14529 lines
507 KiB
Scheme
14529 lines
507 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2016, 2017 Ben Woodcroft <donttrustben@gmail.com>
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;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
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;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
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;;; Copyright © 2017 Raoul Bonnal <ilpuccio.febo@gmail.com>
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;;; Copyright © 2018 Vijayalakshmi Vedantham <vijimay12@gmail.com>
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;;; Copyright © 2018 Sahithi Yarlagadda <sahi@swecha.net>
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;;; Copyright © 2018 Sandeep Subramanian <sandeepsubramanian94@gmail.com>
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;;; Copyright © 2018 Charlie Ritter <chewzeirta@posteo.net>
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;;; Copyright © 2018 Konrad Hinsen <konrad.hinsen@fastmail.net>
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;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
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;;; Copyright © 2018 Laura Lazzati <laura.lazzati.15@gmail.com>
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;;; Copyright © 2018 Leo Famulari <leo@famulari.name>
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;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
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;;; Copyright © 2018, 2019 Brett Gilio <brettg@posteo.net>
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;;; Copyright © 2019 Nicolò Balzarotti <anothersms@gmail.com>
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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 git-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 algebra)
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|
#:use-module (gnu packages base)
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#:use-module (gnu packages bioinformatics)
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|
#:use-module (gnu packages c)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages curl)
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|
#:use-module (gnu packages databases)
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|
#:use-module (gnu packages fontutils)
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|
#:use-module (gnu packages gcc)
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|
#:use-module (gnu packages geo)
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#:use-module (gnu packages ghostscript)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages gnome)
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#:use-module (gnu packages graph)
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#:use-module (gnu packages gtk)
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#:use-module (gnu packages haskell)
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#:use-module (gnu packages icu4c)
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#:use-module (gnu packages image)
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#:use-module (gnu packages imagemagick)
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#:use-module (gnu packages java)
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#:use-module (gnu packages javascript)
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#:use-module (gnu packages lisp)
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#:use-module (gnu packages machine-learning)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages multiprecision)
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#:use-module (gnu packages networking)
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#:use-module (gnu packages pcre)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages web)
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#:use-module (gnu packages xorg))
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(define-public r-clipr
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(package
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(name "r-clipr")
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(version "0.6.0")
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(source
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(origin
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|
(method url-fetch)
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(uri (cran-uri "clipr" version))
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(sha256
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|
(base32
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|
"0k9kimkmmj9k7290sxiqn4kd1vvm4w7q9a44wp0w30b7yjpavx2m"))))
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(build-system r-build-system)
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(home-page "https://github.com/mdlincoln/clipr")
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(synopsis "Read and write from the system clipboard")
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(description
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"This package provides simple utility functions to read from and write to
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the system clipboards.")
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(license license:gpl3)))
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(define-public r-ellipsis
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(package
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(name "r-ellipsis")
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(version "0.1.0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "ellipsis" version))
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(sha256
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(base32
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"0pw94qpg81xmsdsagpqxddv7m2cmdszmyyq99dk3caqqj01z7wg6"))))
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(build-system r-build-system)
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(home-page "https://github.com/hadley/ellipsis")
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(synopsis "Tools for working with additional arguments")
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(description
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"In S3 generics, it's useful to take @code{...} so that methods can have
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additional arguments. But this flexibility comes at a cost: misspelled
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arguments will be silently ignored. The @code{ellipsis} package is an
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experiment that allows a generic to warn if any arguments passed in @code{...}
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are not used.")
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(license license:gpl3)))
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|
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(define-public r-sys
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(package
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(name "r-sys")
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(version "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 "sys" version))
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(sha256
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|
(base32
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|
"1k5vk5q9wa5sin0n226i05nymg469s24f6lx64yyhb7yc624j698"))))
|
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(build-system r-build-system)
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(home-page "https://github.com/jeroen/sys")
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(synopsis "Powerful and reliable tools for running system commands in R")
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(description
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"This package provides drop-in replacements for the base @code{system2()}
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function with fine control and consistent behavior across platforms. It
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supports clean interruption, timeout, background tasks, and streaming STDIN /
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STDOUT / STDERR over binary or text connections. The package also provides
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functions for evaluating expressions inside a temporary fork. Such
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evaluations have no side effects on the main R process, and support reliable
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interrupts and timeouts. This provides the basis for a sandboxing
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mechanism.")
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(license license:expat)))
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(define-public r-askpass
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(package
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(name "r-askpass")
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(version "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 "askpass" version))
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(sha256
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(base32
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|
"07q0ik8jzk44vpwh48rr3fnpd7dzsdhjjsl4l850rffv3dyq4h6v"))))
|
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(build-system r-build-system)
|
|
(propagated-inputs `(("r-sys" ,r-sys)))
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(home-page "https://github.com/jeroen/askpass")
|
|
(synopsis "Safe password entry for R")
|
|
(description
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|
"This package provides cross-platform utilities for prompting the user
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for credentials or a passphrase, for example to authenticate with a server or
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read a protected key.")
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(license license:expat)))
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|
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(define-public r-vegan
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(package
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(name "r-vegan")
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(version "2.5-5")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "vegan" version))
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|
(sha256
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|
(base32
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|
"0wb90ng02gi13854bjq0b8a2vrknyhb0s0l1v3z38c4zy9k54sw7"))))
|
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(build-system r-build-system)
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|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)
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|
("r-knitr" ,r-knitr) ; needed for vignettes
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("r-lattice" ,r-lattice)
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("r-mass" ,r-mass)
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("r-mgcv" ,r-mgcv)
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("r-permute" ,r-permute)))
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|
(home-page "https://cran.r-project.org/web/packages/vegan")
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(synopsis "Functions for community ecology")
|
|
(description
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|
"The vegan package provides tools for descriptive community ecology. It
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has most basic functions of diversity analysis, community ordination and
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dissimilarity analysis. Most of its multivariate tools can be used for other
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data types as well.")
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(license license:gpl2+)))
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(define-public r-tidyverse
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(package
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(name "r-tidyverse")
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(version "1.2.1")
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|
(source
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|
(origin
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|
(method url-fetch)
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|
(uri (cran-uri "tidyverse" version))
|
|
(sha256
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|
(base32
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|
"0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
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|
("r-cli" ,r-cli)
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|
("r-crayon" ,r-crayon)
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("r-dbplyr" ,r-dbplyr)
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|
("r-dplyr" ,r-dplyr)
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|
("r-forcats" ,r-forcats)
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|
("r-ggplot2" ,r-ggplot2)
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("r-haven" ,r-haven)
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|
("r-hms" ,r-hms)
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|
("r-httr" ,r-httr)
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("r-jsonlite" ,r-jsonlite)
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|
("r-lubridate" ,r-lubridate)
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|
("r-magrittr" ,r-magrittr)
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|
("r-modelr" ,r-modelr)
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|
("r-purrr" ,r-purrr)
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("r-readr" ,r-readr)
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|
("r-readxl" ,r-readxl)
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|
("r-reprex" ,r-reprex)
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|
("r-rlang" ,r-rlang)
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|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-rvest" ,r-rvest)
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|
("r-stringr" ,r-stringr)
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|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://tidyverse.tidyverse.org")
|
|
(synopsis "Install and load packages from the \"Tidyverse\"")
|
|
(description
|
|
"The @code{tidyverse} is a set of packages that work in harmony because
|
|
they share common data representations and API design. This package is
|
|
designed to make it easy to install and load multiple tidyverse packages in a
|
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single step.")
|
|
(license license:gpl3)))
|
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|
|
(define-public r-rvest
|
|
(package
|
|
(name "r-rvest")
|
|
(version "0.3.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rvest" version))
|
|
(sha256
|
|
(base32
|
|
"0ji5lk8g1gbv4d9c4jg1fg6rgsqrrwkm05j1id7drdw9kqdifgj1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-httr" ,r-httr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-selectr" ,r-selectr)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://github.com/hadley/rvest")
|
|
(synopsis "Simple web scraping for R")
|
|
(description
|
|
"@code{r-rvest} helps you scrape information from web pages. It is
|
|
designed to work with @code{magrittr} to make it easy to express common web
|
|
scraping tasks, inspired by libraries like @code{BeautifulSoup}.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-selectr
|
|
(package
|
|
(name "r-selectr")
|
|
(version "0.4-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "selectr" version))
|
|
(sha256
|
|
(base32
|
|
"1jp27rxks4w29l47k42869hp8hnkzq2rnvsqbr44wd19fqb2zm4b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-stringr" ,r-stringr)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://sjp.co.nz/projects/selectr/")
|
|
(synopsis "Translate CSS selectors to XPath expressions")
|
|
(description
|
|
"@code{r-selectr} translates a CSS3 selector into an equivalent XPath
|
|
expression. This allows you to use CSS selectors when working with the XML
|
|
package as it can only evaluate XPath expressions. Also provided are
|
|
convenience functions useful for using CSS selectors on XML nodes. This
|
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package is a port of the Python package @code{cssselect}.")
|
|
(license license:bsd-3)))
|
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|
|
(define-public r-reprex
|
|
(package
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|
(name "r-reprex")
|
|
(version "0.3.0")
|
|
(source
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|
(origin
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|
(method url-fetch)
|
|
(uri (cran-uri "reprex" version))
|
|
(sha256
|
|
(base32
|
|
"0v7vxzs8alwz8y1cjicpimp5yimf1g9gb8x5wy3zhvrz6kk2lg10"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-callr" ,r-callr)
|
|
("r-clipr" ,r-clipr)
|
|
("r-fs" ,r-fs)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-whisker" ,r-whisker)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/tidyverse/reprex")
|
|
(synopsis "Prepare reproducible R code examples for sharing")
|
|
(description
|
|
"This package provides a convenience wrapper that uses the
|
|
@code{rmarkdown} package to render small snippets of code to target formats
|
|
that include both code and output. The goal is to encourage the sharing of
|
|
small, reproducible, and runnable examples on code-oriented websites or email.
|
|
@code{reprex} also extracts clean, runnable R code from various common formats,
|
|
such as copy/paste from an R session.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-callr
|
|
(package
|
|
(name "r-callr")
|
|
(version "3.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "callr" version))
|
|
(sha256
|
|
(base32
|
|
"1s5h2k7c1vgbry90xczin66q89cbkc6mvh4679l5rsz83087pd2b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-r6" ,r-r6)
|
|
("r-processx" ,r-processx)))
|
|
(home-page "https://github.com/r-lib/callr#readme")
|
|
(synopsis "Call R from R")
|
|
(description
|
|
"It is sometimes useful to perform a computation in a separate R process,
|
|
without affecting the current R process at all. This package does exactly
|
|
that.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-readxl
|
|
(package
|
|
(name "r-readxl")
|
|
(version "1.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "readxl" version))
|
|
(sha256
|
|
(base32
|
|
"15mambxr8c7k2ikdfsl1w3vxvm54dsnk0cl1qvks6iig7rql3d14"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cellranger" ,r-cellranger)
|
|
("r-progress" ,r-progress)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://readxl.tidyverse.org")
|
|
(synopsis "Read Excel files")
|
|
(description
|
|
"This package lets you import Excel files into R. It supports
|
|
@file{.xls} via the embedded @code{libxls} C library and @file{.xlsx} via
|
|
the embedded @code{RapidXML} C++ library.")
|
|
;; XXX: This package bundles a copy of 'libxsl' which is BSD-2 and
|
|
;; 'rapidxml' which is Boost.
|
|
(license (list license:gpl3 license:bsd-2 license:boost1.0))))
|
|
|
|
(define-public r-modelr
|
|
(package
|
|
(name "r-modelr")
|
|
(version "0.1.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "modelr" version))
|
|
(sha256
|
|
(base32
|
|
"1ngxphbjkv7yl1rg30sj36mfwhc76g452drjrq9abgab4k0pgnml"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-purrr" ,r-purrr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/tidyverse/modelr")
|
|
(synopsis "Helper functions for modelling in pipelines")
|
|
(description
|
|
"Functions for modelling that help you seamlessly integrate modelling
|
|
into a pipeline of data manipulation and visualisation.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-httpuv
|
|
(package
|
|
(name "r-httpuv")
|
|
(version "1.5.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "httpuv" version))
|
|
(sha256
|
|
(base32
|
|
"042piypg4c8sqrlcdl3dwajkafkbglsky3x7d0jpjv8s5wxnpfxm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-later" ,r-later)
|
|
("r-promises" ,r-promises)
|
|
("r-r6" ,r-r6)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/rstudio/httpuv")
|
|
(synopsis "HTTP and WebSocket server library for R")
|
|
(description
|
|
"The httpuv package provides low-level socket and protocol support for
|
|
handling HTTP and WebSocket requests directly from within R. It is primarily
|
|
intended as a building block for other packages, rather than making it
|
|
particularly easy to create complete web applications using httpuv alone.")
|
|
;; This package includes third-party code that was originally released
|
|
;; under various non-copyleft licenses. Full licensing information can be
|
|
;; obtained here: https://github.com/rstudio/httpuv/blob/master/LICENSE
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-jsonlite
|
|
(package
|
|
(name "r-jsonlite")
|
|
(version "1.6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "jsonlite" version))
|
|
(sha256
|
|
(base32
|
|
"0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://arxiv.org/abs/1403.2805")
|
|
(synopsis "Robust, high performance JSON parser and generator for R")
|
|
(description
|
|
"The jsonlite package provides a fast JSON parser and generator optimized
|
|
for statistical data and the web. It offers flexible, robust, high
|
|
performance tools for working with JSON in R and is particularly powerful for
|
|
building pipelines and interacting with a web API. In addition to converting
|
|
JSON data from/to R objects, jsonlite contains functions to stream, validate,
|
|
and prettify JSON data. The unit tests included with the package verify that
|
|
all edge cases are encoded and decoded consistently for use with dynamic data
|
|
in systems and applications.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-servr
|
|
(package
|
|
(name "r-servr")
|
|
(version "0.14")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "servr" version))
|
|
(sha256
|
|
(base32
|
|
"0zjjnfgas9d16fihksyk24kgkkqswb4sd0rz51id2ni1ymdyasjk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-httpuv" ,r-httpuv)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-mime" ,r-mime)
|
|
("r-xfun" ,r-xfun)))
|
|
(home-page "https://github.com/yihui/servr")
|
|
(synopsis "Simple HTTP server to serve static files or dynamic documents")
|
|
(description
|
|
"Servr provides an HTTP server in R to serve static files, or dynamic
|
|
documents that can be converted to HTML files (e.g., R Markdown) under a given
|
|
directory.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-htmltools
|
|
(package
|
|
(name "r-htmltools")
|
|
(version "0.3.6")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "htmltools" version))
|
|
(sha256
|
|
(base32
|
|
"18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
;; See https://github.com/rstudio/htmltools/pull/68
|
|
;; The resource files are in the store and have mode 444. After
|
|
;; copying the files R fails to remove them again because it doesn't
|
|
;; have write access to them.
|
|
(add-after 'unpack 'copy-files-without-mode
|
|
(lambda _
|
|
(substitute* "R/html_dependency.R"
|
|
(("file.copy\\(from, to, " prefix)
|
|
(string-append prefix
|
|
"copy.mode = FALSE, ")))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/htmltools")
|
|
(synopsis "R tools for HTML")
|
|
(description
|
|
"This package provides tools for HTML generation and output in R.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-htmlwidgets
|
|
(package
|
|
(name "r-htmlwidgets")
|
|
(version "1.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "htmlwidgets" version))
|
|
(sha256
|
|
(base32
|
|
"04jsdh14l2zifbjpbbh23w7bxz1wpsas0zb2gy2zwv4yqamzzr7i"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-yaml" ,r-yaml)))
|
|
(home-page "https://github.com/ramnathv/htmlwidgets")
|
|
(synopsis "HTML Widgets for R")
|
|
(description
|
|
"HTML widgets is a framework for creating HTML widgets that render in
|
|
various contexts including the R console, R Markdown documents, and Shiny web
|
|
applications.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-htmltable
|
|
(package
|
|
(name "r-htmltable")
|
|
(version "1.13.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "htmlTable" version))
|
|
(sha256
|
|
(base32
|
|
"1l44b33xgj2698k6nz17r8fl0ink14ryzng803apm9d6bnv357v8"))))
|
|
(properties `((upstream-name . "htmlTable")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-checkmate" ,r-checkmate)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-knitr" ,r-knitr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-stringr" ,r-stringr)))
|
|
(home-page "http://gforge.se/packages/")
|
|
(synopsis "Advanced tables for Markdown/HTML")
|
|
(description
|
|
"This package provides functions to build tables with advanced layout
|
|
elements such as row spanners, column spanners, table spanners, zebra
|
|
striping, and more. While allowing advanced layout, the underlying
|
|
CSS-structure is simple in order to maximize compatibility with word
|
|
processors such as LibreOffice. The package also contains a few text
|
|
formatting functions that help outputting text compatible with HTML or
|
|
LaTeX.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-curl
|
|
(package
|
|
(name "r-curl")
|
|
(version "3.3")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "curl" version))
|
|
(sha256
|
|
(base32
|
|
"1gd5i25anzi28lg1f8p7g63z9d46xi0qaw4lxpml5p0f52lvkc0c"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
;; The environment variable CURL_CA_BUNDLE is only respected when
|
|
;; running Windows, so we disable the platform checks.
|
|
;; This can be removed once the libcurl has been patched.
|
|
(add-after 'unpack 'allow-CURL_CA_BUNDLE
|
|
(lambda _
|
|
(substitute* "R/onload.R"
|
|
(("if \\(!grepl\\(\"mingw\".*")
|
|
"if (FALSE)\n"))
|
|
(substitute* "src/handle.c"
|
|
(("#ifdef _WIN32") "#if 1"))
|
|
#t)))))
|
|
(inputs
|
|
`(("libcurl" ,curl)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "https://github.com/jeroenooms/curl")
|
|
(synopsis "HTTP client for R")
|
|
(description
|
|
"The @code{curl()} and @code{curl_download()} functions provide highly
|
|
configurable drop-in replacements for base @code{url()} and
|
|
@code{download.file()} with better performance, support for encryption, gzip
|
|
compression, authentication, and other @code{libcurl} goodies. The core of
|
|
the package implements a framework for performing fully customized requests
|
|
where data can be processed either in memory, on disk, or streaming via the
|
|
callback or connection interfaces.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-hwriter
|
|
(package
|
|
(name "r-hwriter")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hwriter" version))
|
|
(sha256
|
|
(base32
|
|
"0arjsz854rfkfqhgvpqbm9lfni97dcjs66isdsfvwfd2wz932dbb"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/hwriter")
|
|
(synopsis "Output R objects in HTML format")
|
|
(description
|
|
"This package provides easy-to-use and versatile functions to output R
|
|
objects in HTML format.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public r-rjson
|
|
(package
|
|
(name "r-rjson")
|
|
(version "0.2.20")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rjson" version))
|
|
(sha256
|
|
(base32
|
|
"0v1zvdd3svnavklh7y5xbwrrkbvx6053r4c5hgnk7hz7bqg7qa1s"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rjson")
|
|
(synopsis "JSON library for R")
|
|
(description
|
|
"This package provides functions to convert R objects into JSON objects
|
|
and vice-versa.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-shiny
|
|
(package
|
|
(name "r-shiny")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/rstudio/shiny.git")
|
|
(commit (string-append "v" version))))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1kl3dh68h4cnrm3rqn9pddk5n6bsmr5x0626bkfv0qqi0q92zin4"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build r-build-system)
|
|
(guix build minify-build-system)
|
|
(guix build utils)
|
|
(ice-9 match))
|
|
#:imported-modules (,@%r-build-system-modules
|
|
(guix build minify-build-system))
|
|
#:phases
|
|
(modify-phases (@ (guix build r-build-system) %standard-phases)
|
|
(add-after 'unpack 'replace-bundled-minified-JavaScript
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((replace-file (lambda (old new)
|
|
(format #t "replacing ~a with ~a\n" old new)
|
|
(delete-file old)
|
|
(symlink new old))))
|
|
;; NOTE: Files in ./inst/www/shared/datepicker/js/locales/
|
|
;; contain just data. They are not minified code, so we don't
|
|
;; replace them.
|
|
(with-directory-excursion "inst/www/shared"
|
|
(replace-file "bootstrap/shim/respond.min.js"
|
|
(string-append (assoc-ref inputs "js-respond")
|
|
"/share/javascript/respond.min.js"))
|
|
(replace-file "bootstrap/shim/html5shiv.min.js"
|
|
(string-append (assoc-ref inputs "js-html5shiv")
|
|
"/share/javascript/html5shiv.min.js"))
|
|
(replace-file "json2-min.js"
|
|
(string-append (assoc-ref inputs "js-json2")
|
|
"/share/javascript/json2.min.js"))
|
|
(replace-file "strftime/strftime-min.js"
|
|
(string-append (assoc-ref inputs "js-strftime")
|
|
"/share/javascript/strftime.min.js"))
|
|
(replace-file "highlight/highlight.pack.js"
|
|
(string-append (assoc-ref inputs "js-highlight")
|
|
"/share/javascript/highlight.min.js"))
|
|
(replace-file "datatables/js/jquery.dataTables.min.js"
|
|
(string-append (assoc-ref inputs "js-datatables")
|
|
"/share/javascript/jquery.dataTables.min.js"))
|
|
(replace-file "selectize/js/selectize.min.js"
|
|
(string-append (assoc-ref inputs "js-selectize")
|
|
"/share/javascript/selectize.min.js"))
|
|
(replace-file "selectize/js/es5-shim.min.js"
|
|
(string-append (assoc-ref inputs "js-es5-shim")
|
|
"/share/javascript/es5-shim.min.js"))
|
|
(for-each (match-lambda
|
|
((source . target)
|
|
(delete-file target)
|
|
(minify source #:target target)))
|
|
'(("jqueryui/jquery-ui.js" .
|
|
"jqueryui/jquery-ui.min.js")
|
|
("datepicker/js/bootstrap-datepicker.js" .
|
|
"datepicker/js/bootstrap-datepicker.min.js")
|
|
("ionrangeslider/js/ion.rangeSlider.js" .
|
|
"ionrangeslider/js/ion.rangeSlider.min.js")
|
|
("bootstrap/js/bootstrap.js" .
|
|
"bootstrap/js/bootstrap.min.js")
|
|
("shiny.js" .
|
|
"shiny.min.js")
|
|
("jquery.js" .
|
|
"jquery.min.js")))))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-crayon" ,r-crayon)
|
|
("r-httpuv" ,r-httpuv)
|
|
("r-mime" ,r-mime)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-xtable" ,r-xtable)
|
|
("r-digest" ,r-digest)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-r6" ,r-r6)
|
|
("r-sourcetools" ,r-sourcetools)))
|
|
(inputs
|
|
`(("js-datatables" ,js-datatables)
|
|
("js-html5shiv" ,js-html5shiv)
|
|
("js-json2" ,js-json2)
|
|
("js-respond" ,js-respond)
|
|
("js-selectize" ,js-selectize)
|
|
("js-strftime" ,js-strftime)
|
|
("js-highlight" ,js-highlight)
|
|
("js-es5-shim" ,js-es5-shim)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)))
|
|
(home-page "http://shiny.rstudio.com")
|
|
(synopsis "Easy interactive web applications with 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 license:artistic2.0)))
|
|
|
|
(define-public r-shinydashboard
|
|
(package
|
|
(name "r-shinydashboard")
|
|
(version "0.7.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinydashboard" version))
|
|
(sha256
|
|
(base32
|
|
"0khac8b27q3swdw07kl609hm0fjfjsjv591b388q99mqqr2rk92i"))))
|
|
(build-system r-build-system)
|
|
;; The directory inst/AdminLTE/ contains a minified JavaScript file.
|
|
;; Regenerate it from the included sources.
