
26440 "This is a subset of the original spatstat package, containing all of the
26441 user-level code from spatstat, except for the code for linear networks.")
26442 (license license:gpl2+)))
26444 (define-public r-spatstat-linnet
26446 (name "r-spatstat-linnet")
26451 (uri (cran-uri "spatstat.linnet" version))
26454 "1hrqa2i6mp7d79jw4h56b8hk9590959s79vh9xcsj6k5vbisd6qi"))))
26456 `((upstream-name . "spatstat.linnet")))
26457 (build-system r-build-system)
26465 (home-page "http://spatstat.org/")
26466 (synopsis "Linear networks functionality of the spatstat package")
26468 "This is a subset of the spatstat package, containing its functionality
26469 for spatial data on a linear network.")
26470 (license license:gpl2+)))
26472 (define-public r-spatstat
26474 (name "r-spatstat")
26479 (uri (cran-uri "spatstat" version))
26482 "01jckks3j39854mhsarzyzn4rj82h1xrnyd2b6fyzizj48vl80ns"))))
26483 (properties `((upstream-name . "spatstat")))
26484 (build-system r-build-system)
26486 (list r-spatstat-core r-spatstat-data r-spatstat-geom
26487 r-spatstat-linnet r-spatstat-utils))
26488 (home-page "http://www.spatstat.org")
26489 (synopsis "Spatial Point Pattern analysis, model-fitting, simulation, tests")
26491 "This package provides a comprehensive toolbox for analysing Spatial
26492 Point Patterns. It is focused mainly on two-dimensional point patterns,
26493 including multitype/marked points, in any spatial region. It also supports
26494 three-dimensional point patterns, space-time point patterns in any number of
26495 dimensions, point patterns on a linear network, and patterns of other
26496 geometrical objects. It supports spatial covariate data such as pixel images
26497 and contains over 2000 functions for plotting spatial data, exploratory data
26498 analysis, model-fitting, simulation, spatial sampling, model diagnostics, and
26499 formal inference.")
26500 (license license:gpl2+)))
26502 (define-public r-gaston
26509 (uri (cran-uri "gaston" version))
26512 "14z94dpln4dvgrv2w7w9ik7h6rpvbf02qhq1hqzx8c2cndzxr21i"))))
26513 (properties `((upstream-name . "gaston")))
26514 (build-system r-build-system)
26515 (inputs (list zlib))
26517 (list r-rcpp r-rcppeigen r-rcppparallel))
26518 (native-inputs (list r-knitr))
26519 (home-page "https://cran.r-project.org/web/packages/gaston/")
26520 (synopsis "Genetic data handling (QC, GRM, LD, PCA) and linear mixed models")
26522 "This is a package for the manipulation of genetic data (SNPs).
26523 Computation of @dfn{genetic relationship matrix} (GRM) and dominance matrix,
26524 @dfn{linkage disequilibrium} (LD), and heritability with efficient algorithms
26525 for linear mixed models (AIREML).")
26526 (license license:gpl3)))
26528 (define-public r-cpp11
26535 (uri (cran-uri "cpp11" version))
26538 "16cvjfkbc7c0ymdmbcqg9px6pjsqx6qhyfq5frqj739mhazy0g20"))))
26539 (properties `((upstream-name . "cpp11")))
26540 (build-system r-build-system)
26541 (native-inputs (list r-knitr))
26542 (home-page "https://github.com/r-lib/cpp11")
26543 (synopsis "C++11 Interface for R's C Interface")
26545 "This package provides a header only, C++11 interface to R's C interface.
26546 Compared to other approaches @code{cpp11} strives to be safe against long
26547 jumps from the C API as well as C++ exceptions, conform to normal R function
26548 semantics and supports interaction with @code{ALTREP} vectors.")
26549 (license license:expat)))
26551 (define-public r-rcpptoml
26553 (name "r-rcpptoml")
26558 (uri (cran-uri "RcppTOML" version))
26560 (base32 "0h8517ipwqhqkhcfiyqmvsb585g01p0ra0azbpzyxip6pq6g029g"))))
26561 (properties `((upstream-name . "RcppTOML")))
26562 (build-system r-build-system)
26563 (propagated-inputs (list r-rcpp))
26564 (home-page "http://dirk.eddelbuettel.com/code/rcpp.toml.html")
26565 (synopsis "Rcpp bindings to TOML parser")
26567 "The TOML configuration format specifies an excellent format suitable for
26568 both human editing as well as the common uses of a machine-readable format.
26569 This package provides Rcpp bindings to a TOML parser.")
26570 (license license:gpl2+)))
26572 (define-public r-rcppziggurat
26574 (name "r-rcppziggurat")
26579 (uri (cran-uri "RcppZiggurat" version))
26582 "0wgd1v2p7zajnbrjf3hfi56p3pk3ld6iwkanbb04bjbnlif2ay4w"))))
26583 (properties `((upstream-name . "RcppZiggurat")))
26584 (build-system r-build-system)
26586 (list r-rcpp r-rcppgsl))
26587 (native-inputs (list r-knitr))
26588 (home-page "https://cran.r-project.org/web/packages/RcppZiggurat/")
26589 (synopsis "Rcpp integration of different \"Ziggurat\" normal RNG implementations")
26591 "The Ziggurat generator for normally distributed random numbers,
26592 originally proposed by Marsaglia and Tsang (2000,
26593 @url{https://doi.org/10.18637/jss.v005.i08}) has been improved upon a few
26594 times starting with Leong et al (2005,
26595 @url{https://doi.org/10.18637/jss.v012.i07}). This package provides an
26596 aggregation for comparing different implementations in order to provide a
26597 'faster but good enough' alternative for use with R and C++ code.")
26598 (license license:gpl2+)))
26600 (define-public r-rfast
26607 (uri (cran-uri "Rfast" version))
26610 "1n9imwkkq14ickp0g34jyha4jkr180xj0ar8xh3hqqi4dvihg6cm"))))
26611 (properties `((upstream-name . "Rfast")))
26612 (build-system r-build-system)
26614 (list r-rcpp r-rcpparmadillo r-rcppziggurat))
26615 (home-page "https://github.com/RfastOfficial/Rfast")
26616 (synopsis "Collection of efficient and fast R functions")
26618 "This package provides a collection of fast (utility) functions for data
26619 analysis. Column- and row- wise means, medians, variances, minimums,
26620 maximums, many t, F and G-square tests, many regressions (normal, logistic,
26621 Poisson), are some of the many fast functions.")
26622 (license license:gpl2+)))
26624 (define-public r-rffc
26630 (uri (string-append
26631 "https://download.r-forge.r-project.org/src/contrib/"
26632 "rfFC_" version ".tar.gz"))
26635 "05x9wgzsmx4vb12lmcspymgmpb2xw8bwryb8ysg7vzg2nkh0ma3g"))))
26636 (build-system r-build-system)
26638 (list r-randomforest))
26639 (home-page "https://r-forge.r-project.org/projects/rffc/")
26640 (synopsis "Random Forest Feature Contributions")
26641 (description "This package provides functions for extracting feature
26642 contributions from a random forest model from package @code{randomForest}.
26643 Feature contributions provide detailed information about the relationship
26644 between data variables and the predicted value returned by random forest
26646 (license license:gpl2)))
26648 (define-public r-clusterr
26650 (name "r-clusterr")
26655 (uri (cran-uri "ClusterR" version))
26658 "1fsb9pzs1paw1cbyr5a56lfh8h2d50232p6isk0xg5sl110ql7kx"))))
26659 (properties `((upstream-name . "ClusterR")))
26660 (build-system r-build-system)
26662 (list r-ggplot2 r-gmp r-gtools r-rcpp r-rcpparmadillo))
26663 (native-inputs (list r-knitr))
26664 (home-page "https://github.com/mlampros/ClusterR")
26665 (synopsis "Clustering")
26667 "This package provides Gaussian mixture models, k-means,
26668 mini-batch-kmeans, k-medoids and affinity propagation clustering with the
26669 option to plot, validate, predict (new data) and estimate the optimal number
26670 of clusters. The package takes advantage of @code{RcppArmadillo} to speed up
26671 the computationally intensive parts of the functions. For more information,
26675 @item \"Clustering in an Object-Oriented Environment\" by Anja Struyf, Mia
26676 Hubert, Peter Rousseeuw (1997), Journal of Statistical Software,
26677 @url{https://doi.org/10.18637/jss.v001.i04};
26678 @item \"Web-scale k-means clustering\" by D. Sculley (2010), ACM Digital
26679 Library, @url{https://doi.org/10.1145/1772690.1772862};
26680 @item \"Armadillo: a template-based C++ library
26681 for linear algebra\" by Sanderson et al (2016), The Journal of Open Source
26682 Software, @url{https://doi.org/10.21105/joss.00026};
26683 @item \"Clustering by Passing Messages Between Data Points\" by Brendan
26684 J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814,
26685 pp. 972-976, @url{https://doi.org/10.1126/science.1136800}.
26688 (license license:gpl3)))
26690 (define-public r-spectrum
26692 (name "r-spectrum")
26697 (uri (cran-uri "Spectrum" version))
26700 "0n38d360azkck6vvhr771zsh0gbvd9qsf9ygg5r18vhz0pb1xcfw"))))
26701 (properties `((upstream-name . "Spectrum")))
26702 (build-system r-build-system)
26704 (list r-clusterr r-diptest r-ggplot2 r-rfast))
26705 (native-inputs (list r-knitr))
26706 (home-page "https://cran.r-project.org/web/packages/Spectrum/")
26707 (synopsis "Fast adaptive spectral clustering for single and multi-view data")
26709 "This package provides a self-tuning spectral clustering method for
26710 single or multi-view data. Spectrum uses a new type of adaptive density aware
26711 kernel that strengthens connections in the graph based on common nearest
26712 neighbours. It uses a tensor product graph data integration and diffusion
26713 procedure to integrate different data sources and reduce noise. Spectrum uses
26714 either the eigengap or multimodality gap heuristics to determine the number of
26715 clusters. The method is sufficiently flexible so that a wide range of
26716 Gaussian and non-Gaussian structures can be clustered with automatic selection
26718 (license license:agpl3+)))
26720 (define-public r-nabor
26727 (uri (cran-uri "nabor" version))
26730 "1nj39cdfwrmhgsi3cq8imxv3n6xzc1v6dzdb2cf2hybjk368v4s7"))))
26731 (properties `((upstream-name . "nabor")))
26732 (build-system r-build-system)
26734 (list r-bh r-rcpp r-rcppeigen))
26735 (home-page "https://cran.r-project.org/web/packages/nabor/")
26736 (synopsis "Wrapper for K nearest neighbour library for low dimensions")
26738 "This package provides an R wrapper for libnabo, an exact or approximate
26739 k nearest neighbour library which is optimised for low dimensional
26740 spaces (e.g. 3D). @code{nabor} includes a @code{knn} function that is
26741 designed as a drop-in replacement for the RANN function @code{nn2}. In
26742 addition, objects which include the k-d tree search structure can be returned
26743 to speed up repeated queries of the same set of target points.")
26744 (license license:bsd-3)))
26746 (define-public r-naturalsort
26748 (name "r-naturalsort")
26752 (uri (cran-uri "naturalsort" version))
26755 "0mz801y9mzld9ypp3xmsjw2d8l9q97sdnv09wrci9xi3yg2sjf6d"))))
26756 (build-system r-build-system)
26757 (home-page "https://cran.r-project.org/web/packages/naturalsort/")
26758 (synopsis "Natural ordering")
26759 (description "This package provides functions related to human natural
26760 ordering. It handles adjacent digits in a character sequence as a number
26761 so that natural sort function arranges a character vector by their numbers,
26762 not digit characters.")
26763 (license license:bsd-3)))
26765 (define-public r-visdat
26771 (uri (cran-uri "visdat" version))
26774 "1ikqp29nncbw1xlwyb9dqqgcdk9q0bs3wxhnhnjpb11vcjv7cz2j"))))
26775 (build-system r-build-system)
26787 (home-page "https://visdat.njtierney.com/")
26788 (synopsis "Preliminary Visualisation of Data")
26789 (description "This package provides procedures to create preliminary exploratory
26790 data visualisations of an entire dataset to identify problems or unexpected features
26791 using @code{ggplot2}.")
26792 (license license:expat)))
26794 (define-public r-muhaz
26797 (version "1.2.6.4")
26801 (uri (cran-uri "muhaz" version))
26804 "1ddy8ayr4rdhzcipdvxdwd7z5g9hfp0ppacl7xf6f2612cn1185g"))))
26805 (properties `((upstream-name . "muhaz")))
26806 (build-system r-build-system)
26811 (home-page "https://cran.r-project.org/web/packages/muhaz/")
26812 (synopsis "Hazard function estimation in survival analysis")
26814 "This package produces a smooth estimate of the hazard function for
26816 ;; Any version of the GPL.
26817 (license license:gpl3+)))
26819 (define-public r-flexsurv
26821 (name "r-flexsurv")
26826 (uri (cran-uri "flexsurv" version))
26829 "0kwij9nkdvnsn1kn12fj3hjkd2qpgw7bdda4qad7basq5p6divlp"))))
26830 (properties `((upstream-name . "flexsurv")))
26831 (build-system r-build-system)
26854 (home-page "https://github.com/chjackson/flexsurv-dev")
26855 (synopsis "Flexible parametric survival and multi-state models")
26857 "This package provides flexible parametric models for time-to-event data,
26858 including the Royston-Parmar spline model, generalized gamma and generalized F
26859 distributions. Any user-defined parametric distribution can be fitted, given
26860 at least an R function defining the probability density or hazard. There are
26861 also tools for fitting and predicting from fully parametric multi-state
26863 (license license:gpl2+)))
26865 (define-public r-transphylo
26867 (name "r-transphylo")
26872 (uri (cran-uri "TransPhylo" version))
26875 "0g92kwi1nlmpc8m4pc9kv9xhczryr2kn9icfr3js7da7vy8g50xy"))))
26876 (properties `((upstream-name . "TransPhylo")))
26877 (build-system r-build-system)
26879 (list r-ape r-rcpp))
26882 (home-page "https://cran.r-project.org/web/packages/TransPhylo/")
26883 (synopsis "Inference of transmission tree from a dated phylogeny")
26885 "This is a package to infer transmission trees from a dated phylogeny.
26886 It includes methods to simulate and analyze outbreaks. The methodology is
26887 described in @url{https://doi.org/10.1093/molbev/msu121,Didelot et al. (2014)}
26888 and @url{https://doi.org/10.1093/molbev/msw275,Didelot et al. (2017)}.")
26889 (license license:gpl2+)))
26891 (define-public r-km-ci
26898 (uri (cran-uri "km.ci" version))
26901 "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
26902 (properties `((upstream-name . "km.ci")))
26903 (build-system r-build-system)
26906 (home-page "https://cran.r-project.org/web/packages/km.ci/")
26907 (synopsis "Confidence intervals for the Kaplan-Meier estimator")
26909 "This package computes various @dfn{confidence intervals} (CI) for the
26910 Kaplan-Meier estimator, namely: Petos CI, Rothman CI, CIs based on Greenwoods
26911 variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by
26912 Nair and Hall and Wellner.")
26913 (license license:gpl2+)))
26915 (define-public r-kmsurv
26922 (uri (cran-uri "KMsurv" version))
26925 "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
26926 (properties `((upstream-name . "KMsurv")))
26927 (build-system r-build-system)
26928 (home-page "https://cran.r-project.org/web/packages/KMsurv/")
26929 (synopsis "Data sets from Klein and Moeschberger (1997), Survival Analysis")
26931 "This package provides data sets and functions for Klein and Moeschberger
26932 (1997), \"Survival Analysis, Techniques for Censored and Truncated Data\",
26934 (license license:gpl3+)))
26936 (define-public r-survmisc
26938 (name "r-survmisc")
26943 (uri (cran-uri "survMisc" version))
26946 "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
26947 (properties `((upstream-name . "survMisc")))
26948 (build-system r-build-system)
26961 (home-page "https://cran.r-project.org/web/packages/survMisc/")
26962 (synopsis "Miscellaneous functions for survival data")
26964 "This package provides a collection of functions to help in the analysis
26965 of right-censored survival data. These extend the methods available in
26966 the @code{survival} package.")
26967 (license license:gpl2)))
26969 (define-public r-exactranktests
26971 (name "r-exactranktests")
26976 (uri (cran-uri "exactRankTests" version))
26979 "1i4mwz61mjlh1ai3dww2pjkicx9ww8c4mljnr8xlawh91479lva9"))))
26981 `((upstream-name . "exactRankTests")))
26982 (build-system r-build-system)
26983 (home-page "https://cran.r-project.org/web/packages/exactRankTests/")
26984 (synopsis "Exact distributions for rank and permutation tests")
26986 "This package computes exact conditional p-values and quantiles using an
26987 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
26988 (license license:gpl2+)))
26990 (define-public r-maxstat
26997 (uri (cran-uri "maxstat" version))
27000 "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
27001 (properties `((upstream-name . "maxstat")))
27002 (build-system r-build-system)
27004 (list r-exactranktests r-mvtnorm))
27005 (home-page "https://cran.r-project.org/web/packages/maxstat/")
27006 (synopsis "Maximally selected rank statistics")
27008 "This package provides maximally selected rank statistics with several
27009 p-value approximations.")
27010 (license license:gpl2+)))
27012 (define-public r-survminer
27014 (name "r-survminer")
27019 (uri (cran-uri "survminer" version))
27022 "0byh0wxdbjfwdrzsnqv4xlmnik6lj0vkkzfxy7lssk8dv5zmj7nz"))))
27023 (properties `((upstream-name . "survminer")))
27024 (build-system r-build-system)
27043 (home-page "https://rpkgs.datanovia.com/survminer/index.html")
27044 (synopsis "Drawing survival curves using ggplot2")
27046 "This package contains the function @code{ggsurvplot()} for easily
27047 drawing beautiful and 'ready-to-publish' survival curves with the 'number at
27048 risk' table and 'censoring count plot'. Other functions are also available to
27049 plot adjusted curves for Cox model and to visually examine Cox model
27051 (license license:gpl2)))
27053 (define-public r-forge
27060 (uri (cran-uri "forge" version))
27063 "0pjfzsc35agkh0zfw2czwajkbsyn6liys5irl5bhz5r1vim3jmwa"))))
27064 (properties `((upstream-name . "forge")))
27065 (build-system r-build-system)
27067 (list r-magrittr r-rlang))
27068 (home-page "https://cran.r-project.org/web/packages/forge/")
27069 (synopsis "Cast values into shape")
27071 "This package provides helper functions with a consistent interface to
27072 coerce and verify the types and shapes of values for input checking.")
27073 (license license:asl2.0)))
27075 (define-public r-config
27082 (uri (cran-uri "config" version))
27085 "0l2zp7v6qaz72dclcbjrlis633zlwp8rsi5azr7iw127iyz7i26l"))))
27086 (properties `((upstream-name . "config")))
27087 (build-system r-build-system)
27092 (home-page "https://github.com/rstudio/config")
27093 (synopsis "Manage environment specific configuration values")
27095 "This package lets you manage configuration values across multiple
27096 environments (e.g. development, test, production). It reads values using a
27097 function that determines the current environment and returns the appropriate
27099 (license license:gpl3)))
27101 (define-public r-adaptivesparsity
27103 (name "r-adaptivesparsity")
27107 (uri (cran-uri "AdaptiveSparsity" version))
27110 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
27112 `((upstream-name . "AdaptiveSparsity")))
27113 (build-system r-build-system)
27116 (modify-phases %standard-phases
27117 (add-after 'unpack 'link-against-armadillo
27119 (substitute* "src/Makevars"
27120 (("PKG_LIBS=" prefix)
27121 (string-append prefix "-larmadillo")))
27124 (list r-mass r-matrix r-rcpp r-rcpparmadillo))
27127 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
27128 (synopsis "Adaptive sparsity models")
27130 "This package implements the Figueiredo machine learning algorithm for
27131 adaptive sparsity and the Wong algorithm for adaptively sparse Gaussian
27132 geometric models.")
