r.scm

(define-module (nextjournal packages r)
  #:use-module (guix licenses)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system r)
  #:use-module (gnu packages image)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages web)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages statistics))

(define-public r-maps
  (package
   (name "r-maps")
   (version "3.2.0")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "maps" version))
       (sha256
         (base32
           "0577f3b5d3a7djl7r0miy9mzr6xq6jb32p8nyrma7m2azasbwyj3"))))
   (build-system r-build-system)
   (home-page
     "http://cran.r-project.org/web/packages/maps")
   (synopsis "Draw Geographical Maps")
   (description
     "Display of maps.  Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').")
   (license gpl2)))

(define-public r-ggmap
  (package
   (name "r-ggmap")
   (version "2.6.1")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "ggmap" version))
       (sha256
         (base32
           "0mssb09w818jv58h7mly9y181pzv22sgcd4a079cfpq04bs0wigw"))))
   (build-system r-build-system)
   (propagated-inputs
     `(("r-digest" ,r-digest)
       ("r-geosphere" ,r-geosphere)
       ("r-ggplot2" ,r-ggplot2)
       ("r-jpeg" ,r-jpeg)
       ("r-mapproj" ,r-mapproj)
       ("r-plyr" ,r-plyr)
       ("r-png" ,r-png)
       ("r-proto" ,r-proto)
       ("r-reshape2" ,r-reshape2)
       ("r-rgooglemaps" ,r-rgooglemaps)
       ("r-rjson" ,r-rjson)
       ("r-scales" ,r-scales)))
   (home-page "https://github.com/dkahle/ggmap")
   (synopsis "Spatial Visualization with ggplot2")
   (description
     "This package provides a collection of functions to visualize spatial data and models on top of static maps from various online sources (e.g Google Maps and Stamen Maps).  It includes tools common to those tasks, including functions for geolocation and routing.")
   (license gpl2)))

(define-public r-geosphere
  (package
   (name "r-geosphere")
   (version "1.5-5")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "geosphere" version))
       (sha256
         (base32
           "0vffppnyxp7ryg7rvsb1ww9z0ghh1vk20vzgw245pi2gfh9f0vwb"))))
   (build-system r-build-system)
   (propagated-inputs `(("r-sp" ,r-sp)))
   (home-page
     "http://cran.r-project.org/web/packages/geosphere")
   (synopsis "Spherical Trigonometry")
   (description
     "Spherical trigonometry for geographic applications.  That is, compute distances and related measures for angular (longitude/latitude) locations.")
   (license gpl3+)))

(define-public r-jpeg
  (package
   (name "r-jpeg")
   (version "0.1-8")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "jpeg" version))
       (sha256
         (base32
           "05hawv5qcb82ljc1l2nchx1wah8mq2k2kfkhpzyww554ngzbwcnh"))))
   (build-system r-build-system)
   (inputs `(("libjpeg" ,libjpeg)))
   (home-page "http://www.rforge.net/jpeg/")
   (synopsis "Read and write JPEG images")
   (description
     "This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format.  It can read and write both files and in-memory raw vectors.")
   (license #f)))

(define-public r-mapproj
  (package
   (name "r-mapproj")
   (version "1.2-5")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "mapproj" version))
       (sha256
         (base32
           "0rjz37r4rizk2c6jaf54f0kfb60dqv6b262cnhiwjl55d4x6l0pk"))))
   (build-system r-build-system)
   (propagated-inputs `(("r-maps" ,r-maps)))
   (home-page
     "http://cran.r-project.org/web/packages/mapproj")
   (synopsis "Map Projections")
   (description
     "Converts latitude/longitude into projected coordinates.")
   (license #f)))

(define-public r-png
  (package
   (name "r-png")
   (version "0.1-7")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "png" version))
       (sha256
         (base32
           "0g2mcp55lvvpx4kd3mn225mpbxqcq73wy5qx8b4lyf04iybgysg2"))))
   (build-system r-build-system)
   (inputs `(("libpng" ,libpng)))
   (home-page "http://www.rforge.net/png/")
   (synopsis "Read and write PNG images")
   (description
     "This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format.  It can read and write both files and in-memory raw vectors.")
   (license #f)))