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(ice-9 popen))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'generate-minified-javascript
|
|
(lambda _
|
|
(with-directory-excursion "inst/AdminLTE"
|
|
(delete-file "app.min.js")
|
|
(let ((minified (open-pipe* OPEN_READ "uglify-js" "app.js")))
|
|
(call-with-output-file "app.min.js"
|
|
(lambda (port)
|
|
(dump-port minified port))))))))))
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-promises" ,r-promises)
|
|
("r-shiny" ,r-shiny)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)))
|
|
(home-page "http://rstudio.github.io/shinydashboard/")
|
|
(synopsis "Create dashboards with shiny")
|
|
(description "This package provides an extension to the Shiny web
|
|
application framework for R, making it easy to create attractive dashboards.")
|
|
;; This package includes software that was released under the Expat
|
|
;; license, but the whole package is released under GPL version 2 or
|
|
;; later.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-shinyfiles
|
|
(package
|
|
(name "r-shinyfiles")
|
|
(version "0.7.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinyFiles" version))
|
|
(sha256
|
|
(base32
|
|
"01as3l9ffj5dwac0vviais2x5l3027zxlj67kcvkdwxaj5hql33i"))))
|
|
(properties `((upstream-name . "shinyFiles")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-fs" ,r-fs)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-shiny" ,r-shiny)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/thomasp85/shinyFiles")
|
|
(synopsis "Server-side file system viewer for Shiny")
|
|
(description
|
|
"This package provides functionality for client-side navigation of the
|
|
server side file system in shiny apps. In case the app is running locally
|
|
this gives the user direct access to the file system without the need to
|
|
\"download\" files to a temporary location. Both file and folder selection as
|
|
well as file saving is available.")
|
|
(license license:gpl2+)))
|
|
|
|
(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
|
|
"This package provides building blocks for allowing HTML widgets to
|
|
communicate with each other, with Shiny or without (i.e. static @code{.html}
|
|
files). It currently supports linked brushing and filtering.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-rook
|
|
(package
|
|
(name "r-rook")
|
|
(version "1.1-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rook" version))
|
|
(sha256
|
|
(base32
|
|
"00s9a0kr9rwxvlq433daxjk4ji8m0w60hjdprf502msw9kxfrx00"))))
|
|
(properties `((upstream-name . "Rook")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-brew" ,r-brew)))
|
|
(home-page "https://cran.r-project.org/web/packages/Rook")
|
|
(synopsis "Web server interface for R")
|
|
(description
|
|
"This package contains the Rook specification and convenience software
|
|
for building and running Rook applications. A Rook application is an R
|
|
reference class object that implements a @code{call} method or an R closure
|
|
that takes exactly one argument, an environment, and returns a list with three
|
|
named elements: the @code{status}, the @code{headers}, and the @code{body}.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-miniui
|
|
(package
|
|
(name "r-miniui")
|
|
(version "0.1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "miniUI" version))
|
|
(sha256
|
|
(base32
|
|
"1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"))))
|
|
(properties `((upstream-name . "miniUI")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-shiny" ,r-shiny)))
|
|
(home-page "https://cran.r-project.org/web/packages/miniUI/")
|
|
(synopsis "Shiny UI widgets for small screens")
|
|
(description
|
|
"This package provides UI widget and layout functions for writing Shiny apps that
|
|
work well on small screens.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-feather
|
|
(package
|
|
(name "r-feather")
|
|
(version "0.3.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "feather" version))
|
|
(sha256
|
|
(base32
|
|
"0ls8lmygyjq60467s88h66d7fczjp1d3a2106rfq4dx9lyfvdfsa"))))
|
|
(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 license:asl2.0)))
|
|
|
|
(define-public r-maps
|
|
(package
|
|
(name "r-maps")
|
|
(version "3.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "maps" version))
|
|
(sha256
|
|
(base32
|
|
"05i2ppl5z4p8rawgqmy3z4ia05fcblpq1vvrmrkgkkpdlhczx6hr"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/maps")
|
|
(synopsis "Draw geographical maps")
|
|
(description "This package provides an R module for display of maps.
|
|
Projection code and larger maps are in separate packages (@code{mapproj} and
|
|
@code{mapdata}).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-mapproj
|
|
(package
|
|
(name "r-mapproj")
|
|
(version "1.2.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mapproj" version))
|
|
(sha256
|
|
(base32
|
|
"1rggww8cbwv0vzlj5afzhbsbngg4bzj5znbkz7wmxsbshfbsm9b2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-maps" ,r-maps)))
|
|
(home-page "https://cran.r-project.org/web/packages/mapproj")
|
|
(synopsis "Map projection in R")
|
|
(description "This package converts latitude/longitude into projected
|
|
coordinates.")
|
|
(license (list license:gpl2 ; The R interface
|
|
(license:non-copyleft ; The C code
|
|
"https://www.gnu.org/licenses/license-list.en.html#lucent102"
|
|
"Lucent Public License Version 1.02")))))
|
|
|
|
(define-public r-rgooglemaps
|
|
(package
|
|
(name "r-rgooglemaps")
|
|
(version "1.4.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RgoogleMaps" version))
|
|
(sha256
|
|
(base32
|
|
"06ab3lg1rwm93hkshf1vxfm8mlxq5qsjan0wx43lhnrysay65js4"))))
|
|
(properties `((upstream-name . "RgoogleMaps")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-png" ,r-png)))
|
|
(home-page "https://cran.r-project.org/web/packages/RgoogleMaps")
|
|
(synopsis "Use Google Maps in R")
|
|
(description "This package serves two purposes:
|
|
@enumerate
|
|
@item Provide a comfortable R interface to query the Google server for static
|
|
maps, and
|
|
@item Use the map as a background image to overlay plots within R. This
|
|
requires proper coordinate scaling.
|
|
@end enumerate\n")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-geosphere
|
|
(package
|
|
(name "r-geosphere")
|
|
(version "1.5-10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "geosphere" version))
|
|
(sha256
|
|
(base32
|
|
"15xlgsmn0vwky1l13n6acdz6jn2b2na3gf6x367y3qh1f5w4zkan"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-sp" ,r-sp)))
|
|
(home-page "https://cran.r-project.org/web/packages/geosphere")
|
|
(synopsis "Spherical trigonometry")
|
|
(description "This package computes spherical trigonometry for geographic
|
|
applications. That is, compute distances and related measures for angular
|
|
(longitude/latitude) locations.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-ggmap
|
|
(package
|
|
(name "r-ggmap")
|
|
(version "3.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggmap" version))
|
|
(sha256
|
|
(base32
|
|
"13dmzl6z62pzjiffilarkji46vy0sacxa8a7mhrhc3biq3ylzhln"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bitops" ,r-bitops)
|
|
("r-digest" ,r-digest)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-glue" ,r-glue)
|
|
("r-httr" ,r-httr)
|
|
("r-jpeg" ,r-jpeg)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-plyr" ,r-plyr)
|
|
("r-png" ,r-png)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rgooglemaps" ,r-rgooglemaps)
|
|
("r-rjson" ,r-rjson)
|
|
("r-scales" ,r-scales)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(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 license:gpl2)))
|
|
|
|
(define-public r-haven
|
|
(package
|
|
(name "r-haven")
|
|
(version "2.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "haven" version))
|
|
(sha256
|
|
(base32
|
|
"0x5fwc4q2gdxwwp5sxdd6q17jhpisd769y9kv0xgnjcm0cdwz8f0"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-forcats" ,r-forcats)
|
|
("r-hms" ,r-hms)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-readr" ,r-readr)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://haven.tidyverse.org")
|
|
(synopsis "Import and Export 'SPSS', 'Stata' and 'SAS' Files")
|
|
(description
|
|
"This package lets you mport foreign statistical formats into R via the
|
|
embedded @url{https://github.com/WizardMac/ReadStat,ReadStat} C library.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-amap
|
|
(package
|
|
(name "r-amap")
|
|
(version "0.8-17")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "amap" version))
|
|
(sha256
|
|
(base32
|
|
"1il94bkhl8192vawq4gr2gwyhqhid27jr2312rhvr72ssg8p713b"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://mulcyber.toulouse.inra.fr/projects/amap/")
|
|
(synopsis "Another multidimensional analysis package")
|
|
(description "This package provides tools for clustering and principal
|
|
component analysis (with robust methods, and parallelized functions).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ape
|
|
(package
|
|
(name "r-ape")
|
|
(version "5.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ape" version))
|
|
(sha256
|
|
(base32
|
|
"08wbk1kxhs32bmmvqlqanbdg1w235amd35k8m00fngsj9h9xzc08"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-nlme" ,r-nlme)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "http://ape-package.ird.fr/")
|
|
(synopsis "Analyses of phylogenetics and evolution")
|
|
(description
|
|
"This package provides functions for reading, writing, plotting, and
|
|
manipulating phylogenetic trees, analyses of comparative data in a
|
|
phylogenetic framework, ancestral character analyses, analyses of
|
|
diversification and macroevolution, computing distances from DNA sequences,
|
|
and several other tools.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-abbyyr
|
|
(package
|
|
(name "r-abbyyr")
|
|
(version "0.5.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abbyyR" version))
|
|
(sha256
|
|
(base32
|
|
"1vldnd3dg89aj6a73nhirirqddbfdrnzhb5m3679i60sark8nk6r"))))
|
|
(properties `((upstream-name . "abbyyR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-httr" ,r-httr)
|
|
("r-plyr" ,r-plyr)
|
|
("r-progress" ,r-progress)
|
|
("r-readr" ,r-readr)
|
|
("r-xml" ,r-xml)))
|
|
(home-page "https://github.com/soodoku/abbyyR")
|
|
(synopsis "Access to Abbyy Optical Character Recognition (OCR) API")
|
|
(description
|
|
"This package provides tools to get text from images of text using Abbyy
|
|
Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily
|
|
OCR images, barcodes, forms, documents with machine readable zones, e.g.
|
|
passports and get the results in a variety of formats including plain text and
|
|
XML. To learn more about the Abbyy OCR API, see @url{http://ocrsdk.com/}.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-colorspace
|
|
(package
|
|
(name "r-colorspace")
|
|
(version "1.4-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "colorspace" version))
|
|
(sha256
|
|
(base32 "0wyny3ah2d74hqv80s6imrarpna09gq3j9rjnz6zx2qg0lx72gb9"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://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 "1.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "glue" version))
|
|
(sha256
|
|
(base32
|
|
"1a1ycg9r3gd91visp49q49rsrdgyf8kr9dxdy3hk99kikn4z5hag"))))
|
|
(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-pastecs
|
|
(package
|
|
(name "r-pastecs")
|
|
(version "1.3.21")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pastecs" version))
|
|
(sha256
|
|
(base32
|
|
"0z4dic94ar646w7zc2ggi5hgvf2qnznsani94c5pyql8zspz47lc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-boot" ,r-boot)))
|
|
(home-page "http://www.sciviews.org/pastecs")
|
|
(synopsis "Analysis of space-time ecological series")
|
|
(description
|
|
"This package provides functions for regulation, decomposition and analysis
|
|
of space-time series. The @code{pastecs} library is a PNEC-Art4 and IFREMER
|
|
initiative to bring PASSTEC 2000 functionalities to R.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-plogr
|
|
(package
|
|
(name "r-plogr")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plogr" version))
|
|
(sha256
|
|
(base32
|
|
"0a8dhzlna79ggyhfr0nncgh15a9n6r0dsz664pz0ah323wpblqqf"))))
|
|
(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-pls
|
|
(package
|
|
(name "r-pls")
|
|
(version "2.7-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pls" version))
|
|
(sha256
|
|
(base32
|
|
"0jw3zl5z06023zxr74phnvwax8m3i4a4i6lsqiq6j15aq9zq3zgq"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://mevik.net/work/software/pls.html")
|
|
(synopsis "Partial Least Squares and Principal Component Regression")
|
|
(description
|
|
"The pls package implements multivariate regression methods: Partial Least
|
|
Squares Regression (@dfn{PLSR}), Principal Component Regression (@dfn{PCR}), and
|
|
Canonical Powered Partial Least Squares (@dfn{CPPLS}). It supports:
|
|
|
|
@itemize
|
|
@item several algorithms: the traditional orthogonal scores (@dfn{NIPALS}) PLS
|
|
algorithm, kernel PLS, wide kernel PLS, Simpls, and PCR through @code{svd}
|
|
@item multi-response models (or @dfn{PLS2})
|
|
@item flexible cross-validation
|
|
@item Jackknife variance estimates of regression coefficients
|
|
@item extensive and flexible plots: scores, loadings, predictions, coefficients,
|
|
(R)MSEP, R², and correlation loadings
|
|
@item formula interface, modelled after @code{lm()}, with methods for predict,
|
|
print, summary, plot, update, etc.
|
|
@item extraction functions for coefficients, scores, and loadings
|
|
@item MSEP, RMSEP, and R² estimates
|
|
@item multiplicative scatter correction (@dfn{MSC})
|
|
@end itemize\n")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ps
|
|
(package
|
|
(name "r-ps")
|
|
(version "1.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ps" version))
|
|
(sha256
|
|
(base32 "1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://ps.r-lib.org")
|
|
(synopsis "List, query, and manipulate system processes")
|
|
(description
|
|
"The ps package implements an API to list, query, and manipulate system
|
|
processes. Most of its code is based on the @code{psutil} Python package.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-pkgbuild
|
|
(package
|
|
(name "r-pkgbuild")
|
|
(version "1.0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pkgbuild" version))
|
|
(sha256
|
|
(base32
|
|
"0k8zwa66rm1ncx19ld5mbaxcjxkswiczpdqyssy44vl8k6scwfn9"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-callr" ,r-callr)
|
|
("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-desc" ,r-desc)
|
|
("r-prettyunits" ,r-prettyunits)
|
|
("r-r6" ,r-r6)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/r-pkgs/pkgbuild")
|
|
(synopsis "Find tools needed to build R packages")
|
|
(description
|
|
"This package provides functions used to build R packages. It locates
|
|
compilers needed to build R packages on various platforms and ensures the PATH
|
|
is configured appropriately so R can use them.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-pkgload
|
|
(package
|
|
(name "r-pkgload")
|
|
(version "1.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pkgload" version))
|
|
(sha256
|
|
(base32
|
|
"0z7jvharafahi2gv5547mk1n499isjzw06kfwymmxc0gd575d1ii"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-desc" ,r-desc)
|
|
("r-pkgbuild" ,r-pkgbuild)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/r-lib/pkgload")
|
|
(synopsis "Simulate package installation and attach")
|
|
(description
|
|
"This package simulates the process of installing a package and then
|
|
attaching it. This is a key part of the @code{devtools} package as it allows
|
|
you to rapidly iterate while developing a package.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-rcpp
|
|
(package
|
|
(name "r-rcpp")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rcpp" version))
|
|
(sha256
|
|
(base32 "015rmxns8mhmnd9wnz9bmma4iwx2sf4bcwkkp9hcgvdmblzf0vg7"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; for vignettes
|
|
(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
|
|
@code{Rcpp Gallery} site at <http://gallery.rcpp.org>, the paper by Eddelbuettel
|
|
and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see
|
|
@code{citation(\"Rcpp\")} for details on these last two.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-bindr
|
|
(package
|
|
(name "r-bindr")
|
|
(version "0.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bindr" version))
|
|
(sha256
|
|
(base32
|
|
"1l05fpk2yql3jka321c0bdgx6mqq9pvfrg2844lbjfpbgjkmqy3w"))))
|
|
(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 "0.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bindrcpp" version))
|
|
(sha256
|
|
(base32
|
|
"0rz4ibjdjsxl99ff3ha79z7cnjmilx4rx58fk9kk7ld9xc4hf4s8"))))
|
|
(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 "https://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 "https://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 "1.4.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shape" version))
|
|
(sha256
|
|
(base32
|
|
"0hadk3mapkhbh8xjkiz52vxdagmmgvm15xwpzb90ikw4giyipjzl"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://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 "0.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GlobalOptions" version))
|
|
(sha256
|
|
(base32
|
|
"1wlyqz1yhmhjwslrd7q69jbd9vsbjkjfc01g60kl3cdpyr8hlyjn"))))
|
|
(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 "0.4.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "circlize" version))
|
|
(sha256
|
|
(base32
|
|
"1yjnb88pnzk5c1p0vjxykc7cr3394ln5axviqcf12ajibvy8rj6f"))))
|
|
(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 to visualise huge amounts of
|
|
information. This package provides an implementation of circular layout
|
|
generation in R as well as an enhancement of available software. Its
|
|
flexibility 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
|
|
multi-dimensional data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-powerlaw
|
|
(package
|
|
(name "r-powerlaw")
|
|
(version "0.70.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "poweRlaw" version))
|
|
(sha256
|
|
(base32
|
|
"1asr6ikr7hmj78jyg8r1gwvcjg14addkxdiz92nh06lv71a183r4"))))
|
|
(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 "https://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 "1.12.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dendextend" version))
|
|
(sha256
|
|
(base32
|
|
"0mgsc9qkr5p6hss3wychdjvk263ay48yx543wawj72l7q7cgx1xl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-viridis" ,r-viridis)))
|
|
(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 "0.1.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GetoptLong" version))
|
|
(sha256
|
|
(base32
|
|
"1fl3w2n602ldybc5qj7qw4xmzzb804bsjkqwf6dswzj0vf0qiadr"))))
|
|
(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 "2.2-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ff" version))
|
|
(sha256
|
|
(base32
|
|
"1w724q4jpzbvzpilb2ifviaxkjgk9lzwxz9gksnvicbmfa20fqqw"))))
|
|
(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.")
|
|
;; error Architecture not supported.
|
|
(supported-systems (delete "aarch64-linux" %supported-systems))
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ffbase
|
|
(package
|
|
(name "r-ffbase")
|
|
(version "0.12.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ffbase" version))
|
|
(sha256
|
|
(base32
|
|
"04kxx2f3f0743c5nvpb7x1x0pcd220dazpd5ag1pidxbz3xa85nw"))))
|
|
(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 "0.8.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reshape" version))
|
|
(sha256
|
|
(base32
|
|
"0s6i0sqxg1vldxs6miv8mi0zydxbqzgpmzfiwkj8y7jix3yrfmad"))))
|
|
(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 "1.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "progress" version))
|
|
(sha256
|
|
(base32
|
|
"0dgzb362641aqm8xd88iqa8jmpdm43xs0aba0d5kk6fvapnxi95l"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-crayon" ,r-crayon)
|
|
("r-hms" ,r-hms)
|
|
("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 "1.4.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GGally" version))
|
|
(sha256
|
|
(base32
|
|
"1zjmcc5bzagvy7c5cmdcl39xmx07fwi98yrj4i05w7y40kqcsiws"))))
|
|
(properties `((upstream-name . "GGally")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libressl" ,libressl)))
|
|
(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)
|
|
("r-rlang" ,r-rlang)))
|
|
(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 "0.4-23")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "proxy" version))
|
|
(sha256
|
|
(base32
|
|
"17b6qfllqrhzrxqgx7dccffgybnkcria5a68ap5ly3plg04ypm4x"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://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 "1.3-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sp" version))
|
|
(sha256
|
|
(base32
|
|
"17xm1ig80p9wc860hm3bgishz6lj9fxgwqidj7rkbk4ap99qp62p"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)))
|
|
(home-page "https://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+)))
|
|
|
|
(define-public r-rmtstat
|
|
(package
|
|
(name "r-rmtstat")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RMTstat" version))
|
|
(sha256
|
|
(base32
|
|
"1nn25q4kmh9kj975sxkrpa97vh5irqrlqhwsfinbck6h6ia4rsw1"))))
|
|
(properties `((upstream-name . "RMTstat")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/RMTstat")
|
|
(synopsis "Distributions, statistics and tests derived from random matrix theory")
|
|
(description
|
|
"This package provides functions for working with the Tracy-Widom laws
|
|
and other distributions related to the eigenvalues of large Wishart
|
|
matrices.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-rmpi
|
|
(package
|
|
(name "r-rmpi")
|
|
(version "0.6-9")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rmpi" version))
|
|
(sha256
|
|
(base32
|
|
"1rhycla98hxgnnxlxxldr1x51djak7c2jjvlrv3jcsvgwp1ymqdj"))))
|
|
(properties `((upstream-name . "Rmpi")))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:configure-flags '("--configure-args=\"--with-Rmpi-type=OPENMPI\"")
|
|
#:phases (modify-phases %standard-phases
|
|
(add-before 'install 'mpi-setup
|
|
,%openmpi-setup))))
|
|
(inputs
|
|
`(("openmpi" ,openmpi)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://www.stats.uwo.ca/faculty/yu/Rmpi")
|
|
(synopsis "R interface to message-passing interface (MPI)")
|
|
(description
|
|
"This package provides an interface (wrapper) to MPI APIs. It also
|
|
provides an interactive R manager and worker environment.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-lmoments
|
|
(package
|
|
(name "r-lmoments")
|
|
(version "1.3-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Lmoments" version))
|
|
(sha256
|
|
(base32
|
|
"0pc63bj9a8hzr5m3yssrc4kin39fffwkl8rggs3sagzr12d4i7bw"))))
|
|
(properties `((upstream-name . "Lmoments")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)))
|
|
(home-page "http://www.tilastotiede.fi/juha_karvanen.html")
|
|
(synopsis "L-moments and quantile mixtures")
|
|
(description
|
|
"This package contains functions to estimate L-moments and trimmed
|
|
L-moments from the data. It also contains functions to estimate the
|
|
parameters of the normal polynomial quantile mixture and the Cauchy polynomial
|
|
quantile mixture from L-moments and trimmed L-moments.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-distillery
|
|
(package
|
|
(name "r-distillery")
|
|
(version "1.0-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "distillery" version))
|
|
(sha256
|
|
(base32
|
|
"1mi3ig9jq0kd7yrwc5m37lmrw04p1b4lirnbsxi10z3n5yay4429"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.ral.ucar.edu/staff/ericg")
|
|
(synopsis "Functions for confidence intervals and object information")
|
|
(description
|
|
"This package provides some very simple method functions for confidence
|
|
interval calculation and to distill pertinent information from a potentially
|
|
complex object; primarily used in common with the packages extRemes and
|
|
SpatialVx.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-extremes
|
|
(package
|
|
(name "r-extremes")
|
|
(version "2.0-10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "extRemes" version))
|
|
(sha256
|
|
(base32
|
|
"08fj72gpq2d6695hbm3cgwgal64z009ykrirby7g6r0akfcsx5ic"))))
|
|
(properties `((upstream-name . "extRemes")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-distillery" ,r-distillery)
|
|
("r-lmoments" ,r-lmoments)))
|
|
(home-page "http://www.assessment.ucar.edu/toolkit/")
|
|
(synopsis "Extreme value analysis")
|
|
(description
|
|
"ExtRemes is a suite of functions for carrying out analyses on the
|
|
extreme values of a process of interest; be they block maxima over long blocks
|
|
or excesses over a high threshold.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-lmtest
|
|
(package
|
|
(name "r-lmtest")
|
|
(version "0.9-37")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lmtest" version))
|
|
(sha256
|
|
(base32
|
|
"02nasm0j2vwkhz11dxqixs23msy1s3yj0jps6949fmgh9gwjkjfx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-zoo" ,r-zoo)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/lmtest")
|
|
(synopsis "Testing linear regression models")
|
|
(description
|
|
"This package provides a collection of tests, data sets, and examples for
|
|
diagnostic checking in linear regression models. Furthermore, some generic
|
|
tools for inference in parametric models are provided.")
|
|
;; Either version is okay
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-idr
|
|
(package
|
|
(name "r-idr")
|
|
(version "1.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "idr" version))
|
|
(sha256
|
|
(base32
|
|
"05nvgw1xdg670bsjjrxkgd1mrdkciccpw4krn0zcgdf2r21dzgwb"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/idr/")
|
|
(synopsis "Irreproducible discovery rate")
|
|
(description
|
|
"This is a package for estimating the copula mixture model and plotting
|
|
correspondence curves in \"Measuring reproducibility of high-throughput
|
|
experiments\" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779,
|
|
by Li, Brown, Huang, and Bickel")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-inline
|
|
(package
|
|
(name "r-inline")
|
|
(version "0.3.15")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "inline" version))
|
|
(sha256
|
|
(base32
|
|
"0s4wssvpan189fijahknxq5s22ww9bzmdlmyhnra748r7khky17z"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/inline")
|
|
(synopsis "Functions to inline C, C++, Fortran function calls from R")
|
|
(description
|
|
"This package provides functionality to dynamically define R functions
|
|
and S4 methods with inlined C, C++ or Fortran code supporting @code{.C} and
|
|
@code{.Call} calling conventions.")
|
|
;; Any version of the LGPL.
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public r-bbmle
|
|
(package
|
|
(name "r-bbmle")
|
|
(version "1.0.20")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bbmle" version))
|
|
(sha256
|
|
(base32
|
|
"1xzij7swrrzl5ly8l3lw6awh486zcm00251dwqws1y23fbgyh3vc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-numderiv" ,r-numderiv)))
|
|
(home-page "https://cran.r-project.org/web/packages/bbmle")
|
|
(synopsis "Tools for General Maximum Likelihood Estimation")
|
|
(description
|
|
"This package provides methods and functions for fitting maximum
|
|
likelihood models in R. This package modifies and extends the @code{mle}
|
|
classes in the @code{stats4} package.")
|
|
;; Any version of the GPL
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-emdbook
|
|
(package
|
|
(name "r-emdbook")
|
|
(version "1.3.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "emdbook" version))
|
|
(sha256
|
|
(base32
|
|
"0a515jdzvg87npvrh7md7zp0v5nlz7c2jr7pba5dql6slb0d8j7q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bbmle" ,r-bbmle)
|
|
("r-coda" ,r-coda)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-plyr" ,r-plyr)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "http://www.math.mcmaster.ca/bolker/emdbook")
|
|
(synopsis "Support functions and data for \"Ecological Models and Data\"")
|
|
(description
|
|
"This package provides auxiliary functions and data sets for \"Ecological
|
|
Models and Data\", a book presenting maximum likelihood estimation and related
|
|
topics for ecologists (ISBN 978-0-691-12522-0).")
|
|
;; Any GPL version
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-lpsolve
|
|
(package
|
|
(name "r-lpsolve")
|
|
(version "5.6.13.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lpSolve" version))
|
|
(sha256
|
|
(base32
|
|
"1f10ywlaaldgjj84vs108ly0nsbkrdgbn5d6qj7nk93j1x1xrn3a"))))
|
|
(properties `((upstream-name . "lpSolve")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/lpSolve")
|
|
(synopsis "R interface to Lp_solve to solve linear/integer programs")
|
|
(description
|
|
"Lp_solve is software for solving linear, integer and mixed integer
|
|
programs. This implementation supplies a \"wrapper\" function in C and some R
|
|
functions that solve general linear/integer problems, assignment problems, and
|
|
transportation problems.")
|
|
(license license:lgpl2.0)))
|
|
|
|
(define-public r-limsolve
|
|
(package
|
|
(name "r-limsolve")
|
|
(version "1.5.5.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "limSolve" version))
|
|
(sha256
|
|
(base32
|
|
"1ll6ir42h3g2fzf0wqai213bm82gpwjj2hfma2np3mz024sc09rg"))))
|
|
(properties `((upstream-name . "limSolve")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lpsolve" ,r-lpsolve)
|
|
("r-mass" ,r-mass)
|
|
("r-quadprog" ,r-quadprog)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/limSolve")
|
|
(synopsis "Solving linear inverse models")
|
|
(description
|
|
"This package provides functions that:
|
|
|
|
@enumerate
|
|
@item find the minimum/maximum of a linear or quadratic function,
|
|
@item sample an underdetermined or overdetermined system,
|
|
@item solve a linear system Ax=B for the unknown x.
|
|
@end enumerate
|
|
|
|
It includes banded and tridiagonal linear systems. The package calls Fortran
|
|
functions from LINPACK.")
|
|
;; Any GPL version.
