gnu: Add r-foreach.

[jackhill/guix/guix.git] / gnu / packages / statistics.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com>
;;; Copyright © 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;;
;;; 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 (guix build-system python)
  #:use-module (gnu packages)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages haskell)
  #: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 python)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages ssh)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages base)
  #:use-module (gnu packages web)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (gnu packages zip)
  #:use-module (srfi srfi-1))

(define-public r
  (package
    (name "r")
    (version "3.2.3")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://cran/src/base/R-"
                                  (version-prefix version 1) "/R-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "1hdnv77ralzcx5k5b88jq1r8l6zqnywpq00g2qs949rqh63psfxr"))))
    (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))
         (add-after 'build 'make-info
          (lambda _ (zero? (system* "make" "info"))))
         (add-after 'build 'install-info
          (lambda _ (zero? (system* "make" "install-info")))))
       #:configure-flags
       '("--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")))
    ;; R has some support for Java.  When the JDK is available at configure
    ;; time environment variables pointing to the JDK will be recorded under
    ;; $R_HOME/etc and ./tools/getsp.java will be compiled which is used by "R
    ;; CMD javareconf".  "R CMD javareconf" appears to only be used to update
    ;; the recorded environment variables in $R_HOME/etc.  Refer to
    ;; https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Java-support
    ;; for additional information.

    ;; As the JDK is a rather large input with only very limited effects on R,
    ;; we decided to drop it.
    (native-inputs
     `(("bzip2" ,bzip2)
       ("perl" ,perl)
       ("pkg-config" ,pkg-config)
       ("texinfo" ,texinfo) ; for building HTML manuals
       ("which" ,which) ; for tests/Examples/base-Ex.R
       ("xz" ,xz)))
    (inputs
     `(("cairo" ,cairo)
       ("gfortran" ,gfortran)
       ("icu4c" ,icu4c)
       ("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 (cran-uri "colorspace" version))
       (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 (cran-uri "dichromat" version))
       (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 (cran-uri "digest" version))
       (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 (cran-uri "gtable" version))
       (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 (cran-uri "labeling" version))
       (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 (cran-uri "magrittr" version))
       (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 (cran-uri "munsell" version))
       (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 (cran-uri "Rcpp" version))
       (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+)))

(define-public r-plyr
  (package
    (name "r-plyr")
    (version "1.8.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "plyr" version))
       (sha256
        (base32 "06v4zxawpjz37rp2q2ii5q43g664z9s29j4ydn0cz3crn7lzl6pk"))))
    (build-system r-build-system)
    (native-inputs `(("r-rcpp" ,r-rcpp)))
    (home-page "http://had.co.nz/plyr")
    (synopsis "Tools for Splitting, Applying and Combining Data")
    (description
     "Plyr is a set of tools that solves a common set of problems: you need to
break a big problem down into manageable pieces, operate on each piece and
then put all the pieces back together.  For example, you might want to fit a
model to each spatial location or time point in your study, summarise data by
panels or collapse high-dimensional arrays to simpler summary statistics.")
    (license license:expat)))

(define-public r-proto
  (package
    (name "r-proto")
    (version "0.3-10")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "proto" version))
       (sha256
        (base32 "03mvzi529y6kjcp9bkpk7zlgpcakb3iz73hca6rpjy14pyzl3nfh"))))
    (build-system r-build-system)
    (home-page "http://r-proto.googlecode.com")
    (synopsis "Prototype object-based programming")
    (description
     "Proto is an object oriented system using object-based, also called
prototype-based, rather than class-based object oriented ideas.")
    (license license:gpl2+)))

(define-public r-rcolorbrewer
  (package
    (name "r-rcolorbrewer")
    (version "1.1-2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "RColorBrewer" version))
       (sha256
        (base32 "1pfcl8z1pnsssfaaz9dvdckyfnnc6rcq56dhislbf571hhg7isgk"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/RColorBrewer")
    (synopsis "ColorBrewer palettes")
    (description
     "This package provides color schemes for maps (and other graphics)
designed by Cynthia Brewer as described at http://colorbrewer2.org")
    ;; Includes code licensed under bsd-4
    (license license:asl2.0)))

(define-public r-stringi
  (package
    (name "r-stringi")
    (version "0.5-5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "stringi" version))
       (sha256
        (base32
         "183wrrjhpgl1wbnn9lhghyvhz7l2mc64mpcmzplckal7y9j7pmhw"))))
    (build-system r-build-system)
    (inputs `(("icu4c" ,icu4c)))
    (native-inputs `(("pkg-config" ,pkg-config)))
    (home-page "http://stringi.rexamine.com/")
    (synopsis "Character string processing facilities")
    (description
     "This package allows for fast, correct, consistent, portable, as well as
convenient character string/text processing in every locale and any native
encoding.  Owing to the use of the ICU library, the package provides R users
with platform-independent functions known to Java, Perl, Python, PHP, and Ruby
programmers.  Among available features there are: pattern searching
 (e.g.  via regular expressions), random string generation, string collation,
transliteration, concatenation, date-time formatting and parsing, etc.")
    (license license:bsd-3)))

(define-public r-stringr
  (package
    (name "r-stringr")
    (version "1.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "stringr" version))
       (sha256
        (base32 "0jnz6r9yqyf7dschr2fnn1slg4wn6b4ik5q00j4zrh43bfw7s9pq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-magrittr" ,r-magrittr)
       ("r-stringi" ,r-stringi)))
    (home-page "https://github.com/hadley/stringr")
    (synopsis "Simple, consistent wrappers for common string operations")
    (description
     "Stringr is a consistent, simple and easy to use set of wrappers around
the fantastic 'stringi' package.  All function and argument names (and
positions) are consistent, all functions deal with \"NA\"'s and zero length
vectors in the same way, and the output from one function is easy to feed into
the input of another.")
    (license license:gpl2+)))

(define-public r-reshape2
  (package
    (name "r-reshape2")
    (version "1.4.1")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "reshape2" version))
       (sha256
        (base32 "0hl082dyk3pk07nqprpn5dvnrkqhnf6zjnjig1ijddxhlmsrzm7v"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-plyr" ,r-plyr)
       ("r-rcpp" ,r-rcpp)
       ("r-stringr" ,r-stringr)))
    (home-page "https://github.com/hadley/reshape")
    (synopsis "Flexibly reshape data: a reboot of the \"reshape\" package")
    (description
     "Reshape2 is an R library to flexibly restructure and aggregate data
using just two functions: melt and dcast (or acast).")
    (license license:expat)))

(define-public r-scales
  (package
    (name "r-scales")
    (version "0.3.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "scales" version))
       (sha256
        (base32 "1kkgpqzb0a6lnpblhcprr4qzyfk5lhicdv4639xs5cq16n7bkqgl"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-dichromat" ,r-dichromat)
       ("r-labeling" ,r-labeling)
       ("r-munsell" ,r-munsell)
       ("r-plyr" ,r-plyr)
       ("r-rcolorbrewer" ,r-rcolorbrewer)
       ("r-rcpp" ,r-rcpp)))
    (home-page "https://github.com/hadley/scales")
    (synopsis "Scale functions for visualization")
    (description
     "This package provides graphical scales that map data to aesthetics, and
provides methods for automatically determining breaks and labels for axes and
legends.")
    (license license:expat)))

