1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
4 ;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
5 ;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
7 ;;; This file is part of GNU Guix.
9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
10 ;;; under the terms of the GNU General Public License as published by
11 ;;; the Free Software Foundation; either version 3 of the License, or (at
12 ;;; your option) any later version.
14 ;;; GNU Guix is distributed in the hope that it will be useful, but
15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 ;;; GNU General Public License for more details.
19 ;;; You should have received a copy of the GNU General Public License
20 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
22 (define-module (gnu packages cran)
23 #:use-module ((guix licenses) #:prefix license:)
24 #:use-module (guix packages)
25 #:use-module (guix download)
26 #:use-module (guix utils)
27 #:use-module (guix build-system r)
28 #:use-module (gnu packages gcc)
29 #:use-module (gnu packages machine-learning)
30 #:use-module (gnu packages maths)
31 #:use-module (gnu packages mpi)
32 #:use-module (gnu packages perl)
33 #:use-module (gnu packages statistics)
34 #:use-module (gnu packages web))
43 (uri (cran-uri "ape" version))
46 "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
47 (build-system r-build-system)
49 `(("r-lattice" ,r-lattice)
52 (home-page "http://ape-package.ird.fr/")
53 (synopsis "Analyses of phylogenetics and evolution")
55 "This package provides functions for reading, writing, plotting, and
56 manipulating phylogenetic trees, analyses of comparative data in a
57 phylogenetic framework, ancestral character analyses, analyses of
58 diversification and macroevolution, computing distances from DNA sequences,
59 and several other tools.")
60 (license license:gpl2+)))
62 (define-public r-colorspace
69 (uri (cran-uri "colorspace" version))
71 (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
72 (build-system r-build-system)
73 (home-page "https://cran.r-project.org/web/packages/colorspace")
74 (synopsis "Color space manipulation")
76 "This package carries out a mapping between assorted color spaces
77 including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
78 CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
79 colors are provided.")
80 (license license:bsd-3)))
89 (uri (cran-uri "glue" version))
92 "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr"))))
93 (build-system r-build-system)
94 (home-page "https://github.com/tidyverse/glue")
95 (synopsis "Interpreted string literals")
97 "This package provides an implementation of interpreted string literals,
98 inspired by Python's Literal String Interpolation (PEP-0498) and
99 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
100 (license license:expat)))
102 (define-public r-plogr
109 (uri (cran-uri "plogr" version))
112 "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92"))))
113 (build-system r-build-system)
114 (home-page "https://github.com/krlmlr/plogr")
115 (synopsis "R bindings for the plog C++ logging library")
117 "This package provides the header files for a stripped-down version of
118 the plog header-only C++ logging library, and a method to log to R's standard
120 (license license:expat)))
122 (define-public r-rcpp
129 (uri (cran-uri "Rcpp" version))
131 (base32 "1pnv6sl4vdn69ygmgrb1b3gsigfdcfb56wnzikic93l8gkvdsvxv"))))
132 (build-system r-build-system)
133 (home-page "http://www.rcpp.org")
134 (synopsis "Seamless R and C++ integration")
136 "The Rcpp package provides R functions as well as C++ classes which offer
137 a seamless integration of R and C++. Many R data types and objects can be
138 mapped back and forth to C++ equivalents which facilitates both writing of new
139 code as well as easier integration of third-party libraries. Documentation
140 about Rcpp is provided by several vignettes included in this package, via the
141 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
142 and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
143 'citation(\"Rcpp\")' for details on these last two.")
144 (license license:gpl2+)))
146 (define-public r-bindr
153 (uri (cran-uri "bindr" version))
156 "0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc"))))
157 (build-system r-build-system)
158 (home-page "https://github.com/krlmlr/bindr")
159 (synopsis "Parametrized active bindings")
161 "This package provides a simple interface for creating active bindings
162 where the bound function accepts additional arguments.")
163 (license license:expat)))
165 (define-public r-bindrcpp
172 (uri (cran-uri "bindrcpp" version))
175 "0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh"))))
176 (build-system r-build-system)
178 `(("r-bindr" ,r-bindr)
181 (home-page "https://github.com/krlmlr/bindrcpp")
182 (synopsis "Rcpp interface to active bindings")
184 "This package provides an easy way to fill an environment with active
185 bindings that call a C++ function.")
186 (license license:expat)))
195 (uri (cran-uri "AUC" version))
198 "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
199 (properties `((upstream-name . "AUC")))
200 (build-system r-build-system)
201 (home-page "https://cran.r-project.org/web/packages/AUC")
202 (synopsis "Compute the area under the curve of selected measures")
204 "This package includes functions to compute the area under the curve of
205 selected measures: the area under the sensitivity curve (AUSEC), the area
206 under the specificity curve (AUSPC), the area under the accuracy
207 curve (AUACC), and the area under the receiver operating characteristic
208 curve (AUROC). The curves can also be visualized. Support for partial areas
210 (license license:gpl2+)))
212 (define-public r-calibrate
219 (uri (cran-uri "calibrate" version))
222 "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
223 (build-system r-build-system)
225 `(("r-mass" ,r-mass)))
226 (home-page "https://cran.r-project.org/web/packages/calibrate")
227 (synopsis "Calibration of scatterplot and biplot axes")
229 "This is a package for drawing calibrated scales with tick marks
230 on (non-orthogonal) variable vectors in scatterplots and biplots.")
231 (license license:gpl2)))
233 (define-public r-shape
240 (uri (cran-uri "shape" version))
243 "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
244 (build-system r-build-system)
245 (home-page "https://cran.r-project.org/web/packages/shape")
246 (synopsis "Functions for plotting graphical shapes")
248 "This package provides functions for plotting graphical shapes such as
249 ellipses, circles, cylinders, arrows, ...")
250 (license license:gpl3+)))
252 (define-public r-globaloptions
254 (name "r-globaloptions")
259 (uri (cran-uri "GlobalOptions" version))
262 "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0"))))
263 (properties `((upstream-name . "GlobalOptions")))
264 (build-system r-build-system)
265 (home-page "https://github.com/jokergoo/GlobalOptions")
266 (synopsis "Generate functions to get or set global options")
268 "This package provides more controls on the option values such as
269 validation and filtering on the values, making options invisible or private.")
270 (license license:gpl2+)))
272 (define-public r-circlize
279 (uri (cran-uri "circlize" version))
282 "0pg947gkryygikfbv6admx8gsg02b6g219j6a1sdnqij2908yxna"))))
283 (build-system r-build-system)
285 `(("r-colorspace" ,r-colorspace)
286 ("r-globaloptions" ,r-globaloptions)
287 ("r-shape" ,r-shape)))
288 (home-page "https://github.com/jokergoo/circlize")
289 (synopsis "Circular visualization")
291 "Circular layout is an efficient way to visualise huge amounts of
292 information. This package provides an implementation of circular layout
293 generation in R as well as an enhancement of available software. Its
294 flexibility is based on the usage of low-level graphics functions such that
295 self-defined high-level graphics can be easily implemented by users for
296 specific purposes. Together with the seamless connection between the powerful
297 computational and visual environment in R, it gives users more convenience and
298 freedom to design figures for better understanding complex patterns behind
299 multi-dimensional data.")
300 (license license:gpl2+)))
302 (define-public r-powerlaw
309 (uri (cran-uri "poweRlaw" version))
312 "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m"))))
313 (properties `((upstream-name . "poweRlaw")))
314 (build-system r-build-system)
316 `(("r-vgam" ,r-vgam)))
317 (home-page "https://github.com/csgillespie/poweRlaw")
318 (synopsis "Tools for the analysis of heavy tailed distributions")
320 "This package provides an implementation of maximum likelihood estimators
321 for a variety of heavy tailed distributions, including both the discrete and
322 continuous power law distributions. Additionally, a goodness-of-fit based
323 approach is used to estimate the lower cut-off for the scaling region.")
324 ;; Any of these GPL versions.
325 (license (list license:gpl2 license:gpl3))))
327 (define-public r-compare
334 (uri (cran-uri "compare" version))
337 "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
338 (build-system r-build-system)
339 (home-page "https://cran.r-project.org/web/packages/compare")
340 (synopsis "Comparing objects for differences")
342 "This package provides functions to compare a model object to a
343 comparison object. If the objects are not identical, the functions can be
344 instructed to explore various modifications of the objects (e.g., sorting
345 rows, dropping names) to see if the modified versions are identical.")
346 (license license:gpl2+)))
348 (define-public r-dendextend
350 (name "r-dendextend")
355 (uri (cran-uri "dendextend" version))
358 "1krvqadnnh53xx5ql7bwzxaif6a317jzbs1m00gnc6jnj03rfl5d"))))
359 (build-system r-build-system)
362 ("r-ggplot2" ,r-ggplot2)
363 ("r-magrittr" ,r-magrittr)
364 ("r-viridis" ,r-viridis)
365 ("r-whisker" ,r-whisker)))
366 (home-page "https://cran.r-project.org/web/packages/dendextend")
367 (synopsis "Extending 'dendrogram' functionality in R")
369 "This package offers a set of functions for extending @code{dendrogram}
370 objects in R, letting you visualize and compare trees of hierarchical
371 clusterings. You can adjust a tree's graphical parameters (the color, size,
372 type, etc of its branches, nodes and labels) and visually and statistically
373 compare different dendrograms to one another.")
374 ;; Any of these versions
375 (license (list license:gpl2 license:gpl3))))
377 (define-public r-getoptlong
379 (name "r-getoptlong")
384 (uri (cran-uri "GetoptLong" version))
387 "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm"))))
388 (properties `((upstream-name . "GetoptLong")))
389 (build-system r-build-system)
393 `(("r-globaloptions" ,r-globaloptions)
394 ("r-rjson" ,r-rjson)))
395 (home-page "https://github.com/jokergoo/GetoptLong")
396 (synopsis "Parsing command-line arguments and variable interpolation")
398 "This is yet another command-line argument parser which wraps the
399 powerful Perl module @code{Getopt::Long} and with some adaptation for easier
400 use in R. It also provides a simple way for variable interpolation in R.")
401 (license license:gpl2+)))
403 (define-public r-fastmatch
410 (uri (cran-uri "fastmatch" version))
413 "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
414 (build-system r-build-system)
415 (home-page "http://www.rforge.net/fastmatch")
416 (synopsis "Fast match function")
418 "This package provides a fast @code{match} replacement for cases that
419 require repeated look-ups. It is slightly faster that R's built-in
420 @code{match} function on first match against a table, but extremely fast on
421 any subsequent lookup as it keeps the hash table in memory.")
