1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
5 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
6 ;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
7 ;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
8 ;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
9 ;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
10 ;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
11 ;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
13 ;;; This file is part of GNU Guix.
15 ;;; GNU Guix is free software; you can redistribute it and/or modify it
16 ;;; under the terms of the GNU General Public License as published by
17 ;;; the Free Software Foundation; either version 3 of the License, or (at
18 ;;; your option) any later version.
20 ;;; GNU Guix is distributed in the hope that it will be useful, but
21 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
22 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 ;;; GNU General Public License for more details.
25 ;;; You should have received a copy of the GNU General Public License
26 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
28 (define-module (gnu packages cran)
29 #:use-module ((guix licenses) #:prefix license:)
30 #:use-module (guix packages)
31 #:use-module (guix download)
32 #:use-module (guix utils)
33 #:use-module (guix build-system r)
34 #:use-module (gnu packages compression)
35 #:use-module (gnu packages gcc)
36 #:use-module (gnu packages machine-learning)
37 #:use-module (gnu packages maths)
38 #:use-module (gnu packages mpi)
39 #:use-module (gnu packages perl)
40 #:use-module (gnu packages pkg-config)
41 #:use-module (gnu packages python)
42 #:use-module (gnu packages statistics)
43 #:use-module (gnu packages tls)
44 #:use-module (gnu packages web))
46 (define-public r-clipr
53 (uri (cran-uri "clipr" version))
56 "061x84ildc7g1p91yw5iyj8lpqdf4hqv36as85lw8c6qv9ywbsqv"))))
57 (build-system r-build-system)
58 (home-page "https://github.com/mdlincoln/clipr")
59 (synopsis "Read and write from the system clipboard")
61 "This package provides simple utility functions to read from and write to
62 the system clipboards.")
63 (license license:gpl3)))
65 (define-public r-tidyverse
72 (uri (cran-uri "tidyverse" version))
75 "0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"))))
76 (build-system r-build-system)
78 `(("r-broom" ,r-broom)
80 ("r-crayon" ,r-crayon)
81 ("r-dbplyr" ,r-dbplyr)
83 ("r-forcats" ,r-forcats)
84 ("r-ggplot2" ,r-ggplot2)
88 ("r-jsonlite" ,r-jsonlite)
89 ("r-lubridate" ,r-lubridate)
90 ("r-magrittr" ,r-magrittr)
91 ("r-modelr" ,r-modelr)
94 ("r-readxl" ,r-readxl)
95 ("r-reprex" ,r-reprex)
97 ("r-rstudioapi" ,r-rstudioapi)
99 ("r-stringr" ,r-stringr)
100 ("r-tibble" ,r-tibble)
103 (home-page "https://tidyverse.tidyverse.org")
104 (synopsis "Install and load packages from the \"Tidyverse\"")
106 "The @code{tidyverse} is a set of packages that work in harmony because
107 they share common data representations and API design. This package is
108 designed to make it easy to install and load multiple tidyverse packages in a
110 (license license:gpl3)))
112 (define-public r-rvest
119 (uri (cran-uri "rvest" version))
122 "04mv99z8dixywx96kfy4215g6ib23s7qvd77hcf9pxqxzcvqhvhd"))))
123 (build-system r-build-system)
126 ("r-magrittr" ,r-magrittr)
127 ("r-selectr" ,r-selectr)
129 (home-page "https://github.com/hadley/rvest")
130 (synopsis "Simple web scraping for R")
132 "@code{r-rvest} helps you scrape information from web pages. It is
133 designed to work with @code{magrittr} to make it easy to express common web
134 scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
135 (license license:gpl3)))
137 (define-public r-selectr
144 (uri (cran-uri "selectr" version))
147 "1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b"))))
148 (build-system r-build-system)
150 `(("r-stringr" ,r-stringr)
152 (home-page "https://sjp.co.nz/projects/selectr/")
153 (synopsis "Translate CSS selectors to XPath expressions")
155 "@code{r-selectr} translates a CSS3 selector into an equivalent XPath
156 expression. This allows you to use CSS selectors when working with the XML
157 package as it can only evaluate XPath expressions. Also provided are
158 convenience functions useful for using CSS selectors on XML nodes. This
159 package is a port of the Python package @code{cssselect}.")
160 (license license:bsd-3)))
162 (define-public r-reprex
169 (uri (cran-uri "reprex" version))
172 "105d9vsmqfilgpw8psfb2wyiz1hvcycvh4cqhb3ab37lm3rcavvs"))))
173 (build-system r-build-system)
175 `(("r-callr" ,r-callr)
177 ("r-rmarkdown" ,r-rmarkdown)
178 ("r-whisker" ,r-whisker)))
179 (home-page "https://github.com/tidyverse/reprex")
180 (synopsis "Prepare reproducible R code examples for sharing")
182 "This package provides a convenience wrapper that uses the
183 @code{rmarkdown} package to render small snippets of code to target formats
184 that include both code and output. The goal is to encourage the sharing of
185 small, reproducible, and runnable examples on code-oriented websites or email.
186 @code{reprex} also extracts clean, runnable R code from various common formats,
187 such as copy/paste from an R session.")
188 (license license:expat)))
190 (define-public r-callr
197 (uri (cran-uri "callr" version))
200 "1053qqq632z94pqq2v5dynjpgyv1b1c8zvidmcllw7zn8zha8gqf"))))
201 (build-system r-build-system)
204 ("r-processx" ,r-processx)))
205 (home-page "https://github.com/r-lib/callr#readme")
206 (synopsis "Call R from R")
208 "It is sometimes useful to perform a computation in a separate R process,
209 without affecting the current R process at all. This packages does exactly
211 (license license:expat)))
213 (define-public r-readxl
220 (uri (cran-uri "readxl" version))
223 "05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn"))))
224 (build-system r-build-system)
226 `(("r-cellranger" ,r-cellranger)
228 ("r-tibble" ,r-tibble)))
229 (home-page "https://readxl.tidyverse.org")
230 (synopsis "Read Excel files")
232 "This package lets you import Excel files into R. It supports
233 @file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
234 the embedded @code{RapidXML} C++ library.")
235 ;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
236 ;; 'rapidxml' which is Boost.
237 (license (list license:gpl3 license:bsd-2 license:boost1.0))))
239 (define-public r-modelr
246 (uri (cran-uri "modelr" version))
249 "09whg3q5xq6csbqwgwfwav09vda8vgady5j70sk52xcn232k363a"))))
250 (build-system r-build-system)
252 `(("r-broom" ,r-broom)
254 ("r-lazyeval" ,r-lazyeval)
255 ("r-magrittr" ,r-magrittr)
257 ("r-tibble" ,r-tibble)
258 ("r-tidyr" ,r-tidyr)))
259 (home-page "https://github.com/tidyverse/modelr")
260 (synopsis "Helper functions for modelling in pipelines")
262 "Functions for modelling that help you seamlessly integrate modelling
263 into a pipeline of data manipulation and visualisation.")
264 (license license:gpl3)))
266 (define-public r-haven
273 (uri (cran-uri "haven" version))
276 "0pp8xjf5lzqg1wr8cwxj4njx99vxwlflwjrd7jvyzwlfpwh7n1qa"))))
277 (build-system r-build-system)
281 `(("r-forcats" ,r-forcats)
285 ("r-tibble" ,r-tibble)))
286 (home-page "https://haven.tidyverse.org")
287 (synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
289 "This package lets you mport foreign statistical formats into R via the
290 embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
291 (license license:expat)))
293 (define-public r-amap
299 (uri (cran-uri "amap" version))
302 "1qnl2x98x64iaipkx5126rsddq2sx5ml43h75xyiyn30yvbmlxyk"))))
303 (build-system r-build-system)
305 `(("gfortran" ,gfortran)))
306 (home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
307 (synopsis "Another multidimensional analysis package")
308 (description "This package provides tools for clustering and principal
309 component analysis (with robust methods, and parallelized functions).")
310 (license license:gpl2+)))
319 (uri (cran-uri "ape" version))
322 "0vm2065993wf4hdqarxqykhfz9aaj0rrb98alhkq4qw1d2kdrmdp"))))
323 (build-system r-build-system)
325 `(("r-lattice" ,r-lattice)
328 (home-page "http://ape-package.ird.fr/")
329 (synopsis "Analyses of phylogenetics and evolution")
331 "This package provides functions for reading, writing, plotting, and
332 manipulating phylogenetic trees, analyses of comparative data in a
333 phylogenetic framework, ancestral character analyses, analyses of
334 diversification and macroevolution, computing distances from DNA sequences,
335 and several other tools.")
336 (license license:gpl2+)))
338 (define-public r-abbyyr
345 (uri (cran-uri "abbyyR" version))
348 "1jh1c1ad6mgw7brdh2isnza1qpjlfxnqr7jl76yd93axyfl76xjx"))))
349 (properties `((upstream-name . "abbyyR")))
350 (build-system r-build-system)
355 ("r-progress" ,r-progress)
358 (home-page "https://github.com/soodoku/abbyyR")
359 (synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
361 "This package provides tools to get text from images of text using Abbyy
362 Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
363 OCR images, barcodes, forms, documents with machine readable zones, e.g.
364 passports and get the results in a variety of formats including plain text and
365 XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
366 (license license:expat)))
368 (define-public r-colorspace
370 (name "r-colorspace")
375 (uri (cran-uri "colorspace" version))
377 (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
378 (build-system r-build-system)
379 (home-page "https://cran.r-project.org/web/packages/colorspace")
380 (synopsis "Color space manipulation")
382 "This package carries out a mapping between assorted color spaces
383 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
384 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
385 colors are provided.")
386 (license license:bsd-3)))
388 (define-public r-glue
395 (uri (cran-uri "glue" version))
398 "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr"))))
399 (build-system r-build-system)
400 (home-page "https://github.com/tidyverse/glue")
401 (synopsis "Interpreted string literals")
403 "This package provides an implementation of interpreted string literals,
404 inspired by Python's Literal String Interpolation (PEP-0498) and
405 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
406 (license license:expat)))
408 (define-public r-pastecs
414 (uri (cran-uri "pastecs" version))
417 "0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
418 (build-system r-build-system)
420 `(("r-boot" ,r-boot)))
421 (home-page "http://www.sciviews.org/pastecs")
422 (synopsis "Analysis of space-time ecological series")
424 "This package provides functions for regulation, decomposition and analysis
425 of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
426 initiative to bring PASSTEC 2000 functionalities to R.")
427 (license license:gpl2+)))
429 (define-public r-plogr
436 (uri (cran-uri "plogr" version))
439 "0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
440 (build-system r-build-system)
441 (home-page "https://github.com/krlmlr/plogr")
442 (synopsis "R bindings for the plog C++ logging library")
444 "This package provides the header files for a stripped-down version of
445 the plog header-only C++ logging library, and a method to log to R's standard
447 (license license:expat)))
456 (uri (cran-uri "pls" version))
459 "15j59p5x0rkdrk7iqzkipsy50rsyjl31w8zxc4w3v1j5gzxhi1rx"))))
460 (build-system r-build-system)
461 (home-page "http://mevik.net/work/software/pls.html")
462 (synopsis "Partial Least Squares and Principal Component Regression")
464 "The pls package implements multivariate regression methods: Partial Least
465 Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
466 Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
469 @item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
470 algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
471 @item multi-response models (or @dfn{PLS2})
472 @item flexible cross-validation
473 @item Jackknife variance estimates of regression coefficients
474 @item extensive and flexible plots: scores, loadings, predictions, coefficients,
475 (R)MSEP, R², and correlation loadings
476 @item formula interface, modelled after @code{lm()}, with methods for predict,
477 print, summary, plot, update, etc.
478 @item extraction functions for coefficients, scores, and loadings
479 @item MSEP, RMSEP, and R² estimates
480 @item multiplicative scatter correction (@dfn{MSC})
482 (license license:gpl2)))
491 (uri (cran-uri "ps" version))
493 (base32 "1zm9qkyvy1fvcjvmgw51iqw8x1xzkpy7rx7xnchwfj0xpzal0ljx"))))
494 (build-system r-build-system)
495 (home-page "http://ps.r-lib.org")
496 (synopsis "List, query, and manipulate system processes")
498 "The ps package implements an API to list, query, and manipulate system
499 processes. Most of its code is based on the @code{psutil} Python package.")
500 (license license:bsd-3)))
502 (define-public r-pkgbuild
509 (uri (cran-uri "pkgbuild" version))
512 "10iz8057mixl9j73pq2cbp4ib6dadfsgi3fcsjjm7l3wwb9issd9"))))
513 (build-system r-build-system)
515 `(("r-callr" ,r-callr)
516 ("r-crayon" ,r-crayon)
519 ("r-rprojroot" ,r-rprojroot)
520 ("r-withr" ,r-withr)))
521 (home-page "https://github.com/r-pkgs/pkgbuild")
522 (synopsis "Find tools needed to build R packages")
524 "This package provides functions used to build R packages. It locates
525 compilers needed to build R packages on various platforms and ensures the PATH
526 is configured appropriately so R can use them.")
527 (license license:gpl3)))
529 (define-public r-pkgload
536 (uri (cran-uri "pkgload" version))
539 "1rjj229nq9fsl4ki4m75ybsavjgpqqhsr1zjzapwicsrxv6212px"))))
540 (build-system r-build-system)
543 ("r-pkgbuild" ,r-pkgbuild)
545 ("r-rprojroot" ,r-rprojroot)
546 ("r-rstudioapi" ,r-rstudioapi)
547 ("r-withr" ,r-withr)))
548 (home-page "https://github.com/r-lib/pkgload")
549 (synopsis "Simulate package installation and attach")
551 "This package simulates the process of installing a package and then
552 attaching it. This is a key part of the @code{devtools} package as it allows
553 you to rapidly iterate while developing a package.")
554 (license license:gpl3)))
556 (define-public r-rcpp
563 (uri (cran-uri "Rcpp" version))
565 (base32 "006kpg2ph109rh1l13lqk26pp4as4fvl5661vrcczjygacgd1v7w"))))
566 (build-system r-build-system)
567 (home-page "http://www.rcpp.org")
568 (synopsis "Seamless R and C++ integration")
570 "The Rcpp package provides R functions as well as C++ classes which offer
571 a seamless integration of R and C++. Many R data types and objects can be
572 mapped back and forth to C++ equivalents which facilitates both writing of new
573 code as well as easier integration of third-party libraries. Documentation
574 about Rcpp is provided by several vignettes included in this package, via the
575 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
576 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
577 'citation(\"Rcpp\")' for details on these last two.")
578 (license license:gpl2+)))
580 (define-public r-bindr
587 (uri (cran-uri "bindr" version))
590 "1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
591 (build-system r-build-system)
592 (home-page "https://github.com/krlmlr/bindr")
593 (synopsis "Parametrized active bindings")
595 "This package provides a simple interface for creating active bindings
596 where the bound function accepts additional arguments.")
597 (license license:expat)))
599 (define-public r-bindrcpp
606 (uri (cran-uri "bindrcpp" version))
609 "0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
610 (build-system r-build-system)
612 `(("r-bindr" ,r-bindr)
615 (home-page "https://github.com/krlmlr/bindrcpp")
616 (synopsis "Rcpp interface to active bindings")
618 "This package provides an easy way to fill an environment with active
619 bindings that call a C++ function.")
620 (license license:expat)))
629 (uri (cran-uri "AUC" version))
632 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
633 (properties `((upstream-name . "AUC")))
634 (build-system r-build-system)
635 (home-page "https://cran.r-project.org/web/packages/AUC")
636 (synopsis "Compute the area under the curve of selected measures")
638 "This package includes functions to compute the area under the curve of
639 selected measures: the area under the sensitivity curve (AUSEC), the area
640 under the specificity curve (AUSPC), the area under the accuracy
641 curve (AUACC), and the area under the receiver operating characteristic
642 curve (AUROC). The curves can also be visualized. Support for partial areas
644 (license license:gpl2+)))
646 (define-public r-calibrate
653 (uri (cran-uri "calibrate" version))
656 "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
657 (build-system r-build-system)
659 `(("r-mass" ,r-mass)))
660 (home-page "https://cran.r-project.org/web/packages/calibrate")
661 (synopsis "Calibration of scatterplot and biplot axes")
663 "This is a package for drawing calibrated scales with tick marks
664 on (non-orthogonal) variable vectors in scatterplots and biplots.")
665 (license license:gpl2)))
667 (define-public r-shape
674 (uri (cran-uri "shape" version))
677 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
678 (build-system r-build-system)
679 (home-page "https://cran.r-project.org/web/packages/shape")
680 (synopsis "Functions for plotting graphical shapes")
682 "This package provides functions for plotting graphical shapes such as
683 ellipses, circles, cylinders, arrows, ...")
684 (license license:gpl3+)))
686 (define-public r-globaloptions
688 (name "r-globaloptions")
693 (uri (cran-uri "GlobalOptions" version))
696 "1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn"))))
697 (properties `((upstream-name . "GlobalOptions")))
698 (build-system r-build-system)
699 (home-page "https://github.com/jokergoo/GlobalOptions")
700 (synopsis "Generate functions to get or set global options")
702 "This package provides more controls on the option values such as
703 validation and filtering on the values, making options invisible or private.")
704 (license license:gpl2+)))
706 (define-public r-circlize
713 (uri (cran-uri "circlize" version))
716 "1l28maiqi549z191srncxgabx5fnvf0lld7smzwfd3vr5cx8nqww"))))
717 (build-system r-build-system)
719 `(("r-colorspace" ,r-colorspace)
720 ("r-globaloptions" ,r-globaloptions)
721 ("r-shape" ,r-shape)))
722 (home-page "https://github.com/jokergoo/circlize")
723 (synopsis "Circular visualization")
725 "Circular layout is an efficient way to visualise huge amounts of
726 information. This package provides an implementation of circular layout
727 generation in R as well as an enhancement of available software. Its
728 flexibility is based on the usage of low-level graphics functions such that
729 self-defined high-level graphics can be easily implemented by users for
730 specific purposes. Together with the seamless connection between the powerful
731 computational and visual environment in R, it gives users more convenience and
732 freedom to design figures for better understanding complex patterns behind
733 multi-dimensional data.")