(define-public r-ggplot2
  (package
    (name "r-ggplot2")
    (version "2.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ggplot2" version))
       (sha256
        (base32 "07r5zw0ccv4sf1mdxcz9wa86p2c6j61cnnq18qdjrh3zhhcbmdp2"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-digest" ,r-digest)
       ("r-gtable" ,r-gtable)
       ("r-plyr" ,r-plyr)
       ("r-proto" ,r-proto)
       ("r-reshape2" ,r-reshape2)
       ("r-scales" ,r-scales)))
    (home-page "http://ggplot2.org")
    (synopsis "An implementation of the grammar of graphics")
    (description
     "Ggplot2 is an implementation of the grammar of graphics in R.  It
combines the advantages of both base and lattice graphics: conditioning and
shared axes are handled automatically, and you can still build up a plot step
by step from multiple data sources.  It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map data to
aesthetic attributes.")
    (license license:gpl2+)))

(define-public r-assertthat
  (package
    (name "r-assertthat")
    (version "0.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "assertthat" version))
              (sha256
               (base32
                "0dwsqajyglfscqilj843qfqn1ndbqpswa7b4l1d633qjk9d68qqk"))))
    (build-system r-build-system)
    (home-page "https://github.com/hadley/assertthat")
    (synopsis "Easy pre and post assertions")
    (description
     "Assertthat is an extension to stopifnot() that makes it easy to declare
the pre and post conditions that your code should satisfy, while also
producing friendly error messages so that your users know what they've done
wrong.")
    (license license:gpl3+)))

(define-public r-lazyeval
  (package
    (name "r-lazyeval")
    (version "0.1.10")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "lazyeval" version))
              (sha256
               (base32
                "02qfpn2fmy78vx4jxr7g7rhqzcm1kcivfwai7lbh0vvpawia0qwh"))))
    (build-system r-build-system)
    (home-page "https://github.com/hadley/lazyeval")
    (synopsis "Lazy (non-standard) evaluation in R")
    (description
     "This package provides the tools necessary to do non-standard
evaluation (NSE) in R.")
    (license license:gpl3+)))

(define-public r-dbi
  (package
    (name "r-dbi")
    (version "0.3.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "DBI" version))
              (sha256
               (base32
                "0xj5baxwnhl23rd5nskhjvranrwrc68f3xlyrklglipi41bm69hw"))))
    (build-system r-build-system)
    (home-page "https://github.com/rstats-db/DBI")
    (synopsis "R database interface")
    (description
     "The DBI package provides a database interface (DBI) definition for
communication between R and relational database management systems.  All
classes in this package are virtual and need to be extended by the various
R/DBMS implementations.")
    (license license:lgpl2.0+)))

(define-public r-bh
  (package
    (name "r-bh")
    (version "1.58.0-1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "BH" version))
              (sha256
               (base32
                "17rnwyw9ib2pvm60iixzkbz7ff4fslpifp1nlx4czp42hy67kqpf"))))
    (build-system r-build-system)
    (home-page "https://github.com/eddelbuettel/bh")
    (synopsis "R package providing subset of Boost headers")
    (description
     "This package aims to provide the most useful subset of Boost libraries
for template use among CRAN packages.")
    (license license:boost1.0)))

(define-public r-evaluate
  (package
    (name "r-evaluate")
    (version "0.8")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "evaluate" version))
              (sha256
               (base32
                "137gc35jlizhqnx19mxim3llrkm403abj8ghb2b7v5ls9rvd40pq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-stringr" ,r-stringr)))
    (home-page "https://github.com/hadley/evaluate")
    (synopsis "Parsing and evaluation tools for R")
    (description
     "This package provides tools that allow you to recreate the parsing,
evaluation and display of R code, with enough information that you can
accurately recreate what happens at the command line.  The tools can easily be
adapted for other output formats, such as HTML or LaTeX.")
    (license license:gpl3+)))

(define-public r-formatr
  (package
    (name "r-formatr")
    (version "1.2.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "formatR" version))
              (sha256
               (base32
                "0f4cv2zv5wayyqx99ybfyl0p83kgjvnsv8dhcwa4s49kw6jsx1lr"))))
    (build-system r-build-system)
    (home-page "http://yihui.name/formatR")
    (synopsis "Format R code automatically")
    (description
     "This package provides a function to format R source code.  Spaces and
indent will be added to the code automatically, and comments will be preserved
under certain conditions, so that R code will be more human-readable and tidy.
There is also a Shiny app as a user interface in this package.")
    (license license:gpl3+)))

(define-public r-highr
  (package
    (name "r-highr")
    (version "0.5.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "highr" version))
              (sha256
               (base32
                "11hyawzhaw3ph5y5xphi7alx6df1d0i6wh0a2n5m4sxxhdrzswnb"))))
    (build-system r-build-system)
    (home-page "https://github.com/yihui/highr")
    (synopsis "Syntax highlighting for R source code")
    (description
     "This package provides syntax highlighting for R source code.  Currently
it supports LaTeX and HTML output.  Source code of other languages is
supported via Andre Simon's highlight package.")
    (license license:gpl3+)))

(define-public r-mime
  (package
    (name "r-mime")
    (version "0.4")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "mime" version))
              (sha256
               (base32
                "145cdcg252w2zsq67dmvmsqka60msfp7agymlxs3gl3ihgiwg46p"))))
    (build-system r-build-system)
    (home-page "https://github.com/yihui/mime")
    (synopsis "R package to map filenames to MIME types")
    (description
     "This package guesses the MIME type from a filename extension using the
data derived from /etc/mime.types in UNIX-type systems.")
    (license license:gpl2)))

(define-public r-markdown
  (package
    (name "r-markdown")
    (version "0.7.7")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "markdown" version))
              (sha256
               (base32
                "00j1hlib3il50azs2vlcyhi0bjpx1r50mxr9w9dl5g1bwjjc71hb"))))
    (build-system r-build-system)
    ;; Skip check phase because the tests require the r-knitr package to be
    ;; installed. This prevents installation failures. Knitr normally
    ;; shouldn't be available since r-markdown is a dependency of the r-knitr
    ;; package.
    (arguments `(#:tests? #f))
    (propagated-inputs
     `(("r-mime" ,r-mime)))
    (home-page "https://github.com/rstudio/markdown")
    (synopsis "Markdown rendering for R")
    (description
     "This package provides R bindings to the Sundown Markdown rendering
library (https://github.com/vmg/sundown).  Markdown is a plain-text formatting
syntax that can be converted to XHTML or other formats.")
    (license license:gpl2)))