27133 (license license:lgpl3+)))
27135 (define-public r-add2ggplot
27137 (name "r-add2ggplot")
27142 (uri (cran-uri "add2ggplot" version))
27144 (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
27145 (properties `((upstream-name . "add2ggplot")))
27146 (build-system r-build-system)
27148 (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
27149 (native-inputs (list r-knitr))
27150 (home-page "https://github.com/JiaxiangBU/add2ggplot")
27151 (synopsis "Extension for ggplot2")
27152 (description "This packages provides tools to create themes and color
27153 palettes for the package ggplot2.")
27154 (license license:expat)))
27156 (define-public r-diffusionmap
27158 (name "r-diffusionmap")
27163 (uri (cran-uri "diffusionMap" version))
27166 "1rvk7069brlm1s9kqj4c31mwwr3mw4hmhay95cjjjfmw5xclff2j"))))
27167 (properties `((upstream-name . "diffusionMap")))
27168 (build-system r-build-system)
27170 (list r-igraph r-matrix r-scatterplot3d))
27171 (home-page "https://www.r-project.org")
27172 (synopsis "Diffusion map")
27173 (description "This package implements the diffusion map method of data
27174 parametrization, including creation and visualization of diffusion maps,
27175 clustering with diffusion K-means and regression using the adaptive regression
27177 (license license:gpl2)))
27179 (define-public r-igraph
27186 (uri (cran-uri "igraph" version))
27189 "1ph042yinl8ig2x7laha5j1xr14fky9771l5ha87svhynrg732qw"))))
27190 (build-system r-build-system)
27194 (list gmp glpk libxml2 zlib))
27196 (list r-magrittr r-matrix r-pkgconfig))
27197 (home-page "https://igraph.org")
27198 (synopsis "Network analysis and visualization")
27200 "This package provides routines for simple graphs and network analysis.
27201 It can handle large graphs very well and provides functions for generating
27202 random and regular graphs, graph visualization, centrality methods and much
27204 (license license:gpl2+)))
27206 (define-public r-workflows
27208 (name "r-workflows")
27213 (uri (cran-uri "workflows" version))
27216 "1sxrgza922p137z41jcj2iwk19lxzwh6kp4kz7h9kw0b8rvfqwab"))))
27217 (properties `((upstream-name . "workflows")))
27218 (build-system r-build-system)
27232 (home-page "https://github.com/tidymodels/workflows")
27233 (synopsis "Modeling workflows")
27235 "A workflow is an object that can bundle together your pre-processing,
27236 modeling, and post-processing requests. For example, if you have a
27237 @code{recipe} and @code{parsnip} model, these can be combined into a
27238 workflow. The advantages are:
27241 @item You don’t have to keep track of separate objects in your workspace.
27242 @item The recipe prepping and model fitting can be executed using a single
27243 call to @code{fit()}.
27244 @item If you have custom tuning parameter settings, these can be defined using
27245 a simpler interface when combined with @code{tune}.
27246 @item In the future, workflows will be able to add post-processing operations,
27247 such as modifying the probability cutoff for two-class models.
27250 (license license:expat)))
27252 (define-public r-lobstr
27259 (uri (cran-uri "lobstr" version))
27262 "0vkif17825x33cz8r89j0qph4wj5l8fzfgl8nh2g7m2v140cxjdq"))))
27263 (properties `((upstream-name . "lobstr")))
27264 (build-system r-build-system)
27266 (list r-crayon r-rcpp r-rlang))
27267 (home-page "https://github.com/r-lib/lobstr")
27268 (synopsis "Visualize R data structures with trees")
27270 "This package provides a set of tools for inspecting and understanding R
27271 data structures inspired by @code{str}. It includes @code{ast} for
27272 visualizing abstract syntax trees, @code{ref} for showing shared references,
27273 @code{cst} for showing call stack trees, and @code{obj_size} for computing
27275 (license license:gpl3)))
27277 (define-public r-gpfit
27284 (uri (cran-uri "GPfit" version))
27287 "05mpiyi2vxv0wqp422n1mnxa8msc4daq40cwpnpngbcwqhlgqkby"))))
27288 (properties `((upstream-name . "GPfit")))
27289 (build-system r-build-system)
27291 (list r-lattice r-lhs))
27292 (home-page "https://cran.r-project.org/web/packages/GPfit/")
27293 (synopsis "Gaussian Processes modeling")
27295 "This package provides a computationally stable approach of fitting a
27296 @dfn{Gaussian Process} (GP) model to a deterministic simulator.")
27297 (license license:gpl2)))
27299 (define-public r-yardstick
27301 (name "r-yardstick")
27306 (uri (cran-uri "yardstick" version))
27309 "00hv4gk1ba4dab8i3dcq7lim4bll7l572rgc8km9x4ja8by95j8h"))))
27310 (properties `((upstream-name . "yardstick")))
27311 (build-system r-build-system)
27321 (home-page "https://github.com/tidymodels/yardstick")
27322 (synopsis "Tidy characterizations of model performance")
27324 "This package provides tidy tools for quantifying how well a model fits
27325 to a data set such as confusion matrices, class probability curve summaries,
27326 and regression metrics (e.g., RMSE).")
27327 (license license:gpl2)))
27329 (define-public r-warp
27336 (uri (cran-uri "warp" version))
27339 "0s0acddc5h14245hi1faycxp0fyvw6nlgaz2df7da4fpyd2f638f"))))
27340 (properties `((upstream-name . "warp")))
27341 (build-system r-build-system)
27342 (native-inputs (list r-knitr))
27343 (home-page "https://github.com/DavisVaughan/warp")
27344 (synopsis "Group dates")
27346 "This package provides tooling to group dates by a variety of periods
27347 including: yearly, monthly, by second, by week of the month, and more. The
27348 groups are defined in such a way that they also represent the distance between
27349 dates in terms of the period. This extracts valuable information that can be
27350 used in further calculations that rely on a specific temporal spacing between
27352 (license license:expat)))
27354 (define-public r-scico
27361 (uri (cran-uri "scico" version))
27363 (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
27364 (properties `((upstream-name . "scico")))
27365 (build-system r-build-system)
27366 (propagated-inputs (list r-scales))
27367 (home-page "https://github.com/thomasp85/scico")
27368 (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
27370 "This package provides colour choice in information visualisation. It
27371 important in order to avoid being mislead by inherent bias in the used colour
27372 palette. This package provides access to the perceptually uniform and
27373 colour-blindness friendly palettes developed by Fabio Crameri and released
27374 under the \"Scientific Colour-Maps\" moniker. The package contains 24
27375 different palettes and includes both diverging and sequential types.")
27376 (license license:expat)))
27378 (define-public r-slider
27385 (uri (cran-uri "slider" version))
27388 "1vxk2bc33svwcki2j8zr5jcxswh27i0fqgzjw2a5a1pp9dh3fmd3"))))
27389 (properties `((upstream-name . "slider")))
27390 (build-system r-build-system)
27392 (list r-ellipsis r-glue r-rlang r-vctrs r-warp))
27393 (native-inputs (list r-knitr))
27394 (home-page "https://github.com/DavisVaughan/slider")
27395 (synopsis "Sliding window functions")
27397 "This package provides type-stable rolling window functions over any R
27398 data type. Cumulative and expanding windows are also supported. For more
27399 advanced usage, an index can be used as a secondary vector that defines how
27400 sliding windows are to be created.")
27401 (license license:expat)))
27403 (define-public r-rlist
27406 (version "0.4.6.2")
27410 (uri (cran-uri "rlist" version))
27412 (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
27413 (properties `((upstream-name . "rlist")))
27414 (build-system r-build-system)
27415 (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
27416 (home-page "https://renkun-ken.github.io/rlist/")
27417 (synopsis "A Toolbox for Non-Tabular Data Manipulation")
27419 "This package provides a set of functions for data manipulation with
27420 list objects, including mapping, filtering, grouping, sorting, updating,
27421 searching, and other useful functions. Most functions are designed to be
27422 pipeline friendly so that data processing with lists can be chained.")
27423 (license license:expat)))
27425 (define-public r-rsample
27432 (uri (cran-uri "rsample" version))
27435 "01xwhj4zfvxbv9cjb6mbz3aphxqc3cnjjx1xy2yx2wd94fbka42z"))))
27436 (properties `((upstream-name . "rsample")))
27437 (build-system r-build-system)
27453 (home-page "https://rsample.tidymodels.org")
27454 (synopsis "General resampling infrastructure")
27456 "This package provides classes and functions to create and summarize
27457 different types of resampling objects (e.g. bootstrap, cross-validation).")
27458 (license license:gpl2)))
27460 (define-public r-dicedesign
27462 (name "r-dicedesign")
27467 (uri (cran-uri "DiceDesign" version))
27470 "1a8ixa65xgyfri03cviic8qi2plbhdyz8m02bwif8w94w0q3ghlk"))))
27471 (properties `((upstream-name . "DiceDesign")))
27472 (build-system r-build-system)
27473 (home-page "http://dice.emse.fr/")
27474 (synopsis "Designs of computer experiments")
27476 "This package provides tools to create some specific @code{Space-Filling
27477 Design} (SFD) and to test their quality.")
27478 (license license:gpl3)))
27480 (define-public r-dials
27487 (uri (cran-uri "dials" version))
27490 "1vhqcfwgic01pkw0i3000fvqq9yxfzsv26c0psfjhxkkdcz8h2px"))))
27491 (properties `((upstream-name . "dials")))
27492 (build-system r-build-system)
27503 (native-inputs (list r-knitr))
27504 (home-page "https://dials.tidymodels.org/")
27505 (synopsis "Tools for creating tuning parameter values")
27507 "Many models contain tuning parameters (i.e. parameters that cannot be
27508 directly estimated from the data). These tools can be used to define objects
27509 for creating, simulating, or validating values for such parameters.")
27510 (license license:gpl2)))
27512 (define-public r-tune
27519 (uri (cran-uri "tune" version))
27522 "1356w98ljiay8fwa7narr7j5hfbvi69gy03gr7kqiwnfglyksrza"))))
27523 (properties `((upstream-name . "tune")))
27524 (build-system r-build-system)
27547 (home-page "https://github.com/tidymodels/tune")
27548 (synopsis "Tidy tuning tools")
27550 "The ability to tune models is important. @code{tune} contains functions
27551 and classes to be used in conjunction with other @code{tidymodels} packages
27552 for finding reasonable values of hyper-parameters in models, pre-processing
27553 methods, and post-processing steps.")
27554 (license license:expat)))
27556 (define-public r-workflowsets
27558 (name "r-workflowsets")
27563 (uri (cran-uri "workflowsets" version))
27566 "0596hb17mshpag3vjy2wl6fi2mdw54i9gc5za10vzy8vpkigb9jy"))))
27567 (properties `((upstream-name . "workflowsets")))
27568 (build-system r-build-system)
27588 (home-page "https://github.com/tidymodels/workflowsets")
27589 (synopsis "Create a collection of tidymodels workflows")
27591 "A workflow is a combination of a model and preprocessors (e.g, a
27592 formula, recipe, etc.). In order to try different combinations of these, an
27593 object can be created that contains many workflows. There are functions to
27594 create workflows en masse as well as training them and visualizing the
27596 (license license:expat)))
27598 (define-public r-tidyposterior
27600 (name "r-tidyposterior")
27605 (uri (cran-uri "tidyposterior" version))
27608 "1h1664sjrg6akph6nrk8ynn2kjiswv6gshy35gamam1h4axf6wah"))))
27609 (properties `((upstream-name . "tidyposterior")))
27610 (build-system r-build-system)
27626 (home-page "https://tidyposterior.tidymodels.org")
27627 (synopsis "Bayesian analysis to compare models using resampling statistics")
27629 "This package can be used to conduct post hoc analyses of resampling
27630 results generated by models. For example, if two models are evaluated with
27631 the @dfn{root mean squared error} (RMSE) using 10-fold cross-validation, there
27632 are 10 paired statistics. These can be used to make comparisons between
27633 models without involving a test set.")
27634 (license license:gpl2)))
27636 (define-public r-tidypredict
27638 (name "r-tidypredict")
27643 (uri (cran-uri "tidypredict" version))
27646 "0fff349pkksss8h1k2qza78l81ha6avx63pxziv6dfa8h62qmrdy"))))
27647 (properties `((upstream-name . "tidypredict")))
27648 (build-system r-build-system)
27660 (home-page "https://tidypredict.tidymodels.org")
27661 (synopsis "Run predictions inside the database")
27663 "This package parses a fitted R model object, and returns a formula in
27664 Tidy Eval code that calculates the predictions. It works with several
27665 database backends because it leverages @code{dplyr} and @code{dbplyr} for the
27666 final SQL translation of the algorithm. It currently supports @code{lm()},
27667 @code{glm()}, @code{randomForest()}, @code{ranger()}, @code{earth()},
27668 @code{xgb.Booster.complete()}, @code{cubist()}, and @code{ctree()} models.")
27669 (license license:gpl3)))
27671 (define-public r-janeaustenr
27673 (name "r-janeaustenr")
27678 (uri (cran-uri "janeaustenr" version))
27681 "1wyn4qc28a3sval8shmyi2d7s4nl3jh96s8pzq871brxcmrncbwr"))))
27682 (properties `((upstream-name . "janeaustenr")))
27683 (build-system r-build-system)
27684 (home-page "https://github.com/juliasilge/janeaustenr")
27685 (synopsis "Jane Austen's complete novels")
27687 "This package provides the full texts for Jane Austen's six completed
27688 novels, ready for text analysis. These novels are \"Sense and Sensibility\",
27689 \"Pride and Prejudice\", \"Mansfield Park\", \"Emma\", \"Northanger Abbey\",
27690 and \"Persuasion\".")
27691 (license license:expat)))
27693 (define-public r-tokenizers
27695 (name "r-tokenizers")
27700 (uri (cran-uri "tokenizers" version))
27703 "006xf1vdrmp9skhpss9ldhmk4cwqk512cjp1pxm2gxfybpf7qq98"))))
27704 (properties `((upstream-name . "tokenizers")))
27705 (build-system r-build-system)
27707 (list r-rcpp r-snowballc r-stringi))
27710 (home-page "https://lincolnmullen.com/software/tokenizers/")
27711 (synopsis "Fast, consistent tokenization of natural language text")
27713 "This is a package for converting natural language text into tokens.
27714 It includes tokenizers for shingled n-grams, skip n-grams, words, word stems,
27715 sentences, paragraphs, characters, shingled characters, lines, tweets, Penn
27716 Treebank, regular expressions, as well as functions for counting characters,
27717 words, and sentences, and a function for splitting longer texts into separate
27718 documents, each with the same number of words. The tokenizers have a
27719 consistent interface, and the package is built on the @code{stringi} and
27720 @code{Rcpp} packages for fast yet correct tokenization in UTF-8 encoding.")
27721 (license license:expat)))
27723 (define-public r-hunspell
27725 (name "r-hunspell")
27730 (uri (cran-uri "hunspell" version))
27733 "0ql6y05d4xxpm468rslb0wxdp1x9l3flxzmb5w6pjg617f8vpv8z"))))
27734 (properties `((upstream-name . "hunspell")))
27735 (build-system r-build-system)
27737 (list r-digest r-rcpp))
27740 (home-page "https://github.com/ropensci/hunspell#readme")
27741 (synopsis "High-performance stemmer, tokenizer, and spell checker")
27743 "This package provides a low-level spell checker and morphological
27744 analyzer based on the famous @code{hunspell} library. The package can analyze
27745 or check individual words as well as parse text, LaTeX, HTML or XML documents.
27746 For a more user-friendly interface use the @code{spelling} package which
27747 builds on this package to automate checking of files, documentation and
27748 vignettes in all common formats.")
27749 ;; The hunspell library itself is available under one of GPL2, LGPL2.1, or
27750 ;; MPL; in addition to these licenses the rest of the R wrapper is also
27751 ;; available under the Expat license.
27752 (license (list license:gpl2
27757 (define-public r-tidytext
27759 (name "r-tidytext")
27764 (uri (cran-uri "tidytext" version))
27767 "0as7lscjl6ywk85almmb4f71vxmgkfds46g52ryggkg2isksvq3g"))))
27768 (properties `((upstream-name . "tidytext")))
27769 (build-system r-build-system)
27785 (home-page "https://github.com/juliasilge/tidytext")
27786 (synopsis "Text mining using dplyr, ggplot2, and other Tidy tools")
27788 "This is a package for text mining for word processing and sentiment
27789 analysis using @code{dplyr}, @code{ggplot2}, and other Tidy tools.")
27790 (license license:expat)))
27792 (define-public r-parsnip
27799 (uri (cran-uri "parsnip" version))
27802 "12chngdzplwkk1c9k8y7cwaqlyy72yamlknp7ksg7g9p3b58f1fb"))))
27803 (properties `((upstream-name . "parsnip")))
27804 (build-system r-build-system)
27821 (home-page "https://parsnip.tidymodels.org")
27822 (synopsis "Common API to modeling and analysis functions")
27824 "This package provides a common interface to allow users to specify a
27825 model without having to remember the different argument names across different
27826 functions or computational engines (e.g. R, Spark, Stan, etc).")
27827 (license license:gpl2)))
27829 (define-public r-infer
27836 (uri (cran-uri "infer" version))
27839 "1qbpcn7jqbvgwnpiyylj021j8m33p58a204yd1pfkpzd3x2lbsm6"))))
27840 (properties `((upstream-name . "infer")))
27841 (build-system r-build-system)
27856 (home-page "https://github.com/tidymodels/infer")
27857 (synopsis "Tidy statistical inference")
27859 "The objective of this package is to perform inference using an
27860 expressive statistical grammar that coheres with the Tidy design framework.")
27861 (license license:cc0)))
27863 (define-public r-modeldata
27865 (name "r-modeldata")
27870 (uri (cran-uri "modeldata" version))
27873 "0jgrwf9k8p9j3ywg3yv2wzwsx3snlwm3dd9vfqwhlr7j63jg3cm4"))))
27874 (properties `((upstream-name . "modeldata")))
27875 (build-system r-build-system)
27876 (home-page "https://modeldata.tidymodels.org")
27877 (synopsis "Data sets useful for modeling packages")
27879 "This package provides data sets used for demonstrating or testing
27880 model-related packages.")