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-fitdistrplus
|
|
(package
|
|
(name "r-fitdistrplus")
|
|
(version "1.0-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fitdistrplus" version))
|
|
(sha256
|
|
(base32
|
|
"10q08wsv8v3w7797jdvvv60bgrf1bi6438wf0jcqv81ays82a245"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-npsurv" ,r-npsurv)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "http://riskassessment.r-forge.r-project.org")
|
|
(synopsis "Fitting a parametric distribution from data")
|
|
(description
|
|
"This package extends the @code{fitdistr} function of the MASS package
|
|
with several functions to help the fit of a parametric distribution to
|
|
non-censored or censored data. Censored data may contain left-censored,
|
|
right-censored and interval-censored values, with several lower and upper
|
|
bounds. In addition to @dfn{maximum likelihood estimation} (MLE), the package
|
|
provides moment matching (MME), quantile matching (QME) and maximum
|
|
goodness-of-fit estimation (MGE) methods (available only for non-censored
|
|
data). Weighted versions of MLE, MME and QME are available.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-energy
|
|
(package
|
|
(name "r-energy")
|
|
(version "1.7-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "energy" version))
|
|
(sha256
|
|
(base32
|
|
"15k9dg0a82cs9ypm0wpcsff3il1hzhnnv86dv5ngby1r144czhi4"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-boot" ,r-boot)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/energy")
|
|
(synopsis "Multivariate inference via the energy of data")
|
|
(description
|
|
"This package provides e-statistics (energy) tests and statistics for
|
|
multivariate and univariate inference, including distance correlation,
|
|
one-sample, two-sample, and multi-sample tests for comparing multivariate
|
|
distributions, are implemented. Measuring and testing multivariate
|
|
independence based on distance correlation, partial distance correlation,
|
|
multivariate goodness-of-fit tests, clustering based on energy distance,
|
|
testing for multivariate normality, distance components (disco) for
|
|
non-parametric analysis of structured data, and other energy
|
|
statistics/methods are implemented.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-suppdists
|
|
(package
|
|
(name "r-suppdists")
|
|
(version "1.1-9.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "SuppDists" version))
|
|
(sha256
|
|
(base32
|
|
"1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"))))
|
|
(properties `((upstream-name . "SuppDists")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/SuppDists")
|
|
(synopsis "Supplementary distributions")
|
|
(description
|
|
"This package provides ten distributions supplementing those built into
|
|
R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared,
|
|
Spearman's rho, maximum F ratio, the Pearson product moment correlation
|
|
coefficient, Johnson distributions, normal scores and generalized
|
|
hypergeometric distributions. In addition two random number generators of
|
|
George Marsaglia are included.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ksamples
|
|
(package
|
|
(name "r-ksamples")
|
|
(version "1.2-9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "kSamples" version))
|
|
(sha256
|
|
(base32
|
|
"1zs22p68d6320kcylisnk0b5wmpapxkyz15py09czxzw7npw8gms"))))
|
|
(properties `((upstream-name . "kSamples")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-suppdists" ,r-suppdists)))
|
|
(home-page "https://cran.r-project.org/web/packages/kSamples")
|
|
(synopsis "K-Sample rank tests and their combinations")
|
|
(description
|
|
"This package provides tools to compares k samples using the
|
|
Anderson-Darling test, Kruskal-Wallis type tests with different rank score
|
|
criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT)
|
|
test. It computes asymptotic, simulated or (limited) exact P-values, all
|
|
valid under randomization, with or without ties, or conditionally under random
|
|
sampling from populations, given the observed tie pattern. Except for Steel's
|
|
test and the JT test it also combines these tests across several blocks of
|
|
samples.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-cvst
|
|
(package
|
|
(name "r-cvst")
|
|
(version "0.2-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "CVST" version))
|
|
(sha256
|
|
(base32
|
|
"05l3yzkfrbds09ah9cdwn2sn4ryhq78lz33ryzrgkv176jc8qjw5"))))
|
|
(properties `((upstream-name . "CVST")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-kernlab" ,r-kernlab)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "https://cran.r-project.org/web/packages/CVST")
|
|
(synopsis "Fast cross-validation via sequential testing")
|
|
(description
|
|
"This package implements the fast cross-validation via sequential
|
|
testing (CVST) procedure. CVST is an improved cross-validation procedure
|
|
which uses non-parametric testing coupled with sequential analysis to
|
|
determine the best parameter set on linearly increasing subsets of the data.
|
|
Additionally to the CVST the package contains an implementation of the
|
|
ordinary k-fold cross-validation with a flexible and powerful set of helper
|
|
objects and methods to handle the overall model selection process. The
|
|
implementations of the Cochran's Q test with permutations and the sequential
|
|
testing framework of Wald are generic and can therefore also be used in other
|
|
contexts.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-squarem
|
|
(package
|
|
(name "r-squarem")
|
|
(version "2017.10-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "SQUAREM" version))
|
|
(sha256
|
|
(base32
|
|
"10xj26x7qjyvzndnbjl5krr9wabnb9cbrnp3m7xg673g8ddr12cv"))))
|
|
(properties `((upstream-name . "SQUAREM")))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html")
|
|
(synopsis "Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms")
|
|
(description
|
|
"This package provides algorithms for accelerating the convergence of
|
|
slow, monotone sequences from smooth, contraction mapping such as the EM
|
|
algorithm. It can be used to accelerate any smooth, linearly convergent
|
|
acceleration scheme. A tutorial style introduction to this package is
|
|
available in a vignette.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-lava
|
|
(package
|
|
(name "r-lava")
|
|
(version "1.6.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lava" version))
|
|
(sha256
|
|
(base32
|
|
"13rlqdg42ylnz4hc932bl50xismrcr4d9ykcd9zs19cw5mckjx0f"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-numderiv" ,r-numderiv)
|
|
("r-squarem" ,r-squarem)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://github.com/kkholst/lava")
|
|
(synopsis "Latent variable models")
|
|
(description
|
|
"This package provides tools for the estimation and simulation of latent
|
|
variable models.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-drr
|
|
(package
|
|
(name "r-drr")
|
|
(version "0.0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DRR" version))
|
|
(sha256
|
|
(base32
|
|
"1yd1fvllfkcrwg9v322n4wkk4q4q84nvy58y4vac9pdr3yf3i4vl"))))
|
|
(properties `((upstream-name . "DRR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cvst" ,r-cvst)
|
|
("r-kernlab" ,r-kernlab)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "https://cran.r-project.org/web/packages/DRR")
|
|
(synopsis "Dimensionality reduction via regression")
|
|
(description
|
|
"This package provides an implementation of dimensionality reduction via
|
|
regression using Kernel Ridge Regression.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-prodlim
|
|
(package
|
|
(name "r-prodlim")
|
|
(version "2018.04.18")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "prodlim" version))
|
|
(sha256
|
|
(base32
|
|
"1aslq87sqwikh8chxc378r38146y7kv79zz0kcq3j93ivx7va8jb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-kernsmooth" ,r-kernsmooth)
|
|
("r-lava" ,r-lava)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://cran.r-project.org/web/packages/prodlim")
|
|
(synopsis "Product-limit estimation for censored event history analysis")
|
|
(description
|
|
"This package provides a fast and user-friendly implementation of
|
|
nonparametric estimators for censored event history (survival) analysis with
|
|
the Kaplan-Meier and Aalen-Johansen methods.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-dimred
|
|
(package
|
|
(name "r-dimred")
|
|
(version "0.2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dimRed" version))
|
|
(sha256
|
|
(base32
|
|
"110d6y83ib1nfpxzmvkvb3fn3brskwkdbsk4dqrdrswrd4znxrg6"))))
|
|
(properties `((upstream-name . "dimRed")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-drr" ,r-drr)
|
|
("r-magrittr" ,r-magrittr)))
|
|
(home-page "https://github.com/gdkrmr/dimRed")
|
|
(synopsis "Framework for dimensionality reduction")
|
|
(description
|
|
"This package provides a collection of dimensionality reduction
|
|
techniques from R packages and provides a common interface for calling the
|
|
methods.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-timedate
|
|
(package
|
|
(name "r-timedate")
|
|
(version "3043.102")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "timeDate" version))
|
|
(sha256
|
|
(base32
|
|
"0wvl5pq261rvbgly7vilk3x3m9xk3ly6il1i5scwdf6srl1vlz1p"))))
|
|
(properties `((upstream-name . "timeDate")))
|
|
(build-system r-build-system)
|
|
(home-page "https://www.rmetrics.org")
|
|
(synopsis "Chronological and calendar objects")
|
|
(description
|
|
"This package provides an environment for teaching \"Financial
|
|
Engineering and Computational Finance\" and for managing chronological and
|
|
calendar objects.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-magic
|
|
(package
|
|
(name "r-magic")
|
|
(version "1.5-9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "magic" version))
|
|
(sha256
|
|
(base32
|
|
"0snmdh6vk0p6ar1swsihisinxrx7l8371dri5lk0z24ysgr5w7gs"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-abind" ,r-abind)))
|
|
(home-page "https://github.com/RobinHankin/magic.git")
|
|
(synopsis "Create and investigate magic squares")
|
|
(description
|
|
"This package provides a collection of efficient, vectorized algorithms
|
|
for the creation and investigation of magic squares and hypercubes, including
|
|
a variety of functions for the manipulation and analysis of arbitrarily
|
|
dimensioned arrays.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rmysql
|
|
(package
|
|
(name "r-rmysql")
|
|
(version "0.10.17")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RMySQL" version))
|
|
(sha256
|
|
(base32
|
|
"1xamf99ih44dvaxg5x4ivj0hkqssmabgqd7gh8b8q1srw7yg8kbm"))))
|
|
(properties `((upstream-name . "RMySQL")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("mariadb" ,mariadb)
|
|
("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-dbi" ,r-dbi)))
|
|
(home-page "https://github.com/r-dbi/RMySQL")
|
|
(synopsis "Database interface and MySQL driver for R")
|
|
(description
|
|
"This package provides a DBI interface to MySQL / MariaDB. The RMySQL
|
|
package contains an old implementation based on legacy code from S-PLUS which
|
|
is being phased out. A modern MySQL client based on Rcpp is available from
|
|
the RMariaDB package.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rpostgresql
|
|
(package
|
|
(name "r-rpostgresql")
|
|
(version "0.6-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RPostgreSQL" version))
|
|
(sha256
|
|
(base32
|
|
"1mdhw5821v2h7hpa53v10wz53k4i90r0vb6a3dia5gq8f9j1h088"))))
|
|
(properties `((upstream-name . "RPostgreSQL")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("postgresql" ,postgresql)))
|
|
(propagated-inputs
|
|
`(("r-dbi" ,r-dbi)))
|
|
(home-page "https://github.com/tomoakin/RPostgreSQL")
|
|
(synopsis "R interface to the PostgreSQL database system")
|
|
(description
|
|
"This package provides a Database Interface (DBI) compliant driver for R
|
|
to access PostgreSQL database systems.")
|
|
;; The whole package is released under GPL version 2. It includes code
|
|
;; under the PostgreSQL license.
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-geometry
|
|
(package
|
|
(name "r-geometry")
|
|
(version "0.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "geometry" version))
|
|
(sha256
|
|
(base32
|
|
"0v3ivaw8vbjyxg08dd573qk3kqfyknj5hli9503dza6p6xz0dzmm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-magic" ,r-magic)
|
|
("r-lpsolve" ,r-lpsolve)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcppprogress" ,r-rcppprogress)))
|
|
(home-page "http://geometry.r-forge.r-project.org/")
|
|
(synopsis "Mesh generation and surface tesselation")
|
|
(description
|
|
"This package makes the qhull library available in R, in a similar manner
|
|
as in Octave. Qhull computes convex hulls, Delaunay triangulations, halfspace
|
|
intersections about a point, Voronoi diagrams, furthest-site Delaunay
|
|
triangulations, and furthest-site Voronoi diagrams. It runs in 2-d, 3-d, 4-d,
|
|
and higher dimensions. It implements the Quickhull algorithm for computing
|
|
the convex hull. Qhull does not support constrained Delaunay triangulations,
|
|
or mesh generation of non-convex objects, but the package does include some R
|
|
functions that allow for this. Currently the package only gives access to
|
|
Delaunay triangulation and convex hull computation.")
|
|
;; The Qhull sources are included and are distributed under a custom
|
|
;; non-copyleft license. The R sources are released under GPL version 2.
|
|
(license (list license:gpl2
|
|
(license:non-copyleft "http://www.qhull.org/COPYING.txt")))))
|
|
|
|
(define-public r-ddalpha
|
|
(package
|
|
(name "r-ddalpha")
|
|
(version "1.3.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ddalpha" version))
|
|
(sha256
|
|
(base32
|
|
"1vzs0cvl6xw3h9i00rg3hs02xwgxcnh8326y10kxmhs3qq4m7nb2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-class" ,r-class)
|
|
("r-geometry" ,r-geometry)
|
|
("r-mass" ,r-mass)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-robustbase" ,r-robustbase)
|
|
("r-sfsmisc" ,r-sfsmisc)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/ddalpha")
|
|
(synopsis "Depth-Based classification and calculation of data depth")
|
|
(description
|
|
"This package contains procedures for depth-based supervised learning,
|
|
which are entirely non-parametric, in particular the DDalpha-procedure (Lange,
|
|
Mosler and Mozharovskyi, 2014). The training data sample is transformed by a
|
|
statistical depth function to a compact low-dimensional space, where the final
|
|
classification is done. It also offers an extension to functional data and
|
|
routines for calculating certain notions of statistical depth functions. 50
|
|
multivariate and 5 functional classification problems are included.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-gower
|
|
(package
|
|
(name "r-gower")
|
|
(version "0.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gower" version))
|
|
(sha256
|
|
(base32
|
|
"007ivwn1nagpi26qq8iih1c2l61c53glvv60n90hi341ry8vwgxg"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/markvanderloo/gower")
|
|
(synopsis "Gower's distance")
|
|
(description
|
|
"This package provides tools to compute Gower's distance (or similarity)
|
|
coefficient between records, and to compute the top-n matches between records.
|
|
Core algorithms are executed in parallel on systems supporting OpenMP.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-rcpproll
|
|
(package
|
|
(name "r-rcpproll")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppRoll" version))
|
|
(sha256
|
|
(base32
|
|
"0srzfhzkk42kzrdjnhbb37946jp1p688rgysy6k3i2is8jb21zyb"))))
|
|
(properties `((upstream-name . "RcppRoll")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/RcppRoll")
|
|
(synopsis "Efficient rolling and windowed operations")
|
|
(description
|
|
"This package provides fast and efficient routines for common rolling /
|
|
windowed operations. Routines for the efficient computation of windowed mean,
|
|
median, sum, product, minimum, maximum, standard deviation and variance are
|
|
provided.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ipred
|
|
(package
|
|
(name "r-ipred")
|
|
(version "0.9-9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ipred" version))
|
|
(sha256
|
|
(base32
|
|
"0vs1hqfx7yd0xdbmfsf2gim7spkni0845cj6gswn0nhdfdq7ma0d"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-class" ,r-class)
|
|
("r-mass" ,r-mass)
|
|
("r-nnet" ,r-nnet)
|
|
("r-prodlim" ,r-prodlim)
|
|
("r-rpart" ,r-rpart)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://cran.r-project.org/web/packages/ipred")
|
|
(synopsis "Improved predictors")
|
|
(description
|
|
"This package provides improved predictive models by indirect
|
|
classification and bagging for classification, regression and survival
|
|
problems as well as resampling based estimators of prediction error.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-psych
|
|
(package
|
|
(name "r-psych")
|
|
(version "1.8.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "psych" version))
|
|
(sha256
|
|
(base32
|
|
"0hvp0dkkkn0szaf5rkirr3kb8qmr4bxwl775m5wmpvn1kc25w5vf"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-foreign" ,r-foreign)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mnormt" ,r-mnormt)
|
|
("r-nlme" ,r-nlme)))
|
|
(home-page "https://cran.r-project.org/web/packages/psych/")
|
|
(synopsis "Procedures for psychological, psychometric, and personality research")
|
|
(description
|
|
"This package provides a general purpose toolbox for personality,
|
|
psychometric theory and experimental psychology. Functions are primarily for
|
|
multivariate analysis and scale construction using factor analysis, principal
|
|
component analysis, cluster analysis and reliability analysis, although others
|
|
provide basic descriptive statistics. Item Response Theory is done using
|
|
factor analysis of tetrachoric and polychoric correlations. Functions for
|
|
analyzing data at multiple levels include within and between group statistics,
|
|
including correlations and factor analysis. Functions for simulating and
|
|
testing particular item and test structures are included. Several functions
|
|
serve as a useful front end for structural equation modeling. Graphical
|
|
displays of path diagrams, factor analysis and structural equation models are
|
|
created using basic graphics.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-generics
|
|
(package
|
|
(name "r-generics")
|
|
(version "0.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "generics" version))
|
|
(sha256
|
|
(base32
|
|
"0xk1xhpy7gpv3pvaygzhpfdxj72zmb38pb4nscfyg2ff36vx3cvi"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/r-lib/generics")
|
|
(synopsis "Common S3 generics not provided by base R methods")
|
|
(description
|
|
"In order to reduce potential package dependencies and conflicts,
|
|
generics provides a number of commonly used S3 generics that are not provided
|
|
by base R methods related to model fitting.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-broom
|
|
(package
|
|
(name "r-broom")
|
|
(version "0.5.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "broom" version))
|
|
(sha256
|
|
(base32
|
|
"0qmclih5dm5sqzy4hplcfy677kr12pm9pnpv3r319g14dd27pbqn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-generics" ,r-generics)
|
|
("r-nlme" ,r-nlme)
|
|
("r-purrr" ,r-purrr)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/tidyverse/broom")
|
|
(synopsis "Convert statistical analysis objects into tidy data frames")
|
|
(description
|
|
"This package provides tools to convert statistical analysis objects from
|
|
R into tidy data frames, so that they can more easily be combined, reshaped
|
|
and otherwise processed with tools like @code{dplyr}, @code{tidyr} and
|
|
@code{ggplot2}. The package provides three S3 generics: @code{tidy}, which
|
|
summarizes a model's statistical findings such as coefficients of a
|
|
regression; @code{augment}, which adds columns to the original data such as
|
|
predictions, residuals and cluster assignments; and @code{glance}, which
|
|
provides a one-row summary of model-level statistics.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-recipes
|
|
(package
|
|
(name "r-recipes")
|
|
(version "0.1.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "recipes" version))
|
|
(sha256
|
|
(base32
|
|
"056zv4vhayyy8q9izcdknbb9hff2gxivg21g5mkssia78vw8g3mg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-generics" ,r-generics)
|
|
("r-glue" ,r-glue)
|
|
("r-gower" ,r-gower)
|
|
("r-ipred" ,r-ipred)
|
|
("r-lubridate" ,r-lubridate)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-matrix" ,r-matrix)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rcpproll" ,r-rcpproll)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-tidyselect" ,r-tidyselect)
|
|
("r-timedate" ,r-timedate)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/topepo/recipes")
|
|
(synopsis "Preprocessing tools to create design matrices")
|
|
(description
|
|
"Recipes is an extensible framework to create and preprocess design
|
|
matrices. Recipes consist of one or more data manipulation and analysis
|
|
\"steps\". Statistical parameters for the steps can be estimated from an
|
|
initial data set and then applied to other data sets. The resulting design
|
|
matrices can then be used as inputs into statistical or machine learning
|
|
models.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-pdist
|
|
(package
|
|
(name "r-pdist")
|
|
(version "1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pdist" version))
|
|
(sha256
|
|
(base32
|
|
"18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/jeffwong/pdist")
|
|
(synopsis "Partitioned distance function")
|
|
(description
|
|
"Pdist computes the euclidean distance between rows of a matrix X and
|
|
rows of another matrix Y. Previously, this could be done by binding the two
|
|
matrices together and calling @code{dist}, but this creates unnecessary
|
|
computation by computing the distances between a row of X and another row of
|
|
X, and likewise for Y. Pdist strictly computes distances across the two
|
|
matrices, not within the same matrix, making computations significantly faster
|
|
for certain use cases.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-ggrepel
|
|
(package
|
|
(name "r-ggrepel")
|
|
(version "0.8.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggrepel" version))
|
|
(sha256
|
|
(base32
|
|
"10vjrcmx8yknfbx93d9a4y3z8gafri0fhimw6hcq733dmdvkml6m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "http://github.com/slowkow/ggrepel")
|
|
(synopsis "Repulsive text and label geometries for ggplot2")
|
|
(description
|
|
"This package provides text and label geometries for ggplot2 that help to
|
|
avoid overlapping text labels. Labels repel away from each other and away
|
|
from the data points.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-corrplot
|
|
(package
|
|
(name "r-corrplot")
|
|
(version "0.84")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "corrplot" version))
|
|
(sha256
|
|
(base32
|
|
"1k03qd8db7pwg1v318xapx5mpiypiz2n07qr19c4b45diri5xkhd"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/taiyun/corrplot")
|
|
(synopsis "Visualization of a correlation matrix")
|
|
(description
|
|
"This package provides a graphical display of a correlation matrix or
|
|
general matrix. It also contains some algorithms to do matrix reordering. In
|
|
addition, corrplot is good at details, including choosing color, text labels,
|
|
color labels, layout, etc.")
|
|
;; Any version of the GPL
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-stringdist
|
|
(package
|
|
(name "r-stringdist")
|
|
(version "0.9.5.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stringdist" version))
|
|
(sha256
|
|
(base32
|
|
"0nw8c317qkfq63pr0prl0hx522ddfq4cbgixb5r4pq3fxk9z303l"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/markvanderloo/stringdist")
|
|
(synopsis "Approximate string matching and string distance functions")
|
|
(description
|
|
"This package implements an approximate string matching version of R's
|
|
native @code{match} function. It can calculate various string distances based
|
|
on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal sting alignment),
|
|
qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro,
|
|
Jaro-Winkler). An implementation of soundex is provided as well. Distances
|
|
can be computed between character vectors while taking proper care of encoding
|
|
or between integer vectors representing generic sequences.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-ucminf
|
|
(package
|
|
(name "r-ucminf")
|
|
(version "1.1-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ucminf" version))
|
|
(sha256
|
|
(base32
|
|
"01vggwg1w71k98qs6fhb0x1843vi322mf4g3hbclks94kcpkisx2"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/ucminf/")
|
|
(synopsis "General-purpose unconstrained non-linear optimization")
|
|
(description
|
|
"This package provides an implementation of an algorithm for
|
|
general-purpose unconstrained non-linear optimization. The algorithm is of
|
|
quasi-Newton type with BFGS updating of the inverse Hessian and soft line
|
|
search with a trust region type monitoring of the input to the line search
|
|
algorithm. The interface of @code{ucminf} is designed for easy interchange
|
|
with the package @code{optim}.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ordinal
|
|
(package
|
|
(name "r-ordinal")
|
|
(version "2019.4-25")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ordinal" version))
|
|
(sha256
|
|
(base32
|
|
"1pvrkly4x12w32n7w1qljdwzqnlkv7rfa7rx0nz5vbiw29xas4i8"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-numderiv" ,r-numderiv)
|
|
("r-ucminf" ,r-ucminf)))
|
|
(home-page "https://github.com/runehaubo/ordinal")
|
|
(synopsis "Regression models for ordinal data")
|
|
(description
|
|
"This package provides an implementation of cumulative link (mixed)
|
|
models also known as ordered regression models, proportional odds models,
|
|
proportional hazards models for grouped survival times and ordered models.
|
|
Estimation is via maximum likelihood and mixed models are fitted with the
|
|
Laplace approximation and adaptive Gauss-Hermite quadrature.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-jomo
|
|
(package
|
|
(name "r-jomo")
|
|
(version "2.6-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "jomo" version))
|
|
(sha256
|
|
(base32
|
|
"097zfdcqc3a45ay8xxbraqh8xsfyivskkdmc2b4ca4n979lx8vyb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lme4" ,r-lme4)
|
|
("r-mass" ,r-mass)
|
|
("r-ordinal" ,r-ordinal)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://cran.r-project.org/web/packages/jomo/")
|
|
(synopsis "Multilevel Joint Modelling Multiple Imputation")
|
|
(description
|
|
"Similarly to Schafer's package pan, jomo is a package for multilevel
|
|
joint modelling multiple imputation @url{Carpenter and Kenward (2013),
|
|
http://doi.org/10.1002/9781119942283}. Novel aspects of jomo are the
|
|
possibility of handling binary and categorical data through latent normal
|
|
variables, the option to use cluster-specific covariance matrices and to
|
|
impute compatibly with the substantive model.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-pan
|
|
(package
|
|
(name "r-pan")
|
|
(version "1.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pan" version))
|
|
(sha256
|
|
(base32
|
|
"1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/pan/")
|
|
(synopsis "Multiple imputation for multivariate panel or clustered data")
|
|
(description
|
|
"This package implements multiple imputation for multivariate panel or
|
|
clustered data.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-mitml
|
|
(package
|
|
(name "r-mitml")
|
|
(version "0.3-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mitml" version))
|
|
(sha256
|
|
(base32
|
|
"0yqyxkyi1kmv5k63wxj5kkg5g8igk1axk2csb4xhj6wz0p89dxy6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-haven" ,r-haven)
|
|
("r-jomo" ,r-jomo)
|
|
("r-pan" ,r-pan)))
|
|
(home-page "https://cran.r-project.org/web/packages/mitml/")
|
|
(synopsis "Tools for multiple imputation in multilevel modeling")
|
|
(description
|
|
"This package provides tools for multiple imputation of missing data in
|
|
multilevel modeling. It includes a user-friendly interface to the packages
|
|
pan and jomo, and several functions for visualization, data management and the
|
|
analysis of multiply imputed data sets.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-mice
|
|
(package
|
|
(name "r-mice")
|
|
(version "3.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mice" version))
|
|
(sha256
|
|
(base32
|
|
"0icydc312sbvzbp0r0mhs2r77a2ly2xvz5w5amirz3wdkvgyrk2g"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-mitml" ,r-mitml)
|
|
("r-nnet" ,r-nnet)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rpart" ,r-rpart)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://cran.r-project.org/web/packages/mice/")
|
|
(synopsis "Multivariate imputation by chained equations")
|
|
(description
|
|
"Multiple imputation using @dfn{Fully Conditional Specification} (FCS)
|
|
implemented by the MICE algorithm as described in @url{Van Buuren and
|
|
Groothuis-Oudshoorn (2011), http://doi.org/10.18637/jss.v045.i03}. Each
|
|
variable has its own imputation model. Built-in imputation models are
|
|
provided for continuous data (predictive mean matching, normal), binary
|
|
data (logistic regression), unordered categorical data (polytomous logistic
|
|
regression) and ordered categorical data (proportional odds). MICE can also
|
|
impute continuous two-level data (normal model, pan, second-level variables).
|
|
Passive imputation can be used to maintain consistency between variables.
|
|
Various diagnostic plots are available to inspect the quality of the
|
|
imputations.")
|
|
;; Any of these two versions.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-truncnorm
|
|
(package
|
|
(name "r-truncnorm")
|
|
(version "1.0-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "truncnorm" version))
|
|
(sha256
|
|
(base32
|
|
"0zn88wdd58223kibk085rhsikl4yhlrwiyq109hzjg06hy6lwmj9"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/truncnorm/")
|
|
(synopsis "Truncated normal distribution")
|
|
(description "This package provides functions for the truncated normal
|
|
distribution with mean equal to @code{mean} and standard deviation equal to
|
|
@code{sd}. It includes density, distribution, quantile, and expected value
|
|
functions, as well as a random generation function.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rsolnp
|
|
(package
|
|
(name "r-rsolnp")
|
|
(version "1.16")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rsolnp" version))
|
|
(sha256
|
|
(base32
|
|
"0w7nkj6igr0gi7r7jg950lsx7dj6aipgxi6vbjsf5f5yc9h7fhii"))))
|
|
(properties `((upstream-name . "Rsolnp")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-truncnorm" ,r-truncnorm)))
|
|
(home-page "https://cran.r-project.org/web/packages/Rsolnp/")
|
|
(synopsis "General non-linear optimization")
|
|
(description "The Rsolnp package implements a general non-linear augmented
|
|
Lagrange multiplier method solver, a @dfn{sequential quadratic
|
|
programming} (SQP) based solver).")
