;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages cran)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system r)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages web))

(define-public r-ape
  (package
    (name "r-ape")
    (version "5.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ape" version))
       (sha256
        (base32
         "0q59pmxawz498cb9mv5m49lhiwxib8ak94yyydz7qg8b6lpd4bn3"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lattice" ,r-lattice)
       ("r-nlme" ,r-nlme)
       ("r-rcpp" ,r-rcpp)))
    (home-page "http://ape-package.ird.fr/")
    (synopsis "Analyses of phylogenetics and evolution")
    (description
     "This package provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data in a
phylogenetic framework, ancestral character analyses, analyses of
diversification and macroevolution, computing distances from DNA sequences,
and several other tools.")
    (license license:gpl2+)))

(define-public r-colorspace
  (package
    (name "r-colorspace")
    (version "1.3-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "colorspace" version))
       (sha256
        (base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/colorspace")
    (synopsis "Color space manipulation")
    (description
     "This package carries out a mapping between assorted color spaces
including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
CIELAB.  Qualitative, sequential, and diverging color palettes based on HCL
colors are provided.")
    (license license:bsd-3)))

(define-public r-glue
  (package
    (name "r-glue")
    (version "1.2.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "glue" version))
       (sha256
        (base32
         "0vi9y8ix95g6hjqdz9c9y4119apbdjcypdv0ag8cl6vaxqs5n9qr"))))
    (build-system r-build-system)
    (home-page "https://github.com/tidyverse/glue")
    (synopsis "Interpreted string literals")
    (description
     "This package provides an implementation of interpreted string literals,
inspired by Python's Literal String Interpolation (PEP-0498) and
Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
    (license license:expat)))

(define-public r-plogr
  (package
    (name "r-plogr")
    (version "0.1-1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "plogr" version))
       (sha256
        (base32
         "13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92"))))
    (build-system r-build-system)
    (home-page "https://github.com/krlmlr/plogr")
    (synopsis "R bindings for the plog C++ logging library")
    (description
     "This package provides the header files for a stripped-down version of
the plog header-only C++ logging library, and a method to log to R's standard
error stream.")
    (license license:expat)))

(define-public r-rcpp
  (package
    (name "r-rcpp")
    (version "0.12.15")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "Rcpp" version))
       (sha256
        (base32 "1pnv6sl4vdn69ygmgrb1b3gsigfdcfb56wnzikic93l8gkvdsvxv"))))
    (build-system r-build-system)
    (home-page "http://www.rcpp.org")
    (synopsis "Seamless R and C++ integration")
    (description
     "The Rcpp package provides R functions as well as C++ classes which offer
a seamless integration of R and C++.  Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries.  Documentation
about Rcpp is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
'citation(\"Rcpp\")' for details on these last two.")
    (license license:gpl2+)))

(define-public r-bindr
  (package
    (name "r-bindr")
    (version "0.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "bindr" version))
       (sha256
        (base32
         "0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc"))))
    (build-system r-build-system)
    (home-page "https://github.com/krlmlr/bindr")
    (synopsis "Parametrized active bindings")
    (description
     "This package provides a simple interface for creating active bindings
where the bound function accepts additional arguments.")
    (license license:expat)))

(define-public r-bindrcpp
  (package
    (name "r-bindrcpp")
    (version "0.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "bindrcpp" version))
       (sha256
        (base32
         "0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bindr" ,r-bindr)
       ("r-plogr" ,r-plogr)
       ("r-rcpp" ,r-rcpp)))
    (home-page "https://github.com/krlmlr/bindrcpp")
    (synopsis "Rcpp interface to active bindings")
    (description
     "This package provides an easy way to fill an environment with active
bindings that call a C++ function.")
    (license license:expat)))

(define-public r-auc
  (package
    (name "r-auc")
    (version "0.3.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "AUC" version))
       (sha256
        (base32
         "0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
    (properties `((upstream-name . "AUC")))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/AUC")
    (synopsis "Compute the area under the curve of selected measures")
    (description
     "This package includes functions to compute the area under the curve of
selected measures: the area under the sensitivity curve (AUSEC), the area
under the specificity curve (AUSPC), the area under the accuracy
curve (AUACC), and the area under the receiver operating characteristic
curve (AUROC).  The curves can also be visualized.  Support for partial areas
is provided.")
    (license license:gpl2+)))

(define-public r-calibrate
  (package
    (name "r-calibrate")
    (version "1.7.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "calibrate" version))
       (sha256
        (base32
         "010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-mass" ,r-mass)))
    (home-page "https://cran.r-project.org/web/packages/calibrate")
    (synopsis "Calibration of scatterplot and biplot axes")
    (description
     "This is a package for drawing calibrated scales with tick marks
on (non-orthogonal) variable vectors in scatterplots and biplots.")
    (license license:gpl2)))

(define-public r-shape
  (package
    (name "r-shape")
    (version "1.4.4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "shape" version))
       (sha256
        (base32
         "0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/shape")
    (synopsis "Functions for plotting graphical shapes")
    (description
     "This package provides functions for plotting graphical shapes such as
ellipses, circles, cylinders, arrows, ...")
    (license license:gpl3+)))

(define-public r-globaloptions
  (package
    (name "r-globaloptions")
    (version "0.0.12")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "GlobalOptions" version))
       (sha256
        (base32
         "1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0"))))
    (properties `((upstream-name . "GlobalOptions")))
    (build-system r-build-system)
    (home-page "https://github.com/jokergoo/GlobalOptions")
    (synopsis "Generate functions to get or set global options")
    (description
     "This package provides more controls on the option values such as
validation and filtering on the values, making options invisible or private.")
    (license license:gpl2+)))

(define-public r-circlize
  (package
    (name "r-circlize")
    (version "0.4.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "circlize" version))
       (sha256
        (base32
         "0pg947gkryygikfbv6admx8gsg02b6g219j6a1sdnqij2908yxna"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-colorspace" ,r-colorspace)
       ("r-globaloptions" ,r-globaloptions)
       ("r-shape" ,r-shape)))
    (home-page "https://github.com/jokergoo/circlize")
    (synopsis "Circular visualization")
    (description
     "Circular layout is an efficient way to visualise huge amounts of
information.  This package provides an implementation of circular layout
generation in R as well as an enhancement of available software.  Its
flexibility is based on the usage of low-level graphics functions such that
self-defined high-level graphics can be easily implemented by users for
specific purposes.  Together with the seamless connection between the powerful
computational and visual environment in R, it gives users more convenience and
freedom to design figures for better understanding complex patterns behind
multi-dimensional data.")
    (license license:gpl2+)))

(define-public r-powerlaw
  (package
    (name "r-powerlaw")
    (version "0.70.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "poweRlaw" version))
       (sha256
        (base32
         "04sr0nhdd1v915m0zf5gasznzgi08ykcy20kkwdw0l5mvvdbic8m"))))
    (properties `((upstream-name . "poweRlaw")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-vgam" ,r-vgam)))
    (home-page "https://github.com/csgillespie/poweRlaw")
    (synopsis "Tools for the analysis of heavy tailed distributions")
    (description
     "This package provides an implementation of maximum likelihood estimators
for a variety of heavy tailed distributions, including both the discrete and
continuous power law distributions.  Additionally, a goodness-of-fit based
approach is used to estimate the lower cut-off for the scaling region.")
    ;; Any of these GPL versions.
    (license (list license:gpl2 license:gpl3))))

(define-public r-compare
  (package
    (name "r-compare")
    (version "0.2-6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "compare" version))
       (sha256
        (base32
         "0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/compare")
    (synopsis "Comparing objects for differences")
    (description
     "This package provides functions to compare a model object to a
comparison object.  If the objects are not identical, the functions can be
instructed to explore various modifications of the objects (e.g., sorting
rows, dropping names) to see if the modified versions are identical.")
    (license license:gpl2+)))

(define-public r-dendextend
  (package
    (name "r-dendextend")
    (version "1.7.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "dendextend" version))
       (sha256
        (base32
         "1krvqadnnh53xx5ql7bwzxaif6a317jzbs1m00gnc6jnj03rfl5d"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-fpc" ,r-fpc)
       ("r-ggplot2" ,r-ggplot2)
       ("r-magrittr" ,r-magrittr)
       ("r-viridis" ,r-viridis)
       ("r-whisker" ,r-whisker)))
    (home-page "https://cran.r-project.org/web/packages/dendextend")
    (synopsis "Extending 'dendrogram' functionality in R")
    (description
     "This package offers a set of functions for extending @code{dendrogram}
objects in R, letting you visualize and compare trees of hierarchical
clusterings.  You can adjust a tree's graphical parameters (the color, size,
type, etc of its branches, nodes and labels) and visually and statistically
compare different dendrograms to one another.")
    ;; Any of these versions
    (license (list license:gpl2 license:gpl3))))

(define-public r-getoptlong
  (package
    (name "r-getoptlong")
    (version "0.1.6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "GetoptLong" version))
       (sha256
        (base32
         "1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm"))))
    (properties `((upstream-name . "GetoptLong")))
    (build-system r-build-system)
    (inputs
     `(("perl" ,perl)))
    (propagated-inputs
     `(("r-globaloptions" ,r-globaloptions)
       ("r-rjson" ,r-rjson)))
    (home-page "https://github.com/jokergoo/GetoptLong")
    (synopsis "Parsing command-line arguments and variable interpolation")
    (description
     "This is yet another command-line argument parser which wraps the
powerful Perl module @code{Getopt::Long} and with some adaptation for easier
use in R.  It also provides a simple way for variable interpolation in R.")
    (license license:gpl2+)))

(define-public r-fastmatch
  (package
    (name "r-fastmatch")
    (version "1.1-0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "fastmatch" version))
       (sha256
        (base32
         "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
    (build-system r-build-system)
    (home-page "http://www.rforge.net/fastmatch")
    (synopsis "Fast match function")
    (description
     "This package provides a fast @code{match} replacement for cases that
require repeated look-ups.  It is slightly faster that R's built-in
@code{match} function on first match against a table, but extremely fast on
any subsequent lookup as it keeps the hash table in memory.")
    (license license:gpl2)))

(define-public r-ff
  (package
    (name "r-ff")
    (version "2.2-13")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ff" version))
       (sha256
        (base32
         "1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-bit" ,r-bit)))
    (home-page "http://ff.r-forge.r-project.org/")
    (synopsis "Memory-efficient storage of large data on disk and access functions")
    (description
     "This package provides data structures that are stored on disk but
behave (almost) as if they were in RAM by transparently mapping only a section
in main memory.")
    ;; error Architecture not supported.
    (supported-systems (delete "aarch64-linux" %supported-systems))
    (license license:gpl2)))

(define-public r-ffbase
  (package
    (name "r-ffbase")
    (version "0.12.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ffbase" version))
       (sha256
        (base32
         "1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bit" ,r-bit)
       ("r-fastmatch" ,r-fastmatch)
       ("r-ff" ,r-ff)))
    (home-page "http://github.com/edwindj/ffbase")
    (synopsis "Basic statistical functions for package 'ff'")
    (description
     "This package extends the out of memory vectors of @code{ff} with
statistical functions and other utilities to ease their usage.")
    (license license:gpl3)))