734 (license license:gpl2+)))
736 (define-public r-powerlaw
743 (uri (cran-uri "poweRlaw" version))
746 "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m"))))
747 (properties `((upstream-name . "poweRlaw")))
748 (build-system r-build-system)
750 `(("r-vgam" ,r-vgam)))
751 (home-page "https://github.com/csgillespie/poweRlaw")
752 (synopsis "Tools for the analysis of heavy tailed distributions")
754 "This package provides an implementation of maximum likelihood estimators
755 for a variety of heavy tailed distributions, including both the discrete and
756 continuous power law distributions. Additionally, a goodness-of-fit based
757 approach is used to estimate the lower cut-off for the scaling region.")
758 ;; Any of these GPL versions.
759 (license (list license:gpl2 license:gpl3))))
761 (define-public r-compare
768 (uri (cran-uri "compare" version))
771 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
772 (build-system r-build-system)
773 (home-page "https://cran.r-project.org/web/packages/compare")
774 (synopsis "Comparing objects for differences")
776 "This package provides functions to compare a model object to a
777 comparison object. If the objects are not identical, the functions can be
778 instructed to explore various modifications of the objects (e.g., sorting
779 rows, dropping names) to see if the modified versions are identical.")
780 (license license:gpl2+)))
782 (define-public r-dendextend
784 (name "r-dendextend")
789 (uri (cran-uri "dendextend" version))
792 "1virn3c232xwcq3d0hhkgjh5gpzl01s39iwii5gxcm9mnsxjzdrh"))))
793 (build-system r-build-system)
796 ("r-ggplot2" ,r-ggplot2)
797 ("r-magrittr" ,r-magrittr)
798 ("r-viridis" ,r-viridis)
799 ("r-whisker" ,r-whisker)))
800 (home-page "https://cran.r-project.org/web/packages/dendextend")
801 (synopsis "Extending 'dendrogram' functionality in R")
803 "This package offers a set of functions for extending @code{dendrogram}
804 objects in R, letting you visualize and compare trees of hierarchical
805 clusterings. You can adjust a tree's graphical parameters (the color, size,
806 type, etc of its branches, nodes and labels) and visually and statistically
807 compare different dendrograms to one another.")
808 ;; Any of these versions
809 (license (list license:gpl2 license:gpl3))))
811 (define-public r-getoptlong
813 (name "r-getoptlong")
818 (uri (cran-uri "GetoptLong" version))
821 "1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
822 (properties `((upstream-name . "GetoptLong")))
823 (build-system r-build-system)
827 `(("r-globaloptions" ,r-globaloptions)
828 ("r-rjson" ,r-rjson)))
829 (home-page "https://github.com/jokergoo/GetoptLong")
830 (synopsis "Parsing command-line arguments and variable interpolation")
832 "This is yet another command-line argument parser which wraps the
833 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
834 use in R. It also provides a simple way for variable interpolation in R.")
835 (license license:gpl2+)))
837 (define-public r-fastmatch
844 (uri (cran-uri "fastmatch" version))
847 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
848 (build-system r-build-system)
849 (home-page "http://www.rforge.net/fastmatch")
850 (synopsis "Fast match function")
852 "This package provides a fast @code{match} replacement for cases that
853 require repeated look-ups. It is slightly faster that R's built-in
854 @code{match} function on first match against a table, but extremely fast on
855 any subsequent lookup as it keeps the hash table in memory.")
856 (license license:gpl2)))
865 (uri (cran-uri "ff" version))
868 "1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
869 (build-system r-build-system)
870 (propagated-inputs `(("r-bit" ,r-bit)))
871 (home-page "http://ff.r-forge.r-project.org/")
872 (synopsis "Memory-efficient storage of large data on disk and access functions")
874 "This package provides data structures that are stored on disk but
875 behave (almost) as if they were in RAM by transparently mapping only a section
877 ;; error Architecture not supported.
878 (supported-systems (delete "aarch64-linux" %supported-systems))
879 (license license:gpl2)))
881 (define-public r-ffbase
888 (uri (cran-uri "ffbase" version))
891 "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5"))))
892 (build-system r-build-system)
895 ("r-fastmatch" ,r-fastmatch)
897 (home-page "http://github.com/edwindj/ffbase")
898 (synopsis "Basic statistical functions for package 'ff'")
900 "This package extends the out of memory vectors of @code{ff} with
901 statistical functions and other utilities to ease their usage.")
902 (license license:gpl3)))
904 (define-public r-prettyunits
906 (name "r-prettyunits")
911 (uri (cran-uri "prettyunits" version))
914 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
915 (build-system r-build-system)
917 `(("r-assertthat" ,r-assertthat)
918 ("r-magrittr" ,r-magrittr)))
919 (home-page "https://github.com/gaborcsardi/prettyunits")
920 (synopsis "Pretty, human readable formatting of quantities")
922 "This package provides tools for pretty, human readable formatting of
924 (license license:expat)))
926 (define-public r-reshape
933 (uri (cran-uri "reshape" version))
936 "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig"))))
937 (build-system r-build-system)
941 (home-page "http://had.co.nz/reshape")
942 (synopsis "Flexibly reshape data")
944 "Flexibly restructure and aggregate data using just two functions:
945 @code{melt} and @code{cast}. This package provides them.")
946 (license license:expat)))
948 (define-public r-progress
955 (uri (cran-uri "progress" version))
958 "1rhwm0bdw30z3rvl0bn56xprjl3zrdy7150w4gl4bkvn2d6h9fav"))))
959 (build-system r-build-system)
961 `(("r-crayon" ,r-crayon)
963 ("r-prettyunits" ,r-prettyunits)
965 (home-page "https://github.com/gaborcsardi/progress")
966 (synopsis "Terminal progress bars")
968 "This package provides configurable progress bars. They may include
969 percentage, elapsed time, and/or the estimated completion time. They work in
970 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
971 package also provides a C++ API, that works with or without Rcpp.")
972 (license license:expat)))
974 (define-public r-ggally
981 (uri (cran-uri "GGally" version))
984 "1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
985 (properties `((upstream-name . "GGally")))
986 (build-system r-build-system)
988 `(("libressl" ,libressl)))
990 `(("r-ggplot2" ,r-ggplot2)
991 ("r-gtable" ,r-gtable)
993 ("r-progress" ,r-progress)
994 ("r-rcolorbrewer" ,r-rcolorbrewer)
995 ("r-reshape" ,r-reshape)
996 ("r-rlang" ,r-rlang)))
997 (home-page "https://ggobi.github.io/ggally")
998 (synopsis "Extension to ggplot2")
1000 "The R package ggplot2 is a plotting system based on the grammar of
1001 graphics. GGally extends ggplot2 by adding several functions to reduce the
1002 complexity of combining geometric objects with transformed data. Some of
1003 these functions include a pairwise plot matrix, a two group pairwise plot
1004 matrix, a parallel coordinates plot, a survival plot, and several functions to
1006 (license license:gpl2+)))
1008 (define-public r-proxy
1015 (uri (cran-uri "proxy" version))
1018 "0l0ff8irmmvic941is290hd5vszyhaj5nfwna4v3w9c1zk5nr1ma"))))
1019 (build-system r-build-system)
1020 (home-page "https://cran.r-project.org/web/packages/proxy")
1021 (synopsis "Distance and similarity measures")
1023 "This package provides an extensible framework for the efficient
1024 calculation of auto- and cross-proximities, along with implementations of the
1025 most popular ones.")
1026 (license license:gpl2)))
1035 (uri (cran-uri "sp" version))
1038 "17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p"))))
1039 (build-system r-build-system)
1041 `(("r-lattice" ,r-lattice)))
1042 (home-page "https://cran.r-project.org/web/packages/sp")
1043 (synopsis "Classes and methods for spatial data")
1045 "This package provides classes and methods for spatial data; the classes
1046 document where the spatial location information resides, for 2D or 3D data.
1047 Utility functions are provided, e.g. for plotting data as maps, spatial
1048 selection, as well as methods for retrieving coordinates, for subsetting,
1049 print, summary, etc.")
1050 (license license:gpl2+)))
1052 (define-public r-rmtstat
1059 (uri (cran-uri "RMTstat" version))
1062 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
1063 (properties `((upstream-name . "RMTstat")))
1064 (build-system r-build-system)
1065 (home-page "https://cran.r-project.org/web/packages/RMTstat")
1066 (synopsis "Distributions, statistics and tests derived from random matrix theory")
1068 "This package provides functions for working with the Tracy-Widom laws
1069 and other distributions related to the eigenvalues of large Wishart
1071 (license license:bsd-3)))
1073 (define-public r-rmpi
1079 (uri (cran-uri "Rmpi" version))
1082 "1b62gs7w1xqadqd7ir41jnxlcf14gcqfxd0915kn9ckdlsdrh0sw"))))
1083 (properties `((upstream-name . "Rmpi")))
1084 (build-system r-build-system)
1086 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")))
1088 `(("openmpi" ,openmpi)))
1090 `(("pkg-config" ,pkg-config)))
1091 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
1092 (synopsis "R interface to message-passing interface (MPI)")
1094 "This package provides an interface (wrapper) to MPI APIs. It also
1095 provides an interactive R manager and worker environment.")
1096 (license license:gpl2+)))
1098 (define-public r-lmoments
1105 (uri (cran-uri "Lmoments" version))
1108 "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79"))))
1109 (properties `((upstream-name . "Lmoments")))
1110 (build-system r-build-system)
1111 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
1112 (synopsis "L-moments and quantile mixtures")
1114 "This package contains functions to estimate L-moments and trimmed
1115 L-moments from the data. It also contains functions to estimate the
1116 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
1117 quantile mixture from L-moments and trimmed L-moments.")
1118 (license license:gpl2)))
1120 (define-public r-distillery
1122 (name "r-distillery")
1127 (uri (cran-uri "distillery" version))
1130 "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix"))))
1131 (build-system r-build-system)
1132 (home-page "http://www.ral.ucar.edu/staff/ericg")
1133 (synopsis "Functions for confidence intervals and object information")
1135 "This package provides some very simple method functions for confidence
1136 interval calculation and to distill pertinent information from a potentially
1137 complex object; primarily used in common with the packages extRemes and
1139 (license license:gpl2+)))
1141 (define-public r-extremes
1148 (uri (cran-uri "extRemes" version))
1151 "0cpvcajk9xyy7662nqkyx333vrxpwsc5nmv0bfnhsbgijz5y0hvm"))))
1152 (properties `((upstream-name . "extRemes")))
1153 (build-system r-build-system)
1156 ("r-distillery" ,r-distillery)
1157 ("r-lmoments" ,r-lmoments)))
1158 (home-page "http://www.assessment.ucar.edu/toolkit/")
1159 (synopsis "Extreme value analysis")
1161 "ExtRemes is a suite of functions for carrying out analyses on the
1162 extreme values of a process of interest; be they block maxima over long blocks
1163 or excesses over a high threshold.")
1164 (license license:gpl2+)))
1166 (define-public r-lmtest
1173 (uri (cran-uri "lmtest" version))
1176 "0sym9sm1vl6bbgq01jhz1plxqmgh8hrgrn7rw0mwvsalcn6id7xy"))))
1177 (build-system r-build-system)
1179 `(("r-zoo" ,r-zoo)))
1181 `(("gfortran" ,gfortran)))
1182 (home-page "https://cran.r-project.org/web/packages/lmtest")
1183 (synopsis "Testing linear regression models")
1185 "This package provides a collection of tests, data sets, and examples for
1186 diagnostic checking in linear regression models. Furthermore, some generic
1187 tools for inference in parametric models are provided.")
1188 ;; Either version is okay
1189 (license (list license:gpl2 license:gpl3))))
1191 (define-public r-idr
1197 (uri (cran-uri "idr" version))
1200 "05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
1201 (build-system r-build-system)
1202 (home-page "https://cran.r-project.org/web/packages/idr/")
1203 (synopsis "Irreproducible discovery rate")
1205 "This is a package for estimating the copula mixture model and plotting
1206 correspondence curves in \"Measuring reproducibility of high-throughput
1207 experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
1208 by Li, Brown, Huang, and Bickel")
1209 (license license:gpl2+)))
1211 (define-public r-inline
1217 (uri (cran-uri "inline" version))
1220 "0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
1221 (build-system r-build-system)
1222 (home-page "https://cran.r-project.org/web/packages/inline")
1223 (synopsis "Functions to inline C, C++, Fortran function calls from R")
1225 "This package provides functionality to dynamically define R functions
1226 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
1227 @code{.Call} calling conventions.")
1228 ;; Any version of the LGPL.
1229 (license license:lgpl3+)))
1231 (define-public r-bbmle
1238 (uri (cran-uri "bbmle" version))
1241 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
1242 (build-system r-build-system)
1244 `(("r-lattice" ,r-lattice)
1246 ("r-numderiv" ,r-numderiv)))
1247 (home-page "https://cran.r-project.org/web/packages/bbmle")
1248 (synopsis "Tools for General Maximum Likelihood Estimation")
1250 "This package provides methods and functions for fitting maximum
1251 likelihood models in R. This package modifies and extends the @code{mle}
1252 classes in the @code{stats4} package.")
1253 ;; Any version of the GPL
1254 (license license:gpl2+)))
1256 (define-public r-emdbook
1263 (uri (cran-uri "emdbook" version))
1266 "0880cx6rqm9vgd2zxnd2k0igfl80gy7ak15w36clwlzavab59hmv"))))
1267 (build-system r-build-system)
1269 `(("r-bbmle" ,r-bbmle)
1271 ("r-lattice" ,r-lattice)
1274 ("r-rcpp" ,r-rcpp)))
1275 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
1276 (synopsis "Support functions and data for \"Ecological Models and Data\"")
1278 "This package provides auxiliary functions and data sets for \"Ecological
1279 Models and Data\", a book presenting maximum likelihood estimation and related
1280 topics for ecologists (ISBN 978-0-691-12522-0).")
1282 (license (list license:gpl2 license:gpl3))))
1284 (define-public r-lpsolve
1291 (uri (cran-uri "lpSolve" version))
1294 "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
1295 (properties `((upstream-name . "lpSolve")))
1296 (build-system r-build-system)
1297 (home-page "https://cran.r-project.org/web/packages/lpSolve")
1298 (synopsis "R interface to Lp_solve to solve linear/integer programs")
1300 "Lp_solve is software for solving linear, integer and mixed integer
1301 programs. This implementation supplies a \"wrapper\" function in C and some R
1302 functions that solve general linear/integer problems, assignment problems, and
1303 transportation problems.")
1304 (license license:lgpl2.0)))
1306 (define-public r-limsolve
1313 (uri (cran-uri "limSolve" version))
1316 "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
1317 (properties `((upstream-name . "limSolve")))
1318 (build-system r-build-system)
1320 `(("r-lpsolve" ,r-lpsolve)
1322 ("r-quadprog" ,r-quadprog)))
1323 (native-inputs `(("gfortran" ,gfortran)))
1324 (home-page "https://cran.r-project.org/web/packages/limSolve")
1325 (synopsis "Solving linear inverse models")
1327 "This package provides functions that:
1330 @item find the minimum/maximum of a linear or quadratic function,
1331 @item sample an underdetermined or overdetermined system,
1332 @item solve a linear system Ax=B for the unknown x.
1335 It includes banded and tridiagonal linear systems. The package calls Fortran
1336 functions from LINPACK.")
1338 (license (list license:gpl2+ license:gpl3+))))
1340 (define-public r-fitdistrplus
1342 (name "r-fitdistrplus")
1347 (uri (cran-uri "fitdistrplus" version))
1350 "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6"))))
1351 (build-system r-build-system)
1353 `(("r-mass" ,r-mass)
1354 ("r-survival" ,r-survival)))
1355 (home-page "http://riskassessment.r-forge.r-project.org")
1356 (synopsis "Fitting a parametric distribution from data")
1358 "This package extends the @code{fitdistr} function of the MASS package
1359 with several functions to help the fit of a parametric distribution to
1360 non-censored or censored data. Censored data may contain left-censored,
1361 right-censored and interval-censored values, with several lower and upper
1362 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
1363 provides moment matching (MME), quantile matching (QME) and maximum
1364 goodness-of-fit estimation (MGE) methods (available only for non-censored
1365 data). Weighted versions of MLE, MME and QME are available.")
1366 (license license:gpl2+)))
1368 (define-public r-energy
1375 (uri (cran-uri "energy" version))
1378 "15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4"))))
1379 (build-system r-build-system)
1381 `(("r-boot" ,r-boot)
1382 ("r-rcpp" ,r-rcpp)))
1383 (home-page "https://cran.r-project.org/web/packages/energy")
1384 (synopsis "Multivariate inference via the energy of data")
1386 "This package provides e-statistics (energy) tests and statistics for
1387 multivariate and univariate inference, including distance correlation,
1388 one-sample, two-sample, and multi-sample tests for comparing multivariate
1389 distributions, are implemented. Measuring and testing multivariate
1390 independence based on distance correlation, partial distance correlation,
1391 multivariate goodness-of-fit tests, clustering based on energy distance,
1392 testing for multivariate normality, distance components (disco) for
1393 non-parametric analysis of structured data, and other energy
1394 statistics/methods are implemented.")
1395 (license license:gpl2+)))
1397 (define-public r-suppdists
1399 (name "r-suppdists")
1404 (uri (cran-uri "SuppDists" version))
1407 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
1408 (properties `((upstream-name . "SuppDists")))
1409 (build-system r-build-system)
1410 (home-page "https://cran.r-project.org/web/packages/SuppDists")
1411 (synopsis "Supplementary distributions")
1413 "This package provides ten distributions supplementing those built into
1414 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
1415 Spearman's rho, maximum F ratio, the Pearson product moment correlation
1416 coefficient, Johnson distributions, normal scores and generalized
1417 hypergeometric distributions. In addition two random number generators of
1418 George Marsaglia are included.")
1419 (license license:gpl2+)))
1421 (define-public r-ksamples
1428 (uri (cran-uri "kSamples" version))
1431 "15d5q5vpp4wx5rk5kjxjdxpwc8mkq5sbdz8gi07iscrvhzb5rzfr"))))
1432 (properties `((upstream-name . "kSamples")))
1433 (build-system r-build-system)
1435 `(("r-suppdists" ,r-suppdists)))
1436 (home-page "https://cran.r-project.org/web/packages/kSamples")
1437 (synopsis "K-Sample rank tests and their combinations")
1439 "This package provides tools to compares k samples using the
1440 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
1441 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
1442 test. It computes asymptotic, simulated or (limited) exact P-values, all
1443 valid under randomization, with or without ties, or conditionally under random
1444 sampling from populations, given the observed tie pattern. Except for Steel's
1445 test and the JT test it also combines these tests across several blocks of
1447 (license license:gpl2+)))
1449 (define-public r-cvst
1456 (uri (cran-uri "CVST" version))
1459 "05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
1460 (properties `((upstream-name . "CVST")))
1461 (build-system r-build-system)
1463 `(("r-kernlab" ,r-kernlab)
1464 ("r-matrix" ,r-matrix)))
1465 (home-page "https://cran.r-project.org/web/packages/CVST")
1466 (synopsis "Fast cross-validation via sequential testing")
1468 "This package implements the fast cross-validation via sequential
1469 testing (CVST) procedure. CVST is an improved cross-validation procedure
1470 which uses non-parametric testing coupled with sequential analysis to
1471 determine the best parameter set on linearly increasing subsets of the data.