|
|
;; Any version of the GPL.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-hardyweinberg
|
|
(package
|
|
(name "r-hardyweinberg")
|
|
(version "1.6.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "HardyWeinberg" version))
|
|
(sha256
|
|
(base32
|
|
"15i7b444hikkfgqmx2ki827998xwra38k9v7a7kavwz6zmq5mmv9"))))
|
|
(properties `((upstream-name . "HardyWeinberg")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mice" ,r-mice)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rsolnp" ,r-rsolnp)))
|
|
(home-page "https://cran.r-project.org/package=HardyWeinberg")
|
|
(synopsis "Statistical tests and graphics for Hardy-Weinberg equilibrium")
|
|
(description
|
|
"This package contains tools for exploring Hardy-Weinberg equilibrium for
|
|
diallelic genetic marker data. All classical tests (chi-square, exact,
|
|
likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium are
|
|
included in the package, as well as functions for power computation and for
|
|
the simulation of marker data under equilibrium and disequilibrium. Routines
|
|
for dealing with markers on the X-chromosome are included. Functions for
|
|
testing equilibrium in the presence of missing data by using multiple
|
|
imputation are also provided. Implements several graphics for exploring the
|
|
equilibrium status of a large set of diallelic markers: ternary plots with
|
|
acceptance regions, log-ratio plots and Q-Q plots.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-sm
|
|
(package
|
|
(name "r-sm")
|
|
(version "2.2-5.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sm" version))
|
|
(sha256
|
|
(base32
|
|
"0c4whcx879gb4lwvqnzxl5n9xgpcqh2c54ip9ami3mwfprzcv45q"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "http://www.stats.gla.ac.uk/~adrian/sm/")
|
|
(synopsis "Smoothing methods for nonparametric regression and density estimation")
|
|
(description
|
|
"This is software accompanying the book 'Applied Smoothing Techniques for
|
|
Data Analysis---The Kernel Approach with S-Plus Illustrations', Oxford
|
|
University Press. It provides smoothing methods for nonparametric regression
|
|
and density estimation")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-venndiagram
|
|
(package
|
|
(name "r-venndiagram")
|
|
(version "1.6.20")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "VennDiagram" version))
|
|
(sha256
|
|
(base32
|
|
"1ic1jaxzw98si2p4n1fl4n3myhd7fpw0njb634cwhviwybzv6775"))))
|
|
(properties `((upstream-name . "VennDiagram")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-futile-logger" ,r-futile-logger)))
|
|
(home-page "https://cran.r-project.org/web/packages/VennDiagram/")
|
|
(synopsis "Generate High-Resolution Venn and Euler Plots")
|
|
(description
|
|
"This package provides a set of functions to generate high-resolution
|
|
Venn and Euler plots. It includes handling for several special cases,
|
|
including two-case scaling, and extensive customization of plot shape and
|
|
structure.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-vioplot
|
|
(package
|
|
(name "r-vioplot")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "vioplot" version))
|
|
(sha256
|
|
(base32
|
|
"1ddmmqq7qrnvr5q518afnysrl7ccr8am9njknv3dpwaqzcdr9akn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-sm" ,r-sm)
|
|
("r-zoo" ,r-zoo)))
|
|
(home-page "http://wsopuppenkiste.wiso.uni-goettingen.de/~dadler")
|
|
(synopsis "Violin plot")
|
|
(description
|
|
"This package provides a violin plot, which is a combination of a box
|
|
plot and a kernel density plot.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-rsofia
|
|
(package
|
|
(name "r-rsofia")
|
|
(version "1.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
;; This package has been removed from CRAN, so we can
|
|
;; only fetch it from the archives.
|
|
(uri (string-append "https://cran.r-project.org/src/"
|
|
"contrib/Archive/RSofia/RSofia_"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0q931y9rcf6slb0s2lsxhgqrzy4yqwh8hb1124nxg0bjbxvjbihn"))))
|
|
(properties `((upstream-name . "RSofia")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/src/contrib/Archive/RSofia")
|
|
(synopsis "Port of sofia-ml to R")
|
|
(description "This package is a port of sofia-ml to R. Sofia-ml is a
|
|
suite of fast incremental algorithms for machine learning that can be used for
|
|
training models for classification or ranking.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-xts
|
|
(package
|
|
(name "r-xts")
|
|
(version "0.11-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xts" version))
|
|
(sha256
|
|
(base32
|
|
"1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-zoo" ,r-zoo)))
|
|
(home-page "https://github.com/joshuaulrich/xts")
|
|
(synopsis "Extensible time series")
|
|
(description
|
|
"This package provides for uniform handling of R's different time-based
|
|
data classes by extending @code{zoo}, maximizing native format information
|
|
preservation and allowing for user-level customization and extension, while
|
|
simplifying cross-class interoperability.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-performanceanalytics
|
|
(package
|
|
(name "r-performanceanalytics")
|
|
(version "1.5.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "PerformanceAnalytics" version))
|
|
(sha256
|
|
(base32
|
|
"0jhjldwyxwq7a47zmk5y1jjck7hvq92p8rlgjvdfy51hx2dmlqqd"))))
|
|
(properties
|
|
`((upstream-name . "PerformanceAnalytics")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-quadprog" ,r-quadprog)
|
|
("r-xts" ,r-xts)
|
|
("r-zoo" ,r-zoo)))
|
|
(home-page "https://r-forge.r-project.org/projects/returnanalytics/")
|
|
(synopsis "Econometric tools for performance and risk analysis")
|
|
(description "This is a collection of econometric functions for
|
|
performance and risk analysis. This package aims to aid practitioners and
|
|
researchers in utilizing the latest research in analysis of non-normal return
|
|
streams. In general, it is most tested on return (rather than price) data on
|
|
a regular scale, but most functions will work with irregular return data as
|
|
well, and increasing numbers of functions will work with P&L or price data
|
|
where possible.")
|
|
;; Either version may be picked.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-laeken
|
|
(package
|
|
(name "r-laeken")
|
|
(version "0.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "laeken" version))
|
|
(sha256
|
|
(base32
|
|
"1g9r3y7b0gl91hijk9awa8rjk97mqpkxinzq2cgmx0m38ng9ylpa"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-boot" ,r-boot)
|
|
("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/laeken/")
|
|
(synopsis "Estimation of indicators on social exclusion and poverty")
|
|
(description "This package provides tools for the estimation of indicators
|
|
on social exclusion and poverty, as well as an implementation of Pareto tail
|
|
modeling for empirical income distributions.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-vcd
|
|
(package
|
|
(name "r-vcd")
|
|
(version "1.4-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "vcd" version))
|
|
(sha256
|
|
(base32
|
|
"1lp99h0wvsc61l1dgcqjxdrcgpgw88ak430cdsv43kmm43qssqd5"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-colorspace" ,r-colorspace)
|
|
("r-lmtest" ,r-lmtest)
|
|
("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/vcd/")
|
|
(synopsis "Visualizing categorical data")
|
|
(description "This package provides visualization techniques, data sets,
|
|
summary and inference procedures aimed particularly at categorical data.
|
|
Special emphasis is given to highly extensible grid graphics. The package was
|
|
originally inspired by the book \"Visualizing Categorical Data\" by Michael
|
|
Friendly and is now the main support package for a new book, \"Discrete Data
|
|
Analysis with R\" by Michael Friendly and David Meyer (2015).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ica
|
|
(package
|
|
(name "r-ica")
|
|
(version "1.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ica" version))
|
|
(sha256
|
|
(base32
|
|
"0ya1nph1zwhad0bfz4yxs27kl45yk1dhnphdlrq34p8pqrpmj8g7"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/ica/")
|
|
(synopsis "Independent component analysis")
|
|
(description "This package provides tools for @dfn{Independent Component
|
|
Analysis} (ICA) using various algorithms: FastICA,
|
|
Information-Maximization (Infomax), and @dfn{Joint Approximate Diagonalization
|
|
of Eigenmatrices} (JADE).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-dtw
|
|
(package
|
|
(name "r-dtw")
|
|
(version "1.20-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dtw" version))
|
|
(sha256
|
|
(base32
|
|
"1w301xwizncy5r8v9rwwdxfshydgp3l1pnjla1fjn6n8lx3imjj3"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-proxy" ,r-proxy)))
|
|
(home-page "http://dtw.r-forge.r-project.org/")
|
|
(synopsis "Dynamic Time Warping Algorithms")
|
|
(description "This package provides a comprehensive implementation of
|
|
@dfn{dynamic time warping} (DTW) algorithms in R. DTW computes the
|
|
optimal (least cumulative distance) alignment between points of two time
|
|
series. Common DTW variants covered include local (slope) and global (window)
|
|
constraints, subsequence matches, arbitrary distance definitions,
|
|
normalizations, minimum variance matching, and so on.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-sdmtools
|
|
(package
|
|
(name "r-sdmtools")
|
|
(version "1.1-221.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "SDMTools" version))
|
|
(sha256
|
|
(base32
|
|
"1fsgnlc7glawimzijp11j53g5bnfp1mdq9wb0754idmxcdi8a99q"))))
|
|
(properties `((upstream-name . "SDMTools")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-r-utils" ,r-r-utils)))
|
|
(home-page "http://www.rforge.net/SDMTools/")
|
|
(synopsis "Species distribution modelling tools")
|
|
(description "This package provides a set of tools for post processing
|
|
the outcomes of species distribution modeling exercises. It includes novel
|
|
methods for comparing models and tracking changes in distributions through
|
|
time. It further includes methods for visualizing outcomes, selecting
|
|
thresholds, calculating measures of accuracy and landscape fragmentation
|
|
statistics, etc.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-scatterplot3d
|
|
(package
|
|
(name "r-scatterplot3d")
|
|
(version "0.3-41")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "scatterplot3d" version))
|
|
(sha256
|
|
(base32
|
|
"152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/scatterplot3d/")
|
|
(synopsis "3D scatter plot")
|
|
(description "This package provides an implementation of scatter plots for
|
|
plotting. a three dimensional point cloud.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ggridges
|
|
(package
|
|
(name "r-ggridges")
|
|
(version "0.5.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggridges" version))
|
|
(sha256
|
|
(base32
|
|
"0dhwcpy785ac2ny5bjp284595nnybi3554wd0yffsli0vzf7ry01"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-plyr" ,r-plyr)
|
|
("r-scales" ,r-scales)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/clauswilke/ggridges")
|
|
(synopsis "Ridgeline plots in ggplot2")
|
|
(description
|
|
"Ridgeline plots provide a convenient way of visualizing changes in
|
|
distributions over time or space. This package enables the creation of such
|
|
plots in @code{ggplot2}.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ggjoy
|
|
(package
|
|
(name "r-ggjoy")
|
|
(version "0.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggjoy" version))
|
|
(sha256
|
|
(base32
|
|
"012md2m0jqfcccb933j423m3ck31v3p0pd41gjxpyg9082y7ixyj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-ggridges" ,r-ggridges)))
|
|
(home-page "https://github.com/clauswilke/ggjoy")
|
|
(synopsis "Joyplots in ggplot2")
|
|
(description "Joyplots provide a convenient way of visualizing changes in
|
|
distributions over time or space. This package enables the creation of such
|
|
plots in @code{ggplot2}.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-cli
|
|
(package
|
|
(name "r-cli")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cli" version))
|
|
(sha256
|
|
(base32
|
|
"02hdwvdq5nic6dhxj88jbgsc9m8yrz3yibigg6szkggxyk6hzh2g"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-crayon" ,r-crayon)))
|
|
(home-page "https://github.com/r-lib/cli#readme")
|
|
(synopsis "Helpers for developing command line interfaces")
|
|
(description "This package provides a suite of tools designed to build
|
|
attractive command line interfaces (CLIs). It includes tools for drawing
|
|
rules, boxes, trees, and Unicode symbols with ASCII alternatives.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-argparser
|
|
(package
|
|
(name "r-argparser")
|
|
(version "0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "argparser" version))
|
|
(sha256
|
|
(base32
|
|
"0s1wxshx4jk69wfxhycx973q6y8cmqrfymyjklhq1i8xrj0kmmx9"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://bitbucket.org/djhshih/argparser")
|
|
(synopsis "Command-line argument parser")
|
|
(description
|
|
"This package provides a cross-platform command-line argument parser
|
|
written purely in R with no external dependencies. It is useful with the
|
|
Rscript front-end and facilitates turning an R script into an executable
|
|
script.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-debugme
|
|
(package
|
|
(name "r-debugme")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "debugme" version))
|
|
(sha256
|
|
(base32
|
|
"1c9sg55zvf10h8198jdnpamm6f66lzw3c3jnmdp9ls6na0j0xbjd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-crayon" ,r-crayon)))
|
|
(home-page "https://github.com/r-lib/debugme#readme")
|
|
(synopsis "Debug R packages")
|
|
(description
|
|
"This package allows the user to specify debug messages as special string
|
|
constants, and control debugging of packages via environment variables.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-processx
|
|
(package
|
|
(name "r-processx")
|
|
(version "3.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "processx" version))
|
|
(sha256
|
|
(base32
|
|
"1bhbfacx2z2d97pz5bch45nvbvywhx2zp049czlfbdivkzgxn8v1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ps" ,r-ps)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://github.com/r-lib/processx3")
|
|
(synopsis "Execute and control system processes")
|
|
(description
|
|
"This package provides portable tools to run system processes in the
|
|
background. It can check if a background process is running; wait on a
|
|
background process to finish; get the exit status of finished processes; kill
|
|
background processes and their children; restart processes. It can read the
|
|
standard output and error of the processes, using non-blocking connections.
|
|
@code{processx} can poll a process for standard output or error, with a
|
|
timeout. It can also poll several processes at once.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-tsp
|
|
(package
|
|
(name "r-tsp")
|
|
(version "1.1-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "TSP" version))
|
|
(sha256
|
|
(base32
|
|
"0rxxhvqi55869dg2p82hzg5kvgcqf9h60cjcg00k3pv9aw4x07kb"))))
|
|
(properties `((upstream-name . "TSP")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-foreach" ,r-foreach)))
|
|
(home-page "https://cran.r-project.org/web/packages/TSP/")
|
|
(synopsis "Traveling salesperson problem (TSP)")
|
|
(description "This package provides basic infrastructure and some
|
|
algorithms for the @dfn{traveling salesperson problem}(TSP) (also known as the
|
|
traveling salesman problem).")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-qap
|
|
(package
|
|
(name "r-qap")
|
|
(version "0.1-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "qap" version))
|
|
(sha256
|
|
(base32
|
|
"0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/qap/")
|
|
(synopsis "Heuristics for the quadratic assignment problem (QAP)")
|
|
(description "This package implements heuristics for the @dfn{quadratic
|
|
assignment problem} (QAP). Currently only a simulated annealing heuristic is
|
|
available.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-gclus
|
|
(package
|
|
(name "r-gclus")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gclus" version))
|
|
(sha256
|
|
(base32
|
|
"1cz0g0i972955hhaji30rx8448x7f3as7z1sww9i5h86ybgirilw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-cluster" ,r-cluster)))
|
|
(home-page "https://cran.r-project.org/web/packages/gclus/")
|
|
(synopsis "Clustering graphics")
|
|
(description "This package orders panels in scatterplot matrices and
|
|
parallel coordinate displays by some merit index. It contains various indices
|
|
of merit, ordering functions, and enhanced versions of @code{pairs} and
|
|
@code{parcoord} which color panels according to their merit level.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-webshot
|
|
(package
|
|
(name "r-webshot")
|
|
(version "0.5.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "webshot" version))
|
|
(sha256
|
|
(base32
|
|
"08sb1xi376pfy1vwilk2d68zljsg9yiv04n2dkqz383gdhh0sxdr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-callr" ,r-callr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-magrittr" ,r-magrittr)))
|
|
(home-page "https://github.com/wch/webshot/")
|
|
(synopsis "Take screenshots of web pages")
|
|
(description
|
|
"Webshot makes it easy to take screenshots of web pages from within R.
|
|
It can also run Shiny applications locally and take screenshots of the
|
|
application; and it can render and screenshot static as well as interactive R
|
|
Markdown documents.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-seriation
|
|
(package
|
|
(name "r-seriation")
|
|
(version "1.2-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "seriation" version))
|
|
(sha256
|
|
(base32
|
|
"0dbz5b5msy4fr2whhphyriqk1xc6305zpjq59rrwxyz3d7rzwpa6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)
|
|
("r-colorspace" ,r-colorspace)
|
|
("r-dendextend" ,r-dendextend)
|
|
("r-gclus" ,r-gclus)
|
|
("r-gplots" ,r-gplots)
|
|
("r-mass" ,r-mass)
|
|
("r-qap" ,r-qap)
|
|
("r-registry" ,r-registry)
|
|
("r-tsp" ,r-tsp)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "http://s2.smu.edu/IDA/seriation/")
|
|
(synopsis "Infrastructure for ordering objects using seriation")
|
|
(description
|
|
"This package provides infrastructure for seriation with an
|
|
implementation of several seriation/sequencing techniques to reorder matrices,
|
|
dissimilarity matrices, and dendrograms. It also provides (optimally)
|
|
reordered heatmaps, color images and clustering visualizations like
|
|
dissimilarity plots, and visual assessment of cluster tendency plots (VAT and
|
|
iVAT).")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-xfun
|
|
(package
|
|
(name "r-xfun")
|
|
(version "0.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xfun" version))
|
|
(sha256
|
|
(base32
|
|
"05jlbi5byqpw0fkhmmxqglnaxh9gwbcigx77kcpw1pkxnpwfry62"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/yihui/xfun")
|
|
(synopsis "Miscellaneous functions")
|
|
(description
|
|
"This package provides miscellaneous functions commonly used in other
|
|
packages maintained by Yihui Xie.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-utf8
|
|
(package
|
|
(name "r-utf8")
|
|
(version "1.1.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "utf8" version))
|
|
(sha256
|
|
(base32
|
|
"0m0ywg8k3blfiahxvh1i4zn9dksrlc937d2lbza5fc38zjnrrnpn"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/patperry/r-utf8")
|
|
(synopsis "Unicode text processing")
|
|
(description
|
|
"This package provides tools to process and print UTF-8 encoded
|
|
international text (Unicode). Input, validate, normalize, encode, format, and
|
|
display.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-zeallot
|
|
(package
|
|
(name "r-zeallot")
|
|
(version "0.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "zeallot" version))
|
|
(sha256
|
|
(base32
|
|
"1sd1igcfnv27pa3bqxlbyxchi562h7grnjg1l7wxx3bwr49i57s3"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/nteetor/zeallot")
|
|
(synopsis "Multiple, unpacking, and destructuring assignment")
|
|
(description
|
|
"This package provides a @code{%<-%} operator to perform multiple,
|
|
unpacking, and destructuring assignment in R. The operator unpacks the
|
|
right-hand side of an assignment into multiple values and assigns these values
|
|
to variables on the left-hand side of the assignment.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-vctrs
|
|
(package
|
|
(name "r-vctrs")
|
|
(version "0.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "vctrs" version))
|
|
(sha256
|
|
(base32
|
|
"13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)
|
|
("r-digest" ,r-digest)
|
|
("r-glue" ,r-glue)
|
|
("r-rlang" ,r-rlang)
|
|
("r-zeallot" ,r-zeallot)))
|
|
(home-page "https://github.com/r-lib/vctrs")
|
|
(synopsis "Vector helpers")
|
|
(description
|
|
"There are three main goals to the @code{vctrs} package:
|
|
|
|
@enumerate
|
|
@item To propose @code{vec_size()} and @code{vec_type()} as alternatives to
|
|
@code{length()} and @code{class()}. These definitions are paired with a
|
|
framework for type-coercion and size-recycling.
|
|
@item To define type- and size-stability as desirable function properties, use
|
|
them to analyse existing base function, and to propose better alternatives.
|
|
This work has been particularly motivated by thinking about the ideal
|
|
properties of @code{c()}, @code{ifelse()}, and @code{rbind()}.
|
|
@item To provide a new @code{vctr} base class that makes it easy to create new
|
|
S3 vectors. @code{vctrs} provides methods for many base generics in terms of
|
|
a few new @code{vctrs} generics, making implementation considerably simpler
|
|
and more robust.
|
|
@end enumerate\n")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-pillar
|
|
(package
|
|
(name "r-pillar")
|
|
(version "1.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pillar" version))
|
|
(sha256
|
|
(base32
|
|
"0mcc09caxm69pghhz6b8vawj9ni63aijv5qba53pg4ph7rxclwgm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-fansi" ,r-fansi)
|
|
("r-rlang" ,r-rlang)
|
|
("r-utf8" ,r-utf8)
|
|
("r-vctrs" ,r-vctrs)))
|
|
(home-page "https://github.com/r-lib/pillar")
|
|
(synopsis "Coloured formatting for columns")
|
|
(description
|
|
"This package provides a @code{pillar} generic designed for formatting
|
|
columns of data using the full range of colours provided by modern
|
|
terminals.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-uuid
|
|
(package
|
|
(name "r-uuid")
|
|
(version "0.1-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "uuid" version))
|
|
(sha256
|
|
(base32
|
|
"1gmisd630fc8ybg845hbg13wmm3pk3npaamrh5wqbc1nqd6p0wfx"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.rforge.net/uuid")
|
|
(synopsis "Tools for generating and handling of UUIDs")
|
|
(description
|
|
"This package provides tools for generating and handling of
|
|
@dfn{Universally Unique Identifiers} (UUIDs).")
|
|
(license license:expat)))
|
|
|
|
(define-public r-tinytex
|
|
(package
|
|
(name "r-tinytex")
|
|
(version "0.13")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tinytex" version))
|
|
(sha256
|
|
(base32
|
|
"1bbphyrbk2rnyi0jhw4hj2w4l84kyhb0km901qd5qnnl0cy6dzvb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-xfun" ,r-xfun)))
|
|
(home-page "https://github.com/yihui/tinytex")
|
|
(synopsis "Helper functions for TeX Live and compiling LaTeX documents")
|
|
(description
|
|
"This package provides helper functions to install and maintain the LaTeX
|
|
distribution named TinyTeX, a lightweight, cross-platform, portable, and
|
|
easy-to-maintain version of TeX Live. This package also contains helper
|
|
functions to compile LaTeX documents, and install missing LaTeX packages
|
|
automatically.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-metap
|
|
(package
|
|
(name "r-metap")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "metap" version))
|
|
(sha256
|
|
(base32
|
|
"10kv7z8pik5iy374h399vws0ldf41y2nczlwh8axqf9dcwl084i0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-rdpack" ,r-rdpack)))
|
|
(home-page "http://www.dewey.myzen.co.uk/meta/meta.html")
|
|
(synopsis "Meta-analysis of significance values")
|
|
(description
|
|
"The canonical way to perform meta-analysis involves using effect sizes.