422 (license license:gpl2)))
431 (uri (cran-uri "ff" version))
434 "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb"))))
435 (build-system r-build-system)
436 (propagated-inputs `(("r-bit" ,r-bit)))
437 (home-page "http://ff.r-forge.r-project.org/")
438 (synopsis "Memory-efficient storage of large data on disk and access functions")
440 "This package provides data structures that are stored on disk but
441 behave (almost) as if they were in RAM by transparently mapping only a section
443 ;; error Architecture not supported.
444 (supported-systems (delete "aarch64-linux" %supported-systems))
445 (license license:gpl2)))
447 (define-public r-ffbase
454 (uri (cran-uri "ffbase" version))
457 "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5"))))
458 (build-system r-build-system)
461 ("r-fastmatch" ,r-fastmatch)
463 (home-page "http://github.com/edwindj/ffbase")
464 (synopsis "Basic statistical functions for package 'ff'")
466 "This package extends the out of memory vectors of @code{ff} with
467 statistical functions and other utilities to ease their usage.")
468 (license license:gpl3)))
470 (define-public r-prettyunits
472 (name "r-prettyunits")
477 (uri (cran-uri "prettyunits" version))
480 "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
481 (build-system r-build-system)
483 `(("r-assertthat" ,r-assertthat)
484 ("r-magrittr" ,r-magrittr)))
485 (home-page "https://github.com/gaborcsardi/prettyunits")
486 (synopsis "Pretty, human readable formatting of quantities")
488 "This package provides tools for pretty, human readable formatting of
490 (license license:expat)))
492 (define-public r-reshape
499 (uri (cran-uri "reshape" version))
502 "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig"))))
503 (build-system r-build-system)
507 (home-page "http://had.co.nz/reshape")
508 (synopsis "Flexibly reshape data")
510 "Flexibly restructure and aggregate data using just two functions:
511 @code{melt} and @code{cast}. This package provides them.")
512 (license license:expat)))
514 (define-public r-progress
521 (uri (cran-uri "progress" version))
524 "1fxakchfjr5vj59s9sxynd7crpz97xj42438rmkhkf3rjpyspx59"))))
525 (build-system r-build-system)
527 `(("r-prettyunits" ,r-prettyunits)
529 (home-page "https://github.com/gaborcsardi/progress")
530 (synopsis "Terminal progress bars")
532 "This package provides configurable progress bars. They may include
533 percentage, elapsed time, and/or the estimated completion time. They work in
534 terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The
535 package also provides a C++ API, that works with or without Rcpp.")
536 (license license:expat)))
538 (define-public r-ggally
545 (uri (cran-uri "GGally" version))
548 "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l"))))
549 (properties `((upstream-name . "GGally")))
550 (build-system r-build-system)
552 `(("r-ggplot2" ,r-ggplot2)
553 ("r-gtable" ,r-gtable)
555 ("r-progress" ,r-progress)
556 ("r-rcolorbrewer" ,r-rcolorbrewer)
557 ("r-reshape" ,r-reshape)))
558 (home-page "https://ggobi.github.io/ggally")
559 (synopsis "Extension to ggplot2")
561 "The R package ggplot2 is a plotting system based on the grammar of
562 graphics. GGally extends ggplot2 by adding several functions to reduce the
563 complexity of combining geometric objects with transformed data. Some of
564 these functions include a pairwise plot matrix, a two group pairwise plot
565 matrix, a parallel coordinates plot, a survival plot, and several functions to
567 (license license:gpl2+)))
569 (define-public r-proxy
576 (uri (cran-uri "proxy" version))
579 "1vih8gsfzv97h5c8ixd1qjnn02i7fzla2p9fdj2wpisqhx0p0xv0"))))
580 (build-system r-build-system)
581 (home-page "https://cran.r-project.org/web/packages/proxy")
582 (synopsis "Distance and similarity measures")
584 "This package provides an extensible framework for the efficient
585 calculation of auto- and cross-proximities, along with implementations of the
587 (license license:gpl2)))
596 (uri (cran-uri "sp" version))
599 "0q04yfgyjannsrzl0ppwcv0simrxrrbx2iz5mzaafc5x38zf0q3d"))))
600 (build-system r-build-system)
602 `(("r-lattice" ,r-lattice)))
603 (home-page "https://cran.r-project.org/web/packages/sp")
604 (synopsis "Classes and methods for spatial data")
606 "This package provides classes and methods for spatial data; the classes
607 document where the spatial location information resides, for 2D or 3D data.
608 Utility functions are provided, e.g. for plotting data as maps, spatial
609 selection, as well as methods for retrieving coordinates, for subsetting,
610 print, summary, etc.")
611 (license license:gpl2+)))
613 (define-public r-rmtstat
620 (uri (cran-uri "RMTstat" version))
623 "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
624 (properties `((upstream-name . "RMTstat")))
625 (build-system r-build-system)
626 (home-page "https://cran.r-project.org/web/packages/RMTstat")
627 (synopsis "Distributions, statistics and tests derived from random matrix theory")
629 "This package provides functions for working with the Tracy-Widom laws
630 and other distributions related to the eigenvalues of large Wishart
632 (license license:bsd-3)))
634 (define-public r-rmpi
640 (uri (cran-uri "Rmpi" version))
643 "0fm6z049aaq2c9xagm8n64d9560hg9d8hyb0m359fii672nhkz6q"))))
644 (properties `((upstream-name . "Rmpi")))
645 (build-system r-build-system)
647 `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")))
649 `(("openmpi" ,openmpi)))
650 (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
651 (synopsis "R interface to message-passing interface (MPI)")
653 "This package provides an interface (wrapper) to MPI APIs. It also
654 provides an interactive R manager and worker environment.")
655 (license license:gpl2+)))
657 (define-public r-lmoments
664 (uri (cran-uri "Lmoments" version))
667 "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79"))))
668 (properties `((upstream-name . "Lmoments")))
669 (build-system r-build-system)
670 (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
671 (synopsis "L-moments and quantile mixtures")
673 "This package contains functions to estimate L-moments and trimmed
674 L-moments from the data. It also contains functions to estimate the
675 parameters of the normal polynomial quantile mixture and the Cauchy polynomial
676 quantile mixture from L-moments and trimmed L-moments.")
677 (license license:gpl2)))
679 (define-public r-distillery
681 (name "r-distillery")
686 (uri (cran-uri "distillery" version))
689 "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix"))))
690 (build-system r-build-system)
691 (home-page "http://www.ral.ucar.edu/staff/ericg")
692 (synopsis "Functions for confidence intervals and object information")
694 "This package provides some very simple method functions for confidence
695 interval calculation and to distill pertinent information from a potentially
696 complex object; primarily used in common with the packages extRemes and
698 (license license:gpl2+)))
700 (define-public r-extremes
707 (uri (cran-uri "extRemes" version))
710 "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm"))))
711 (properties `((upstream-name . "extRemes")))
712 (build-system r-build-system)
715 ("r-distillery" ,r-distillery)
716 ("r-lmoments" ,r-lmoments)))
717 (home-page "http://www.assessment.ucar.edu/toolkit/")
718 (synopsis "Extreme value analysis")
720 "ExtRemes is a suite of functions for carrying out analyses on the
721 extreme values of a process of interest; be they block maxima over long blocks
722 or excesses over a high threshold.")
723 (license license:gpl2+)))
725 (define-public r-lmtest
732 (uri (cran-uri "lmtest" version))
735 "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g"))))
736 (build-system r-build-system)
740 `(("gfortran" ,gfortran)))
741 (home-page "https://cran.r-project.org/web/packages/lmtest")
742 (synopsis "Testing linear regression models")
744 "This package provides a collection of tests, data sets, and examples for
745 diagnostic checking in linear regression models. Furthermore, some generic
746 tools for inference in parametric models are provided.")
747 ;; Either version is okay
748 (license (list license:gpl2 license:gpl3))))
750 (define-public r-inline
756 (uri (cran-uri "inline" version))
759 "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
760 (build-system r-build-system)
761 (home-page "https://cran.r-project.org/web/packages/inline")
762 (synopsis "Functions to inline C, C++, Fortran function calls from R")
764 "This package provides functionality to dynamically define R functions
765 and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
766 @code{.Call} calling conventions.")
767 ;; Any version of the LGPL.
768 (license license:lgpl3+)))
770 (define-public r-bbmle
777 (uri (cran-uri "bbmle" version))
780 "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
781 (build-system r-build-system)
783 `(("r-lattice" ,r-lattice)
785 ("r-numderiv" ,r-numderiv)))
786 (home-page "https://cran.r-project.org/web/packages/bbmle")
787 (synopsis "Tools for General Maximum Likelihood Estimation")
789 "This package provides methods and functions for fitting maximum
790 likelihood models in R. This package modifies and extends the @code{mle}
791 classes in the @code{stats4} package.")
792 ;; Any version of the GPL
793 (license license:gpl2+)))
795 (define-public r-emdbook
802 (uri (cran-uri "emdbook" version))
805 "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69"))))
806 (build-system r-build-system)
808 `(("r-bbmle" ,r-bbmle)
810 ("r-lattice" ,r-lattice)
814 (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
815 (synopsis "Support functions and data for \"Ecological Models and Data\"")
817 "This package provides auxiliary functions and data sets for \"Ecological
818 Models and Data\", a book presenting maximum likelihood estimation and related
819 topics for ecologists (ISBN 978-0-691-12522-0).")
821 (license (list license:gpl2 license:gpl3))))
823 (define-public r-lpsolve
830 (uri (cran-uri "lpSolve" version))
833 "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
834 (properties `((upstream-name . "lpSolve")))
835 (build-system r-build-system)
836 (home-page "https://cran.r-project.org/web/packages/lpSolve")
837 (synopsis "R interface to Lp_solve to solve linear/integer programs")
839 "Lp_solve is software for solving linear, integer and mixed integer
840 programs. This implementation supplies a \"wrapper\" function in C and some R
841 functions that solve general linear/integer problems, assignment problems, and
842 transportation problems.")