1472 Additionally to the CVST the package contains an implementation of the
1473 ordinary k-fold cross-validation with a flexible and powerful set of helper
1474 objects and methods to handle the overall model selection process. The
1475 implementations of the Cochran's Q test with permutations and the sequential
1476 testing framework of Wald are generic and can therefore also be used in other
1478 (license license:gpl2+)))
1480 (define-public r-squarem
1483 (version "2017.10-1")
1487 (uri (cran-uri "SQUAREM" version))
1490 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
1491 (properties `((upstream-name . "SQUAREM")))
1492 (build-system r-build-system)
1493 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
1494 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
1496 "This package provides algorithms for accelerating the convergence of
1497 slow, monotone sequences from smooth, contraction mapping such as the EM
1498 algorithm. It can be used to accelerate any smooth, linearly convergent
1499 acceleration scheme. A tutorial style introduction to this package is
1500 available in a vignette.")
1501 (license license:gpl2+)))
1503 (define-public r-lava
1510 (uri (cran-uri "lava" version))
1513 "0cayjspry3r2lcbvl77v5v52b2zarri3b8xsf87pw5a3jn9anxcf"))))
1514 (build-system r-build-system)
1516 `(("r-numderiv" ,r-numderiv)
1517 ("r-squarem" ,r-squarem)
1518 ("r-survival" ,r-survival)))
1519 (home-page "https://github.com/kkholst/lava")
1520 (synopsis "Latent variable models")
1522 "This package provides tools for the estimation and simulation of latent
1524 (license license:gpl3)))
1526 (define-public r-drr
1533 (uri (cran-uri "DRR" version))
1536 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
1537 (properties `((upstream-name . "DRR")))
1538 (build-system r-build-system)
1540 `(("r-cvst" ,r-cvst)
1541 ("r-kernlab" ,r-kernlab)
1542 ("r-matrix" ,r-matrix)))
1543 (home-page "https://cran.r-project.org/web/packages/DRR")
1544 (synopsis "Dimensionality reduction via regression")
1546 "This package provides an implementation of dimensionality reduction via
1547 regression using Kernel Ridge Regression.")
1548 (license license:gpl3)))
1550 (define-public r-prodlim
1553 (version "2018.04.18")
1557 (uri (cran-uri "prodlim" version))
1560 "1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb"))))
1561 (build-system r-build-system)
1563 `(("r-kernsmooth" ,r-kernsmooth)
1566 ("r-survival" ,r-survival)))
1567 (home-page "https://cran.r-project.org/web/packages/prodlim")
1568 (synopsis "Product-limit estimation for censored event history analysis")
1570 "This package provides a fast and user-friendly implementation of
1571 nonparametric estimators for censored event history (survival) analysis with
1572 the Kaplan-Meier and Aalen-Johansen methods.")
1573 (license license:gpl2+)))
1575 (define-public r-dimred
1582 (uri (cran-uri "dimRed" version))
1585 "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v"))))
1586 (properties `((upstream-name . "dimRed")))
1587 (build-system r-build-system)
1588 (propagated-inputs `(("r-drr" ,r-drr)))
1589 (home-page "https://github.com/gdkrmr/dimRed")
1590 (synopsis "Framework for dimensionality reduction")
1592 "This package provides a collection of dimensionality reduction
1593 techniques from R packages and provides a common interface for calling the
1595 (license license:gpl3)))
1597 (define-public r-timedate
1600 (version "3043.102")
1604 (uri (cran-uri "timeDate" version))
1607 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
1608 (properties `((upstream-name . "timeDate")))
1609 (build-system r-build-system)
1610 (home-page "https://www.rmetrics.org")
1611 (synopsis "Chronological and calendar objects")
1613 "This package provides an environment for teaching \"Financial
1614 Engineering and Computational Finance\" and for managing chronological and
1616 (license license:gpl2+)))
1618 (define-public r-magic
1625 (uri (cran-uri "magic" version))
1628 "083cgpp3v03li0h8597b3g21pd9lkbmn9pyssblnhc800mpc52vz"))))
1629 (build-system r-build-system)
1631 `(("r-abind" ,r-abind)))
1632 (home-page "https://github.com/RobinHankin/magic.git")
1633 (synopsis "Create and investigate magic squares")
1635 "This package provides a collection of efficient, vectorized algorithms
1636 for the creation and investigation of magic squares and hypercubes, including
1637 a variety of functions for the manipulation and analysis of arbitrarily
1638 dimensioned arrays.")
1639 (license license:gpl2)))
1641 (define-public r-geometry
1648 (uri (cran-uri "geometry" version))
1651 "0s09vi0rr0smys3an83mz6fk41bplxyz4myrbiinf4qpk6n33qib"))))
1652 (build-system r-build-system)
1653 (propagated-inputs `(("r-magic" ,r-magic)))
1654 (home-page "http://geometry.r-forge.r-project.org/")
1655 (synopsis "Mesh generation and surface tesselation")
1657 "This package makes the qhull library available in R, in a similar manner
1658 as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
1659 intersections about a point, Voronoi diagrams, furthest-site Delaunay
1660 triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
1661 and higher dimensions. It implements the Quickhull algorithm for computing
1662 the convex hull. Qhull does not support constrained Delaunay triangulations,
1663 or mesh generation of non-convex objects, but the package does include some R
1664 functions that allow for this. Currently the package only gives access to
1665 Delaunay triangulation and convex hull computation.")
1666 ;; The Qhull sources are included and are distributed under a custom
1667 ;; non-copyleft license. The R sources are released under GPL version 2.
1668 (license (list license:gpl2
1669 (license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
1671 (define-public r-ddalpha
1678 (uri (cran-uri "ddalpha" version))
1681 "16cn0bhbaz9l9k4y79sv2d4f7pvs7dyka273y89igs5jvr99kfj1"))))
1682 (build-system r-build-system)
1685 ("r-class" ,r-class)
1686 ("r-geometry" ,r-geometry)
1689 ("r-robustbase" ,r-robustbase)
1690 ("r-sfsmisc" ,r-sfsmisc)))
1692 `(("gfortran" ,gfortran)))
1693 (home-page "https://cran.r-project.org/web/packages/ddalpha")
1694 (synopsis "Depth-Based classification and calculation of data depth")
1696 "This package contains procedures for depth-based supervised learning,
1697 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
1698 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
1699 statistical depth function to a compact low-dimensional space, where the final
1700 classification is done. It also offers an extension to functional data and
1701 routines for calculating certain notions of statistical depth functions. 50
1702 multivariate and 5 functional classification problems are included.")
1703 (license license:gpl2)))
1705 (define-public r-gower
1712 (uri (cran-uri "gower" version))
1715 "1mbrj1lam3jfbby2j32shmmj5cn09zx3rkxbamq7q8sdg39b54gb"))))
1716 (build-system r-build-system)
1718 `(("r-knitr" ,r-knitr)))
1719 (home-page "https://github.com/markvanderloo/gower")
1720 (synopsis "Gower's distance")
1722 "This package provides tools to compute Gower's distance (or similarity)
1723 coefficient between records, and to compute the top-n matches between records.
1724 Core algorithms are executed in parallel on systems supporting OpenMP.")
1725 (license license:gpl3)))
1727 (define-public r-rcpproll
1734 (uri (cran-uri "RcppRoll" version))
1737 "0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
1738 (properties `((upstream-name . "RcppRoll")))
1739 (build-system r-build-system)
1741 `(("r-rcpp" ,r-rcpp)))
1742 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
1743 (synopsis "Efficient rolling and windowed operations")
1745 "This package provides fast and efficient routines for common rolling /
1746 windowed operations. Routines for the efficient computation of windowed mean,
1747 median, sum, product, minimum, maximum, standard deviation and variance are
1749 (license license:gpl2+)))
1751 (define-public r-ipred
1758 (uri (cran-uri "ipred" version))
1761 "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq"))))
1762 (build-system r-build-system)
1764 `(("r-class" ,r-class)
1767 ("r-prodlim" ,r-prodlim)
1768 ("r-rpart" ,r-rpart)
1769 ("r-survival" ,r-survival)))
1770 (home-page "https://cran.r-project.org/web/packages/ipred")
1771 (synopsis "Improved predictors")
1773 "This package provides improved predictive models by indirect
1774 classification and bagging for classification, regression and survival
1775 problems as well as resampling based estimators of prediction error.")
1776 (license license:gpl2+)))
1778 (define-public r-psych
1785 (uri (cran-uri "psych" version))
1788 "1kzv9nc7rwn1sj1zxd8xrbs6c7qlka7j2c8lsr4f20znkd3qx8gf"))))
1789 (build-system r-build-system)
1791 `(("r-foreign" ,r-foreign)
1792 ("r-lattice" ,r-lattice)
1793 ("r-mnormt" ,r-mnormt)
1794 ("r-nlme" ,r-nlme)))
1795 (home-page "https://cran.r-project.org/web/packages/psych/")
1796 (synopsis "Procedures for psychological, psychometric, and personality research")
1798 "This package provides a general purpose toolbox for personality,
1799 psychometric theory and experimental psychology. Functions are primarily for
1800 multivariate analysis and scale construction using factor analysis, principal
1801 component analysis, cluster analysis and reliability analysis, although others
1802 provide basic descriptive statistics. Item Response Theory is done using
1803 factor analysis of tetrachoric and polychoric correlations. Functions for
1804 analyzing data at multiple levels include within and between group statistics,
1805 including correlations and factor analysis. Functions for simulating and
1806 testing particular item and test structures are included. Several functions
1807 serve as a useful front end for structural equation modeling. Graphical
1808 displays of path diagrams, factor analysis and structural equation models are
1809 created using basic graphics.")
1810 (license license:gpl2+)))
1812 (define-public r-broom
1819 (uri (cran-uri "broom" version))
1822 "1mrrqqw1bmjf2v88ziqwb5y86g29h0a3rsx2jpw0hrzrzb8i5kcb"))))
1823 (build-system r-build-system)
1825 `(("r-dplyr" ,r-dplyr)
1828 ("r-psych" ,r-psych)
1829 ("r-reshape2" ,r-reshape2)
1830 ("r-stringr" ,r-stringr)
1831 ("r-tidyr" ,r-tidyr)))
1832 (home-page "https://github.com/tidyverse/broom")
1833 (synopsis "Convert statistical analysis objects into tidy data frames")
1835 "This package provides tools to convert statistical analysis objects from
1836 R into tidy data frames, so that they can more easily be combined, reshaped
1837 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
1838 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
1839 summarizes a model's statistical findings such as coefficients of a
1840 regression; @code{augment}, which adds columns to the original data such as
1841 predictions, residuals and cluster assignments; and @code{glance}, which
1842 provides a one-row summary of model-level statistics.")
1843 (license license:expat)))
1845 (define-public r-recipes
1852 (uri (cran-uri "recipes" version))
1855 "1vqh3pxs4n1azhnd1lzg91vasya6g323kllhbrw177j7kdxqyimy"))))
1856 (build-system r-build-system)
1858 `(("r-broom" ,r-broom)
1859 ("r-ddalpha" ,r-ddalpha)
1860 ("r-dimred" ,r-dimred)
1861 ("r-dplyr" ,r-dplyr)
1862 ("r-gower" ,r-gower)
1863 ("r-ipred" ,r-ipred)
1864 ("r-lubridate" ,r-lubridate)
1865 ("r-magrittr" ,r-magrittr)
1866 ("r-matrix" ,r-matrix)
1868 ("r-purrr" ,r-purrr)
1869 ("r-rcpproll" ,r-rcpproll)
1870 ("r-rlang" ,r-rlang)
1871 ("r-tibble" ,r-tibble)
1872 ("r-tidyselect" ,r-tidyselect)
1873 ("r-timedate" ,r-timedate)))
1874 (home-page "https://github.com/topepo/recipes")
1875 (synopsis "Preprocessing tools to create design matrices")
1877 "Recipes is an extensible framework to create and preprocess design
1878 matrices. Recipes consist of one or more data manipulation and analysis
1879 \"steps\". Statistical parameters for the steps can be estimated from an
1880 initial data set and then applied to other data sets. The resulting design
1881 matrices can then be used as inputs into statistical or machine learning
1883 (license license:gpl2)))
1885 (define-public r-pdist
1892 (uri (cran-uri "pdist" version))
1895 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
1896 (build-system r-build-system)
1897 (home-page "https://github.com/jeffwong/pdist")
1898 (synopsis "Partitioned distance function")
1900 "Pdist computes the euclidean distance between rows of a matrix X and
1901 rows of another matrix Y. Previously, this could be done by binding the two
1902 matrices together and calling @code{dist}, but this creates unnecessary
1903 computation by computing the distances between a row of X and another row of
1904 X, and likewise for Y. Pdist strictly computes distances across the two
1905 matrices, not within the same matrix, making computations significantly faster
1906 for certain use cases.")
1907 (license license:gpl3+)))
1909 (define-public r-ggrepel
1916 (uri (cran-uri "ggrepel" version))
1919 "1m3p84d6nh9mzzvxb82vgig3ngcvkz86rjwzl9a66ckdf5p611k3"))))
1920 (build-system r-build-system)
1922 `(("r-ggplot2" ,r-ggplot2)
1924 ("r-scales" ,r-scales)))
1925 (home-page "http://github.com/slowkow/ggrepel")
1926 (synopsis "Repulsive text and label geometries for ggplot2")
1928 "This package provides text and label geometries for ggplot2 that help to
1929 avoid overlapping text labels. Labels repel away from each other and away
1930 from the data points.")
1931 (license license:gpl3)))
1933 (define-public r-corrplot
1940 (uri (cran-uri "corrplot" version))
1943 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
1944 (build-system r-build-system)
1945 (home-page "https://github.com/taiyun/corrplot")
1946 (synopsis "Visualization of a correlation matrix")
1948 "This package provides a graphical display of a correlation matrix or
1949 general matrix. It also contains some algorithms to do matrix reordering. In
1950 addition, corrplot is good at details, including choosing color, text labels,
1951 color labels, layout, etc.")
1952 ;; Any version of the GPL
1953 (license license:gpl2+)))
1955 (define-public r-stringdist
1957 (name "r-stringdist")
1962 (uri (cran-uri "stringdist" version))
1965 "0gap1g9xwhp0zxqsznkc2carpvi80z03prr4q8m528684lznx2xa"))))
1966 (build-system r-build-system)
1967 (home-page "https://github.com/markvanderloo/stringdist")
1968 (synopsis "Approximate string matching and string distance functions")
1970 "This package implements an approximate string matching version of R's
1971 native @code{match} function. It can calculate various string distances based
1972 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
1973 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
1974 Jaro-Winkler). An implementation of soundex is provided as well. Distances
1975 can be computed between character vectors while taking proper care of encoding
1976 or between integer vectors representing generic sequences.")
1977 (license license:gpl3+)))
1979 (define-public r-jomo
1986 (uri (cran-uri "jomo" version))
1989 "14s8q0j5zgl1g1pfxg3a4y1jzvs0wl61ir4992wsj7safskj7zvi"))))
1990 (build-system r-build-system)
1992 `(("r-lme4" ,r-lme4)
1993 ("r-survival" ,r-survival)))
1994 (home-page "https://cran.r-project.org/web/packages/jomo/")
1995 (synopsis "Multilevel Joint Modelling Multiple Imputation")
1997 "Similarly to Schafer's package pan, jomo is a package for multilevel
1998 joint modelling multiple imputation @url{Carpenter and Kenward (2013),
1999 http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
2000 possibility of handling binary and categorical data through latent normal
2001 variables, the option to use cluster-specific covariance matrices and to
2002 impute compatibly with the substantive model.")
2003 (license license:gpl2)))
2005 (define-public r-pan
2012 (uri (cran-uri "pan" version))
2015 "1p3nigmhrnlch86g89hn7l0wvkifx3k9n59g0psi95yck43kza76"))))
2016 (build-system r-build-system)
2017 (native-inputs `(("gfortran" ,gfortran)))
2018 (home-page "https://cran.r-project.org/web/packages/pan/")
2019 (synopsis "Multiple imputation for multivariate panel or clustered data")
2021 "This package implements multiple imputation for multivariate panel or
2023 (license license:gpl3)))
2025 (define-public r-mitml
2032 (uri (cran-uri "mitml" version))
2035 "1pkqv4qazih3byws5z6629pp232n8ra56lip7502727b0b4bsndw"))))
2036 (build-system r-build-system)
2038 `(("r-haven" ,r-haven)
2041 (home-page "https://cran.r-project.org/web/packages/mitml/")
2042 (synopsis "Tools for multiple imputation in multilevel modeling")
2044 "This package provides tools for multiple imputation of missing data in
2045 multilevel modeling. It includes a user-friendly interface to the packages
2046 pan and jomo, and several functions for visualization, data management and the
2047 analysis of multiply imputed data sets.")
2048 (license license:gpl2+)))
2050 (define-public r-mice
2057 (uri (cran-uri "mice" version))
2060 "0xpn215yfzib4hw09cwilnyg9zbvq460njavfvm84mvgwbm25byi"))))
2061 (build-system r-build-system)
2063 `(("r-broom" ,r-broom)
2064 ("r-dplyr" ,r-dplyr)
2065 ("r-lattice" ,r-lattice)
2067 ("r-mitml" ,r-mitml)
2070 ("r-rlang" ,r-rlang)
2071 ("r-rpart" ,r-rpart)
2072 ("r-survival" ,r-survival)))
2073 (home-page "https://cran.r-project.org/web/packages/mice/")
2074 (synopsis "Multivariate imputation by chained equations")
2076 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
2077 implemented by the MICE algorithm as described in @url{Van Buuren and
2078 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
2079 variable has its own imputation model. Built-in imputation models are
2080 provided for continuous data (predictive mean matching, normal), binary
2081 data (logistic regression), unordered categorical data (polytomous logistic
2082 regression) and ordered categorical data (proportional odds). MICE can also
2083 impute continuous two-level data (normal model, pan, second-level variables).