|
|
When they are not available this package provides a number of methods for
|
|
meta-analysis of significance values including the methods of Edgington,
|
|
Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate
|
|
published results; and a routine for graphical display.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-network
|
|
(package
|
|
(name "r-network")
|
|
(version "1.15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "network" version))
|
|
(sha256
|
|
(base32
|
|
"1cscw5978fyixhkicf06c4b2g1yf6gyi8vx86cz3dy75d41mrgjw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-magrittr" ,r-magrittr)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://statnet.org/")
|
|
(synopsis "Classes for relational data")
|
|
(description
|
|
"This package provides tools to create and modify network objects. The
|
|
@code{network} class can represent a range of relational data types, and
|
|
supports arbitrary vertex/edge/graph attributes.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-statnet-common
|
|
(package
|
|
(name "r-statnet-common")
|
|
(version "4.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "statnet.common" version))
|
|
(sha256
|
|
(base32
|
|
"0ng90i0wm9wlyhjbnmnylc1bbqw396p1dr7f402dyry9x9ck6jl3"))))
|
|
(properties
|
|
`((upstream-name . "statnet.common")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-coda" ,r-coda)))
|
|
(home-page "https://statnet.org")
|
|
(synopsis "R scripts and utilities used by the Statnet software")
|
|
(description "This package provides non-statistical utilities used by the
|
|
software developed by the Statnet Project.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-sna
|
|
(package
|
|
(name "r-sna")
|
|
(version "2.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sna" version))
|
|
(sha256
|
|
(base32
|
|
"1ks8819qvpdfansfqj9p32s1rhvl26frvbi78m4rx1wd1qcv74i2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-network" ,r-network)
|
|
("r-statnet-common" ,r-statnet-common)))
|
|
(home-page "https://statnet.org")
|
|
(synopsis "Tools for social network analysis")
|
|
(description
|
|
"This package provides a range of tools for social network analysis,
|
|
including node and graph-level indices, structural distance and covariance
|
|
methods, structural equivalence detection, network regression, random graph
|
|
generation, and 2D/3D network visualization.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ttr
|
|
(package
|
|
(name "r-ttr")
|
|
(version "0.23-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "TTR" version))
|
|
(sha256
|
|
(base32
|
|
"18mzyv6cmxmqyqsfwlx2b2k055887mfgc2jgj8xkn8c6m56n05zb"))))
|
|
(properties `((upstream-name . "TTR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-xts" ,r-xts)
|
|
("r-zoo" ,r-zoo)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://github.com/joshuaulrich/TTR")
|
|
(synopsis "Technical trading rules")
|
|
(description
|
|
"This package provides functions and data to construct technical trading
|
|
rules with R.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-leaps
|
|
(package
|
|
(name "r-leaps")
|
|
(version "3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "leaps" version))
|
|
(sha256
|
|
(base32
|
|
"11gjmn1azrjw5xlvdb4gknj9985kck9x8zb9np1rnk2smp6pka2m"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/leaps/")
|
|
(synopsis "Regression subset selection")
|
|
(description
|
|
"This package provides tools for regression subset selection, including
|
|
exhaustive search.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-splus2r
|
|
(package
|
|
(name "r-splus2r")
|
|
(version "1.2-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "splus2R" version))
|
|
(sha256
|
|
(base32
|
|
"0xrbj8vxy0pc6hl7m8abv71d3hjw47cl51s7j7priadyqczkq6sz"))))
|
|
(properties `((upstream-name . "splus2R")))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/splus2R/")
|
|
(synopsis "Supplemental S-PLUS functionality in R")
|
|
(description
|
|
"Currently there are many functions in S-PLUS that are missing in R. To
|
|
facilitate the conversion of S-PLUS packages to R packages, this package
|
|
provides some missing S-PLUS functionality in R.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ifultools
|
|
(package
|
|
(name "r-ifultools")
|
|
(version "2.0-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ifultools" version))
|
|
(sha256
|
|
(base32
|
|
"040kvbczcmmbaiaz0k0pdq9af541pjj6iwzh1a3w4szh9w6b5a3j"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-splus2r" ,r-splus2r)))
|
|
(home-page "https://cran.r-project.org/web/packages/ifultools/")
|
|
(synopsis "Insightful research tools")
|
|
(description "This package provides C code used by the wmtsa, fractal, and
|
|
sapa R packages.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-sapa
|
|
(package
|
|
(name "r-sapa")
|
|
(version "2.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sapa" version))
|
|
(sha256
|
|
(base32
|
|
"056xlh14dnzq4x7sbp7ff2k61jxy7110a742b502vz549qfrr5ds"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ifultools" ,r-ifultools)
|
|
("r-splus2r" ,r-splus2r)))
|
|
(home-page "https://cran.r-project.org/web/packages/sapa/")
|
|
(synopsis "Spectral analysis for physical applications")
|
|
(description "This package provides software for the book Spectral
|
|
Analysis for Physical Applications, Donald B. Percival and Andrew T. Walden,
|
|
Cambridge University Press, 1993.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-aggregation
|
|
(package
|
|
(name "r-aggregation")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "aggregation" version))
|
|
(sha256
|
|
(base32
|
|
"0j9g604m2ccc7hcy02539yja9cf3xcbl25gvp838bp4x8w18my46"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/aggregation/")
|
|
(synopsis "Methods for p-value aggregation")
|
|
(description
|
|
"This package contains functionality for performing the following methods
|
|
of p-value aggregation: Fisher's method, the Lancaster method (weighted
|
|
Fisher's method), and Sidak correction.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-quantmod
|
|
(package
|
|
(name "r-quantmod")
|
|
(version "0.4-14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "quantmod" version))
|
|
(sha256
|
|
(base32
|
|
"1csljagnpkr1mmc18h70b64zbyj07kx972nip9dng39jfg7ilnyr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-ttr" ,r-ttr)
|
|
("r-xts" ,r-xts)
|
|
("r-zoo" ,r-zoo)))
|
|
(home-page "https://cran.r-project.org/web/packages/quantmod/")
|
|
(synopsis "Quantitative financial modelling framework")
|
|
(description "This package provides a quantitative financial modelling
|
|
framework to allow users to specify, build, trade, and analyse quantitative
|
|
financial trading strategies.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-tseries
|
|
(package
|
|
(name "r-tseries")
|
|
(version "0.10-47")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tseries" version))
|
|
(sha256
|
|
(base32
|
|
"0yzvc9djp3angvxdxqi60wi726y76ablsb71q88ycvw0avgpf8r0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-quadprog" ,r-quadprog)
|
|
("r-quantmod" ,r-quantmod)
|
|
("r-zoo" ,r-zoo)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/tseries/")
|
|
(synopsis "Time series analysis and computational finance")
|
|
(description
|
|
"This package provides functions relating to time series analysis and
|
|
computational finance.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-wmtsa
|
|
(package
|
|
(name "r-wmtsa")
|
|
(version "2.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "wmtsa" version))
|
|
(sha256
|
|
(base32
|
|
"1q436krz5p1f4a7a7sya6a9rh9x9mi8zzcgq66gbk9w9w4hcqcj6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ifultools" ,r-ifultools)
|
|
("r-mass" ,r-mass)
|
|
("r-splus2r" ,r-splus2r)))
|
|
(home-page "https://cran.r-project.org/web/packages/wmtsa/")
|
|
(synopsis "Wavelet methods for time series analysis")
|
|
(description
|
|
"This package provides software to accompany the book \"Wavelet Methods
|
|
for Time Series Analysis\", Donald B. Percival and Andrew T. Walden, Cambridge
|
|
University Press, 2000.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-tsa
|
|
(package
|
|
(name "r-tsa")
|
|
(version "1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "TSA" version))
|
|
(sha256
|
|
(base32
|
|
"0gjfqibwdznz0nka95k4fjm935svxjpnqfywwz403crn2lh30h6q"))))
|
|
(properties `((upstream-name . "TSA")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-leaps" ,r-leaps)
|
|
("r-locfit" ,r-locfit)
|
|
("r-mgcv" ,r-mgcv)))
|
|
(home-page "http://www.stat.uiowa.edu/~kchan/TSA.htm")
|
|
(synopsis "Time series analysis")
|
|
(description
|
|
"This package contains R functions and datasets detailed in the book
|
|
\"Time Series Analysis with Applications in R (second edition)\" by Jonathan
|
|
Cryer and Kung-Sik Chan.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-extradistr
|
|
(package
|
|
(name "r-extradistr")
|
|
(version "1.8.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "extraDistr" version))
|
|
(sha256
|
|
(base32
|
|
"1vvqv1d4hxa025gmm8cbiph63qsqy87l3ri5idd524gyz3chbcl3"))))
|
|
(properties `((upstream-name . "extraDistr")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/twolodzko/extraDistr")
|
|
(synopsis "Additional univariate and multivariate distributions")
|
|
(description
|
|
"This package implements density, distribution functions, quantile
|
|
functions and random generation functions for a large number of univariate and
|
|
multivariate distributions.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-fractal
|
|
(package
|
|
(name "r-fractal")
|
|
(version "2.0-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fractal" version))
|
|
(sha256
|
|
(base32
|
|
"18lr9z0gslvfc3z8vyj3krqj3bfhg60zv1fzinrwwkc4cpk1w7mp"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ifultools" ,r-ifultools)
|
|
("r-mass" ,r-mass)
|
|
("r-sapa" ,r-sapa)
|
|
("r-scatterplot3d" ,r-scatterplot3d)
|
|
("r-splus2r" ,r-splus2r)
|
|
("r-wmtsa" ,r-wmtsa)))
|
|
(home-page "https://cran.r-project.org/web/packages/fractal/")
|
|
(synopsis "Fractal time series modeling and analysis")
|
|
(description
|
|
"This package provides tools for stochastic fractal and deterministic
|
|
chaotic time series analysis.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-urca
|
|
(package
|
|
(name "r-urca")
|
|
(version "1.3-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "urca" version))
|
|
(sha256
|
|
(base32
|
|
"1akaqwf3fvvvx4sgfn641fd4sj51s0701pvfl6s5hnz2k0iwh732"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-nlme" ,r-nlme)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/urca/")
|
|
(synopsis "Unit root and cointegration tests for time series data")
|
|
(description
|
|
"This package provides unit root and cointegration tests encountered in
|
|
applied econometric analysis.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-cubature
|
|
(package
|
|
(name "r-cubature")
|
|
(version "2.0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cubature" version))
|
|
(sha256
|
|
(base32
|
|
"0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/bnaras/cubature")
|
|
(synopsis "Adaptive multivariate integration over hypercubes")
|
|
(description
|
|
"This package is an R wrapper around the cubature C library for adaptive
|
|
multivariate integration over hypercubes. This version provides both
|
|
@code{hcubature} and @code{pcubature} routines in addition to a vector
|
|
interface.")
|
|
;; The included cubature C library is released under GPLv2+, but the
|
|
;; wrapper declares the license to be GPLv3+.
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-trend
|
|
(package
|
|
(name "r-trend")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "trend" version))
|
|
(sha256
|
|
(base32
|
|
"1bd567n15k2vpmgbx02584k5kglrc58mlb5kgd07wdss3knpa48q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-extradistr" ,r-extradistr)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/trend/")
|
|
(synopsis "Non-parametric trend tests and change-point detection")
|
|
(description
|
|
"The analysis of environmental data often requires the detection of
|
|
trends and change-points. This package includes tests for trend
|
|
detection (Cox-Stuart Trend Test, Mann-Kendall Trend Test, (correlated)
|
|
Hirsch-Slack Test, partial Mann-Kendall Trend Test, multivariate (multisite)
|
|
Mann-Kendall Trend Test, (Seasonal) Sen's slope, partial Pearson and Spearman
|
|
correlation trend test), change-point detection (Lanzante's test procedures,
|
|
Pettitt's test, Buishand Range Test, Buishand U Test, Standard Normal
|
|
Homogeinity Test), detection of non-randomness (Wallis-Moore Phase Frequency
|
|
Test, Bartels rank von Neumann's ratio test, Wald-Wolfowitz Test) and the two
|
|
sample Robust Rank-Order Distributional Test.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-expm
|
|
(package
|
|
(name "r-expm")
|
|
(version "0.999-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "expm" version))
|
|
(sha256
|
|
(base32
|
|
"15k0acg2aqb2ajhwal6l7vhhp03m4lg579805d34554cl0kn9l2q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-matrix" ,r-matrix)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://r-forge.r-project.org/projects/expm/")
|
|
(synopsis "Tools for matrix exponentials and related quantities")
|
|
(description
|
|
"This package provides tools for the computation of the matrix
|
|
exponential, logarithm, square root, and related quantities.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-complexplus
|
|
(package
|
|
(name "r-complexplus")
|
|
(version "2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "complexplus" version))
|
|
(sha256
|
|
(base32
|
|
"16w9v7d1ckavqmr86l34frr37pkvdn0iqnb17ssb8xaggns5lgqx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-expm" ,r-expm)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "https://cran.r-project.org/web/packages/complexplus/")
|
|
(synopsis "Functions of complex or real variables")
|
|
(description
|
|
"This package extends several functions to the complex domain, including
|
|
the matrix exponential and logarithm, and the determinant.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-phontools
|
|
(package
|
|
(name "r-phontools")
|
|
(version "0.2-2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "phonTools" version))
|
|
(sha256
|
|
(base32
|
|
"01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"))))
|
|
(properties `((upstream-name . "phonTools")))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.santiagobarreda.com/rscripts.html")
|
|
(synopsis "Tools for phonetic and acoustic analyses")
|
|
(description
|
|
"This package contains tools for the organization, display, and analysis
|
|
of the sorts of data frequently encountered in phonetics research and
|
|
experimentation, including the easy creation of IPA vowel plots, and the
|
|
creation and manipulation of WAVE audio files.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public r-np
|
|
(package
|
|
(name "r-np")
|
|
(version "0.60-9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "np" version))
|
|
(sha256
|
|
(base32
|
|
"1z4jcpx8bbgwslv42wrphfd1qfq965qjn0kmfxm5f6hbbycahcgy"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-boot" ,r-boot)
|
|
("r-cubature" ,r-cubature)
|
|
("r-quadprog" ,r-quadprog)
|
|
("r-quantreg" ,r-quantreg)))
|
|
(home-page "https://github.com/JeffreyRacine/R-Package-np")
|
|
(synopsis "Non-parametric kernel smoothing methods for mixed data types")
|
|
(description "This package provides non-parametric (and semi-parametric)
|
|
kernel methods that seamlessly handle a mix of continuous, unordered, and
|
|
ordered factor data types.")
|
|
;; Any version of the GPL.
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-powerplus
|
|
(package
|
|
(name "r-powerplus")
|
|
(version "3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "powerplus" version))
|
|
(sha256
|
|
(base32
|
|
"0ayp6x34hkzgris4j3zbbs0r23n81bhww3wgfyy630ri4sk6brrn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-complexplus" ,r-complexplus)
|
|
("r-expm" ,r-expm)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-phontools" ,r-phontools)))
|
|
(home-page "https://cran.r-project.org/web/packages/powerplus/")
|
|
(synopsis "Exponentiation operations")
|
|
(description
|
|
"This package provides tools for the computation of matrix and scalar
|
|
exponentiation.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-heatmaply
|
|
(package
|
|
(name "r-heatmaply")
|
|
(version "0.16.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "heatmaply" version))
|
|
(sha256
|
|
(base32
|
|
"1qhxk48qh61qjxdlhl0qffdh3yh8iiwccid5ssngdv433q0cmyc1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-colorspace" ,r-colorspace)
|
|
("r-dendextend" ,r-dendextend)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-plotly" ,r-plotly)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-scales" ,r-scales)
|
|
("r-seriation" ,r-seriation)
|
|
("r-viridis" ,r-viridis)
|
|
("r-webshot" ,r-webshot)))
|
|
(home-page "https://cran.r-project.org/package=heatmaply")
|
|
(synopsis "Interactive cluster heat maps using plotly")
|
|
(description
|
|
"This package enables you to create interactive cluster heatmaps that can
|
|
be saved as a stand-alone HTML file, embedded in R Markdown documents or in a
|
|
Shiny app, and made available in the RStudio viewer pane. Hover the mouse
|
|
pointer over a cell to show details or drag a rectangle to zoom. A heatmap is
|
|
a popular graphical method for visualizing high-dimensional data, in which a
|
|
table of numbers is encoded as a grid of colored cells. The rows and columns
|
|
of the matrix are ordered to highlight patterns and are often accompanied by
|
|
dendrograms.")
|
|
;; Either version of the license.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-h5
|
|
(package
|
|
(name "r-h5")
|
|
(version "0.9.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "h5" version))
|
|
(sha256
|
|
(base32
|
|
"14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("zlib" ,zlib)
|
|
("hdf5" ,hdf5)))
|
|
(native-inputs
|
|
`(("which" ,which)))
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/mannau/h5")
|
|
(synopsis "Interface to the HDF5 Library")
|
|
(description
|
|
"This package provides an S4 interface to the HDF5 library supporting
|
|
fast storage and retrieval of R-objects like vectors, matrices and arrays to
|
|
binary files in a language independent format. The HDF5 format can therefore
|
|
be used as an alternative to R's save/load mechanism. Since h5 is able to
|
|
access only subsets of stored data it can also handle data sets which do not
|
|
fit into memory.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public r-cgdsr
|
|
(package
|
|
(name "r-cgdsr")
|
|
(version "1.2.10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cgdsr" version))
|
|
(sha256
|
|
(base32
|
|
"1xyhw7mhmjichr1l6f9y1qvfj9wm87kfbm87ji7lcwf36gxh5g23"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-r-methodss3" ,r-r-methodss3)
|
|
("r-r-oo" ,r-r-oo)))
|
|
(home-page "https://github.com/cBioPortal/cgdsr")
|
|
(synopsis "R-based API for accessing the MSKCC Cancer Genomics Data Server")
|
|
(description
|
|
"This package provides a basic set of R functions for querying the Cancer
|
|
Genomics Data Server (CGDS), hosted by the Computational Biology Center at
|
|
Memorial-Sloan-Kettering Cancer Center (MSKCC).")
|
|
(license license:lgpl3)))
|
|
|
|
(define-public r-import
|
|
(package
|
|
(name "r-import")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "import" version))
|
|
(sha256
|
|
(base32
|
|
"0blf9539rbfwcmw8zsb4k58slb4pdnc075v34vmyjw752fznhcji"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/smbache/import")
|
|
(synopsis "Import mechanism for R")
|
|
(description
|
|
"This is an alternative mechanism for importing objects from packages.
|
|
The syntax allows for importing multiple objects from a package with a single
|
|
command in an expressive way. The import package bridges some of the gap
|
|
between using @code{library} (or @code{require}) and direct (single-object)
|
|
imports. Furthermore the imported objects are not placed in the current
|
|
environment. It is also possible to import objects from stand-alone @code{.R}
|
|
files.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-shinyace
|
|
(package
|
|
(name "r-shinyace")
|
|
(version "0.3.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinyAce" version))
|
|
(sha256
|
|
(base32
|
|
"02q6wqw349nlyf3mbf18cxif1xv9cal5qzccrdlnv73szqn9jk7j"))))
|
|
(properties `((upstream-name . "shinyAce")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-shiny" ,r-shiny)
|
|
("r-jsonlite" ,r-jsonlite)))
|
|
(home-page "http://cran.r-project.org/web/packages/shinyAce")
|
|
(synopsis "Ace editor bindings for Shiny")
|
|
(description
|
|
"This package provides Ace editor bindings to enable a rich text editing
|
|
environment within Shiny.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-base64url
|
|
(package
|
|
(name "r-base64url")
|
|
(version "1.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "base64url" version))
|
|
(sha256
|
|
(base32
|
|
"0n1c2b68vza1dh7sk38v6biiwm72c4jpl79kpdg1bsb0hq9qy18x"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)))
|
|
(home-page "https://github.com/mllg/base64url")
|
|
(synopsis "Fast and URL-safe base64 encoder and decoder")
|
|
(description
|
|
"This package provides a URL-safe base64 encoder and decoder. In
|
|
contrast to RFC3548, the 62nd character (@code{+}) is replaced with @code{-},
|
|
the 63rd character (@code{/}) is replaced with @code{_}. Furthermore, the
|
|
encoder does not fill the string with trailing @code{=}. The resulting
|
|
encoded strings comply to the regular expression pattern @code{[A-Za-z0-9_-]}
|
|
and thus are safe to use in URLs or for file names. The package also comes
|
|
with a simple base32 encoder/decoder suited for case insensitive file
|
|
systems.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-radiant-data
|
|
(package
|
|
(name "r-radiant-data")
|
|
(version "0.9.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "radiant.data" version))
|
|
(sha256
|
|
(base32
|
|
"17mgm0sggh4f7ihqmj9m3996p3pqc7h2cwx6ll1ha3kg5mx0znyn"))
|
|
(modules '((guix build utils)))
|
|
(snippet
|
|
'(begin
|
|
;; Delete files that are under CC-NC-SA.
|
|
(delete-file-recursively "inst/app/tools/help")
|
|
#t))))
|
|
(properties `((upstream-name . "radiant.data")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-broom" ,r-broom)
|
|
("r-car" ,r-car)
|
|
("r-curl" ,r-curl)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-dt" ,r-dt)
|
|
("r-glue" ,r-glue)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-import" ,r-import)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-knitr" ,r-knitr)
|
|
("r-lubridate" ,r-lubridate)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-markdown" ,r-markdown)
|
|
("r-plotly" ,r-plotly)
|
|
("r-psych" ,r-psych)
|
|
("r-readr" ,r-readr)
|
|
("r-readxl" ,r-readxl)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-scales" ,r-scales)
|
|
("r-shiny" ,r-shiny)
|
|
("r-shinyfiles" ,r-shinyfiles)
|
|
("r-shinyace" ,r-shinyace)
|
|
("r-stringi" ,r-stringi)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)
|
|
("r-writexl" ,r-writexl)))
|
|
(home-page "https://github.com/radiant-rstats/radiant.data")
|
|
(synopsis "Data menu for Radiant: business analytics using R and Shiny")
|
|
(description
|
|
"The Radiant Data menu includes interfaces for loading, saving, viewing,
|
|
visualizing, summarizing, transforming, and combining data. It also contains
|
|
functionality to generate reproducible reports of the analyses conducted in
|
|
the application.")
|
|
(license license:agpl3)))
|
|
|
|
(define-public r-algdesign
|
|
(package
|
|
(name "r-algdesign")
|
|
(version "1.1-7.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "AlgDesign" version))
|
|
(sha256
|
|
(base32
|
|
"0bl7mx4dnmkgs2x1fj7cqnrp7jx18mqwxyga0rzlniq12h8mc3fz"))))
|
|
(properties `((upstream-name . "AlgDesign")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/jvbraun/AlgDesign")
|
|
(synopsis "Algorithmic experimental design")
|
|
(description
|
|
"This package provides tools to calculate exact and approximate theory
|
|
experimental designs for D, A, and I criteria. Very large designs may be
|
|
created. Experimental designs may be blocked or blocked designs created from
|
|
a candidate list, using several criteria. The blocking can be done when whole
|
|
and within plot factors interact.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-signal
|
|
(package
|
|
(name "r-signal")
|
|
(version "0.7-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "signal" version))
|
|
(sha256
|
|
(base32
|
|
"1vsxramz5qd9q9s3vlqzmfdpmwl2rhlb2n904zw6f0fg0xxjfq3b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mass" ,r-mass)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/signal/")
|
|
(synopsis "Signal processing")
|
|
(description
|
|
"This package provides a set of signal processing functions originally
|
|
written for Matlab and GNU Octave. It includes filter generation utilities,
|
|
filtering functions, resampling routines, and visualization of filter models.
|
|
It also includes interpolation functions.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-gsubfn
|
|
(package
|
|
(name "r-gsubfn")
|
|
(version "0.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gsubfn" version))
|
|
(sha256
|
|
(base32
|
|
"00j6b8b6xsx6v370h220x233rpk6asca78165y3d48jpwvwisdc9"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-proto" ,r-proto)))
|
|
(home-page "http://gsubfn.googlecode.com")
|
|
(synopsis "Utilities for strings and function arguments.")
|
|
(description
|
|
"This package provides @code{gsubfn} which is like @code{gsub} but can
|
|
take a replacement function or certain other objects instead of the
|
|
replacement string. Matches and back references are input to the replacement
|
|
function and replaced by the function output. @code{gsubfn} can be used to
|
|
split strings based on content rather than delimiters and for quasi-perl-style
|
|
string interpolation. The package also has facilities for translating
|
|
formulas to functions and allowing such formulas in function calls instead of
|
|
functions.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-sqldf
|
|
(package
|
|
(name "r-sqldf")
|
|
(version "0.4-11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sqldf" version))
|
|
(sha256
|
|
(base32
|
|
"0q12vsb53p2wchgp8wfz5bk08wfnm0jxjrakclj4jyy6x3a7ksff"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-chron" ,r-chron)
|
|
("r-dbi" ,r-dbi)
|
|
("r-gsubfn" ,r-gsubfn)
|
|
("r-proto" ,r-proto)
|
|
("r-rsqlite" ,r-rsqlite)))
|
|
(home-page "https://github.com/ggrothendieck/sqldf")
|
|
(synopsis "Manipulate R data frames using SQL")
|
|
(description
|
|
"The @code{sqldf} function is typically passed a single argument which is
|
|
an SQL select statement where the table names are ordinary R data frame names.
|
|
@code{sqldf} transparently sets up a database, imports the data frames into
|
|
that database, performs the SQL statement and returns the result using a
|
|
heuristic to determine which class to assign to each column of the returned
|
|
data frame. The @code{sqldf} or @code{read.csv.sql} functions can also be
|
|
used to read filtered files into R even if the original files are larger than
|
|
R itself can handle.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-abind
|
|
(package
|
|
(name "r-abind")
|
|
(version "1.4-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abind" version))
|
|
(sha256
|
|
(base32
|
|
"0b1zd8jbnl6l292cr9rb50m09fy3ylxvzkpgi5lfb1nbzddcwfis"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/abind/")
|
|
(synopsis "Combine multidimensional arrays")
|
|
(description
|
|
"This package provides tools to combine multidimensional arrays into a
|
|
single array. This is a generalization of @code{cbind} and @code{rbind}. It
|
|
works with vectors, matrices, and higher-dimensional arrays. It also provides
|
|
the functions @code{adrop}, @code{asub}, and @code{afill} for manipulating,
|
|
extracting and replacing data in arrays.")
|
|
(license license:lgpl2.0+)))
|
|
|
|
(define-public r-prroc
|
|
(package
|
|
(name "r-prroc")
|
|
(version "1.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "PRROC" version))
|
|
(sha256
|
|
(base32
|
|
"1m28h8pcd78049lz2qixhkcr9h5b3jik3maqzfbvq9y58z71i4a7"))))
|
|
(properties `((upstream-name . "PRROC")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/PRROC/")
|
|
(synopsis "Precision-Recall and ROC curves for weighted and unweighted data")
|
|
(description
|
|
"This package computes the areas under the @dfn{precision-recall} (PR)
|
|
and ROC curve for weighted (e.g. soft-labeled) and unweighted data. In
|
|
contrast to other implementations, the interpolation between points of the PR
|
|
curve is done by a non-linear piecewise function. In addition to the areas
|
|
under the curves, the curves themselves can also be computed and plotted by a
|
|
specific S3-method.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-vim
|
|
(package
|
|
(name "r-vim")
|
|
(version "4.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "VIM" version))
|
|
(sha256
|
|
(base32
|
|
"08x4a4yzgp8adgrv7a3666yma4b60n64mcsnvhzmwdy023f4ysrw"))))
|
|
(properties `((upstream-name . "VIM")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-car" ,r-car)
|
|
("r-colorspace" ,r-colorspace)
|
|
("r-data-table" ,r-data-table)
|
|
("r-e1071" ,r-e1071)
|
|
("r-laeken" ,r-laeken)
|
|
("r-mass" ,r-mass)
|
|
("r-nnet" ,r-nnet)
|
|
("r-ranger" ,r-ranger)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-robustbase" ,r-robustbase)
|
|
("r-sp" ,r-sp)
|
|
("r-vcd" ,r-vcd)))
|
|
(home-page "https://github.com/alexkowa/VIM")
|
|
(synopsis "Visualization and imputation of missing values")
|
|
(description
|
|
"This package provides tools for the visualization of missing and/or
|
|
imputed values are introduced, which can be used for exploring the data and
|
|
the structure of the missing and/or imputed values. Depending on this
|
|
structure of the missing values, the corresponding methods may help to
|
|
identify the mechanism generating the missing values and allows to explore the
|
|
data including missing values. In addition, the quality of imputation can be
|
|
visually explored using various univariate, bivariate, multiple and
|
|
multivariate plot methods.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-fnn
|
|
(package
|
|
(name "r-fnn")
|
|
(version "1.1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "FNN" version))
|
|
(sha256
|
|
(base32
|
|
"0cllqlnynm5yaj4r64mqyyfc8phkb38rwssq8k8ikgfgr4jklxny"))))
|
|
(properties `((upstream-name . "FNN")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/FNN")
|
|
(synopsis "Fast nearest neighbor search algorithms and applications")
|
|
(description
|
|
"This package provides cover-tree and kd-tree fast k-nearest neighbor
|
|
search algorithms. Related applications including KNN classification,
|
|
regression and information measures are implemented.")
|
|
;; The DESCRIPTION file erroneously states that GPL version 2.1 or
|
|
;; later can be used.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-smoother
|
|
(package
|
|
(name "r-smoother")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "smoother" version))
|
|
(sha256
|
|
(base32
|
|
"0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ttr" ,r-ttr)))
|
|
(home-page "http://cran.r-project.org/web/packages/smoother")
|
|
(synopsis "Functions relating to the smoothing of numerical data")
|
|
(description
|
|
"This package provides a collection of methods for smoothing numerical
|
|
data, commencing with a port of the Matlab gaussian window smoothing function.