843 (license license:lgpl2.0)))
845 (define-public r-limsolve
852 (uri (cran-uri "limSolve" version))
855 "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
856 (properties `((upstream-name . "limSolve")))
857 (build-system r-build-system)
859 `(("r-lpsolve" ,r-lpsolve)
861 ("r-quadprog" ,r-quadprog)))
862 (native-inputs `(("gfortran" ,gfortran)))
863 (home-page "https://cran.r-project.org/web/packages/limSolve")
864 (synopsis "Solving linear inverse models")
866 "This package provides functions that:
869 @item find the minimum/maximum of a linear or quadratic function,
870 @item sample an underdetermined or overdetermined system,
871 @item solve a linear system Ax=B for the unknown x.
874 It includes banded and tridiagonal linear systems. The package calls Fortran
875 functions from LINPACK.")
877 (license (list license:gpl2+ license:gpl3+))))
879 (define-public r-fitdistrplus
881 (name "r-fitdistrplus")
886 (uri (cran-uri "fitdistrplus" version))
889 "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6"))))
890 (build-system r-build-system)
893 ("r-survival" ,r-survival)))
894 (home-page "http://riskassessment.r-forge.r-project.org")
895 (synopsis "Fitting a parametric distribution from data")
897 "This package extends the @code{fitdistr} function of the MASS package
898 with several functions to help the fit of a parametric distribution to
899 non-censored or censored data. Censored data may contain left-censored,
900 right-censored and interval-censored values, with several lower and upper
901 bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
902 provides moment matching (MME), quantile matching (QME) and maximum
903 goodness-of-fit estimation (MGE) methods (available only for non-censored
904 data). Weighted versions of MLE, MME and QME are available.")
905 (license license:gpl2+)))
907 (define-public r-energy
914 (uri (cran-uri "energy" version))
917 "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p"))))
918 (build-system r-build-system)
922 (home-page "https://cran.r-project.org/web/packages/energy")
923 (synopsis "Multivariate inference via the energy of data")
925 "This package provides e-statistics (energy) tests and statistics for
926 multivariate and univariate inference, including distance correlation,
927 one-sample, two-sample, and multi-sample tests for comparing multivariate
928 distributions, are implemented. Measuring and testing multivariate
929 independence based on distance correlation, partial distance correlation,
930 multivariate goodness-of-fit tests, clustering based on energy distance,
931 testing for multivariate normality, distance components (disco) for
932 non-parametric analysis of structured data, and other energy
933 statistics/methods are implemented.")
934 (license license:gpl2+)))
936 (define-public r-suppdists
943 (uri (cran-uri "SuppDists" version))
946 "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
947 (properties `((upstream-name . "SuppDists")))
948 (build-system r-build-system)
949 (home-page "https://cran.r-project.org/web/packages/SuppDists")
950 (synopsis "Supplementary distributions")
952 "This package provides ten distributions supplementing those built into
953 R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
954 Spearman's rho, maximum F ratio, the Pearson product moment correlation
955 coefficient, Johnson distributions, normal scores and generalized
956 hypergeometric distributions. In addition two random number generators of
957 George Marsaglia are included.")
958 (license license:gpl2+)))
960 (define-public r-ksamples
967 (uri (cran-uri "kSamples" version))
970 "0f19rjngk0lg6s8c6h5l55qpxp8sl4vxj3kpi05cizzncny9b9bj"))))
971 (properties `((upstream-name . "kSamples")))
972 (build-system r-build-system)
974 `(("r-suppdists" ,r-suppdists)))
975 (home-page "https://cran.r-project.org/web/packages/kSamples")
976 (synopsis "K-Sample rank tests and their combinations")
978 "This package provides tools to compares k samples using the
979 Anderson-Darling test, Kruskal-Wallis type tests with different rank score
980 criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
981 test. It computes asymptotic, simulated or (limited) exact P-values, all
982 valid under randomization, with or without ties, or conditionally under random
983 sampling from populations, given the observed tie pattern. Except for Steel's
984 test and the JT test it also combines these tests across several blocks of
986 (license license:gpl2+)))
988 (define-public r-cvst
995 (uri (cran-uri "CVST" version))
998 "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2"))))
999 (properties `((upstream-name . "CVST")))
1000 (build-system r-build-system)
1002 `(("r-kernlab" ,r-kernlab)
1003 ("r-matrix" ,r-matrix)))
1004 (home-page "https://cran.r-project.org/web/packages/CVST")
1005 (synopsis "Fast cross-validation via sequential testing")
1007 "This package implements the fast cross-validation via sequential
1008 testing (CVST) procedure. CVST is an improved cross-validation procedure
1009 which uses non-parametric testing coupled with sequential analysis to
1010 determine the best parameter set on linearly increasing subsets of the data.
1011 Additionally to the CVST the package contains an implementation of the
1012 ordinary k-fold cross-validation with a flexible and powerful set of helper
1013 objects and methods to handle the overall model selection process. The
1014 implementations of the Cochran's Q test with permutations and the sequential
1015 testing framework of Wald are generic and can therefore also be used in other
1017 (license license:gpl2+)))
1019 (define-public r-squarem
1022 (version "2017.10-1")
1026 (uri (cran-uri "SQUAREM" version))
1029 "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
1030 (properties `((upstream-name . "SQUAREM")))
1031 (build-system r-build-system)
1032 (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
1033 (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
1035 "This package provides algorithms for accelerating the convergence of
1036 slow, monotone sequences from smooth, contraction mapping such as the EM
1037 algorithm. It can be used to accelerate any smooth, linearly convergent
1038 acceleration scheme. A tutorial style introduction to this package is
1039 available in a vignette.")
1040 (license license:gpl2+)))
1042 (define-public r-lava
1049 (uri (cran-uri "lava" version))
1052 "02xf5d968raz9gnq5ywy04wz29xpdyca1hm79vbbg1mcxvzdl1dz"))))
1053 (build-system r-build-system)
1055 `(("r-numderiv" ,r-numderiv)
1056 ("r-squarem" ,r-squarem)
1057 ("r-survival" ,r-survival)))
1058 (home-page "https://github.com/kkholst/lava")
1059 (synopsis "Latent variable models")
1061 "This package provides tools for the estimation and simulation of latent
1063 (license license:gpl3)))
1065 (define-public r-drr
1072 (uri (cran-uri "DRR" version))
1075 "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
1076 (properties `((upstream-name . "DRR")))
1077 (build-system r-build-system)
1079 `(("r-cvst" ,r-cvst)
1080 ("r-kernlab" ,r-kernlab)
1081 ("r-matrix" ,r-matrix)))
1082 (home-page "https://cran.r-project.org/web/packages/DRR")
1083 (synopsis "Dimensionality reduction via regression")
1085 "This package provides an implementation of dimensionality reduction via
1086 regression using Kernel Ridge Regression.")
1087 (license license:gpl3)))
1089 (define-public r-prodlim
1096 (uri (cran-uri "prodlim" version))
1099 "0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz"))))
1100 (build-system r-build-system)
1102 `(("r-kernsmooth" ,r-kernsmooth)
1105 ("r-survival" ,r-survival)))
1106 (home-page "https://cran.r-project.org/web/packages/prodlim")
1107 (synopsis "Product-limit estimation for censored event history analysis")
1109 "This package provides a fast and user-friendly implementation of
1110 nonparametric estimators for censored event history (survival) analysis with
1111 the Kaplan-Meier and Aalen-Johansen methods.")
1112 (license license:gpl2+)))
1114 (define-public r-dimred
1121 (uri (cran-uri "dimRed" version))
1124 "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v"))))
1125 (properties `((upstream-name . "dimRed")))
1126 (build-system r-build-system)
1127 (propagated-inputs `(("r-drr" ,r-drr)))
1128 (home-page "https://github.com/gdkrmr/dimRed")
1129 (synopsis "Framework for dimensionality reduction")
1131 "This package provides a collection of dimensionality reduction
1132 techniques from R packages and provides a common interface for calling the
1134 (license license:gpl3)))
1136 (define-public r-timedate
1139 (version "3043.102")
1143 (uri (cran-uri "timeDate" version))
1146 "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
1147 (properties `((upstream-name . "timeDate")))
1148 (build-system r-build-system)
1149 (home-page "https://www.rmetrics.org")
1150 (synopsis "Chronological and calendar objects")
1152 "This package provides an environment for teaching \"Financial
1153 Engineering and Computational Finance\" and for managing chronological and
1155 (license license:gpl2+)))
1157 (define-public r-ddalpha
1164 (uri (cran-uri "ddalpha" version))
1167 "13w8ir5rd80rka4mq343zd4wn93vfw870lzfqrd3cxgwb1bwcw7y"))))
1168 (build-system r-build-system)
1171 ("r-class" ,r-class)
1174 ("r-robustbase" ,r-robustbase)
1175 ("r-sfsmisc" ,r-sfsmisc)))
1177 `(("gfortran" ,gfortran)))
1178 (home-page "https://cran.r-project.org/web/packages/ddalpha")
1179 (synopsis "Depth-Based classification and calculation of data depth")
1181 "This package contains procedures for depth-based supervised learning,
1182 which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
1183 Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
1184 statistical depth function to a compact low-dimensional space, where the final
1185 classification is done. It also offers an extension to functional data and
1186 routines for calculating certain notions of statistical depth functions. 50
1187 multivariate and 5 functional classification problems are included.")
1188 (license license:gpl2)))
1190 (define-public r-gower
1197 (uri (cran-uri "gower" version))
1200 "1mbrj1lam3jfbby2j32shmmj5cn09zx3rkxbamq7q8sdg39b54gb"))))
1201 (build-system r-build-system)
1203 `(("r-knitr" ,r-knitr)))
1204 (home-page "https://github.com/markvanderloo/gower")
1205 (synopsis "Gower's distance")
1207 "This package provides tools to compute Gower's distance (or similarity)
1208 coefficient between records, and to compute the top-n matches between records.