(define-public r-rgooglemaps
  (package
   (name "r-rgooglemaps")
   (version "1.4.1")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "RgoogleMaps" version))
       (sha256
         (base32
           "0fsmlnhl4kw2j4972kfanzw9njhnzk695gsyw8g6yppsmz2clcaq"))))
   (properties `((upstream-name . "RgoogleMaps")))
   (build-system r-build-system)
   (propagated-inputs `(("r-png" ,r-png)))
   (home-page
     "http://cran.r-project.org/web/packages/RgoogleMaps")
   (synopsis "Overlays on Static Maps")
   (description
     "Serves two purposes: (i) Provide a comfortable R interface to query the Google server for static maps, and (ii) Use the map as a background image to overlay plots within R.  This requires proper coordinate scaling.")
   (license (list gpl2+ gpl3+))))

(define-public r-sp
  (package
   (name "r-sp")
   (version "1.2-4")
   (source
     (origin
       (method url-fetch)
       (uri (cran-uri "sp" version))
       (sha256
         (base32
           "0crba3j00mb2xv2yk60rpa57gn97xq4ql3a6p9cjzqjxzv2cknk2"))))
   (build-system r-build-system)
   (propagated-inputs `(("r-lattice" ,r-lattice)))
   (home-page
     "http://cran.r-project.org/web/packages/sp")
   (synopsis "Classes and Methods for Spatial Data")
   (description
     "Classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data.  Utility functions are provided, e.g.  for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.")
   (license gpl2+)))

(define-public r-feather
   (package
     (name "r-feather")
     (version "0.3.1")
     (source
       (origin
         (method url-fetch)
         (uri (cran-uri "feather" version))
         (sha256
           (base32
             "1q6dbkfnkpnabq8lb6bm9ma44cfcghx2lm23pyk3vg7943wrn1pi"))))
     (build-system r-build-system)
     (propagated-inputs
       `(("r-hms" ,r-hms)
         ("r-rcpp" ,r-rcpp)
         ("r-tibble" ,r-tibble)))
     (home-page "https://github.com/wesm/feather")
     (synopsis "R Bindings to the Feather 'API'")
     (description
       "Read and write feather files, a lightweight binary columnar data store designed for maximum speed.")
     (license asl2.0)))

(define-public r-diversitree
     (package
       (name "r-diversitree")
       (version "0.9-10")
       (source
         (origin
           (method url-fetch)
           (uri (cran-uri "diversitree" version))
           (sha256
             (base32
               "0gh4rcrp0an3jh8915i1fsxlgyfk7njywgbd5ln5r2jhr085kpz7"))))
       (build-system r-build-system)
       (native-inputs
            `(("gfortran" ,gfortran)))
       (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
       (propagated-inputs
         `(("r-ape" ,r-ape)
           ("r-desolve" ,r-desolve)
           ("r-rcpp" ,r-rcpp)
           ("r-subplex" ,r-subplex)))
       (home-page
         "http://www.zoology.ubc.ca/prog/diversitree")
       (synopsis
         "Comparative 'Phylogenetic' Analyses of Diversification")
       (description
         "Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution.  Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.")
       (license gpl2+)))

(define-public r-desolve
      (package
        (name "r-desolve")
        (version "1.14")
        (source
          (origin
            (method url-fetch)
            (uri (cran-uri "deSolve" version))
            (sha256
              (base32
                "1c4yv5xjk36xwjs0ywxfas1f2xcg05ppf4380s0l3k7gl7vx44g4"))))
        (properties `((upstream-name . "deSolve")))
        (build-system r-build-system)
        (native-inputs
             `(("gfortran" ,gfortran)))
        ;(arguments
        ;  `(#:phases
        ;      (modify-phases %standard-phases
        ;        (delete 'check))))
        (home-page
          "http://desolve.r-forge.r-project.org/")
        (synopsis
          "Solvers for Initial Value Problems of Differential Equations (ODE, DAE, DDE)")
        (description
          "Functions that solve initial value problems of a system of first-order ordinary differential equations (ODE), of partial differential equations (PDE), of differential algebraic equations (DAE), and of delay differential equations.  The functions provide an interface to the FORTRAN functions lsoda, lsodar, lsode, lsodes of the ODEPACK collection, to the FORTRAN functions dvode and daspk and a C-implementation of solvers of the Runge-Kutta family with fixed or variable time steps.  The package contains routines designed for solving ODEs resulting from 1-D, 2-D and 3-D partial differential equations (PDE) that have been converted to ODEs by numerical differencing.")
        (license gpl2+)))