(define-public r-prettyunits
  (package
    (name "r-prettyunits")
    (version "1.0.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "prettyunits" version))
       (sha256
        (base32
         "0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-assertthat" ,r-assertthat)
       ("r-magrittr" ,r-magrittr)))
    (home-page "https://github.com/gaborcsardi/prettyunits")
    (synopsis "Pretty, human readable formatting of quantities")
    (description
     "This package provides tools for pretty, human readable formatting of
quantities.")
    (license license:expat)))

(define-public r-reshape
  (package
    (name "r-reshape")
    (version "0.8.7")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "reshape" version))
       (sha256
        (base32
         "14ir3w4bb3bsz8jsak27nj7kpn227pdgr9653gjq5wc93rywi9ig"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-plyr" ,r-plyr)
       ("r-rcpp" ,r-rcpp)))
    (home-page "http://had.co.nz/reshape")
    (synopsis "Flexibly reshape data")
    (description
     "Flexibly restructure and aggregate data using just two functions:
@code{melt} and @code{cast}.  This package provides them.")
    (license license:expat)))

(define-public r-progress
  (package
    (name "r-progress")
    (version "1.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "progress" version))
       (sha256
        (base32
         "1fxakchfjr5vj59s9sxynd7crpz97xj42438rmkhkf3rjpyspx59"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-prettyunits" ,r-prettyunits)
       ("r-r6" ,r-r6)))
    (home-page "https://github.com/gaborcsardi/progress")
    (synopsis "Terminal progress bars")
    (description
     "This package provides configurable progress bars.  They may include
percentage, elapsed time, and/or the estimated completion time.  They work in
terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app.  The
package also provides a C++ API, that works with or without Rcpp.")
    (license license:expat)))

(define-public r-ggally
  (package
    (name "r-ggally")
    (version "1.3.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "GGally" version))
       (sha256
        (base32
         "02px7j28wzbhcgcwm2m0pxb6g7s5zvphl64ix55pkvag4m2ky57l"))))
    (properties `((upstream-name . "GGally")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ggplot2" ,r-ggplot2)
       ("r-gtable" ,r-gtable)
       ("r-plyr" ,r-plyr)
       ("r-progress" ,r-progress)
       ("r-rcolorbrewer" ,r-rcolorbrewer)
       ("r-reshape" ,r-reshape)))
    (home-page "https://ggobi.github.io/ggally")
    (synopsis "Extension to ggplot2")
    (description
     "The R package ggplot2 is a plotting system based on the grammar of
graphics.  GGally extends ggplot2 by adding several functions to reduce the
complexity of combining geometric objects with transformed data.  Some of
these functions include a pairwise plot matrix, a two group pairwise plot
matrix, a parallel coordinates plot, a survival plot, and several functions to
plot networks.")
    (license license:gpl2+)))

(define-public r-proxy
  (package
    (name "r-proxy")
    (version "0.4-21")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "proxy" version))
       (sha256
        (base32
         "1vih8gsfzv97h5c8ixd1qjnn02i7fzla2p9fdj2wpisqhx0p0xv0"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/proxy")
    (synopsis "Distance and similarity measures")
    (description
     "This package provides an extensible framework for the efficient
calculation of auto- and cross-proximities, along with implementations of the
most popular ones.")
    (license license:gpl2)))

(define-public r-sp
  (package
    (name "r-sp")
    (version "1.2-7")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "sp" version))
       (sha256
        (base32
         "0q04yfgyjannsrzl0ppwcv0simrxrrbx2iz5mzaafc5x38zf0q3d"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lattice" ,r-lattice)))
    (home-page "https://cran.r-project.org/web/packages/sp")
    (synopsis "Classes and methods for spatial data")
    (description
     "This package provides classes and methods for spatial data; the classes
document where the spatial location information resides, for 2D or 3D data.
Utility functions are provided, e.g. for plotting data as maps, spatial
selection, as well as methods for retrieving coordinates, for subsetting,
print, summary, etc.")
    (license license:gpl2+)))

(define-public r-rmtstat
  (package
    (name "r-rmtstat")
    (version "0.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "RMTstat" version))
       (sha256
        (base32
         "1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
    (properties `((upstream-name . "RMTstat")))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/RMTstat")
    (synopsis "Distributions, statistics and tests derived from random matrix theory")
    (description
     "This package provides functions for working with the Tracy-Widom laws
and other distributions related to the eigenvalues of large Wishart
matrices.")
    (license license:bsd-3)))

(define-public r-rmpi
  (package
    (name "r-rmpi")
    (version "0.6-6")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "Rmpi" version))
              (sha256
               (base32
                "0fm6z049aaq2c9xagm8n64d9560hg9d8hyb0m359fii672nhkz6q"))))
    (properties `((upstream-name . "Rmpi")))
    (build-system r-build-system)
    (arguments
     `(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")))
    (inputs
     `(("openmpi" ,openmpi)))
    (home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
    (synopsis "R interface to message-passing interface (MPI)")
    (description
     "This package provides an interface (wrapper) to MPI APIs.  It also
provides an interactive R manager and worker environment.")
    (license license:gpl2+)))

(define-public r-lmoments
  (package
    (name "r-lmoments")
    (version "1.2-3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "Lmoments" version))
       (sha256
        (base32
         "13p0r4w16jvjnyjmkhkp3dwdfr1gap2l0k4k5jy41m8nc5fvcx79"))))
    (properties `((upstream-name . "Lmoments")))
    (build-system r-build-system)
    (home-page "http://www.tilastotiede.fi/juha_karvanen.html")
    (synopsis "L-moments and quantile mixtures")
    (description
     "This package contains functions to estimate L-moments and trimmed
L-moments from the data.  It also contains functions to estimate the
parameters of the normal polynomial quantile mixture and the Cauchy polynomial
quantile mixture from L-moments and trimmed L-moments.")
    (license license:gpl2)))

(define-public r-distillery
  (package
    (name "r-distillery")
    (version "1.0-4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "distillery" version))
       (sha256
        (base32
         "1m0pgmlvk7bsb6q3kxagnq422babk61sf73naavac68v8x2q8fix"))))
    (build-system r-build-system)
    (home-page "http://www.ral.ucar.edu/staff/ericg")
    (synopsis "Functions for confidence intervals and object information")
    (description
     "This package provides some very simple method functions for confidence
interval calculation and to distill pertinent information from a potentially
complex object; primarily used in common with the packages extRemes and
SpatialVx.")
    (license license:gpl2+)))

(define-public r-extremes
  (package
    (name "r-extremes")
    (version "2.0-8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "extRemes" version))
       (sha256
        (base32
         "0pnpib3g2r9x8hfqhvq23j8m3jh62lp28ipnqir5yadnzv850gfm"))))
    (properties `((upstream-name . "extRemes")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-car" ,r-car)
       ("r-distillery" ,r-distillery)
       ("r-lmoments" ,r-lmoments)))
    (home-page "http://www.assessment.ucar.edu/toolkit/")
    (synopsis "Extreme value analysis")
    (description
     "ExtRemes is a suite of functions for carrying out analyses on the
extreme values of a process of interest; be they block maxima over long blocks
or excesses over a high threshold.")
    (license license:gpl2+)))

(define-public r-lmtest
  (package
    (name "r-lmtest")
    (version "0.9-35")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "lmtest" version))
       (sha256
        (base32
         "107br1l7p52wxvazs031f4h5ryply97qywg9dzrkw4ydnvqq4j9g"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-zoo" ,r-zoo)))
    (native-inputs
     `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/lmtest")
    (synopsis "Testing linear regression models")
    (description
     "This package provides a collection of tests, data sets, and examples for
diagnostic checking in linear regression models.  Furthermore, some generic
tools for inference in parametric models are provided.")
    ;; Either version is okay
    (license (list license:gpl2 license:gpl3))))

(define-public r-inline
  (package
    (name "r-inline")
    (version "0.3.14")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "inline" version))
              (sha256
               (base32
                "0cf9vya9h4znwgp6s1nayqqmh6mwyw7jl0isk1nx4j2ijszxcd7x"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/inline")
    (synopsis "Functions to inline C, C++, Fortran function calls from R")
    (description
     "This package provides functionality to dynamically define R functions
and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
@code{.Call} calling conventions.")
    ;; Any version of the LGPL.
    (license license:lgpl3+)))

(define-public r-bbmle
  (package
    (name "r-bbmle")
    (version "1.0.20")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "bbmle" version))
       (sha256
        (base32
         "1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lattice" ,r-lattice)
       ("r-mass" ,r-mass)
       ("r-numderiv" ,r-numderiv)))
    (home-page "https://cran.r-project.org/web/packages/bbmle")
    (synopsis "Tools for General Maximum Likelihood Estimation")
    (description
     "This package provides methods and functions for fitting maximum
likelihood models in R.  This package modifies and extends the @code{mle}
classes in the @code{stats4} package.")
    ;; Any version of the GPL
    (license license:gpl2+)))

(define-public r-emdbook
  (package
    (name "r-emdbook")
    (version "1.3.9")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "emdbook" version))
       (sha256
        (base32
         "09xbdyw8a4pvrsg3ryr8drby0njy4avc5wsjj4ffibdaicpchy69"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bbmle" ,r-bbmle)
       ("r-coda" ,r-coda)
       ("r-lattice" ,r-lattice)
       ("r-mass" ,r-mass)
       ("r-plyr" ,r-plyr)
       ("r-rcpp" ,r-rcpp)))
    (home-page "http://www.math.mcmaster.ca/bolker/emdbook")
    (synopsis "Support functions and data for \"Ecological Models and Data\"")
    (description
     "This package provides auxiliary functions and data sets for \"Ecological
Models and Data\", a book presenting maximum likelihood estimation and related
topics for ecologists (ISBN 978-0-691-12522-0).")
    ;; Any GPL version
    (license (list license:gpl2 license:gpl3))))

(define-public r-lpsolve
  (package
    (name "r-lpsolve")
    (version "5.6.13")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "lpSolve" version))
       (sha256
        (base32
         "13a9ry8xf5j1f2j6imqrxdgxqz3nqp9sj9b4ivyx9sid459irm6m"))))
    (properties `((upstream-name . "lpSolve")))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/lpSolve")
    (synopsis "R interface to Lp_solve to solve linear/integer programs")
    (description
     "Lp_solve is software for solving linear, integer and mixed integer
programs.  This implementation supplies a \"wrapper\" function in C and some R
functions that solve general linear/integer problems, assignment problems, and
transportation problems.")
    (license license:lgpl2.0)))

(define-public r-limsolve
  (package
    (name "r-limsolve")
    (version "1.5.5.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "limSolve" version))
       (sha256
        (base32
         "1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
    (properties `((upstream-name . "limSolve")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lpsolve" ,r-lpsolve)
       ("r-mass" ,r-mass)
       ("r-quadprog" ,r-quadprog)))
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/limSolve")
    (synopsis "Solving linear inverse models")
    (description
     "This package provides functions that:

@enumerate
@item find the minimum/maximum of a linear or quadratic function,
@item sample an underdetermined or overdetermined system,
@item solve a linear system Ax=B for the unknown x.
@end enumerate

It includes banded and tridiagonal linear systems.  The package calls Fortran
functions from LINPACK.")
    ;; Any GPL version.
    (license (list license:gpl2+ license:gpl3+))))

(define-public r-fitdistrplus
  (package
    (name "r-fitdistrplus")
    (version "1.0-9")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "fitdistrplus" version))
       (sha256
        (base32
         "18x9454g598d54763k3hvi33iszifk7sxvhd1zg5r8z1vpixx3z6"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-mass" ,r-mass)
       ("r-survival" ,r-survival)))
    (home-page "http://riskassessment.r-forge.r-project.org")
    (synopsis "Fitting a parametric distribution from data")
    (description
     "This package extends the @code{fitdistr} function of the MASS package
with several functions to help the fit of a parametric distribution to
non-censored or censored data.  Censored data may contain left-censored,
right-censored and interval-censored values, with several lower and upper
bounds.  In addition to @dfn{maximum likelihood estimation} (MLE), the package
provides moment matching (MME), quantile matching (QME) and maximum
goodness-of-fit estimation (MGE) methods (available only for non-censored
data).  Weighted versions of MLE, MME and QME are available.")
    (license license:gpl2+)))

(define-public r-energy
  (package
    (name "r-energy")
    (version "1.7-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "energy" version))
       (sha256
        (base32
         "19c7bgjnm4ggf7w5mk64c5shkma3sa9wc8x117iqv7pk1bvvyy3p"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-boot" ,r-boot)
       ("r-rcpp" ,r-rcpp)))
    (home-page "https://cran.r-project.org/web/packages/energy")
    (synopsis "Multivariate inference via the energy of data")
    (description
     "This package provides e-statistics (energy) tests and statistics for
multivariate and univariate inference, including distance correlation,
one-sample, two-sample, and multi-sample tests for comparing multivariate
distributions, are implemented.  Measuring and testing multivariate
independence based on distance correlation, partial distance correlation,
multivariate goodness-of-fit tests, clustering based on energy distance,
testing for multivariate normality, distance components (disco) for
non-parametric analysis of structured data, and other energy
statistics/methods are implemented.")
    (license license:gpl2+)))

(define-public r-suppdists
  (package
    (name "r-suppdists")
    (version "1.1-9.4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "SuppDists" version))
       (sha256
        (base32
         "1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
    (properties `((upstream-name . "SuppDists")))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/SuppDists")
    (synopsis "Supplementary distributions")
    (description
     "This package provides ten distributions supplementing those built into
R.  Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
Spearman's rho, maximum F ratio, the Pearson product moment correlation
coefficient, Johnson distributions, normal scores and generalized
hypergeometric distributions.  In addition two random number generators of
George Marsaglia are included.")
    (license license:gpl2+)))

(define-public r-ksamples
  (package
    (name "r-ksamples")
    (version "1.2-7")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "kSamples" version))
       (sha256
        (base32
         "0f19rjngk0lg6s8c6h5l55qpxp8sl4vxj3kpi05cizzncny9b9bj"))))
    (properties `((upstream-name . "kSamples")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-suppdists" ,r-suppdists)))
    (home-page "https://cran.r-project.org/web/packages/kSamples")
    (synopsis "K-Sample rank tests and their combinations")
    (description
     "This package provides tools to compares k samples using the
Anderson-Darling test, Kruskal-Wallis type tests with different rank score
criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
test.  It computes asymptotic, simulated or (limited) exact P-values, all
valid under randomization, with or without ties, or conditionally under random
sampling from populations, given the observed tie pattern.  Except for Steel's
test and the JT test it also combines these tests across several blocks of
samples.")
    (license license:gpl2+)))

(define-public r-cvst
  (package
    (name "r-cvst")
    (version "0.2-1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "CVST" version))
       (sha256
        (base32
         "17xacyi8cf37rr2xswx96qy7pwkaqq394awdlswykz3qlyzx4zx2"))))
    (properties `((upstream-name . "CVST")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-kernlab" ,r-kernlab)
       ("r-matrix" ,r-matrix)))
    (home-page "https://cran.r-project.org/web/packages/CVST")
    (synopsis "Fast cross-validation via sequential testing")
    (description
     "This package implements the fast cross-validation via sequential
testing (CVST) procedure.  CVST is an improved cross-validation procedure
which uses non-parametric testing coupled with sequential analysis to
determine the best parameter set on linearly increasing subsets of the data.
Additionally to the CVST the package contains an implementation of the
ordinary k-fold cross-validation with a flexible and powerful set of helper
objects and methods to handle the overall model selection process.  The
implementations of the Cochran's Q test with permutations and the sequential
testing framework of Wald are generic and can therefore also be used in other
contexts.")
    (license license:gpl2+)))

(define-public r-squarem
  (package
    (name "r-squarem")
    (version "2017.10-1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "SQUAREM" version))
       (sha256
        (base32
         "10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
    (properties `((upstream-name . "SQUAREM")))
    (build-system r-build-system)
    (home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
    (synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
    (description
     "This package provides algorithms for accelerating the convergence of
slow, monotone sequences from smooth, contraction mapping such as the EM
algorithm.  It can be used to accelerate any smooth, linearly convergent
acceleration scheme.  A tutorial style introduction to this package is
available in a vignette.")
    (license license:gpl2+)))

(define-public r-lava
  (package
    (name "r-lava")
    (version "1.6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "lava" version))
       (sha256
        (base32
         "02xf5d968raz9gnq5ywy04wz29xpdyca1hm79vbbg1mcxvzdl1dz"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-numderiv" ,r-numderiv)
       ("r-squarem" ,r-squarem)
       ("r-survival" ,r-survival)))
    (home-page "https://github.com/kkholst/lava")
    (synopsis "Latent variable models")
    (description
     "This package provides tools for the estimation and simulation of latent
variable models.")
    (license license:gpl3)))

(define-public r-drr
  (package
    (name "r-drr")
    (version "0.0.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "DRR" version))
       (sha256
        (base32
         "1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
    (properties `((upstream-name . "DRR")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-cvst" ,r-cvst)
       ("r-kernlab" ,r-kernlab)
       ("r-matrix" ,r-matrix)))
    (home-page "https://cran.r-project.org/web/packages/DRR")
    (synopsis "Dimensionality reduction via regression")
    (description
     "This package provides an implementation of dimensionality reduction via
regression using Kernel Ridge Regression.")
    (license license:gpl3)))

(define-public r-prodlim
  (package
    (name "r-prodlim")
    (version "1.6.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "prodlim" version))
       (sha256
        (base32
         "0m51rkivx1zr6whdqwj66jpnkmp4385m06kkha3dp8qqf4jna9iz"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-kernsmooth" ,r-kernsmooth)
       ("r-lava" ,r-lava)
       ("r-rcpp" ,r-rcpp)
       ("r-survival" ,r-survival)))
    (home-page "https://cran.r-project.org/web/packages/prodlim")
    (synopsis "Product-limit estimation for censored event history analysis")
    (description
     "This package provides a fast and user-friendly implementation of
nonparametric estimators for censored event history (survival) analysis with
the Kaplan-Meier and Aalen-Johansen methods.")
    (license license:gpl2+)))

(define-public r-dimred
  (package
    (name "r-dimred")
    (version "0.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "dimRed" version))
       (sha256
        (base32
         "0fasca5fsbrxdwv30hch7vb9snb844l7l8p5fjf239dq45xfy37v"))))
    (properties `((upstream-name . "dimRed")))
    (build-system r-build-system)
    (propagated-inputs `(("r-drr" ,r-drr)))
    (home-page "https://github.com/gdkrmr/dimRed")
    (synopsis "Framework for dimensionality reduction")
    (description
     "This package provides a collection of dimensionality reduction
techniques from R packages and provides a common interface for calling the
methods.")
    (license license:gpl3)))

(define-public r-timedate
  (package
    (name "r-timedate")
    (version "3043.102")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "timeDate" version))
       (sha256
        (base32
         "0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
    (properties `((upstream-name . "timeDate")))
    (build-system r-build-system)
    (home-page "https://www.rmetrics.org")
    (synopsis "Chronological and calendar objects")
    (description
     "This package provides an environment for teaching \"Financial
Engineering and Computational Finance\" and for managing chronological and
calendar objects.")
    (license license:gpl2+)))

(define-public r-ddalpha
  (package
    (name "r-ddalpha")
    (version "1.3.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ddalpha" version))
       (sha256
        (base32
         "13w8ir5rd80rka4mq343zd4wn93vfw870lzfqrd3cxgwb1bwcw7y"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bh" ,r-bh)
       ("r-class" ,r-class)
       ("r-mass" ,r-mass)
       ("r-rcpp" ,r-rcpp)
       ("r-robustbase" ,r-robustbase)
       ("r-sfsmisc" ,r-sfsmisc)))
    (native-inputs
     `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/ddalpha")
    (synopsis "Depth-Based classification and calculation of data depth")
    (description
     "This package contains procedures for depth-based supervised learning,
which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
Mosler and Mozharovskyi, 2014).  The training data sample is transformed by a
statistical depth function to a compact low-dimensional space, where the final
classification is done.  It also offers an extension to functional data and
routines for calculating certain notions of statistical depth functions.  50
multivariate and 5 functional classification problems are included.")
    (license license:gpl2)))

(define-public r-gower
  (package
    (name "r-gower")
    (version "0.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "gower" version))
       (sha256
        (base32
         "1mbrj1lam3jfbby2j32shmmj5cn09zx3rkxbamq7q8sdg39b54gb"))))
    (build-system r-build-system)
    (native-inputs
     `(("r-knitr" ,r-knitr)))
    (home-page "https://github.com/markvanderloo/gower")
    (synopsis "Gower's distance")
    (description
     "This package provides tools to compute Gower's distance (or similarity)
coefficient between records, and to compute the top-n matches between records.
Core algorithms are executed in parallel on systems supporting OpenMP.")
    (license license:gpl3)))

(define-public r-rcpproll
  (package
    (name "r-rcpproll")
    (version "0.2.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "RcppRoll" version))
       (sha256
        (base32
         "19xzvxym8zbighndygkq4imfwc0abh4hqyq3qrr8aakyd096iisi"))))
    (properties `((upstream-name . "RcppRoll")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-rcpp" ,r-rcpp)))
    (home-page "https://cran.r-project.org/web/packages/RcppRoll")
    (synopsis "Efficient rolling and windowed operations")
    (description
     "This package provides fast and efficient routines for common rolling /
windowed operations.  Routines for the efficient computation of windowed mean,
median, sum, product, minimum, maximum, standard deviation and variance are
provided.")
    (license license:gpl2+)))