1209 Core algorithms are executed in parallel on systems supporting OpenMP.")
1210 (license license:gpl3)))
1212 (define-public r-rcpproll
1219 (uri (cran-uri "RcppRoll" version))
1222 "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi"))))
1223 (properties `((upstream-name . "RcppRoll")))
1224 (build-system r-build-system)
1226 `(("r-rcpp" ,r-rcpp)))
1227 (home-page "https://cran.r-project.org/web/packages/RcppRoll")
1228 (synopsis "Efficient rolling and windowed operations")
1230 "This package provides fast and efficient routines for common rolling /
1231 windowed operations. Routines for the efficient computation of windowed mean,
1232 median, sum, product, minimum, maximum, standard deviation and variance are
1234 (license license:gpl2+)))
1236 (define-public r-ipred
1243 (uri (cran-uri "ipred" version))
1246 "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq"))))
1247 (build-system r-build-system)
1249 `(("r-class" ,r-class)
1252 ("r-prodlim" ,r-prodlim)
1253 ("r-rpart" ,r-rpart)
1254 ("r-survival" ,r-survival)))
1255 (home-page "https://cran.r-project.org/web/packages/ipred")
1256 (synopsis "Improved predictors")
1258 "This package provides improved predictive models by indirect
1259 classification and bagging for classification, regression and survival
1260 problems as well as resampling based estimators of prediction error.")
1261 (license license:gpl2+)))
1263 (define-public r-psych
1270 (uri (cran-uri "psych" version))
1273 "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
1274 (build-system r-build-system)
1276 `(("r-foreign" ,r-foreign)
1277 ("r-lattice" ,r-lattice)
1278 ("r-mnormt" ,r-mnormt)
1279 ("r-nlme" ,r-nlme)))
1280 (home-page "https://cran.r-project.org/web/packages/psych/")
1281 (synopsis "Procedures for psychological, psychometric, and personality research")
1283 "This package provides a general purpose toolbox for personality,
1284 psychometric theory and experimental psychology. Functions are primarily for
1285 multivariate analysis and scale construction using factor analysis, principal
1286 component analysis, cluster analysis and reliability analysis, although others
1287 provide basic descriptive statistics. Item Response Theory is done using
1288 factor analysis of tetrachoric and polychoric correlations. Functions for
1289 analyzing data at multiple levels include within and between group statistics,
1290 including correlations and factor analysis. Functions for simulating and
1291 testing particular item and test structures are included. Several functions
1292 serve as a useful front end for structural equation modeling. Graphical
1293 displays of path diagrams, factor analysis and structural equation models are
1294 created using basic graphics.")
1295 (license license:gpl2+)))
1297 (define-public r-broom
1304 (uri (cran-uri "broom" version))
1307 "119pc2jnxvm13cvd77c7d14p3bn68f4jm310vj3yfck40101n9if"))))
1308 (build-system r-build-system)
1310 `(("r-dplyr" ,r-dplyr)
1313 ("r-psych" ,r-psych)
1314 ("r-reshape2" ,r-reshape2)
1315 ("r-stringr" ,r-stringr)
1316 ("r-tidyr" ,r-tidyr)))
1317 (home-page "http://github.com/tidyverse/broom")
1318 (synopsis "Convert statistical analysis objects into tidy data frames")
1320 "This package provides tools to convert statistical analysis objects from
1321 R into tidy data frames, so that they can more easily be combined, reshaped
1322 and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
1323 @code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
1324 summarizes a model's statistical findings such as coefficients of a
1325 regression; @code{augment}, which adds columns to the original data such as
1326 predictions, residuals and cluster assignments; and @code{glance}, which
1327 provides a one-row summary of model-level statistics.")
1328 (license license:expat)))
1330 (define-public r-recipes
1337 (uri (cran-uri "recipes" version))
1340 "1car3a3mqn87pz049cbgkaayz86970mvkapk6al2k7jjw76306l9"))))
1341 (build-system r-build-system)
1343 `(("r-broom" ,r-broom)
1344 ("r-ddalpha" ,r-ddalpha)
1345 ("r-dimred" ,r-dimred)
1346 ("r-dplyr" ,r-dplyr)
1347 ("r-gower" ,r-gower)
1348 ("r-ipred" ,r-ipred)
1349 ("r-lubridate" ,r-lubridate)
1350 ("r-magrittr" ,r-magrittr)
1351 ("r-matrix" ,r-matrix)
1352 ("r-purrr" ,r-purrr)
1353 ("r-rcpproll" ,r-rcpproll)
1354 ("r-rlang" ,r-rlang)
1355 ("r-tibble" ,r-tibble)
1356 ("r-tidyselect" ,r-tidyselect)
1357 ("r-timedate" ,r-timedate)))
1358 (home-page "https://github.com/topepo/recipes")
1359 (synopsis "Preprocessing tools to create design matrices")
1361 "Recipes is an extensible framework to create and preprocess design
1362 matrices. Recipes consist of one or more data manipulation and analysis
1363 \"steps\". Statistical parameters for the steps can be estimated from an
1364 initial data set and then applied to other data sets. The resulting design
1365 matrices can then be used as inputs into statistical or machine learning
1367 (license license:gpl2)))
1369 (define-public r-pdist
1376 (uri (cran-uri "pdist" version))
1379 "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
1380 (build-system r-build-system)
1381 (home-page "https://github.com/jeffwong/pdist")
1382 (synopsis "Partitioned distance function")
1384 "Pdist computes the euclidean distance between rows of a matrix X and
1385 rows of another matrix Y. Previously, this could be done by binding the two
1386 matrices together and calling @code{dist}, but this creates unnecessary
1387 computation by computing the distances between a row of X and another row of
1388 X, and likewise for Y. Pdist strictly computes distances across the two
1389 matrices, not within the same matrix, making computations significantly faster
1390 for certain use cases.")
1391 (license license:gpl3+)))
1393 (define-public r-ggrepel
1400 (uri (cran-uri "ggrepel" version))
1403 "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618"))))
1404 (build-system r-build-system)
1406 `(("r-ggplot2" ,r-ggplot2)
1408 ("r-scales" ,r-scales)))
1409 (home-page "http://github.com/slowkow/ggrepel")
1410 (synopsis "Repulsive text and label geometries for ggplot2")
1412 "This package provides text and label geometries for ggplot2 that help to
1413 avoid overlapping text labels. Labels repel away from each other and away
1414 from the data points.")
1415 (license license:gpl3)))
1417 (define-public r-corrplot
1424 (uri (cran-uri "corrplot" version))
1427 "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
1428 (build-system r-build-system)
1429 (home-page "https://github.com/taiyun/corrplot")
1430 (synopsis "Visualization of a correlation matrix")
1432 "This package provides a graphical display of a correlation matrix or
1433 general matrix. It also contains some algorithms to do matrix reordering. In
1434 addition, corrplot is good at details, including choosing color, text labels,
1435 color labels, layout, etc.")
1436 ;; Any version of the GPL
1437 (license license:gpl2+)))
1439 (define-public r-stringdist
1441 (name "r-stringdist")
1446 (uri (cran-uri "stringdist" version))
1449 "0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci"))))
1450 (build-system r-build-system)
1451 (home-page "https://github.com/markvanderloo/stringdist")
1452 (synopsis "Approximate string matching and string distance functions")
1454 "This package implements an approximate string matching version of R's
1455 native @code{match} function. It can calculate various string distances based
1456 on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
1457 qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
1458 Jaro-Winkler). An implementation of soundex is provided as well. Distances
1459 can be computed between character vectors while taking proper care of encoding
1460 or between integer vectors representing generic sequences.")
1461 (license license:gpl3+)))
1463 (define-public r-mice
1470 (uri (cran-uri "mice" version))
1473 "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax"))))
1474 (build-system r-build-system)
1476 `(("r-lattice" ,r-lattice)
1480 ("r-rpart" ,r-rpart)
1481 ("r-survival" ,r-survival)))
1482 (home-page "https://cran.r-project.org/web/packages/mice/")
1483 (synopsis "Multivariate imputation by chained equations")
1485 "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
1486 implemented by the MICE algorithm as described in @url{Van Buuren and
1487 Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
1488 variable has its own imputation model. Built-in imputation models are
1489 provided for continuous data (predictive mean matching, normal), binary
1490 data (logistic regression), unordered categorical data (polytomous logistic
1491 regression) and ordered categorical data (proportional odds). MICE can also
1492 impute continuous two-level data (normal model, pan, second-level variables).
1493 Passive imputation can be used to maintain consistency between variables.
1494 Various diagnostic plots are available to inspect the quality of the
1496 ;; Any of these two versions.
1497 (license (list license:gpl2 license:gpl3))))
1499 (define-public r-truncnorm
1501 (name "r-truncnorm")
1506 (uri (cran-uri "truncnorm" version))
1509 "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
1510 (build-system r-build-system)
1511 (home-page "https://cran.r-project.org/web/packages/truncnorm/")
1512 (synopsis "Truncated normal distribution")
1513 (description "This package provides functions for the truncated normal
1514 distribution with mean equal to @code{mean} and standard deviation equal to
1515 @code{sd}. It includes density, distribution, quantile, and expected value
1516 functions, as well as a random generation function.")
1517 (license license:gpl2)))
1519 (define-public r-rsolnp
1526 (uri (cran-uri "Rsolnp" version))
1529 "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
1530 (properties `((upstream-name . "Rsolnp")))
1531 (build-system r-build-system)
1533 `(("r-truncnorm" ,r-truncnorm)))
1534 (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
1535 (synopsis "General non-linear optimization")
1536 (description "The Rsolnp package implements a general non-linear augmented
1537 Lagrange multiplier method solver, a @dfn{sequential quadratic
1538 programming} (SQP) based solver).")
1539 ;; Any version of the GPL.
1540 (license license:gpl2+)))
1542 (define-public r-hardyweinberg
1544 (name "r-hardyweinberg")
1549 (uri (cran-uri "HardyWeinberg" version))
1552 "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz"))))
1553 (properties `((upstream-name . "HardyWeinberg")))
1554 (build-system r-build-system)
1556 `(("r-mice" ,r-mice)
1558 ("r-rsolnp" ,r-rsolnp)))
1559 (home-page "https://cran.r-project.org/package=HardyWeinberg")
1560 (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
1562 "This package contains tools for exploring Hardy-Weinberg equilibrium for
1563 diallelic genetic marker data. All classical tests (chi-square, exact,
1564 likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
1565 included in the package, as well as functions for power computation and for
1566 the simulation of marker data under equilibrium and disequilibrium. Routines
1567 for dealing with markers on the X-chromosome are included. Functions for
1568 testing equilibrium in the presence of missing data by using multiple
1569 imputation are also provided. Implements several graphics for exploring the
1570 equilibrium status of a large set of diallelic markers: ternary plots with
1571 acceptance regions, log-ratio plots and Q-Q plots.")