27881 (license license:expat)))
27883 (define-public r-conflicted
27885 (name "r-conflicted")
27890 (uri (cran-uri "conflicted" version))
27893 "1qg9ar114r98wm0pnf65mss4v2ksq3924rlpm13mqp4s3p6j9yi4"))))
27894 (properties `((upstream-name . "conflicted")))
27895 (build-system r-build-system)
27897 (list r-memoise r-rlang))
27898 (home-page "https://github.com/r-lib/conflicted")
27899 (synopsis "Alternative conflict resolution strategy")
27901 "R's default conflict management system gives the most recently loaded
27902 package precedence. This can make it hard to detect conflicts, particularly
27903 when they arise because a package update creates ambiguity that did not
27904 previously exist. The @code{conflicted} package takes a different approach,
27905 making every conflict an error and forcing you to choose which function to
27907 (license license:gpl3)))
27909 (define-public r-tidymodels
27911 (name "r-tidymodels")
27916 (uri (cran-uri "tidymodels" version))
27919 "18krycdn0h1i8swrq6bgj8qnb200rr0pqhr6maq3h1jc66x0y7nd"))))
27920 (properties `((upstream-name . "tidymodels")))
27921 (build-system r-build-system)
27945 (list r-knitr r-rmarkdown pandoc))
27946 (home-page "https://github.com/tidymodels/tidymodels")
27947 (synopsis "Tidy collection for modeling and statistical analysis")
27949 "The tidy modeling \"verse\" is a collection of packages for modeling and
27950 statistical analysis that share the underlying design philosophy, grammar, and
27951 data structures of the tidyverse.")
27952 (license license:gpl3)))
27954 (define-public r-lsa
27961 (uri (cran-uri "lsa" version))
27964 "1a33irqa6qvbc02z12rgbgv8kxq2gmahy7j5bg8b23lvvaxif06b"))))
27965 (properties `((upstream-name . "lsa")))
27966 (build-system r-build-system)
27968 (list r-snowballc))
27969 (home-page "https://cran.r-project.org/package=lsa")
27970 (synopsis "Latent semantic analysis")
27972 "The basic idea of latent semantic analysis (LSA) is, that text do have a
27973 higher order (=latent semantic) structure which, however, is obscured by word
27974 usage (e.g. through the use of synonyms or polysemy). By using conceptual
27975 indices that are derived statistically via a truncated singular value
27976 decomposition (a two-mode factor analysis) over a given document-term matrix,
27977 this variability problem can be overcome.")
27978 (license license:gpl2+)))
27980 (define-public r-mlecens
27987 (uri (cran-uri "MLEcens" version))
27990 "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))
27991 (properties `((upstream-name . "MLEcens")))
27992 (build-system r-build-system)
27993 (home-page "http://stat.ethz.ch/~maathuis/")
27994 (synopsis "Computation of the MLE for bivariate (interval) censored data")
27996 "This package contains functions to compute the nonparametric
27997 @dfn{maximum likelihood estimator} (MLE) for the bivariate distribution of
27998 @code{(X,Y)}, when realizations of @code{(X,Y)} cannot be observed directly.
27999 To be more precise, we consider the situation where we observe a set of
28000 rectangles that are known to contain the unobservable realizations of (X,Y).
28001 We compute the MLE based on such a set of rectangles. The methods can also be
28002 used for univariate censored data (see data set @code{cosmesis}), and for
28003 censored data with competing risks (see data set @code{menopause}). The
28004 package also provides functions to visualize the observed data and the MLE.")
28005 (license license:gpl2+)))
28007 (define-public r-metafor
28014 (uri (cran-uri "metafor" version))
28017 "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
28018 (properties `((upstream-name . "metafor")))
28019 (build-system r-build-system)
28021 (list r-matrix r-nlme))
28022 (home-page "https://cran.r-project.org/web/packages/metafor/")
28023 (synopsis "Meta-analysis package for R")
28025 "This package provides a comprehensive collection of functions for
28026 conducting meta-analyses in R. The package includes functions to calculate
28027 various effect sizes or outcome measures, fit fixed-, random-, and
28028 mixed-effects models to such data, carry out moderator and meta-regression
28029 analyses, and create various types of meta-analytical plots (e.g., forest,
28030 funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial
28031 and person-time data, the package also provides functions that implement
28032 specialized methods, including the Mantel-Haenszel method, Peto's method, and
28033 a variety of suitable generalized linear (mixed-effects) models (i.e.
28034 mixed-effects logistic and Poisson regression models). Finally, the package
28035 provides functionality for fitting meta-analytic multivariate/multilevel
28036 models that account for non-independent sampling errors and/or true
28037 effects (e.g. due to the inclusion of multiple treatment studies, multiple
28038 endpoints, or other forms of clustering). Network meta-analyses and
28039 meta-analyses accounting for known correlation structures (e.g. due to
28040 phylogenetic relatedness) can also be conducted.")
28041 (license license:gpl2+)))
28043 (define-public r-altmeta
28050 (uri (cran-uri "altmeta" version))
28053 "1xq12hnzxh7kgv2i36xprg4lkvqfmxwz3sq4a1jlq2d5g3narvcm"))))
28054 (properties `((upstream-name . "altmeta")))
28055 (build-system r-build-system)
28057 (list r-coda r-lme4 r-matrix r-metafor r-rjags))
28058 (home-page "https://cran.r-project.org/web/packages/altmeta/")
28059 (synopsis "Alternative meta-analysis methods")
28061 "This package provides alternative statistical methods for meta-analysis,
28065 @item bivariate generalized linear mixed models for synthesizing odds ratios,
28066 relative risks, and risk differences
28067 @item heterogeneity tests and measures that are robust to outliers;
28068 @item measures, tests, and visualization tools for publication bias or
28069 small-study effects;
28070 @item meta-analysis of diagnostic tests for synthesizing sensitivities,
28071 specificities, etc.;
28072 @item meta-analysis methods for synthesizing proportions;
28073 @item models for multivariate meta-analysis.
28076 (license license:gpl2+)))
28078 (define-public r-perm
28081 (version "1.0-0.2")
28085 (uri (cran-uri "perm" version))
28088 "182ac1y91yzb34zwdcmx5fdfr5z0cha0gx2bgk36gwxhgfc994kj"))))
28089 (properties `((upstream-name . "perm")))
28090 (build-system r-build-system)
28091 (home-page "https://cran.r-project.org/web/packages/perm/")
28092 (synopsis "Exact or asymptotic permutation tests")
28094 "This package provides several methods for performing permutation tests.
28095 It has three main functions, to perform linear permutation tests. These tests
28096 are tests where the test statistic is the sum of the product of a
28097 covariate (usually group indicator) and the scores.")
28098 ;; Any version of the GPL
28099 (license license:gpl2+)))
28101 (define-public r-qtl
28108 (uri (cran-uri "qtl" version))
28111 "1mcy9wlp5lj5f3z4mf3n5li7x32vj67rmhjnzsp8fhfw0ipnaf1d"))))
28112 (build-system r-build-system)
28113 (home-page "https://rqtl.org/")
28114 (synopsis "R package for analyzing QTL experiments in genetics")
28115 (description "R/qtl is an extension library for the R statistics system.
28116 It is used to analyze experimental crosses for identifying genes contributing
28117 to variation in quantitative traits (so-called quantitative trait loci, QTLs).
28119 Using a hidden Markov model, R/qtl estimates genetic maps, to identify
28120 genotyping errors, and to perform single-QTL and two-QTL, two-dimensional
28122 (license license:gpl3)))
28124 (define-public r-qtl2
28130 (uri (cran-uri "qtl2" version))
28132 (base32 "0ppc6dzlq77mppxc6bczai9gi40jrbxd1466y2cn2s8a4ah1jg9y"))))
28133 (build-system r-build-system)
28141 (home-page "https://kbroman.org/qtl2/")
28142 (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
28144 "This package provides a set of tools to perform @dfn{Quantitative Trait
28145 Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
28146 @code{R/qtl} package to better handle high-dimensional data and complex cross
28147 designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
28148 (license license:gpl3)))
28150 (define-public r-seqminer
28152 (name "r-seqminer")
28157 (uri (cran-uri "seqminer" version))
28160 "097313x72jr2q6dp8ma33w8kyp3gfw71snf1qx2maxbwwnysk085"))))
28161 (build-system r-build-system)
28164 (home-page "http://seqminer.genomic.codes")
28165 (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
28167 "This package provides tools to integrate nucleotide sequencing
28168 data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
28169 ;; Any version of the GPL is acceptable
28170 (license (list license:gpl2+ license:gpl3+))))
28172 (define-public r-maldiquant
28174 (name "r-maldiquant")
28179 (uri (cran-uri "MALDIquant" version))
28182 "1y1g3819ss06dry70kfhg2syddw71682qmzkcyppfsma6hhghw87"))))
28183 (properties `((upstream-name . "MALDIquant")))
28184 (build-system r-build-system)
28187 (home-page "https://cran.r-project.org/web/packages/MALDIquant")
28188 (synopsis "Quantitative analysis of mass spectrometry data")
28190 "This package provides a complete analysis pipeline for matrix-assisted
28191 laser desorption/ionization-time-of-flight (MALDI-TOF) and other
28192 two-dimensional mass spectrometry data. In addition to commonly used plotting
28193 and processing methods it includes distinctive features, namely baseline
28194 subtraction methods such as morphological filters (TopHat) or the
28195 statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
28196 alignment using warping functions, handling of replicated measurements as well
28197 as allowing spectra with different resolutions.")
28198 (license license:gpl3+)))
28200 (define-public r-scattermore
28202 (name "r-scattermore")
28207 (uri (cran-uri "scattermore" version))
28210 "18nzlprmphkvjg946h10h2qq0wbkmv2526p8di6k2xl4gccq0qpk"))))
28211 (properties `((upstream-name . "scattermore")))
28212 (build-system r-build-system)
28214 (list r-ggplot2 r-scales))
28215 (home-page "https://github.com/exaexa/scattermore")
28216 (synopsis "Scatterplots with more points")
28218 "This package provides C-based tools for converting large scatterplot
28219 data to rasters. It speeds up plotting of data with millions of points.")
28220 (license license:gpl3+)))
28222 (define-public r-seuratobject
28224 (name "r-seuratobject")
28229 (uri (cran-uri "SeuratObject" version))
28232 "1308hjbs8br3gp9vwm65awgp6vimwgi2jyl1ryn96l84savn2ljq"))))
28233 (properties `((upstream-name . "SeuratObject")))
28234 (build-system r-build-system)
28236 (list r-matrix r-rcpp r-rcppeigen r-rlang))
28237 (home-page "https://satijalab.org/seurat")
28238 (synopsis "Data structures for single cell data")
28240 "This package defines S4 classes for single-cell genomic data and
28241 associated information, such as dimensionality reduction embeddings,
28242 nearest-neighbor graphs, and spatially-resolved coordinates. It provides data
28243 access methods and R-native hooks to ensure the Seurat object is familiar to
28245 (license license:gpl3)))
28247 (define-public r-seurat
28253 (uri (cran-uri "Seurat" version))
28256 "0p9i3fnkqa3vranr7c7ckzp1kq42d7p0gcfi9ml4kr334yd84195"))))
28257 (properties `((upstream-name . "Seurat")))
28258 (build-system r-build-system)
28303 (home-page "http://www.satijalab.org/seurat")
28304 (synopsis "Seurat is an R toolkit for single cell genomics")
28306 "This package is an R package designed for QC, analysis, and
28307 exploration of single cell RNA-seq data. It easily enables widely-used
28308 analytical techniques, including the identification of highly variable genes,
28309 dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
28310 algorithms; density clustering, hierarchical clustering, k-means, and the
28311 discovery of differentially expressed genes and markers.")
28312 (license license:gpl3)))
28314 (define-public r-seuratdisk
28315 (let ((commit "163f1aade5bac38ed1e9e9c912283a7e74781610")
28318 (name "r-seuratdisk")
28319 (version (git-version "0.0.0.9019" revision commit))
28323 (uri (git-reference
28324 (url "https://github.com/mojaveazure/seurat-disk")
28326 (file-name (git-file-name name version))
28328 (base32 "1d1v8qi6kknzy5fj6bl8akwy74h5h143i00lyidsnqjbwp9n4qnw"))))
28329 (properties `((upstream-name . "SeuratDisk")))
28330 (build-system r-build-system)
28344 (home-page "https://github.com/mojaveazure/seurat-disk")
28345 (synopsis "Interfaces for HDF5-based single cell file formats")
28347 "The h5Seurat file format is specifically designed for the storage and
28348 analysis of multi-modal single-cell and spatially-resolved expression
28349 experiments, for example, from CITE-seq or 10X Visium technologies. It holds
28350 all molecular information and associated metadata, including (for example)
28351 nearest-neighbor graphs, dimensional reduction information, spatial
28352 coordinates and image data, and cluster labels. This package also supports
28353 rapid and on-disk conversion between h5Seurat and AnnData objects, with the
28354 goal of enhancing interoperability between Seurat and Scanpy.")
28355 (license license:gpl3))))
28357 (define-public r-seuratdata
28358 (let ((commit "b59556b24d7d6728a5744c9c715dd5f7f32ed7a5")
28361 (name "r-seuratdata")
28362 (version (git-version "0.2.1" revision commit))
28366 (uri (git-reference
28367 (url "https://github.com/satijalab/seurat-data")
28369 (file-name (git-file-name name version))
28371 (base32 "1xfdmdmgn4r0z6w4cxa98ic6xk8i6qz054r215dvqbjs1vydsbf9"))))
28372 (properties `((upstream-name . "SeuratData")))
28373 (build-system r-build-system)
28376 (modify-phases %standard-phases
28377 ;; When there is no HOME directory, this package will fail to load
28378 ;; the included list of packages.
28379 (add-after 'unpack 'set-HOME
28380 (lambda _ (setenv "HOME" "/tmp"))))))
28382 (list r-cli r-crayon r-rappdirs))
28383 (home-page "https://github.com/satijalab/seurat-data")
28384 (synopsis "Install and manage Seurat datasets")
28386 "Single cell RNA sequencing datasets can be large, consisting of
28387 matrices that contain expression data for several thousand features across
28388 several thousand cells. This package is designed to easily install, manage,
28389 and learn about various single-cell datasets, provided Seurat objects and
28390 distributed as independent packages.")
28391 (license license:gpl3))))
28393 (define-public r-phangorn
28395 (name "r-phangorn")
28400 (uri (cran-uri "phangorn" version))
28403 "0xfwi7adl1pcfcwk72fj7lkwfm0wiip96ij7m4252xr9mq818ivd"))))
28404 (build-system r-build-system)
28414 (home-page "https://github.com/KlausVigo/phangorn")
28415 (synopsis "Phylogenetic analysis in R")
28417 "Phangorn is a package for phylogenetic analysis in R. It supports
28418 estimation of phylogenetic trees and networks using Maximum Likelihood,
28419 Maximum Parsimony, distance methods and Hadamard conjugation.")
28420 (license license:gpl2+)))
28422 (define-public r-diversitree
28424 (name "r-diversitree")
28429 (uri (cran-uri "diversitree" version))
28432 "0rzrk7xsn4gy271pbcw3azndhx0c06bmsgrg6libjmlfnmq6j8sc"))))
28433 (build-system r-build-system)
28436 (inputs (list fftw gsl))
28438 (list r-ape r-desolve r-rcpp r-subplex))
28439 (home-page "https://www.zoology.ubc.ca/prog/diversitree")
28440 (synopsis "Comparative 'phylogenetic' analyses of diversification")
28441 (description "This package contains a number of comparative \"phylogenetic\"
28442 methods, mostly focusing on analysing diversification and character evolution.
28443 Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
28444 and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
28445 Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
28446 include Markov models of discrete and continuous trait evolution and constant
28447 rate speciation and extinction.")
28448 (license license:gpl2+)))
28450 (define-public r-calculus
28452 (name "r-calculus")
28457 (uri (cran-uri "calculus" version))
28460 "1x3bcdd422wqv9gk9r2m8g19qcga220sm5rxdp4bgfc6vlqzzz7y"))))
28461 (properties `((upstream-name . "calculus")))
28462 (build-system r-build-system)
28467 (home-page "https://github.com/eguidotti/calculus")
28468 (synopsis "High dimensional numerical and symbolic calculus")
28470 "Efficient C++ optimized functions for numerical and symbolic calculus.
28471 It includes basic symbolic arithmetic, tensor calculus, Einstein summing
28472 convention, fast computation of the Levi-Civita symbol and generalized
28473 Kronecker delta, Taylor series expansion, multivariate Hermite polynomials,
28474 accurate high-order derivatives, differential operators (Gradient, Jacobian,
28475 Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary
28476 orthogonal coordinate systems: cartesian, polar, spherical, cylindrical,
28477 parabolic or user defined by custom scale factors.")
28478 (license license:gpl3)))
28480 (define-public r-decon
28487 (uri (cran-uri "decon" version))
28490 "036cv56wf42q2p3d5h15hbrp5rc29xxy20qwv4k1qzhkq6hmw0qs"))))
28491 (properties `((upstream-name . "decon")))
28492 (build-system r-build-system)
28496 "https://cran.r-project.org/web/packages/decon/")
28497 (synopsis "Deconvolution Estimation in Measurement Error Models")
28499 "This package contains a collection of functions to deal with
28500 nonparametric measurement error problems using deconvolution
28501 kernel methods. We focus two measurement error models in the
28502 package: (1) an additive measurement error model, where the
28503 goal is to estimate the density or distribution function from
28504 contaminated data; (2) nonparametric regression model with
28505 errors-in-variables. The R functions allow the measurement errors
28506 to be either homoscedastic or heteroscedastic. To make the
28507 deconvolution estimators computationally more efficient in R,
28508 we adapt the \"Fast Fourier Transform\" (FFT) algorithm for
28509 density estimation with error-free data to the deconvolution
28510 kernel estimation. Several methods for the selection of the
28511 data-driven smoothing parameter are also provided in the package.
28512 See details in: Wang, X.F. and Wang, B. (2011). Deconvolution
28513 estimation in measurement error models: The R package decon.
28514 Journal of Statistical Software, 39(10), 1-24.")
28515 (license license:gpl3+)))
28517 (define-public r-densestbayes
28519 (name "r-densestbayes")
28524 (uri (cran-uri "densEstBayes" version))
28526 (base32 "16fb7vkic9q5p8s4f0f215zmb36fcizqr4r2vm9dxxj9rasrg2f3"))))
28527 (properties `((upstream-name . "densEstBayes")))
28528 (build-system r-build-system)
28540 (home-page "https://cran.r-project.org/package=densEstBayes")
28541 (synopsis "Density estimation via Bayesian inference engines")
28543 "Bayesian density estimates for univariate continuous random samples are
28544 provided using the Bayesian inference engine paradigm. The engine options
28545 are: Hamiltonian Monte Carlo, the no U-turn sampler, semiparametric mean field
28546 variational Bayes and slice sampling. The methodology is described in Wand
28547 and Yu (2020), arXiv:2009.06182.")
28548 (license license:gpl2+)))
28550 (define-public r-locpol
28557 (uri (cran-uri "locpol" version))
28560 "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))
28561 (properties `((upstream-name . "locpol")))
28562 (build-system r-build-system)
28564 "https://cran.r-project.org/web/packages/locpol/")
28565 (synopsis "Kernel Local Polynomial Regression")
28567 "Computes local polynomial estimators for the regression and
28568 also density. It comprises several different utilities to handle
28569 kernel estimators.")
28570 (license license:gpl2+)))
28572 (define-public r-lpme
28579 (uri (cran-uri "lpme" version))
28582 "1b0w5ji8hjayni1sh5id193cmanf6n11p16fijkxln4sv4lks4aw"))))
28583 (properties `((upstream-name . "lpme")))
28584 (build-system r-build-system)
28586 (list r-decon r-flexmix r-locpol r-rcpp r-rcpparmadillo))
28588 "https://cran.r-project.org/web/packages/lpme/")
28589 (synopsis "Nonparametric Estimation of Measurement Error Models")
28591 "Provide nonparametric methods for mean regression model,
28592 modal regression and conditional density estimation in the
28593 presence/absence of measurement error. Bandwidth selection is
28594 also provided for each method.")