(define-public r-ipred
  (package
    (name "r-ipred")
    (version "0.9-6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ipred" version))
       (sha256
        (base32
         "1vrw1pqcpnc04x1r2h9grdfm6bivs358sww5gg90jwlvxcw69lxq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-class" ,r-class)
       ("r-mass" ,r-mass)
       ("r-nnet" ,r-nnet)
       ("r-prodlim" ,r-prodlim)
       ("r-rpart" ,r-rpart)
       ("r-survival" ,r-survival)))
    (home-page "https://cran.r-project.org/web/packages/ipred")
    (synopsis "Improved predictors")
    (description
     "This package provides improved predictive models by indirect
classification and bagging for classification, regression and survival
problems as well as resampling based estimators of prediction error.")
    (license license:gpl2+)))

(define-public r-psych
  (package
    (name "r-psych")
    (version "1.7.8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "psych" version))
       (sha256
        (base32
         "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-foreign" ,r-foreign)
       ("r-lattice" ,r-lattice)
       ("r-mnormt" ,r-mnormt)
       ("r-nlme" ,r-nlme)))
    (home-page "https://cran.r-project.org/web/packages/psych/")
    (synopsis "Procedures for psychological, psychometric, and personality research")
    (description
     "This package provides a general purpose toolbox for personality,
psychometric theory and experimental psychology.  Functions are primarily for
multivariate analysis and scale construction using factor analysis, principal
component analysis, cluster analysis and reliability analysis, although others
provide basic descriptive statistics.  Item Response Theory is done using
factor analysis of tetrachoric and polychoric correlations.  Functions for
analyzing data at multiple levels include within and between group statistics,
including correlations and factor analysis.  Functions for simulating and
testing particular item and test structures are included.  Several functions
serve as a useful front end for structural equation modeling.  Graphical
displays of path diagrams, factor analysis and structural equation models are
created using basic graphics.")
    (license license:gpl2+)))

(define-public r-broom
  (package
    (name "r-broom")
    (version "0.4.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "broom" version))
       (sha256
        (base32
         "119pc2jnxvm13cvd77c7d14p3bn68f4jm310vj3yfck40101n9if"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-dplyr" ,r-dplyr)
       ("r-nlme" ,r-nlme)
       ("r-plyr" ,r-plyr)
       ("r-psych" ,r-psych)
       ("r-reshape2" ,r-reshape2)
       ("r-stringr" ,r-stringr)
       ("r-tidyr" ,r-tidyr)))
    (home-page "http://github.com/tidyverse/broom")
    (synopsis "Convert statistical analysis objects into tidy data frames")
    (description
     "This package provides tools to convert statistical analysis objects from
R into tidy data frames, so that they can more easily be combined, reshaped
and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
@code{ggplot2}.  The package provides three S3 generics: @code{tidy}, which
summarizes a model's statistical findings such as coefficients of a
regression; @code{augment}, which adds columns to the original data such as
predictions, residuals and cluster assignments; and @code{glance}, which
provides a one-row summary of model-level statistics.")
    (license license:expat)))

(define-public r-recipes
  (package
    (name "r-recipes")
    (version "0.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "recipes" version))
       (sha256
        (base32
         "1car3a3mqn87pz049cbgkaayz86970mvkapk6al2k7jjw76306l9"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-broom" ,r-broom)
       ("r-ddalpha" ,r-ddalpha)
       ("r-dimred" ,r-dimred)
       ("r-dplyr" ,r-dplyr)
       ("r-gower" ,r-gower)
       ("r-ipred" ,r-ipred)
       ("r-lubridate" ,r-lubridate)
       ("r-magrittr" ,r-magrittr)
       ("r-matrix" ,r-matrix)
       ("r-purrr" ,r-purrr)
       ("r-rcpproll" ,r-rcpproll)
       ("r-rlang" ,r-rlang)
       ("r-tibble" ,r-tibble)
       ("r-tidyselect" ,r-tidyselect)
       ("r-timedate" ,r-timedate)))
    (home-page "https://github.com/topepo/recipes")
    (synopsis "Preprocessing tools to create design matrices")
    (description
     "Recipes is an extensible framework to create and preprocess design
matrices.  Recipes consist of one or more data manipulation and analysis
\"steps\".  Statistical parameters for the steps can be estimated from an
initial data set and then applied to other data sets.  The resulting design
matrices can then be used as inputs into statistical or machine learning
models.")
    (license license:gpl2)))

(define-public r-pdist
  (package
    (name "r-pdist")
    (version "1.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "pdist" version))
       (sha256
        (base32
         "18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
    (build-system r-build-system)
    (home-page "https://github.com/jeffwong/pdist")
    (synopsis "Partitioned distance function")
    (description
     "Pdist computes the euclidean distance between rows of a matrix X and
rows of another matrix Y.  Previously, this could be done by binding the two
matrices together and calling @code{dist}, but this creates unnecessary
computation by computing the distances between a row of X and another row of
X, and likewise for Y.  Pdist strictly computes distances across the two
matrices, not within the same matrix, making computations significantly faster
for certain use cases.")
    (license license:gpl3+)))

(define-public r-ggrepel
  (package
    (name "r-ggrepel")
    (version "0.7.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ggrepel" version))
       (sha256
        (base32
         "0g0qfm6g71rv27423c1x846ipilnj213knyzrcr09vrpxc87l618"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ggplot2" ,r-ggplot2)
       ("r-rcpp" ,r-rcpp)
       ("r-scales" ,r-scales)))
    (home-page "http://github.com/slowkow/ggrepel")
    (synopsis "Repulsive text and label geometries for ggplot2")
    (description
     "This package provides text and label geometries for ggplot2 that help to
avoid overlapping text labels.  Labels repel away from each other and away
from the data points.")
    (license license:gpl3)))

(define-public r-corrplot
  (package
    (name "r-corrplot")
    (version "0.84")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "corrplot" version))
       (sha256
        (base32
         "1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
    (build-system r-build-system)
    (home-page "https://github.com/taiyun/corrplot")
    (synopsis "Visualization of a correlation matrix")
    (description
     "This package provides a graphical display of a correlation matrix or
general matrix.  It also contains some algorithms to do matrix reordering.  In
addition, corrplot is good at details, including choosing color, text labels,
color labels, layout, etc.")
    ;; Any version of the GPL
    (license license:gpl2+)))

(define-public r-stringdist
  (package
    (name "r-stringdist")
    (version "0.9.4.6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "stringdist" version))
       (sha256
        (base32
         "0j5b7hr53nr9xq44famkpwzi4khix93ffani5pwldqkf8bpdvhci"))))
    (build-system r-build-system)
    (home-page "https://github.com/markvanderloo/stringdist")
    (synopsis "Approximate string matching and string distance functions")
    (description
     "This package implements an approximate string matching version of R's
native @code{match} function.  It can calculate various string distances based
on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
Jaro-Winkler).  An implementation of soundex is provided as well.  Distances
can be computed between character vectors while taking proper care of encoding
or between integer vectors representing generic sequences.")
    (license license:gpl3+)))

(define-public r-mice
  (package
    (name "r-mice")
    (version "2.46.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "mice" version))
       (sha256
        (base32
         "1gjvlk67zvgipfczsca8zqk97vg3sivv82hblsdwp14s7smhjcax"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lattice" ,r-lattice)
       ("r-mass" ,r-mass)
       ("r-nnet" ,r-nnet)
       ("r-rcpp" ,r-rcpp)
       ("r-rpart" ,r-rpart)
       ("r-survival" ,r-survival)))
    (home-page "https://cran.r-project.org/web/packages/mice/")
    (synopsis "Multivariate imputation by chained equations")
    (description
     "Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
implemented by the MICE algorithm as described in @url{Van Buuren and
Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}.  Each
variable has its own imputation model.  Built-in imputation models are
provided for continuous data (predictive mean matching, normal), binary
data (logistic regression), unordered categorical data (polytomous logistic
regression) and ordered categorical data (proportional odds).  MICE can also
impute continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.")
    ;; Any of these two versions.
    (license (list license:gpl2 license:gpl3))))

(define-public r-truncnorm
  (package
    (name "r-truncnorm")
    (version "1.0-8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "truncnorm" version))
       (sha256
        (base32
         "0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/truncnorm/")
    (synopsis "Truncated normal distribution")
    (description "This package provides functions for the truncated normal
distribution with mean equal to @code{mean} and standard deviation equal to
@code{sd}.  It includes density, distribution, quantile, and expected value
functions, as well as a random generation function.")
    (license license:gpl2)))

(define-public r-rsolnp
  (package
    (name "r-rsolnp")
    (version "1.16")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "Rsolnp" version))
       (sha256
        (base32
         "0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
    (properties `((upstream-name . "Rsolnp")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-truncnorm" ,r-truncnorm)))
    (home-page "https://cran.r-project.org/web/packages/Rsolnp/")
    (synopsis "General non-linear optimization")
    (description "The Rsolnp package implements a general non-linear augmented
Lagrange multiplier method solver, a @dfn{sequential quadratic
programming} (SQP) based solver).")
    ;; Any version of the GPL.
    (license license:gpl2+)))

(define-public r-hardyweinberg
  (package
    (name "r-hardyweinberg")
    (version "1.5.9")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "HardyWeinberg" version))
       (sha256
        (base32
         "0qk3lly5qczn61rj0q9xzscppspvk238yjgr4p71pkzkjhiv40jz"))))
    (properties `((upstream-name . "HardyWeinberg")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-mice" ,r-mice)
       ("r-rcpp" ,r-rcpp)
       ("r-rsolnp" ,r-rsolnp)))
    (home-page "https://cran.r-project.org/package=HardyWeinberg")
    (synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
    (description
     "This package contains tools for exploring Hardy-Weinberg equilibrium for
diallelic genetic marker data.  All classical tests (chi-square, exact,
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
included in the package, as well as functions for power computation and for
the simulation of marker data under equilibrium and disequilibrium.  Routines
for dealing with markers on the X-chromosome are included.  Functions for
testing equilibrium in the presence of missing data by using multiple
imputation are also provided.  Implements several graphics for exploring the
equilibrium status of a large set of diallelic markers: ternary plots with
acceptance regions, log-ratio plots and Q-Q plots.")
    (license license:gpl2+)))

(define-public r-sm
  (package
    (name "r-sm")
    (version "2.2-5.4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "sm" version))
       (sha256
        (base32
         "0hnq5s2fv94gaj0nyqc1vjdjd64vsp9z23nqa8hxvjcaf996rwj9"))))
    (build-system r-build-system)
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
    (synopsis "Smoothing methods for nonparametric regression and density estimation")
    (description
     "This is software accompanying the book 'Applied Smoothing Techniques for
Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
University Press.  It provides smoothing methods for nonparametric regression
and density estimation")
    (license license:gpl2+)))

(define-public r-vioplot
  (package
    (name "r-vioplot")
    (version "0.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "vioplot" version))
       (sha256
        (base32
         "16wkb26kv6qr34hv5zgqmgq6zzgysg9i78pvy2c097lr60v087v0"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-sm" ,r-sm)))
    (home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
    (synopsis "Violin plot")
    (description
     "This package provides a violin plot, which is a combination of a box
plot and a kernel density plot.")
    (license license:bsd-3)))