1572 (license license:gpl2+)))
1581 (uri (cran-uri "sm" version))
1584 "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9"))))
1585 (build-system r-build-system)
1586 (native-inputs `(("gfortran" ,gfortran)))
1587 (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
1588 (synopsis "Smoothing methods for nonparametric regression and density estimation")
1590 "This is software accompanying the book 'Applied Smoothing Techniques for
1591 Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
1592 University Press. It provides smoothing methods for nonparametric regression
1593 and density estimation")
1594 (license license:gpl2+)))
1596 (define-public r-vioplot
1603 (uri (cran-uri "vioplot" version))
1606 "16wkb26kv6qr34hv5zgqmgq6zzgysg9i78pvy2c097lr60v087v0"))))
1607 (build-system r-build-system)
1608 (propagated-inputs `(("r-sm" ,r-sm)))
1609 (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
1610 (synopsis "Violin plot")
1612 "This package provides a violin plot, which is a combination of a box
1613 plot and a kernel density plot.")
1614 (license license:bsd-3)))
1616 (define-public r-rsofia
1622 ;; This package has been removed from CRAN, so we can
1623 ;; only fetch it from the archives.
1624 (uri (string-append "https://cran.r-project.org/src/"
1625 "contrib/Archive/RSofia/RSofia_"
1629 "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
1630 (properties `((upstream-name . "RSofia")))
1631 (build-system r-build-system)
1633 `(("r-rcpp" ,r-rcpp)))
1634 (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
1635 (synopsis "Port of sofia-ml to R")
1636 (description "This package is a port of sofia-ml to R. Sofia-ml is a
1637 suite of fast incremental algorithms for machine learning that can be used for
1638 training models for classification or ranking.")
1639 (license license:asl2.0)))
1641 (define-public r-xts
1648 (uri (cran-uri "xts" version))
1651 "1j9ddh9v9081zrqlpylsk13fldilhjdyaw6r6pa726fhgnrsf8a2"))))
1652 (build-system r-build-system)
1653 (propagated-inputs `(("r-zoo" ,r-zoo)))
1654 (native-inputs `(("gfortran" ,gfortran)))
1655 (home-page "https://github.com/joshuaulrich/xts")
1656 (synopsis "Extensible time series")
1658 "This package provides for uniform handling of R's different time-based
1659 data classes by extending @code{zoo}, maximizing native format information
1660 preservation and allowing for user-level customization and extension, while
1661 simplifying cross-class interoperability.")
1662 (license license:gpl2+)))
1664 (define-public r-performanceanalytics
1666 (name "r-performanceanalytics")
1671 (uri (cran-uri "PerformanceAnalytics" version))
1674 "01bgm57z079g6r505w3bj293zkbd49fwa8sg55z87vizwavipml6"))))
1676 `((upstream-name . "PerformanceAnalytics")))
1677 (build-system r-build-system)
1679 `(("r-quadprog" ,r-quadprog)
1682 (home-page "http://r-forge.r-project.org/projects/returnanalytics/")
1683 (synopsis "Econometric tools for performance and risk analysis")
1684 (description "This is a collection of econometric functions for
1685 performance and risk analysis. This package aims to aid practitioners and
1686 researchers in utilizing the latest research in analysis of non-normal return
1687 streams. In general, it is most tested on return (rather than price) data on
1688 a regular scale, but most functions will work with irregular return data as
1689 well, and increasing numbers of functions will work with P&L or price data
1691 ;; Either version may be picked.
1692 (license (list license:gpl2 license:gpl3))))
1694 (define-public r-laeken
1701 (uri (cran-uri "laeken" version))
1704 "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6"))))
1705 (build-system r-build-system)
1707 `(("r-boot" ,r-boot)
1708 ("r-mass" ,r-mass)))
1709 (home-page "https://cran.r-project.org/web/packages/laeken/")
1710 (synopsis "Estimation of indicators on social exclusion and poverty")
1711 (description "This package provides tools for the estimation of indicators
1712 on social exclusion and poverty, as well as an implementation of Pareto tail
1713 modeling for empirical income distributions.")
1714 (license license:gpl2+)))
1716 (define-public r-vcd
1723 (uri (cran-uri "vcd" version))
1726 "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
1727 (build-system r-build-system)
1729 `(("r-colorspace" ,r-colorspace)
1730 ("r-lmtest" ,r-lmtest)
1731 ("r-mass" ,r-mass)))
1732 (home-page "https://cran.r-project.org/web/packages/vcd/")
1733 (synopsis "Visualizing categorical data")
1734 (description "This package provides visualization techniques, data sets,
1735 summary and inference procedures aimed particularly at categorical data.
1736 Special emphasis is given to highly extensible grid graphics. The package was
1737 originally inspired by the book \"Visualizing Categorical Data\" by Michael
1738 Friendly and is now the main support package for a new book, \"Discrete Data
1739 Analysis with R\" by Michael Friendly and David Meyer (2015).")
1740 (license license:gpl2)))
1742 (define-public r-ica
1749 (uri (cran-uri "ica" version))
1752 "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq"))))
1753 (build-system r-build-system)
1754 (home-page "https://cran.r-project.org/web/packages/ica/")
1755 (synopsis "Independent component analysis")
1756 (description "This package provides tools for @dfn{Independent Component
1757 Analysis} (ICA) using various algorithms: FastICA,
1758 Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
1759 of Eigenmatrices} (JADE).")
1760 (license license:gpl2+)))
1762 (define-public r-dtw
1769 (uri (cran-uri "dtw" version))
1772 "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr"))))
1773 (build-system r-build-system)
1774 (propagated-inputs `(("r-proxy" ,r-proxy)))
1775 (home-page "http://dtw.r-forge.r-project.org/")
1776 (synopsis "Dynamic Time Warping Algorithms")
1777 (description "This package provides a comprehensive implementation of
1778 @dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
1779 optimal (least cumulative distance) alignment between points of two time
1780 series. Common DTW variants covered include local (slope) and global (window)
1781 constraints, subsequence matches, arbitrary distance definitions,
1782 normalizations, minimum variance matching, and so on.")
1783 (license license:gpl2+)))
1785 (define-public r-sdmtools
1792 (uri (cran-uri "SDMTools" version))
1795 "1kacrpamshv7wz83yn45sfbw4m9c44xrrngzcklnwx8gcxx2knm6"))))
1796 (properties `((upstream-name . "SDMTools")))
1797 (build-system r-build-system)
1798 (propagated-inputs `(("r-r-utils" ,r-r-utils)))
1799 (home-page "http://www.rforge.net/SDMTools/")
1800 (synopsis "Species distribution modelling tools")
1801 (description "This packages provides a set of tools for post processing
1802 the outcomes of species distribution modeling exercises. It includes novel
1803 methods for comparing models and tracking changes in distributions through
1804 time. It further includes methods for visualizing outcomes, selecting
1805 thresholds, calculating measures of accuracy and landscape fragmentation
1807 (license license:gpl3+)))
1809 (define-public r-scatterplot3d
1811 (name "r-scatterplot3d")
1816 (uri (cran-uri "scatterplot3d" version))
1819 "0ababcj87kx7860mica9y2ydlhskxmgj9n46crx036cila512jc2"))))
1820 (build-system r-build-system)
1821 (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
1822 (synopsis "3D scatter plot")
1823 (description "This package provides an implementation of scatter plots for
1824 plotting. a three dimensional point cloud.")
1825 (license license:gpl2)))
1827 (define-public r-ggridges
1834 (uri (cran-uri "ggridges" version))
1837 "0kfa3icqdalqdg1klxjrhfl7if35d3wnsiyl86bprw5dyqyh3lh3"))))
1838 (build-system r-build-system)
1840 `(("r-ggplot2" ,r-ggplot2)
1842 ("r-scales" ,r-scales)))
1843 (home-page "https://github.com/clauswilke/ggridges")
1844 (synopsis "Ridgeline plots in ggplot2")
1846 "Ridgeline plots provide a convenient way of visualizing changes in
1847 distributions over time or space. This package enables the creation of such
1848 plots in @code{ggplot2}.")
1849 (license license:gpl2)))
1851 (define-public r-ggjoy
1858 (uri (cran-uri "ggjoy" version))
1861 "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb"))))
1862 (build-system r-build-system)
1864 `(("r-ggplot2" ,r-ggplot2)
1865 ("r-ggridges" ,r-ggridges)))
1866 (home-page "https://github.com/clauswilke/ggjoy")
1867 (synopsis "Joyplots in ggplot2")
1868 (description "Joyplots provide a convenient way of visualizing changes in
1869 distributions over time or space. This package enables the creation of such
1870 plots in @code{ggplot2}.")
1871 (license license:gpl2)))
1873 (define-public r-cli
1880 (uri (cran-uri "cli" version))
1883 "07as3dr7vwx02p3qgzlmxz1dlrd3x3lysrzp222ip9jcjpydp8wg"))))
1884 (build-system r-build-system)
1886 `(("r-assertthat" ,r-assertthat)
1887 ("r-crayon" ,r-crayon)))
1888 (home-page "https://github.com/r-lib/cli#readme")
1889 (synopsis "Helpers for developing command line interfaces")
1890 (description "This package provides a suite of tools designed to build
1891 attractive command line interfaces (CLIs). It includes tools for drawing
1892 rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
1893 (license license:expat)))
1895 (define-public r-argparser
1897 (name "r-argparser")
1902 (uri (cran-uri "argparser" version))
1905 "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
1906 (build-system r-build-system)
1907 (home-page "https://bitbucket.org/djhshih/argparser")
1908 (synopsis "Command-line argument parser")
1910 "This package provides a cross-platform command-line argument parser
1911 written purely in R with no external dependencies. It is useful with the
1912 Rscript front-end and facilitates turning an R script into an executable
1914 (license license:gpl3+)))
1916 (define-public r-debugme
1923 (uri (cran-uri "debugme" version))
1926 "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
1927 (build-system r-build-system)
1928 (propagated-inputs `(("r-crayon" ,r-crayon)))
1929 (home-page "https://github.com/r-lib/debugme#readme")
1930 (synopsis "Debug R packages")
1932 "This package allows the user to specify debug messages as special string
1933 constants, and control debugging of packages via environment variables.")