(define-public r-yaml
  (package
    (name "r-yaml")
    (version "2.1.13")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "yaml" version))
              (sha256
               (base32
                "18kz5mfn7qpif5pn91w4vbrc5bkycsj85vwm5wxwzjlb02i9mxi6"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/yaml/")
    (synopsis "Methods to convert R data to YAML and back")
    (description
     "This package implements the libyaml YAML 1.1 parser and
emitter (http://pyyaml.org/wiki/LibYAML) for R.")
    (license license:bsd-3)))

(define-public r-knitr
  (package
    (name "r-knitr")
    (version "1.11")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "knitr" version))
              (sha256
               (base32
                "1ikjla0hnpjfkdbydqhhqypc0aiizbi4nyn8c694sdk9ca4jasdd"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-evaluate" ,r-evaluate)
       ("r-digest" ,r-digest)
       ("r-formatr" ,r-formatr)
       ("r-highr" ,r-highr)
       ("r-markdown" ,r-markdown)
       ("r-stringr" ,r-stringr)
       ("r-yaml" ,r-yaml)))
    (home-page "http://yihui.name/knitr/")
    (synopsis "General-purpose package for dynamic report generation in R")
    (description
     "This package provides a general-purpose tool for dynamic report
generation in R using Literate Programming techniques.")
    ;; The code is released under any version of the GPL.  As it is used by
    ;; r-markdown which is available under GPLv2 only, we have chosen GPLv2+
    ;; here.
    (license license:gpl2+)))

(define-public r-microbenchmark
  (package
    (name "r-microbenchmark")
    (version "1.4-2")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "microbenchmark" version))
              (sha256
               (base32
                "05yxvdnkxr2ll94h6f2m5sn3gg7vrlm9nbdxgmj2g8cp8gfxpfkg"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ggplot2" ,r-ggplot2)))
    (home-page "https://cran.r-project.org/web/packages/microbenchmark/")
    (synopsis "Accurate timing functions for R")
    (description
     "This package provides infrastructure to accurately measure and compare
the execution time of R expressions.")
    (license license:bsd-2)))

(define-public r-codetools
  (package
    (name "r-codetools")
    (version "0.2-14")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "codetools" version))
              (sha256
               (base32
                "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
    (build-system r-build-system)
    (home-page "https://cran.r-project.org/web/packages/codetools/index.html")
    (synopsis "Code analysis tools for R")
    (description "This package provides code analysis tools for R.")
    (license license:gpl3+)))

(define-public r-pryr
  (package
    (name "r-pryr")
    (version "0.1.2")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "pryr" version))
              (sha256
               (base32
                "1in350a8hxwf580afavasvn3jc7x2p1b7nlwmj1scakfz74vghk5"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-stringr" ,r-stringr)
       ("r-codetools" ,r-codetools)))
    (native-inputs
     `(("r-rcpp" ,r-rcpp)))
    (home-page "https://github.com/hadley/pryr")
    (synopsis "Tools for computing on the R language")
    (description
     "This package provides useful tools to pry back the covers of R and
understand the language at a deeper level.")
    (license license:gpl2)))

(define-public r-memoise
  (package
    (name "r-memoise")
    (version "0.2.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "memoise" version))
              (sha256
               (base32
                "19wm4b3kq6xva43kga3xydnl7ybl5mq7b4y2fczgzzjz63jd75y4"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-digest" ,r-digest)))
    (home-page "http://github.com/hadley/memoise")
    (synopsis "Memoise functions for R")
    (description
     "This R package allows to cache the results of a function so that when
you call it again with the same arguments it returns the pre-computed value.")
    (license license:expat)))

(define-public r-crayon
  (package
    (name "r-crayon")
    (version "1.3.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "crayon" version))
              (sha256
               (base32
                "0d38fm06h272a8iqlc0d45m2rh36giwqw7mwq4z8hkp4vs975fmm"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-memoise" ,r-memoise)))
    (home-page "https://github.com/gaborcsardi/crayon")
    (synopsis "Colored terminal output for R")
    (description
     "Colored terminal output on terminals that support ANSI color and
highlight codes.  It also works in Emacs ESS.  ANSI color support is
automatically detected.  Colors and highlighting can be combined and nested.
New styles can also be created easily.  This package was inspired by the
\"chalk\" JavaScript project.")
    (license license:expat)))

(define-public r-testthat
  (package
    (name "r-testthat")
    (version "0.10.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "testthat" version))
              (sha256
               (base32
                "0b3akwcx5mv9dmi8vssbk91hr3yrrdxd2fm6zhr31fnyz8kjx4pw"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-digest" ,r-digest)
       ("r-crayon" ,r-crayon)))
    (home-page "https://github.com/hadley/testthat")
    (synopsis "Unit testing for R")
    (description
     "This package provides a unit testing system for R designed to be fun,
flexible and easy to set up.")
    (license license:expat)))

(define-public r-r6
  (package
    (name "r-r6")
    (version "2.1.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "R6" version))
              (sha256
               (base32
                "16qq35bgxgswf989yvsqkb6fv7srpf8n8dv2s2c0z9n6zgmwq66m"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-knitr" ,r-knitr)
       ("r-microbenchmark" ,r-microbenchmark)
       ("r-pryr" ,r-pryr)
       ("r-testthat" ,r-testthat)
       ("r-ggplot2" ,r-ggplot2)
       ("r-scales" ,r-scales)))
    (home-page "https://github.com/wch/R6/")
    (synopsis "Classes with reference semantics in R")
    (description
     "The R6 package allows the creation of classes with reference semantics,
similar to R's built-in reference classes.  Compared to reference classes, R6
classes are simpler and lighter-weight, and they are not built on S4 classes
so they do not require the methods package.  These classes allow public and
private members, and they support inheritance, even when the classes are
defined in different packages.")
    (license license:expat)))

(define-public r-dplyr
  (package
    (name "r-dplyr")
    (version "0.4.3")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "dplyr" version))
              (sha256
               (base32
                "1p8rbn4p4yrx2840dapwiahf9iqa8gnvd35nyc200wfhmrxlqdlc"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-assertthat" ,r-assertthat)
       ("r-r6" ,r-r6)
       ("r-magrittr" ,r-magrittr)
       ("r-lazyeval" ,r-lazyeval)
       ("r-dbi" ,r-dbi)))
    (native-inputs
     `(("r-rcpp" ,r-rcpp)
       ("r-bh" ,r-bh)))
    (home-page "https://github.com/hadley/dplyr")
    (synopsis "Tools for working with data frames in R")
    (description
     "dplyr is the next iteration of plyr.  It is focussed on tools for
working with data frames.  It has three main goals: 1) identify the most
important data manipulation tools needed for data analysis and make them easy
to use in R; 2) provide fast performance for in-memory data by writing key
pieces of code in C++; 3) use the same code interface to work with data no
matter where it is stored, whether in a data frame, a data table or
database.")
    (license license:expat)))