28595 (license license:gpl2+)))
28597 (define-public r-aws-signature
28599 (name "r-aws-signature")
28604 (uri (cran-uri "aws.signature" version))
28607 "15llpcnrdq4y6jsn7079yjmgbr5d1wgy2ymsm3jj3gkrd5l4zzpp"))))
28608 (properties `((upstream-name . "aws.signature")))
28609 (build-system r-build-system)
28611 (list r-base64enc r-digest))
28612 (home-page "https://github.com/cloudyr/aws.signature")
28613 (synopsis "Amazon Web Services Request Signatures")
28615 "This package generates version 2 and 4 request signatures for Amazon Web
28616 Services (AWS) and provides a mechanism for retrieving credentials from
28617 environment variables, AWS credentials files, and EC2 instance metadata. For
28618 use on EC2 instances, the package 'aws.ec2metadata' is suggested.")
28619 (license license:gpl2+)))
28621 (define-public r-aws-s3
28628 (uri (cran-uri "aws.s3" version))
28631 "132cczq0ml7lpp2yl6l4p99dn1zihrncnpa6wyad4m9mnr50a8dx"))))
28632 (properties `((upstream-name . "aws.s3")))
28633 (build-system r-build-system)
28635 (list r-aws-signature
28641 (home-page "https://github.com/cloudyr/aws.s3")
28642 (synopsis "AWS S3 Client Package")
28644 "This package provides a simple client package for the Amazon Web
28645 Services (AWS) Simple Storage Service (S3) REST API.")
28646 (license license:gpl2+)))
28648 (define-public r-lgr
28654 (uri (cran-uri "lgr" version))
28657 "18s92qyakhvp336kk2777ydypwfrfwfz6a1gqkq812zy3kcb4mcc"))))
28658 (build-system r-build-system)
28663 (home-page "https://s-fleck.github.io/lgr/")
28664 (synopsis "Fully featured logging framework")
28665 (description "This package offers a flexible, feature-rich yet
28666 light-weight logging framework based on @code{R6} classes. It supports
28667 hierarchical loggers, custom log levels, arbitrary data fields in log events,
28668 logging to plaintext, JSON, (rotating) files, memory buffers, and databases, as
28669 well as email and push notifications.")
28670 (license license:expat)))
28672 (define-public r-mhg
28679 (uri (cran-uri "mHG" version))
28682 "1rz5ncrvvv9h9grls15apa63v2nh9j87fmp4mwjjil37jx6a5zki"))))
28683 (properties `((upstream-name . "mHG")))
28684 (build-system r-build-system)
28685 (home-page "https://cran.r-project.org/package=mHG")
28686 (synopsis "Minimum-hypergeometric test")
28688 "This package runs a minimum-hypergeometric (mHG) test as described in
28689 \"Discovering Motifs in Ranked Lists of DNA Sequences\" by Eran Eden.")
28690 (license license:gpl2)))
28692 (define-public r-mlr3measures
28694 (name "r-mlr3measures")
28698 (uri (cran-uri "mlr3measures" version))
28701 "1kbw3xd7c9x65v9zzs8i5skmrvl0mf2wsbyssmiif0lvrbzfhcmb"))))
28702 (build-system r-build-system)
28704 (list r-checkmate r-prroc))
28705 (home-page "https://mlr3measures.mlr-org.com/")
28706 (synopsis "Performance measures for mlr3")
28707 (description "This package implements multiple performance measures for
28708 supervised learning. It includes over 40 measures for regression and
28709 classification. Additionally, meta information about the performance measures
28710 can be queried, e.g. what the best and worst possible performances scores
28712 (license license:lgpl3)))
28714 (define-public r-mlr3misc
28716 (name "r-mlr3misc")
28720 (uri (cran-uri "mlr3misc" version))
28723 "1wnzyij1x67smkb3gjb9gpp7iy5andfl0s1c78xx4wylhycc6m11"))))
28724 (build-system r-build-system)
28726 (list r-backports r-checkmate r-data-table r-digest r-r6))
28727 (home-page "https://mlr3misc.mlr-org.com/")
28728 (synopsis "Helper functions for mlr3")
28729 (description "@code{mlr3misc} provides frequently used helper functions
28730 and assertions used in @code{mlr3} and its companion packages. It comes with
28731 helper functions for functional programming, for printing, to work with
28732 @code{data.table}, as well as some generally useful @code{R6} classes. This
28733 package also supersedes the package @code{BBmisc}.")
28734 (license license:lgpl3)))
28736 (define-public r-mlr3pipelines
28738 (name "r-mlr3pipelines")
28742 (uri (cran-uri "mlr3pipelines" version))
28745 "0913f67c1r9bi68gxh1prsp0vch21bl6plahnvjrlbq8rrs1sr6p"))))
28746 (build-system r-build-system)
28758 (home-page "https://mlr3pipelines.mlr-org.com/")
28759 (synopsis "Preprocessing Operators and Pipelines for @code{mlr3}")
28760 (description "@code{mlr3pipelines} enriches @code{mlr3} with a diverse
28761 set of pipelining operators (PipeOps) that can be composed into graphs.
28762 Operations exist for data preprocessing, model fitting, and ensemble learning.
28763 Graphs can themselves be treated as @code{mlr3} Learners and can therefore be
28764 resampled, benchmarked, and tuned.")
28765 (license license:lgpl3)))
28767 (define-public r-mlr3ordinal
28768 (let ((commit "9febac983b11b7b1f477e5cf0212e5999cd2ed44")
28771 (name "r-mlr3ordinal")
28772 (version (git-version "0.1.0-9000" revision commit))
28775 (uri (git-reference
28776 (url "https://github.com/mlr-org/mlr3ordinal")
28778 (file-name (git-file-name name version))
28781 "1icfhz1pjm0mlsn2y60gsrbk31b2p7xmpx3xsg7639rcgdb5f9gl"))))
28782 (build-system r-build-system)
28793 (home-page "https://mlr3ordinal.mlr-org.com/")
28794 (synopsis "Ordinal Regression for mlr3")
28795 (description "This package extends @code{mlr3} with support for
28796 performing ordinal regression.")
28797 (license license:expat))))
28799 (define-public r-paradox
28805 (uri (cran-uri "paradox" version))
28808 "1difp0bzsfxcmbm1snahh3i6417k1a2w4mnjx65p20n2yiclmrgs"))))
28809 (build-system r-build-system)
28811 (list r-backports r-checkmate r-data-table r-mlr3misc r-r6))
28812 (home-page "https://paradox.mlr-org.com/")
28813 (synopsis "Define and work with parameter spaces for complex algorithms")
28814 (description "With this package it is possible to define parameter spaces,
28815 constraints and dependencies for arbitrary algorithms, and to program on such
28816 spaces. It also includes statistical designs and random samplers. Objects are
28817 implemented as @code{R6} classes.")
28818 (license license:lgpl3)))
28820 (define-public r-mlr3
28826 (uri (cran-uri "mlr3" version))
28829 "052685d08cfsrh3r31yn05ngwi6z3fmz26gwiy32z7cpcigz8jjs"))))
28830 (build-system r-build-system)
28846 (home-page "https://mlr3.mlr-org.com/")
28847 (synopsis "Machine Learning in R - Next Generation")
28848 (description "@code{mlr3} enables efficient, object-oriented programming
28849 on the building blocks of machine learning. It provides @code{R6} objects for
28850 tasks, learners, resamplings, and measures. The package is geared towards
28851 scalability and larger datasets by supporting parallelization and out-of-memory
28852 data-backends like databases. While @code{mlr3} focuses on the core
28853 computational operations, add-on packages provide additional functionality.")
28854 (license license:lgpl3)))
28856 (define-public r-mlr3learners
28858 (name "r-mlr3learners")
28862 (uri (cran-uri "mlr3learners" version))
28865 "1yc3mrk1b9h1k342wnw7sm4zmcw7w31l5ybh558g88f5hmibdl98"))))
28866 (build-system r-build-system)
28874 (home-page "https://mlr3learners.mlr-org.com/")
28875 (synopsis "Recommended Learners for @code{mlr3}")
28876 (description "@code{mlr3learners} extends @code{mlr3} and @code{mlr3proba}
28877 with interfaces to essential machine learning packages on CRAN. This includes,
28878 but is not limited to: (penalized) linear and logistic regression, linear and
28879 quadratic discriminant analysis, k-nearest neighbors, naive Bayes, support
28880 vector machines, and gradient boosting.")
28881 (license license:lgpl3)))
28883 (define-public r-bbotk
28890 (uri (cran-uri "bbotk" version))
28893 "15y1w3mi1g91p73786ql1mmqld011757vax17i1vq7zw1s51yzxz"))))
28894 (properties `((upstream-name . "bbotk")))
28895 (build-system r-build-system)
28905 (home-page "https://bbotk.mlr-org.com")
28906 (synopsis "Black-Box Optimization Toolkit")
28907 (description "This package provides a common framework for optimization of
28908 black-box functions for other packages, e.g. @code{mlr3}. It offers various
28909 optimization methods e.g. grid search, random search and generalized simulated
28911 (license license:lgpl3)))
28913 (define-public r-mlr3tuning
28915 (name "r-mlr3tuning")
28919 (uri (cran-uri "mlr3tuning" version))
28922 "0cqbqp53053v7lvi9ynpr860n8fm9w9842hai5z6xvmgzqdmjiyp"))))
28923 (build-system r-build-system)
28933 (home-page "https://mlr3tuning.mlr-org.com/")
28934 (synopsis "Tuning for @code{mlr3}")
28935 (description "@code{mlr3tuning} implements methods for hyperparameter
28936 tuning, e.g. Grid Search, Random Search, or Simulated Annealing. Various
28937 termination criteria can be set and combined. The class @code{AutoTuner} provides a
28938 convenient way to perform nested resampling in combination with @code{mlr3}.")
28939 (license license:lgpl3)))
28941 (define-public r-fontliberation
28943 (name "r-fontliberation")
28948 (uri (cran-uri "fontLiberation" version))
28951 "1w1rl0g4ayyp8lwppmz9yzj9cizg7i50g07216jkm1q5w0is9pmc"))))
28953 `((upstream-name . "fontLiberation")))
28954 (build-system r-build-system)
28955 (home-page "https://cran.r-project.org/package=fontLiberation")
28956 (synopsis "Liberation fonts")
28958 "This package provides a placeholder for the Liberation fontset intended
28959 for the fontquiver package. This fontset covers the 12 combinations of
28960 families (sans, serif, mono) and faces (plain, bold, italic, bold italic)
28961 supported in R graphics devices.")
28962 (license license:silofl1.1)))
28964 (define-public r-fontbitstreamvera
28966 (name "r-fontbitstreamvera")
28971 (uri (cran-uri "fontBitstreamVera" version))
28974 "0nipdlmhjv1wr3aidcl97nk6mppdkd65krgwqnhdsnv0jpfv761j"))))
28976 `((upstream-name . "fontBitstreamVera")))
28977 (build-system r-build-system)
28978 (home-page "https://cran.r-project.org/package=fontBitstreamVera")
28979 (synopsis "Fonts for fontquiver")
28981 "This package is a placeholder for the Bitstream Vera font. It is
28982 intended for the fontquiver package.")
28984 (license:fsdg-compatible
28985 "https://www.gnome.org/fonts/#Final_Bitstream_Vera_Fonts"
28986 "The Font Software may be sold as part of a larger software package but
28987 no copy of one or more of the Font Software typefaces may be sold by
28990 (define-public r-fontquiver
28992 (name "r-fontquiver")
28997 (uri (cran-uri "fontquiver" version))
29000 "0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"))))
29001 (properties `((upstream-name . "fontquiver")))
29002 (build-system r-build-system)
29004 (list r-fontbitstreamvera r-fontliberation))
29005 (home-page "https://cran.r-project.org/package=fontquiver")
29006 (synopsis "Set of installed fonts")
29008 "This package provides a set of fonts. This is useful when you want to
29009 avoid system fonts to make sure your outputs are reproducible.")
29010 (license license:gpl3)))
29012 (define-public r-freetypeharfbuzz
29014 (name "r-freetypeharfbuzz")
29019 (uri (cran-uri "freetypeharfbuzz" version))
29022 "0r3icgnq3jk4fm6z92cmhzdmflbk5df8zsmjg0dzpc4y48xafnk7"))))
29024 `((upstream-name . "freetypeharfbuzz")))
29025 (build-system r-build-system)
29028 (modify-phases %standard-phases
29029 (add-after 'unpack 'prepare-static-libraries
29030 (lambda* (#:key inputs #:allow-other-keys)
29031 (mkdir-p "src/target/include")
29032 (let ((freetype (assoc-ref inputs "static-freetype"))
29033 (harfbuzz (assoc-ref inputs "static-harfbuzz")))
29034 (substitute* "src/Makevars.in"
29035 (("include @MK_FILE@") "") ; do not build static libs
29036 (("^HB_STATIC_LIB =.*")
29037 (string-append "HB_STATIC_LIB = " harfbuzz "/lib/libharfbuzz.a\n"))
29038 (("^FT_STATIC_LIB =.*")
29039 (string-append "FT_STATIC_LIB = " freetype "/lib/libfreetype.a\n")))
29040 (copy-recursively (string-append freetype "/include")
29041 "src/target/include")
29042 (copy-recursively (string-append harfbuzz "/include")
29043 "src/target/include")))))))
29045 (list r-fontquiver))
29046 ;; This may defeat the purpose of this package as our versions of freetype
29047 ;; and harfbuzz obviously differ from the tarballs offered by this
29048 ;; project. On the other hand, Guix arguably does a better job at
29049 ;; "ensur[ing] deterministic computation".
29051 `(("static-freetype"
29053 (inherit (static-package freetype))
29055 `(#:configure-flags
29056 (list "--enable-static=yes"
29061 "--without-harfbuzz")))))
29064 (inherit (static-package harfbuzz))
29066 `(#:tests? #false ; fail because shared library is disabled
29068 (list "--enable-static=yes"
29069 "--enable-shared=no"
29071 "--with-freetype=yes"
29074 "--without-fontconfig"
29075 "--without-glib")))))))
29078 (home-page "https://cran.r-project.org/package=freetypeharfbuzz")
29079 (synopsis "Deterministic computation of text box metrics")
29081 "Unlike other tools that dynamically link to the Cairo stack,
29082 freetypeharfbuzz is statically linked to specific versions of the FreeType and
29083 harfbuzz libraries. This ensures deterministic computation of text box
29084 extents for situations where reproducible results are crucial (for instance
29085 unit tests of graphics).")
29086 (license license:gpl3)))
29088 (define-public r-vdiffr
29095 (uri (cran-uri "vdiffr" version))
29098 "1zjwjw8lqqnx7cxj2aik5rn1g67zsyf0bq08yfwwmsi7v2x6ly3x"))))
29099 (properties `((upstream-name . "vdiffr")))
29100 (build-system r-build-system)
29102 (list libpng zlib))
29112 (home-page "https://github.com/r-lib/vdiffr")
29113 (synopsis "Visual regression testing and graphical diffing")
29115 "This package is an extension to the testthat package that makes it easy
29116 to add graphical unit tests. It provides a Shiny application to manage the
29118 (license license:gpl3)))
29120 (define-public r-highlight
29122 (name "r-highlight")
29127 (uri (cran-uri "highlight" version))
29130 "1shar4y07wyixg0ichdrn2xhgwkl3mv2pxkalqzisc69w605b3hf"))))
29131 (properties `((upstream-name . "highlight")))
29132 (build-system r-build-system)
29133 (home-page "https://github.com/hadley/highlight")
29134 (synopsis "Syntax highlighter for R code")
29136 "This package provides a syntax highlighter for R code based on the
29137 results of the R parser. It supports rendering in HTML and LaTeX markup. It
29138 includes a custom Sweave driver performing syntax highlighting of R code
29140 (license license:gpl3+)))
29142 (define-public r-clustree
29144 (name "r-clustree")
29149 (uri (cran-uri "clustree" version))
29152 "0vwmicajl7c0rmjdmf4f857fii0xrxz25vjkn888svlsikw00qbs"))))
29153 (properties `((upstream-name . "clustree")))
29154 (build-system r-build-system)
29167 (home-page "https://github.com/lazappi/clustree")
29168 (synopsis "Visualize clusterings at different resolutions")
29170 "Deciding what resolution to use can be a difficult question when
29171 approaching a clustering analysis. One way to approach this problem is to
29172 look at how samples move as the number of clusters increases. This package
29173 allows you to produce clustering trees, a visualization for interrogating
29174 clusterings as resolution increases.")
29175 (license license:gpl3)))
29177 (define-public r-textshaping
29179 (name "r-textshaping")
29184 (uri (cran-uri "textshaping" version))
29187 "1niaj1dh09rqrg9hrh98ddnc0f2nkyq9iizv24lcwm9gjs3w1ql0"))))
29188 (properties `((upstream-name . "textshaping")))
29189 (build-system r-build-system)
29191 (list freetype fribidi harfbuzz zlib))
29193 (list r-cpp11 r-systemfonts))
29195 (list pkg-config r-knitr))
29196 (home-page "https://github.com/r-lib/textshaping")
29197 (synopsis "Bindings to the HarfBuzz and Fribidi libraries for text shaping")
29199 "This package provides access to the text shaping functionality in the
29200 HarfBuzz library and the bidirectional algorithm in the Fribidi library. This
29201 is a low-level utility package mainly for graphic devices that expands upon
29202 the font tool-set provided by the @code{systemfonts} package.")
29203 (license license:expat)))
29205 (define-public r-ragg
29212 (uri (cran-uri "ragg" version))
29215 "08dknkibmmwllycga2cp2732idsi3jfkkl5ghh6r2g2wdli1n2y1"))))
29216 (properties `((upstream-name . "ragg")))
29217 (build-system r-build-system)
29219 (list freetype libjpeg-turbo libpng libtiff zlib))
29221 (list r-systemfonts r-textshaping))
29224 (home-page "https://ragg.r-lib.org")
29225 (synopsis "Graphic devices based on AGG")
29227 "Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D
29228 drawing library. The ragg package provides a set of graphic devices based on
29229 AGG to use as alternative to the raster devices provided through the
29230 @code{grDevices} package.")
29231 (license license:expat)))
29233 (define-public r-downlit
29240 (uri (cran-uri "downlit" version))
29243 "10zvrqdpwavdy97h3q26bqh3k63z61fmc04w9vwsnvmnv8hnh3vl"))))
29244 (properties `((upstream-name . "downlit")))
29245 (build-system r-build-system)
29256 (home-page "https://downlit.r-lib.org/")
29257 (synopsis "Syntax highlighting and automatic linking")
29259 "This package provides syntax highlighting of R code, specifically
29260 designed for the needs of RMarkdown packages like @code{pkgdown},
29261 @code{hugodown}, and @code{bookdown}. It includes linking of function calls
29262 to their documentation on the web, and automatic translation of ANSI escapes
29263 in output to the equivalent HTML.")