(define-public r-rsofia
  (package
    (name "r-rsofia")
    (version "1.1")
    (source (origin
              (method url-fetch)
              ;; This package has been removed from CRAN, so we can
              ;; only fetch it from the archives.
              (uri (string-append "https://cran.r-project.org/src/"
                                  "contrib/Archive/RSofia/RSofia_"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
    (properties `((upstream-name . "RSofia")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-rcpp" ,r-rcpp)))
    (home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
    (synopsis "Port of sofia-ml to R")
    (description "This package is a port of sofia-ml to R.  Sofia-ml is a
suite of fast incremental algorithms for machine learning that can be used for
training models for classification or ranking.")
    (license license:asl2.0)))

(define-public r-xts
  (package
    (name "r-xts")
    (version "0.10-1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "xts" version))
       (sha256
        (base32
         "1j9ddh9v9081zrqlpylsk13fldilhjdyaw6r6pa726fhgnrsf8a2"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-zoo" ,r-zoo)))
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://github.com/joshuaulrich/xts")
    (synopsis "Extensible time series")
    (description
     "This package provides for uniform handling of R's different time-based
data classes by extending @code{zoo}, maximizing native format information
preservation and allowing for user-level customization and extension, while
simplifying cross-class interoperability.")
    (license license:gpl2+)))

(define-public r-performanceanalytics
  (package
    (name "r-performanceanalytics")
    (version "1.5.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "PerformanceAnalytics" version))
       (sha256
        (base32
         "01bgm57z079g6r505w3bj293zkbd49fwa8sg55z87vizwavipml6"))))
    (properties
     `((upstream-name . "PerformanceAnalytics")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-quadprog" ,r-quadprog)
       ("r-xts" ,r-xts)
       ("r-zoo" ,r-zoo)))
    (home-page "https://r-forge.r-project.org/projects/returnanalytics/")
    (synopsis "Econometric tools for performance and risk analysis")
    (description "This is a collection of econometric functions for
performance and risk analysis.  This package aims to aid practitioners and
researchers in utilizing the latest research in analysis of non-normal return
streams.  In general, it is most tested on return (rather than price) data on
a regular scale, but most functions will work with irregular return data as
well, and increasing numbers of functions will work with P&L or price data
where possible.")
    ;; Either version may be picked.
    (license (list license:gpl2 license:gpl3))))

(define-public r-laeken
  (package
    (name "r-laeken")
    (version "0.4.6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "laeken" version))
       (sha256
        (base32
         "1rhkv1kk508pwln1d325iq4fink2ncssps0ypxi52j9d7wk78la6"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-boot" ,r-boot)
       ("r-mass" ,r-mass)))
    (home-page "https://cran.r-project.org/web/packages/laeken/")
    (synopsis "Estimation of indicators on social exclusion and poverty")
    (description "This package provides tools for the estimation of indicators
on social exclusion and poverty, as well as an implementation of Pareto tail
modeling for empirical income distributions.")
    (license license:gpl2+)))

(define-public r-vcd
  (package
    (name "r-vcd")
    (version "1.4-4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "vcd" version))
       (sha256
        (base32
         "1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-colorspace" ,r-colorspace)
       ("r-lmtest" ,r-lmtest)
       ("r-mass" ,r-mass)))
    (home-page "https://cran.r-project.org/web/packages/vcd/")
    (synopsis "Visualizing categorical data")
    (description "This package provides visualization techniques, data sets,
summary and inference procedures aimed particularly at categorical data.
Special emphasis is given to highly extensible grid graphics.  The package was
originally inspired by the book \"Visualizing Categorical Data\" by Michael
Friendly and is now the main support package for a new book, \"Discrete Data
Analysis with R\" by Michael Friendly and David Meyer (2015).")
    (license license:gpl2)))

(define-public r-ica
  (package
    (name "r-ica")
    (version "1.0-1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ica" version))
       (sha256
        (base32
         "1bkl4a72l0k6gm82l3jxnib898z20cw17zg81jj39l9dn65rlmcq"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/ica/")
    (synopsis "Independent component analysis")
    (description "This package provides tools for @dfn{Independent Component
Analysis} (ICA) using various algorithms: FastICA,
Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
of Eigenmatrices} (JADE).")
    (license license:gpl2+)))

(define-public r-dtw
  (package
    (name "r-dtw")
    (version "1.18-1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "dtw" version))
       (sha256
        (base32
         "1b91vahba09cqlb8b1ry4dlv4rbldb4s2p6w52gmyw31vxdv5nnr"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-proxy" ,r-proxy)))
    (home-page "http://dtw.r-forge.r-project.org/")
    (synopsis "Dynamic Time Warping Algorithms")
    (description "This package provides a comprehensive implementation of
@dfn{dynamic time warping} (DTW) algorithms in R.  DTW computes the
optimal (least cumulative distance) alignment between points of two time
series.  Common DTW variants covered include local (slope) and global (window)
constraints, subsequence matches, arbitrary distance definitions,
normalizations, minimum variance matching, and so on.")
    (license license:gpl2+)))

(define-public r-sdmtools
  (package
    (name "r-sdmtools")
    (version "1.1-221")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "SDMTools" version))
       (sha256
        (base32
         "1kacrpamshv7wz83yn45sfbw4m9c44xrrngzcklnwx8gcxx2knm6"))))
    (properties `((upstream-name . "SDMTools")))
    (build-system r-build-system)
    (propagated-inputs `(("r-r-utils" ,r-r-utils)))
    (home-page "http://www.rforge.net/SDMTools/")
    (synopsis "Species distribution modelling tools")
    (description "This packages provides a set of tools for post processing
the outcomes of species distribution modeling exercises.  It includes novel
methods for comparing models and tracking changes in distributions through
time.  It further includes methods for visualizing outcomes, selecting
thresholds, calculating measures of accuracy and landscape fragmentation
statistics, etc.")
    (license license:gpl3+)))

(define-public r-scatterplot3d
  (package
    (name "r-scatterplot3d")
    (version "0.3-41")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "scatterplot3d" version))
       (sha256
        (base32
         "152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
    (synopsis "3D scatter plot")
    (description "This package provides an implementation of scatter plots for
plotting.  a three dimensional point cloud.")
    (license license:gpl2)))

(define-public r-ggridges
  (package
    (name "r-ggridges")
    (version "0.4.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ggridges" version))
       (sha256
        (base32
         "0kfa3icqdalqdg1klxjrhfl7if35d3wnsiyl86bprw5dyqyh3lh3"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ggplot2" ,r-ggplot2)
       ("r-plyr" ,r-plyr)
       ("r-scales" ,r-scales)))
    (home-page "https://github.com/clauswilke/ggridges")
    (synopsis "Ridgeline plots in ggplot2")
    (description
     "Ridgeline plots provide a convenient way of visualizing changes in
distributions over time or space.  This package enables the creation of such
plots in @code{ggplot2}.")
    (license license:gpl2)))

(define-public r-ggjoy
  (package
    (name "r-ggjoy")
    (version "0.4.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ggjoy" version))
       (sha256
        (base32
         "1s24zn7gmk52bvjjhanxby7rxbnc2yfl0nx5nv7x7z0zja8gg7nb"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ggplot2" ,r-ggplot2)
       ("r-ggridges" ,r-ggridges)))
    (home-page "https://github.com/clauswilke/ggjoy")
    (synopsis "Joyplots in ggplot2")
    (description "Joyplots provide a convenient way of visualizing changes in
distributions over time or space.  This package enables the creation of such
plots in @code{ggplot2}.")
    (license license:gpl2)))

(define-public r-cli
  (package
    (name "r-cli")
    (version "1.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "cli" version))
       (sha256
        (base32
         "07as3dr7vwx02p3qgzlmxz1dlrd3x3lysrzp222ip9jcjpydp8wg"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-assertthat" ,r-assertthat)
       ("r-crayon" ,r-crayon)))
    (home-page "https://github.com/r-lib/cli#readme")
    (synopsis "Helpers for developing command line interfaces")
    (description "This package provides a suite of tools designed to build
attractive command line interfaces (CLIs).  It includes tools for drawing
rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
    (license license:expat)))

(define-public r-argparser
  (package
    (name "r-argparser")
    (version "0.4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "argparser" version))
       (sha256
        (base32
         "0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
    (build-system r-build-system)
    (home-page "https://bitbucket.org/djhshih/argparser")
    (synopsis "Command-line argument parser")
    (description
     "This package provides a cross-platform command-line argument parser
written purely in R with no external dependencies.  It is useful with the
Rscript front-end and facilitates turning an R script into an executable
script.")
    (license license:gpl3+)))

(define-public r-debugme
  (package
    (name "r-debugme")
    (version "1.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "debugme" version))
       (sha256
        (base32
         "1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-crayon" ,r-crayon)))
    (home-page "https://github.com/r-lib/debugme#readme")
    (synopsis "Debug R packages")
    (description
     "This package allows the user to specify debug messages as special string
constants, and control debugging of packages via environment variables.")
    (license license:expat)))

(define-public r-processx
  (package
    (name "r-processx")
    (version "2.0.0.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "processx" version))
       (sha256
        (base32
         "0yw23lp9xjvbpswzghkmjiayw7p19hbvmgv58k3i6b8g5nav4qcg"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-assertthat" ,r-assertthat)
       ("r-crayon" ,r-crayon)
       ("r-debugme" ,r-debugme)
       ("r-r6" ,r-r6)))
    (home-page "https://github.com/r-lib/processx3")
    (synopsis "Execute and control system processes")
    (description
     "This package provides portable tools to run system processes in the
background.  It can check if a background process is running; wait on a
background process to finish; get the exit status of finished processes; kill
background processes and their children; restart processes.  It can read the
standard output and error of the processes, using non-blocking connections.
@code{processx} can poll a process for standard output or error, with a
timeout.  It can also poll several processes at once.")
    (license license:expat)))

(define-public r-tsp
  (package
    (name "r-tsp")
    (version "1.1-5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "TSP" version))
       (sha256
        (base32
         "03xxfr5kk4zhzpb1q1pwncdp0dhchm9b48wzhvvxn2dxf3mnby2w"))))
    (properties `((upstream-name . "TSP")))
    (build-system r-build-system)
    (propagated-inputs `(("r-foreach" ,r-foreach)))
    (home-page "https://cran.r-project.org/web/packages/TSP/")
    (synopsis "Traveling salesperson problem (TSP)")
    (description "This package provides basic infrastructure and some
algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
traveling salesman problem).")
    (license license:gpl3)))

(define-public r-qap
  (package
    (name "r-qap")
    (version "0.1-1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "qap" version))
       (sha256
        (base32
         "0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
    (build-system r-build-system)
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/qap/")
    (synopsis "Heuristics for the quadratic assignment problem (QAP)")
    (description "This package implements heuristics for the @dfn{quadratic
assignment problem} (QAP).  Currently only a simulated annealing heuristic is
available.")
    (license license:gpl3)))