(define-public r-chron
  (package
    (name "r-chron")
    (version "2.3-47")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "chron" version))
              (sha256
               (base32
                "1xj50kk8b8mbjpszp8i0wbripb5a4b36jcscwlbyap8n4487g34s"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/chron")
    (synopsis "Chronological R objects which can handle dates and times")
    (description
     "This package provides chronological R objects which can handle dates and
times.")
    (license license:gpl2)))

(define-public r-data-table
  (package
    (name "r-data-table")
    (version "1.9.6")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "data.table" version))
              (sha256
               (base32
                "0vi3zplpxqbg78z9ifjfs1kl2i8qhkqxr7l9ysp2663kq54w6x3g"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-chron" ,r-chron)))
    (home-page "https://github.com/Rdatatable/data.table/wiki")
    (synopsis "Enhanced version of data.frame R object")
    (description
     "The R package @code{data.table} is an extension of @code{data.frame}
providing functions for fast aggregation of large data (e.g. 100GB in RAM),
fast ordered joins, fast add/modify/delete of columns by group, column listing
and fast file reading.")
    (license license:gpl3+)))

(define-public python-patsy
  (package
    (name "python-patsy")
    (version "0.4.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "patsy" version ".zip"))
              (sha256
               (base32
                "1m6knyq8hbqlx242y4da02j0x86j4qggs1j7q186w3jv0j0c476w"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check (lambda _ (zero? (system* "nosetests" "-v"))))
         (add-after 'unpack 'prevent-generation-of-egg-archive
          (lambda _
            (substitute* "setup.py"
              (("from setuptools import setup")
               "from distutils.core import setup"))
            #t)))))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-scipy" ,python-scipy)
       ("python-six" ,python-six)))
    (native-inputs
     `(("python-nose" ,python-nose)
       ("unzip" ,unzip)))
    (home-page "https://github.com/pydata/patsy")
    (synopsis "Describe statistical models and build design matrices")
    (description
     "Patsy is a Python package for describing statistical models and for
building design matrices.")
    ;; The majority of the code is distributed under BSD-2.  The module
    ;; patsy.compat contains code derived from the Python standard library,
    ;; and is covered by the PSFL.
    (license (list license:bsd-2 license:psfl))
    (properties `((python2-variant . ,(delay python2-patsy))))))

(define-public python2-patsy
  (let ((patsy (package-with-python2 (strip-python2-variant python-patsy))))
    (package (inherit patsy)
      (native-inputs
       `(("python2-setuptools" ,python2-setuptools)
         ,@(package-native-inputs patsy))))))

(define-public python-statsmodels
  (package
    (name "python-statsmodels")
    (version "0.6.1")
    (source
     (origin
       (method url-fetch)
       (uri (string-append "https://pypi.python.org/packages/source/"
                           "s/statsmodels/statsmodels-" version ".tar.gz"))
       (sha256
        (base32
         "0xn67sqr0cc1lmlhzm71352hrb4hw7g318p5ff5q97pc98vl8kmy"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         ;; tests must be run after installation
         (delete 'check)
         (add-after 'unpack 'set-matplotlib-backend-to-agg
          (lambda _
            ;; Set the matplotlib backend to Agg to avoid problems using the
            ;; GTK backend without a display.
            (substitute* (find-files "statsmodels/graphics/tests" "\\.py")
              (("import matplotlib\\.pyplot as plt" line)
               (string-append "import matplotlib;matplotlib.use('Agg');"
                              line)))
            #t))
         (add-after 'install 'check
          (lambda _
            (with-directory-excursion "/tmp"
              (zero? (system* "nosetests"
                              "--stop"
                              "-v" "statsmodels"))))))))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-scipy" ,python-scipy)
       ("python-pandas" ,python-pandas)
       ("python-patsy" ,python-patsy)
       ("python-matplotlib" ,python-matplotlib)))
    (native-inputs
     `(("python-cython" ,python-cython)
       ("python-nose" ,python-nose)
       ("python-sphinx" ,python-sphinx)))
    (home-page "http://statsmodels.sourceforge.net/")
    (synopsis "Statistical modeling and econometrics in Python")
    (description
     "Statsmodels is a Python package that provides a complement to scipy for
statistical computations including descriptive statistics and estimation and
inference for statistical models.")
    (license license:bsd-3)))

(define-public python2-statsmodels
  (let ((stats (package-with-python2 python-statsmodels)))
    (package (inherit stats)
      (propagated-inputs
       `(("python2-numpy" ,python2-numpy)
         ("python2-scipy" ,python2-scipy)
         ("python2-pandas" ,python2-pandas)
         ("python2-patsy" ,python2-patsy)
         ("python2-matplotlib" ,python2-matplotlib)))
      (native-inputs
       `(("python2-setuptools" ,python2-setuptools)
         ,@(package-native-inputs stats))))))

(define-public r-xml2
  (package
    (name "r-xml2")
    (version "0.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "xml2" version))
       (sha256
        (base32
         "0jjilz36h7vbdbkpvjnja1vgjf6d1imql3z4glqn2m2b74w5qm4c"))))
    (build-system r-build-system)
    (inputs
     `(("libxml2" ,libxml2)))
    (propagated-inputs
     `(("r-rcpp" ,r-rcpp)
       ("r-bh" ,r-bh)))
    (home-page "https://github.com/hadley/xml2")
    (synopsis "Parse XML with R")
    (description
     "This package provides a simple, consistent interface to working with XML
files in R.  It is built on top of the libxml2 C library.")
    (license license:gpl2+)))

(define-public r-rversions
  (package
    (name "r-rversions")
    (version "1.0.2")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "rversions" version))
              (sha256
               (base32
                "0xmi461g1rf5ngb7r1sri798jn6icld1xq25wj9jii2ca8j8xv68"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-curl" ,r-curl)
       ("r-xml2" ,r-xml2)))
    (home-page "https://github.com/metacran/rversions")
    (synopsis "Query R versions, including 'r-release' and 'r-oldrel'")
    (description
     "This package provides functions to query the main R repository to find
the versions that @code{r-release} and @code{r-oldrel} refer to, and also all
previous R versions and their release dates.")
    (license license:expat)))

(define-public r-whisker
  (package
    (name "r-whisker")
    (version "0.3-2")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "whisker" version))
              (sha256
               (base32
                "0z4cn115gxcl086d6bnqr8afi67b6a7xqg6ivmk3l4ng1x8kcj28"))))
    (build-system r-build-system)
    (home-page "http://github.com/edwindj/whisker")
    (synopsis "Logicless mustache templating for R")
    (description
     "This package provides logicless templating, with a syntax that is not
limited to R.")
    (license license:gpl3+)))

(define-public r-brew
  (package
    (name "r-brew")
    (version "1.0-6")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "brew" version))
              (sha256
               (base32
                "1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/brew")
    (synopsis "Templating framework for report generation")
    (description
     "The brew package implements a templating framework for mixing text and R
code for report generation.  The template syntax is similar to PHP, Ruby's erb
module, Java Server Pages, and Python's psp module.")
    (license license:gpl2+)))

