;;; 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 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 "1.4.2")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "shape" version))
       (sha256
        (base32
         "0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66"))))
    (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 "0.4.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "circlize" version))
       (sha256
        (base32
         "0p1zx1aawkblz48kzzfn5w1k3lbwv9wrk1k5gcfjrr2b4sz1pp5b"))))
    (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 "0.70.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "poweRlaw" version))
       (sha256
        (base32
         "1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh"))))
    (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 "0.8.6")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "reshape" version))
       (sha256
        (base32
         "1f1ngalc22knhdm9djv1m6abnjqpv1frdzxfkpakhph2l67bk7fq"))))
    (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 "1.3.0")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "GGally" version))
       (sha256
        (base32
         "12ddab0nd0f9c7bb6cx3c22mliyvc8xsxv26aqz3cvfbla8crp3b"))))
    (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+)))