;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015 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 statistics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system r)
  #:use-module (gnu packages)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages icu4c)
  #:use-module (gnu packages image)
  #:use-module (gnu packages java)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages texlive)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages base)
  #:use-module (gnu packages xorg))

(define-public r
  (package
    (name "r")
    (version "3.2.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://cran/src/base/R-"
                                  (version-prefix version 1) "/R-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "07a6s865bjnh7w0fqsrkv1pva76w99v86w0w787qpdil87km54cw"))))
    (build-system gnu-build-system)
    (arguments
     `(#:make-flags
       (list (string-append "LDFLAGS=-Wl,-rpath="
                            (assoc-ref %outputs "out")
                            "/lib/R/lib"))
       #:phases
       (modify-phases %standard-phases
         (add-before
          'configure 'set-default-pager
          ;; Set default pager to "cat", because otherwise it is "false",
          ;; making "help()" print nothing at all.
          (lambda _ (setenv "PAGER" "cat") #t))
         (add-before
          'check 'set-timezone
          ;; Some tests require the timezone to be set.
          (lambda _ (setenv "TZ" "UTC") #t)))
       #:configure-flags
       '("--with-blas=openblas"
         "--with-lapack"
         "--with-cairo"
         "--with-libpng"
         "--with-jpeglib"
         "--with-libtiff"
         "--with-ICU"
         "--enable-R-shlib"
         "--enable-BLAS-shlib"
         "--with-system-zlib"
         "--with-system-bzlib"
         "--with-system-pcre"
         "--with-system-tre"
         "--with-system-xz")))
    (native-inputs
     `(("bzip2" ,bzip2)
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)
       ("texlive" ,texlive) ; needed to make vignettes
       ("texinfo" ,texinfo) ; for building HTML manuals
       ("which" ,which) ; for tests/Examples/base-Ex.R
       ("xz" ,xz)))
    (inputs
     `(("openblas" ,openblas)
       ("cairo" ,cairo)
       ("gfortran" ,gfortran)
       ("icu4c" ,icu4c)
       ("icedtea6" ,icedtea6 "jdk")
       ("lapack" ,lapack)
       ("libjpeg" ,libjpeg)
       ("libpng" ,libpng)
       ("libtiff" ,libtiff)
       ("libxt" ,libxt)
       ("pcre" ,pcre)
       ("readline" ,readline)
       ("zlib" ,zlib)))
    (native-search-paths
     (list (search-path-specification
            (variable "R_LIBS_SITE")
            (files (list "site-library/")))))
    (home-page "http://www.r-project.org/")
    (synopsis "Environment for statistical computing and graphics")
    (description
     "R is a language and environment for statistical computing and graphics.
It provides a variety of statistical techniques, such as linear and nonlinear
modeling, classical statistical tests, time-series analysis, classification
and clustering.  It also provides robust support for producing
publication-quality data plots.  A large amount of 3rd-party packages are
available, greatly increasing its breadth and scope.")
    (license license:gpl3+)))

(define-public r-colorspace
  (package
    (name "r-colorspace")
    (version "1.2-6")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/colorspace_"
                           version ".tar.gz"))
       (sha256
        (base32 "0y8n4ljwhbdvkysdwgqzcnpv107pb3px1jip3k6svv86p72nacds"))))
    (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-dichromat
  (package
    (name "r-dichromat")
    (version "2.0-0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/dichromat_"
                           version ".tar.gz"))
       (sha256
        (base32 "1l8db1nk29ccqg3mkbafvfiw0775iq4gapysf88xq2zp6spiw59i"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/dichromat")
    (synopsis "Color schemes for dichromats")
    (description
     "Dichromat collapses red-green or green-blue distinctions to simulate the
effects of different types of color-blindness.")
    (license license:gpl2+)))

(define-public r-digest
  (package
    (name "r-digest")
    (version "0.6.8")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/digest_"
                           version ".tar.gz"))
       (sha256
        (base32 "0m9grqv67hhf51lz10whymhw0g0d98466ka694kya5x95hn44qih"))))
    (build-system r-build-system)
    (home-page "http://dirk.eddelbuettel.com/code/digest.html")
    (synopsis "Create cryptographic hash digests of R objects")
    (description
     "This package contains an implementation of a function 'digest()' for the
creation of hash digests of arbitrary R objects (using the md5, sha-1,
sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison
of R language objects, as well as a function 'hmac()' to create hash-based
message authentication code.

Please note that this package is not meant to be deployed for cryptographic
purposes for which more comprehensive (and widely tested) libraries such as
OpenSSL should be used.")
    (license license:gpl2+)))

(define-public r-gtable
  (package
    (name "r-gtable")
    (version "0.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/gtable_"
                           version ".tar.gz"))
       (sha256
        (base32 "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/gtable")
    (synopsis "R library to arrange grobs in tables")
    (description
     "Gtable is a collection of tools to make it easier to work with
\"tables\" of grobs.")
    (license license:gpl2+)))

(define-public r-labeling
  (package
    (name "r-labeling")
    (version "0.3")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/labeling_"
                           version ".tar.gz"))
       (sha256
        (base32 "13sk7zrrrzry6ky1bp8mmnzcl9jhvkig8j4id9nny7z993mnk00d"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/labeling")
    (synopsis "Axis labeling algorithms")
    (description "The labeling package provides a range of axis labeling
algorithms.")
    (license license:expat)))

(define-public r-magrittr
  (package
    (name "r-magrittr")
    (version "1.5")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/magrittr_"
                           version ".tar.gz"))
       (sha256
        (base32 "1s1ar6rag8m277qcqmdp02gn4awn9bdj9ax0r8s32i59mm1mki05"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/magrittr/index.html")
    (synopsis "A forward-pipe operator for R")
    (description
     "Magrittr provides a mechanism for chaining commands with a new
forward-pipe operator, %>%.  This operator will forward a value, or the result
of an expression, into the next function call/expression.  There is flexible
support for the type of right-hand side expressions.  For more information,
see package vignette.  To quote Rene Magritte, \"Ceci n'est pas un pipe.\"")
    (license license:expat)))

(define-public r-munsell
  (package
    (name "r-munsell")
    (version "0.4.2")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/munsell_"
                           version ".tar.gz"))
       (sha256
        (base32 "1bi5yi0i80778bbzx2rm4f0glpc34kvh24pwwfhm4v32izsqgrw4"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-colorspace" ,r-colorspace)))
    (home-page "http://cran.r-project.org/web/packages/munsell")
    (synopsis "Munsell colour system")
    (description
     "The Munsell package contains Functions for exploring and using the
Munsell colour system.")
    (license license:expat)))

(define-public r-rcpp
  (package
    (name "r-rcpp")
    (version "0.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "mirror://cran/src/contrib/Rcpp_"
                           version ".tar.gz"))
       (sha256
        (base32 "182109z0yc1snqgd833ssl2cix6cbq83bcxmy5344b15ym820y38"))))
    (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+)))