(define-public r-roxygen2
  (package
    (name "r-roxygen2")
    (version "5.0.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "roxygen2" version))
              (sha256
               (base32
                "0xjdphjs7l1v71lylmqgp76cbcxzvm9z1a40jgkdwvz072nn08vr"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-brew" ,r-brew)
       ("r-digest" ,r-digest)
       ("r-rcpp" ,r-rcpp)
       ("r-stringi" ,r-stringi)
       ("r-stringr" ,r-stringr)))
    (home-page "https://github.com/klutometis/roxygen")
    (synopsis "In-source documentation system for R")
    (description
     "Roxygen2 is a Doxygen-like in-source documentation system for Rd,
collation, and NAMESPACE files.")
    (license license:gpl2+)))

(define-public r-httr
  (package
    (name "r-httr")
    (version "1.0.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "httr" version))
              (sha256
               (base32
                "1yprw8p4g8026jhravgg1hdwj1g51cpdgycyr5a58jwm4i5f79cq"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-curl" ,r-curl)
       ("r-digest" ,r-digest)
       ("r-jsonlite" ,r-jsonlite)
       ("r-mime" ,r-mime)
       ("r-r6" ,r-r6)
       ("r-stringr" ,r-stringr)))
    (home-page "https://github.com/hadley/httr")
    (synopsis "Tools for working with URLs and HTTP")
    (description
     "The aim of httr is to provide a wrapper for RCurl customised to the
demands of modern web APIs.  It provides useful tools for working with HTTP
organised by HTTP verbs (@code{GET()}, @code{POST()}, etc).  Configuration
functions make it easy to control additional request components.")
    (license license:expat)))

(define-public r-git2r
  (package
    (name "r-git2r")
    (version "0.11.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "git2r" version))
              (sha256
               (base32
                "1h5ag8sm512jsn2sp4yhiqspc7hjq5y8z0kqz24sdznxa3b7rpn9"))))
    (build-system r-build-system)
    ;; This R package contains modified sources of libgit2.  This modified
    ;; version of libgit2 is built as the package is built.  Hence libgit2 is
    ;; not among the inputs of this package.
    (inputs
     `(("libssh2" ,libssh2)
       ("openssl" ,openssl)
       ("zlib" ,zlib)))
    (home-page "https://github.com/ropensci/git2r")
    (synopsis "Access Git repositories with R")
    (description
     "This package provides an R interface to the libgit2 library, which is a
pure C implementation of the Git core methods.")
    ;; GPLv2 only with linking exception.
    (license license:gpl2)))

(define-public r-rstudioapi
  (package
    (name "r-rstudioapi")
    (version "0.3.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "rstudioapi" version))
              (sha256
               (base32
                "0q7671d924nzqsqhs8d9p7l907bcam56wjwm7vvz44xgj0saj8bs"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/rstudioapi")
    (synopsis "Safely access the RStudio API")
    (description
     "This package provides functions to access the RStudio API and provide
informative error messages when it's not available.")
    (license license:expat)))

(define-public r-devtools
  (package
    (name "r-devtools")
    (version "1.9.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "devtools" version))
              (sha256
               (base32
                "10ycx3kkiz5x8nmgw31d9wa5hhlx2fhda2nqzxfrczqpz1jik6ci"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-curl" ,r-curl)
       ("r-digest" ,r-digest)
       ("r-evaluate" ,r-evaluate)
       ("r-git2r" ,r-git2r)
       ("r-httr" ,r-httr)
       ("r-jsonlite" ,r-jsonlite)
       ("r-memoise" ,r-memoise)
       ("r-roxygen2" ,r-roxygen2)
       ("r-rstudioapi" ,r-rstudioapi)
       ("r-rversions" ,r-rversions)
       ("r-whisker" ,r-whisker)))
    (home-page "https://github.com/hadley/devtools")
    (synopsis "Tools to make developing R packages easier")
    (description "The devtools package is a collection of package development
tools to simplify the devolpment of R packages.")
    (license license:gpl2+)))

(define-public r-readr
  (package
    (name "r-readr")
    (version "0.2.2")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "readr" version))
              (sha256
               (base32
                "156422xwvskynna5kjc8h1qqnn50kxgjrihl2h2b7vm9sxxdyr2m"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-curl" ,r-curl)
       ("r-rcpp" ,r-rcpp)
       ("r-bh" ,r-bh)))
    (home-page "https://github.com/hadley/readr")
    (synopsis "Read tabular data")
    (description
     "This package provides functions to read flat or tabular text files from
disk (or a connection).")
    (license license:gpl2+)))

(define-public r-plotrix
  (package
    (name "r-plotrix")
    (version "3.6")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "plotrix" version))
              (sha256
               (base32
                "0zn6k8azh40v0lg7q9yd4sy30a26bcc0fjvndn4z7k36avlw4i25"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/plotrix")
    (synopsis "Various plotting functions")
    (description
     "This package provides lots of plotting, various labeling, axis and color
scaling functions for R.")
    (license license:gpl2+)))

(define-public r-gridbase
  (package
    (name "r-gridbase")
    (version "0.4-7")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "gridBase" version))
              (sha256
               (base32
                "09jzw4rzwf2y5lcz7b16mb68pn0fqigv34ff7lr6w3yi9k91i1xy"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/gridBase")
    (synopsis "Integration of base and grid graphics")
    (description
     "This package provides an integration of base and grid graphics for R.")
    (license license:gpl2+)))

(define-public r-lattice
  (package
    (name "r-lattice")
    (version "0.20-33")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "lattice" version))
              (sha256
               (base32
                "0car12x5vl9k180i9pc86lq3cvwqakdpqn3lgdf98k9n2h52cilg"))))
    (build-system r-build-system)
    (home-page "http://lattice.r-forge.r-project.org/")
    (synopsis "High-level data visualization system")
    (description
     "The lattice package provides a powerful and elegant high-level data
visualization system inspired by Trellis graphics, with an emphasis on
multivariate data.  Lattice is sufficient for typical graphics needs, and is
also flexible enough to handle most nonstandard requirements.")
    (license license:gpl2+)))