2084 Passive imputation can be used to maintain consistency between variables.
2085 Various diagnostic plots are available to inspect the quality of the
2087 ;; Any of these two versions.
2088 (license (list license:gpl2 license:gpl3))))
2090 (define-public r-truncnorm
2092 (name "r-truncnorm")
2097 (uri (cran-uri "truncnorm" version))
2100 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
2101 (build-system r-build-system)
2102 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
2103 (synopsis "Truncated normal distribution")
2104 (description "This package provides functions for the truncated normal
2105 distribution with mean equal to @code{mean} and standard deviation equal to
2106 @code{sd}. It includes density, distribution, quantile, and expected value
2107 functions, as well as a random generation function.")
2108 (license license:gpl2)))
2110 (define-public r-rsolnp
2117 (uri (cran-uri "Rsolnp" version))
2120 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
2121 (properties `((upstream-name . "Rsolnp")))
2122 (build-system r-build-system)
2124 `(("r-truncnorm" ,r-truncnorm)))
2125 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
2126 (synopsis "General non-linear optimization")
2127 (description "The Rsolnp package implements a general non-linear augmented
2128 Lagrange multiplier method solver, a @dfn{sequential quadratic
2129 programming} (SQP) based solver).")
2130 ;; Any version of the GPL.
2131 (license license:gpl2+)))
2133 (define-public r-hardyweinberg
2135 (name "r-hardyweinberg")
2140 (uri (cran-uri "HardyWeinberg" version))
2143 "16n8qanxx0p5ny5zqxafn8hwb1xv94y1wig1iql8as5a5qh8lwcz"))))
2144 (properties `((upstream-name . "HardyWeinberg")))
2145 (build-system r-build-system)
2147 `(("r-mice" ,r-mice)
2149 ("r-rsolnp" ,r-rsolnp)))
2150 (home-page "https://cran.r-project.org/package=HardyWeinberg")
2151 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
2153 "This package contains tools for exploring Hardy-Weinberg equilibrium for
2154 diallelic genetic marker data. All classical tests (chi-square, exact,
2155 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
2156 included in the package, as well as functions for power computation and for
2157 the simulation of marker data under equilibrium and disequilibrium. Routines
2158 for dealing with markers on the X-chromosome are included. Functions for
2159 testing equilibrium in the presence of missing data by using multiple
2160 imputation are also provided. Implements several graphics for exploring the
2161 equilibrium status of a large set of diallelic markers: ternary plots with
2162 acceptance regions, log-ratio plots and Q-Q plots.")
2163 (license license:gpl2+)))
2172 (uri (cran-uri "sm" version))
2175 "1rw2mxygxsmk8mn4wag1ppjgzk0rlvh6zd8q02qrhjrn9jhi5qj3"))))
2176 (build-system r-build-system)
2177 (native-inputs `(("gfortran" ,gfortran)))
2178 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
2179 (synopsis "Smoothing methods for nonparametric regression and density estimation")
2181 "This is software accompanying the book 'Applied Smoothing Techniques for
2182 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
2183 University Press. It provides smoothing methods for nonparametric regression
2184 and density estimation")
2185 (license license:gpl2+)))
2187 (define-public r-venndiagram
2189 (name "r-venndiagram")
2193 (uri (cran-uri "VennDiagram" version))
2196 "1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
2197 (properties `((upstream-name . "VennDiagram")))
2198 (build-system r-build-system)
2200 `(("r-futile-logger" ,r-futile-logger)))
2201 (home-page "https://cran.r-project.org/web/packages/VennDiagram/")
2202 (synopsis "Generate High-Resolution Venn and Euler Plots")
2204 "This package provides a set of functions to generate high-resolution
2205 Venn and Euler plots. It includes handling for several special cases,
2206 including two-case scaling, and extensive customization of plot shape and
2208 (license license:gpl2+)))
2210 (define-public r-vioplot
2217 (uri (cran-uri "vioplot" version))
2220 "16wkb26kv6qr34hv5zgqmgq6zzgysg9i78pvy2c097lr60v087v0"))))
2221 (build-system r-build-system)
2222 (propagated-inputs `(("r-sm" ,r-sm)))
2223 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
2224 (synopsis "Violin plot")
2226 "This package provides a violin plot, which is a combination of a box
2227 plot and a kernel density plot.")
2228 (license license:bsd-3)))
2230 (define-public r-rsofia
2236 ;; This package has been removed from CRAN, so we can
2237 ;; only fetch it from the archives.
2238 (uri (string-append "https://cran.r-project.org/src/"
2239 "contrib/Archive/RSofia/RSofia_"
2243 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
2244 (properties `((upstream-name . "RSofia")))
2245 (build-system r-build-system)
2247 `(("r-rcpp" ,r-rcpp)))
2248 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
2249 (synopsis "Port of sofia-ml to R")
2250 (description "This package is a port of sofia-ml to R. Sofia-ml is a
2251 suite of fast incremental algorithms for machine learning that can be used for
2252 training models for classification or ranking.")
2253 (license license:asl2.0)))
2255 (define-public r-xts
2262 (uri (cran-uri "xts" version))
2265 "1i11fczks4lh8rpi6xbm9bm7f3jpcp6xw03kv178g3n3361qhmc1"))))
2266 (build-system r-build-system)
2267 (propagated-inputs `(("r-zoo" ,r-zoo)))
2268 (native-inputs `(("gfortran" ,gfortran)))
2269 (home-page "https://github.com/joshuaulrich/xts")
2270 (synopsis "Extensible time series")
2272 "This package provides for uniform handling of R's different time-based
2273 data classes by extending @code{zoo}, maximizing native format information
2274 preservation and allowing for user-level customization and extension, while
2275 simplifying cross-class interoperability.")
2276 (license license:gpl2+)))
2278 (define-public r-performanceanalytics
2280 (name "r-performanceanalytics")
2285 (uri (cran-uri "PerformanceAnalytics" version))
2288 "01bgm57z079g6r505w3bj293zkbd49fwa8sg55z87vizwavipml6"))))
2290 `((upstream-name . "PerformanceAnalytics")))
2291 (build-system r-build-system)
2293 `(("r-quadprog" ,r-quadprog)
2296 (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
2297 (synopsis "Econometric tools for performance and risk analysis")
2298 (description "This is a collection of econometric functions for
2299 performance and risk analysis. This package aims to aid practitioners and
2300 researchers in utilizing the latest research in analysis of non-normal return
2301 streams. In general, it is most tested on return (rather than price) data on
2302 a regular scale, but most functions will work with irregular return data as
2303 well, and increasing numbers of functions will work with P&L or price data
2305 ;; Either version may be picked.
2306 (license (list license:gpl2 license:gpl3))))
2308 (define-public r-laeken
2315 (uri (cran-uri "laeken" version))
2318 "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6"))))
2319 (build-system r-build-system)
2321 `(("r-boot" ,r-boot)
2322 ("r-mass" ,r-mass)))
2323 (home-page "https://cran.r-project.org/web/packages/laeken/")
2324 (synopsis "Estimation of indicators on social exclusion and poverty")
2325 (description "This package provides tools for the estimation of indicators
2326 on social exclusion and poverty, as well as an implementation of Pareto tail
2327 modeling for empirical income distributions.")
2328 (license license:gpl2+)))
2330 (define-public r-vcd
2337 (uri (cran-uri "vcd" version))
2340 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
2341 (build-system r-build-system)
2343 `(("r-colorspace" ,r-colorspace)
2344 ("r-lmtest" ,r-lmtest)
2345 ("r-mass" ,r-mass)))
2346 (home-page "https://cran.r-project.org/web/packages/vcd/")
2347 (synopsis "Visualizing categorical data")
2348 (description "This package provides visualization techniques, data sets,
2349 summary and inference procedures aimed particularly at categorical data.
2350 Special emphasis is given to highly extensible grid graphics. The package was
2351 originally inspired by the book \"Visualizing Categorical Data\" by Michael
2352 Friendly and is now the main support package for a new book, \"Discrete Data
2353 Analysis with R\" by Michael Friendly and David Meyer (2015).")
2354 (license license:gpl2)))
2356 (define-public r-ica
2363 (uri (cran-uri "ica" version))
2366 "0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
2367 (build-system r-build-system)
2368 (home-page "https://cran.r-project.org/web/packages/ica/")
2369 (synopsis "Independent component analysis")
2370 (description "This package provides tools for @dfn{Independent Component
2371 Analysis} (ICA) using various algorithms: FastICA,
2372 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
2373 of Eigenmatrices} (JADE).")
2374 (license license:gpl2+)))
2376 (define-public r-dtw
2383 (uri (cran-uri "dtw" version))
2386 "1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
2387 (build-system r-build-system)
2388 (propagated-inputs `(("r-proxy" ,r-proxy)))
2389 (home-page "http://dtw.r-forge.r-project.org/")
2390 (synopsis "Dynamic Time Warping Algorithms")
2391 (description "This package provides a comprehensive implementation of
2392 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
2393 optimal (least cumulative distance) alignment between points of two time
2394 series. Common DTW variants covered include local (slope) and global (window)
2395 constraints, subsequence matches, arbitrary distance definitions,
2396 normalizations, minimum variance matching, and so on.")
2397 (license license:gpl2+)))
2399 (define-public r-sdmtools
2406 (uri (cran-uri "SDMTools" version))
2409 "1kacrpamshv7wz83yn45sfbw4m9c44xrrngzcklnwx8gcxx2knm6"))))
2410 (properties `((upstream-name . "SDMTools")))
2411 (build-system r-build-system)
2412 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
2413 (home-page "http://www.rforge.net/SDMTools/")
2414 (synopsis "Species distribution modelling tools")
2415 (description "This packages provides a set of tools for post processing
2416 the outcomes of species distribution modeling exercises. It includes novel
2417 methods for comparing models and tracking changes in distributions through
2418 time. It further includes methods for visualizing outcomes, selecting
2419 thresholds, calculating measures of accuracy and landscape fragmentation
2421 (license license:gpl3+)))
2423 (define-public r-scatterplot3d
2425 (name "r-scatterplot3d")
2430 (uri (cran-uri "scatterplot3d" version))
2433 "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
2434 (build-system r-build-system)
2435 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
2436 (synopsis "3D scatter plot")
2437 (description "This package provides an implementation of scatter plots for
2438 plotting. a three dimensional point cloud.")
2439 (license license:gpl2)))
2441 (define-public r-ggridges
2448 (uri (cran-uri "ggridges" version))
2451 "1znvsbl3px8dddpjgdrygnpz4s685wizi0jnjvx2hrz58i0chjqj"))))
2452 (build-system r-build-system)
2454 `(("r-ggplot2" ,r-ggplot2)
2456 ("r-scales" ,r-scales)
2457 ("r-withr" ,r-withr)))
2458 (home-page "https://github.com/clauswilke/ggridges")
2459 (synopsis "Ridgeline plots in ggplot2")
2461 "Ridgeline plots provide a convenient way of visualizing changes in
2462 distributions over time or space. This package enables the creation of such
2463 plots in @code{ggplot2}.")
2464 (license license:gpl2)))
2466 (define-public r-ggjoy
2473 (uri (cran-uri "ggjoy" version))
2476 "012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
2477 (build-system r-build-system)
2479 `(("r-ggplot2" ,r-ggplot2)
2480 ("r-ggridges" ,r-ggridges)))
2481 (home-page "https://github.com/clauswilke/ggjoy")
2482 (synopsis "Joyplots in ggplot2")
2483 (description "Joyplots provide a convenient way of visualizing changes in
2484 distributions over time or space. This package enables the creation of such
2485 plots in @code{ggplot2}.")
2486 (license license:gpl2)))
2488 (define-public r-cli
2495 (uri (cran-uri "cli" version))
2498 "07as3dr7vwx02p3qgzlmxz1dlrd3x3lysrzp222ip9jcjpydp8wg"))))
2499 (build-system r-build-system)
2501 `(("r-assertthat" ,r-assertthat)
2502 ("r-crayon" ,r-crayon)))
2503 (home-page "https://github.com/r-lib/cli#readme")
2504 (synopsis "Helpers for developing command line interfaces")
2505 (description "This package provides a suite of tools designed to build
2506 attractive command line interfaces (CLIs). It includes tools for drawing
2507 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
2508 (license license:expat)))
2510 (define-public r-argparser
2512 (name "r-argparser")
2517 (uri (cran-uri "argparser" version))
2520 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
2521 (build-system r-build-system)
2522 (home-page "https://bitbucket.org/djhshih/argparser")
2523 (synopsis "Command-line argument parser")
2525 "This package provides a cross-platform command-line argument parser
2526 written purely in R with no external dependencies. It is useful with the
2527 Rscript front-end and facilitates turning an R script into an executable
2529 (license license:gpl3+)))
2531 (define-public r-debugme
2538 (uri (cran-uri "debugme" version))
2541 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
2542 (build-system r-build-system)
2543 (propagated-inputs `(("r-crayon" ,r-crayon)))
2544 (home-page "https://github.com/r-lib/debugme#readme")
2545 (synopsis "Debug R packages")
2547 "This package allows the user to specify debug messages as special string
2548 constants, and control debugging of packages via environment variables.")
2549 (license license:expat)))
2551 (define-public r-processx
2558 (uri (cran-uri "processx" version))
2561 "1pzx4ap4xa07gf9zkd6hacdsnb9sp3kb60a7v7ljl0ywrcpn1fn4"))))
2562 (build-system r-build-system)
2564 `(("r-assertthat" ,r-assertthat)
2565 ("r-crayon" ,r-crayon)
2568 ("r-testthat" ,r-testthat)))
2569 (home-page "https://github.com/r-lib/processx3")
2570 (synopsis "Execute and control system processes")
2572 "This package provides portable tools to run system processes in the
2573 background. It can check if a background process is running; wait on a
2574 background process to finish; get the exit status of finished processes; kill
2575 background processes and their children; restart processes. It can read the
2576 standard output and error of the processes, using non-blocking connections.
2577 @code{processx} can poll a process for standard output or error, with a
2578 timeout. It can also poll several processes at once.")
2579 (license license:expat)))
2581 (define-public r-tsp
2588 (uri (cran-uri "TSP" version))
2591 "1ym97xl2icjpfkrici0wig29w06bb704hp51v7h5liygjlwpkhlc"))))
2592 (properties `((upstream-name . "TSP")))
2593 (build-system r-build-system)
2594 (propagated-inputs `(("r-foreach" ,r-foreach)))
2595 (home-page "https://cran.r-project.org/web/packages/TSP/")
2596 (synopsis "Traveling salesperson problem (TSP)")
2597 (description "This package provides basic infrastructure and some
2598 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
2599 traveling salesman problem).")
2600 (license license:gpl3)))
2602 (define-public r-qap
2609 (uri (cran-uri "qap" version))
2612 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
2613 (build-system r-build-system)
2614 (native-inputs `(("gfortran" ,gfortran)))
2615 (home-page "https://cran.r-project.org/web/packages/qap/")
2616 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
2617 (description "This package implements heuristics for the @dfn{quadratic
2618 assignment problem} (QAP). Currently only a simulated annealing heuristic is
2620 (license license:gpl3)))
2622 (define-public r-gclus
2629 (uri (cran-uri "gclus" version))
2632 "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn"))))
2633 (build-system r-build-system)
2634 (propagated-inputs `(("r-cluster" ,r-cluster)))
2635 (home-page "https://cran.r-project.org/web/packages/gclus/")
2636 (synopsis "Clustering graphics")
2637 (description "This package orders panels in scatterplot matrices and
2638 parallel coordinate displays by some merit index. It contains various indices
2639 of merit, ordering functions, and enhanced versions of @code{pairs} and
2640 @code{parcoord} which color panels according to their merit level.")
2641 (license license:gpl2+)))
2643 (define-public r-webshot
2650 (uri (cran-uri "webshot" version))
2653 "07r71zzmggp4jf92x4ws4wg6v1x98vaj01lsar85bnb30n5vx8gh"))))
2654 (build-system r-build-system)
2656 `(("r-jsonlite" ,r-jsonlite)
2657 ("r-magrittr" ,r-magrittr)
2658 ("r-processx" ,r-processx)
2659 ("r-withr" ,r-withr)))
2660 (home-page "https://github.com/wch/webshot/")
2661 (synopsis "Take screenshots of web pages")
2663 "Webshot makes it easy to take screenshots of web pages from within R.
2664 It can also run Shiny applications locally and take screenshots of the
2665 application; and it can render and screenshot static as well as interactive R
2666 Markdown documents.")
2667 (license license:gpl2)))
2669 (define-public r-seriation
2671 (name "r-seriation")
2676 (uri (cran-uri "seriation" version))
2679 "1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92"))))
2680 (build-system r-build-system)
2682 `(("r-cluster" ,r-cluster)
2683 ("r-colorspace" ,r-colorspace)
2684 ("r-dendextend" ,r-dendextend)
2685 ("r-gclus" ,r-gclus)
2686 ("r-gplots" ,r-gplots)
2689 ("r-registry" ,r-registry)
2691 (native-inputs `(("gfortran" ,gfortran)))
2692 (home-page "http://s2.smu.edu/IDA/seriation/")
2693 (synopsis "Infrastructure for ordering objects using seriation")
2695 "This package provides infrastructure for seriation with an
2696 implementation of several seriation/sequencing techniques to reorder matrices,
2697 dissimilarity matrices, and dendrograms. It also provides (optimally)
2698 reordered heatmaps, color images and clustering visualizations like
2699 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
2701 (license license:gpl3)))
2703 (define-public r-xfun
2710 (uri (cran-uri "xfun" version))
2713 "1r11dd49ngmjgbjdv28a9c1jp8cg1l50x0acbsamzz576p8i2wl9"))))
2714 (build-system r-build-system)
2715 (home-page "https://github.com/yihui/xfun")
2716 (synopsis "Miscellaneous functions")
2718 "This package provides miscellaneous functions commonly used in other
2719 packages maintained by Yihui Xie.")