|
|
In addition, several functions typically used in smoothing of financial data
|
|
are included.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-riverplot
|
|
(package
|
|
(name "r-riverplot")
|
|
(version "0.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "riverplot" version))
|
|
(sha256
|
|
(base32
|
|
"0q1icpny8nkxyjhawyjzwrw8qlz0ayn2xyrsqrm4vkxyv6c9xk8z"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://logfc.wordpress.com")
|
|
(synopsis "Sankey or ribbon plots")
|
|
(description
|
|
"Sankey plots are a type of diagram that is convenient to illustrate how
|
|
flow of information, resources etc. separates and joins, much like observing
|
|
how rivers split and merge. For example, they can be used to compare
|
|
different clusterings. This package provides an implementation of Sankey
|
|
plots for R.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-dyn
|
|
(package
|
|
(name "r-dyn")
|
|
(version "0.2-9.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dyn" version))
|
|
(sha256
|
|
(base32
|
|
"16fqv9k7yxdgybwzafjkyqm16qpgqz13lcjpi6a1nc8xbzlzh0gb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-zoo" ,r-zoo)))
|
|
(home-page "https://cran.r-project.org/web/packages/dyn")
|
|
(synopsis "Time series regression")
|
|
(description
|
|
"This package provides the dyn class interfaces @code{ts}, @code{irts},
|
|
@code{zoo} and @code{zooreg} time series classes to @code{lm}, @code{glm},
|
|
@code{loess}, @code{quantreg::rq}, @code{MASS::rlm},
|
|
@code{MCMCpack::MCMCregress()}, @code{quantreg::rq()},
|
|
@code{randomForest::randomForest()} and other regression functions, allowing
|
|
those functions to be used with time series including specifications that may
|
|
contain lags, diffs and missing values.")
|
|
;; Any GPL version.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-catdap
|
|
(package
|
|
(name "r-catdap")
|
|
(version "1.3.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "catdap" version))
|
|
(sha256
|
|
(base32
|
|
"0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/catdap/")
|
|
(synopsis "Tools for categorical data analysis")
|
|
(description
|
|
"This package provides functions for analyzing multivariate data.
|
|
Dependencies of the distribution of the specified variable (response
|
|
variable) to other variables (explanatory variables) are derived and
|
|
evaluated by the @dfn{Akaike Information Criterion} (AIC).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-arules
|
|
(package
|
|
(name "r-arules")
|
|
(version "1.6-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "arules" version))
|
|
(sha256
|
|
(base32
|
|
"0dimrq1pz449z0mz9m87nhm5bpc0v789bcc3lghhh97wwi5zah9y"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)))
|
|
(home-page "https://github.com/mhahsler/arules")
|
|
(synopsis "Mining association rules and frequent itemsets")
|
|
(description
|
|
"This package provides an infrastructure for representing, manipulating
|
|
and analyzing transaction data and patterns (frequent itemsets and association rules).
|
|
It also provides C implementations of the association mining algorithms Apriori
|
|
and Eclat.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-parsedate
|
|
(package
|
|
(name "r-parsedate")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "parsedate" version))
|
|
(sha256
|
|
(base32
|
|
"0gb3w6hmwxayhijpf36p5dk4h6bbdps57x3cgikwvvxkgi83rarr"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rematch2" ,r-rematch2)))
|
|
(home-page "https://github.com/gaborcsardi/parsedate")
|
|
(synopsis
|
|
"Recognize and parse dates in various formats")
|
|
(description
|
|
"This package provides three functions for dealing with dates:
|
|
@code{parse_iso_8601} recognizes and parses all valid ISO 8601 date and
|
|
time formats, @code{parse_date} parses dates in unspecified formats,
|
|
and @code{format_iso_8601} formats a date in ISO 8601 format.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-abc-data
|
|
(package
|
|
(name "r-abc-data")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abc.data" version))
|
|
(sha256
|
|
(base32
|
|
"1bv1n68ah714ws58cf285n2s2v5vn7382lfjca4jxph57lyg8hmj"))))
|
|
(properties `((upstream-name . "abc.data")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/abc.data/")
|
|
(synopsis "Data for Approximate Bayesian Computation (ABC) package")
|
|
(description
|
|
"This package contains data which are used by functions of the abc
|
|
package which implements several @dfn{Approximate Bayesian Computation} (ABC)
|
|
algorithms for performing parameter estimation, model selection, and
|
|
goodness-of-fit.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-abc
|
|
(package
|
|
(name "r-abc")
|
|
(version "2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abc" version))
|
|
(sha256
|
|
(base32
|
|
"0ngzaaz2y2s03fhngvwipmy4kq38xrmyddaz6a6l858rxvadrlhb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-abc-data" ,r-abc-data)
|
|
("r-locfit" ,r-locfit)
|
|
("r-mass" ,r-mass)
|
|
("r-nnet" ,r-nnet)
|
|
("r-quantreg" ,r-quantreg)))
|
|
(home-page "https://cran.r-project.org/web/packages/abc/")
|
|
(synopsis "Tools for Approximate Bayesian Computation (ABC)")
|
|
(description
|
|
"This package implements several @dfn{Approximate Bayesian
|
|
Computation} (ABC) algorithms for performing parameter estimation, model
|
|
selection, and goodness-of-fit. Cross-validation tools are also available for
|
|
measuring the accuracy of ABC estimates, and to calculate the
|
|
misclassification probabilities of different models.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-zip
|
|
(package
|
|
(name "r-zip")
|
|
(version "2.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "zip" version))
|
|
(sha256
|
|
(base32
|
|
"1xvgs7mhxi0sdp5ix4nisqm9lf8f75b7ip7b1hqpq9bzh0x6z8ix"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/gaborcsardi/zip")
|
|
(synopsis "Cross-platform Zip compression")
|
|
(description
|
|
"This package provides a cross-platform Zip compression library for R.
|
|
It is a replacement for the @code{zip} function, that does not require any
|
|
additional external tools on any platform.")
|
|
(license license:cc0)))
|
|
|
|
(define-public r-openxlsx
|
|
(package
|
|
(name "r-openxlsx")
|
|
(version "4.1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "openxlsx" version))
|
|
(sha256
|
|
(base32
|
|
"1lflygpi1z4rlb1c6g6wsmi334maiiy7jhpg6ph4sw8lpvg12w4b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-zip" ,r-zip)))
|
|
(home-page "https://github.com/awalker89/openxlsx")
|
|
(synopsis "Read, write and edit XLSX files")
|
|
(description
|
|
"This package simplifies the creation of Excel @code{.xlsx} files by
|
|
providing a high level interface to writing, styling and editing worksheets.
|
|
Through the use of Rcpp, read/write times are comparable to the @code{xlsx}
|
|
and @code{XLConnect} packages with the added benefit of removing the
|
|
dependency on Java.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-rio
|
|
(package
|
|
(name "r-rio")
|
|
(version "0.5.16")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rio" version))
|
|
(sha256
|
|
(base32
|
|
"0rfl56fdawlhc98451a9lcb6a6m56kw0i7dvd5hx58z025d8vsyk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-data-table" ,r-data-table)
|
|
("r-foreign" ,r-foreign)
|
|
("r-haven" ,r-haven)
|
|
("r-openxlsx" ,r-openxlsx)
|
|
("r-readxl" ,r-readxl)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/leeper/rio")
|
|
(synopsis "Swiss-army knife for data I/O")
|
|
(description
|
|
"This package provides streamlined data import and export infrastructure
|
|
by making assumptions that the user is probably willing to make: @code{import}
|
|
and @code{export} determine the data structure from the file extension,
|
|
reasonable defaults are used for data import and export (e.g.,
|
|
@code{stringsAsFactors=FALSE}), web-based import is natively
|
|
supported (including from SSL/HTTPS), compressed files can be read directly
|
|
without explicit decompression, and fast import packages are used where
|
|
appropriate. An additional convenience function, @code{convert}, provides a
|
|
simple method for converting between file types.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-maptools
|
|
(package
|
|
(name "r-maptools")
|
|
(version "0.9-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "maptools" version))
|
|
(sha256
|
|
(base32
|
|
"1pbvcn9xfx0hxq1ppbfg9xm5j04q4c15nj983yjmg7dlkzq135ax"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-foreign" ,r-foreign)
|
|
("r-lattice" ,r-lattice)
|
|
("r-sp" ,r-sp)))
|
|
(home-page "http://r-forge.r-project.org/projects/maptools/")
|
|
(synopsis "Tools for reading and handling spatial objects")
|
|
(description
|
|
"This package provides a set of tools for manipulating and reading
|
|
geographic data, in particular ESRI Shapefiles. It includes binary access to
|
|
GSHHG shoreline files. The package also provides interface wrappers for
|
|
exchanging spatial objects with other R packages.")
|
|
;; The C source files from shapelib are released under the Expat license.
|
|
;; The R code is released under GPL version 2 or later.
|
|
(license (list license:gpl2+
|
|
license:expat))))
|
|
|
|
(define-public r-later
|
|
(package
|
|
(name "r-later")
|
|
(version "0.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "later" version))
|
|
(sha256
|
|
(base32
|
|
"08g503xjxrfxvrzj0cavsrz4m8ykbha64344j1w2r6v17js2hakb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)))
|
|
(home-page "https://github.com/r-lib/later")
|
|
(synopsis "Utilities for delaying function execution")
|
|
(description
|
|
"This package provides tools to execute arbitrary R or C functions some
|
|
time after the current time, after the R execution stack has emptied.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-promises
|
|
(package
|
|
(name "r-promises")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "promises" version))
|
|
(sha256
|
|
(base32
|
|
"0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-later" ,r-later)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-r6" ,r-r6)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)))
|
|
(home-page "https://rstudio.github.io/promises")
|
|
(synopsis "Abstractions for promise-based asynchronous programming")
|
|
(description
|
|
"This package provides fundamental abstractions for doing asynchronous
|
|
programming in R using promises. Asynchronous programming is useful for
|
|
allowing a single R process to orchestrate multiple tasks in the background
|
|
while also attending to something else. Semantics are similar to JavaScript
|
|
promises, but with a syntax that is idiomatic R.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-dosnow
|
|
(package
|
|
(name "r-dosnow")
|
|
(version "1.0.16")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "doSNOW" version))
|
|
(sha256
|
|
(base32
|
|
"13ir4a8252h4yvp5ir9xnwack1kn58i4ny6sf2qdc12zspn3850n"))))
|
|
(properties `((upstream-name . "doSNOW")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-foreach" ,r-foreach)
|
|
("r-iterators" ,r-iterators)
|
|
("r-snow" ,r-snow)))
|
|
(home-page "https://cran.r-project.org/web/packages/doSNOW")
|
|
(synopsis "Foreach parallel adaptor for the snow package")
|
|
(description
|
|
"This package provides a parallel backend for the @code{%dopar%} function
|
|
using the @code{snow} package.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-snowfall
|
|
(package
|
|
(name "r-snowfall")
|
|
(version "1.84-6.1")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "snowfall" version))
|
|
(sha256
|
|
(base32 "13941rlw1jsdjsndp1plzj1cq5aqravizkrqn6l25r9im7rnsi2w"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-snow" ,r-snow)))
|
|
(home-page "http://cran.r-project.org/web/packages/snowfall/")
|
|
(synopsis "Easier cluster computing")
|
|
(description "This package is a usability wrapper around snow for easier
|
|
development of parallel R programs. This package offers e.g. extended error
|
|
checks, and additional functions. All functions work in sequential mode, too,
|
|
if no cluster is present or wished. The package is also designed as connector
|
|
to the cluster management tool @code{sfCluster}, but can also used without
|
|
it.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rappdirs
|
|
(package
|
|
(name "r-rappdirs")
|
|
(version "0.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rappdirs" version))
|
|
(sha256
|
|
(base32
|
|
"0ji6sg3bdn5gazkq14xmmcq7jnbsyxw4lzmmbgv6526j2vn93n1g"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rappdirs/")
|
|
(synopsis "Determine where to save data, caches, and logs")
|
|
(description
|
|
"This package provides an easy way to determine which directories on the
|
|
user's computer should be used to save data, caches and logs. It is a port of
|
|
Python's @url{https://github.com/ActiveState/appdirs,Appdirs} to R.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-learnr
|
|
(package
|
|
(name "r-learnr")
|
|
(version "0.9.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "learnr" version))
|
|
(sha256
|
|
(base32
|
|
"0jbk0g6fkw7zs8ykzhsvh9vvz8xmc4v03bqzjsa5mmpxpqan5vx5"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-evaluate" ,r-evaluate)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-knitr" ,r-knitr)
|
|
("r-markdown" ,r-markdown)
|
|
("r-rappdirs" ,r-rappdirs)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-shiny" ,r-shiny)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://rstudio.github.io/learnr/")
|
|
(synopsis "Interactive tutorials for R")
|
|
(description
|
|
"This package provides tools to create interactive tutorials using R
|
|
Markdown. Use a combination of narrative, figures, videos, exercises, and
|
|
quizzes to create self-paced tutorials for learning about R and R packages.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-analytics
|
|
(package
|
|
(name "r-analytics")
|
|
(version "3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "analytics" version))
|
|
(sha256
|
|
(base32
|
|
"0js3c8lwj3knccb55nq03cbjlf4w390p9aid2mi5x80l3ayd9in1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-car" ,r-car)
|
|
("r-cluster" ,r-cluster)
|
|
("r-fractal" ,r-fractal)
|
|
("r-lmtest" ,r-lmtest)
|
|
("r-mass" ,r-mass)
|
|
("r-np" ,r-np)
|
|
("r-powerplus" ,r-powerplus)
|
|
("r-robust" ,r-robust)
|
|
("r-trend" ,r-trend)
|
|
("r-tsa" ,r-tsa)
|
|
("r-urca" ,r-urca)
|
|
("r-vim" ,r-vim)))
|
|
(home-page "https://cran.r-project.org/web/packages/analytics/")
|
|
(synopsis "Collection of data analysis tools")
|
|
(description
|
|
"This package is a collection of data analysis tools. It includes tools
|
|
for regression outlier detection in a fitted linear model, stationary
|
|
bootstrap using a truncated geometric distribution, a comprehensive test for
|
|
weak stationarity, column means by group, weighted biplots, and a heuristic to
|
|
obtain a better initial configuration in non-metric MDS.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-reticulate
|
|
(package
|
|
(name "r-reticulate")
|
|
(version "1.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reticulate" version))
|
|
(sha256
|
|
(base32
|
|
"0pqr1rcs8yg9nlh729mvlws93cqhpmv49j9bcgarh7vxzkwyv0kb"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("python" ,python)))
|
|
(propagated-inputs
|
|
`(("r-jsonlite" ,r-jsonlite)
|
|
("r-matrix" ,r-matrix)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/rstudio/reticulate")
|
|
(synopsis "R interface to Python")
|
|
(description
|
|
"This package provides an interface from R to Python modules, classes,
|
|
and functions. When calling into Python, R data types are automatically
|
|
converted to their equivalent Python types. When values are returned from
|
|
Python to R they are converted back to R types.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-bibtex
|
|
(package
|
|
(name "r-bibtex")
|
|
(version "0.4.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bibtex" version))
|
|
(sha256
|
|
(base32
|
|
"0wl3925ryd54g1nv3ncwllc493d39dpgy5md61940h69c0van1hz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-stringr" ,r-stringr)))
|
|
(home-page "https://github.com/romainfrancois/bibtex")
|
|
(synopsis "Bibtex parser")
|
|
(description "This package provides a utility for R to parse a bibtex
|
|
file.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ggseqlogo
|
|
(package
|
|
(name "r-ggseqlogo")
|
|
(version "0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggseqlogo" version))
|
|
(sha256
|
|
(base32
|
|
"13q6kcpxrqxqbji889fx63p0nsi08lk5yymkchig75r5k1d18ky1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
|
|
(home-page "https://github.com/omarwagih/ggseqlogo")
|
|
(synopsis "ggplot2 extension for drawing genetic sequence logos")
|
|
(description
|
|
"The range of functions provided by this package makes it possible to
|
|
draw highly versatile genomic sequence logos. Features include, but are not
|
|
limited to, modifying colour schemes and fonts used to draw the logo,
|
|
generating multiple logo plots, and aiding the visualisation with annotations.
|
|
Sequence logos can easily be combined with other ggplot2 plots.")
|
|
;; Unspecified version of the LGPL.
|
|
(license license:lgpl3+)))
|
|
|
|
(define-public r-ggsci
|
|
(package
|
|
(name "r-ggsci")
|
|
(version "2.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggsci" version))
|
|
(sha256
|
|
(base32
|
|
"0g73x6grbka7ahjh6z23m3wrcifp5rdfdiasbl8lq4sp6rplxwaa"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "https://nanx.me/ggsci/")
|
|
(synopsis "Scientific journal and sci-fi themed color palettes for ggplot2")
|
|
(description
|
|
"This package provides a collection of ggplot2 color palettes inspired by
|
|
plots in scientific journals, data visualization libraries, science fiction
|
|
movies, and TV shows.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ggsignif
|
|
(package
|
|
(name "r-ggsignif")
|
|
(version "0.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggsignif" version))
|
|
(sha256
|
|
(base32
|
|
"0z04g5kqdj66fyfxb5d2m7njkqd7idbiy4xgsnxdh5pbh3cr643x"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)))
|
|
(home-page "https://github.com/const-ae/ggsignif")
|
|
(synopsis "Significance brackets for ggplot2")
|
|
(description
|
|
"Enrich your ggplots with group-wise comparisons. This package provides
|
|
an easy way to indicate if two groups are significantly different. Commonly
|
|
this is shown by a bracket on top connecting the groups of interest which
|
|
itself is annotated with the level of significance. The package provides a
|
|
single layer that takes the groups for comparison and the test as arguments
|
|
and adds the annotation to the plot.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ggpubr
|
|
(package
|
|
(name "r-ggpubr")
|
|
(version "0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggpubr" version))
|
|
(sha256
|
|
(base32
|
|
"0rkpcjb1x7lvhj68aam5airbi534jqyiq12x5xk40a25iifhghq6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cowplot" ,r-cowplot)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-ggrepel" ,r-ggrepel)
|
|
("r-ggsci" ,r-ggsci)
|
|
("r-ggsignif" ,r-ggsignif)
|
|
("r-glue" ,r-glue)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-polynom" ,r-polynom)
|
|
("r-purrr" ,r-purrr)
|
|
("r-scales" ,r-scales)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "http://www.sthda.com/english/rpkgs/ggpubr")
|
|
(synopsis "ggplot2-based publication-ready plots")
|
|
(description
|
|
"The ggplot2 package is an excellent and flexible package for elegant
|
|
data visualization in R. However the default generated plots require some
|
|
formatting before we can send them for publication. The ggpubr package
|
|
provides some easy-to-use functions for creating and customizing ggplot2-based
|
|
publication-ready plots.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ellipse
|
|
(package
|
|
(name "r-ellipse")
|
|
(version "0.4.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ellipse" version))
|
|
(sha256
|
|
(base32
|
|
"0g82vc51m3c1k0hnpp2zla6amxxgk2mmkl8ssnsc49jv3599r6hs"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/ellipse/")
|
|
(synopsis "Functions for drawing ellipses and ellipse-like confidence regions")
|
|
(description
|
|
"This package contains various routines for drawing ellipses and
|
|
ellipse-like confidence regions, implementing the plots described in Murdoch
|
|
and Chow (1996), A graphical display of large correlation matrices, The
|
|
American Statistician 50, 178-180. There are also routines implementing the
|
|
profile plots described in Bates and Watts (1988), Nonlinear Regression
|
|
Analysis and its Applications.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-flashclust
|
|
(package
|
|
(name "r-flashclust")
|
|
(version "1.01-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "flashClust" version))
|
|
(sha256
|
|
(base32
|
|
"0l4lpz451ll7f7lfxmb7ds24ppzhfg1c3ypvydglcc35p2dq99s8"))))
|
|
(properties `((upstream-name . "flashClust")))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/flashClust/")
|
|
(synopsis "Implementation of optimal hierarchical clustering")
|
|
(description
|
|
"This package provides a fast implementation of hierarchical
|
|
clustering.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-factominer
|
|
(package
|
|
(name "r-factominer")
|
|
(version "1.41")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "FactoMineR" version))
|
|
(sha256
|
|
(base32
|
|
"1h20hydav6l2b7bngqw1av4l5rrh0wk58nhailga1f4qw9lrv259"))))
|
|
(properties `((upstream-name . "FactoMineR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-car" ,r-car)
|
|
("r-cluster" ,r-cluster)
|
|
("r-ellipse" ,r-ellipse)
|
|
("r-flashclust" ,r-flashclust)
|
|
("r-lattice" ,r-lattice)
|
|
("r-leaps" ,r-leaps)
|
|
("r-mass" ,r-mass)
|
|
("r-scatterplot3d" ,r-scatterplot3d)))
|
|
(home-page "http://factominer.free.fr")
|
|
(synopsis "Multivariate exploratory data analysis and data mining")
|
|
(description
|
|
"This package provides exploratory data analysis methods to summarize,
|
|
visualize and describe datasets. The main principal component methods are
|
|
available, those with the largest potential in terms of applications:
|
|
principal component analysis (PCA) when variables are quantitative,
|
|
correspondence analysis (CA) and multiple correspondence analysis (MCA) when
|
|
variables are categorical, Multiple Factor Analysis when variables are
|
|
structured in groups, etc. and hierarchical cluster analysis.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-factoextra
|
|
(package
|
|
(name "r-factoextra")
|
|
(version "1.0.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "factoextra" version))
|
|
(sha256
|
|
(base32
|
|
"1l6m8k7qhdw8ndar8nhmym0lfyd1i2iszl1cicjax0vq23ss6xw1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-abind" ,r-abind)
|
|
("r-cluster" ,r-cluster)
|
|
("r-dendextend" ,r-dendextend)
|
|
("r-factominer" ,r-factominer)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-ggpubr" ,r-ggpubr)
|
|
("r-ggrepel" ,r-ggrepel)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "http://www.sthda.com/english/rpkgs/factoextra")
|
|
(synopsis "Extract and visualize the results of multivariate data analyses")
|
|
(description
|
|
"This package provides some easy-to-use functions to extract and
|
|
visualize the output of multivariate data analyses, including
|
|
@code{PCA} (Principal Component Analysis), @code{CA} (Correspondence
|
|
Analysis), @code{MCA} (Multiple Correspondence Analysis), @code{FAMD} (Factor
|
|
Analysis of Mixed Data), @code{MFA} (Multiple Factor Analysis) and
|
|
@code{HMFA} (Hierarchical Multiple Factor Analysis) functions from different R
|
|
packages. It contains also functions for simplifying some clustering analysis
|
|
steps and provides ggplot2-based elegant data visualization.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-fansi
|
|
(package
|
|
(name "r-fansi")
|
|
(version "0.4.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fansi" version))
|
|
(sha256
|
|
(base32
|
|
"02f2rx7v7wz6w97m2slwky2i5y8f9iafycmkyr3siy3z3k8fj171"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; for vignettes
|
|
(home-page "https://github.com/brodieG/fansi")
|
|
(synopsis "ANSI control sequence aware string functions")
|
|
(description
|
|
"This package provides counterparts to R string manipulation functions
|
|
that account for the effects of ANSI text formatting control sequences.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-nbclust
|
|
(package
|
|
(name "r-nbclust")
|
|
(version "3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "NbClust" version))
|
|
(sha256
|
|
(base32
|
|
"1vwb48zy6ln1ddpqmfngii1i80n8qmqyxnzdp6gbaq96lakl3w3c"))))
|
|
(properties `((upstream-name . "NbClust")))
|
|
(build-system r-build-system)
|
|
(home-page "https://sites.google.com/site/malikacharrad/research/nbclust-package")
|
|
(synopsis "Determine the best number of clusters in a data set")
|
|
(description
|
|
"NbClust provides 30 indexes for determining the optimal number of
|
|
clusters in a data set and offers the best clustering scheme from different
|
|
results to the user.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-hdf5r
|
|
(package
|
|
(name "r-hdf5r")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hdf5r" version))
|
|
(sha256
|
|
(base32
|
|
"10gynjwaaxks8y9c2fl8k040j0nbwn372nil70009yfk9wrkx0aq"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("hdf5" ,hdf5)
|
|
("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-bit64" ,r-bit64)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://hhoeflin.github.io/hdf5r")
|
|
(synopsis "Interface to the HDF5 binary data format")
|
|
(description
|
|
"HDF5 is a data model, library and file format for storing and managing
|
|
large amounts of data. This package provides a nearly feature complete,
|
|
object oriented wrapper for the HDF5 API using R6 classes. Additionally,
|
|
functionality is added so that HDF5 objects behave very similar to their
|
|
corresponding R counterparts.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-itertools
|
|
(package
|
|
(name "r-itertools")
|
|
(version "0.1-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "itertools" version))
|
|
(sha256
|
|
(base32
|
|
"1ls5biiva10pb1dj3ph4griykb9vam02hkrdmlr5a5wf660hg6xn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-iterators" ,r-iterators)))
|
|
(home-page "https://cran.r-project.org/web/packages/itertools/")
|
|
(synopsis "Iterator tools")
|
|
(description
|
|
"This package provides various tools for creating iterators, many
|
|
patterned after functions in the Python @code{itertools} module, and others
|
|
patterned after functions in the snow package.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-polynom
|
|
(package
|
|
(name "r-polynom")
|
|
(version "1.4-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "polynom" version))
|
|
(sha256
|
|
(base32
|
|
"1pflscwc0qzdf0y60j7s0dkglgmz18xajywfbn6s263idyr8idy5"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/polynom/")
|
|
(synopsis "Functions for univariate polynomial manipulations")
|
|
(description
|
|
"This package provides a collection of functions to implement a class for
|
|
univariate polynomial manipulations.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-gbrd
|
|
(package
|
|
(name "r-gbrd")
|
|
(version "0.4-11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gbRd" version))
|
|
(sha256
|
|
(base32
|
|
"06x97rw5i6v6cgjxkfhxnw4dn7lghn5q6ra7ri5ag1x9dkfzcl82"))))
|
|
(properties `((upstream-name . "gbRd")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/gbRd/")
|
|
(synopsis "Utilities for processing Rd objects and files")
|
|
(description
|
|
"This package provides utilities for processing Rd objects and files.