(define-public r-rcpparmadillo
  (package
    (name "r-rcpparmadillo")
    (version "0.6.200.2.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "RcppArmadillo" version))
              (sha256
               (base32
                "137wqqga776yj6synx5awhrzgkz7mmqnvgmggh9l4k6d99vwp9gj"))
              (modules '((guix build utils)))
              ;; Remove bundled armadillo sources
              (snippet
               '(begin
                  (delete-file-recursively "inst/include/armadillo_bits")
                  (delete-file "inst/include/armadillo")))))
    (properties `((upstream-name . "RcppArmadillo")))
    (build-system r-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'link-against-armadillo
           (lambda _
             (substitute* "src/Makevars"
               (("PKG_LIBS=" prefix)
                (string-append prefix "-larmadillo"))))))))
    (propagated-inputs
     `(("r-rcpp" ,r-rcpp)
       ("armadillo" ,armadillo-for-rcpparmadillo)))
    (home-page "https://github.com/RcppCore/RcppArmadillo")
    (synopsis "Rcpp integration for the Armadillo linear algebra library")
    (description
     "Armadillo is a templated C++ linear algebra library that aims towards a
good balance between speed and ease of use.  Integer, floating point and
complex numbers are supported, as well as a subset of trigonometric and
statistics functions.  Various matrix decompositions are provided through
optional integration with LAPACK and ATLAS libraries.  This package includes
the header files from the templated Armadillo library.")
    ;; Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
    ;; bindings to Armadillo) is licensed under the GNU GPL version 2 or
    ;; later, as is the rest of 'Rcpp'.
    (license license:gpl2+)))

(define-public r-bitops
  (package
    (name "r-bitops")
    (version "1.0-6")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "bitops" version))
              (sha256
               (base32
                "176nr5wpnkavn5z0yy9f7d47l37ndnn2w3gv854xav8nnybi6wwv"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/bitops")
    (synopsis "Bitwise operations")
    (description
     "This package provides functions for bitwise operations on integer
vectors.")
    (license license:gpl2+)))

(define-public r-catools
  (package
    (name "r-catools")
    (version "1.17.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "caTools" version))
              (sha256
               (base32
                "1x4szsn2qmbzpyjfdaiz2q7jwhap2gky9wq0riah74q0pzz76ank"))))
    (properties `((upstream-name . "caTools")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bitops" ,r-bitops)))
    (home-page "http://cran.r-project.org/web/packages/caTools")
    (synopsis "Various tools including functions for moving window statistics")
    (description
     "This package contains several basic utility functions including:
moving (rolling, running) window statistic functions, read/write for GIF and
ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64
encoder/decoder, round-off-error-free sum and cumsum, etc.")
    (license license:gpl3+)))

(define-public r-rmarkdown
  (package
    (name "r-rmarkdown")
    (version "0.8.1")
    (source
      (origin
        (method url-fetch)
        (uri (cran-uri "rmarkdown" version))
        (sha256
          (base32
            "07q5g9dvac5j3vnf4sjc60mnkij1k6y7vnzjz6anf499rwdwbxza"))))
    (properties `((upstream-name . "rmarkdown")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-catools" ,r-catools)
       ("r-htmltools" ,r-htmltools)
       ("r-knitr" ,r-knitr)
       ("r-yaml" ,r-yaml)
       ("ghc-pandoc" ,ghc-pandoc)))
    (home-page "http://rmarkdown.rstudio.com")
    (synopsis "Convert R Markdown documents into a variety of formats")
    (description
     "This package provides tools to convert R Markdown documents into a
variety of formats.")
    (license license:gpl3+)))

(define-public r-gtable
  (package
    (name "r-gtable")
    (version "0.1.2")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "gtable" version))
              (sha256
               (base32
                "0k9hfj6r5y238gqh92s3cbdn34biczx3zfh79ix5xq0c5vkai2xh"))))
    (properties `((upstream-name . "gtable")))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/gtable")
    (synopsis "Arrange grobs in tables")
    (description
     "This package provides tools to make it easier to work with tables of
grobs.")
    (license license:gpl2+)))

(define-public r-gridextra
  (package
    (name "r-gridextra")
    (version "2.0.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "gridExtra" version))
              (sha256
               (base32
                "19yyrfd37c5hxlavb9lca9l26wjhc80rlqhgmfj9k3xhbvvpdp17"))))
    (properties `((upstream-name . "gridExtra")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-gtable" ,r-gtable)))
    (native-inputs
     `(("r-knitr" ,r-knitr))) ;for building vignettes
    (home-page "https://github.com/baptiste/gridextra")
    (synopsis "Miscellaneous functions for \"Grid\" graphics")
    (description
     "This package provides a number of user-level functions to work with
@code{grid} graphics, notably to arrange multiple grid-based plots on a page,
and draw tables.")
    (license license:gpl2+)))

(define-public r-rsqlite
  (package
    (name "r-rsqlite")
    (version "1.0.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "RSQLite" version))
              (sha256
               (base32
                "08b1syv8z887gxiw8i09dpqh0zisfb6ihq6qqr01zipvkahzq34f"))))
    (properties `((upstream-name . "RSQLite")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-dbi" ,r-dbi)))
    (home-page "https://github.com/rstats-db/RSQLite")
    (synopsis "SQLite interface for R")
    (description
     "This package embeds the SQLite database engine in R and provides an
interface compliant with the DBI package.  The source for the SQLite
engine (version 3.8.6) is included.")
    (license license:lgpl2.0+)))

(define-public r-rcurl
  (package
    (name "r-rcurl")
    (version "1.95-0.1.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "http://www.bioconductor.org/packages/"
                                  "release/extra/src/"
                                  "contrib/RCurl_" version ".tar.gz"))
              (sha256
               (base32
                "0l7qi45jxlf898n0jazabnam1yyczvqfdknd00bdirhhiplpd1sc"))))
    (properties `((upstream-name . "RCurl")))
    (build-system r-build-system)
    (inputs
     `(("libcurl" ,curl)))
    (propagated-inputs
     `(("r-bitops" ,r-bitops)))
    (home-page "http://www.omegahat.org/RCurl")
    (synopsis "General network client interface for R")
    (description
     "The package allows one to compose general HTTP requests and provides
convenient functions to fetch URIs, GET and POST forms, etc. and process the
results returned by the Web server.  This provides a great deal of control
over the HTTP/FTP/... connection and the form of the request while providing a
higher-level interface than is available just using R socket connections.
Additionally, the underlying implementation is robust and extensive,
supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict,
ldap, and also supports cookies, redirects, authentication, etc.")
    (license license:bsd-3)))

(define-public r-xml
  (package
    (name "r-xml")
    (version "3.98-1.3")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "XML" version))
              (sha256
               (base32
                "0j9ayp8a35g0227a4zd8nbmvnbfnj5w687jal6qvj4lbhi3va7sy"))))
    (properties
     `((upstream-name . "XML")))
    (build-system r-build-system)
    (inputs
     `(("libxml2" ,libxml2)))
    (propagated-inputs
     `(("r-rcurl" ,r-rcurl)))
    (home-page "http://www.omegahat.org/RSXML")
    (synopsis "Tools for parsing and generating XML within R")
    (description
     "Many approaches for both reading and creating XML (and HTML)
documents (including DTDs), both local and accessible via HTTP or FTP.  Also
offers access to an XPath \"interpreter\".")
    (license license:bsd-2)))