1934 (license license:expat)))
1936 (define-public r-processx
1943 (uri (cran-uri "processx" version))
1946 "0yw23lp9xjvbpswzghkmjiayw7p19hbvmgv58k3i6b8g5nav4qcg"))))
1947 (build-system r-build-system)
1949 `(("r-assertthat" ,r-assertthat)
1950 ("r-crayon" ,r-crayon)
1951 ("r-debugme" ,r-debugme)
1953 (home-page "https://github.com/r-lib/processx3")
1954 (synopsis "Execute and control system processes")
1956 "This package provides portable tools to run system processes in the
1957 background. It can check if a background process is running; wait on a
1958 background process to finish; get the exit status of finished processes; kill
1959 background processes and their children; restart processes. It can read the
1960 standard output and error of the processes, using non-blocking connections.
1961 @code{processx} can poll a process for standard output or error, with a
1962 timeout. It can also poll several processes at once.")
1963 (license license:expat)))
1965 (define-public r-tsp
1972 (uri (cran-uri "TSP" version))
1975 "03xxfr5kk4zhzpb1q1pwncdp0dhchm9b48wzhvvxn2dxf3mnby2w"))))
1976 (properties `((upstream-name . "TSP")))
1977 (build-system r-build-system)
1978 (propagated-inputs `(("r-foreach" ,r-foreach)))
1979 (home-page "https://cran.r-project.org/web/packages/TSP/")
1980 (synopsis "Traveling salesperson problem (TSP)")
1981 (description "This package provides basic infrastructure and some
1982 algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
1983 traveling salesman problem).")
1984 (license license:gpl3)))
1986 (define-public r-qap
1993 (uri (cran-uri "qap" version))
1996 "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
1997 (build-system r-build-system)
1998 (native-inputs `(("gfortran" ,gfortran)))
1999 (home-page "http://cran.r-project.org/web/packages/qap/")
2000 (synopsis "Heuristics for the quadratic assignment problem (QAP)")
2001 (description "This package implements heuristics for the @dfn{quadratic
2002 assignment problem} (QAP). Currently only a simulated annealing heuristic is
2004 (license license:gpl3)))
2006 (define-public r-gclus
2013 (uri (cran-uri "gclus" version))
2016 "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn"))))
2017 (build-system r-build-system)
2018 (propagated-inputs `(("r-cluster" ,r-cluster)))
2019 (home-page "http://cran.r-project.org/web/packages/gclus/")
2020 (synopsis "Clustering graphics")
2021 (description "This package orders panels in scatterplot matrices and
2022 parallel coordinate displays by some merit index. It contains various indices
2023 of merit, ordering functions, and enhanced versions of @code{pairs} and
2024 @code{parcoord} which color panels according to their merit level.")
2025 (license license:gpl2+)))
2027 (define-public r-webshot
2034 (uri (cran-uri "webshot" version))
2037 "07r71zzmggp4jf92x4ws4wg6v1x98vaj01lsar85bnb30n5vx8gh"))))
2038 (build-system r-build-system)
2040 `(("r-jsonlite" ,r-jsonlite)
2041 ("r-magrittr" ,r-magrittr)
2042 ("r-processx" ,r-processx)
2043 ("r-withr" ,r-withr)))
2044 (home-page "https://github.com/wch/webshot/")
2045 (synopsis "Take screenshots of web pages")
2047 "Webshot makes it easy to take screenshots of web pages from within R.
2048 It can also run Shiny applications locally and take screenshots of the
2049 application; and it can render and screenshot static as well as interactive R
2050 Markdown documents.")
2051 (license license:gpl2)))
2053 (define-public r-seriation
2055 (name "r-seriation")
2060 (uri (cran-uri "seriation" version))
2063 "1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92"))))
2064 (build-system r-build-system)
2066 `(("r-cluster" ,r-cluster)
2067 ("r-colorspace" ,r-colorspace)
2068 ("r-dendextend" ,r-dendextend)
2069 ("r-gclus" ,r-gclus)
2070 ("r-gplots" ,r-gplots)
2073 ("r-registry" ,r-registry)
2075 (native-inputs `(("gfortran" ,gfortran)))
2076 (home-page "http://s2.smu.edu/IDA/seriation/")
2077 (synopsis "Infrastructure for ordering objects using seriation")
2079 "This package provides infrastructure for seriation with an
2080 implementation of several seriation/sequencing techniques to reorder matrices,
2081 dissimilarity matrices, and dendrograms. It also provides (optimally)
2082 reordered heatmaps, color images and clustering visualizations like
2083 dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
2085 (license license:gpl3)))
2087 (define-public r-heatmaply
2089 (name "r-heatmaply")
2094 (uri (cran-uri "heatmaply" version))
2097 "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc"))))
2098 (build-system r-build-system)
2100 `(("r-assertthat" ,r-assertthat)
2101 ("r-colorspace" ,r-colorspace)
2102 ("r-dendextend" ,r-dendextend)
2103 ("r-ggplot2" ,r-ggplot2)
2104 ("r-gplots" ,r-gplots)
2105 ("r-htmlwidgets" ,r-htmlwidgets)
2106 ("r-magrittr" ,r-magrittr)
2107 ("r-plotly" ,r-plotly)
2108 ("r-rcolorbrewer" ,r-rcolorbrewer)
2109 ("r-reshape2" ,r-reshape2)
2110 ("r-scales" ,r-scales)
2111 ("r-seriation" ,r-seriation)
2112 ("r-viridis" ,r-viridis)
2113 ("r-webshot" ,r-webshot)))
2114 (home-page "https://cran.r-project.org/package=heatmaply")
2115 (synopsis "Interactive cluster heat maps using plotly")
2116 (description "Heatmaps are used in many fields for visualizing
2117 observations, correlations, missing values patterns, and more. Interactive
2118 heatmaps allow the inspection of specific value by hovering the mouse over a
2119 cell, as well as zooming into a region of the heatmap by dragging a rectangle
2120 around the relevant area. This work is based on the @code{ggplot2} and
2121 @code{plotly.js} engine. It produces similar heatmaps as @code{heatmap.2} or
2122 @code{d3heatmap}, with the advantage of speed, the ability to zoom from the
2123 dendrogram panes, and the placing of factor variables in the sides of the
2125 (license (list license:gpl2 license:gpl3))))
2127 (define-public r-xfun
2134 (uri (cran-uri "xfun" version))
2137 "1sm51gmwgw876d6d1q8smxmfgfh6zsnykfx8qp8z6jmh0fvd89pj"))))
2138 (build-system r-build-system)
2139 (home-page "https://github.com/yihui/xfun")
2140 (synopsis "Miscellaneous functions")
2142 "This package provides miscellaneous functions commonly used in other
2143 packages maintained by Yihui Xie.")
2144 (license license:expat)))
2146 (define-public r-utf8
2153 (uri (cran-uri "utf8" version))
2156 "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3"))))
2157 (build-system r-build-system)
2158 (home-page "https://github.com/patperry/r-utf8")
2159 (synopsis "Unicode text processing")
2161 "This package provides tools to process and print UTF-8 encoded
2162 international text (Unicode). Input, validate, normalize, encode, format, and
2164 (license license:asl2.0)))
2166 (define-public r-pillar
2173 (uri (cran-uri "pillar" version))
2176 "1ryd7m570y6q3w71wd5dz042b3d0dv24g2rbkw1kdx0n6jj9gsbd"))))
2177 (build-system r-build-system)
2180 ("r-crayon" ,r-crayon)
2181 ("r-rlang" ,r-rlang)
2182 ("r-utf8" ,r-utf8)))
2183 (home-page "https://github.com/r-lib/pillar")
2184 (synopsis "Coloured formatting for columns")
2186 "This package provides a @code{pillar} generic designed for formatting
2187 columns of data using the full range of colours provided by modern
2189 (license license:gpl3)))
2191 (define-public r-uuid
2198 (uri (cran-uri "uuid" version))
2201 "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
2202 (build-system r-build-system)
2203 (home-page "http://www.rforge.net/uuid")
2204 (synopsis "Tools for generating and handling of UUIDs")
2206 "This package provides tools for generating and handling of
2207 @dfn{Universally Unique Identifiers} (UUIDs).")
2208 (license license:expat)))
2210 (define-public r-tinytex
2217 (uri (cran-uri "tinytex" version))
2220 "0mhxlr4709mca9jshnah5i7yjyy6k12s933619p7p9c8nbqj39cn"))))
2221 (build-system r-build-system)
2222 (home-page "https://github.com/yihui/tinytex")
2223 (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
2225 "This package provides helper functions to install and maintain the LaTeX
2226 distribution named TinyTeX, a lightweight, cross-platform, portable, and
2227 easy-to-maintain version of TeX Live. This package also contains helper
2228 functions to compile LaTeX documents, and install missing LaTeX packages
2230 (license license:expat)))
2232 (define-public r-metap
2239 (uri (cran-uri "metap" version))
2242 "06ny9zkilawdy0s8yiwhnygs3yppw89bbyf76zgdavykbzscz5lh"))))
2243 (build-system r-build-system)
2245 `(("r-lattice" ,r-lattice)))
2246 (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
2247 (synopsis "Meta-analysis of significance values")
2249 "The canonical way to perform meta-analysis involves using effect sizes.
2250 When they are not available this package provides a number of methods for
2251 meta-analysis of significance values including the methods of Edgington,
2252 Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
2253 published results; and a routine for graphical display.")
2254 (license license:gpl2)))
2256 (define-public r-network
2263 (uri (cran-uri "network" version))
2266 "11sg330xb7gcnl3f6lwhhjdabz6mk43828i2np635pqw4s4yl13s"))))
2267 (build-system r-build-system)
2268 (home-page "http://statnet.org/")
2269 (synopsis "Classes for relational data")
2271 "This package provides tools to create and modify network objects. The
2272 @code{network} class can represent a range of relational data types, and
2273 supports arbitrary vertex/edge/graph attributes.")
2274 (license license:gpl2+)))
2276 (define-public r-statnet-common
2278 (name "r-statnet-common")
2283 (uri (cran-uri "statnet.common" version))
2286 "0yw6l5b4qv0jqlg4zyczas7m12a5pyqghs6ydxy2f6v6vxkijvi0"))))
2288 `((upstream-name . "statnet.common")))
2289 (build-system r-build-system)
2290 (home-page "http://www.statnet.org")
2291 (synopsis "R scripts and utilities used by the Statnet software")
2292 (description "This package provides non-statistical utilities used by the
2293 software developed by the Statnet Project.")