(define-public r-gclus
  (package
    (name "r-gclus")
    (version "1.3.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "gclus" version))
       (sha256
        (base32
         "02ba6zj9bjwrzykamjp40ajynx9xjx9h2i85n0ym0r5lcki4x6fn"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-cluster" ,r-cluster)))
    (home-page "https://cran.r-project.org/web/packages/gclus/")
    (synopsis "Clustering graphics")
    (description "This package orders panels in scatterplot matrices and
parallel coordinate displays by some merit index.  It contains various indices
of merit, ordering functions, and enhanced versions of @code{pairs} and
@code{parcoord} which color panels according to their merit level.")
    (license license:gpl2+)))

(define-public r-webshot
  (package
    (name "r-webshot")
    (version "0.5.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "webshot" version))
       (sha256
        (base32
         "07r71zzmggp4jf92x4ws4wg6v1x98vaj01lsar85bnb30n5vx8gh"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-jsonlite" ,r-jsonlite)
       ("r-magrittr" ,r-magrittr)
       ("r-processx" ,r-processx)
       ("r-withr" ,r-withr)))
    (home-page "https://github.com/wch/webshot/")
    (synopsis "Take screenshots of web pages")
    (description
     "Webshot makes it easy to take screenshots of web pages from within R.
It can also run Shiny applications locally and take screenshots of the
application; and it can render and screenshot static as well as interactive R
Markdown documents.")
    (license license:gpl2)))

(define-public r-seriation
  (package
    (name "r-seriation")
    (version "1.2-3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "seriation" version))
       (sha256
        (base32
         "1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-cluster" ,r-cluster)
       ("r-colorspace" ,r-colorspace)
       ("r-dendextend" ,r-dendextend)
       ("r-gclus" ,r-gclus)
       ("r-gplots" ,r-gplots)
       ("r-mass" ,r-mass)
       ("r-qap" ,r-qap)
       ("r-registry" ,r-registry)
       ("r-tsp" ,r-tsp)))
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "http://s2.smu.edu/IDA/seriation/")
    (synopsis "Infrastructure for ordering objects using seriation")
    (description
     "This package provides infrastructure for seriation with an
implementation of several seriation/sequencing techniques to reorder matrices,
dissimilarity matrices, and dendrograms.  It also provides (optimally)
reordered heatmaps, color images and clustering visualizations like
dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
iVAT).")
    (license license:gpl3)))

(define-public r-heatmaply
  (package
    (name "r-heatmaply")
    (version "0.14.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "heatmaply" version))
       (sha256
        (base32
         "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-assertthat" ,r-assertthat)
       ("r-colorspace" ,r-colorspace)
       ("r-dendextend" ,r-dendextend)
       ("r-ggplot2" ,r-ggplot2)
       ("r-gplots" ,r-gplots)
       ("r-htmlwidgets" ,r-htmlwidgets)
       ("r-magrittr" ,r-magrittr)
       ("r-plotly" ,r-plotly)
       ("r-rcolorbrewer" ,r-rcolorbrewer)
       ("r-reshape2" ,r-reshape2)
       ("r-scales" ,r-scales)
       ("r-seriation" ,r-seriation)
       ("r-viridis" ,r-viridis)
       ("r-webshot" ,r-webshot)))
    (home-page "https://cran.r-project.org/package=heatmaply")
    (synopsis "Interactive cluster heat maps using plotly")
    (description "Heatmaps are used in many fields for visualizing
observations, correlations, missing values patterns, and more.  Interactive
heatmaps allow the inspection of specific value by hovering the mouse over a
cell, as well as zooming into a region of the heatmap by dragging a rectangle
around the relevant area.  This work is based on the @code{ggplot2} and
@code{plotly.js} engine.  It produces similar heatmaps as @code{heatmap.2} or
@code{d3heatmap}, with the advantage of speed, the ability to zoom from the
dendrogram panes, and the placing of factor variables in the sides of the
heatmap.")
    (license (list license:gpl2 license:gpl3))))

(define-public r-xfun
  (package
    (name "r-xfun")
    (version "0.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "xfun" version))
       (sha256
        (base32
         "1sm51gmwgw876d6d1q8smxmfgfh6zsnykfx8qp8z6jmh0fvd89pj"))))
    (build-system r-build-system)
    (home-page "https://github.com/yihui/xfun")
    (synopsis "Miscellaneous functions")
    (description
     "This package provides miscellaneous functions commonly used in other
packages maintained by Yihui Xie.")
    (license license:expat)))

(define-public r-utf8
  (package
    (name "r-utf8")
    (version "1.1.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "utf8" version))
       (sha256
        (base32
         "03s4j6059q0nly68vpk6wy3p3f5ypakw93fj35kzd82b4z1r9cs3"))))
    (build-system r-build-system)
    (home-page "https://github.com/patperry/r-utf8")
    (synopsis "Unicode text processing")
    (description
     "This package provides tools to process and print UTF-8 encoded
international text (Unicode).  Input, validate, normalize, encode, format, and
display.")
    (license license:asl2.0)))

(define-public r-pillar
  (package
    (name "r-pillar")
    (version "1.2.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "pillar" version))
       (sha256
        (base32
         "1ryd7m570y6q3w71wd5dz042b3d0dv24g2rbkw1kdx0n6jj9gsbd"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-cli" ,r-cli)
       ("r-crayon" ,r-crayon)
       ("r-rlang" ,r-rlang)
       ("r-utf8" ,r-utf8)))
    (home-page "https://github.com/r-lib/pillar")
    (synopsis "Coloured formatting for columns")
    (description
     "This package provides a @code{pillar} generic designed for formatting
columns of data using the full range of colours provided by modern
terminals.")
    (license license:gpl3)))

(define-public r-uuid
  (package
    (name "r-uuid")
    (version "0.1-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "uuid" version))
       (sha256
        (base32
         "1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
    (build-system r-build-system)
    (home-page "http://www.rforge.net/uuid")
    (synopsis "Tools for generating and handling of UUIDs")
    (description
     "This package provides tools for generating and handling of
@dfn{Universally Unique Identifiers} (UUIDs).")
    (license license:expat)))

(define-public r-tinytex
  (package
    (name "r-tinytex")
    (version "0.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "tinytex" version))
       (sha256
        (base32
         "0mhxlr4709mca9jshnah5i7yjyy6k12s933619p7p9c8nbqj39cn"))))
    (build-system r-build-system)
    (home-page "https://github.com/yihui/tinytex")
    (synopsis "Helper functions for TeX Live and compiling LaTeX documents")
    (description
     "This package provides helper functions to install and maintain the LaTeX
distribution named TinyTeX, a lightweight, cross-platform, portable, and
easy-to-maintain version of TeX Live.  This package also contains helper
functions to compile LaTeX documents, and install missing LaTeX packages
automatically.")
    (license license:expat)))

(define-public r-metap
  (package
    (name "r-metap")
    (version "0.8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "metap" version))
       (sha256
        (base32
         "06ny9zkilawdy0s8yiwhnygs3yppw89bbyf76zgdavykbzscz5lh"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lattice" ,r-lattice)))
    (home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
    (synopsis "Meta-analysis of significance values")
    (description
     "The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington,
Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
published results; and a routine for graphical display.")
    (license license:gpl2)))

(define-public r-network
  (package
    (name "r-network")
    (version "1.13.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "network" version))
       (sha256
        (base32
         "11sg330xb7gcnl3f6lwhhjdabz6mk43828i2np635pqw4s4yl13s"))))
    (build-system r-build-system)
    (home-page "http://statnet.org/")
    (synopsis "Classes for relational data")
    (description
     "This package provides tools to create and modify network objects.  The
@code{network} class can represent a range of relational data types, and
supports arbitrary vertex/edge/graph attributes.")
    (license license:gpl2+)))

(define-public r-statnet-common
  (package
    (name "r-statnet-common")
    (version "4.0.0")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "statnet.common" version))
        (sha256
          (base32
            "0yw6l5b4qv0jqlg4zyczas7m12a5pyqghs6ydxy2f6v6vxkijvi0"))))
    (properties
      `((upstream-name . "statnet.common")))
    (build-system r-build-system)
    (home-page "http://www.statnet.org")
    (synopsis "R scripts and utilities used by the Statnet software")
    (description "This package provides non-statistical utilities used by the
software developed by the Statnet Project.")
    (license license:gpl3)))

(define-public r-sna
  (package
    (name "r-sna")
    (version "2.4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "sna" version))
       (sha256
        (base32
         "1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-network" ,r-network)
       ("r-statnet-common" ,r-statnet-common)))
    (home-page "http://www.statnet.org")
    (synopsis "Tools for social network analysis")
    (description
     "This package provides a range of tools for social network analysis,
including node and graph-level indices, structural distance and covariance
methods, structural equivalence detection, network regression, random graph
generation, and 2D/3D network visualization.")
    (license license:gpl2+)))

(define-public r-ttr
  (package
    (name "r-ttr")
    (version "0.23-3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "TTR" version))
       (sha256
        (base32
         "07r62ngyzjl4aszdxnr3n6bnbcgcap32yhd430jsilicg8n06di1"))))
    (properties `((upstream-name . "TTR")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-curl" ,r-curl)
       ("r-xts" ,r-xts)
       ("r-zoo" ,r-zoo)))
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://github.com/joshuaulrich/TTR")
    (synopsis "Technical trading rules")
    (description
     "This package provides functions and data to construct technical trading
rules with R.")
    (license license:gpl2)))

(define-public r-leaps
  (package
    (name "r-leaps")
    (version "3.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "leaps" version))
       (sha256
        (base32
         "11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
    (build-system r-build-system)
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/leaps/")
    (synopsis "Regression subset selection")
    (description
     "This package provides tools for regression subset selection, including
exhaustive search.")
    (license license:gpl2+)))

(define-public r-splus2r
  (package
    (name "r-splus2r")
    (version "1.2-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "splus2R" version))
       (sha256
        (base32
         "0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
    (properties `((upstream-name . "splus2R")))
    (build-system r-build-system)
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/splus2R/")
    (synopsis "Supplemental S-PLUS functionality in R")
    (description
     "Currently there are many functions in S-PLUS that are missing in R.  To
facilitate the conversion of S-PLUS packages to R packages, this package
provides some missing S-PLUS functionality in R.")
    (license license:gpl2)))

(define-public r-ifultools
  (package
    (name "r-ifultools")
    (version "2.0-4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ifultools" version))
       (sha256
        (base32
         "0pv2msaa1rmj8csxdclzi2jwg9pfdvh87blj9j3xa3myisglq092"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-mass" ,r-mass)
       ("r-splus2r" ,r-splus2r)))
    (home-page "https://cran.r-project.org/web/packages/ifultools/")
    (synopsis "Insightful research tools")
    (description "This package provides C code used by the wmtsa, fractal, and
sapa R packages.")
    (license license:gpl2)))

(define-public r-sapa
  (package
    (name "r-sapa")
    (version "2.0-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "sapa" version))
       (sha256
        (base32
         "056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ifultools" ,r-ifultools)
       ("r-splus2r" ,r-splus2r)))
    (home-page "https://cran.r-project.org/web/packages/sapa/")
    (synopsis "Spectral analysis for physical applications")
    (description "This package provides software for the book Spectral
Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
Cambridge University Press, 1993.")
    (license license:gpl2)))