(define-public r-lambda-r
  (package
    (name "r-lambda-r")
    (version "1.1.7")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "lambda.r" version))
              (sha256
               (base32
                "1lxzrwyminc3dfb07pbn1rmj45kplxgsb17b06pzflj728knbqwa"))))
    (properties `((upstream-name . "lambda.r")))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/lambda.r")
    (synopsis "Functional programming extension for R")
    (description
     "This package provides a language extension to efficiently write
functional programs in R.  Syntax extensions include multi-part function
definitions, pattern matching, guard statements, built-in (optional) type
safety.")
    (license license:lgpl3+)))

(define-public r-futile-options
  (package
    (name "r-futile-options")
    (version "1.0.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "futile.options" version))
              (sha256
               (base32
                "1hp82h6xqq5cck67h7lpf22n3j7mg3v1mla5y5ivnzrrb7iyr17f"))))
    (properties
     `((upstream-name . "futile.options")))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/futile.options")
    (synopsis "Options management framework")
    (description
     "The futile.options subsystem provides an easy user-defined options
management system that is properly scoped.  This means that options created
via @code{futile.options} are fully self-contained and will not collide with
options defined in other packages.")
    (license license:lgpl3+)))

(define-public r-futile-logger
  (package
    (name "r-futile-logger")
    (version "1.4.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "futile.logger" version))
              (sha256
               (base32
                "1plld1icxrcay7llplbd4i8inpg97crpnczk58mbk26j8glqbr51"))))
    (properties `((upstream-name . "futile.logger")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-futile-options" ,r-futile-options)
       ("r-lambda-r" ,r-lambda-r)))
    (home-page "http://cran.r-project.org/web/packages/futile.logger")
    (synopsis "Logging utility for R")
    (description
     "This package provides a simple yet powerful logging utility.  Based
loosely on log4j, futile.logger takes advantage of R idioms to make logging a
convenient and easy to use replacement for @code{cat} and @code{print}
statements.")
    (license license:lgpl3+)))

(define-public r-snow
  (package
    (name "r-snow")
    (version "0.4-1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "snow" version))
              (sha256
               (base32
                "19r2yq8aqw99vwyx81p6ay4afsfqffal1wzvizk3dj882s2n4j8w"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/snow")
    (synopsis "Support for simple parallel computing in R")
    (description
     "The snow package provides support for simple parallel computing on a
network of workstations using R.  A master R process calls @code{makeCluster}
to start a cluster of worker processes; the master process then uses functions
such as @code{clusterCall} and @code{clusterApply} to execute R code on the
worker processes and collect and return the results on the master.")
    (license (list license:gpl2+ license:gpl3+))))

(define-public r-sparsem
  (package
    (name "r-sparsem")
    (version "1.7")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "SparseM" version))
              (sha256
               (base32
                "0s9kab5khk7daqf6nfp1wm1qnhkssnnwnymisfwyk3kz4q5maqfz"))))
    (properties
     `((upstream-name . "SparseM")))
    (inputs
     `(("gfortran" ,gfortran)))
    (build-system r-build-system)
    (home-page "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html")
    (synopsis "Sparse linear algebra")
    (description
     "This package provides some basic linear algebra functionality for sparse
matrices.  It includes Cholesky decomposition and backsolving as well as
standard R subsetting and Kronecker products.")
    (license license:gpl2+)))

(define-public r-iterators
  (package
    (name "r-iterators")
    (version "1.0.8")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "iterators" version))
       (sha256
        (base32
         "1f057pabs7ss9h1n244can26qsi5n2k3salrdk0b0vkphlrs4kmf"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/iterators")
    (synopsis "Iterator construct for R")
    (description
     "This package provides support for iterators, which allow a programmer to
traverse through all the elements of a vector, list, or other collection of
data.")
    (license license:asl2.0)))

(define-public r-codetools
  (package
    (name "r-codetools")
    (version "0.2-14")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "codetools" version))
       (sha256
        (base32
         "0y9r4m2b8xgavr89sc179knzwpz54xljbc1dinpq2q07i4xn0397"))))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/codetools")
    (synopsis "Code analysis tools for R")
    (description "This package provides code analysis tools for R to check R
code for possible problems.")
    (license (list license:gpl2+ license:gpl3+))))

(define-public r-foreach
  (package
    (name "r-foreach")
    (version "1.4.3")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "foreach" version))
       (sha256
        (base32
         "10aqsd3rxz03s1qdb6gsb1cj89mj4vmh491zfpin4skj1xvkzw0y"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-codetools" ,r-codetools)
       ("r-iterators" ,r-iterators)))
    (home-page "http://cran.r-project.org/web/packages/foreach")
    (synopsis "Foreach looping construct for R")
    (description
     "This package provides support for the @code{foreach} looping construct.
@code{foreach} is an idiom that allows for iterating over elements in a
collection, without the use of an explicit loop counter.  This package in
particular is intended to be used for its return value, rather than for its
side effects.  In that sense, it is similar to the standard @code{lapply}
function, but doesn't require the evaluation of a function.  Using
@code{foreach} without side effects also facilitates executing the loop in
parallel.")
    (license license:asl2.0)))

(define-public r-dt
  (package
    (name "r-dt")
    (version "0.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "DT" version))
              (sha256
               (base32
                "0mj7iiy1gglw7kixybmb7kr1bcl5r006zcb3klkw7p6vvvzdm6qj"))))
    (properties
     `((upstream-name . "DT")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-htmltools" ,r-htmltools)
       ("r-htmlwidgets" ,r-htmlwidgets)
       ("r-magrittr" ,r-magrittr)))
    (home-page "http://rstudio.github.io/DT")
    (synopsis "R wrapper of the DataTables JavaScript library")
    (description
     "This package allows for data objects in R to be rendered as HTML tables
using the JavaScript library 'DataTables' (typically via R Markdown or Shiny).
The 'DataTables' library has been included in this R package.")
    ;; The DT package as a whole is distributed under GPLv3.  The DT package
    ;; inludes other software components under different licenses:
    ;;
    ;;   * Expat: jQuery, jquery.highlight.js, DataTables
    ;;   * ASL2.0: selectize.js
    ;;   * WTFPL: noUiSlider
    (license (list license:gpl3
                   license:expat
                   license:asl2.0
                   (license:non-copyleft "http://www.wtfpl.net/txt/copying/")))))

(define-public r-base64enc
  (package
    (name "r-base64enc")
    (version "0.1-3")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "base64enc" version))
              (sha256
               (base32
                "13b89fhg1nx7zds82a0biz847ixphg9byf5zl2cw9kab6s56v1bd"))))
    (build-system r-build-system)
    (home-page "http://www.rforge.net/base64enc")
    (synopsis "Tools for Base64 encoding")
    (description
     "This package provides tools for handling Base64 encoding.  It is more
flexible than the orphaned \"base64\" package.")
    (license license:gpl2+)))