2720 (license license:expat)))
2722 (define-public r-utf8
2729 (uri (cran-uri "utf8" version))
2732 "0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
2733 (build-system r-build-system)
2734 (home-page "https://github.com/patperry/r-utf8")
2735 (synopsis "Unicode text processing")
2737 "This package provides tools to process and print UTF-8 encoded
2738 international text (Unicode). Input, validate, normalize, encode, format, and
2740 (license license:asl2.0)))
2742 (define-public r-pillar
2749 (uri (cran-uri "pillar" version))
2752 "1rzhssprqgam1nq3s0f5rzxhxsq02azcghvxf6k8kmsmddf1n7f8"))))
2753 (build-system r-build-system)
2756 ("r-crayon" ,r-crayon)
2757 ("r-rlang" ,r-rlang)
2758 ("r-utf8" ,r-utf8)))
2759 (home-page "https://github.com/r-lib/pillar")
2760 (synopsis "Coloured formatting for columns")
2762 "This package provides a @code{pillar} generic designed for formatting
2763 columns of data using the full range of colours provided by modern
2765 (license license:gpl3)))
2767 (define-public r-uuid
2774 (uri (cran-uri "uuid" version))
2777 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
2778 (build-system r-build-system)
2779 (home-page "http://www.rforge.net/uuid")
2780 (synopsis "Tools for generating and handling of UUIDs")
2782 "This package provides tools for generating and handling of
2783 @dfn{Universally Unique Identifiers} (UUIDs).")
2784 (license license:expat)))
2786 (define-public r-tinytex
2793 (uri (cran-uri "tinytex" version))
2796 "16y9dldaff2kx1fkm92p7zlph0dcrdmlmavpdgf5y9jbhmc8g83f"))))
2797 (build-system r-build-system)
2799 `(("r-xfun" ,r-xfun)))
2800 (home-page "https://github.com/yihui/tinytex")
2801 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
2803 "This package provides helper functions to install and maintain the LaTeX
2804 distribution named TinyTeX, a lightweight, cross-platform, portable, and
2805 easy-to-maintain version of TeX Live. This package also contains helper
2806 functions to compile LaTeX documents, and install missing LaTeX packages
2808 (license license:expat)))
2810 (define-public r-metap
2817 (uri (cran-uri "metap" version))
2820 "03vg0mb6q7j2z0pkxykbak0hcp6dcak7zxs1lw9hswz9kqrq5jhz"))))
2821 (build-system r-build-system)
2823 `(("r-lattice" ,r-lattice)))
2824 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
2825 (synopsis "Meta-analysis of significance values")
2827 "The canonical way to perform meta-analysis involves using effect sizes.
2828 When they are not available this package provides a number of methods for
2829 meta-analysis of significance values including the methods of Edgington,
2830 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
2831 published results; and a routine for graphical display.")
2832 (license license:gpl2)))
2834 (define-public r-network
2837 (version "1.13.0.1")
2841 (uri (cran-uri "network" version))
2844 "1bbkbqkqf1d7irfwh08c13c2pfypir1ssvlqrln83irqns1ikdv0"))))
2845 (build-system r-build-system)
2846 (home-page "https://statnet.org/")
2847 (synopsis "Classes for relational data")
2849 "This package provides tools to create and modify network objects. The
2850 @code{network} class can represent a range of relational data types, and
2851 supports arbitrary vertex/edge/graph attributes.")
2852 (license license:gpl2+)))
2854 (define-public r-statnet-common
2856 (name "r-statnet-common")
2861 (uri (cran-uri "statnet.common" version))
2864 "0h3g687214rlycca0fjrpy1lqbqsrginxqhmhl2mb2jinqqxcfgd"))))
2866 `((upstream-name . "statnet.common")))
2867 (build-system r-build-system)
2869 `(("r-coda" ,r-coda)))
2870 (home-page "https://statnet.org")
2871 (synopsis "R scripts and utilities used by the Statnet software")
2872 (description "This package provides non-statistical utilities used by the
2873 software developed by the Statnet Project.")
2874 (license license:gpl3)))
2876 (define-public r-sna
2883 (uri (cran-uri "sna" version))
2886 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
2887 (build-system r-build-system)
2889 `(("r-network" ,r-network)
2890 ("r-statnet-common" ,r-statnet-common)))
2891 (home-page "https://statnet.org")
2892 (synopsis "Tools for social network analysis")
2894 "This package provides a range of tools for social network analysis,
2895 including node and graph-level indices, structural distance and covariance
2896 methods, structural equivalence detection, network regression, random graph
2897 generation, and 2D/3D network visualization.")
2898 (license license:gpl2+)))
2900 (define-public r-ttr
2907 (uri (cran-uri "TTR" version))
2910 "07r62ngyzjl4aszdxnr3n6bnbcgcap32yhd430jsilicg8n06di1"))))
2911 (properties `((upstream-name . "TTR")))
2912 (build-system r-build-system)
2914 `(("r-curl" ,r-curl)
2917 (native-inputs `(("gfortran" ,gfortran)))
2918 (home-page "https://github.com/joshuaulrich/TTR")
2919 (synopsis "Technical trading rules")
2921 "This package provides functions and data to construct technical trading
2923 (license license:gpl2)))
2925 (define-public r-leaps
2932 (uri (cran-uri "leaps" version))
2935 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
2936 (build-system r-build-system)
2937 (native-inputs `(("gfortran" ,gfortran)))
2938 (home-page "https://cran.r-project.org/web/packages/leaps/")
2939 (synopsis "Regression subset selection")
2941 "This package provides tools for regression subset selection, including
2942 exhaustive search.")
2943 (license license:gpl2+)))
2945 (define-public r-splus2r
2952 (uri (cran-uri "splus2R" version))
2955 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
2956 (properties `((upstream-name . "splus2R")))
2957 (build-system r-build-system)
2958 (native-inputs `(("gfortran" ,gfortran)))
2959 (home-page "https://cran.r-project.org/web/packages/splus2R/")
2960 (synopsis "Supplemental S-PLUS functionality in R")
2962 "Currently there are many functions in S-PLUS that are missing in R. To
2963 facilitate the conversion of S-PLUS packages to R packages, this package
2964 provides some missing S-PLUS functionality in R.")
2965 (license license:gpl2)))
2967 (define-public r-ifultools
2969 (name "r-ifultools")
2974 (uri (cran-uri "ifultools" version))
2977 "0pv2msaa1rmj8csxdclzi2jwg9pfdvh87blj9j3xa3myisglq092"))))
2978 (build-system r-build-system)
2980 `(("r-mass" ,r-mass)
2981 ("r-splus2r" ,r-splus2r)))
2982 (home-page "https://cran.r-project.org/web/packages/ifultools/")
2983 (synopsis "Insightful research tools")
2984 (description "This package provides C code used by the wmtsa, fractal, and
2986 (license license:gpl2)))
2988 (define-public r-sapa
2995 (uri (cran-uri "sapa" version))
2998 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
2999 (build-system r-build-system)
3001 `(("r-ifultools" ,r-ifultools)
3002 ("r-splus2r" ,r-splus2r)))
3003 (home-page "https://cran.r-project.org/web/packages/sapa/")
3004 (synopsis "Spectral analysis for physical applications")
3005 (description "This package provides software for the book Spectral
3006 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
3007 Cambridge University Press, 1993.")
3008 (license license:gpl2)))
3010 (define-public r-quantmod
3017 (uri (cran-uri "quantmod" version))
3020 "16aldg96z7amp5mr90nb8127yy04gxsihfr26km5p3cx3j117yv0"))))
3021 (build-system r-build-system)
3023 `(("r-curl" ,r-curl)
3027 (home-page "https://cran.r-project.org/web/packages/quantmod/")
3028 (synopsis "Quantitative financial modelling framework")
3029 (description "This package provides a quantitative financial modelling
3030 framework to allow users to specify, build, trade, and analyse quantitative
3031 financial trading strategies.")
3032 (license license:gpl3)))
3034 (define-public r-tseries
3041 (uri (cran-uri "tseries" version))
3044 "14s1glh5zzdvdl05a2z7ymhgf962svxf8xircghg5sc649lb33n0"))))
3045 (build-system r-build-system)
3047 `(("r-quadprog" ,r-quadprog)
3048 ("r-quantmod" ,r-quantmod)
3051 `(("gfortran" ,gfortran)))
3052 (home-page "https://cran.r-project.org/web/packages/tseries/")
3053 (synopsis "Time series analysis and computational finance")
3055 "This package provides functions relating to time series analysis and
3056 computational finance.")
3057 (license license:gpl2)))
3059 (define-public r-wmtsa
3066 (uri (cran-uri "wmtsa" version))
3069 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
3070 (build-system r-build-system)
3072 `(("r-ifultools" ,r-ifultools)
3074 ("r-splus2r" ,r-splus2r)))
3075 (home-page "https://cran.r-project.org/web/packages/wmtsa/")
3076 (synopsis "Wavelet methods for time series analysis")
3078 "This package provides software to accompany the book \"Wavelet Methods
3079 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
3080 University Press, 2000.")
3081 (license license:gpl2)))
3083 (define-public r-tsa
3090 (uri (cran-uri "TSA" version))
3093 "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx"))))
3094 (properties `((upstream-name . "TSA")))
3095 (build-system r-build-system)
3097 `(("r-leaps" ,r-leaps)
3098 ("r-locfit" ,r-locfit)
3100 ("r-tseries" ,r-tseries)))
3101 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
3102 (synopsis "Time series analysis")
3104 "This package contains R functions and datasets detailed in the book
3105 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
3106 Cryer and Kung-Sik Chan.")
3107 (license license:gpl2+)))
3109 (define-public r-extradistr
3111 (name "r-extradistr")
3116 (uri (cran-uri "extraDistr" version))
3119 "1fg8vjpal33y51iqzglk1yvy46d7js0l0wfbdy698lq8a06hq19p"))))
3120 (properties `((upstream-name . "extraDistr")))
3121 (build-system r-build-system)
3123 `(("r-rcpp" ,r-rcpp)))
3124 (home-page "https://github.com/twolodzko/extraDistr")
3125 (synopsis "Additional univariate and multivariate distributions")
3127 "This package implements density, distribution functions, quantile
3128 functions and random generation functions for a large number of univariate and
3129 multivariate distributions.")
3130 (license license:gpl2)))
3132 (define-public r-fractal
3139 (uri (cran-uri "fractal" version))
3142 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
3143 (build-system r-build-system)
3145 `(("r-ifultools" ,r-ifultools)
3148 ("r-scatterplot3d" ,r-scatterplot3d)
3149 ("r-splus2r" ,r-splus2r)
3150 ("r-wmtsa" ,r-wmtsa)))
3151 (home-page "https://cran.r-project.org/web/packages/fractal/")
3152 (synopsis "Fractal time series modeling and analysis")
3154 "This package provides tools for stochastic fractal and deterministic
3155 chaotic time series analysis.")
3156 (license license:gpl2)))
3158 (define-public r-urca
3165 (uri (cran-uri "urca" version))
3168 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
3169 (build-system r-build-system)
3170 (propagated-inputs `(("r-nlme" ,r-nlme)))
3171 (native-inputs `(("gfortran" ,gfortran)))
3172 (home-page "https://cran.r-project.org/web/packages/urca/")
3173 (synopsis "Unit root and cointegration tests for time series data")
3175 "This package provides unit root and cointegration tests encountered in
3176 applied econometric analysis.")
3177 (license license:gpl2+)))
3179 (define-public r-cubature
3186 (uri (cran-uri "cubature" version))
3189 "1hd23b8v2kpqp5gr0va8p2q7j8w9rik6ks7zrr4b8mb2mwrakk74"))))
3190 (build-system r-build-system)
3192 `(("r-rcpp" ,r-rcpp)))
3193 (home-page "https://github.com/bnaras/cubature")
3194 (synopsis "Adaptive multivariate integration over hypercubes")
3196 "This package is an R wrapper around the cubature C library for adaptive
3197 multivariate integration over hypercubes. This version provides both
3198 @code{hcubature} and @code{pcubature} routines in addition to a vector
3200 ;; The included cubature C library is released under GPLv2+, but the
3201 ;; wrapper declares the license to be GPLv3+.
3202 (license (list license:gpl2+ license:gpl3+))))
3204 (define-public r-trend
3211 (uri (cran-uri "trend" version))
3214 "1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
3215 (build-system r-build-system)
3217 `(("r-extradistr" ,r-extradistr)))
3219 `(("gfortran" ,gfortran)))
3220 (home-page "https://cran.r-project.org/web/packages/trend/")
3221 (synopsis "Non-parametric trend tests and change-point detection")
3223 "The analysis of environmental data often requires the detection of
3224 trends and change-points. This package includes tests for trend
3225 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
3226 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
3227 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
3228 correlation trend test), change-point detection (Lanzante's test procedures,
3229 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
3230 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
3231 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
3232 sample Robust Rank-Order Distributional Test.")
3233 (license license:gpl3)))
3235 (define-public r-expm
3242 (uri (cran-uri "expm" version))
3245 "1mihl67kvv1xv0figp25jkmwfn4iwkcx15cng2348y8gm6zybw9q"))))
3246 (build-system r-build-system)
3247 (propagated-inputs `(("r-matrix" ,r-matrix)))
3248 (native-inputs `(("gfortran" ,gfortran)))
3249 (home-page "https://r-forge.r-project.org/projects/expm/")
3250 (synopsis "Tools for matrix exponentials and related quantities")
3252 "This package provides tools for the computation of the matrix
3253 exponential, logarithm, square root, and related quantities.")
3254 (license license:gpl2+)))
3256 (define-public r-complexplus
3258 (name "r-complexplus")
3263 (uri (cran-uri "complexplus" version))
3266 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
3267 (build-system r-build-system)
3269 `(("r-expm" ,r-expm)
3270 ("r-matrix" ,r-matrix)))
3271 (home-page "https://cran.r-project.org/web/packages/complexplus/")
3272 (synopsis "Functions of complex or real variables")
3274 "This package extends several functions to the complex domain, including
3275 the matrix exponential and logarithm, and the determinant.")
3276 (license license:gpl2)))
3278 (define-public r-phontools
3280 (name "r-phontools")
3285 (uri (cran-uri "phonTools" version))
3288 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
3289 (properties `((upstream-name . "phonTools")))
3290 (build-system r-build-system)
3291 (home-page "http://www.santiagobarreda.com/rscripts.html")
3292 (synopsis "Tools for phonetic and acoustic analyses")
3294 "This package contains tools for the organization, display, and analysis
3295 of the sorts of data frequently encountered in phonetics research and
3296 experimentation, including the easy creation of IPA vowel plots, and the
3297 creation and manipulation of WAVE audio files.")
3298 (license license:bsd-2)))
3307 (uri (cran-uri "np" version))
3310 "17h67a510wh83800ri6g02wvznrlhigxni8shyijz1iaxcpk8k4j"))))
3311 (build-system r-build-system)
3313 `(("r-boot" ,r-boot)
3314 ("r-cubature" ,r-cubature)
3315 ("r-quadprog" ,r-quadprog)
3316 ("r-quantreg" ,r-quantreg)))
3317 (home-page "https://github.com/JeffreyRacine/R-Package-np")
3318 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
3319 (description "This package provides non-parametric (and semi-parametric)
3320 kernel methods that seamlessly handle a mix of continuous, unordered, and
3321 ordered factor data types.")
3322 ;; Any version of the GPL.
3323 (license license:gpl3+)))
3325 (define-public r-powerplus
3327 (name "r-powerplus")
3332 (uri (cran-uri "powerplus" version))
3335 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
3336 (build-system r-build-system)
3338 `(("r-complexplus" ,r-complexplus)
3341 ("r-matrix" ,r-matrix)
3342 ("r-phontools" ,r-phontools)))
3343 (home-page "https://cran.r-project.org/web/packages/powerplus/")
3344 (synopsis "Exponentiation operations")
3346 "This package provides tools for the computation of matrix and scalar
3348 (license license:gpl2)))
3350 (define-public r-heatmaply
3352 (name "r-heatmaply")
3357 (uri (cran-uri "heatmaply" version))
3360 "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc"))))
3361 (build-system r-build-system)
3363 `(("r-assertthat" ,r-assertthat)
3364 ("r-colorspace" ,r-colorspace)
3365 ("r-dendextend" ,r-dendextend)
3366 ("r-ggplot2" ,r-ggplot2)
3367 ("r-gplots" ,r-gplots)
3368 ("r-htmlwidgets" ,r-htmlwidgets)
3369 ("r-knitr" ,r-knitr) ; needed for vignettes
3370 ("r-magrittr" ,r-magrittr)
3371 ("r-plotly" ,r-plotly)
3372 ("r-rcolorbrewer" ,r-rcolorbrewer)
3373 ("r-reshape2" ,r-reshape2)
3374 ("r-scales" ,r-scales)
3375 ("r-seriation" ,r-seriation)
3376 ("r-viridis" ,r-viridis)
3377 ("r-webshot" ,r-webshot)))
3378 (home-page "https://cran.r-project.org/package=heatmaply")
3379 (synopsis "Interactive cluster heat maps using plotly")
3381 "This package enables you to create interactive cluster heatmaps that can
3382 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
3383 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
3384 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
3385 a popular graphical method for visualizing high-dimensional data, in which a
3386 table of numbers is encoded as a grid of colored cells. The rows and columns
3387 of the matrix are ordered to highlight patterns and are often accompanied by
3389 ;; Either version of the license.
3390 (license (list license:gpl2 license:gpl3))))
3392 (define-public r-cgdsr
3399 (uri (cran-uri "cgdsr" version))
3402 "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23"))))
3403 (build-system r-build-system)
3405 `(("r-r-methodss3" ,r-r-methodss3)
3406 ("r-r-oo" ,r-r-oo)))
3407 (home-page "https://github.com/cBioPortal/cgdsr")
3408 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
3410 "This package provides a basic set of R functions for querying the Cancer
3411 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
3412 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
3413 (license license:lgpl3)))
3415 (define-public r-import
3422 (uri (cran-uri "import" version))
3425 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
3426 (build-system r-build-system)
3427 (home-page "https://github.com/smbache/import")
3428 (synopsis "Import mechanism for R")
3430 "This is an alternative mechanism for importing objects from packages.