29264 (license license:expat)))
29266 (define-public r-pkgdown
29273 (uri (cran-uri "pkgdown" version))
29276 "11grx7a2rz6b4kwspm7c8crjav677c22hysnp4bkwh5g8kr5nm2h"))))
29277 (properties `((upstream-name . "pkgdown")))
29278 (build-system r-build-system)
29279 (inputs (list pandoc))
29303 (home-page "https://pkgdown.r-lib.org")
29304 (synopsis "Make static HTML documentation for an R package")
29306 "The goal of this package is to generate an attractive and useful website
29307 from a source package. @code{pkgdown} converts your documentation, vignettes,
29308 README file, and more to HTML making it easy to share information about your
29310 (license license:expat)))
29312 (define-public r-prereg
29319 (uri (cran-uri "prereg" version))
29322 "039nrl5cirsx1ysh214dr6xnn1h6h3f90im6k9dgmzfksxdqigpw"))))
29323 (properties `((upstream-name . "prereg")))
29324 (build-system r-build-system)
29326 (list r-rmarkdown))
29327 (home-page "https://github.com/crsh/prereg")
29329 "R Markdown Templates to preregister Scientific Studies")
29331 "This package provides a collection of templates to author
29332 preregistration documents for scientific studies in PDF format.")
29333 (license license:gpl3)))
29335 (define-public r-ez
29342 (uri (cran-uri "ez" version))
29345 "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq"))))
29346 (properties `((upstream-name . "ez")))
29347 (build-system r-build-system)
29359 (home-page "https://github.com/mike-lawrence/ez")
29360 (synopsis "Easy Analysis and Visualization of Factorial Experiments")
29362 "Facilitates easy analysis of factorial experiments, including purely
29363 within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss designs,
29364 and mixed within-and-between-Ss designs. The functions in this package aim to
29365 provide simple, intuitive and consistent specification of data analysis and
29366 visualization. Visualization functions also include design visualization for
29367 pre-analysis data auditing, and correlation matrix visualization. Finally,
29368 this package includes functions for non-parametric analysis, including
29369 permutation tests and bootstrap resampling. The bootstrap function obtains
29370 predictions either by cell means or by more advanced/powerful mixed effects
29371 models, yielding predictions and confidence intervals that may be easily
29372 visualized at any level of the experiment's design.")
29373 (license license:gpl2+)))
29375 (define-public r-qdapregex
29377 (name "r-qdapregex")
29382 (uri (cran-uri "qdapRegex" version))
29385 "1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"))))
29386 (properties `((upstream-name . "qdapRegex")))
29387 (build-system r-build-system)
29388 (propagated-inputs (list r-stringi))
29390 "https://trinker.github.com/qdapRegex/")
29392 "Regular Expression Removal, Extraction, and Replacement Tools")
29394 "This package provides a collection of regular expression tools
29395 associated with the @code{qdap} package that may be useful outside of the
29396 context of discourse analysis. Tools include removal/extraction/replacement of
29397 abbreviations, dates, dollar amounts, email addresses, hash tags, numbers,
29398 percentages, citations, person tags, phone numbers, times, and zip codes.")
29399 (license license:gpl2)))
29401 (define-public r-mgsub
29408 (uri (cran-uri "mgsub" version))
29411 "1mci6x65h94qiz9cwikx2inbrwkykv43zbs8abfbx416zrh2bbn9"))))
29412 (properties `((upstream-name . "mgsub")))
29413 (build-system r-build-system)
29414 (native-inputs (list r-knitr))
29416 "https://cran.r-project.org/package=mgsub")
29418 "Safe, Multiple, Simultaneous String Substitution")
29420 "Designed to enable simultaneous substitution in strings in a safe
29421 fashion. Safe means it does not rely on placeholders (which can cause errors
29422 in same length matches).")
29423 (license license:expat)))
29425 (define-public r-textshape
29427 (name "r-textshape")
29432 (uri (cran-uri "textshape" version))
29435 "0k9injxykgj2qprc7dygd7gafvcbh3r9x84qzaa1al21pk0dz7ds"))))
29436 (properties `((upstream-name . "textshape")))
29437 (build-system r-build-system)
29439 (list r-data-table r-slam r-stringi))
29440 (home-page "https://github.com/trinker/textshape")
29441 (synopsis "Tools for Reshaping Text")
29443 "Tools that can be used to reshape and restructure text data.")
29444 (license license:gpl2)))
29446 (define-public r-syuzhet
29453 (uri (cran-uri "syuzhet" version))
29456 "16iccqdbw02iw82nah6kwz3gwfghi864j2y698n4b9dyc386ijzv"))))
29457 (properties `((upstream-name . "syuzhet")))
29458 (build-system r-build-system)
29467 (native-inputs (list r-knitr))
29468 (home-page "https://github.com/mjockers/syuzhet")
29470 "Extracts Sentiment and Sentiment-Derived Plot Arcs from Text")
29472 "Extracts sentiment and sentiment-derived plot arcs from text using a
29473 variety of sentiment dictionaries conveniently packaged for consumption by R
29474 users. Implemented dictionaries include @dfn{syuzhet} (default) developed in the
29475 Nebraska Literary Lab, @dfn{afinn} developed by Finn Arup Nielsen, @dfn{bing}
29476 developed by Minqing Hu and Bing Liu, and @dfn{nrc} developed by Mohammad, Saif
29477 M. and Turney, Peter D. Applicable references are available in
29478 @file{README.md} and in the documentation for the @code{get_sentiment}
29479 function. The package also provides a hack for implementing Stanford's coreNLP
29480 sentiment parser. The package provides several methods for plot arc
29482 (license license:gpl3)))
29484 (define-public r-lexicon
29491 (uri (cran-uri "lexicon" version))
29494 "0x7rscsh6par2lj11sby7bmz41cxn63iiw51lgh29z09cg8j606c"))))
29495 (properties `((upstream-name . "lexicon")))
29496 (build-system r-build-system)
29498 (list r-data-table r-syuzhet))
29499 (home-page "https://github.com/trinker/lexicon")
29500 (synopsis "Lexicons for Text Analysis")
29502 "This package provides a collection of lexical hash tables, dictionaries,
29504 (license license:gpl3)))
29506 (define-public r-english
29513 (uri (cran-uri "english" version))
29516 "1g3nmy5p8wj3ix1vp1qmkmy3dyqisrw0md8cjrx4klqkp0wqlms9"))))
29517 (properties `((upstream-name . "english")))
29518 (build-system r-build-system)
29519 (native-inputs (list r-knitr))
29521 "https://cran.r-project.org/package=english")
29522 (synopsis "Translate Integers into English")
29524 "Allow numbers to be presented in an English language version, one, two,
29525 three, ... Ordinals are also available, first, second, third, ... and
29526 indefinite article choice, \"a\" or \"an\".")
29527 (license license:gpl2)))
29529 (define-public r-textclean
29531 (name "r-textclean")
29536 (uri (cran-uri "textclean" version))
29539 "0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"))))
29540 (properties `((upstream-name . "textclean")))
29541 (build-system r-build-system)
29552 "https://github.com/trinker/textclean")
29553 (synopsis "Text Cleaning Tools")
29555 "Tools to clean and process text. Tools are geared at checking for
29556 substrings that are not optimal for analysis and replacing or removing them
29557 (normalizing) with more analysis friendly substrings (see Sproat, Black, Chen,
29558 Kumar, Ostendorf, & Richards (2001) @url{doi:10.1006/csla.2001.0169}) or
29559 extracting them into new variables. For example, emoticons are often used in
29560 text but not always easily handled by analysis algorithms. The
29561 @code{replace_emoticon()} function replaces emoticons with word equivalents.")
29562 (license license:gpl2)))
29564 (define-public r-striprtf
29566 (name "r-striprtf")
29571 (uri (cran-uri "striprtf" version))
29574 "0dqcsh3fb8j0mmmxvxjl77rryhmrjm7a3scqvk2xkgxk4xq6q316"))))
29575 (properties `((upstream-name . "striprtf")))
29576 (build-system r-build-system)
29578 (list r-magrittr r-rcpp r-stringr))
29579 (home-page "https://github.com/kota7/striprtf")
29580 (synopsis "Extract Text from RTF File")
29582 "Extracts plain text from @dfn{Rich Text Format} (RTF) file.")
29583 (license license:expat)))
29585 (define-public r-ndjson
29592 (uri (cran-uri "ndjson" version))
29595 "0lvzbgfi1sg4kya1mvv67z14qk3vz9q57x22qh57xq8ampdkg812"))
29596 (modules '((guix build utils)))
29599 ;; unvendor gzstream
29600 (for-each delete-file '("src/gzstream.cpp" "src/gzstream.h"))
29602 (properties `((upstream-name . "ndjson")))
29603 (build-system r-build-system)
29606 (modify-phases %standard-phases
29607 (add-after 'unpack 'use-system-gzstream
29608 (lambda* (#:key inputs #:allow-other-keys)
29609 (substitute* "src/Makevars"
29610 (("PKG_LIBS = " all)
29611 (string-append all "-lgzstream ")))
29613 (inputs (list zlib gzstream))
29615 (list r-data-table r-rcpp r-tibble))
29616 (home-page "https://gitlab.com/hrbrmstr/ndjson")
29618 "Wicked-Fast @dfn{Streaming JSON} (ndjson) Reader")
29620 "@dfn{Streaming JSON} (ndjson) has one JSON record per-line and many
29621 modern ndjson files contain large numbers of records. These constructs may not
29622 be columnar in nature, but it is often useful to read in these files and
29623 \"flatten\" the structure out to enable working with the data in an R
29624 @code{data.frame}-like context. Functions are provided that make it possible
29625 to read in plain ndjson files or compressed (@code{gz}) ndjson files and either
29626 validate the format of the records or create \"flat\" @code{data.table}
29627 structures from them.")
29628 (license license:expat)))
29630 (define-public r-streamr
29637 (uri (cran-uri "streamR" version))
29640 "1clx3b0j2515r1nmnl6ki7qw5n54q3x2jvqv3zrc00kq71mlj7ix"))))
29641 (properties `((upstream-name . "streamR")))
29642 (build-system r-build-system)
29644 (list r-ndjson r-rcurl r-rjson))
29646 "https://cran.r-project.org/package=streamR")
29648 "Access to Twitter Streaming API via R")
29650 "This package provides functions to access Twitter's filter, sample, and
29651 user streams, and to parse the output into data frames.")
29652 (license license:gpl2)))
29654 (define-public r-readods
29661 (uri (cran-uri "readODS" version))
29664 "1hi217ab7hp15jsbzi5ak57cqf8jn2rv78bnn74q72gn9mrfra7n"))))
29665 (properties `((upstream-name . "readODS")))
29666 (build-system r-build-system)
29668 (list r-cellranger r-readr r-stringi r-xml2))
29669 (native-inputs (list r-knitr))
29671 "https://cran.r-project.org/package=readODS")
29672 (synopsis "Read and Write ODS Files")
29674 "Import @dfn{OpenDocument Spreadsheet} (ODS) into R as a data frame.
29675 Also support writing data frame into ODS file.")
29676 (license license:gpl3)))
29678 (define-public r-qpdf
29685 (uri (cran-uri "qpdf" version))
29688 "03lnfncw8qd1fwfyqh1mjvnsjr3b63wxbah0wp5g7z7gba90dwbi"))
29689 (modules '((guix build utils)))
29692 ;; unvendor libqpdf
29693 (delete-file-recursively "src/libqpdf")
29694 (delete-file-recursively "src/include/qpdf")
29696 (properties `((upstream-name . "qpdf")))
29697 (build-system r-build-system)
29700 (modify-phases %standard-phases
29701 (add-after 'unpack 'configure
29703 (setenv "EXTERNAL_QPDF" "1")
29708 (list r-askpass r-curl r-rcpp))
29709 (native-inputs (list pkg-config))
29710 (home-page "https://github.com/ropensci/qpdf")
29712 "Split, Combine and Compress PDF Files")
29714 "Content-preserving transformations transformations of PDF files such as
29715 split, combine, and compress. This package interfaces directly to the
29716 @code{qpdf} C++ API and does not require any command line utilities. Note that
29717 @code{qpdf} does not read actual content from PDF files: to extract text and
29718 data you need the @code{pdftools} package.")
29719 (license license:asl2.0)))
29721 (define-public r-pdftools
29723 (name "r-pdftools")
29728 (uri (cran-uri "pdftools" version))
29731 "1dcbs5n5y8zi7bbyx491m9ik8kkmjr301x8ms85fmwdfb5a97m8k"))))
29732 (properties `((upstream-name . "pdftools")))
29733 (build-system r-build-system)
29735 (list zlib poppler))
29737 (list r-qpdf r-rcpp))
29738 (native-inputs (list pkg-config))
29740 "https://docs.ropensci.org/pdftools/")
29742 "Text Extraction, Rendering and Converting of PDF Documents")
29744 "Utilities based on @code{libpoppler} for extracting text, fonts,
29745 attachments and metadata from a PDF file. Also supports high quality rendering
29746 of PDF documents into PNG, JPEG, TIFF format, or into raw bitmap vectors for
29747 further processing in R.")
29748 (license license:expat)))
29750 (define-public r-antiword
29752 (name "r-antiword")
29757 (uri (cran-uri "antiword" version))
29760 "034znb0g9wwb8gi1r3z75v3sbb4mh83qrc4y8mbfx5lbgh8zhj6j"))
29761 (modules '((guix build utils)))
29764 ;; unvendor libantiword
29765 (delete-file-recursively "src")
29767 (properties `((upstream-name . "antiword")))
29768 (build-system r-build-system)
29771 (modify-phases %standard-phases
29772 (add-after 'unpack 'use-system-antiword
29773 (lambda* (#:key inputs #:allow-other-keys)
29774 (substitute* "R/antiword.R"
29775 (("system.file\\(\"bin\", package = \"antiword\"\\)")
29776 (string-append "\"" (assoc-ref inputs "antiword") "/bin\"")))
29778 (inputs (list antiword))
29779 (propagated-inputs (list r-sys))
29781 "https://github.com/ropensci/antiword#readme")
29783 "Extract Text from Microsoft Word Documents")
29785 "Wraps the @code{AntiWord} utility to extract text from Microsoft Word
29786 documents. The utility only supports the old @code{doc} format, not the new
29787 xml based @code{docx} format. Use the @code{xml2} package to read the
29789 (license license:gpl2)))
29791 (define-public r-readtext
29793 (name "r-readtext")
29798 (uri (cran-uri "readtext" version))
29801 "0k782h5hns5v5h8a6qyfqck2hc15nq0awg8bsp196q4zviv5jw3c"))))
29802 (properties `((upstream-name . "readtext")))
29803 (build-system r-build-system)
29818 (native-inputs (list r-knitr))
29820 "https://github.com/quanteda/readtext")
29822 "Import and Handling for Plain and Formatted Text Files")
29824 "This package provides functions for importing and handling text files
29825 and formatted text files with additional meta-data, such including @code{.csv},
29826 @code{.tab}, @code{.json}, @code{.xml}, @code{.html}, @code{.pdf}, @code{.doc},
29827 @code{.docx}, @code{.rtf}, @code{.xls}, @code{.xlsx}, and others.")
29828 (license license:gpl3)))
29830 (define-public r-packcircles
29832 (name "r-packcircles")
29837 (uri (cran-uri "packcircles" version))
29840 "05pv5c4k4njkr0xw6i6ksiy34hcyx2lbiqpv5gxw81yrkm0rxfyk"))))
29841 (properties `((upstream-name . "packcircles")))
29842 (build-system r-build-system)
29843 (propagated-inputs (list r-rcpp))
29844 (native-inputs (list r-knitr))
29846 "https://github.com/mbedward/packcircles")
29847 (synopsis "Circle Packing")
29849 "Algorithms to find arrangements of non-overlapping circles.")
29850 (license license:expat)))
29852 ;; Cannot unbundle liblwgeom, because PostGIS does not support building it on
29854 (define-public r-lwgeom
29861 (uri (cran-uri "lwgeom" version))
29864 "0d4b1djwrzla91mmyya2m1250mb44fzmq3d36w5mk81d4bg952pl"))))
29865 (properties `((upstream-name . "lwgeom")))
29866 (build-system r-build-system)
29868 (list geos proj sqlite zlib))
29870 (list r-rcpp r-sf r-units))
29871 (native-inputs (list pkg-config))
29872 (home-page "https://github.com/r-spatial/lwgeom/")
29873 (synopsis "Bindings to Selected 'liblwgeom' Functions for Simple Features")
29875 "Access to selected functions found in
29876 @url{https://github.com/postgis/postgis/tree/master/liblwgeom,liblwgeom}, the
29877 light-weight geometry library used by @url{http://postgis.net/,PostGIS}.")
29878 (license license:gpl2)))
29880 (define-public r-stars
29887 (uri (cran-uri "stars" version))
29890 "0hcbzr8c7wk30qjwrvx6bflzwkjpms79pavaxawnq1h8kry5fngk"))))
29891 (properties `((upstream-name . "stars")))
29892 (build-system r-build-system)
29900 (native-inputs (list r-knitr))
29901 (home-page "https://r-spatial.github.io/stars/")
29903 "Spatiotemporal Arrays, Raster and Vector Data Cubes")
29905 "Reading, manipulating, writing and plotting spatiotemporal arrays
29906 (raster and vector data cubes) in @code{R}, using @code{GDAL} bindings provided
29907 by @code{sf}, and @code{NetCDF} bindings by @code{ncmeta} and @code{RNetCDF}.")
29908 (license license:asl2.0)))
29910 (define-public r-tmaptools
29912 (name "r-tmaptools")
29917 (uri (cran-uri "tmaptools" version))
29920 "0bal3czrdr93qig8s5cf5szld5vjbbks67rismfhlkmlgw6wp2gx"))))
29921 (properties `((upstream-name . "tmaptools")))
29922 (build-system r-build-system)
29934 "https://github.com/mtennekes/tmaptools")
29935 (synopsis "Thematic Map Tools")
29937 "Set of tools for reading and processing spatial data. The aim is to
29938 supply the workflow to create thematic maps. This package also facilitates
29939 @code{tmap}, the package for visualizing thematic maps.")
29940 (license license:gpl3)))
29942 (define-public r-rworldmap
29944 (name "r-rworldmap")
29949 (uri (cran-uri "rworldmap" version))
29952 "1q1h0n9qr0m5pdx10swrh9ddsvdj8kv5nqngrf3lnx9rg9iwivjk"))))
29953 (properties `((upstream-name . "rworldmap")))
29954 (build-system r-build-system)
29956 (list r-fields r-maptools r-sp))
29958 "https://github.com/AndySouth/rworldmap/")
29959 (synopsis "Mapping Global Data")
29961 "Enables mapping of country level and gridded user datasets.")
29962 (license license:gpl2+)))
29964 (define-public r-rtweet
29971 (uri (cran-uri "rtweet" version))
29974 "05pbvxm2vmf6935b9s6663k3aifnkr3m52wh2jvnplmrwyrfpn9n"))))
29975 (properties `((upstream-name . "rtweet")))
29976 (build-system r-build-system)
29985 (native-inputs (list r-knitr))
29987 "https://docs.ropensci.org/rtweet/")
29988 (synopsis "Collecting Twitter Data")
29990 "An implementation of calls designed to collect and organize Twitter data
29991 via @url{https://developer.twitter.com/en/docs,Twitter's REST and stream
29992 Application Program Interfaces (API)}.")
29993 (license license:expat)))
29995 (define-public r-intervals
29997 (name "r-intervals")
30002 (uri (cran-uri "intervals" version))
30005 "0mvwfwc03ifb30a3dzbmkv9adwqb8ajxhcw24d8xip8px063plhb"))))
30006 (properties `((upstream-name . "intervals")))
30007 (build-system r-build-system)
30008 (home-page "https://github.com/edzer/intervals")
30010 "Tools for Working with Points and Intervals")
30012 "Tools for working with and comparing sets of points and intervals.")