(define-public r-r-methodss3
  (package
    (name "r-r-methodss3")
    (version "1.7.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "R.methodsS3" version))
              (sha256
               (base32
                "1dg4bbrwr8jcsqisjrrwxs942mrjq72zw8yvl2br4djdm0md8zz5"))))
    (properties `((upstream-name . "R.methodsS3")))
    (build-system r-build-system)
    (home-page "http://cran.r-project.org/web/packages/R.methodsS3")
    (synopsis "S3 methods simplified")
    (description
     "This package provides methods that simplify the setup of S3 generic
functions and S3 methods.  Major effort has been made in making definition of
methods as simple as possible with a minimum of maintenance for package
developers.  For example, generic functions are created automatically, if
missing, and naming conflict are automatically solved, if possible.  The
method @code{setMethodS3()} is a good start for those who in the future may
want to migrate to S4.")
    (license license:lgpl2.1+)))

(define-public r-r-oo
  (package
    (name "r-r-oo")
    (version "1.19.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "R.oo" version))
              (sha256
               (base32
                "15rm1qb9a212bqazhcpk7m48hcp7jq8rh4yhd9c6zfyvdqszfmsb"))))
    (properties `((upstream-name . "R.oo")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-r-methodss3" ,r-r-methodss3)))
    (home-page "https://github.com/HenrikBengtsson/R.oo")
    (synopsis "R object-oriented programming with or without references")
    (description
     "This package provides methods and classes for object-oriented
programming in R with or without references.  Large effort has been made on
making definition of methods as simple as possible with a minimum of
maintenance for package developers.")
    (license license:lgpl2.1+)))

(define-public r-r-utils
  (package
    (name "r-r-utils")
    (version "2.1.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "R.utils" version))
              (sha256
               (base32
                "03pi6pkcsq65fv7cn4x74cj050dc8x5d4xyg930p6f7flk788xaz"))))
    (properties `((upstream-name . "R.utils")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-r-methodss3" ,r-r-methodss3)
       ("r-r-oo" ,r-r-oo)))
    (home-page "https://github.com/HenrikBengtsson/R.utils")
    (synopsis "Various programming utilities")
    (description
     "This package provides utility functions useful when programming and
developing R packages.")
    (license license:lgpl2.1+)))

(define-public r-r-cache
  (package
    (name "r-r-cache")
    (version "0.12.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "R.cache" version))
              (sha256
               (base32
                "006x52w9r8phw5hgqmyp0bz8z42vn8p5yibibnzi1sfa1xlw8iyx"))))
    (properties `((upstream-name . "R.cache")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-digest" ,r-digest)
       ("r-r-methodss3" ,r-r-methodss3)
       ("r-r-oo" ,r-r-oo)
       ("r-r-utils" ,r-r-utils)))
    (home-page "https://github.com/HenrikBengtsson/R.cache")
    (synopsis "Light-weight caching of objects and results")
    (description
     "This package provides methods for caching or memoization of objects and
results.  With this package, any R object can be cached in a key-value storage
where the key can be an arbitrary set of R objects.  The cache memory is
persistent (on the file system).")
    (license license:lgpl2.1+)))

(define-public r-r-rsp
  (package
    (name "r-r-rsp")
    (version "0.20.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "R.rsp" version))
              (sha256
               (base32
                "06vq9qq5hdz3hqc99q82622mab6ix7jwap20h4za6ap6gnwqs0fv"))))
    (properties `((upstream-name . "R.rsp")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-r-cache" ,r-r-cache)
       ("r-r-methodss3" ,r-r-methodss3)
       ("r-r-oo" ,r-r-oo)
       ("r-r-utils" ,r-r-utils)))
    (home-page "https://github.com/HenrikBengtsson/R.rsp")
    (synopsis "Dynamic generation of scientific reports")
    (description
     "The RSP markup language provides a powerful markup for controlling the
content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr
documents (and more), e.g. @code{Today's date is <%=Sys.Date()%>}.  Contrary
to many other literate programming languages, with RSP it is straightforward
to loop over mixtures of code and text sections, e.g.  in month-by-month
summaries.  RSP has also several preprocessing directives for incorporating
static and dynamic contents of external files (local or online) among other
things.  RSP is ideal for self-contained scientific reports and R package
vignettes.")
    (license license:lgpl2.1+)))

(define-public r-matrixstats
  (package
    (name "r-matrixstats")
    (version "0.15.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "matrixStats" version))
              (sha256
               (base32
                "1068k85s6rlwfzlszw790c2rndydvrsw7rpck6k6z17896m8drfa"))))
    (properties `((upstream-name . "matrixStats")))
    (build-system r-build-system)
    (native-inputs
     `(("r-r-rsp" ,r-r-rsp))) ;used to build vignettes
    (home-page "https://github.com/HenrikBengtsson/matrixStats")
    (synopsis "Methods applying to vectors and matrix rows and columns")
    (description
     "This package provides methods operating on rows and columns of matrices,
e.g.  @code{rowMedians()}, @code{rowRanks()}, and @code{rowSds()}.  There are
also some vector-based methods, e.g. @code{binMeans()}, @code{madDiff()} and
@code{weightedMedians()}.  All methods have been optimized for speed and
memory usage.")
    (license license:artistic2.0)))

(define-public r-viridis
  (package
    (name "r-viridis")
    (version "0.3.1")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "viridis" version))
              (sha256
               (base32
                "0zz9i874s1fwhl9bcbiprlzaz7zsy1rj6c729zn3k525d63qbnj7"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ggplot2" ,r-ggplot2)
       ("r-gridextra" ,r-gridextra)))
    (home-page "https://github.com/sjmgarnier/viridis")
    (synopsis "Matplotlib default color map")
    (description
     "This package is a port of the new @url{matplotlib,
http://matplotlib.org/} color maps (@code{viridis}--the default--,
@code{magma}, @code{plasma}, and @code{inferno}) to R.  These color maps are
designed in such a way that they will analytically be perfectly
perceptually-uniform, both in regular form and also when converted to
black-and-white.  They are also designed to be perceived by readers with the
most common form of color blindness.")
    (license license:x11)))

(define-public r-plotly
  (package
    (name "r-plotly")
    (version "2.0.3")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "plotly" version))
              (sha256
               (base32
                "16pqycns8qf0y1j21n009qf242lv0izwyidlx40zv88izxhg1vs0"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-base64enc" ,r-base64enc)
       ("r-digest" ,r-digest)
       ("r-ggplot2" ,r-ggplot2)
       ("r-htmlwidgets" ,r-htmlwidgets)
       ("r-httr" ,r-httr)
       ("r-jsonlite" ,r-jsonlite)
       ("r-magrittr" ,r-magrittr)
       ("r-plyr" ,r-plyr)
       ("r-viridis" ,r-viridis)))
    (home-page "https://plot.ly/r")
    (synopsis "Create interactive web graphics")
    (description
     "This package enables the translation of ggplot2 graphs to an interactive
web-based version and/or the creation of custom web-based visualizations
directly from R.  Once uploaded to a plotly account, plotly graphs (and the
data behind them) can be viewed and modified in a web browser.")
    (license license:x11)))