2294 (license license:gpl3)))
2296 (define-public r-sna
2303 (uri (cran-uri "sna" version))
2306 "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
2307 (build-system r-build-system)
2309 `(("r-network" ,r-network)
2310 ("r-statnet-common" ,r-statnet-common)))
2311 (home-page "http://www.statnet.org")
2312 (synopsis "Tools for social network analysis")
2314 "This package provides a range of tools for social network analysis,
2315 including node and graph-level indices, structural distance and covariance
2316 methods, structural equivalence detection, network regression, random graph
2317 generation, and 2D/3D network visualization.")
2318 (license license:gpl2+)))
2320 (define-public r-ttr
2327 (uri (cran-uri "TTR" version))
2330 "07r62ngyzjl4aszdxnr3n6bnbcgcap32yhd430jsilicg8n06di1"))))
2331 (properties `((upstream-name . "TTR")))
2332 (build-system r-build-system)
2334 `(("r-curl" ,r-curl)
2337 (native-inputs `(("gfortran" ,gfortran)))
2338 (home-page "https://github.com/joshuaulrich/TTR")
2339 (synopsis "Technical trading rules")
2341 "This package provides functions and data to construct technical trading
2343 (license license:gpl2)))
2345 (define-public r-leaps
2352 (uri (cran-uri "leaps" version))
2355 "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
2356 (build-system r-build-system)
2357 (native-inputs `(("gfortran" ,gfortran)))
2358 (home-page "http://cran.r-project.org/web/packages/leaps/")
2359 (synopsis "Regression subset selection")
2361 "This package provides tools for regression subset selection, including
2362 exhaustive search.")
2363 (license license:gpl2+)))
2365 (define-public r-splus2r
2372 (uri (cran-uri "splus2R" version))
2375 "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
2376 (properties `((upstream-name . "splus2R")))
2377 (build-system r-build-system)
2378 (native-inputs `(("gfortran" ,gfortran)))
2379 (home-page "http://cran.r-project.org/web/packages/splus2R/")
2380 (synopsis "Supplemental S-PLUS functionality in R")
2382 "Currently there are many functions in S-PLUS that are missing in R. To
2383 facilitate the conversion of S-PLUS packages to R packages, this package
2384 provides some missing S-PLUS functionality in R.")
2385 (license license:gpl2)))
2387 (define-public r-ifultools
2389 (name "r-ifultools")
2394 (uri (cran-uri "ifultools" version))
2397 "0pv2msaa1rmj8csxdclzi2jwg9pfdvh87blj9j3xa3myisglq092"))))
2398 (build-system r-build-system)
2400 `(("r-mass" ,r-mass)
2401 ("r-splus2r" ,r-splus2r)))
2402 (home-page "http://cran.r-project.org/web/packages/ifultools/")
2403 (synopsis "Insightful research tools")
2404 (description "This package provides C code used by the wmtsa, fractal, and
2406 (license license:gpl2)))
2408 (define-public r-sapa
2415 (uri (cran-uri "sapa" version))
2418 "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
2419 (build-system r-build-system)
2421 `(("r-ifultools" ,r-ifultools)
2422 ("r-splus2r" ,r-splus2r)))
2423 (home-page "http://cran.r-project.org/web/packages/sapa/")
2424 (synopsis "Spectral analysis for physical applications")
2425 (description "This package provides software for the book Spectral
2426 Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
2427 Cambridge University Press, 1993.")
2428 (license license:gpl2)))
2430 (define-public r-quantmod
2437 (uri (cran-uri "quantmod" version))
2440 "0y7gh0k1s10vdsfch8777avbhf99mc9crikvx7ahqrw0j631vmhq"))))
2441 (build-system r-build-system)
2443 `(("r-curl" ,r-curl)
2447 (home-page "http://cran.r-project.org/web/packages/quantmod/")
2448 (synopsis "Quantitative financial modelling framework")
2449 (description "This package provides a quantitative financial modelling
2450 framework to allow users to specify, build, trade, and analyse quantitative
2451 financial trading strategies.")
2452 (license license:gpl3)))
2454 (define-public r-tseries
2461 (uri (cran-uri "tseries" version))
2464 "1yjxhj7l1p2przczl6frggfcr5iwda9lbcsmh0y75gbbbps14yf2"))))
2465 (build-system r-build-system)
2467 `(("r-quadprog" ,r-quadprog)
2468 ("r-quantmod" ,r-quantmod)
2471 `(("gfortran" ,gfortran)))
2472 (home-page "http://cran.r-project.org/web/packages/tseries/")
2473 (synopsis "Time series analysis and computational finance")
2475 "This package provides functions relating to time series analysis and
2476 computational finance.")
2477 (license license:gpl2)))
2479 (define-public r-wmtsa
2486 (uri (cran-uri "wmtsa" version))
2489 "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
2490 (build-system r-build-system)
2492 `(("r-ifultools" ,r-ifultools)
2494 ("r-splus2r" ,r-splus2r)))
2495 (home-page "http://cran.r-project.org/web/packages/wmtsa/")
2496 (synopsis "Wavelet methods for time series analysis")
2498 "This package provides software to accompany the book \"Wavelet Methods
2499 for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
2500 University Press, 2000.")
2501 (license license:gpl2)))
2503 (define-public r-tsa
2510 (uri (cran-uri "TSA" version))
2513 "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx"))))
2514 (properties `((upstream-name . "TSA")))
2515 (build-system r-build-system)
2517 `(("r-leaps" ,r-leaps)
2518 ("r-locfit" ,r-locfit)
2520 ("r-tseries" ,r-tseries)))
2521 (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
2522 (synopsis "Time series analysis")
2524 "This package contains R functions and datasets detailed in the book
2525 \"Time Series Analysis with Applications in R (second edition)\" by Jonathan
2526 Cryer and Kung-Sik Chan.")
2527 (license license:gpl2+)))
2529 (define-public r-extradistr
2531 (name "r-extradistr")
2536 (uri (cran-uri "extraDistr" version))
2539 "0ywn4qwnamv36l1hw27l9y5kh3v6ha5781wsv2bz6szqjgg7kdb3"))))
2540 (properties `((upstream-name . "extraDistr")))
2541 (build-system r-build-system)
2543 `(("r-rcpp" ,r-rcpp)))
2544 (home-page "https://github.com/twolodzko/extraDistr")
2545 (synopsis "Additional univariate and multivariate distributions")
2547 "This package implements density, distribution functions, quantile
2548 functions and random generation functions for a large number of univariate and
2549 multivariate distributions.")
2550 (license license:gpl2)))
2552 (define-public r-fractal
2559 (uri (cran-uri "fractal" version))
2562 "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
2563 (build-system r-build-system)
2565 `(("r-ifultools" ,r-ifultools)
2568 ("r-scatterplot3d" ,r-scatterplot3d)
2569 ("r-splus2r" ,r-splus2r)
2570 ("r-wmtsa" ,r-wmtsa)))
2571 (home-page "http://cran.r-project.org/web/packages/fractal/")
2572 (synopsis "Fractal time series modeling and analysis")
2574 "This package provides tools for stochastic fractal and deterministic
2575 chaotic time series analysis.")
2576 (license license:gpl2)))
2578 (define-public r-urca
2585 (uri (cran-uri "urca" version))
2588 "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
2589 (build-system r-build-system)
2590 (propagated-inputs `(("r-nlme" ,r-nlme)))
2591 (native-inputs `(("gfortran" ,gfortran)))
2592 (home-page "http://cran.r-project.org/web/packages/urca/")
2593 (synopsis "Unit root and cointegration tests for time series data")
2595 "This package provides unit root and cointegration tests encountered in
2596 applied econometric analysis.")
2597 (license license:gpl2+)))
2599 (define-public r-cubature
2606 (uri (cran-uri "cubature" version))
2609 "06f6gsvbb732p80r6hxvzh4ik546icxfvx21dyh65ypmw3kgm64k"))))
2610 (build-system r-build-system)
2612 `(("r-rcpp" ,r-rcpp)))
2613 (home-page "https://github.com/bnaras/cubature")
2614 (synopsis "Adaptive multivariate integration over hypercubes")
2616 "This package is an R wrapper around the cubature C library for adaptive
2617 multivariate integration over hypercubes. This version provides both
2618 @code{hcubature} and @code{pcubature} routines in addition to a vector
2620 ;; The included cubature C library is released under GPLv2+, but the
2621 ;; wrapper declares the license to be GPLv3+.
2622 (license (list license:gpl2+ license:gpl3+))))
2624 (define-public r-trend
2631 (uri (cran-uri "trend" version))
2634 "06yifqbsvxbmk5gld4z2nnyhf59v8ks5xjwacmb25mv9r6bn388b"))))
2635 (build-system r-build-system)
2637 `(("r-extradistr" ,r-extradistr)))
2639 `(("gfortran" ,gfortran)))
2640 (home-page "http://cran.r-project.org/web/packages/trend/")
2641 (synopsis "Non-parametric trend tests and change-point detection")
2643 "The analysis of environmental data often requires the detection of
2644 trends and change-points. This package includes tests for trend
2645 detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
2646 Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
2647 Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
2648 correlation trend test), change-point detection (Lanzante's test procedures,
2649 Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
2650 Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
2651 Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
2652 sample Robust Rank-Order Distributional Test.")
2653 (license license:gpl3)))
2655 (define-public r-expm
2662 (uri (cran-uri "expm" version))
2665 "1mihl67kvv1xv0figp25jkmwfn4iwkcx15cng2348y8gm6zybw9q"))))
2666 (build-system r-build-system)
2667 (propagated-inputs `(("r-matrix" ,r-matrix)))
2668 (native-inputs `(("gfortran" ,gfortran)))
2669 (home-page "http://r-forge.r-project.org/projects/expm/")
2670 (synopsis "Tools for matrix exponentials and related quantities")
2672 "This package provides tools for the computation of the matrix
2673 exponential, logarithm, square root, and related quantities.")
2674 (license license:gpl2+)))
2676 (define-public r-complexplus
2678 (name "r-complexplus")
2683 (uri (cran-uri "complexplus" version))
2686 "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
2687 (build-system r-build-system)
2689 `(("r-expm" ,r-expm)
2690 ("r-matrix" ,r-matrix)))
2691 (home-page "http://cran.r-project.org/web/packages/complexplus/")
2692 (synopsis "Functions of complex or real variables")
2694 "This package extends several functions to the complex domain, including
2695 the matrix exponential and logarithm, and the determinant.")