30013 (license license:artistic2.0)))
30015 (define-public r-eyelinker
30017 (name "r-eyelinker")
30022 (uri (cran-uri "eyelinker" version))
30025 "0wijd45p6j2qal6wnj7zywks8p9v3m9cmyp7axmk44mrjdjx2i71"))))
30026 (properties `((upstream-name . "eyelinker")))
30027 (build-system r-build-system)
30029 (list r-intervals r-readr r-stringi r-stringr r-tibble))
30030 (native-inputs (list r-knitr))
30032 "https://github.com/a-hurst/eyelinker")
30034 "Import ASC Files from EyeLink Eye Trackers")
30036 "Imports plain-text ASC data files from EyeLink eye trackers into
30037 (relatively) tidy data frames for analysis and visualization.")
30038 (license license:gpl3)))
30040 (define-public r-btm
30047 (uri (cran-uri "BTM" version))
30050 "0ab0wr8nbwn1w1j9hpwfz52lm1sw0qk93713y9k0hpm3pw9dq4jr"))))
30051 (properties `((upstream-name . "BTM")))
30052 (build-system r-build-system)
30053 (propagated-inputs (list r-rcpp))
30054 (home-page "https://github.com/bnosac/BTM")
30055 (synopsis "Biterm Topic Models for Short Text")
30057 "Biterm Topic Models find topics in collections of short texts. It is a
30058 word co-occurrence based topic model that learns topics by modeling word-word
30059 co-occurrences patterns which are called biterms. This in contrast to
30060 traditional topic models like Latent Dirichlet Allocation and Probabilistic
30061 Latent Semantic Analysis which are word-document co-occurrence topic models. A
30062 biterm consists of two words co-occurring in the same short text window. This
30063 context window can for example be a twitter message, a short answer on a
30064 survey, a sentence of a text or a document identifier. The techniques are
30065 explained in detail in the paper 'A Biterm Topic Model For Short Text' by
30066 Xiaohui Yan, Jiafeng Guo, Yanyan Lan, Xueqi Cheng (2013)
30067 @url{https://github.com/xiaohuiyan/xiaohuiyan.github.io/blob/master/paper/\
30069 (license license:asl2.0)))
30071 (define-public r-delaporte
30073 (name "r-delaporte")
30078 (uri (cran-uri "Delaporte" version))
30081 "10xsmms2jfw7x4hmgpd35dv4n4azpjzmfid6585kg6qfh2zg23g5"))))
30082 (properties `((upstream-name . "Delaporte")))
30083 (build-system r-build-system)
30084 (native-inputs (list gfortran))
30085 (home-page "https://github.com/aadler/Delaporte")
30086 (synopsis "Statistical functions for the Delaporte distribution")
30088 "This package provides probability mass, distribution, quantile,
30089 random-variate generation, and method-of-moments parameter-estimation
30090 functions for the Delaporte distribution with parameterization based on
30091 Vose (2008). The Delaporte is a discrete probability distribution which can
30092 be considered the convolution of a negative binomial distribution with a
30093 Poisson distribution. Alternatively, it can be considered a counting
30094 distribution with both Poisson and negative binomial components. It has been
30095 studied in actuarial science as a frequency distribution which has more
30096 variability than the Poisson, but less than the negative binomial.")
30097 (license license:bsd-2)))
30099 (define-public r-rjsonio
30102 (version "1.3-1.6")
30106 (uri (cran-uri "RJSONIO" version))
30109 "17x0ayk7daprbc8w2hvb2jl9mfnw4dic9yc3sr5adcjqfzmcklc2"))))
30110 (properties `((upstream-name . "RJSONIO")))
30111 (build-system r-build-system)
30112 (home-page "https://cran.r-project.org/package=RJSONIO")
30113 (synopsis "Serialize R objects to JSON")
30115 "This is a package that allows conversion to and from data in JavaScript
30116 Object Notation (JSON) format. This allows R objects to be inserted into
30117 Javascript/ECMAScript/ActionScript code and allows R programmers to read and
30118 convert JSON content to R objects. This is an alternative to the @code{rjson}
30120 (license license:bsd-3)))
30122 (define-public r-revgeo
30129 (uri (cran-uri "revgeo" version))
30132 "1ns7d1817475lriss6wwgvdm6lj760p40yxqaifla13c2xb73a55"))))
30133 (properties `((upstream-name . "revgeo")))
30134 (build-system r-build-system)
30136 (list r-rcurl r-rjsonio))
30137 (home-page "https://cran.r-project.org/package=revgeo")
30138 (synopsis "Reverse geocoding")
30140 "The @code{revgeo} procedure allows you to use the Photon geocoder for
30141 OpenStreetMap, Google Maps, and Bing to reverse geocode coordinate pairs with
30143 (license license:gpl3+)))
30145 (define-public r-qpcr
30152 (uri (cran-uri "qpcR" version))
30155 "1r01q7jv3w59yx1gc0qw91rq7rvdhqsi8y57sqqkmwyqfw2x2vsv"))))
30156 (properties `((upstream-name . "qpcR")))
30157 (build-system r-build-system)
30159 (list r-mass r-matrix r-minpack-lm r-rgl r-robustbase))
30160 (home-page "https://cran.r-project.org/package=qpcR")
30161 (synopsis "Modelling and analysis of real-time PCR data")
30163 "This is a package for model fitting, optimal model selection and
30164 calculation of various features that are essential in the analysis of
30165 quantitative real-time polymerase chain reaction (qPCR).")
30166 (license license:gpl2+)))
30168 (define-public r-textplot
30170 (name "r-textplot")
30175 (uri (cran-uri "textplot" version))
30178 "10nxh9axhy6kyp6f3rz7smq08yl35ydx9jx47bs7i0bmcl2kwxvl"))))
30179 (properties `((upstream-name . "textplot")))
30180 (build-system r-build-system)
30182 (list r-data-table r-lattice r-matrix))
30183 (native-inputs (list r-knitr))
30184 (home-page "https://github.com/bnosac/textplot")
30185 (synopsis "Text Plots")
30187 "Visualise complex relations in texts. This is done by providing
30188 functionalities for displaying text co-occurrence networks, text correlation
30189 networks, dependency relationships as well as text clustering. Feel free to
30190 join the effort of providing interesting text visualisations.")
30191 (license license:gpl2)))
30193 (define-public r-gsa
30200 (uri (cran-uri "GSA" version))
30203 "05x9wspah1cdznjpncqam1iawsxdiigyl8v2anyhss2k7wwd94p1"))))
30204 (properties `((upstream-name . "GSA")))
30205 (build-system r-build-system)
30206 (home-page "https://statweb.stanford.edu/~tibs/GSA/")
30207 (synopsis "Gene set analysis")
30208 (description "This package lets you determine the significance of
30209 pre-defined sets of genes with respect to an outcome variable, such as a group
30210 indicator, a quantitative variable or a survival time.")
30211 ;; Any version of the LGPL
30212 (license license:lgpl3+)))
30214 (define-public r-randomforestsrc
30216 (name "r-randomforestsrc")
30221 (uri (cran-uri "randomForestSRC" version))
30224 "05ifvj49jv0n5p6k46milpgj9r10sc5aw23fypyyibdgwpwvwixw"))))
30226 `((upstream-name . "randomForestSRC")))
30227 (build-system r-build-system)
30228 (home-page "https://cran.r-project.org/web/packages/randomForestSRC/")
30229 (synopsis "Random forests for survival, regression, and classification")
30231 "This package implements fast OpenMP parallel computing of Breiman's
30232 random forests for survival, competing risks, regression and classification
30233 based on Ishwaran and Kogalur's popular random survival forests (RSF) package.
30234 It handles missing data and now includes multivariate, unsupervised forests,
30235 quantile regression and solutions for class imbalanced data. It provides a
30236 fast interface using subsampling and confidence regions for variable
30238 (license license:gpl3+)))
30240 (define-public r-contfrac
30242 (name "r-contfrac")
30247 (uri (cran-uri "contfrac" version))
30250 "0sq5c7ny235yrkv2xc4insgxby6rvzc1qsj8h301cd2if3lwbgwm"))))
30251 (properties `((upstream-name . "contfrac")))
30252 (build-system r-build-system)
30254 "https://github.com/RobinHankin/contfrac")
30255 (synopsis "Continued Fractions")
30257 "Various utilities for evaluating continued fractions.")
30258 (license license:gpl2)))
30260 (define-public r-elliptic
30262 (name "r-elliptic")
30267 (uri (cran-uri "elliptic" version))
30270 "1dhba0yfxjd5rlqsxp5a7s2hclfkla9wigsr39dlma67l6qjjmxn"))))
30271 (properties `((upstream-name . "elliptic")))
30272 (build-system r-build-system)
30273 (inputs (list pari-gp))
30274 (propagated-inputs (list r-mass))
30276 "https://github.com/RobinHankin/elliptic")
30278 "Weierstrass and Jacobi Elliptic Functions")
30280 "A suite of elliptic and related functions including Weierstrass and
30281 Jacobi forms. Also includes various tools for manipulating and visualizing
30282 complex functions.")
30283 (license license:gpl2)))
30285 (define-public r-hypergeo
30287 (name "r-hypergeo")
30292 (uri (cran-uri "hypergeo" version))
30295 "13jdiy216znwhr91iqnh03mvkmyscw439syb3h4i67dd78sphnvd"))))
30296 (properties `((upstream-name . "hypergeo")))
30297 (build-system r-build-system)
30299 (list r-contfrac r-desolve r-elliptic))
30301 "https://cran.r-project.org/web/packages/hypergeo/")
30302 (synopsis "The Gauss Hypergeometric Function")
30304 "The Gaussian hypergeometric function for complex numbers.")
30305 (license license:gpl2)))
30307 (define-public r-gganimate
30309 (name "r-gganimate")
30314 (uri (cran-uri "gganimate" version))
30317 "046v6j92xxgaghsnh88dy5h8x040qsfa8csvhp4dmsfmrrf0dz0f"))))
30318 (properties `((upstream-name . "gganimate")))
30319 (build-system r-build-system)
30322 (modify-phases %standard-phases
30323 (add-after 'unpack 'absolute-paths
30324 (lambda* (#:key inputs #:allow-other-keys)
30325 (substitute* "R/renderers.R"
30327 (string-append "'" (assoc-ref inputs "ffmpeg") "/bin/ffmpeg'"))))))))
30329 ;; For video output.
30340 ;; For GIF/SVG output. gifski is faster, but depends on Rust.
30342 ;; For HTML output.
30345 (native-inputs (list r-knitr))
30346 (home-page "https://gganimate.com")
30347 (synopsis "Grammar of Animated Graphics")
30349 "This package extends the grammar of graphics as implemented by
30350 @code{ggplot2} to include the description of animation. It does this by
30351 providing a range of new grammar classes that can be added to the plot object
30352 in order to customise how it should change with time.")
30353 (license license:expat)))
30355 ;; This library bundles ‘date’ from (gnu packages calendar). We cannot unbundle
30356 ;; it, because its C++ libtz.so is built with different compiler flags than
30358 (define-public r-tzdb
30365 (uri (cran-uri "tzdb" version))
30368 "1afmav7s29fb5cd920h6vrzg9cvc4jsidfalxpvhlh1b8mfr0df3"))))
30369 (properties `((upstream-name . "tzdb")))
30370 (build-system r-build-system)
30371 (propagated-inputs (list r-cpp11))
30372 (home-page "https://github.com/r-lib/tzdb")
30373 (synopsis "Time Zone Database Information")
30375 "This package provides an up-to-date copy of the Internet Assigned
30376 Numbers Authority (IANA) Time Zone Database. It is updated periodically to
30377 reflect changes made by political bodies to time zone boundaries, UTC offsets,
30378 and daylight saving time rules. Additionally, this package provides a C++
30379 interface for working with the @code{date} library. @code{date} provides
30380 comprehensive support for working with dates and date-times, which this package
30381 exposes to make it easier for other R packages to utilize. Headers are
30382 provided for calendar specific calculations, along with a limited interface for
30383 time zone manipulations.")
30384 (license license:expat)))
30386 (define-public r-vroom
30393 (uri (cran-uri "vroom" version))
30396 "1plz20x6s01gkkcac51lhx4r2s024pgh778ri7y25hkiiwacp1yh"))))
30397 (properties `((upstream-name . "vroom")))
30398 (build-system r-build-system)
30414 (native-inputs (list r-knitr))
30415 (home-page "https://vroom.r-lib.org")
30417 "Read and Write Rectangular Text Data")
30419 "This package reads and writes data files like @acronym{CSV},
30420 @acronym{TSV} and @acronym{FWF}. When reading it uses a quick initial indexing
30421 step, then reads the values lazily, so only the data you actually use needs to
30422 be read. The writer formats the data in parallel and writes to disk
30423 asynchronously from formatting.")
30424 (license license:expat)))
30426 (define-public r-rmisc
30432 (uri (cran-uri "Rmisc" version))
30435 "1ijjhfy3v91fspid77rrkc5dkcb2lav37wc3f4k5lwrn24wzy5y8"))))
30436 (build-system r-build-system)
30438 (list r-plyr r-rcpp r-lattice))
30439 (home-page "https://cran.r-project.org/web/packages/Rmisc/")
30440 (synopsis "Ryan Miscellaneous")
30441 (description "The Rmisc library contains functions for data analysis and
30442 utility operations.")
30443 (license license:gpl3)))
30445 (define-public r-webutils
30447 (name "r-webutils")
30452 (uri (cran-uri "webutils" version))
30454 (base32 "16a6ds0fnb6y8i1r9ba1hf1ydb53am57s070b3hi5jmrs84b9qik"))))
30455 (properties `((upstream-name . "webutils")))
30456 (build-system r-build-system)
30458 (list r-curl r-jsonlite))
30459 (home-page "https://github.com/jeroen/webutils")
30460 (synopsis "Utility functions for developing web applications")
30462 "This package parses HTTP request data in @code{application/json},
30463 @code{multipart/form-data}, or @code{application/x-www-form-urlencoded}
30464 format. It includes an example of hosting and parsing HTML form data in R
30465 using either @code{httpuv} or @code{Rhttpd}.")
30466 (license license:expat)))
30468 (define-public r-protolite
30470 (name "r-protolite")
30475 (uri (cran-uri "protolite" version))
30477 (base32 "0g1r3lzmvx1w44qzqzdvxfn21zmz11srlp6cr76kd7pd5wzjv82p"))))
30478 (properties `((upstream-name . "protolite")))
30479 (build-system r-build-system)
30483 (list r-jsonlite r-rcpp))
30485 (list protobuf pkg-config))
30486 (home-page "https://github.com/jeroen/protolite")
30487 (synopsis "Highly optimized protocol buffer serializers")
30489 "This package provides pure C++ implementations for reading and writing
30490 several common data formats based on Google protocol-buffers. It currently
30491 supports @code{rexp.proto} for serialized R objects, @code{geobuf.proto} for
30492 binary geojson, and @code{mvt.proto} for vector tiles. This package uses the
30493 auto-generated C++ code by protobuf-compiler, hence the entire serialization
30494 is optimized at compile time. The @code{RProtoBuf} package on the other hand
30495 uses the protobuf runtime library to provide a general-purpose toolkit for
30496 reading and writing arbitrary protocol-buffer data in R.")
30497 (license license:expat)))
30499 (define-public r-opencpu
30506 (uri (cran-uri "opencpu" version))
30508 (base32 "0cmjfhkbk4im3x8aas0q5pivlsxgqixf4f3jiindchki7g9nsw91"))))
30509 (properties `((upstream-name . "opencpu")))
30510 (build-system r-build-system)
30530 (home-page "https://www.opencpu.org")
30531 (synopsis "API for embedded scientific computing")
30533 "This package provides a system for embedded scientific computing and
30534 reproducible research with R. The OpenCPU server exposes a simple but
30535 powerful HTTP API for RPC and data interchange with R. This provides a
30536 reliable and scalable foundation for statistical services or building R web
30537 applications. The OpenCPU server runs either as a single-user development
30538 server within the interactive R session, or as a multi-user stack based on
30540 (license license:asl2.0)))
30542 (define-public r-exactextractr
30544 (name "r-exactextractr")
30549 (uri (cran-uri "exactextractr" version))
30552 "0n39dqgsfzybi9yvnpnfdyypl8c9fml80jq0wxssik2n47mvbcif"))))
30553 (properties `((upstream-name . "exactextractr")))
30554 (build-system r-build-system)
30555 (inputs (list geos))
30557 (list r-raster r-rcpp r-sf))
30560 (home-page "https://isciences.gitlab.io/exactextractr/")
30561 (synopsis "Fast extraction from raster datasets using polygons")
30563 "This package provides a replacement for the @code{extract} function from
30564 the @code{raster} package that is suitable for extracting raster values using
30565 @code{sf} polygons.")
30566 (license license:asl2.0)))
30568 (define-public r-stringfish
30570 (name "r-stringfish")
30575 (uri (cran-uri "stringfish" version))
30578 "0ac17wl0fcpmipbvhhg5nyccg055671fnlxvnjd5l3kilx313wlx"))))
30579 (properties `((upstream-name . "stringfish")))
30580 (build-system r-build-system)
30582 (list r-rcpp r-rcppparallel))
30584 (list pkg-config r-knitr))
30585 (home-page "https://github.com/traversc/stringfish")
30586 (synopsis "Alternative string implementation")
30588 "This package provides an extendable, performant and multithreaded
30589 @code{alt-string} implementation backed by C++ vectors and strings.")
30590 (license license:gpl3)))
30592 (define-public r-rapiserialize
30594 (name "r-rapiserialize")
30599 (uri (cran-uri "RApiSerialize" version))
30602 "0gm2j8kh40imhncwwx1sx9kmraaxcxycvgwls53lcyy2ap344k9j"))))
30603 (properties `((upstream-name . "RApiSerialize")))
30604 (build-system r-build-system)
30606 "https://cran.r-project.org/package=RApiSerialize")
30607 (synopsis "R API serialization")
30609 "This package provides other packages with access to the internal R
30610 serialization code. Access to this code is provided at the C function level
30611 by using the registration of native function mechanism. Client packages
30612 simply include a single header file RApiSerializeAPI.h provided by this
30614 (license license:gpl2+)))
30616 (define-public r-qs
30623 (uri (cran-uri "qs" version))
30626 "1gswppmw8rhd7h50hffhss4c4niz0x54r9sc8pgqzy26vkjqlhpy"))))
30627 (properties `((upstream-name . "qs")))
30628 (build-system r-build-system)
30629 (inputs (list zlib))
30631 (list r-rapiserialize r-rcpp r-stringfish))
30633 (list pkg-config r-knitr))
30634 (home-page "https://github.com/traversc/qs")
30635 (synopsis "Quick serialization of R objects")
30637 "This package provides functions for quickly writing and reading any R
30638 object to and from disk.")