(define-public r-quantmod
  (package
    (name "r-quantmod")
    (version "0.4-12")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "quantmod" version))
       (sha256
        (base32
         "0y7gh0k1s10vdsfch8777avbhf99mc9crikvx7ahqrw0j631vmhq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-curl" ,r-curl)
       ("r-ttr" ,r-ttr)
       ("r-xts" ,r-xts)
       ("r-zoo" ,r-zoo)))
    (home-page "https://cran.r-project.org/web/packages/quantmod/")
    (synopsis "Quantitative financial modelling framework")
    (description "This package provides a quantitative financial modelling
framework to allow users to specify, build, trade, and analyse quantitative
financial trading strategies.")
    (license license:gpl3)))

(define-public r-tseries
  (package
    (name "r-tseries")
    (version "0.10-43")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "tseries" version))
       (sha256
        (base32
         "1yjxhj7l1p2przczl6frggfcr5iwda9lbcsmh0y75gbbbps14yf2"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-quadprog" ,r-quadprog)
       ("r-quantmod" ,r-quantmod)
       ("r-zoo" ,r-zoo)))
    (native-inputs
     `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/tseries/")
    (synopsis "Time series analysis and computational finance")
    (description
     "This package provides functions relating to time series analysis and
computational finance.")
    (license license:gpl2)))

(define-public r-wmtsa
  (package
    (name "r-wmtsa")
    (version "2.0-3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "wmtsa" version))
       (sha256
        (base32
         "1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ifultools" ,r-ifultools)
       ("r-mass" ,r-mass)
       ("r-splus2r" ,r-splus2r)))
    (home-page "https://cran.r-project.org/web/packages/wmtsa/")
    (synopsis "Wavelet methods for time series analysis")
    (description
     "This package provides software to accompany the book \"Wavelet Methods
for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
University Press, 2000.")
    (license license:gpl2)))

(define-public r-tsa
  (package
    (name "r-tsa")
    (version "1.01")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "TSA" version))
       (sha256
        (base32
         "0cm97hwxm6vfgy9mc3kgwq6dnmn86p8a4avnfjbai048qnwrn6hx"))))
    (properties `((upstream-name . "TSA")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-leaps" ,r-leaps)
       ("r-locfit" ,r-locfit)
       ("r-mgcv" ,r-mgcv)
       ("r-tseries" ,r-tseries)))
    (home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
    (synopsis "Time series analysis")
    (description
     "This package contains R functions and datasets detailed in the book
\"Time Series Analysis with Applications in R (second edition)\" by Jonathan
Cryer and Kung-Sik Chan.")
    (license license:gpl2+)))

(define-public r-extradistr
  (package
    (name "r-extradistr")
    (version "1.8.8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "extraDistr" version))
       (sha256
        (base32
         "0ywn4qwnamv36l1hw27l9y5kh3v6ha5781wsv2bz6szqjgg7kdb3"))))
    (properties `((upstream-name . "extraDistr")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-rcpp" ,r-rcpp)))
    (home-page "https://github.com/twolodzko/extraDistr")
    (synopsis "Additional univariate and multivariate distributions")
    (description
     "This package implements density, distribution functions, quantile
functions and random generation functions for a large number of univariate and
multivariate distributions.")
    (license license:gpl2)))

(define-public r-fractal
  (package
    (name "r-fractal")
    (version "2.0-4")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "fractal" version))
       (sha256
        (base32
         "18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ifultools" ,r-ifultools)
       ("r-mass" ,r-mass)
       ("r-sapa" ,r-sapa)
       ("r-scatterplot3d" ,r-scatterplot3d)
       ("r-splus2r" ,r-splus2r)
       ("r-wmtsa" ,r-wmtsa)))
    (home-page "https://cran.r-project.org/web/packages/fractal/")
    (synopsis "Fractal time series modeling and analysis")
    (description
     "This package provides tools for stochastic fractal and deterministic
chaotic time series analysis.")
    (license license:gpl2)))

(define-public r-urca
  (package
    (name "r-urca")
    (version "1.3-0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "urca" version))
       (sha256
        (base32
         "1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-nlme" ,r-nlme)))
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/urca/")
    (synopsis "Unit root and cointegration tests for time series data")
    (description
     "This package provides unit root and cointegration tests encountered in
applied econometric analysis.")
    (license license:gpl2+)))

(define-public r-cubature
  (package
    (name "r-cubature")
    (version "1.3-11")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "cubature" version))
       (sha256
        (base32
         "06f6gsvbb732p80r6hxvzh4ik546icxfvx21dyh65ypmw3kgm64k"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-rcpp" ,r-rcpp)))
    (home-page "https://github.com/bnaras/cubature")
    (synopsis "Adaptive multivariate integration over hypercubes")
    (description
     "This package is an R wrapper around the cubature C library for adaptive
multivariate integration over hypercubes.  This version provides both
@code{hcubature} and @code{pcubature} routines in addition to a vector
interface.")
    ;; The included cubature C library is released under GPLv2+, but the
    ;; wrapper declares the license to be GPLv3+.
    (license (list license:gpl2+ license:gpl3+))))

(define-public r-trend
  (package
    (name "r-trend")
    (version "1.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "trend" version))
       (sha256
        (base32
         "06yifqbsvxbmk5gld4z2nnyhf59v8ks5xjwacmb25mv9r6bn388b"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-extradistr" ,r-extradistr)))
    (native-inputs
     `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/trend/")
    (synopsis "Non-parametric trend tests and change-point detection")
    (description
     "The analysis of environmental data often requires the detection of
trends and change-points.  This package includes tests for trend
detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
correlation trend test), change-point detection (Lanzante's test procedures,
Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
sample Robust Rank-Order Distributional Test.")
    (license license:gpl3)))

(define-public r-expm
  (package
    (name "r-expm")
    (version "0.999-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "expm" version))
       (sha256
        (base32
         "1mihl67kvv1xv0figp25jkmwfn4iwkcx15cng2348y8gm6zybw9q"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-matrix" ,r-matrix)))
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://r-forge.r-project.org/projects/expm/")
    (synopsis "Tools for matrix exponentials and related quantities")
    (description
     "This package provides tools for the computation of the matrix
exponential, logarithm, square root, and related quantities.")
    (license license:gpl2+)))

(define-public r-complexplus
  (package
    (name "r-complexplus")
    (version "2.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "complexplus" version))
       (sha256
        (base32
         "16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-expm" ,r-expm)
       ("r-matrix" ,r-matrix)))
    (home-page "https://cran.r-project.org/web/packages/complexplus/")
    (synopsis "Functions of complex or real variables")
    (description
     "This package extends several functions to the complex domain, including
the matrix exponential and logarithm, and the determinant.")
    (license license:gpl2)))

(define-public r-phontools
  (package
    (name "r-phontools")
    (version "0.2-2.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "phonTools" version))
       (sha256
        (base32
         "01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
    (properties `((upstream-name . "phonTools")))
    (build-system r-build-system)
    (home-page "http://www.santiagobarreda.com/rscripts.html")
    (synopsis "Tools for phonetic and acoustic analyses")
    (description
     "This package contains tools for the organization, display, and analysis
of the sorts of data frequently encountered in phonetics research and
experimentation, including the easy creation of IPA vowel plots, and the
creation and manipulation of WAVE audio files.")
    (license license:bsd-2)))

(define-public r-np
  (package
    (name "r-np")
    (version "0.60-6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "np" version))
       (sha256
        (base32
         "1y72x5j9j9mcgcy2xizk31gl843hfkngxdn8s4qw7yhw2qj79hsr"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-boot" ,r-boot)
       ("r-cubature" ,r-cubature)
       ("r-quantreg" ,r-quantreg)))
    (home-page "https://github.com/JeffreyRacine/R-Package-np")
    (synopsis "Non-parametric kernel smoothing methods for mixed data types")
    (description "This package provides non-parametric (and semi-parametric)
kernel methods that seamlessly handle a mix of continuous, unordered, and
ordered factor data types.")
    ;; Any version of the GPL.
    (license license:gpl3+)))

(define-public r-powerplus
  (package
    (name "r-powerplus")
    (version "3.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "powerplus" version))
       (sha256
        (base32
         "0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-complexplus" ,r-complexplus)
       ("r-expm" ,r-expm)
       ("r-mass" ,r-mass)
       ("r-matrix" ,r-matrix)
       ("r-phontools" ,r-phontools)))
    (home-page "https://cran.r-project.org/web/packages/powerplus/")
    (synopsis "Exponentiation operations")
    (description
     "This package provides tools for the computation of matrix and scalar
exponentiation.")
    (license license:gpl2)))

(define-public r-heatmaply
  (package
    (name "r-heatmaply")
    (version "0.14.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "heatmaply" version))
       (sha256
        (base32
         "03p2caclhfgqgpx3wwck5h06jy3mxgs05gjmwkb7hmwghkjh41jc"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-assertthat" ,r-assertthat)
       ("r-colorspace" ,r-colorspace)
       ("r-dendextend" ,r-dendextend)
       ("r-ggplot2" ,r-ggplot2)
       ("r-gplots" ,r-gplots)
       ("r-htmlwidgets" ,r-htmlwidgets)
       ("r-magrittr" ,r-magrittr)
       ("r-plotly" ,r-plotly)
       ("r-rcolorbrewer" ,r-rcolorbrewer)
       ("r-reshape2" ,r-reshape2)
       ("r-scales" ,r-scales)
       ("r-seriation" ,r-seriation)
       ("r-viridis" ,r-viridis)
       ("r-webshot" ,r-webshot)))
    (home-page "https://cran.r-project.org/package=heatmaply")
    (synopsis "Interactive cluster heat maps using plotly")
    (description
     "This package enables you to create interactive cluster heatmaps that can
be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
Shiny app, and made available in the RStudio viewer pane.  Hover the mouse
pointer over a cell to show details or drag a rectangle to zoom.  A heatmap is
a popular graphical method for visualizing high-dimensional data, in which a
table of numbers is encoded as a grid of colored cells.  The rows and columns
of the matrix are ordered to highlight patterns and are often accompanied by
dendrograms.")
    ;; Either version of the license.
    (license (list license:gpl2 license:gpl3))))

(define-public r-cgdsr
  (package
    (name "r-cgdsr")
    (version "1.2.10")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "cgdsr" version))
       (sha256
        (base32
         "1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-r-methodss3" ,r-r-methodss3)
       ("r-r-oo" ,r-r-oo)))
    (home-page "https://github.com/cBioPortal/cgdsr")
    (synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
    (description
     "This package provides a basic set of R functions for querying the Cancer
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
Memorial-Sloan-Kettering Cancer Center (MSKCC).")
    (license license:lgpl3)))

(define-public r-import
  (package
    (name "r-import")
    (version "1.1.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "import" version))
       (sha256
        (base32
         "0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
    (build-system r-build-system)
    (home-page "https://github.com/smbache/import")
    (synopsis "Import mechanism for R")
    (description
     "This is an alternative mechanism for importing objects from packages.
The syntax allows for importing multiple objects from a package with a single
command in an expressive way.  The import package bridges some of the gap
between using @code{library} (or @code{require}) and direct (single-object)
imports.  Furthermore the imported objects are not placed in the current
environment.  It is also possible to import objects from stand-alone @code{.R}
files.")
    (license license:expat)))

