577 lines
20 KiB
Scheme
577 lines
20 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages cran)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix utils)
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#:use-module (guix build-system r)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages web))
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(define-public r-colorspace
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(package
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(name "r-colorspace")
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(version "1.3-2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "colorspace" version))
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(sha256
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(base32 "0d1ya7hx4y58n5ivwmdmq2zgh0g2sbv7ykh13n85c1355csd57yx"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/colorspace")
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(synopsis "Color space manipulation")
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(description
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"This package carries out a mapping between assorted color spaces
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including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar
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CIELAB. Qualitative, sequential, and diverging color palettes based on HCL
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colors are provided.")
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(license license:bsd-3)))
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(define-public r-glue
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(package
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(name "r-glue")
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(version "1.1.1")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "glue" version))
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(sha256
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(base32
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"01awmqby7rwzhzr51m7d87wqibx7ggl6xair8fi3z3q1hkyyv7ih"))))
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(build-system r-build-system)
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(home-page "https://github.com/tidyverse/glue")
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(synopsis "Interpreted string literals")
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(description
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"This package provides an implementation of interpreted string literals,
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inspired by Python's Literal String Interpolation (PEP-0498) and
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Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
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(license license:expat)))
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(define-public r-plogr
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(package
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(name "r-plogr")
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(version "0.1-1")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "plogr" version))
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(sha256
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(base32
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"13zliqlbkl8b04k9ga0sx5jsh7k867gracgl84l2a9kcqy9mqx92"))))
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(build-system r-build-system)
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(home-page "https://github.com/krlmlr/plogr")
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(synopsis "R bindings for the plog C++ logging library")
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(description
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"This package provides the header files for a stripped-down version of
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the plog header-only C++ logging library, and a method to log to R's standard
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error stream.")
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(license license:expat)))
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(define-public r-rcpp
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(package
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(name "r-rcpp")
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(version "0.12.12")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "Rcpp" version))
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(sha256
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(base32 "1byyqvlgb2p46p1gv243k73rk69fa8pa4l5m5asmckag2pkb2glz"))))
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(build-system r-build-system)
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(home-page "http://www.rcpp.org")
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(synopsis "Seamless R and C++ integration")
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(description
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"The Rcpp package provides R functions as well as C++ classes which offer
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a seamless integration of R and C++. Many R data types and objects can be
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mapped back and forth to C++ equivalents which facilitates both writing of new
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code as well as easier integration of third-party libraries. Documentation
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about Rcpp is provided by several vignettes included in this package, via the
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'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
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and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
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'citation(\"Rcpp\")' for details on these last two.")
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(license license:gpl2+)))
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(define-public r-bindr
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(package
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(name "r-bindr")
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(version "0.1")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "bindr" version))
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(sha256
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(base32
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"0d95ifm0x4mrfzi20xf39f5pzd7rfzqsld0vjqf6xzga5rhnd8fc"))))
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(build-system r-build-system)
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(home-page "https://github.com/krlmlr/bindr")
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(synopsis "Parametrized active bindings")
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(description
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"This package provides a simple interface for creating active bindings
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where the bound function accepts additional arguments.")
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(license license:expat)))
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(define-public r-bindrcpp
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(package
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(name "r-bindrcpp")
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(version "0.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "bindrcpp" version))
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(sha256
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(base32
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"0l1l22zl87wiyl79m3gj2vlxmkhxvrkl4alhyy08h55q7hqs3vyh"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-bindr" ,r-bindr)
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("r-plogr" ,r-plogr)
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("r-rcpp" ,r-rcpp)))
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(home-page "https://github.com/krlmlr/bindrcpp")
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(synopsis "Rcpp interface to active bindings")
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(description
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"This package provides an easy way to fill an environment with active
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bindings that call a C++ function.")
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(license license:expat)))
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(define-public r-auc
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(package
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(name "r-auc")
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(version "0.3.0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "AUC" version))
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(sha256
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(base32
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"0ripcib2qz0m7rgr1kiz68nx8f6p408l1ww7j78ljqik7p3g41g7"))))
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(properties `((upstream-name . "AUC")))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/AUC")
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(synopsis "Compute the area under the curve of selected measures")
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(description
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"This package includes functions to compute the area under the curve of
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selected measures: the area under the sensitivity curve (AUSEC), the area
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under the specificity curve (AUSPC), the area under the accuracy
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curve (AUACC), and the area under the receiver operating characteristic
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curve (AUROC). The curves can also be visualized. Support for partial areas
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is provided.")