30639 (license license:gpl3)))
30641 (define-public r-rgeos
30648 (uri (cran-uri "rgeos" version))
30651 "1m73y0nwrdwsjrl48c4fg1kdqnh79835brnmxv9ak01ndbzcp45b"))))
30652 (properties `((upstream-name . "rgeos")))
30653 (build-system r-build-system)
30658 (home-page "https://cran.r-project.org/package=rgeos")
30659 (synopsis "Interface to Geometry Engine (GEOS)")
30661 "This package provides an R interface to Geometry Engine (GEOS) using the
30662 C API for topology operations on geometries.")
30663 (license license:gpl2+)))
30665 (define-public r-tfruns
30672 (uri (cran-uri "tfruns" version))
30675 "04lfckg1if3kfwcl4s4fcc9aw04crwk4m1qr55ag22j2x2jlb2l9"))))
30676 (properties `((upstream-name . "tfruns")))
30677 (build-system r-build-system)
30689 (native-inputs (list r-knitr))
30690 (home-page "https://github.com/rstudio/tfruns")
30691 (synopsis "Training run tools for TensorFlow")
30693 "Create and manage unique directories for each TensorFlow training run.
30694 This package provides a unique, time stamped directory for each run along with
30695 functions to retrieve the directory of the latest run or latest several
30697 (license license:asl2.0)))
30699 (define-public r-tfautograph
30701 (name "r-tfautograph")
30706 (uri (cran-uri "tfautograph" version))
30709 "0fmaq1ggjyxgf2ss7qb8jk74sfwc3s1vc123pd5glclxcy1ib0j2"))))
30710 (properties `((upstream-name . "tfautograph")))
30711 (build-system r-build-system)
30712 (inputs (list tensorflow))
30714 (list r-backports r-reticulate))
30715 (home-page "https://t-kalinowski.github.io/tfautograph/")
30716 (synopsis "Autograph R for Tensorflow")
30718 "This package lets you translate R control flow expressions into
30719 Tensorflow graphs.")
30720 (license license:gpl3)))
30722 (define-public r-tensorflow
30724 (name "r-tensorflow")
30729 (uri (cran-uri "tensorflow" version))
30732 "0xgm8jb1hl8564vviqys3aqwzvfbh0d43m154cj07j9spdz306ng"))))
30733 (properties `((upstream-name . "tensorflow")))
30734 (build-system r-build-system)
30735 (inputs (list tensorflow))
30744 (home-page "https://github.com/rstudio/tensorflow")
30745 (synopsis "R interface to TensorFlow")
30747 "R interface to TensorFlow a library for numerical computation using data
30748 flow graphs. Nodes in the graph represent mathematical operations, while the
30749 graph edges represent the multidimensional data arrays (tensors) communicated
30751 (license license:asl2.0)))
30753 (define-public r-keras
30760 (uri (cran-uri "keras" version))
30763 "004z9aajc0b7lw7g68ri7ndabdwbylmnlyvmziljmm29z6fzk8y5"))))
30764 (properties `((upstream-name . "keras")))
30765 (build-system r-build-system)
30777 (native-inputs (list r-knitr))
30778 (home-page "https://keras.rstudio.com")
30779 (synopsis "R Interface to 'Keras'")
30781 "This package provides an interface to Keras, a high-level neural
30782 networks API. Keras was developed with a focus on enabling fast
30783 experimentation, supports both convolution based networks and recurrent
30784 networks (as well as combinations of the two), and runs seamlessly on both CPU
30786 (license license:expat)))
30788 (define-public r-zzlite
30795 (uri (cran-uri "zzlite" version))
30798 "0vi1slx2s4r5zf82lazqv0c3m12xq73wlgsbz6af4y00h0bkr3ps"))))
30799 (properties `((upstream-name . "zzlite")))
30800 (build-system r-build-system)
30802 (list r-httr r-jsonlite))
30805 (home-page "https://cran.r-project.org/package=zzlite")
30806 (synopsis "Wrapper for the Zamzar file conversion API")
30808 "This package provides a minor collection of HTTP wrappers for the Zamzar
30809 file conversion API. The wrappers makes it easy to utilize the API and thus
30810 convert between more than 100 different file formats (ranging from audio
30811 files, images, movie formats, etc., etc.) through an R session.")
30812 (license license:gpl3)))
30814 (define-public r-ztree
30821 (uri (cran-uri "zTree" version))
30824 "005zk6wpchpss6865ki35yawgf668pn70163ah97rnfkhfaswm6y"))))
30825 (properties `((upstream-name . "zTree")))
30826 (build-system r-build-system)
30829 (home-page "https://cran.r-project.org/package=zTree")
30830 (synopsis "Functions to import data from z-Tree into R")
30832 "This package provides tools for reading @code{.xls} and @code{.sbj}
30833 files which are written by the proprietary program z-Tree for developing and
30834 carrying out economic experiments.")
30835 (license license:gpl3)))
30837 (define-public r-distributionutils
30839 (name "r-distributionutils")
30844 (uri (cran-uri "DistributionUtils" version))
30847 "08vq54pyqxlqsj6q6gsg5ikqa0z3x842j52ld5dxaq272p6xchvl"))))
30849 `((upstream-name . "DistributionUtils")))
30850 (build-system r-build-system)
30853 (home-page "https://cran.r-project.org/package=DistributionUtils")
30854 (synopsis "Distribution utilities")
30856 "This package provides utilities for dealing with distributions.
30857 Functionality includes sample skewness and kurtosis, log-histogram, tail
30858 plots, moments by integration, changing the point about which a moment is
30859 calculated, functions for testing distributions using inversion tests and the
30860 Massart inequality. Also included is an implementation of the incomplete
30861 Bessel K function.")
30862 (license license:gpl2+)))
30864 (define-public r-ztpln
30871 (uri (cran-uri "ztpln" version))
30874 "1b22m72a8117yrgq5k1gzsrbx6yrsrj7bpd49lh7x3vbaz56c0wr"))))
30875 (properties `((upstream-name . "ztpln")))
30876 (build-system r-build-system)
30878 (list r-distributionutils r-mixtools r-rcpp r-rcppeigen
30882 (home-page "https://github.com/mattocci27/ztpln")
30883 (synopsis "Zero-truncated Poisson lognormal distribution")
30885 "This package provides functions for obtaining the density, random
30886 variates and maximum likelihood estimates of the Zero-truncated Poisson
30887 lognormal distribution and their mixture distribution.")
30888 (license license:expat)))
30890 (define-public r-zscorer
30897 (uri (cran-uri "zscorer" version))
30900 "0aijhs0fyird5gq68x4dxchb02mxa7ijk10k9zjhngghxbjj7iqn"))))
30901 (properties `((upstream-name . "zscorer")))
30902 (build-system r-build-system)
30907 (home-page "https://github.com/nutriverse/zscorer")
30908 (synopsis "Child Anthropometry z-Score Calculator")
30910 "This package provides a tool for calculating z-scores and centiles for
30911 weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age,
30912 head circumference-for-age, age circumference-for-age, subscapular
30913 skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth
30915 (license license:agpl3+)))
30917 (define-public r-zra
30924 (uri (cran-uri "ZRA" version))
30927 "1sx1q5yf68hhlb5j1hicpj594rmgajqr25llg7ax416j0m2rnagi"))))
30928 (properties `((upstream-name . "ZRA")))
30929 (build-system r-build-system)
30931 (list r-dygraphs r-forecast))
30932 (home-page "https://cran.r-project.org/package=ZRA")
30933 (synopsis "Dynamic plots for time series forecasting")
30935 "This package combines a forecast of a time series, using the function @code{forecast},
30936 with the dynamic plots from @code{dygraphs}.")
30937 (license license:gpl2+)))
30939 (define-public r-rfigshare
30941 (name "r-rfigshare")
30946 (uri (cran-uri "rfigshare" version))
30949 "1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq"))))
30950 (properties `((upstream-name . "rfigshare")))
30951 (build-system r-build-system)
30960 (home-page "https://github.com/ropensci/rfigshare")
30961 (synopsis "R Interface to figshare")
30963 "This package provides an interface to figshare, a scientific repository
30964 to archive and assign DOIs to data, software, figures, and more.")
30965 (license license:cc0)))
30967 (define-public r-dismo
30974 (uri (cran-uri "dismo" version))
30977 "1rqf6h4imbqvs7hjd1k4my6154wg0qnmnp5byan403rcshr1jbl1"))))
30978 (properties `((upstream-name . "dismo")))
30979 (build-system r-build-system)
30981 (list r-raster r-rcpp r-sp r-terra))
30982 (home-page "https://rspatial.org/raster/sdm/")
30983 (synopsis "Species distribution modeling")
30985 "This package provides methods for species distribution modeling, i.e.,
30986 predicting the environmental similarity of any site to that of the locations
30987 of known occurrences of a species.")
30988 (license license:gpl3+)))
30990 (define-public r-zoon
30997 (uri (cran-uri "zoon" version))
31000 "02y29vr2yn8al69km8faiqrwjrc1r3hsvw3dg8lwjr65cxw1krip"))))
31001 (properties `((upstream-name . "zoon")))
31002 (build-system r-build-system)
31017 (home-page "https://github.com/zoonproject/zoon")
31018 (synopsis "Reproducible, accessible and shareable species distribution modelling")
31020 "This package reads user submitted modules from an online repository,
31021 runs full species distribution modelling workflows and returns output that is
31022 fully reproducible.")
31023 (license license:bsd-3)))
31025 (define-public r-paws-common
31027 (name "r-paws-common")
31032 (uri (cran-uri "paws.common" version))
31035 "0kj5b4253j4rljkj0ibh21kh9r1yq9idz9vf1f4ag775ivsc2dk5"))))
31036 (properties `((upstream-name . "paws.common")))
31037 (build-system r-build-system)
31039 (list r-base64enc r-digest r-httr r-jsonlite r-xml2))
31040 (home-page "https://cran.r-project.org/package=paws.common")
31041 (synopsis "Paws low-level Amazon Web Services API")
31043 "This package provides functions for making low-level API requests to
31044 Amazon Web Services. The functions handle building, signing, and sending
31045 requests, and receiving responses. They are designed to help build
31046 higher-level interfaces to individual services, such as Simple Storage
31048 (license license:asl2.0)))
31050 (define-public r-paws-customer-engagement
31052 (name "r-paws-customer-engagement")
31057 (uri (cran-uri "paws.customer.engagement" version))
31060 "0ac6hzn4ilfjhzdmc9x80999fl18cz16mky31qd3y09m93w2xkdj"))))
31062 `((upstream-name . "paws.customer.engagement")))
31063 (build-system r-build-system)
31065 (list r-paws-common))
31066 (home-page "https://github.com/paws-r/paws")
31067 (synopsis "Amazon Web Services customer engagement services")
31069 "This package provides an interface to Amazon Web Services customer
31070 engagement services, including Simple Email Service, Connect contact center
31071 service, and more.")
31072 (license license:asl2.0)))
31074 (define-public r-paws-cost-management
31076 (name "r-paws-cost-management")
31081 (uri (cran-uri "paws.cost.management" version))
31084 "0in4f8ygw5g2v6vl3lz2y0v51llglh8b1ymbd04d54xxlgn83knh"))))
31086 `((upstream-name . "paws.cost.management")))
31087 (build-system r-build-system)
31089 (list r-paws-common))
31090 (home-page "https://github.com/paws-r/paws")
31091 (synopsis "Amazon Web Services cost management services")
31093 "This package provides an interface to Amazon Web Services cost
31094 management services, including cost and usage reports, budgets, pricing, and
31096 (license license:asl2.0)))
31098 (define-public r-paws-developer-tools
31100 (name "r-paws-developer-tools")
31105 (uri (cran-uri "paws.developer.tools" version))
31107 (base32 "16gb8g8s67al7qdd95fbigxqkih9a9p7slkyf3cga42wb6miiby2"))))
31108 (properties `((upstream-name . "paws.developer.tools")))
31109 (build-system r-build-system)
31111 (list r-paws-common))
31112 (home-page "https://github.com/paws-r/paws")
31113 (synopsis "Amazon Web Services developer tools services")
31115 "This package provides an interface to Amazon Web Services developer
31116 tools services, including version control, continuous integration and
31117 deployment, and more.")
31118 (license license:asl2.0)))
31120 (define-public r-paws-end-user-computing
31122 (name "r-paws-end-user-computing")
31127 (uri (cran-uri "paws.end.user.computing" version))
31129 (base32 "1xxsz86nx128sizym9np8vldzkbym0p3i6vcy94kq1y0cylaicv3"))))
31130 (properties `((upstream-name . "paws.end.user.computing")))
31131 (build-system r-build-system)
31133 (list r-paws-common))
31134 (home-page "https://github.com/paws-r/paws")
31135 (synopsis "Amazon Web Services end user computing services")
31137 "This package provides an interface to Amazon Web Services end user
31138 computing services, including collaborative document editing, mobile intranet,
31140 (license license:asl2.0)))
31142 (define-public r-paws-application-integration
31144 (name "r-paws-application-integration")
31149 (uri (cran-uri "paws.application.integration" version))
31152 "0llyd9hc679pad1ih0rcc38q5xxpzinhwrl8cvrkgsjgbc3agq42"))))
31154 `((upstream-name . "paws.application.integration")))
31155 (build-system r-build-system)
31157 (list r-paws-common))
31158 (home-page "https://github.com/paws-r/paws")
31159 (synopsis "Amazon Web Services application integration services")
31161 "This package provides an interface to Amazon Web Services application
31162 integration services, including Simple Queue Service (SQS) message queue,
31163 Simple Notification Service (SNS) publish/subscribe messaging, and more.")
31164 (license license:asl2.0)))
31166 (define-public r-paws-security-identity
31168 (name "r-paws-security-identity")
31173 (uri (cran-uri "paws.security.identity" version))
31176 "092lz2ipn5iqr593x7ra8c0bj64yf6315mdc3llgwrjyb4vfxif9"))))
31178 `((upstream-name . "paws.security.identity")))
31179 (build-system r-build-system)
31181 (list r-paws-common))
31182 (home-page "https://github.com/paws-r/paws")
31183 (synopsis "Amazon Web Services security, identity, and compliance services")
31185 "This package provides an interface to Amazon Web Services security,
31186 identity, and compliance services, including the Identity and Access
31187 Management (IAM) service for managing access to services and resources, and
31189 (license license:asl2.0)))
31191 (define-public r-paws-analytics
31193 (name "r-paws-analytics")
31198 (uri (cran-uri "paws.analytics" version))
31201 "04gnaxmj21l312xkrsd9bisi0bz9h6h5fyhwlqylcxi077z1yb2g"))))
31203 `((upstream-name . "paws.analytics")))
31204 (build-system r-build-system)
31206 (list r-paws-common))
31207 (home-page "https://github.com/paws-r/paws")
31208 (synopsis "Amazon Web Services analytics services")
31210 "This package provides an interface to Amazon Web Services analytics
31211 services, including Elastic MapReduce Hadoop and Spark big data service,
31212 Elasticsearch search engine, and more.")
31213 (license license:asl2.0)))
31215 (define-public r-paws-machine-learning
31217 (name "r-paws-machine-learning")
31222 (uri (cran-uri "paws.machine.learning" version))
31225 "01w2y5952pk50xjbzby2pc51xrkrzjpfxbmii1b10cl2xgzfkxsa"))))
31227 `((upstream-name . "paws.machine.learning")))
31228 (build-system r-build-system)
31230 (list r-paws-common))
31231 (home-page "https://github.com/paws-r/paws")
31232 (synopsis "Amazon Web Services machine learning services")
31234 "This package provides an interface to Amazon Web Services machine
31235 learning services, including SageMaker managed machine learning service,
31236 natural language processing, speech recognition, translation, and more.")
31237 (license license:asl2.0)))
31239 (define-public r-paws-management
31241 (name "r-paws-management")
31246 (uri (cran-uri "paws.management" version))
31249 "09k7wg0jlj40zs2yb3vldffpkdcjg7ap98n7c5lxr5plpca08swg"))))
31251 `((upstream-name . "paws.management")))
31252 (build-system r-build-system)
31254 (list r-paws-common))
31255 (home-page "https://github.com/paws-r/paws")
31256 (synopsis "Amazon Web Services management and governance services")
31258 "This package provides an interface to Amazon Web Services management and
31259 governance services, including CloudWatch application and infrastructure
31260 monitoring, Auto Scaling for automatically scaling resources, and more.")
31261 (license license:asl2.0)))
31263 (define-public r-paws-networking
31265 (name "r-paws-networking")
31270 (uri (cran-uri "paws.networking" version))
31273 "02hxaa5nlj70mdggh379ij3fn09xm8h5ldzsyf45c342prpl6zwj"))))
31275 `((upstream-name . "paws.networking")))
31276 (build-system r-build-system)
31278 (list r-paws-common))
31279 (home-page "https://github.com/paws-r/paws")
31280 (synopsis "Amazon Web Services networking and content delivery services")
31282 "This package provides an interface to Amazon Web Services networking and
31283 content delivery services, including Route 53 Domain Name System service,
31284 CloudFront content delivery, load balancing, and more.")
31285 (license license:asl2.0)))
31287 (define-public r-paws-database
31289 (name "r-paws-database")
31294 (uri (cran-uri "paws.database" version))
31297 "08jpwz95fw3f68j0wxh2lg57nn60khflldab0ryhkkbcw1iy0qyz"))))
31298 (properties `((upstream-name . "paws.database")))
31299 (build-system r-build-system)
31301 (list r-paws-common))
31302 (home-page "https://github.com/paws-r/paws")
31304 "Amazon Web Services Database Services")
31306 "This package provides an interface to Amazon Web Services database
31307 services, including Relational Database Service (RDS), DynamoDB NoSQL
31308 database, and more.")
31309 (license license:asl2.0)))
31311 (define-public r-paws-storage
31313 (name "r-paws-storage")
31318 (uri (cran-uri "paws.storage" version))
31321 "06m887vpqp5d6k3zxdlga599dsv8v3rladk7xqaxqnld1f17am04"))))
31322 (properties `((upstream-name . "paws.storage")))
31323 (build-system r-build-system)
31325 (list r-paws-common))
31326 (home-page "https://github.com/paws-r/paws")
31327 (synopsis "Amazon Web Services storage services")
31329 "This package provides an interface to Amazon Web Services storage
31330 services, including Simple Storage Service (S3).")
31331 (license license:asl2.0)))
31333 (define-public r-paws-compute
31335 (name "r-paws-compute")
31340 (uri (cran-uri "paws.compute" version))
31343 "1km6fng6il5fcjlrbbndahsw2dr2ql83hwac9wlpd67zm3wy9lky"))))
31344 (properties `((upstream-name . "paws.compute")))
31345 (build-system r-build-system)
31347 (list r-paws-common))
31348 (home-page "https://github.com/paws-r/paws")
31349 (synopsis "Amazon Web Services compute services")
31351 "This package provides an interface to Amazon Web Services compute
31352 services, including Elastic Compute Cloud (EC2), Lambda
31353 functions-as-a-service, containers, batch processing, and more.")