|
|
Extract argument descriptions and other parts of the help pages of
|
|
functions.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rjags
|
|
(package
|
|
(name "r-rjags")
|
|
(version "4-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rjags" version))
|
|
(sha256
|
|
(base32
|
|
"17xmjksj69f9wk4x71jxk4cgiqhaf2fj6bjm0mgzp4qln5x84a8m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-coda" ,r-coda)))
|
|
(inputs
|
|
`(("jags" ,jags)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://mcmc-jags.sourceforge.net")
|
|
(synopsis "Bayesian graphical models using MCMC")
|
|
(description
|
|
"This package provides an R interface to the JAGS MCMC library. JAGS is
|
|
Just Another Gibbs Sampler. It is a program for analysis of Bayesian
|
|
hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rdpack
|
|
(package
|
|
(name "r-rdpack")
|
|
(version "0.11-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rdpack" version))
|
|
(sha256
|
|
(base32
|
|
"11cd27s6zp5cxnwxcvz6rjf00y0r7aq8ywhzwpf1r4xy1z44kd4g"))))
|
|
(properties `((upstream-name . "Rdpack")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bibtex" ,r-bibtex)
|
|
("r-gbrd" ,r-gbrd)))
|
|
(home-page "https://github.com/GeoBosh/Rdpack")
|
|
(synopsis "Update and manipulate Rd documentation objects")
|
|
(description
|
|
"This package provides functions for manipulation of R documentation
|
|
objects, including functions @code{reprompt()} and @code{ereprompt()} for
|
|
updating Rd documentation for functions, methods and classes; it also includes
|
|
Rd macros for citations and import of references from bibtex files for use in
|
|
Rd files and roxygen2 comments, as well as many functions for manipulation of
|
|
references and Rd files.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-officer
|
|
(package
|
|
(name "r-officer")
|
|
(version "0.3.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "officer" version))
|
|
(sha256
|
|
(base32
|
|
"1m4b3mcn5j5q3nq0jp1nranh4rdb8vxcpabn6ryqk9m6709fvhjz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-digest" ,r-digest)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-r6" ,r-r6)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)
|
|
("r-uuid" ,r-uuid)
|
|
("r-xml2" ,r-xml2)
|
|
("r-zip" ,r-zip)))
|
|
(home-page "https://davidgohel.github.io/officer")
|
|
(synopsis "Manipulation of Word and PowerPoint documents")
|
|
(description
|
|
"This package provides tools to access and manipulate Word and PowerPoint
|
|
documents from R. The package focuses on tabular and graphical reporting from
|
|
R; it also provides two functions that let users get document content into
|
|
data objects. A set of functions lets add and remove images, tables and
|
|
paragraphs of text in new or existing documents. When working with PowerPoint
|
|
presentations, slides can be added or removed; shapes inside slides can also
|
|
be added or removed. When working with Word documents, a cursor can be used
|
|
to help insert or delete content at a specific location in the document.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-abn
|
|
(package
|
|
(name "r-abn")
|
|
(version "1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abn" version))
|
|
(sha256
|
|
(base32
|
|
"1q9hzpxwg835711kxwygd0l2awal6f015f8s6fprwz7graz1wbbm"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gsl" ,gsl)))
|
|
(propagated-inputs
|
|
`(("r-cairo" ,r-cairo)
|
|
("r-lme4" ,r-lme4)
|
|
("r-mass" ,r-mass)
|
|
("r-nnet" ,r-nnet)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)
|
|
("r-rjags" ,r-rjags)))
|
|
(home-page "http://www.r-bayesian-networks.org")
|
|
(synopsis "Modelling multivariate data with additive bayesian networks")
|
|
(description
|
|
"Bayesian network analysis is a form of probabilistic graphical models
|
|
which derives from empirical data a directed acyclic graph, DAG, describing
|
|
the dependency structure between random variables. An additive Bayesian
|
|
network model consists of a form of a DAG where each node comprises a
|
|
@dfn{generalized linear model} (GLM). Additive Bayesian network models are
|
|
equivalent to Bayesian multivariate regression using graphical modelling, they
|
|
generalises the usual multivariable regression, GLM, to multiple dependent
|
|
variables. This package provides routines to help determine optimal Bayesian
|
|
network models for a given data set, where these models are used to identify
|
|
statistical dependencies in messy, complex data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-acd
|
|
(package
|
|
(name "r-acd")
|
|
(version "1.5.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ACD" version))
|
|
(sha256
|
|
(base32
|
|
"1a67bi3hklq8nlc50r0qnyr4k7m9kpvijy8sqqpm54by5hsysfd6"))))
|
|
(properties `((upstream-name . "ACD")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/ACD/")
|
|
(synopsis "Categorical data analysis with complete or missing responses")
|
|
(description
|
|
"This package provides tools for categorical data analysis with complete
|
|
or missing responses.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-acdm
|
|
(package
|
|
(name "r-acdm")
|
|
(version "1.0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ACDm" version))
|
|
(sha256
|
|
(base32
|
|
"0b4f02ga5ra66mbrm79g0bnlzmii82rks9kmxixxqgf18yhlyjil"))))
|
|
(properties `((upstream-name . "ACDm")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-plyr" ,r-plyr)
|
|
("r-rsolnp" ,r-rsolnp)
|
|
("r-zoo" ,r-zoo)))
|
|
(home-page "https://cran.r-project.org/web/packages/ACDm/")
|
|
(synopsis "Tools for Autoregressive Conditional Duration Models")
|
|
(description
|
|
"ACDm is a package for Autoregressive Conditional Duration (ACD, Engle
|
|
and Russell, 1998) models. It creates trade, price or volume durations from
|
|
transactions (tic) data, performs diurnal adjustments, fits various ACD models
|
|
and tests them.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-overlap
|
|
(package
|
|
(name "r-overlap")
|
|
(version "0.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "overlap" version))
|
|
(sha256
|
|
(base32
|
|
"1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/overlap/")
|
|
(synopsis "Estimates of coefficient of overlapping for animal activity patterns")
|
|
(description
|
|
"This package provides functions to fit kernel density functions to data
|
|
on temporal activity patterns of animals; estimate coefficients of overlapping
|
|
of densities for two species; and calculate bootstrap estimates of confidence
|
|
intervals.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-snakecase
|
|
(package
|
|
(name "r-snakecase")
|
|
(version "0.11.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "snakecase" version))
|
|
(sha256
|
|
(base32
|
|
"1ky1x2cp5rd0ffd9m1fji9sq4z4jsrpxzg30brw8bb4ihfjj114r"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-stringi" ,r-stringi)
|
|
("r-stringr" ,r-stringr)))
|
|
(home-page "https://github.com/Tazinho/snakecase")
|
|
(synopsis "Convert strings into any case")
|
|
(description
|
|
"This package provides a consistent, flexible and easy to use tool to
|
|
parse and convert strings into cases like snake or camel among others.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-prediction
|
|
(package
|
|
(name "r-prediction")
|
|
(version "0.3.6.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "prediction" version))
|
|
(sha256
|
|
(base32
|
|
"0kx7xbm2j6c8h6gk1iig4vfpg877psg16j74hl7zc2mv40sc6dy5"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-data-table" ,r-data-table)))
|
|
(home-page "https://github.com/leeper/prediction")
|
|
(synopsis "Tidy, type-safe prediction methods")
|
|
(description
|
|
"This package provides the @code{prediction()} function, a type-safe
|
|
alternative to @code{predict()} that always returns a data frame. The package
|
|
currently supports common model types (e.g., @code{\"lm\"}, @code{\"glm\"})
|
|
from the @code{stats} package, as well as numerous other model classes from
|
|
other add-on packages.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-insight
|
|
(package
|
|
(name "r-insight")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "insight" version))
|
|
(sha256
|
|
(base32
|
|
"1r288hc01cpyrk3nias30fw783z2vw20qr1k67vr65anh7mwm7vb"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://easystats.github.io/insight/")
|
|
(synopsis "Easy access to model information for various model objects")
|
|
(description
|
|
"This package provides a tool to provide an easy, intuitive and
|
|
consistent access to information contained in various R models, like model
|
|
formulas, model terms, information about random effects, data that was used to
|
|
fit the model or data from response variables. The package mainly revolves
|
|
around two types of functions: Functions that find (the names of) information,
|
|
starting with @code{find_}, and functions that get the underlying data,
|
|
starting with @code{get_}. The package has a consistent syntax and works with
|
|
many different model objects, where otherwise functions to access these
|
|
information are missing.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-sjlabelled
|
|
(package
|
|
(name "r-sjlabelled")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sjlabelled" version))
|
|
(sha256
|
|
(base32
|
|
"0rnmlwpp41h04dzfjd5ncvzjzs43slaimb4v2in1axznv3haafyc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-haven" ,r-haven)
|
|
("r-insight" ,r-insight)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tidyselect" ,r-tidyselect)))
|
|
(home-page "https://github.com/strengejacke/sjlabelled")
|
|
(synopsis "Labelled data utility functions")
|
|
(description
|
|
"This package provides a collection of functions dealing with labelled
|
|
data, like reading and writing data between R and other statistical software
|
|
packages. This includes easy ways to get, set or change value and variable
|
|
label attributes, to convert labelled vectors into factors or numeric (and
|
|
vice versa), or to deal with multiple declared missing values.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-sjmisc
|
|
(package
|
|
(name "r-sjmisc")
|
|
(version "2.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sjmisc" version))
|
|
(sha256
|
|
(base32
|
|
"0pgavkygsj8fa591pmasx78b4gd32sf2pa067yqvi82xha7dj5k4"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-insight" ,r-insight)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-sjlabelled" ,r-sjlabelled)))
|
|
(home-page "https://github.com/strengejacke/sjmisc")
|
|
(synopsis "Data and variable transformation functions")
|
|
(description
|
|
"This package is a collection of miscellaneous utility functions,
|
|
supporting data transformation tasks like recoding, dichotomizing or grouping
|
|
variables, setting and replacing missing values. The data transformation
|
|
functions also support labelled data, and all integrate seamlessly into a
|
|
tidyverse workflow.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-nortest
|
|
(package
|
|
(name "r-nortest")
|
|
(version "1.0-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nortest" version))
|
|
(sha256
|
|
(base32
|
|
"17r0wpz72z9312c70nwi1i1kp1v9fm1h6jg7q5cx1mc1h420m1d3"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/nortest/")
|
|
(synopsis "Tests for normality")
|
|
(description
|
|
"This package provides five omnibus tests for testing the composite
|
|
hypothesis of normality.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-moonbook
|
|
(package
|
|
(name "r-moonbook")
|
|
(version "0.2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "moonBook" version))
|
|
(sha256
|
|
(base32
|
|
"0hys56mwbm776ff7dibi8wzyf69qiais9rs1jazv79lk6h56s9s6"))))
|
|
(properties `((upstream-name . "moonBook")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-magrittr" ,r-magrittr)
|
|
("r-nortest" ,r-nortest)
|
|
("r-purrr" ,r-purrr)
|
|
("r-sjmisc" ,r-sjmisc)
|
|
("r-stringr" ,r-stringr)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://github.com/cardiomoon/moonBook")
|
|
(synopsis "Functions and datasets for the book by Keon-Woong Moon")
|
|
(description
|
|
"This package provides several analysis-related functions for the book
|
|
entitled \"R statistics and graph for medical articles\" (written in Korean),
|
|
version 1, by Keon-Woong Moon with Korean demographic data with several plot
|
|
functions.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-flextable
|
|
(package
|
|
(name "r-flextable")
|
|
(version "0.5.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "flextable" version))
|
|
(sha256
|
|
(base32
|
|
"0h6ylgz1mn61d2kh1bym8hfl3r7nf4z092lmjsaav3h1ki3avrnl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-data-table" ,r-data-table)
|
|
("r-gdtools" ,r-gdtools)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-knitr" ,r-knitr)
|
|
("r-officer" ,r-officer)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://davidgohel.github.io/flextable")
|
|
(synopsis "Functions for tabular reporting")
|
|
(description
|
|
"This package provides tools to create pretty tables for HTML documents
|
|
and other formats. Functions are provided to let users create tables, modify
|
|
and format their content. It extends the @code{officer} package and can be
|
|
used within R markdown documents when rendering to HTML and to Word
|
|
documents.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-writexl
|
|
(package
|
|
(name "r-writexl")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "writexl" version))
|
|
(sha256
|
|
(base32
|
|
"0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("zlib" ,zlib)))
|
|
(home-page "https://github.com/ropensci/writexl")
|
|
(synopsis "Export data frames to xlsx format")
|
|
(description
|
|
"This package provides a data frame to xlsx exporter based on
|
|
libxlsxwriter.")
|
|
(license license:bsd-2)))
|
|
|
|
(define-public r-biasedurn
|
|
(package
|
|
(name "r-biasedurn")
|
|
(version "1.07")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BiasedUrn" version))
|
|
(sha256
|
|
(base32
|
|
"13i2lgfnjhlbbm2yxfc2l5hswqw6x03pwba5csjmirv8kpjw4xr3"))))
|
|
(properties `((upstream-name . "BiasedUrn")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/BiasedUrn/")
|
|
(synopsis "Biased Urn model distributions")
|
|
(description
|
|
"This package provides statistical models of biased sampling in the form
|
|
of univariate and multivariate noncentral hypergeometric distributions,
|
|
including Wallenius' noncentral hypergeometric distribution and Fisher's
|
|
noncentral hypergeometric distribution (also called extended hypergeometric
|
|
distribution).")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-goplot
|
|
(package
|
|
(name "r-goplot")
|
|
(version "1.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GOplot" version))
|
|
(sha256
|
|
(base32
|
|
"1y8dv0kbzpr9za91njw0x233vx5d13vqml9hmpddcyi9s6va5nix"))))
|
|
(properties `((upstream-name . "GOplot")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggdendro" ,r-ggdendro)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)))
|
|
(home-page "https://github.com/wencke/wencke.github.io")
|
|
(synopsis "Visualization of functional analysis data")
|
|
(description
|
|
"This package provides an implementation of multilayered visualizations
|
|
for enhanced graphical representation of functional analysis data. It
|
|
combines and integrates omics data derived from expression and functional
|
|
annotation enrichment analyses. Its plotting functions have been developed
|
|
with an hierarchical structure in mind: starting from a general overview to
|
|
identify the most enriched categories (modified bar plot, bubble plot) to a
|
|
more detailed one displaying different types of relevant information for the
|
|
molecules in a given set of categories (circle plot, chord plot, cluster plot,
|
|
Venn diagram, heatmap).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-getopt
|
|
(package
|
|
(name "r-getopt")
|
|
(version "1.20.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "getopt" version))
|
|
(sha256
|
|
(base32
|
|
"0zzmzgwl9a4y3s34600vmih22d6y32294f9bvxrnmffnvkgmy7sk"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/trevorld/getopt")
|
|
(synopsis "Command-line option processor for R")
|
|
(description
|
|
"This package is designed to be used with Rscript to write shebang
|
|
scripts that accept short and long options. Many users will prefer to
|
|
use the packages @code{optparse} or @code{argparse} which add extra
|
|
features like automatically generated help options and usage texts,
|
|
support for default values, positional argument support, etc.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-findpython
|
|
(package
|
|
(name "r-findpython")
|
|
(version "1.0.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "findpython" version))
|
|
(sha256
|
|
(base32
|
|
"0icifm4z6hhpmcjrg75a875iph0ci890ss02kdv3725pijc236iy"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/trevorld/findpython")
|
|
(synopsis "Functions to find an acceptable Python binary")
|
|
(description
|
|
"This package was designed to find an acceptable Python binary that
|
|
matches version and feature constraints.")
|
|
(license license:expat)))
|
|
|
|
;; This in not the same as "r-argparser"
|
|
(define-public r-argparse
|
|
(package
|
|
(name "r-argparse")
|
|
(version "2.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "argparse" version))
|
|
(sha256
|
|
(base32
|
|
"1as7h6z7kzgv0fqzpnp76qbm96b4jcd37azd58b7rz0l1n94764l"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("python" ,python)))
|
|
(propagated-inputs
|
|
`(("r-findpython" ,r-findpython)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://github.com/trevorld/argparse")
|
|
(synopsis "Command line optional and positional argument parser")
|
|
(description
|
|
"This package provides a command line parser to be used with Rscript to
|
|
write shebang scripts that gracefully accept positional and optional arguments
|
|
and automatically generate usage notices.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-hash
|
|
(package
|
|
(name "r-hash")
|
|
(version "2.2.6.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hash" version))
|
|
(sha256
|
|
(base32
|
|
"0b3fl0rvgwb992knl81vm99lsldg5clvaqjh6mamm6zqmb6dz056"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/hash/")
|
|
(synopsis "Implementation of hash/associated arrays/dictionaries")
|
|
(description
|
|
"This package implements a data structure similar to hashes in Perl and
|
|
dictionaries in Python but with a purposefully R flavor. For objects of
|
|
appreciable size, access using hashes outperforms native named lists and
|
|
vectors.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-orddom
|
|
(package
|
|
(name "r-orddom")
|
|
(version "3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "orddom" version))
|
|
(sha256
|
|
(base32
|
|
"165axs15fvwhrp89xd87l81q3h2qjll1vrwcsap645cwvb85nwsh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-psych" ,r-psych)))
|
|
(home-page "https://cran.r-project.org/web/packages/orddom/")
|
|
(synopsis "Ordinal dominance statistics")
|
|
(description
|
|
"This package provides tools to compute ordinal, statistics and effect
|
|
sizes as an alternative to mean comparison: Cliff's delta or success rate
|
|
difference (SRD), Vargha and Delaney's A or the Area Under a Receiver
|
|
Operating Characteristic Curve (AUC), the discrete type of McGraw & Wong's
|
|
Common Language Effect Size (CLES) or Grissom & Kim's Probability of
|
|
Superiority (PS), and the Number needed to treat (NNT) effect size. Moreover,
|
|
comparisons to Cohen's d are offered based on Huberty & Lowman's Percentage of
|
|
Group (Non-)Overlap considerations.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-doby
|
|
(package
|
|
(name "r-doby")
|
|
(version "4.6-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "doBy" version))
|
|
(sha256
|
|
(base32
|
|
"02vbv9nfgywg6lsiialkmfnax5z3rkyb9nr8j9l2cp8xi6ml95mb"))))
|
|
(properties `((upstream-name . "doBy")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-plyr" ,r-plyr)))
|
|
(home-page "http://people.math.aau.dk/~sorenh/software/doBy/")
|
|
(synopsis "Groupwise statistics, LSmeans, linear contrasts, and utilities")
|
|
(description
|
|
"This package contains:
|
|
|
|
@itemize
|
|
@item facilities for working with grouped data: @code{do}
|
|
something to data stratified @code{by} some variables.
|
|
@item implementations of least-squares means, general linear contrasts, and
|
|
@item miscellaneous other utilities.
|
|
@end itemize\n")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-refgenome
|
|
(package
|
|
(name "r-refgenome")
|
|
(version "1.7.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "refGenome" version))
|
|
(sha256
|
|
(base32
|
|
"1za89bn3am1zgvm641qi1ab6kaqpll4rb9p9f1sjwvcgqq6065g5"))))
|
|
(properties `((upstream-name . "refGenome")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dbi" ,r-dbi)
|
|
("r-doby" ,r-doby)
|
|
("r-rsqlite" ,r-rsqlite)))
|
|
(home-page "https://cran.r-project.org/web/packages/refGenome/")
|
|
(synopsis
|
|
"Gene and splice site annotation using annotation data from Ensembl and UCSC")
|
|
(description
|
|
"This package contains functionality for importing and managing of
|
|
downloaded genome annotation data from the Ensembl genome browser (European
|
|
Bioinformatics Institute) and from the UCSC genome browser (University of
|
|
California, Santa Cruz) and annotation routines for genomic positions and
|
|
splice site positions.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-basix
|
|
(package
|
|
(name "r-basix")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BASIX" version))
|
|
(sha256
|
|
(base32
|
|
"18dkvv1iwskfnlpl6xridcgqpalbbpm2616mvc3hfrc0b26v01id"))))
|
|
(properties `((upstream-name . "BASIX")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/BASIX/")
|
|
(synopsis "Efficient C/C++ toolset for R")
|
|
(description
|
|
"BASIX provides some efficient C/C++ implementations of native R
|
|
procedures to speed up calculations in R.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-blockfest
|
|
(package
|
|
(name "r-blockfest")
|
|
(version "1.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BlockFeST" version))
|
|
(sha256
|
|
(base32
|
|
"0hj7a5as7nxbgjac7lbj6qfwffx3g8x8phpf9a55f1c9cdzi73a5"))))
|
|
(properties `((upstream-name . "BlockFeST")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-basix" ,r-basix)))
|
|
(home-page "https://cran.r-project.org/web/packages/BlockFeST/")
|
|
(synopsis "Bayesian calculation of region-specific fixation index")
|
|
(description
|
|
"This package provides an R implementation of an extension of the
|
|
BayeScan software for codominant markers, adding the option to group
|
|
individual SNPs into pre-defined blocks. A typical application of this new
|
|
approach is the identification of genomic regions, genes, or gene sets
|
|
containing one or more SNPs that evolved under directional selection.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-proc
|
|
(package
|
|
(name "r-proc")
|
|
(version "1.15.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pROC" version))
|
|
(sha256
|
|
(base32
|
|
"1dxxkwdhxfnj2znq4c5ggrr9m5klh5pmfxg17rz59vr2hfb73m24"))))
|
|
(properties `((upstream-name . "pROC")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-plyr" ,r-plyr)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "http://expasy.org/tools/pROC/")
|
|
(synopsis "Display and analyze ROC curves")
|
|
(description
|
|
"This package provides tools for visualizing, smoothing and comparing
|
|
receiver operating characteristic (ROC curves). The area under the
|
|
curve (AUC) can be compared with statistical tests based on U-statistics or
|
|
bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-rootsolve
|
|
(package
|
|
(name "r-rootsolve")
|
|
(version "1.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rootSolve" version))
|
|
(sha256
|
|
(base32
|
|
"08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8"))))
|
|
(properties `((upstream-name . "rootSolve")))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/rootSolve/")
|
|
(synopsis "Tools for the analysis of ordinary differential equations")
|
|
(description
|
|
"This package provides routines to find the root of nonlinear functions,
|
|
and to perform steady-state and equilibrium analysis of @dfn{ordinary
|
|
differential equations} (ODE). It includes routines that:
|
|
|
|
@enumerate
|
|
@item generate gradient and jacobian matrices (full and banded),
|
|
@item find roots of non-linear equations by the Newton-Raphson method,
|
|
@item estimate steady-state conditions of a system of (differential) equations
|
|
in full, banded or sparse form, using the Newton-Raphson method, or by
|
|
dynamically running,
|
|
@item solve the steady-state conditions for uni- and multicomponent 1-D, 2-D,
|
|
and 3-D partial differential equations, that have been converted to ordinary
|
|
differential equations by numerical differencing (using the method-of-lines
|
|
approach).
|
|
@end enumerate\n")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-abcanalysis
|
|
(package
|
|
(name "r-abcanalysis")
|
|
(version "1.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ABCanalysis" version))
|
|
(sha256
|
|
(base32 "0wac1ksmnxa36v99ca4hv8k0rsh3igwpcllmlv9wf7i9kgqviqwi"))))
|
|
(properties `((upstream-name . "ABCanalysis")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-plotrix" ,r-plotrix)))
|
|
(home-page "https://www.uni-marburg.de/fb12/arbeitsgruppen/datenbionik/software-en/")
|
|
(synopsis "Computed ABC Analysis")
|
|
(description
|
|
"Multivariate data sets often differ in several factors or derived statistical
|
|
parameters, which have to be selected for a valid interpretation. Basing this
|
|
selection on traditional statistical limits leads occasionally to the perception
|
|
of losing information from a data set. This package provides tools to calculate
|
|
these limits on the basis of the mathematical properties of the distribution of
|
|
the analyzed items.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-slam
|
|
(package
|
|
(name "r-slam")
|
|
(version "0.1-45")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "slam" version))
|
|
(sha256
|
|
(base32 "0xvj8va6xd7zkn3l4a5ad7v62s7xmkz8frq7gpcl3b6vqwckkaw4"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/slam/")
|
|
(synopsis "Sparse lightweight arrays and matrices")
|
|
(description
|
|
"This package contains data structures and algorithms for sparse arrays and matrices,
|
|
based on index arrays and simple triplet representations, respectively.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-manipulatewidget
|
|
(package
|
|
(name "r-manipulatewidget")
|
|
(version "0.10.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "manipulateWidget" version))
|
|
(sha256
|
|
(base32 "1zagrbwkn2d50zzw8i2vyb1hsq4cydmfsqiy1a2qlp6zrv8a6q9x"))))
|
|
(properties
|
|
`((upstream-name . "manipulateWidget")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-codetools" ,r-codetools)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-knitr" ,r-knitr)
|
|
("r-miniui" ,r-miniui)
|
|
("r-shiny" ,r-shiny)
|
|
("r-webshot" ,r-webshot)))
|
|
(home-page "https://github.com/rte-antares-rpackage/manipulateWidget/")
|
|
(synopsis "Add even more interactivity to interactive charts")
|
|
(description
|
|
"This package lets you create in just a few lines of R code a nice user interface to
|
|
modify the data or the graphical parameters of one or multiple interactive
|
|
charts. It is useful to quickly explore visually some data or for package
|
|
developers to generate user interfaces easy to maintain.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-a3
|
|
(package
|
|
(name "r-a3")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "A3" version))
|
|
(sha256
|
|
(base32 "017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"))))
|
|
(properties `((upstream-name . "A3")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-pbapply" ,r-pbapply)
|
|
("r-xtable" ,r-xtable)))
|
|
(home-page "https://cran.r-project.org/web/packages/A3/")
|
|
(synopsis "Error metrics for predictive models")
|
|
(description
|
|
"This package supplies tools for tabulating and analyzing the results of predictive
|
|
models. The methods employed are applicable to virtually any predictive model
|
|
and make comparisons between different methodologies straightforward.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-infotheo
|
|
(package
|
|
(name "r-infotheo")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "infotheo" version))
|
|
(sha256
|
|
(base32
|
|
"18xacczfq3z3xpy434js4nf3l19lczngzd0lq26wh22pvg1yniwv"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://homepage.meyerp.com/software")
|
|
(synopsis "Information-theoretic measures")
|
|
(description
|
|
"This package implements various measures of information theory based on
|
|
several entropy estimators.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-abcoptim
|
|
(package
|
|
(name "r-abcoptim")
|
|
(version "0.15.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ABCoptim" version))
|
|
(sha256
|
|
(base32 "1ih0xk88qhsmpvnxf56041wx5sk8as2f4f2gdnpnwdym9mbr9n4b"))))
|
|
(properties `((upstream-name . "ABCoptim")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/gvegayon/ABCoptim/")
|
|
(synopsis "Optimization of Artificial Bee Colony algorithm")
|
|
(description
|
|
"Artificial Bee Colony (ABC) is one of the most recently defined algorithms by Dervis
|
|
Karaboga in 2005, motivated by the intelligent behavior of honey bees. It is as
|
|
simple as Particle Swarm Optimization (PSO) and Differential Evolution (DE)
|
|
algorithms, and uses only common control parameters such as colony size and
|
|
maximum cycle number. The @code{r-abcoptim} implements the Artificial bee
|
|
colony optimization algorithm @url{http://mf.erciyes.edu.tr/abc/pub/tr06_2005.pdf}.