3431 The syntax allows for importing multiple objects from a package with a single
3432 command in an expressive way. The import package bridges some of the gap
3433 between using @code{library} (or @code{require}) and direct (single-object)
3434 imports. Furthermore the imported objects are not placed in the current
3435 environment. It is also possible to import objects from stand-alone @code{.R}
3437 (license license:expat)))
3439 (define-public r-shinyace
3446 (uri (cran-uri "shinyAce" version))
3449 "1hqgszbiv99dibhwr21v21ll4s2hjn3ccqdicsm0z3gk77bh8iyb"))))
3450 (properties `((upstream-name . "shinyAce")))
3451 (build-system r-build-system)
3453 `(("r-shiny" ,r-shiny)
3454 ("r-jsonlite" ,r-jsonlite)))
3455 (home-page "http://cran.r-project.org/web/packages/shinyAce")
3456 (synopsis "Ace editor bindings for Shiny")
3458 "This package provides Ace editor bindings to enable a rich text editing
3459 environment within Shiny.")
3460 (license license:expat)))
3462 (define-public r-radiant-data
3464 (name "r-radiant-data")
3469 (uri (cran-uri "radiant.data" version))
3472 "0mbxfqn79nphii4hb6kxl2wc0w0ra16y378rp2yw9a9926zdb7mb"))
3473 (modules '((guix build utils)))
3476 ;; Delete files that are under CC-NC-SA.
3477 (delete-file-recursively "inst/app/tools/help")
3479 (properties `((upstream-name . "radiant.data")))
3480 (build-system r-build-system)
3482 `(("r-base64enc" ,r-base64enc)
3483 ("r-broom" ,r-broom)
3486 ("r-dplyr" ,r-dplyr)
3489 ("r-ggplot2" ,r-ggplot2)
3490 ("r-gridextra" ,r-gridextra)
3491 ("r-import" ,r-import)
3492 ("r-jsonlite" ,r-jsonlite)
3493 ("r-knitr" ,r-knitr)
3494 ("r-lubridate" ,r-lubridate)
3495 ("r-magrittr" ,r-magrittr)
3496 ("r-markdown" ,r-markdown)
3497 ("r-plotly" ,r-plotly)
3498 ("r-psych" ,r-psych)
3499 ("r-readr" ,r-readr)
3500 ("r-readxl" ,r-readxl)
3501 ("r-rlang" ,r-rlang)
3502 ("r-rmarkdown" ,r-rmarkdown)
3503 ("r-rstudioapi" ,r-rstudioapi)
3504 ("r-scales" ,r-scales)
3505 ("r-shiny" ,r-shiny)
3506 ("r-shinyace" ,r-shinyace)
3507 ("r-tibble" ,r-tibble)
3508 ("r-tidyr" ,r-tidyr)
3509 ("r-writexl" ,r-writexl)))
3510 (home-page "https://github.com/radiant-rstats/radiant.data")
3511 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
3513 "The Radiant Data menu includes interfaces for loading, saving, viewing,
3514 visualizing, summarizing, transforming, and combining data. It also contains
3515 functionality to generate reproducible reports of the analyses conducted in
3517 (license license:agpl3)))
3519 (define-public r-algdesign
3521 (name "r-algdesign")
3526 (uri (cran-uri "AlgDesign" version))
3529 "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
3530 (properties `((upstream-name . "AlgDesign")))
3531 (build-system r-build-system)
3532 (home-page "https://github.com/jvbraun/AlgDesign")
3533 (synopsis "Algorithmic experimental design")
3535 "This package provides tools to calculate exact and approximate theory
3536 experimental designs for D, A, and I criteria. Very large designs may be
3537 created. Experimental designs may be blocked or blocked designs created from
3538 a candidate list, using several criteria. The blocking can be done when whole
3539 and within plot factors interact.")
3540 (license license:gpl2+)))
3542 (define-public r-signal
3549 (uri (cran-uri "signal" version))
3552 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
3553 (build-system r-build-system)
3554 (propagated-inputs `(("r-mass" ,r-mass)))
3555 (native-inputs `(("gfortran" ,gfortran)))
3556 (home-page "https://cran.r-project.org/web/packages/signal/")
3557 (synopsis "Signal processing")
3559 "This package provides a set of signal processing functions originally
3560 written for Matlab and GNU Octave. It includes filter generation utilities,
3561 filtering functions, resampling routines, and visualization of filter models.
3562 It also includes interpolation functions.")
3563 (license license:gpl2)))
3565 (define-public r-gsubfn
3572 (uri (cran-uri "gsubfn" version))
3575 "00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
3576 (build-system r-build-system)
3577 (propagated-inputs `(("r-proto" ,r-proto)))
3578 (home-page "http://gsubfn.googlecode.com")
3579 (synopsis "Utilities for strings and function arguments.")
3581 "This package provides @code{gsubfn} which is like @code{gsub} but can
3582 take a replacement function or certain other objects instead of the
3583 replacement string. Matches and back references are input to the replacement
3584 function and replaced by the function output. @code{gsubfn} can be used to
3585 split strings based on content rather than delimiters and for quasi-perl-style
3586 string interpolation. The package also has facilities for translating
3587 formulas to functions and allowing such formulas in function calls instead of
3589 (license license:gpl2+)))
3591 (define-public r-sqldf
3598 (uri (cran-uri "sqldf" version))
3601 "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
3602 (build-system r-build-system)
3604 `(("r-chron" ,r-chron)
3606 ("r-gsubfn" ,r-gsubfn)
3607 ("r-proto" ,r-proto)
3608 ("r-rsqlite" ,r-rsqlite)))
3609 (home-page "https://github.com/ggrothendieck/sqldf")
3610 (synopsis "Manipulate R data frames using SQL")
3612 "The @code{sqldf} function is typically passed a single argument which is
3613 an SQL select statement where the table names are ordinary R data frame names.
3614 @code{sqldf} transparently sets up a database, imports the data frames into
3615 that database, performs the SQL statement and returns the result using a
3616 heuristic to determine which class to assign to each column of the returned
3617 data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
3618 used to read filtered files into R even if the original files are larger than
3619 R itself can handle.")
3620 (license license:gpl2)))
3622 (define-public r-abind
3629 (uri (cran-uri "abind" version))
3632 "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
3633 (build-system r-build-system)
3634 (home-page "https://cran.r-project.org/web/packages/abind/")
3635 (synopsis "Combine multidimensional arrays")
3637 "This package provides tools to combine multidimensional arrays into a
3638 single array. This is a generalization of @code{cbind} and @code{rbind}. It
3639 works with vectors, matrices, and higher-dimensional arrays. It also provides
3640 the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
3641 extracting and replacing data in arrays.")
3642 (license license:lgpl2.0+)))
3644 (define-public r-prroc
3651 (uri (cran-uri "PRROC" version))
3654 "1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
3655 (properties `((upstream-name . "PRROC")))
3656 (build-system r-build-system)
3657 (home-page "https://cran.r-project.org/web/packages/PRROC/")
3658 (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
3660 "This package computes the areas under the @dfn{precision-recall} (PR)
3661 and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
3662 contrast to other implementations, the interpolation between points of the PR
3663 curve is done by a non-linear piecewise function. In addition to the areas
3664 under the curves, the curves themselves can also be computed and plotted by a
3665 specific S3-method.")
3666 (license license:gpl3)))
3668 (define-public r-vim
3675 (uri (cran-uri "VIM" version))
3678 "1vjcs5wvjv94ln01d94h9rs4j50d3ky4n26mm3prgh13raylrmnd"))))
3679 (properties `((upstream-name . "VIM")))
3680 (build-system r-build-system)
3683 ("r-colorspace" ,r-colorspace)
3684 ("r-data-table" ,r-data-table)
3685 ("r-e1071" ,r-e1071)
3686 ("r-laeken" ,r-laeken)
3690 ("r-robustbase" ,r-robustbase)
3693 (home-page "https://github.com/alexkowa/VIM")
3694 (synopsis "Visualization and imputation of missing values")
3696 "This package provides tools for the visualization of missing and/or
3697 imputed values are introduced, which can be used for exploring the data and
3698 the structure of the missing and/or imputed values. Depending on this
3699 structure of the missing values, the corresponding methods may help to
3700 identify the mechanism generating the missing values and allows to explore the
3701 data including missing values. In addition, the quality of imputation can be
3702 visually explored using various univariate, bivariate, multiple and
3703 multivariate plot methods.")
3704 (license license:gpl2+)))
3706 (define-public r-fnn
3713 (uri (cran-uri "FNN" version))
3716 "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
3717 (properties `((upstream-name . "FNN")))
3718 (build-system r-build-system)
3719 (home-page "https://cran.r-project.org/web/packages/FNN")
3720 (synopsis "Fast nearest neighbor search algorithms and applications")
3722 "This package provides cover-tree and kd-tree fast k-nearest neighbor
3723 search algorithms. Related applications including KNN classification,
3724 regression and information measures are implemented.")
3725 ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
3726 ;; later can be used.
3727 (license license:gpl2+)))
3729 (define-public r-smoother
3736 (uri (cran-uri "smoother" version))
3739 "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
3740 (build-system r-build-system)
3742 `(("r-ttr" ,r-ttr)))
3743 (home-page "http://cran.r-project.org/web/packages/smoother")
3744 (synopsis "Functions relating to the smoothing of numerical data")
3746 "This package provides a collection of methods for smoothing numerical
3747 data, commencing with a port of the Matlab gaussian window smoothing function.
3748 In addition, several functions typically used in smoothing of financial data
3750 (license license:gpl2)))
3752 (define-public r-riverplot
3754 (name "r-riverplot")
3759 (uri (cran-uri "riverplot" version))
3762 "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
3763 (build-system r-build-system)
3764 (home-page "https://logfc.wordpress.com")
3765 (synopsis "Sankey or ribbon plots")
3767 "Sankey plots are a type of diagram that is convenient to illustrate how
3768 flow of information, resources etc. separates and joins, much like observing
3769 how rivers split and merge. For example, they can be used to compare
3770 different clusterings. This package provides an implementation of Sankey
3772 (license license:gpl2+)))
3774 (define-public r-dyn
3781 (uri (cran-uri "dyn" version))
3784 "16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
3785 (build-system r-build-system)
3787 `(("r-zoo" ,r-zoo)))
3788 (home-page "https://cran.r-project.org/web/packages/dyn")
3789 (synopsis "Time series regression")
3791 "This package provides the dyn class interfaces @code{ts}, @code{irts},
3792 @code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
3793 @code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
3794 @code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
3795 @code{randomForest::randomForest()} and other regression functions, allowing
3796 those functions to be used with time series including specifications that may
3797 contain lags, diffs and missing values.")
3799 (license license:gpl2+)))
3801 (define-public r-catdap
3808 (uri (cran-uri "catdap" version))
3811 "0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
3812 (build-system r-build-system)
3814 `(("gfortran" ,gfortran)))
3815 (home-page "https://cran.r-project.org/web/packages/catdap/")
3816 (synopsis "Tools for categorical data analysis")
3818 "This package provides functions for analyzing multivariate data.
3819 Dependencies of the distribution of the specified variable (response
3820 variable) to other variables (explanatory variables) are derived and
3821 evaluated by the @dfn{Akaike Information Criterion} (AIC).")
3822 (license license:gpl2+)))
3824 (define-public r-arules
3831 (uri (cran-uri "arules" version))
3834 "0glfqgxr87900kigmkby2ff7qrjvd6aq595q85y056i5ckjcp615"))))
3835 (build-system r-build-system)
3837 `(("r-matrix" ,r-matrix)))
3838 (home-page "https://github.com/mhahsler/arules")
3839 (synopsis "Mining association rules and frequent itemsets")
3841 "This package provides an infrastructure for representing, manipulating
3842 and analyzing transaction data and patterns (frequent itemsets and association rules).
3843 It also provides C implementations of the association mining algorithms Apriori
3845 (license license:gpl3)))
3847 (define-public r-parsedate
3849 (name "r-parsedate")
3854 (uri (cran-uri "parsedate" version))
3857 "0mg7hbm3903iwvmpn51gjpaaq03rsp72hjb1g8h5g84r81iha002"))))
3858 (build-system r-build-system)
3859 (home-page "https://github.com/gaborcsardi/parsedate")
3861 "Recognize and parse dates in various formats")
3863 "This package provides three functions for dealing with dates:
3864 @code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
3865 time formats, @code{parse_date} parses dates in unspecified formats,
3866 and @code{format_iso_8601} formats a date in ISO 8601 format.")
3867 (license license:gpl2)))
3869 (define-public r-abc-data
3876 (uri (cran-uri "abc.data" version))
3879 "1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
3880 (properties `((upstream-name . "abc.data")))
3881 (build-system r-build-system)
3882 (home-page "https://cran.r-project.org/web/packages/abc.data/")
3883 (synopsis "Data for Approximate Bayesian Computation (ABC) package")
3885 "This package contains data which are used by functions of the abc
3886 package which implements several @dfn{Approximate Bayesian Computation} (ABC)
3887 algorithms for performing parameter estimation, model selection, and
3889 (license license:gpl3+)))
3891 (define-public r-abc
3898 (uri (cran-uri "abc" version))
3901 "0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
3902 (build-system r-build-system)
3904 `(("r-abc-data" ,r-abc-data)
3905 ("r-locfit" ,r-locfit)
3908 ("r-quantreg" ,r-quantreg)))
3909 (home-page "https://cran.r-project.org/web/packages/abc/")
3910 (synopsis "Tools for Approximate Bayesian Computation (ABC)")
3912 "This package implements several @dfn{Approximate Bayesian
3913 Computation} (ABC) algorithms for performing parameter estimation, model
3914 selection, and goodness-of-fit. Cross-validation tools are also available for
3915 measuring the accuracy of ABC estimates, and to calculate the
3916 misclassification probabilities of different models.")
3917 (license license:gpl3+)))
3919 (define-public r-zip
3926 (uri (cran-uri "zip" version))
3929 "0rgr9pcdhdq3k8n29h2ircp3ri1ibhrx81gja1y7331v15xyrabg"))))
3930 (build-system r-build-system)
3931 (home-page "https://github.com/gaborcsardi/zip")
3932 (synopsis "Cross-platform Zip compression")
3934 "This package provides a cross-platform Zip compression library for R.
3935 It is a replacement for the @code{zip} function, that does not require any
3936 additional external tools on any platform.")
3937 (license license:cc0)))
3939 (define-public r-openxlsx
3946 (uri (cran-uri "openxlsx" version))
3949 "1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb"))))
3950 (build-system r-build-system)
3952 `(("r-rcpp" ,r-rcpp)
3954 (home-page "https://github.com/awalker89/openxlsx")
3955 (synopsis "Read, write and edit XLSX files")
3957 "This package simplifies the creation of Excel @code{.xlsx} files by
3958 providing a high level interface to writing, styling and editing worksheets.
3959 Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
3960 and @code{XLConnect} packages with the added benefit of removing the
3961 dependency on Java.")
3962 (license license:gpl3)))
3964 (define-public r-rio
3971 (uri (cran-uri "rio" version))
3974 "158xg3vj0glk3fslwi6fywwmfym2b6kn3fdmjligdfy5lf68khix"))))
3975 (build-system r-build-system)
3977 `(("r-curl" ,r-curl)
3978 ("r-data-table" ,r-data-table)
3979 ("r-foreign" ,r-foreign)
3980 ("r-haven" ,r-haven)
3981 ("r-openxlsx" ,r-openxlsx)
3982 ("r-readxl" ,r-readxl)
3983 ("r-tibble" ,r-tibble)))
3984 (home-page "https://github.com/leeper/rio")
3985 (synopsis "Swiss-army knife for data I/O")
3987 "This package provides streamlined data import and export infrastructure
3988 by making assumptions that the user is probably willing to make: @code{import}
3989 and @code{export} determine the data structure from the file extension,
3990 reasonable defaults are used for data import and export (e.g.,
3991 @code{stringsAsFactors=FALSE}), web-based import is natively
3992 supported (including from SSL/HTTPS), compressed files can be read directly
3993 without explicit decompression, and fast import packages are used where
3994 appropriate. An additional convenience function, @code{convert}, provides a
3995 simple method for converting between file types.")
3996 (license license:gpl2)))
3998 (define-public r-maptools
4005 (uri (cran-uri "maptools" version))
4008 "075lmb3b62171cw2dg8fv1vwmvfzg39r1ji7jwb8s5k9dz88ry1v"))))
4009 (build-system r-build-system)
4011 `(("r-foreign" ,r-foreign)
4012 ("r-lattice" ,r-lattice)
4014 (home-page "http://r-forge.r-project.org/projects/maptools/")
4015 (synopsis "Tools for reading and handling spatial objects")
4017 "This package provides a set of tools for manipulating and reading
4018 geographic data, in particular ESRI Shapefiles. It includes binary access to
4019 GSHHG shoreline files. The package also provides interface wrappers for
4020 exchanging spatial objects with other R packages.")
4021 ;; The C source files from shapelib are released under the Expat license.
4022 ;; The R code is released under GPL version 2 or later.
4023 (license (list license:gpl2+
4026 (define-public r-later
4033 (uri (cran-uri "later" version))
4036 "04j2phymxgkk4hv9pfa5w3s98w5d7fvm11blrdhxmray4n618msw"))))
4037 (build-system r-build-system)
4041 ("r-rlang" ,r-rlang)))
4042 (home-page "https://github.com/r-lib/later")
4043 (synopsis "Utilities for delaying function execution")
4045 "This package provides tools to execute arbitrary R or C functions some
4046 time after the current time, after the R execution stack has emptied.")
4047 (license license:gpl2+)))
4049 (define-public r-promises
4056 (uri (cran-uri "promises" version))
4059 "0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
4060 (build-system r-build-system)
4062 `(("r-later" ,r-later)
4063 ("r-magrittr" ,r-magrittr)
4066 ("r-rlang" ,r-rlang)))
4067 (home-page "https://rstudio.github.io/promises")
4068 (synopsis "Abstractions for promise-based asynchronous programming")
4070 "This package provides fundamental abstractions for doing asynchronous
4071 programming in R using promises. Asynchronous programming is useful for
4072 allowing a single R process to orchestrate multiple tasks in the background
4073 while also attending to something else. Semantics are similar to JavaScript
4074 promises, but with a syntax that is idiomatic R.")