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(license license:gpl2+)))
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(define-public r-calibrate
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(package
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(name "r-calibrate")
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(version "1.7.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "calibrate" version))
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(sha256
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(base32
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"010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-mass" ,r-mass)))
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(home-page "http://cran.r-project.org/web/packages/calibrate")
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(synopsis "Calibration of scatterplot and biplot axes")
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(description
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"This is a package for drawing calibrated scales with tick marks
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on (non-orthogonal) variable vectors in scatterplots and biplots.")
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(license license:gpl2)))
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(define-public r-shape
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(package
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(name "r-shape")
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(version "1.4.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "shape" version))
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(sha256
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(base32
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"0yk3cmsa57svcvbnm21pyr0s0qbhnllka8nmsg4yb41frjlqph66"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/shape")
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(synopsis "Functions for plotting graphical shapes")
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(description
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"This package provides functions for plotting graphical shapes such as
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ellipses, circles, cylinders, arrows, ...")
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(license license:gpl3+)))
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(define-public r-globaloptions
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(package
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(name "r-globaloptions")
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(version "0.0.12")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "GlobalOptions" version))
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(sha256
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(base32
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"1abpc03cfvazbwj2sx6qgngs5pgpzysvxkana20hyvb4n7ws77f0"))))
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(properties `((upstream-name . "GlobalOptions")))
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(build-system r-build-system)
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(home-page "https://github.com/jokergoo/GlobalOptions")
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(synopsis "Generate functions to get or set global options")
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(description
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"This package provides more controls on the option values such as
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validation and filtering on the values, making options invisible or private.")
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(license license:gpl2+)))
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(define-public r-circlize
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(package
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(name "r-circlize")
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(version "0.4.0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "circlize" version))
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(sha256
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(base32
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"0p1zx1aawkblz48kzzfn5w1k3lbwv9wrk1k5gcfjrr2b4sz1pp5b"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-colorspace" ,r-colorspace)
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("r-globaloptions" ,r-globaloptions)
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("r-shape" ,r-shape)))
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(home-page "https://github.com/jokergoo/circlize")
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(synopsis "Circular visualization")
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(description
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"Circular layout is an efficient way for the visualization of huge
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amounts of information. This package provides an implementation of circular
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layout generation in R as well as an enhancement of available software. The
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flexibility of the package is based on the usage of low-level graphics
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functions such that self-defined high-level graphics can be easily implemented
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by users for specific purposes. Together with the seamless connection between
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the powerful computational and visual environment in R, it gives users more
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convenience and freedom to design figures for better understanding complex
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patterns behind multiple dimensional data.")
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(license license:gpl2+)))
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(define-public r-powerlaw
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(package
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(name "r-powerlaw")
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(version "0.70.0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "poweRlaw" version))
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(sha256
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(base32
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"1p2la3hslxq2xa8jkwvci6zcpn47cvyr9xqd5agp1riwwp2xw5gh"))))
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(properties `((upstream-name . "poweRlaw")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-vgam" ,r-vgam)))
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(home-page "https://github.com/csgillespie/poweRlaw")
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(synopsis "Tools for the analysis of heavy tailed distributions")
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(description
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"This package provides an implementation of maximum likelihood estimators
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for a variety of heavy tailed distributions, including both the discrete and
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continuous power law distributions. Additionally, a goodness-of-fit based
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approach is used to estimate the lower cut-off for the scaling region.")
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;; Any of these GPL versions.
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(license (list license:gpl2 license:gpl3))))
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(define-public r-compare
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(package
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(name "r-compare")
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(version "0.2-6")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "compare" version))
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(sha256
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(base32
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"0k9zms930b5dz9gy8414li21wy0zg9x9vp7301v5cvyfi0g7xzgw"))))
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(build-system r-build-system)
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(home-page "http://cran.r-project.org/web/packages/compare")
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(synopsis "Comparing objects for differences")
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(description
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"This package provides functions to compare a model object to a
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comparison object. If the objects are not identical, the functions can be
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instructed to explore various modifications of the objects (e.g., sorting
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rows, dropping names) to see if the modified versions are identical.")
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(license license:gpl2+)))
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(define-public r-dendextend
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(package
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(name "r-dendextend")
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(version "1.5.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "dendextend" version))
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(sha256
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(base32
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"04jz58apibfrkjcrdmw2hmsav6qpb5cs6qdai81k1v1iznfcya42"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-fpc" ,r-fpc)
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("r-ggplot2" ,r-ggplot2)
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("r-magrittr" ,r-magrittr)
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("r-viridis" ,r-viridis)
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("r-whisker" ,r-whisker)))
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(home-page "https://cran.r-project.org/web/packages/dendextend")
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(synopsis "Extending 'dendrogram' functionality in R")
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(description
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"This package offers a set of functions for extending @code{dendrogram}
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objects in R, letting you visualize and compare trees of hierarchical
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clusterings. You can adjust a tree's graphical parameters (the color, size,
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type, etc of its branches, nodes and labels) and visually and statistically
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compare different dendrograms to one another.")