31354 (license license:asl2.0)))
31356 (define-public r-paws
31363 (uri (cran-uri "paws" version))
31366 "0kn1z045r106fwqcaz52hb02bhrcblh479cajfjiq480s1iljcw6"))))
31367 (properties `((upstream-name . "paws")))
31368 (build-system r-build-system)
31370 (list r-paws-analytics
31371 r-paws-application-integration
31373 r-paws-cost-management
31374 r-paws-customer-engagement
31376 r-paws-developer-tools
31377 r-paws-end-user-computing
31378 r-paws-machine-learning
31381 r-paws-security-identity
31383 (home-page "https://github.com/paws-r/paws")
31384 (synopsis "Amazon Web Services software development kit")
31386 "This package provides an interface to Amazon Web Services, including
31387 storage, database, and compute services, such as Simple Storage Service (S3),
31388 DynamoDB NoSQL database, and Lambda functions-as-a-service.")
31389 (license license:asl2.0)))
31391 (define-public r-zoomgroupstats
31393 (name "r-zoomgroupstats")
31398 (uri (cran-uri "zoomGroupStats" version))
31401 "0gndiq92cy6gi7f833hdjvqii3cn83wz5rjvygcvjl3dw4pwv966"))))
31403 `((upstream-name . "zoomGroupStats")))
31404 (build-system r-build-system)
31415 (native-inputs (list r-knitr))
31416 (home-page "http://zoomgroupstats.org")
31417 (synopsis "Analyze text, audio, and video from Zoom meetings")
31419 "This package provides utilities for processing and analyzing the files
31420 that are exported from a recorded Zoom meeting. This includes analyzing data
31421 captured through video cameras and microphones, the text-based chat, and
31422 meta-data. You can analyze aspects of the conversation among meeting
31423 participants and their emotional expressions throughout the meeting.")
31424 (license license:expat)))
31426 (define-public r-zoom
31433 (uri (cran-uri "zoom" version))
31436 "03f5rxfr6ncf1j6vpn7pip21q7ylj4bx0a5xphqb6x6i33lxf1g5"))))
31437 (properties `((upstream-name . "zoom")))
31438 (build-system r-build-system)
31439 (home-page "https://github.com/cbarbu/R-package-zoom")
31440 (synopsis "Spatial data visualization tool")
31442 "This package provides @code{zm}, a utility that allows you to
31443 zoom/navigate any plot when called with any active plot.")
31444 (license license:gpl3+)))
31446 (define-public r-zoolog
31453 (uri (cran-uri "zoolog" version))
31456 "1wxxxscw4ji4p4599vdw6vcrkqm0g75x1gh13m4758lb51wav9ks"))))
31457 (properties `((upstream-name . "zoolog")))
31458 (build-system r-build-system)
31460 (list r-rdpack r-stringi))
31463 (home-page "https://josempozo.github.io/zoolog/")
31464 (synopsis "Zooarchaeological analysis with log-ratios")
31466 "This package includes functions and reference data to generate and
31467 manipulate log-ratios (also known as @dfn{log size index} (LSI) values) from
31468 measurements obtained on zooarchaeological material. Log ratios are used to
31469 compare the relative (rather than the absolute) dimensions of animals from
31470 archaeological contexts. The zoolog package is also able to seamlessly
31471 integrate data and references with heterogeneous nomenclature, which is
31472 internally managed by a zoolog thesaurus.")
31473 (license license:gpl3)))
31475 (define-public r-filehash
31477 (name "r-filehash")
31482 (uri (cran-uri "filehash" version))
31485 "14zv7h5195dmfksgk8qvjgc2qq8253vga6267aa1bqs5bpvmdl5n"))))
31486 (properties `((upstream-name . "filehash")))
31487 (build-system r-build-system)
31488 (home-page "http://github.com/rdpeng/filehash")
31489 (synopsis "Simple key-value database")
31491 "This package implements a simple key-value style database where
31492 character string keys are associated with data values that are stored on the
31493 disk. A simple interface is provided for inserting, retrieving, and deleting
31494 data from the database. Utilities are provided that allow filehash databases
31495 to be treated much like environments and lists are already used in R. These
31496 utilities are provided to encourage interactive and exploratory analysis on
31498 (license license:gpl2+)))
31500 (define-public r-mlearning
31502 (name "r-mlearning")
31507 (uri (cran-uri "mlearning" version))
31510 "0r8xfaxw83s2r27b8x5qd0k4r5ayxpkafzn9b1a0jvsr87i6520r"))))
31511 (properties `((upstream-name . "mlearning")))
31512 (build-system r-build-system)
31520 (home-page "http://www.sciviews.org/zooimage")
31521 (synopsis "Machine learning algorithms with unified interface")
31523 "This package provides a unified interface to various machine learning
31524 algorithms. Confusion matrices are provided too.")
31525 (license license:gpl2+)))
31527 (define-public r-zooimage
31529 (name "r-zooimage")
31534 (uri (cran-uri "zooimage" version))
31537 "0ck8w0zb9l1n9xvjwqshq9q9l8pigy3yslq2hnfbgcwk17kk9mp8"))))
31538 (properties `((upstream-name . "zooimage")))
31539 (build-system r-build-system)
31553 (home-page "http://www.sciviews.org/zooimage")
31554 (synopsis "Analysis of numerical plankton images")
31556 "This package provides a solution for analyzing digital images of
31557 plankton. In combination with ImageJ, an image analysis system, it processes
31558 digital images, measures individuals, trains for automatic classification of
31559 taxa, and finally, measures plankton samples (abundances, total and partial
31560 size spectra or biomasses, etc.).")
31561 (license license:gpl2+)))
31563 (define-public r-zooarch
31570 (uri (cran-uri "zooaRch" version))
31573 "0grc378xppv0303sf4flfqz5002vq5a23nzbq4bsff41rww7dihc"))))
31574 (properties `((upstream-name . "zooaRch")))
31575 (build-system r-build-system)
31576 (propagated-inputs (list r-ggplot2))
31577 (native-inputs (list r-knitr))
31579 "https://cran.r-project.org/package=zooaRch")
31581 "Analytical Tools for Zooarchaeological Data")
31583 "The analysis and inference of faunal remains recovered from
31584 archaeological sites concerns the field of zooarchaeology. The zooaRch
31585 package provides analytical tools to make inferences on zooarchaeological
31586 data. Functions in this package allow users to read, manipulate, visualize,
31587 and analyze zooarchaeological data.")
31588 (license license:gpl2+)))
31590 (define-public r-zonebuilder
31592 (name "r-zonebuilder")
31597 (uri (cran-uri "zonebuilder" version))
31600 "0mxf3dz0d6bi5wwjilqivdxhy5ypnq5svky8zygha0clv45l4dmn"))))
31601 (properties `((upstream-name . "zonebuilder")))
31602 (build-system r-build-system)
31604 (list r-rcolorbrewer r-sf))
31607 (home-page "https://github.com/zonebuilders/zonebuilder")
31608 (synopsis "Create and explore geographic zoning systems")
31610 "This package provides functions, documentation and example data to help
31611 divide geographic space into discrete polygons (zones). The functions are
31612 motivated by research into the merits of different zoning systems. A flexible
31613 @code{ClockBoard} zoning system is provided, which breaks-up space by
31614 concentric rings and radial lines emanating from a central point.")
31615 (license license:gpl3)))
31617 (define-public r-zonator
31624 (uri (cran-uri "zonator" version))
31627 "1plxchpd4ypp36phl13pi9yvlrqi3lk83lv5rldrhdqynhcgfw2k"))))
31628 (properties `((upstream-name . "zonator")))
31629 (build-system r-build-system)
31631 (list r-ggplot2 r-raster r-rcolorbrewer r-reshape2 r-rgdal))
31632 (native-inputs (list r-knitr))
31633 (home-page "https://cbig.github.io/zonator/")
31634 (synopsis "Utilities for Zonation spatial conservation prioritization")
31636 "Create new analysis setups and deal with results of Zonation
31637 conservation prioritization software.")
31638 (license license:bsd-2)))
31640 (define-public r-mmwrweek
31642 (name "r-mmwrweek")
31647 (uri (cran-uri "MMWRweek" version))
31650 "1l1ks44v52iggw9nhs56lfj6804yab5b17k8fzrc6h1kvj3vda0s"))))
31651 (properties `((upstream-name . "MMWRweek")))
31652 (build-system r-build-system)
31653 (home-page "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf")
31654 (synopsis "Convert dates to MMWR day, week, and year")
31656 "The first day of any MMWR week is Sunday. MMWR week numbering is
31657 sequential beginning with 1 and incrementing with each week to a maximum of 52
31658 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at
31659 least four days in the calendar year. This package provides functionality to
31660 convert dates to MMWR day, week, and year and the reverse.")
31661 (license license:gpl2+)))
31663 (define-public r-crul
31670 (uri (cran-uri "crul" version))
31673 "133g0skz4lifl8hm8pqdryd2m2drbrm6mdfzbbsrw8fg46di86my"))))
31674 (properties `((upstream-name . "crul")))
31675 (build-system r-build-system)
31683 (native-inputs (list r-knitr))
31684 (home-page "https://github.com/ropensci/crul")
31685 (synopsis "HTTP client")
31687 "This package provides a simple HTTP client, with tools for making HTTP
31688 requests, and mocking HTTP requests. The package is built on R6, and takes
31689 inspiration from Ruby's @code{faraday} gem.")
31690 (license license:expat)))
31692 (define-public r-gistr
31699 (uri (cran-uri "gistr" version))
31702 "0ac9ikrdg6i8xvlma0gizvsdva46408lk7hvsgkqirhy2ljy02hp"))))
31703 (properties `((upstream-name . "gistr")))
31704 (build-system r-build-system)
31714 (native-inputs (list r-knitr))
31715 (home-page "https://github.com/ropensci/gistr")
31716 (synopsis "Work with Gists in browser")
31718 "This package allows the user to create new Github gists, update gists
31719 with new files, rename files, delete files, get and delete gists, star and
31720 un-star them, fork them, open a gist in your default browser, get an embed
31721 code for a gist, list gist commits, and get rate limit information when
31723 (license license:expat)))
31725 (define-public r-rbokeh
31732 (uri (cran-uri "rbokeh" version))
31735 "1h2fpzqf17pw9d09r1g1iyxsj5qma4fsk8vnar7f1z4fjyypvi6q"))
31737 '(for-each delete-file '("inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js"
31738 "inst/htmlwidgets/lib/bokehjs/bokeh.min.js")))))
31739 (properties `((upstream-name . "rbokeh")))
31740 (build-system r-build-system)
31743 (modify-phases %standard-phases
31744 (add-after 'unpack 'process-javascript
31745 (lambda* (#:key inputs #:allow-other-keys)
31746 (with-directory-excursion "inst/htmlwidgets/lib/bokehjs"
31748 `((,(assoc-ref inputs "js-bokeh-widgets")
31749 . "bokeh-widgets.min.js")
31750 (,(assoc-ref inputs "js-bokeh")
31751 . "bokeh.min.js"))))
31752 (for-each (lambda (source target)
31753 (format #true "Processing ~a --> ~a~%"
31755 (invoke "esbuild" source "--minify"
31756 (string-append "--outfile=" target)))
31758 (map cdr mapping)))))))))
31770 ;; Version 0.12.15 is mentioned in lib/htmlwidgets/rbokeh.yaml.
31772 `(("esbuild" ,esbuild)
31773 ("js-bokeh-widgets"
31776 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh-widgets.js")
31779 "07v9lrkfcbdznpb10qqwi4m660zp65g85vlnfw7kn83zmkxkhhxy"))))
31783 (uri "https://unpkg.com/bokehjs@0.12.15/build/js/bokeh.js")
31786 "1pq0059aad7d2jv50nv9449p3w0gbkxkl0mhblc76m5d9qjqav2q"))))
31787 ("r-knitr" ,r-knitr)))
31788 (home-page "https://cran.r-project.org/web/packages/rbokeh/")
31789 (synopsis "R interface for the Bokeh visualization library")
31791 "This package provides a native R plotting library that provides a
31792 flexible declarative interface for creating interactive web-based graphics,
31793 backed by the @url{https://bokeh.pydata.org/, Bokeh visualization library}.")
31794 (license license:expat)))
31796 (define-public r-fauxpas
31803 (uri (cran-uri "fauxpas" version))
31806 "129fzqb7wsskbn50s8x0marr4wm8jrns6hiycqcsk166k3dnyyy8"))))
31807 (properties `((upstream-name . "fauxpas")))
31808 (build-system r-build-system)
31810 (list r-httpcode r-r6 r-whisker))
31813 (home-page "https://docs.ropensci.org/fauxpas")
31814 (synopsis "HTTP error helpers")
31816 "This package provides HTTP error helpers. Methods are included for
31817 general purpose HTTP error handling, as well as individual methods for every
31818 HTTP status code, both via status code numbers as well as their descriptive
31819 names. It supports the ability to adjust behavior to stop, message or
31820 warning. It includes the ability to use a custom whisker template to have any
31821 configuration of status code, short description, and verbose message.")
31822 (license license:expat)))
31824 (define-public r-webmockr
31826 (name "r-webmockr")
31831 (uri (cran-uri "webmockr" version))
31834 "0j40srwi0yasmllb9wsww4m6zkiyzqd549cis4dxd7c7p24hak8j"))))
31835 (properties `((upstream-name . "webmockr")))
31836 (build-system r-build-system)
31846 (home-page "https://github.com/ropensci/webmockr")
31847 (synopsis "Stubbing and setting expectations on HTTP Requests")
31849 "This is a package for stubbing and setting expectations on HTTP
31850 requests. It includes tools for stubbing HTTP requests, including expected
31851 request conditions and response conditions. You can match on HTTP method,
31852 query parameters, request body, headers and more. It can be used for unit
31853 tests or outside of a testing context.")
31854 (license license:expat)))
31856 (define-public r-mockery
31863 (uri (cran-uri "mockery" version))
31866 "16zayzi2qdmiy513hvlci9f4p8jwry24006yfzrgmrvf6sf293lq"))))
31867 (properties `((upstream-name . "mockery")))
31868 (build-system r-build-system)
31873 (home-page "https://github.com/jfiksel/mockery")
31874 (synopsis "Mocking library for R")
31876 "The two main functionalities of this package are creating mock
31877 objects (functions) and selectively intercepting calls to a given function
31878 that originate in some other function. It can be used with any testing
31879 framework available for R. Mock objects can be injected with either this
31880 package's own @code{stub} function or a similar @code{with_mock} facility
31881 present in the @code{testthat} package.")
31882 (license license:expat)))
31884 (define-public r-zoltr
31891 (uri (cran-uri "zoltr" version))
31894 "12zh7y3pwidclscgvd0b0iaqq9j5y8mc8xd6pz4vs0jy5qs3ahar"))))
31895 (properties `((upstream-name . "zoltr")))
31896 (build-system r-build-system)
31908 (native-inputs (list r-knitr))
31909 (home-page "https://github.com/reichlab/zoltr")
31910 (synopsis "Interface to the Zoltar forecast repository API")
31912 "Zoltar is a website that provides a repository of model forecast results
31913 in a standardized format and a central location. It supports storing,
31914 retrieving, comparing, and analyzing time series forecasts for prediction
31915 challenges of interest to the modeling community. This package provides
31916 functions for working with the Zoltar API, including connecting and
31917 authenticating, getting information about projects, models, and forecasts,
31918 deleting and uploading forecast data, and downloading scores.")
31919 (license license:gpl3)))
31921 (define-public r-zoib
31928 (uri (cran-uri "zoib" version))
31931 "0inm7f2pc68ksqxvq12xp9jc99vj7ydylvs24ip12nksbj5k1n8f"))))
31932 (properties `((upstream-name . "zoib")))
31933 (build-system r-build-system)
31935 (list r-abind r-coda r-formula r-rjags))
31936 (home-page "https://www.r-project.org")
31937 (synopsis "Bayesian inference for beta regression")
31939 "This package lets you fit beta regression and zero-or-one inflated beta
31940 regression and obtain Bayesian inference of the model via the Markov Chain
31941 Monte Carlo approach implemented in JAGS.")
31942 (license license:gpl3+)))
31944 (define-public r-logger
31951 (uri (cran-uri "logger" version))
31953 (base32 "08kym5i5fvbf5xhh9qdszp4jdgyc7j7zpnwzy68wabqz73aff6sg"))))
31954 (properties `((upstream-name . "logger")))
31955 (build-system r-build-system)
31956 (native-inputs (list r-knitr))
31957 (home-page "https://daroczig.github.io/logger/")
31958 (synopsis "Lightweight and flexible logging utility")
31960 "Inspired by the the @code{futile.logger} R package and @code{logging}
31961 Python module, this utility provides a flexible and extensible way of
31962 formatting and delivering log messages with low overhead.")
31963 (license license:agpl3+)))
31965 (define-public r-fasterize
31967 (name "r-fasterize")
31972 (uri (cran-uri "fasterize" version))
31974 (base32 "10bzl77c1b9jhcn1xp467qzp2n8c7s3wpxn53qjh1nwvbri5kd32"))))
31975 (properties `((upstream-name . "fasterize")))
31976 (build-system r-build-system)
31978 (list r-raster r-rcpp r-rcpparmadillo r-sp))
31979 (native-inputs (list r-knitr))
31980 (home-page "https://github.com/ecohealthalliance/fasterize")
31981 (synopsis "Fast Polygon to Raster Conversion")
31983 "This package provides a drop-in replacement for @code{rasterize} from
31984 the @code{raster} package that takes sf-type objects, and is much faster.
31985 There is support for the main options provided by the @code{rasterize}
31986 function, including setting the field used and background value, and
31987 options for aggregating multi-layer rasters.")
31988 (license license:expat)))
31990 (define-public r-bien
31997 (uri (cran-uri "BIEN" version))
31999 (base32 "1dagrs54ciagm2mgqrvxl6k2akahr0qk63ifxqnks7iljm0x1gw6"))))
32000 (properties `((upstream-name . "BIEN")))
32001 (build-system r-build-system)
32003 (list r-knitr r-testthat))
32016 (home-page "https://cran.r-project.org/package=BIEN")
32017 (synopsis "Tools for accessing the BIEN database")
32019 "This package provides tools for accessing the Botanical Information and
32020 Ecology Network (BIEN) database. The BIEN database contains cleaned and
32021 standardized botanical data including occurrence, trait, plot and taxonomic
32022 data. This package provides functions that query the BIEN database by
32023 constructing and executing optimized SQL queries.")
32024 (license license:expat)))
32026 (define-public r-varhandle
32028 (name "r-varhandle")
32033 (uri (cran-uri "varhandle" version))
32035 (base32 "1l42d0s6fbjjc9l28a2m3myxkrx2c0p0b9yj8wjjjgilw19yc3lv"))))
32036 (properties `((upstream-name . "varhandle")))
32037 (build-system r-build-system)
32038 (home-page "https://bitbucket.org/mehrad_mahmoudian/varhandle")
32039 (synopsis "Functions for robust variable handling")
32041 "This package contains some functions to help users (especially data
32042 explorers) to make more sense of their variables and take the most out of
32043 variables and hardware resources. Functions in this package are supposed to
32044 be efficient and easy to use.")
32045 (license license:gpl2+)))
32047 (define-public r-ggh4x
32054 (uri (cran-uri "ggh4x" version))
32057 "1r49yfm5fqv5s7jb92ad6rf8hd9plcry6f500czjhnhhrp16cqfp"))))
32058 (properties `((upstream-name . "ggh4x")))
32059 (build-system r-build-system)
32061 (list r-ggplot2 r-gtable r-rlang r-scales r-vctrs))
32064 (home-page "https://github.com/teunbrand/ggh4x")
32065 (synopsis "Extension for ggplot2")
32066 (description "This package is a @code{ggplot2} extension. It provides some
32067 utility functions that do not entirely fit within the grammar of graphics
32068 concept. The package extends @code{ggpplots} facets through customisation, by
32069 setting individual scales per panel, resizing panels and providing nested
32070 facets. It also allows multiple colour, fill scales per plot and hosts a
32071 smaller collection of stats, geoms and axis guides.")
32072 (license license:expat)))