4075 (license license:expat)))
4077 (define-public r-dosnow
4084 (uri (cran-uri "doSNOW" version))
4087 "13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
4088 (properties `((upstream-name . "doSNOW")))
4089 (build-system r-build-system)
4091 `(("r-foreach" ,r-foreach)
4092 ("r-iterators" ,r-iterators)
4093 ("r-snow" ,r-snow)))
4094 (home-page "https://cran.r-project.org/web/packages/doSNOW")
4095 (synopsis "Foreach parallel adaptor for the snow package")
4097 "This package provides a parallel backend for the @code{%dopar%} function
4098 using the @code{snow} package.")
4099 (license license:gpl2)))
4101 (define-public r-snowfall
4104 (version "1.84-6.1")
4107 (uri (cran-uri "snowfall" version))
4109 (base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
4110 (build-system r-build-system)
4112 `(("r-snow" ,r-snow)))
4113 (home-page "http://cran.r-project.org/web/packages/snowfall/")
4114 (synopsis "Easier cluster computing")
4115 (description "This package is a usability wrapper around snow for easier
4116 development of parallel R programs. This package offers e.g. extended error
4117 checks, and additional functions. All functions work in sequential mode, too,
4118 if no cluster is present or wished. The package is also designed as connector
4119 to the cluster management tool @code{sfCluster}, but can also used without
4121 (license license:gpl2+)))
4123 (define-public r-codedepends
4125 (name "r-codedepends")
4130 (uri (cran-uri "CodeDepends" version))
4133 "03p82s0abca2jimzqvxdzykfzca7c7fhm5xsjxybcksr4gggr5sc"))))
4134 (properties `((upstream-name . "CodeDepends")))
4135 (build-system r-build-system)
4137 `(("r-codetools" ,r-codetools)
4139 (home-page "http://cran.r-project.org/web/packages/CodeDepends")
4140 (synopsis "Analysis of R code for reproducible research and code comprehension")
4142 "This package provides tools for analyzing R expressions or blocks of
4143 code and determining the dependencies between them. It focuses on R scripts,
4144 but can be used on the bodies of functions. There are many facilities
4145 including the ability to summarize or get a high-level view of code,
4146 determining dependencies between variables, code improvement suggestions.")
4147 ;; Any version of the GPL
4148 (license (list license:gpl2+ license:gpl3+))))
4150 (define-public r-rappdirs
4157 (uri (cran-uri "rappdirs" version))
4160 "0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
4161 (build-system r-build-system)
4162 (home-page "https://cran.r-project.org/web/packages/rappdirs/")
4163 (synopsis "Determine where to save data, caches, and logs")
4165 "This package provides an easy way to determine which directories on the
4166 user's computer should be used to save data, caches and logs. It is a port of
4167 Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
4168 (license license:expat)))
4170 (define-public r-learnr
4177 (uri (cran-uri "learnr" version))
4180 "0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5"))))
4181 (build-system r-build-system)
4183 `(("r-evaluate" ,r-evaluate)
4184 ("r-htmltools" ,r-htmltools)
4185 ("r-htmlwidgets" ,r-htmlwidgets)
4186 ("r-jsonlite" ,r-jsonlite)
4187 ("r-knitr" ,r-knitr)
4188 ("r-markdown" ,r-markdown)
4189 ("r-rappdirs" ,r-rappdirs)
4190 ("r-rmarkdown" ,r-rmarkdown)
4191 ("r-rprojroot" ,r-rprojroot)
4192 ("r-shiny" ,r-shiny)
4193 ("r-withr" ,r-withr)))
4194 (home-page "https://rstudio.github.io/learnr/")
4195 (synopsis "Interactive tutorials for R")
4197 "This package provides tools to create interactive tutorials using R
4198 Markdown. Use a combination of narrative, figures, videos, exercises, and
4199 quizzes to create self-paced tutorials for learning about R and R packages.")
4200 (license license:asl2.0)))
4202 (define-public r-analytics
4204 (name "r-analytics")
4209 (uri (cran-uri "analytics" version))
4212 "1jkdjqc3fnvvsgi6x9ncf36rxzq0a55cmgkcv92mfmpcramg2lk6"))))
4213 (build-system r-build-system)
4216 ("r-cluster" ,r-cluster)
4217 ("r-fractal" ,r-fractal)
4218 ("r-lmtest" ,r-lmtest)
4221 ("r-powerplus" ,r-powerplus)
4222 ("r-robust" ,r-robust)
4223 ("r-trend" ,r-trend)
4225 ("r-urca" ,r-urca)))
4226 (home-page "https://cran.r-project.org/web/packages/analytics/")
4227 (synopsis "Collection of data analysis tools")
4229 "This package is a collection of data analysis tools. It includes tools
4230 for regression outlier detection in a fitted linear model, stationary
4231 bootstrap using a truncated geometric distribution, a comprehensive test for
4232 weak stationarity, column means by group, weighted biplots, and a heuristic to
4233 obtain a better initial configuration in non-metric MDS.")
4234 (license license:gpl2)))
4236 (define-public r-reticulate
4238 (name "r-reticulate")
4243 (uri (cran-uri "reticulate" version))
4246 "0zwb4ikf021nw7axdn7qlr6bq4xkph3anfy314idkspy1iil4nmr"))))
4247 (build-system r-build-system)
4248 (inputs `(("python" ,python)))
4250 `(("r-jsonlite" ,r-jsonlite)
4251 ("r-matrix" ,r-matrix)
4252 ("r-rcpp" ,r-rcpp)))
4253 (home-page "https://github.com/rstudio/reticulate")
4254 (synopsis "R interface to Python")
4256 "This package provides an interface from R to Python modules, classes,
4257 and functions. When calling into Python, R data types are automatically
4258 converted to their equivalent Python types. When values are returned from
4259 Python to R they are converted back to R types.")
4260 (license license:asl2.0)))
4262 (define-public r-bibtex
4269 (uri (cran-uri "bibtex" version))
4272 "0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
4273 (build-system r-build-system)
4274 (propagated-inputs `(("r-stringr" ,r-stringr)))
4275 (home-page "https://github.com/romainfrancois/bibtex")
4276 (synopsis "Bibtex parser")
4277 (description "This package provides a utility for R to parse a bibtex
4279 (license license:gpl2+)))
4281 (define-public r-ggseqlogo
4283 (name "r-ggseqlogo")
4288 (uri (cran-uri "ggseqlogo" version))
4291 "13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
4292 (build-system r-build-system)
4293 (propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
4294 (home-page "https://github.com/omarwagih/ggseqlogo")
4295 (synopsis "ggplot2 extension for drawing genetic sequence logos")
4297 "The range of functions provided by this package makes it possible to
4298 draw highly versatile genomic sequence logos. Features include, but are not
4299 limited to, modifying colour schemes and fonts used to draw the logo,
4300 generating multiple logo plots, and aiding the visualisation with annotations.
4301 Sequence logos can easily be combined with other ggplot2 plots.")
4302 ;; Unspecified version of the LGPL.
4303 (license license:lgpl3+)))
4305 (define-public r-ggsci
4312 (uri (cran-uri "ggsci" version))
4315 "0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
4316 (build-system r-build-system)
4318 `(("r-ggplot2" ,r-ggplot2)
4319 ("r-scales" ,r-scales)))
4320 (home-page "https://nanx.me/ggsci/")
4321 (synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
4323 "This package provides a collection of ggplot2 color palettes inspired by
4324 plots in scientific journals, data visualization libraries, science fiction
4325 movies, and TV shows.")
4326 (license license:gpl3)))
4328 (define-public r-ggsignif
4335 (uri (cran-uri "ggsignif" version))
4338 "1rn58d7pb3axk6chiihryykrzw76adaa2yiafq4d0j6qbhax78f7"))))
4339 (build-system r-build-system)
4341 `(("r-ggplot2" ,r-ggplot2)))
4342 (home-page "https://github.com/const-ae/ggsignif")
4343 (synopsis "Significance brackets for ggplot2")
4345 "Enrich your ggplots with group-wise comparisons. This package provides
4346 an easy way to indicate if two groups are significantly different. Commonly
4347 this is shown by a bracket on top connecting the groups of interest which
4348 itself is annotated with the level of significance. The package provides a
4349 single layer that takes the groups for comparison and the test as arguments
4350 and adds the annotation to the plot.")
4351 (license license:gpl3)))
4353 (define-public r-ggpubr
4360 (uri (cran-uri "ggpubr" version))
4363 "110ny8p41kmbz0a5rl0mv9cqpjkx6yr3ybflp1r0fmcvhwv7cr3i"))))
4364 (build-system r-build-system)
4366 `(("r-cowplot" ,r-cowplot)
4367 ("r-dplyr" ,r-dplyr)
4368 ("r-ggplot2" ,r-ggplot2)
4369 ("r-ggrepel" ,r-ggrepel)
4370 ("r-ggsci" ,r-ggsci)
4371 ("r-ggsignif" ,r-ggsignif)
4372 ("r-gridextra" ,r-gridextra)
4373 ("r-magrittr" ,r-magrittr)
4374 ("r-purrr" ,r-purrr)
4375 ("r-scales" ,r-scales)
4376 ("r-tidyr" ,r-tidyr)))
4377 (home-page "http://www.sthda.com/english/rpkgs/ggpubr")
4378 (synopsis "ggplot2-based publication-ready plots")
4380 "The ggplot2 package is an excellent and flexible package for elegant
4381 data visualization in R. However the default generated plots require some
4382 formatting before we can send them for publication. The ggpubr package
4383 provides some easy-to-use functions for creating and customizing ggplot2-based
4384 publication-ready plots.")
4385 (license license:gpl2)))
4387 (define-public r-ellipse
4394 (uri (cran-uri "ellipse" version))
4397 "0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
4398 (build-system r-build-system)
4399 (home-page "https://cran.r-project.org/web/packages/ellipse/")
4400 (synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
4402 "This package contains various routines for drawing ellipses and
4403 ellipse-like confidence regions, implementing the plots described in Murdoch
4404 and Chow (1996), A graphical display of large correlation matrices, The
4405 American Statistician 50, 178-180. There are also routines implementing the
4406 profile plots described in Bates and Watts (1988), Nonlinear Regression
4407 Analysis and its Applications.")
4408 (license license:gpl2+)))
4410 (define-public r-flashclust
4412 (name "r-flashclust")
4417 (uri (cran-uri "flashClust" version))
4420 "0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
4421 (properties `((upstream-name . "flashClust")))
4422 (build-system r-build-system)
4423 (native-inputs `(("gfortran" ,gfortran)))
4424 (home-page "https://cran.r-project.org/web/packages/flashClust/")
4425 (synopsis "Implementation of optimal hierarchical clustering")
4427 "This package provides a fast implementation of hierarchical
4429 (license license:gpl2+)))
4431 (define-public r-factominer
4433 (name "r-factominer")
4438 (uri (cran-uri "FactoMineR" version))
4441 "1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
4442 (properties `((upstream-name . "FactoMineR")))
4443 (build-system r-build-system)
4446 ("r-cluster" ,r-cluster)
4447 ("r-ellipse" ,r-ellipse)
4448 ("r-flashclust" ,r-flashclust)
4449 ("r-lattice" ,r-lattice)
4450 ("r-leaps" ,r-leaps)
4452 ("r-scatterplot3d" ,r-scatterplot3d)))
4453 (home-page "http://factominer.free.fr")
4454 (synopsis "Multivariate exploratory data analysis and data mining")
4456 "This package provides exploratory data analysis methods to summarize,
4457 visualize and describe datasets. The main principal component methods are
4458 available, those with the largest potential in terms of applications:
4459 principal component analysis (PCA) when variables are quantitative,
4460 correspondence analysis (CA) and multiple correspondence analysis (MCA) when
4461 variables are categorical, Multiple Factor Analysis when variables are
4462 structured in groups, etc. and hierarchical cluster analysis.")
4463 (license license:gpl2+)))
4465 (define-public r-factoextra
4467 (name "r-factoextra")
4472 (uri (cran-uri "factoextra" version))
4475 "1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
4476 (build-system r-build-system)
4478 `(("r-abind" ,r-abind)
4479 ("r-cluster" ,r-cluster)
4480 ("r-dendextend" ,r-dendextend)
4481 ("r-factominer" ,r-factominer)
4482 ("r-ggplot2" ,r-ggplot2)
4483 ("r-ggpubr" ,r-ggpubr)
4484 ("r-ggrepel" ,r-ggrepel)
4485 ("r-reshape2" ,r-reshape2)
4486 ("r-tidyr" ,r-tidyr)))
4487 (home-page "http://www.sthda.com/english/rpkgs/factoextra")
4488 (synopsis "Extract and visualize the results of multivariate data analyses")
4490 "This package provides some easy-to-use functions to extract and
4491 visualize the output of multivariate data analyses, including
4492 @code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
4493 Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
4494 Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
4495 @code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
4496 packages. It contains also functions for simplifying some clustering analysis
4497 steps and provides ggplot2-based elegant data visualization.")
4498 (license license:gpl2)))
4500 (define-public r-fansi
4507 (uri (cran-uri "fansi" version))
4510 "135qj7bcc3mwn0vg55hiiadf66lx6zaxvkicfmfw9x0zr7ah2r6x"))))
4511 (build-system r-build-system)
4513 `(("r-knitr" ,r-knitr))) ; for vignettes
4514 (home-page "https://github.com/brodieG/fansi")
4515 (synopsis "ANSI control sequence aware string functions")
4517 "This package provides counterparts to R string manipulation functions
4518 that account for the effects of ANSI text formatting control sequences.")
4519 (license license:gpl2+)))
4521 (define-public r-nbclust
4528 (uri (cran-uri "NbClust" version))
4531 "1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
4532 (properties `((upstream-name . "NbClust")))
4533 (build-system r-build-system)
4534 (home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
4535 (synopsis "Determine the best number of clusters in a data set")
4537 "NbClust provides 30 indexes for determining the optimal number of
4538 clusters in a data set and offers the best clustering scheme from different
4539 results to the user.")
4540 (license license:gpl2)))
4542 (define-public r-hdf5r
4549 (uri (cran-uri "hdf5r" version))
4552 "1s6p4cj909kc635fh5xpl87bqlcdj3dn3r1wk5g40abimk2b0pva"))))
4553 (build-system r-build-system)
4558 `(("r-bit64" ,r-bit64)
4560 (home-page "https://hhoeflin.github.io/hdf5r")
4561 (synopsis "Interface to the HDF5 binary data format")
4563 "HDF5 is a data model, library and file format for storing and managing
4564 large amounts of data. This package provides a nearly feature complete,
4565 object oriented wrapper for the HDF5 API using R6 classes. Additionally,
4566 functionality is added so that HDF5 objects behave very similar to their
4567 corresponding R counterparts.")
4568 (license license:asl2.0)))
4570 (define-public r-itertools
4572 (name "r-itertools")
4577 (uri (cran-uri "itertools" version))
4580 "1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
4581 (build-system r-build-system)
4583 `(("r-iterators" ,r-iterators)))
4584 (home-page "https://cran.r-project.org/web/packages/itertools/")
4585 (synopsis "Iterator tools")
4587 "This package provides various tools for creating iterators, many
4588 patterned after functions in the Python @code{itertools} module, and others
4589 patterned after functions in the snow package.")
4590 (license license:gpl2)))
4592 (define-public r-polynom
4599 (uri (cran-uri "polynom" version))
4602 "1s4xxv5rvpigawknvq27v9vzvs83phfsj5h8mim2lmf5bj950nnk"))))
4603 (build-system r-build-system)
4604 (home-page "https://cran.r-project.org/web/packages/polynom/")
4605 (synopsis "Functions for univariate polynomial manipulations")
4607 "This package provides a collection of functions to implement a class for
4608 univariate polynomial manipulations.")
4609 (license license:gpl2)))
4611 (define-public r-gbrd
4618 (uri (cran-uri "gbRd" version))
4621 "06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
4622 (properties `((upstream-name . "gbRd")))
4623 (build-system r-build-system)
4624 (home-page "https://cran.r-project.org/web/packages/gbRd/")
4625 (synopsis "Utilities for processing Rd objects and files")
4627 "This package provides utilities for processing Rd objects and files.
4628 Extract argument descriptions and other parts of the help pages of
4630 (license license:gpl2+)))
4632 (define-public r-rdpack
4639 (uri (cran-uri "Rdpack" version))
4642 "067w0w6kza0hkzcnx58danl83yfvl9yjacr47mnid2bg856gdd1b"))))
4643 (properties `((upstream-name . "Rdpack")))
4644 (build-system r-build-system)
4646 `(("r-bibtex" ,r-bibtex)
4647 ("r-gbrd" ,r-gbrd)))
4648 (home-page "https://github.com/GeoBosh/Rdpack")
4649 (synopsis "Update and manipulate Rd documentation objects")
4651 "This package provides functions for manipulation of R documentation
4652 objects, including functions @code{reprompt()} and @code{ereprompt()} for
4653 updating Rd documentation for functions, methods and classes; it also includes
4654 Rd macros for citations and import of references from bibtex files for use in
4655 Rd files and roxygen2 comments, as well as many functions for manipulation of
4656 references and Rd files.")
4657 (license license:gpl2+)))
4659 (define-public r-officer
4666 (uri (cran-uri "officer" version))
4669 "14b6ii9h3fi5g8ja929mfhxps9r7x78flqjdy437y9aygkhmiz2i"))))
4670 (build-system r-build-system)
4672 `(("r-base64enc" ,r-base64enc)
4673 ("r-digest" ,r-digest)
4674 ("r-htmltools" ,r-htmltools)
4675 ("r-magrittr" ,r-magrittr)
4681 (home-page "https://davidgohel.github.io/officer")
4682 (synopsis "Manipulation of Word and PowerPoint documents")
4684 "This package provides tools to access and manipulate Word and PowerPoint
4685 documents from R. The package focuses on tabular and graphical reporting from
4686 R; it also provides two functions that let users get document content into
4687 data objects. A set of functions lets add and remove images, tables and
4688 paragraphs of text in new or existing documents. When working with PowerPoint
4689 presentations, slides can be added or removed; shapes inside slides can also
4690 be added or removed. When working with Word documents, a cursor can be used
4691 to help insert or delete content at a specific location in the document.")
