;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; 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 perl)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages web))

(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 "http://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 "1.1.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "glue" version))
       (sha256
        (base32
         "01awmqby7rwzhzr51m7d87wqibx7ggl6xair8fi3z3q1hkyyv7ih"))))
    (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 "0.12.12")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "Rcpp" version))
       (sha256
        (base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz"))))
    (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 "http://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 "http://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 "1.4.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "shape" version))
       (sha256
        (base32
         "1v9xp60p813rnx41vchkh32qmcb4z2zp9l7r1a8a6f8aqylnq3vj"))))
    (build-system r-build-system)
    (home-page "http://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 "0.4.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "circlize" version))
       (sha256
        (base32
         "1w7i3jgxgq510axglzmw54ma9kq7k4c86i9ccndz10mrwc51fji0"))))
    (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 for the visualization of huge
amounts of information.  This package provides an implementation of circular
layout generation in R as well as an enhancement of available software.  The
flexibility of the package 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 multiple 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 "http://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 "1.5.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "dendextend" version))
       (sha256
        (base32
         "04jz58apibfrkjcrdmw2hmsav6qpb5cs6qdai81k1v1iznfcya42"))))
    (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.")
    (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 "0.4-17")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "proxy" version))
       (sha256
        (base32
         "0bg1fn96qrj8whmnl7c3gv244ksm2ykxxsd0zrmw4lb6465pizl2"))))
    (build-system r-build-system)
    (home-page "http://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 "1.2-5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "sp" version))
       (sha256
        (base32
         "09yydnacp33yx0kn537k96fjlbf75fjafqfknpa5gvci4l888bqd"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lattice" ,r-lattice)))
    (home-page "http://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 "http://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-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 "http://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 "http://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 "1.0.19")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "bbmle" version))
       (sha256
        (base32
         "014h6mw16gv4acs2p78dy7lla7s428n633aybsb1mbi6250dg0p8"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-lattice" ,r-lattice)
       ("r-mass" ,r-mass)
       ("r-numderiv" ,r-numderiv)))
    (home-page "http://cran.r-project.org/web/packages/bbmle")
    (synopsis "Tools for General Maximum Likelihood Estimation")
    (description
     "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 (list license:gpl2 license:gpl3))))

(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 "http://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 "http://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 "1.7-0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "energy" version))
       (sha256
        (base32
         "1g4hqi6mgsnd1w4q7dd2m40ljh2jdmvad91ksbq9fscnrqpvji1x"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-boot" ,r-boot)
       ("r-rcpp" ,r-rcpp)))
    (home-page "http://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 "http://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 "http://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 "http://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-lava
  (package
    (name "r-lava")
    (version "1.5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "lava" version))
       (sha256
        (base32
         "0x6s7x111x87a4rh5nbk7vw6j4iq40i1c21w0j795h28rgyc7zc2"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-numderiv" ,r-numderiv)
       ("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 "0.0.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "DRR" version))
       (sha256
        (base32
         "1scfwp6ry6apxzqjclsmn2frxp9qfw6zxsxn5w0j0q3sz42hz1h2"))))
    (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 "http://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 "http://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 "3012.100")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "timeDate" version))
       (sha256
        (base32
         "0cn4h23y2y2bbg62qgm79xx4cvfla5xbpmi9hbdvkvpmm5yfyqk2"))))
    (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 "1.2.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ddalpha" version))
       (sha256
        (base32
         "0nsd515x6bap1qpfyx141hyldmpmyasnhv0f8s9dj6zcklp89af4"))))
    (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)))
    (home-page "http://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 "http://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 "http://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+)))