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;; Any of these versions
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(license (list license:gpl2 license:gpl3))))
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(define-public r-getoptlong
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(package
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(name "r-getoptlong")
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(version "0.1.6")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "GetoptLong" version))
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(sha256
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(base32
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"1d98gcvlvp9nz5lbnzr0kkpc2hbkx74hlhrnybqhg1gdwc3g09pm"))))
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(properties `((upstream-name . "GetoptLong")))
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(build-system r-build-system)
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(inputs
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`(("perl" ,perl)))
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(propagated-inputs
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`(("r-globaloptions" ,r-globaloptions)
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("r-rjson" ,r-rjson)))
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(home-page "https://github.com/jokergoo/GetoptLong")
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(synopsis "Parsing command-line arguments and variable interpolation")
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(description
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"This is yet another command-line argument parser which wraps the
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powerful Perl module @code{Getopt::Long} and with some adaptation for easier
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use in R. It also provides a simple way for variable interpolation in R.")
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(license license:gpl2+)))
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(define-public r-fastmatch
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(package
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(name "r-fastmatch")
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(version "1.1-0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "fastmatch" version))
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(sha256
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(base32
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"0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
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(build-system r-build-system)
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(home-page "http://www.rforge.net/fastmatch")
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(synopsis "Fast match function")
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(description
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"This package provides a fast @code{match} replacement for cases that
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require repeated look-ups. It is slightly faster that R's built-in
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@code{match} function on first match against a table, but extremely fast on
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any subsequent lookup as it keeps the hash table in memory.")
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(license license:gpl2)))
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(define-public r-ff
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(package
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(name "r-ff")
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(version "2.2-13")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "ff" version))
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(sha256
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(base32
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"1nvd6kx46xzyc99a44mgynd94pvd2h495m5a7b1g67k5w2phiywb"))))
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(build-system r-build-system)
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(propagated-inputs `(("r-bit" ,r-bit)))
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(home-page "http://ff.r-forge.r-project.org/")
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(synopsis "Memory-efficient storage of large data on disk and access functions")
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(description
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"This package provides data structures that are stored on disk but
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behave (almost) as if they were in RAM by transparently mapping only a section
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in main memory.")
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(license license:gpl2)))
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(define-public r-ffbase
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(package
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(name "r-ffbase")
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(version "0.12.3")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "ffbase" version))
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(sha256
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(base32
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"1nz97bndxxkzp8rq6va8ff5ky9vkaib1jybm6j852awwb3n9had5"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-bit" ,r-bit)
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("r-fastmatch" ,r-fastmatch)
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("r-ff" ,r-ff)))
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(home-page "http://github.com/edwindj/ffbase")
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(synopsis "Basic statistical functions for package 'ff'")
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(description
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"This package extends the out of memory vectors of @code{ff} with
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statistical functions and other utilities to ease their usage.")
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(license license:gpl3)))
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(define-public r-prettyunits
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(package
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(name "r-prettyunits")
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(version "1.0.2")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "prettyunits" version))
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(sha256
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(base32
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"0p3z42hnk53x7ky4d1dr2brf7p8gv3agxr71i99m01n2hq2ri91m"))))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-assertthat" ,r-assertthat)
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("r-magrittr" ,r-magrittr)))
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(home-page "https://github.com/gaborcsardi/prettyunits")
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(synopsis "Pretty, human readable formatting of quantities")
|
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(description
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"This package provides tools for pretty, human readable formatting of
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quantities.")
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(license license:expat)))
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(define-public r-reshape
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(package
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(name "r-reshape")
|
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(version "0.8.6")
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(source
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(origin
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|
(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+)))
|
|
|
|
(define-public r-proxy
|
|
(package
|
|
(name "r-proxy")
|
|
(version "0.4-17")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "proxy" version))
|
|
(sha256
|
|
(base32
|
|
"0bg1fn96qrj8whmnl7c3gv244ksm2ykxxsd0zrmw4lb6465pizl2"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://cran.r-project.org/web/packages/proxy")
|
|
(synopsis "Distance and similarity measures")
|
|
(description
|
|
"This package provides an extensible framework for the efficient
|
|
calculation of auto- and cross-proximities, along with implementations of the
|
|
most popular ones.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-sp
|
|
(package
|
|
(name "r-sp")
|
|
(version "1.2-4")
|
|
(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
|
|
"This package provides classes and methods for spatial data; the classes
|
|
document where the spatial location information resides, for 2D or 3D data.
|
|
Utility functions are provided, e.g. for plotting data as maps, spatial
|
|
selection, as well as methods for retrieving coordinates, for subsetting,
|
|
print, summary, etc.")
|
|
(license license:gpl2+)))
|