4692 (license license:gpl3)))
4694 (define-public r-snakecase
4696 (name "r-snakecase")
4701 (uri (cran-uri "snakecase" version))
4704 "1g6xai53dl24ws0mwhqrkcv583ziaq505cv3z8v5dhjgy98kilyj"))))
4705 (build-system r-build-system)
4707 `(("r-stringi" ,r-stringi)
4708 ("r-stringr" ,r-stringr)))
4709 (home-page "https://github.com/Tazinho/snakecase")
4710 (synopsis "Convert strings into any case")
4712 "This package provides a consistent, flexible and easy to use tool to
4713 parse and convert strings into cases like snake or camel among others.")
4714 (license license:gpl3)))
4716 (define-public r-prediction
4718 (name "r-prediction")
4723 (uri (cran-uri "prediction" version))
4726 "19d7312f5lkqfglfvlgssnvyw7gl161s0xradcry44r1i6qp05j1"))))
4727 (build-system r-build-system)
4729 `(("r-data-table" ,r-data-table)))
4730 (home-page "https://github.com/leeper/prediction")
4731 (synopsis "Tidy, type-safe prediction methods")
4733 "This package provides the @code{prediction()} function, a type-safe
4734 alternative to @code{predict()} that always returns a data frame. The package
4735 currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
4736 from the @code{stats} package, as well as numerous other model classes from
4737 other add-on packages.")
4738 (license license:expat)))
4740 (define-public r-sjlabelled
4742 (name "r-sjlabelled")
4747 (uri (cran-uri "sjlabelled" version))
4750 "0xizj7mrhnbn8kwjgm076si9w68a7lgrx4vj1sbqmv9jx055h8wv"))))
4751 (build-system r-build-system)
4753 `(("r-broom" ,r-broom)
4754 ("r-dplyr" ,r-dplyr)
4755 ("r-haven" ,r-haven)
4756 ("r-magrittr" ,r-magrittr)
4757 ("r-prediction" ,r-prediction)
4758 ("r-purrr" ,r-purrr)
4759 ("r-rlang" ,r-rlang)
4760 ("r-snakecase" ,r-snakecase)
4761 ("r-tibble" ,r-tibble)
4762 ("r-tidyselect" ,r-tidyselect)))
4763 (home-page "https://github.com/strengejacke/sjlabelled")
4764 (synopsis "Labelled data utility functions")
4766 "This package provides a collection of functions dealing with labelled
4767 data, like reading and writing data between R and other statistical software
4768 packages. This includes easy ways to get, set or change value and variable
4769 label attributes, to convert labelled vectors into factors or numeric (and
4770 vice versa), or to deal with multiple declared missing values.")
4771 (license license:gpl3)))
4773 (define-public r-sjmisc
4780 (uri (cran-uri "sjmisc" version))
4783 "11cy09k1d2y5wwqvafqxr01hzk4x68ji2pqlwj7fnpw27i3ap4q4"))))
4784 (build-system r-build-system)
4786 `(("r-broom" ,r-broom)
4787 ("r-crayon" ,r-crayon)
4788 ("r-dplyr" ,r-dplyr)
4789 ("r-haven" ,r-haven)
4790 ("r-magrittr" ,r-magrittr)
4791 ("r-pillar" ,r-pillar)
4792 ("r-purrr" ,r-purrr)
4793 ("r-rlang" ,r-rlang)
4794 ("r-sjlabelled" ,r-sjlabelled)
4795 ("r-stringdist" ,r-stringdist)
4796 ("r-stringr" ,r-stringr)
4797 ("r-tibble" ,r-tibble)
4798 ("r-tidyr" ,r-tidyr)
4799 ("r-tidyselect" ,r-tidyselect)))
4800 (home-page "https://github.com/strengejacke/sjmisc")
4801 (synopsis "Data and variable transformation functions")
4803 "This package is a collection of miscellaneous utility functions,
4804 supporting data transformation tasks like recoding, dichotomizing or grouping
4805 variables, setting and replacing missing values. The data transformation
4806 functions also support labelled data, and all integrate seamlessly into a
4807 tidyverse workflow.")
4808 (license license:gpl3)))
4810 (define-public r-nortest
4817 (uri (cran-uri "nortest" version))
4820 "17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
4821 (build-system r-build-system)
4822 (home-page "https://cran.r-project.org/web/packages/nortest/")
4823 (synopsis "Tests for normality")
4825 "This package provides five omnibus tests for testing the composite
4826 hypothesis of normality.")
4827 (license license:gpl2+)))
4829 (define-public r-writexl
4836 (uri (cran-uri "writexl" version))
4839 "0r2v12dc4zqmr1agp6vbw0fc48i278018684x84psjjqfmnv14cf"))))
4840 (build-system r-build-system)
4841 (inputs `(("zlib" ,zlib)))
4842 (home-page "https://github.com/ropensci/writexl")
4843 (synopsis "Export data frames to xlsx format")
4845 "This package provides a data frame to xlsx exporter based on
4847 (license license:bsd-2)))
4849 (define-public r-biasedurn
4851 (name "r-biasedurn")
4856 (uri (cran-uri "BiasedUrn" version))
4859 "13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
4860 (properties `((upstream-name . "BiasedUrn")))
4861 (build-system r-build-system)
4862 (home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
4863 (synopsis "Biased Urn model distributions")
4865 "This package provides statistical models of biased sampling in the form
4866 of univariate and multivariate noncentral hypergeometric distributions,
4867 including Wallenius' noncentral hypergeometric distribution and Fisher's
4868 noncentral hypergeometric distribution (also called extended hypergeometric
4870 (license license:gpl3)))
4872 (define-public r-goplot
4879 (uri (cran-uri "GOplot" version))
4882 "1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
4883 (properties `((upstream-name . "GOplot")))
4884 (build-system r-build-system)
4886 `(("r-ggdendro" ,r-ggdendro)
4887 ("r-ggplot2" ,r-ggplot2)
4888 ("r-gridextra" ,r-gridextra)
4889 ("r-rcolorbrewer" ,r-rcolorbrewer)))
4890 (home-page "https://github.com/wencke/wencke.github.io")
4891 (synopsis "Visualization of functional analysis data")
4893 "This package provides an implementation of multilayered visualizations
4894 for enhanced graphical representation of functional analysis data. It
4895 combines and integrates omics data derived from expression and functional
4896 annotation enrichment analyses. Its plotting functions have been developed
4897 with an hierarchical structure in mind: starting from a general overview to
4898 identify the most enriched categories (modified bar plot, bubble plot) to a
4899 more detailed one displaying different types of relevant information for the
4900 molecules in a given set of categories (circle plot, chord plot, cluster plot,
4901 Venn diagram, heatmap).")
4902 (license license:gpl2)))
4904 (define-public r-getopt
4911 (uri (cran-uri "getopt" version))
4914 "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x"))))
4915 (build-system r-build-system)
4916 (home-page "https://github.com/trevorld/getopt")
4917 (synopsis "Command-line option processor for R")
4919 "This package is designed to be used with Rscript to write shebang
4920 scripts that accept short and long options. Many users will prefer to
4921 use the packages @code{optparse} or @code{argparse} which add extra
4922 features like automatically generated help options and usage texts,
4923 support for default values, positional argument support, etc.")
4924 (license license:gpl2+)))
4926 (define-public r-findpython
4928 (name "r-findpython")
4933 (uri (cran-uri "findpython" version))
4936 "1y08jk2ffmkf9zpwiz2xymjhfwqvls9vzsnq62v278ghw9d571jl"))))
4937 (build-system r-build-system)
4938 (home-page "https://github.com/trevorld/findpython")
4939 (synopsis "Functions to find an acceptable Python binary")
4941 "This package was designed to find an acceptable Python binary that
4942 matches version and feature constraints.")
4943 (license license:expat)))
4945 ;; This in not the same as "r-argparser"
4946 (define-public r-argparse
4953 (uri (cran-uri "argparse" version))
4956 "0fzrbj87b274vf96azdnsjxk2nf45d5wy58vzmlah4b4h7q4j524"))))
4957 (build-system r-build-system)
4958 (inputs `(("python" ,python)))
4960 `(("r-findpython" ,r-findpython)
4961 ("r-getopt" ,r-getopt)
4962 ("r-jsonlite" ,r-jsonlite)
4963 ("r-proto" ,r-proto)))
4964 (home-page "https://github.com/trevorld/argparse")
4965 (synopsis "Command line optional and positional argument parser")
4967 "This package provides a command line parser to be used with Rscript to
4968 write shebang scripts that gracefully accept positional and optional arguments
4969 and automatically generate usage notices.")
4970 (license license:gpl2+)))
4972 (define-public r-hash
4979 (uri (cran-uri "hash" version))
4982 "0mkx59bmni3b283znvbndnkbar85fzavzdfgmwrhskidsqcz34yz"))))
4983 (build-system r-build-system)
4984 (home-page "https://cran.r-project.org/web/packages/hash/")
4985 (synopsis "Implementation of hash/associated arrays/dictionaries")
4987 "This package implements a data structure similar to hashes in Perl and
4988 dictionaries in Python but with a purposefully R flavor. For objects of
4989 appreciable size, access using hashes outperforms native named lists and
4991 (license license:gpl2+)))
4993 (define-public r-orddom
5000 (uri (cran-uri "orddom" version))
5003 "165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
5004 (build-system r-build-system)
5005 (propagated-inputs `(("r-psych" ,r-psych)))
5006 (home-page "https://cran.r-project.org/web/packages/orddom/")
5007 (synopsis "Ordinal dominance statistics")
5009 "This package provides tools to compute ordinal, statistics and effect
5010 sizes as an alternative to mean comparison: Cliff's delta or success rate
5011 difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
5012 Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
5013 Common Language Effect Size (CLES) or Grissom & Kim's Probability of
5014 Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
5015 comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
5016 Group (Non-)Overlap considerations.")
5017 (license license:gpl2)))
5019 (define-public r-doby
5026 (uri (cran-uri "doBy" version))
5029 "1y02awzid23bxz8hx6j8pxd6i7jaq8pdw3k60rag8y6m69incrw5"))))
5030 (properties `((upstream-name . "doBy")))
5031 (build-system r-build-system)
5033 `(("r-dplyr" ,r-dplyr)
5034 ("r-magrittr" ,r-magrittr)
5036 ("r-matrix" ,r-matrix)
5037 ("r-plyr" ,r-plyr)))
5038 (home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
5039 (synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
5041 "This package contains:
5044 @item facilities for working with grouped data: @code{do}
5045 something to data stratified @code{by} some variables.
5046 @item implementations of least-squares means, general linear contrasts, and
5047 @item miscellaneous other utilities.
5049 (license license:gpl2+)))
5051 (define-public r-refgenome
5053 (name "r-refgenome")
5058 (uri (cran-uri "refGenome" version))
5061 "15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn"))))
5062 (properties `((upstream-name . "refGenome")))
5063 (build-system r-build-system)
5067 ("r-rsqlite" ,r-rsqlite)))
5068 (home-page "https://cran.r-project.org/web/packages/refGenome/")
5070 "Gene and splice site annotation using annotation data from Ensembl and UCSC")
5072 "This package contains functionality for importing and managing of
5073 downloaded genome annotation data from the Ensembl genome browser (European
5074 Bioinformatics Institute) and from the UCSC genome browser (University of
5075 California, Santa Cruz) and annotation routines for genomic positions and
5076 splice site positions.")
5077 (license license:gpl2)))
5079 (define-public r-basix
5086 (uri (cran-uri "BASIX" version))
5089 "18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
5090 (properties `((upstream-name . "BASIX")))
5091 (build-system r-build-system)
5092 (home-page "https://cran.r-project.org/web/packages/BASIX/")
5093 (synopsis "Efficient C/C++ toolset for R")
5095 "BASIX provides some efficient C/C++ implementations of native R
5096 procedures to speed up calculations in R.")
5097 (license license:gpl2)))
5099 (define-public r-blockfest
5101 (name "r-blockfest")
5106 (uri (cran-uri "BlockFeST" version))
5109 "0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
5110 (properties `((upstream-name . "BlockFeST")))
5111 (build-system r-build-system)
5112 (propagated-inputs `(("r-basix" ,r-basix)))
5113 (home-page "https://cran.r-project.org/web/packages/BlockFeST/")
5114 (synopsis "Bayesian calculation of region-specific fixation index")
5116 "This package provides an R implementation of an extension of the
5117 BayeScan software for codominant markers, adding the option to group
5118 individual SNPs into pre-defined blocks. A typical application of this new
5119 approach is the identification of genomic regions, genes, or gene sets
5120 containing one or more SNPs that evolved under directional selection.")
5121 (license license:gpl2)))
5123 (define-public r-proc
5130 (uri (cran-uri "pROC" version))
5133 "05ad69a6fxy9k903cw3h4q59ch2jv6qfg9yjdbw3cgiiazcafrlj"))))
5134 (properties `((upstream-name . "pROC")))
5135 (build-system r-build-system)
5137 `(("r-ggplot2" ,r-ggplot2)
5139 ("r-rcpp" ,r-rcpp)))
5140 (home-page "http://expasy.org/tools/pROC/")
5141 (synopsis "Display and analyze ROC curves")
5143 "This package provides tools for visualizing, smoothing and comparing
5144 receiver operating characteristic (ROC curves). The area under the
5145 curve (AUC) can be compared with statistical tests based on U-statistics or
5146 bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
5147 (license license:gpl3+)))
5149 (define-public r-rootsolve
5151 (name "r-rootsolve")
5156 (uri (cran-uri "rootSolve" version))
5159 "08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8"))))
5160 (properties `((upstream-name . "rootSolve")))
5161 (build-system r-build-system)
5162 (native-inputs `(("gfortran" ,gfortran)))
5163 (home-page "https://cran.r-project.org/web/packages/rootSolve/")
5164 (synopsis "Tools for the analysis of ordinary differential equations")
5166 "This package provides routines to find the root of nonlinear functions,
5167 and to perform steady-state and equilibrium analysis of @dfn{ordinary
5168 differential equations} (ODE). It includes routines that:
5171 @item generate gradient and jacobian matrices (full and banded),
5172 @item find roots of non-linear equations by the Newton-Raphson method,
5173 @item estimate steady-state conditions of a system of (differential) equations
5174 in full, banded or sparse form, using the Newton-Raphson method, or by
5175 dynamically running,
5176 @item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
5177 and 3-D partial differential equations, that have been converted to ordinary
5178 differential equations by numerical differencing (using the method-of-lines
5181 (license license:gpl2+)))
5183 (define-public r-abcanalysis
5185 (name "r-abcanalysis")
5190 (uri (cran-uri "ABCanalysis" version))
5192 (base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
5193 (properties `((upstream-name . "ABCanalysis")))
5194 (build-system r-build-system)
5195 (propagated-inputs `(("r-plotrix" ,r-plotrix)))
5196 (home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
5197 (synopsis "Computed ABC Analysis")
5199 "Multivariate data sets often differ in several factors or derived statistical
5200 parameters, which have to be selected for a valid interpretation. Basing this
5201 selection on traditional statistical limits leads occasionally to the perception
5202 of losing information from a data set. This package provides tools to calculate
5203 these limits on the basis of the mathematical properties of the distribution of
5204 the analyzed items.")
5205 (license license:gpl3)))
5207 (define-public r-slam
5214 (uri (cran-uri "slam" version))
5216 (base32 "0hy4qzngcgafxxr6ld7n9a9wy979ji998gpcc32vidwyab66dj5h"))))
5217 (build-system r-build-system)
5218 (home-page "https://cran.r-project.org/web/packages/slam/")
5219 (synopsis "Sparse lightweight arrays and matrices")
5221 "This package contains data structures and algorithms for sparse arrays and matrices,
5222 based on index arrays and simple triplet representations, respectively.")
5223 (license license:gpl2)))
5225 (define-public r-manipulatewidget
5227 (name "r-manipulatewidget")
5232 (uri (cran-uri "manipulateWidget" version))
5234 (base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
5236 `((upstream-name . "manipulateWidget")))
5237 (build-system r-build-system)
5239 `(("r-base64enc" ,r-base64enc)
5240 ("r-codetools" ,r-codetools)
5241 ("r-htmltools" ,r-htmltools)
5242 ("r-htmlwidgets" ,r-htmlwidgets)
5243 ("r-knitr" ,r-knitr)
5244 ("r-miniui" ,r-miniui)
5245 ("r-shiny" ,r-shiny)
5246 ("r-webshot" ,r-webshot)))
5247 (home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
5248 (synopsis "Add even more interactivity to interactive charts")
5250 "This package lets you create in just a few lines of R code a nice user interface to
5251 modify the data or the graphical parameters of one or multiple interactive
5252 charts. It is useful to quickly explore visually some data or for package
5253 developers to generate user interfaces easy to maintain.")
5254 (license license:gpl2+)))
5263 (uri (cran-uri "A3" version))
5265 (base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
5266 (properties `((upstream-name . "A3")))
5267 (build-system r-build-system)
5269 `(("r-pbapply" ,r-pbapply)
5270 ("r-xtable" ,r-xtable)))
5271 (home-page "https://cran.r-project.org/web/packages/A3/")
5272 (synopsis "Error metrics for predictive models")
5274 "This package supplies tools for tabulating and analyzing the results of predictive
5275 models. The methods employed are applicable to virtually any predictive model
5276 and make comparisons between different methodologies straightforward.")
5277 (license license:gpl2+)))
5279 (define-public r-infotheo
5286 (uri (cran-uri "infotheo" version))
5289 "18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
5290 (build-system r-build-system)
5291 (home-page "http://homepage.meyerp.com/software")
5292 (synopsis "Information-theoretic measures")
5294 "This package implements various measures of information theory based on
5295 several entropy estimators.")
5296 (license license:gpl3+)))
5298 (define-public r-abcoptim
5305 (uri (cran-uri "ABCoptim" version))
5307 (base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
5308 (properties `((upstream-name . "ABCoptim")))
5309 (build-system r-build-system)
5310 (propagated-inputs `(("r-rcpp" ,r-rcpp)))
5311 (home-page "https://github.com/gvegayon/ABCoptim/")
5312 (synopsis "Optimization of Artificial Bee Colony algorithm")
5314 "Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
5315 Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
5316 simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
5317 algorithms, and uses only common control parameters such as colony size and
5318 maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
5319 colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
5320 This version is a work-in-progress and is written in R code.")
5321 (license license:expat)))