2696 (license license:gpl2)))
2698 (define-public r-phontools
2700 (name "r-phontools")
2705 (uri (cran-uri "phonTools" version))
2708 "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
2709 (properties `((upstream-name . "phonTools")))
2710 (build-system r-build-system)
2711 (home-page "http://www.santiagobarreda.com/rscripts.html")
2712 (synopsis "Tools for phonetic and acoustic analyses")
2714 "This package contains tools for the organization, display, and analysis
2715 of the sorts of data frequently encountered in phonetics research and
2716 experimentation, including the easy creation of IPA vowel plots, and the
2717 creation and manipulation of WAVE audio files.")
2718 (license license:bsd-2)))
2727 (uri (cran-uri "np" version))
2730 "1y72x5j9j9mcgcy2xizk31gl843hfkngxdn8s4qw7yhw2qj79hsr"))))
2731 (build-system r-build-system)
2733 `(("r-boot" ,r-boot)
2734 ("r-cubature" ,r-cubature)
2735 ("r-quantreg" ,r-quantreg)))
2736 (home-page "https://github.com/JeffreyRacine/R-Package-np")
2737 (synopsis "Non-parametric kernel smoothing methods for mixed data types")
2738 (description "This package provides non-parametric (and semi-parametric)
2739 kernel methods that seamlessly handle a mix of continuous, unordered, and
2740 ordered factor data types.")
2741 ;; Any version of the GPL.
2742 (license license:gpl3+)))
2744 (define-public r-powerplus
2746 (name "r-powerplus")
2751 (uri (cran-uri "powerplus" version))
2754 "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
2755 (build-system r-build-system)
2757 `(("r-complexplus" ,r-complexplus)
2760 ("r-matrix" ,r-matrix)
2761 ("r-phontools" ,r-phontools)))
2762 (home-page "http://cran.r-project.org/web/packages/powerplus/")
2763 (synopsis "Exponentiation operations")
2765 "This package provides tools for the computation of matrix and scalar
2767 (license license:gpl2)))
2769 (define-public r-heatmaply
2771 (name "r-heatmaply")
2776 (uri (cran-uri "heatmaply" version))
2779 "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc"))))
2780 (build-system r-build-system)
2782 `(("r-assertthat" ,r-assertthat)
2783 ("r-colorspace" ,r-colorspace)
2784 ("r-dendextend" ,r-dendextend)
2785 ("r-ggplot2" ,r-ggplot2)
2786 ("r-gplots" ,r-gplots)
2787 ("r-htmlwidgets" ,r-htmlwidgets)
2788 ("r-magrittr" ,r-magrittr)
2789 ("r-plotly" ,r-plotly)
2790 ("r-rcolorbrewer" ,r-rcolorbrewer)
2791 ("r-reshape2" ,r-reshape2)
2792 ("r-scales" ,r-scales)
2793 ("r-seriation" ,r-seriation)
2794 ("r-viridis" ,r-viridis)
2795 ("r-webshot" ,r-webshot)))
2796 (home-page "https://cran.r-project.org/package=heatmaply")
2797 (synopsis "Interactive cluster heat maps using plotly")
2799 "This package enables you to create interactive cluster heatmaps that can
2800 be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
2801 Shiny app, and made available in the RStudio viewer pane. Hover the mouse
2802 pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
2803 a popular graphical method for visualizing high-dimensional data, in which a
2804 table of numbers is encoded as a grid of colored cells. The rows and columns
2805 of the matrix are ordered to highlight patterns and are often accompanied by
2807 ;; Either version of the license.
2808 (license (list license:gpl2 license:gpl3))))
2810 (define-public r-cgdsr
2817 (uri (cran-uri "cgdsr" version))
2820 "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23"))))
2821 (build-system r-build-system)
2823 `(("r-r-methodss3" ,r-r-methodss3)
2824 ("r-r-oo" ,r-r-oo)))
2825 (home-page "https://github.com/cBioPortal/cgdsr")
2826 (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
2828 "This package provides a basic set of R functions for querying the Cancer
2829 Genomics Data Server (CGDS), hosted by the Computational Biology Center at
2830 Memorial-Sloan-Kettering Cancer Center (MSKCC).")
2831 (license license:lgpl3)))
2833 (define-public r-import
2840 (uri (cran-uri "import" version))
2843 "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
2844 (build-system r-build-system)
2845 (home-page "https://github.com/smbache/import")
2846 (synopsis "Import mechanism for R")
2848 "This is an alternative mechanism for importing objects from packages.
2849 The syntax allows for importing multiple objects from a package with a single
2850 command in an expressive way. The import package bridges some of the gap
2851 between using @code{library} (or @code{require}) and direct (single-object)
2852 imports. Furthermore the imported objects are not placed in the current
2853 environment. It is also possible to import objects from stand-alone @code{.R}
2855 (license license:expat)))
2857 (define-public r-shinyace
2864 (uri (cran-uri "shinyAce" version))
2867 "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9"))))
2868 (properties `((upstream-name . "shinyAce")))
2869 (build-system r-build-system)
2871 `(("r-shiny" ,r-shiny)))
2872 (home-page "http://cran.r-project.org/web/packages/shinyAce")
2873 (synopsis "Ace editor bindings for Shiny")
2875 "This package provides Ace editor bindings to enable a rich text editing
2876 environment within Shiny.")
2877 (license license:expat)))
2879 (define-public r-radiant-data
2881 (name "r-radiant-data")
2886 (uri (cran-uri "radiant.data" version))
2889 "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1"))
2890 (modules '((guix build utils)))
2893 ;; Delete files that are under CC-NC-SA.
2894 (delete-file-recursively "inst/app/tools/help")
2896 (properties `((upstream-name . "radiant.data")))
2897 (build-system r-build-system)
2899 `(("r-base64enc" ,r-base64enc)
2900 ("r-broom" ,r-broom)
2903 ("r-dplyr" ,r-dplyr)
2905 ("r-ggplot2" ,r-ggplot2)
2906 ("r-gridextra" ,r-gridextra)
2907 ("r-import" ,r-import)
2908 ("r-jsonlite" ,r-jsonlite)
2909 ("r-knitr" ,r-knitr)
2910 ("r-lubridate" ,r-lubridate)
2911 ("r-magrittr" ,r-magrittr)
2912 ("r-markdown" ,r-markdown)
2914 ("r-psych" ,r-psych)
2915 ("r-readr" ,r-readr)
2916 ("r-rmarkdown" ,r-rmarkdown)
2917 ("r-rstudioapi" ,r-rstudioapi)
2918 ("r-scales" ,r-scales)
2919 ("r-shiny" ,r-shiny)
2920 ("r-shinyace" ,r-shinyace)
2921 ("r-tibble" ,r-tibble)
2922 ("r-tidyr" ,r-tidyr)))
2923 (home-page "https://github.com/radiant-rstats/radiant.data")
2924 (synopsis "Data menu for Radiant: business analytics using R and Shiny")
2926 "The Radiant Data menu includes interfaces for loading, saving, viewing,
2927 visualizing, summarizing, transforming, and combining data. It also contains
2928 functionality to generate reproducible reports of the analyses conducted in
2930 (license license:agpl3)))
2932 (define-public r-algdesign
2934 (name "r-algdesign")
2939 (uri (cran-uri "AlgDesign" version))
2942 "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
2943 (properties `((upstream-name . "AlgDesign")))
2944 (build-system r-build-system)
2945 (home-page "https://github.com/jvbraun/AlgDesign")
2946 (synopsis "Algorithmic experimental design")
2948 "This package provides tools to calculate exact and approximate theory
2949 experimental designs for D, A, and I criteria. Very large designs may be
2950 created. Experimental designs may be blocked or blocked designs created from
2951 a candidate list, using several criteria. The blocking can be done when whole
2952 and within plot factors interact.")
2953 (license license:gpl2+)))
2955 (define-public r-signal
2962 (uri (cran-uri "signal" version))
2965 "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
2966 (build-system r-build-system)
2967 (propagated-inputs `(("r-mass" ,r-mass)))
2968 (native-inputs `(("gfortran" ,gfortran)))
2969 (home-page "http://cran.r-project.org/web/packages/signal/")
2970 (synopsis "Signal processing")
2972 "This package provides a set of signal processing functions originally
2973 written for Matlab and GNU Octave. It includes filter generation utilities,
2974 filtering functions, resampling routines, and visualization of filter models.
2975 It also includes interpolation functions.")
2976 (license license:gpl2)))
2978 (define-public r-psych
2985 (uri (cran-uri "psych" version))
2988 "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
2989 (build-system r-build-system)
2991 `(("r-foreign" ,r-foreign)
2992 ("r-lattice" ,r-lattice)
2993 ("r-mnormt" ,r-mnormt)
2994 ("r-nlme" ,r-nlme)))
2995 (home-page "http://cran.r-project.org/web/packages/psych")
2996 (synopsis "Procedures for psychological, psychometric, and personality research")
2998 "This package provides a general purpose toolbox for personality,
2999 psychometric theory and experimental psychology. The functions are primarily
3000 for multivariate analysis and scale construction using factor analysis,
3001 principal component analysis, cluster analysis and reliability analysis,
3002 although others provide basic descriptive statistics. It provides functions
3003 for analyzing data at multiple levels within and between group statistics,
3004 including correlations and factor analysis; functions for simulating and
3005 testing particular item and test structures are included. Several functions
3006 serve as a useful front end for structural equation modeling.")
3007 (license license:gpl2+)))
3009 (define-public r-gsubfn
3016 (uri (cran-uri "gsubfn" version))
3019 "196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv"))))
3020 (build-system r-build-system)
3021 (propagated-inputs `(("r-proto" ,r-proto)))
3022 (home-page "http://gsubfn.googlecode.com")
3023 (synopsis "Utilities for strings and function arguments.")
3025 "This package provides @code{gsubfn} which is like @code{gsub} but can
3026 take a replacement function or certain other objects instead of the
3027 replacement string. Matches and back references are input to the replacement
3028 function and replaced by the function output. @code{gsubfn} can be used to
3029 split strings based on content rather than delimiters and for quasi-perl-style
3030 string interpolation. The package also has facilities for translating
3031 formulas to functions and allowing such formulas in function calls instead of
3033 (license license:gpl2+)))