(define-public r-shinyace
  (package
    (name "r-shinyace")
    (version "0.2.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "shinyAce" version))
       (sha256
        (base32
         "0ycka8rsw0178q9klfid97vdn5cbyx3r778nis5s3dqipdyazdm9"))))
    (properties `((upstream-name . "shinyAce")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-shiny" ,r-shiny)))
    (home-page "http://cran.r-project.org/web/packages/shinyAce")
    (synopsis "Ace editor bindings for Shiny")
    (description
     "This package provides Ace editor bindings to enable a rich text editing
environment within Shiny.")
    (license license:expat)))

(define-public r-radiant-data
  (package
    (name "r-radiant-data")
    (version "0.8.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "radiant.data" version))
       (sha256
        (base32
         "1ylina1jlrmvjkj8pwg0ip5jv1038vnzyckmf542xl7g11x8rvw1"))
       (modules '((guix build utils)))
       (snippet
        '(begin
           ;; Delete files that are under CC-NC-SA.
           (delete-file-recursively "inst/app/tools/help")
           #t))))
    (properties `((upstream-name . "radiant.data")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-base64enc" ,r-base64enc)
       ("r-broom" ,r-broom)
       ("r-car" ,r-car)
       ("r-curl" ,r-curl)
       ("r-dplyr" ,r-dplyr)
       ("r-dt" ,r-dt)
       ("r-ggplot2" ,r-ggplot2)
       ("r-gridextra" ,r-gridextra)
       ("r-import" ,r-import)
       ("r-jsonlite" ,r-jsonlite)
       ("r-knitr" ,r-knitr)
       ("r-lubridate" ,r-lubridate)
       ("r-magrittr" ,r-magrittr)
       ("r-markdown" ,r-markdown)
       ("r-pryr" ,r-pryr)
       ("r-psych" ,r-psych)
       ("r-readr" ,r-readr)
       ("r-rmarkdown" ,r-rmarkdown)
       ("r-rstudioapi" ,r-rstudioapi)
       ("r-scales" ,r-scales)
       ("r-shiny" ,r-shiny)
       ("r-shinyace" ,r-shinyace)
       ("r-tibble" ,r-tibble)
       ("r-tidyr" ,r-tidyr)))
    (home-page "https://github.com/radiant-rstats/radiant.data")
    (synopsis "Data menu for Radiant: business analytics using R and Shiny")
    (description
     "The Radiant Data menu includes interfaces for loading, saving, viewing,
visualizing, summarizing, transforming, and combining data.  It also contains
functionality to generate reproducible reports of the analyses conducted in
the application.")
    (license license:agpl3)))

(define-public r-algdesign
  (package
    (name "r-algdesign")
    (version "1.1-7.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "AlgDesign" version))
       (sha256
        (base32
         "0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
    (properties `((upstream-name . "AlgDesign")))
    (build-system r-build-system)
    (home-page "https://github.com/jvbraun/AlgDesign")
    (synopsis "Algorithmic experimental design")
    (description
     "This package provides tools to calculate exact and approximate theory
experimental designs for D, A, and I criteria.  Very large designs may be
created.  Experimental designs may be blocked or blocked designs created from
a candidate list, using several criteria.  The blocking can be done when whole
and within plot factors interact.")
    (license license:gpl2+)))

(define-public r-signal
  (package
    (name "r-signal")
    (version "0.7-6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "signal" version))
       (sha256
        (base32
         "1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-mass" ,r-mass)))
    (native-inputs `(("gfortran" ,gfortran)))
    (home-page "https://cran.r-project.org/web/packages/signal/")
    (synopsis "Signal processing")
    (description
     "This package provides a set of signal processing functions originally
written for Matlab and GNU Octave.  It includes filter generation utilities,
filtering functions, resampling routines, and visualization of filter models.
It also includes interpolation functions.")
    (license license:gpl2)))

(define-public r-psych
  (package
    (name "r-psych")
    (version "1.7.8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "psych" version))
       (sha256
        (base32
         "0daismb8pdk392vdy304hqx0m3jx62gx3a0hygjygc125rhfla7k"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-foreign" ,r-foreign)
       ("r-lattice" ,r-lattice)
       ("r-mnormt" ,r-mnormt)
       ("r-nlme" ,r-nlme)))
    (home-page "http://cran.r-project.org/web/packages/psych")
    (synopsis "Procedures for psychological, psychometric, and personality research")
    (description
     "This package provides a general purpose toolbox for personality,
psychometric theory and experimental psychology.  The functions are primarily
for multivariate analysis and scale construction using factor analysis,
principal component analysis, cluster analysis and reliability analysis,
although others provide basic descriptive statistics.  It provides functions
for analyzing data at multiple levels within and between group statistics,
including correlations and factor analysis; functions for simulating and
testing particular item and test structures are included.  Several functions
serve as a useful front end for structural equation modeling.")
    (license license:gpl2+)))

(define-public r-gsubfn
  (package
    (name "r-gsubfn")
    (version "0.6-6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "gsubfn" version))
       (sha256
        (base32
         "196x4c3ihf4q3i0v7b1xa6jm8jjld2rsx00qz03n90wfnjdx5idv"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-proto" ,r-proto)))
    (home-page "http://gsubfn.googlecode.com")
    (synopsis "Utilities for strings and function arguments.")
    (description
     "This package provides @code{gsubfn} which is like @code{gsub} but can
take a replacement function or certain other objects instead of the
replacement string.  Matches and back references are input to the replacement
function and replaced by the function output.  @code{gsubfn} can be used to
split strings based on content rather than delimiters and for quasi-perl-style
string interpolation.  The package also has facilities for translating
formulas to functions and allowing such formulas in function calls instead of
functions.")
    (license license:gpl2+)))

(define-public r-sqldf
  (package
    (name "r-sqldf")
    (version "0.4-11")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "sqldf" version))
       (sha256
        (base32
         "0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-chron" ,r-chron)
       ("r-dbi" ,r-dbi)
       ("r-gsubfn" ,r-gsubfn)
       ("r-proto" ,r-proto)
       ("r-rsqlite" ,r-rsqlite)))
    (home-page "https://github.com/ggrothendieck/sqldf")
    (synopsis "Manipulate R data frames using SQL")
    (description
     "The @code{sqldf} function is typically passed a single argument which is
an SQL select statement where the table names are ordinary R data frame names.
@code{sqldf} transparently sets up a database, imports the data frames into
that database, performs the SQL statement and returns the result using a
heuristic to determine which class to assign to each column of the returned
data frame.  The @code{sqldf} or @code{read.csv.sql} functions can also be
used to read filtered files into R even if the original files are larger than
R itself can handle.")
    (license license:gpl2)))

(define-public r-abind
  (package
    (name "r-abind")
    (version "1.4-5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "abind" version))
       (sha256
        (base32
         "0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/abind/")
    (synopsis "Combine multidimensional arrays")
    (description
     "This package provides tools to combine multidimensional arrays into a
single array.  This is a generalization of @code{cbind} and @code{rbind}.  It
works with vectors, matrices, and higher-dimensional arrays.  It also provides
the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
extracting and replacing data in arrays.")
    (license license:lgpl2.0+)))

(define-public r-prroc
  (package
    (name "r-prroc")
    (version "1.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "PRROC" version))
       (sha256
        (base32
         "03hvh92lq4i4w4mla9bvwrwb4626f4hvlxgdn57hamp70960vjyc"))))
    (properties `((upstream-name . "PRROC")))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/PRROC/")
    (synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
    (description
     "This package computes the areas under the @dfn{precision-recall} (PR)
and ROC curve for weighted (e.g. soft-labeled) and unweighted data.  In
contrast to other implementations, the interpolation between points of the PR
curve is done by a non-linear piecewise function.  In addition to the areas
under the curves, the curves themselves can also be computed and plotted by a
specific S3-method.")
    (license license:gpl3)))

(define-public r-vim
  (package
    (name "r-vim")
    (version "4.7.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "VIM" version))
       (sha256
        (base32
         "1vjcs5wvjv94ln01d94h9rs4j50d3ky4n26mm3prgh13raylrmnd"))))
    (properties `((upstream-name . "VIM")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-car" ,r-car)
       ("r-colorspace" ,r-colorspace)
       ("r-data-table" ,r-data-table)
       ("r-e1071" ,r-e1071)
       ("r-laeken" ,r-laeken)
       ("r-mass" ,r-mass)
       ("r-nnet" ,r-nnet)
       ("r-rcpp" ,r-rcpp)
       ("r-robustbase" ,r-robustbase)
       ("r-sp" ,r-sp)
       ("r-vcd" ,r-vcd)))
    (home-page "https://github.com/alexkowa/VIM")
    (synopsis "Visualization and imputation of missing values")
    (description
     "This package provides tools for the visualization of missing and/or
imputed values are introduced, which can be used for exploring the data and
the structure of the missing and/or imputed values.  Depending on this
structure of the missing values, the corresponding methods may help to
identify the mechanism generating the missing values and allows to explore the
data including missing values.  In addition, the quality of imputation can be
visually explored using various univariate, bivariate, multiple and
multivariate plot methods.")
    (license license:gpl2+)))

(define-public r-fnn
  (package
    (name "r-fnn")
    (version "1.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "FNN" version))
       (sha256
        (base32
         "1kncmiaraq1mrykb9fj3fsxswabk3l71fnp1vks0x9aay5xfk8mj"))))
    (properties `((upstream-name . "FNN")))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/FNN")
    (synopsis "Fast nearest neighbor search algorithms and applications")
    (description
     "This package provides cover-tree and kd-tree fast k-nearest neighbor
search algorithms.  Related applications including KNN classification,
regression and information measures are implemented.")
    ;; The DESCRIPTION file erroneously states that GPL version 2.1 or
    ;; later can be used.
    (license license:gpl2+)))

(define-public r-smoother
  (package
    (name "r-smoother")
    (version "1.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "smoother" version))
       (sha256
        (base32
         "0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ttr" ,r-ttr)))
    (home-page "http://cran.r-project.org/web/packages/smoother")
    (synopsis "Functions relating to the smoothing of numerical data")
    (description
     "This package provides a collection of methods for smoothing numerical
data, commencing with a port of the Matlab gaussian window smoothing function.
In addition, several functions typically used in smoothing of financial data
are included.")
    (license license:gpl2)))

(define-public r-riverplot
  (package
    (name "r-riverplot")
    (version "0.6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "riverplot" version))
       (sha256
        (base32
         "0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
    (build-system r-build-system)
    (home-page "https://logfc.wordpress.com")
    (synopsis "Sankey or ribbon plots")
    (description
     "Sankey plots are a type of diagram that is convenient to illustrate how
flow of information, resources etc. separates and joins, much like observing
how rivers split and merge.  For example, they can be used to compare
different clusterings.  This package provides an implementation of Sankey
plots for R.")
    (license license:gpl2+)))