(define-public r-subplex
      (package
        (name "r-subplex")
        (version "1.2-2")
        (source
        (origin
          (method url-fetch)
          (uri (cran-uri "subplex" version))
          (sha256
            (base32
              "10g1hv41w9g0pzj0k071zb3wglk7jl5p99v5maqpkr2v75mfkyry"))))
        (build-system r-build-system)
        (native-inputs
             `(("gfortran" ,gfortran)))
        (home-page
        "http://cran.r-project.org/web/packages/subplex")
        (synopsis
        "Unconstrained Optimization using the Subplex Algorithm")
        (description
        "The subplex algorithm for unconstrained optimization, developed by Tom Rowan <http://www.netlib.org/opt/subplex.tgz>.")
        (license gpl2+)))

(define-public r-plotly
  (package
    (name "r-plotly")
    (version "4.7.0")
    (source (origin
              (method url-fetch)
              (uri (cran-uri "plotly" version))
              (sha256
               (base32
                "1z0qsccdyp0razk40d2yfmzvpvrx3a6ncbdnbf01756wni9szwns"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-base64enc" ,r-base64enc)
       ("r-crosstalk" ,r-crosstalk)
       ("r-data-table" ,r-data-table)
       ("r-digest" ,r-digest)
       ("r-dplyr" ,r-dplyr)
       ("r-ggplot2" ,r-ggplot2)
       ("r-hexbin" ,r-hexbin)
       ("r-htmltools" ,r-htmltools)
       ("r-htmlwidgets" ,r-htmlwidgets)
       ("r-httr" ,r-httr)
       ("r-jsonlite" ,r-jsonlite)
       ("r-lazyeval" ,r-lazyeval)
       ("r-magrittr" ,r-magrittr)
       ("r-purrr" ,r-purrr)
       ("r-scales" ,r-scales)
       ("r-tibble" ,r-tibble)
       ("r-tidyr" ,r-tidyr)
       ("r-viridislite" ,r-viridislite)))
    (home-page "https://plot.ly/r")
    (synopsis "Create interactive web graphics")
    (description
     "Easily translate 'ggplot2' graphs to an interactive web-based version
      and/or create 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 expat)))

(define-public r-crosstalk
  (package
   (name "r-crosstalk")
   (version "1.0.0")
   (source
    (origin
     (method url-fetch)
     (uri (cran-uri "crosstalk" version))
     (sha256
      (base32
       "0lfa89vhrzi7a1rghmygcjr8gzddw35sinb3jx6g49mc9jias7mk"))))
   (build-system r-build-system)
   (propagated-inputs
    `(("r-ggplot2" ,r-ggplot2)
      ("r-htmltools" ,r-htmltools)
      ("r-jsonlite" ,r-jsonlite)
      ("r-lazyeval" ,r-lazyeval)
      ("r-r6" ,r-r6)
      ("r-shiny" ,r-shiny)))
   (home-page
    "https://rstudio.github.io/crosstalk/")
   (synopsis
    "Inter-Widget Interactivity for HTML Widgets")
   (description
    "Provides building blocks for allowing HTML widgets to communicate with each other,
     with Shiny or without (i.e.  static .html files). Currently supports linked brushing
     and filtering.")
   (license expat)))

(define-public r-shiny
  (package
   (name "r-shiny")
   (version "1.0.3")
   (source
    (origin
     (method url-fetch)
     (uri (cran-uri "shiny" version))
     (sha256
      (base32
       "11j4ay1k200hkcb76yx1ahvmkvjrg9k5iy0fchdvmkyv6x25lais"))))
   (build-system r-build-system)
   (propagated-inputs
    `(("r-digest" ,r-digest)
      ("r-htmltools" ,r-htmltools)
      ("r-httpuv" ,r-httpuv)
      ("r-jsonlite" ,r-jsonlite)
      ("r-mime" ,r-mime)
      ("r-r6" ,r-r6)
      ("r-sourcetools" ,r-sourcetools)
      ("r-xtable" ,r-xtable)))
   (home-page "http://shiny.rstudio.com")
   (synopsis "Web Application Framework for R")
   (description
    "Makes it incredibly easy to build interactive web applications with R.  Automatic \"reactive\" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.")
   (license gpl3+)))

;; A version of r-minimal with debugging symbols.
(define-public r-minimal-nextjournal
  (package
    (inherit r-minimal)
    (name "r-minimal-nextjournal")
    (version "3.4.1")
    (source (origin
              (method url-fetch)
              (uri (string-append "https://cran.r-project.org/src/base/R-3/R-"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0y7wlfk3cn1dxn2mpnxwvsk31s0599crbsyah8srm5pa2mfi7c82"))))
    (arguments
      (substitute-keyword-arguments (package-arguments r-minimal)
        ((#:strip-binaries? _ #f) #f)))))