|
|
This version is a work-in-progress and is written in R code.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-abcp2
|
|
(package
|
|
(name "r-abcp2")
|
|
(version "1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ABCp2" version))
|
|
(sha256
|
|
(base32 "1s2skkxpzss7c29i8600psgrp0hl46jcrxqrmy2b4db8hc0kcnbx"))))
|
|
(properties `((upstream-name . "ABCp2")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/ABCp2/")
|
|
(synopsis "Approximate Bayesian Computational Model for Estimating P2")
|
|
(description
|
|
"This package tests the goodness of fit of a distribution of offspring to the Normal,
|
|
Poisson, and Gamma distribution and estimates the proportional paternity of the
|
|
second male (P2) based on the best fit distribution.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-abcrf
|
|
(package
|
|
(name "r-abcrf")
|
|
(version "1.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abcrf" version))
|
|
(sha256
|
|
(base32 "0r31ki89z8zzcffm0yvd2zw3q96rk6g6fnwwkql902mgajbrha1f"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-doparallel" ,r-doparallel)
|
|
("r-foreach" ,r-foreach)
|
|
("r-mass" ,r-mass)
|
|
("r-matrixstats" ,r-matrixstats)
|
|
("r-ranger" ,r-ranger)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)
|
|
("r-readr" ,r-readr)
|
|
("r-stringr" ,r-stringr)))
|
|
(home-page "https://cran.r-project.org/web/packages/abcrf/")
|
|
(synopsis "Approximate bayesian computation via random forests")
|
|
(description
|
|
"This package performs approximate bayesian computation (ABC) model choice and
|
|
parameter inference via random forests. This machine learning tool named random
|
|
forests (RF) can conduct selection among the highly complex models covered by
|
|
ABC algorithms.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-abctools
|
|
(package
|
|
(name "r-abctools")
|
|
(version "1.1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abctools" version))
|
|
(sha256
|
|
(base32 "07s9dg10i8lsxl73b4n2hynca2fjgb0ykb0dz8c3zv6cgw3cyx97"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-abc" ,r-abc)
|
|
("r-abind" ,r-abind)
|
|
("r-hmisc" ,r-hmisc)
|
|
("r-plyr" ,r-plyr)))
|
|
(home-page "https://github.com/dennisprangle/abctools/")
|
|
(synopsis "Tools for ABC analyses")
|
|
(description
|
|
"This @code{r-abctools} package provides tools for approximate Bayesian computation
|
|
including summary statistic selection and assessing coverage. This includes
|
|
recent dimension reduction algorithms to tune the choice of summary statistics,
|
|
and coverage methods to tune the choice of threshold.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ggstance
|
|
(package
|
|
(name "r-ggstance")
|
|
(version "0.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggstance" version))
|
|
(sha256
|
|
(base32 "0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-plyr" ,r-plyr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://cran.r-project.org/web/packages/ggstance/")
|
|
(synopsis "Horizontal and vertical versions of @code{r-ggplot2}")
|
|
(description
|
|
"This package is a @code{r-ggplot2} extension that provides flipped components:
|
|
@enumerate
|
|
@item horizontal versions of @code{r-ggplot2} stats and @code{r-ggplot2} geoms;
|
|
@item vertical versions of @code{r-ggplot2} positions.
|
|
@end enumerate")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-mosaiccore
|
|
(package
|
|
(name "r-mosaiccore")
|
|
(version "0.6.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mosaicCore" version))
|
|
(sha256
|
|
(base32 "1klw97h6lchw1cpcl8s637ikcl428cckmjq0czi7mibh9q9mw72z"))))
|
|
(properties `((upstream-name . "mosaicCore")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-mass" ,r-mass)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/ProjectMOSAIC/mosaicCore/")
|
|
(synopsis "Common utilities for mosaic family packages")
|
|
(description
|
|
"Common utilities used in other Mosaic family packages are collected here.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ggformula
|
|
(package
|
|
(name "r-ggformula")
|
|
(version "0.9.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggformula" version))
|
|
(sha256
|
|
(base32 "01ngx8qh9lhmagng6abx2ky54zi3iyj5bpxlnw59slagwv7l6icx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-ggstance" ,r-ggstance)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-mosaiccore" ,r-mosaiccore)
|
|
("r-rlang" ,r-rlang)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/ProjectMOSAIC/ggformula/")
|
|
(synopsis "Formula interface for the @code{r-ggplot2}")
|
|
(description
|
|
"The @code{r-ggformula} introduces a family of graphics functions, gf_point(),
|
|
gf_density(), and so on, bring the formula interface to ggplot(). This captures
|
|
and extends the excellent simplicity of the lattice-graphics formula interface,
|
|
while providing the intuitive capabilities of @code{r-ggplot2}.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-mosaicdata
|
|
(package
|
|
(name "r-mosaicdata")
|
|
(version "0.17.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mosaicData" version))
|
|
(sha256
|
|
(base32 "04z0mdm52mykqsxsinhmsihn181zf6cw321gayk2rjp7lj7mwdq9"))))
|
|
(properties `((upstream-name . "mosaicData")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/mosaicData/")
|
|
(synopsis "Data sets for project Mosaic")
|
|
(description
|
|
"This package provides data sets from project Mosaic @url{http://mosaic-web.org}
|
|
used to teach mathematics, statistics, computation and modeling.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-raster
|
|
(package
|
|
(name "r-raster")
|
|
(version "2.9-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "raster" version))
|
|
(sha256
|
|
(base32
|
|
"0ljrymsp4zzaxdj1l0mw0a6hi88m5h0h920ixfzrg0szbyxqd0yk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-sp" ,r-sp)))
|
|
(home-page "https://www.rspatial.org/")
|
|
(synopsis "Geographic data analysis and modeling")
|
|
(description
|
|
"The package implements basic and high-level functions for reading,
|
|
writing, manipulating, analyzing and modeling of gridded spatial data.
|
|
Processing of very large files is supported.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-mosaic
|
|
(package
|
|
(name "r-mosaic")
|
|
(version "1.4.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mosaic" version))
|
|
(sha256
|
|
(base32 "10jbrg8kli00kfgbh2f67bymm5cnlancc9dplb1j7fl552yjddn2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggdendro" ,r-ggdendro)
|
|
("r-ggformula" ,r-ggformula)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-ggrepel" ,r-ggrepel)
|
|
("r-glue" ,r-glue)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-lattice" ,r-lattice)
|
|
("r-latticeextra" ,r-latticeextra)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-mosaiccore" ,r-mosaiccore)
|
|
("r-mosaicdata" ,r-mosaicdata)
|
|
("r-readr" ,r-readr)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/ProjectMOSAIC/mosaic/")
|
|
(synopsis "Mathematics, statistics, and computation teaching utilities")
|
|
(description
|
|
"This package contain data sets and utilities from
|
|
@url{http://mosaic-web.org, Project MOSAIC} used to teach mathematics,
|
|
statistics, computation and modeling. Project MOSAIC is a community of
|
|
educators working to tie together aspects of quantitative work that students
|
|
in science, technology, engineering and mathematics will need in their
|
|
professional lives, but which are usually taught in isolation, if at all.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-abd
|
|
(package
|
|
(name "r-abd")
|
|
(version "0.2-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abd" version))
|
|
(sha256
|
|
(base32 "191gspqzdv573vaw624ri0f5cm6v4j524bjs74d4a1hn3kn6r9b7"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-mosaic" ,r-mosaic)
|
|
("r-nlme" ,r-nlme)))
|
|
(home-page "https://cran.r-project.org/web/packages/abd/")
|
|
(synopsis "Analysis of biological data")
|
|
(description
|
|
"The @code{r-abd} package contains data sets and sample code for the Analysis of
|
|
biological data by Michael Whitlock and Dolph Schluter.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-svgui
|
|
(package
|
|
(name "r-svgui")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "svGUI" version))
|
|
(sha256
|
|
(base32 "1r7ab0p4yr8q03gj02hmj7k1ghksgkg4nx750c0ajfs2q9y1dxfc"))))
|
|
(properties `((upstream-name . "svGUI")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/SciViews/svGUI/")
|
|
(synopsis "Functions for managing GUI clients in R")
|
|
(description
|
|
"The SciViews @code{svGUI} package eases the management of Graphical User
|
|
Interfaces (GUI) in R. It is independent from any particular GUI widgets. It
|
|
centralizes info about GUI elements currently used, and it dispatches GUI
|
|
calls to the particular toolkits in use in function of the context.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-svdialogs
|
|
(package
|
|
(name "r-svdialogs")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "svDialogs" version))
|
|
(sha256
|
|
(base32 "0xqppydfawnwk84kb5qiybwbcmv38vn4imgz01mz2pnq4xb80p97"))))
|
|
(properties `((upstream-name . "svDialogs")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("yad" ,yad)
|
|
("zenity" ,zenity)))
|
|
(propagated-inputs
|
|
`(("r-rstudioapi" ,r-rstudioapi)
|
|
("r-svgui" ,r-svgui)))
|
|
(home-page "https://github.com/SciViews/svDialogs/")
|
|
(synopsis "Portable dialog boxes")
|
|
(description
|
|
"This package helps to construct standard dialog boxes for your GUI, including
|
|
message boxes, input boxes, list, file or directory selection, and others. In
|
|
case R cannot display GUI dialog boxes, a simpler command line version of these
|
|
interactive elements is also provided as a fallback solution.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-abe
|
|
(package
|
|
(name "r-abe")
|
|
(version "3.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abe" version))
|
|
(sha256
|
|
(base32
|
|
"1f19h3xzzmjhvwc1rrb8z0rai3ip03y4gdi2gg9bfr5sg2nfklk6"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/abe/")
|
|
(synopsis "Augmented backward elimination")
|
|
(description
|
|
"This package performs augmented backward elimination and checks the
|
|
stability of the obtained model. Augmented backward elimination combines
|
|
significance or information based criteria with the change in estimate to
|
|
either select the optimal model for prediction purposes or to serve as a tool
|
|
to obtain a practically sound, highly interpretable model.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-abf2
|
|
(package
|
|
(name "r-abf2")
|
|
(version "0.7-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abf2" version))
|
|
(sha256
|
|
(base32 "0d65mc1w4pbiv7xaqzdlw1bfsxf25587rv597hh41vs0j0zlfpxx"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/abf2/")
|
|
(synopsis "Load gap-free axon @code{r-abf2} files")
|
|
(description
|
|
"This package loads electrophysiology data from ABF2 files, as created by
|
|
Axon Instruments/Molecular Devices software. Only files recorded in gap-free
|
|
mode are currently supported.")
|
|
(license license:artistic2.0)))
|
|
|
|
(define-public r-abhgenotyper
|
|
(package
|
|
(name "r-abhgenotyper")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ABHgenotypeR" version))
|
|
(sha256
|
|
(base32 "08cpmnaaxsm5c5bjifnfxdlvg5inrf13biqpcl2yq5zpqjmiki0l"))))
|
|
(properties `((upstream-name . "ABHgenotypeR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-reshape2" ,r-reshape2)))
|
|
(home-page "https://github.com/StefanReuscher/ABHgenotypeR/")
|
|
(synopsis "Visualize and manipulate ABH genotypes")
|
|
(description
|
|
"The @code{r-abhgenotyper} package provides simple imputation,
|
|
error-correction and plotting capacities for genotype data. The package is
|
|
supposed to serve as an intermediate but independent analysis tool between the
|
|
TASSEL GBS pipeline and the @code{r-qtl} package. It provides functionalities
|
|
not found in either TASSEL or @code{r-qtl} in addition to visualization of
|
|
genotypes as \"graphical genotypes\".")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-furrr
|
|
(package
|
|
(name "r-furrr")
|
|
(version "0.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "furrr" version))
|
|
(sha256
|
|
(base32
|
|
"1ld9aa9hydna94hgm6p91zjbfv1dz1vsgchjlpknkg6irbvkfafx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-future" ,r-future)
|
|
("r-globals" ,r-globals)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)))
|
|
(home-page "https://github.com/DavisVaughan/furrr")
|
|
(synopsis "Apply mapping functions in parallel using futures")
|
|
(description
|
|
"This package provides implementations of the family of @code{map()}
|
|
functions from the @code{purrr} package that can be resolved using any
|
|
@code{future}-supported backend, e.g. parallel on the local machine or
|
|
distributed on a compute cluster.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public r-abjutils
|
|
(package
|
|
(name "r-abjutils")
|
|
(version "0.2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abjutils" version))
|
|
(sha256
|
|
(base32 "0n4zps65y3zg0gfzlv97w91si52a9izkncirskbkj5x9hk0nhxcv"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-devtools" ,r-devtools)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-furrr" ,r-furrr)
|
|
("r-future" ,r-future)
|
|
("r-glue" ,r-glue)
|
|
("r-httr" ,r-httr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-progress" ,r-progress)
|
|
("r-purrr" ,r-purrr)
|
|
("r-readr" ,r-readr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-scales" ,r-scales)
|
|
("r-stringi" ,r-stringi)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/abjur/abjutils/")
|
|
(synopsis "Collection of tools for jurimetrical analysis")
|
|
(description
|
|
"This package implements general purpose tools, such as functions for
|
|
sampling and basic manipulation of Brazilian lawsuits identification number.
|
|
It also implements functions for text cleaning, such as accentuation
|
|
removal.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-abnormality
|
|
(package
|
|
(name "r-abnormality")
|
|
(version "0.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abnormality" version))
|
|
(sha256
|
|
(base32 "1fzfskl9akl06nliy8hkv2a0pznpj8pwcypg3gj5r2nzvr3kan9v"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "https://cran.r-project.org/web/packages/abnormality/")
|
|
(synopsis "Measure a subject's abnormality with respect to a reference population")
|
|
(description
|
|
"This package contains functions to implement the methodology and
|
|
considerations laid out by Marks et al. in the article \"Measuring abnormality
|
|
in high dimensional spaces: applications in biomechanical gait analysis\".
|
|
Using high-dimensional datasets to measure a subject's overall level of
|
|
abnormality as compared to a reference population is often needed in outcomes
|
|
research.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-abodoutlier
|
|
(package
|
|
(name "r-abodoutlier")
|
|
(version "0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abodOutlier" version))
|
|
(sha256
|
|
(base32 "1pvhgxmh23br84r0fbmv7g53z2427birdja96a67vqgz18r3fdvj"))))
|
|
(properties `((upstream-name . "abodOutlier")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)))
|
|
(home-page "https://cran.r-project.org/web/packages/abodOutlier/")
|
|
(synopsis "Angle-based outlier detection")
|
|
(description
|
|
"This package performs angle-based outlier detection on a given data
|
|
frame. It offers three methods to process data:
|
|
@enumerate
|
|
@item full but slow implementation using all the data that has cubic
|
|
complexity;
|
|
@item a fully randomized method;
|
|
@item a method using k-nearest neighbours.
|
|
@end enumerate
|
|
These algorithms are well suited for high dimensional data outlier
|
|
detection.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-abps
|
|
(package
|
|
(name "r-abps")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ABPS" version))
|
|
(sha256
|
|
(base32 "0n3f66nmfi5v94il1mxy026mi84w01ph2aljk60vn3mrz8kwf2ll"))))
|
|
(properties `((upstream-name . "ABPS")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-kernlab" ,r-kernlab)))
|
|
(home-page "https://cran.r-project.org/web/packages/ABPS/")
|
|
(synopsis "Abnormal blood profile score to detect blood doping")
|
|
(description
|
|
"This package offers an implementation of the @dfn{Abnormal blood profile score} (ABPS).
|
|
The ABPS is a part of the Athlete biological passport program of the World
|
|
anti-doping agency, which combines several blood parameters into a single
|
|
score in order to detect blood doping. The package also contains functions to
|
|
calculate other scores used in anti-doping programs, such as the ratio of
|
|
hemoglobin to reticulocytes (OFF-score), as well as example data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-parmigene
|
|
(package
|
|
(name "r-parmigene")
|
|
(version "1.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "parmigene" version))
|
|
(sha256
|
|
(base32
|
|
"1fsm6pkr17jcbzkj1hbn91jf890fviqk1lq6ls8pihsdgah1zb4d"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/parmigene/")
|
|
(synopsis "Mutual information estimation for gene network reconstruction")
|
|
(description
|
|
"This package provides a parallel estimation of the mutual information
|
|
based on entropy estimates from k-nearest neighbors distances and algorithms
|
|
for the reconstruction of gene regulatory networks.")
|
|
(license license:agpl3+)))
|
|
|
|
(define-public r-pscl
|
|
(package
|
|
(name "r-pscl")
|
|
(version "1.5.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pscl" version))
|
|
(sha256
|
|
(base32 "1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)))
|
|
(home-page "https://github.com/atahk/pscl/")
|
|
(synopsis "Political science computational laboratory")
|
|
(description
|
|
"The @code{pscl} is an R package providing classes and methods for:
|
|
@enumerate
|
|
@item Bayesian analysis of roll call data (item-response models);
|
|
@item elementary Bayesian statistics;
|
|
@item maximum likelihood estimation of zero-inflated and hurdle models for count
|
|
data;
|
|
@item utility functions.
|
|
@end enumerate")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-accelmissing
|
|
(package
|
|
(name "r-accelmissing")
|
|
(version "1.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "accelmissing" version))
|
|
(sha256
|
|
(base32 "1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mice" ,r-mice)
|
|
("r-pscl" ,r-pscl)))
|
|
(home-page "https://cran.r-project.org/web/packages/accelmissing/")
|
|
(synopsis "Missing value imputation for accelerometer data")
|
|
(description
|
|
"This package provides a statistical method to impute the missing values in
|
|
accelerometer data. The methodology includes both parametric and
|
|
semi-parametric multiple imputations under the zero-inflated Poisson lognormal
|
|
model. It also provides multiple functions to preprocess the accelerometer data
|
|
previous to the missing data imputation. These include detecting the wearing
|
|
and the non-wearing time, selecting valid days and subjects, and creating plots.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-mhsmm
|
|
(package
|
|
(name "r-mhsmm")
|
|
(version "0.4.16")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mhsmm" version))
|
|
(sha256
|
|
(base32 "009dj0zkj1zry7jr9hf4cknb686z50a2l967if64xm0dvjmp7dgs"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
|
|
(home-page "https://github.com/jaredo/mhsmm/")
|
|
(synopsis "Inference for hidden Markov and semi-Markov models")
|
|
(description
|
|
"The @code{r-mhsmm} package implements estimation and prediction methods for
|
|
hidden Markov and semi-Markov models for multiple observation sequences. Such
|
|
techniques are of interest when observed data is thought to be dependent on some
|
|
unobserved (or hidden) state. Also, this package is suitable for equidistant
|
|
time series data, with multivariate and/or missing data. Allows user defined
|
|
emission distributions.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-nleqslv
|
|
(package
|
|
(name "r-nleqslv")
|
|
(version "3.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nleqslv" version))
|
|
(sha256
|
|
(base32 "1v9znvncyigw9r25wx2ma0b7ib179b488dl0qsrhp5zrcz7mcjgm"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/nleqslv/")
|
|
(synopsis "Solve systems of nonlinear equations")
|
|
(description
|
|
"The @code{r-nleqslv} package solves a system of nonlinear equations using a
|
|
Broyden or a Newton method with a choice of global strategies such as line
|
|
search and trust region. There are options for using a numerical or user
|
|
supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a
|
|
singular or ill-conditioned Jacobian.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-physicalactivity
|
|
(package
|
|
(name "r-physicalactivity")
|
|
(version "0.2-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "PhysicalActivity" version))
|
|
(sha256
|
|
(base32 "14z6plgwyr46vs9m997rvlz8sdglfs9g087an8668zqkzzs2w4ln"))))
|
|
(properties
|
|
`((upstream-name . "PhysicalActivity")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/PhysicalActivity/")
|
|
(synopsis "Procesing accelerometer data for physical activity measurement")
|
|
(description
|
|
"This @code{r-physicalactivity} package provides a function @code{wearingMarking}
|
|
for classification of monitor wear and nonwear time intervals in accelerometer
|
|
data collected to assess physical activity. The package also contains functions
|
|
for making plots of accelerometer data and obtaining the summary of various
|
|
information including daily monitor wear time and the mean monitor wear time
|
|
during valid days. The revised package version 0.2-1 improved the functions
|
|
regarding speed, robustness and add better support for time zones and daylight
|
|
saving. In addition, several functions were added:
|
|
@enumerate
|
|
@item the @code{markDelivery} can classify days for ActiGraph delivery by mail;
|
|
@item the @code{markPAI} can categorize physical activity intensity level based
|
|
on user-defined cut-points of accelerometer counts.
|
|
@end enumerate
|
|
It also supports importing ActiGraph (AGD) files with @code{readActigraph} and
|
|
@code{queryActigraph} functions.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-acc
|
|
(package
|
|
(name "r-acc")
|
|
(version "1.3.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "acc" version))
|
|
(sha256
|
|
(base32 "1ii2vm47djxbixa75h690q1s2f9m9x6i8nkygik93j6dayr6kr1m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-circlize" ,r-circlize)
|
|
("r-dbi" ,r-dbi)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-iterators" ,r-iterators)
|
|
("r-mhsmm" ,r-mhsmm)
|
|
("r-nleqslv" ,r-nleqslv)
|
|
("r-physicalactivity" ,r-physicalactivity)
|
|
("r-plyr" ,r-plyr)
|
|
("r-r-utils" ,r-r-utils)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)
|
|
("r-rsqlite" ,r-rsqlite)
|
|
("r-zoo" ,r-zoo)))
|
|
(home-page "https://cran.r-project.org/web/packages/acc/")
|
|
(synopsis "Exploring accelerometer data")
|
|
(description
|
|
"This package processes accelerometer data from uni-axial and tri-axial devices
|
|
and generates data summaries. Also, includes functions to plot, analyze, and
|
|
simulate accelerometer data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rbenchmark
|
|
(package
|
|
(name "r-rbenchmark")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rbenchmark" version))
|
|
(sha256
|
|
(base32 "010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rbenchmark/")
|
|
(synopsis "Benchmarking routine for R")
|
|
(description
|
|
"This @code{r-rbenchmark} package is inspired by the Perl module Benchmark,
|
|
and is intended to facilitate benchmarking of arbitrary R code. The library
|
|
consists of just one function, benchmark, which is a simple wrapper around
|
|
system.time. Given a specification of the benchmarking process (counts of
|
|
replications, evaluation environment) and an arbitrary number of expressions,
|
|
benchmark evaluates each of the expressions in the specified environment,
|
|
replicating the evaluation as many times as specified, and returning the results
|
|
conveniently wrapped into a data frame.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-mitools
|
|
(package
|
|
(name "r-mitools")
|
|
(version "2.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mitools" version))
|
|
(sha256
|
|
(base32
|
|
"0c2x2n1p53lcw0vx4vmy5j7m2f95i7g2iwbryl89imr99rvz617j"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-dbi" ,r-dbi)))
|
|
(home-page "https://cran.r-project.org/web/packages/mitools/")
|
|
(synopsis "Tools for multiple imputation of missing data")
|
|
(description
|
|
"This package provides tools to perform analyses and combine results from
|
|
multiple-imputation datasets.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-magick
|
|
(package
|
|
(name "r-magick")
|
|
(version "2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "magick" version))
|
|
(sha256
|
|
(base32
|
|
"18y465325mhf48x2jn3jz9khwq1z2aj13wfbdkv8k3hln1sd572m"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("imagemagick" ,imagemagick)
|
|
("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-curl" ,r-curl)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "https://github.com/ropensci/magick")
|
|
(synopsis "Advanced graphics and image-processing in R")
|
|
(description
|
|
"This package provides bindings to ImageMagick, a comprehensive image
|
|
processing library. It supports many common formats (PNG, JPEG, TIFF, PDF,
|
|
etc.) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All
|
|
operations are vectorized via the Magick++ STL meaning they operate either on
|
|
a single frame or a series of frames for working with layers, collages, or
|
|
animation. In RStudio, images are automatically previewed when printed to the
|
|
console, resulting in an interactive editing environment.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-survey
|
|
(package
|
|
(name "r-survey")
|
|
(version "3.36")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "survey" version))
|
|
(sha256
|
|
(base32
|
|
"0xclsy4ram4k48vzh5m5bpmknnpwxnss85v73s4czsjj5ffjxwwh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-matrix" ,r-matrix)
|
|
("r-minqa" ,r-minqa)
|
|
("r-mitools" ,r-mitools)
|
|
("r-numderiv" ,r-numderiv)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "http://r-survey.r-forge.r-project.org/survey/")
|
|
(synopsis "Analysis of complex survey samples")
|
|
(description
|
|
"This package provides tools for the analysis of complex survey samples.
|
|
The provided features include: summary statistics, two-sample tests, rank
|
|
tests, generalised linear models, cumulative link models, Cox models,
|
|
loglinear models, and general maximum pseudolikelihood estimation for
|
|
multistage stratified, cluster-sampled, unequally weighted survey samples;
|
|
variances by Taylor series linearisation or replicate weights;
|
|
post-stratification, calibration, and raking; two-phase subsampling designs;
|
|
graphics; PPS sampling without replacement; principal components, and factor
|
|
analysis.")
|
|
;; Either version of the GPL.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-dvmisc
|
|
(package
|
|
(name "r-dvmisc")
|
|
(version "1.1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dvmisc" version))
|
|
(sha256
|
|
(base32 "0x391pxg5mqgp5xxc8qwhwxky8ds7d9gr9iwmsb12c92kxfk00bv"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cubature" ,r-cubature)
|
|
("r-data-table" ,r-data-table)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-mass" ,r-mass)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-pracma" ,r-pracma)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rbenchmark" ,r-rbenchmark)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-survey" ,r-survey)))
|
|
(home-page "https://cran.r-project.org/web/packages/dvmisc/")
|
|
(synopsis "Faster computation of common statistics and miscellaneous functions")
|
|
(description
|
|
"This package implements faster versions of base R functions (e.g. mean, standard
|
|
deviation, covariance, weighted mean), mostly written in C++, along with
|
|
miscellaneous functions for various purposes (e.g. create the histogram with
|
|
fitted probability density function or probability mass function curve, create
|
|
the body mass index groups, assess the linearity assumption in logistic
|
|
regression).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-accelerometry
|
|
(package
|
|
(name "r-accelerometry")
|
|
(version "3.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "accelerometry" version))
|
|
(sha256
|
|
(base32 "13xzrwhr4i1nj9c8vrmfdg2rmrc8n446iihcyxmy99sm99hpzyip"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dvmisc" ,r-dvmisc)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/accelerometry/")
|
|
(synopsis "Functions for processing accelerometer data")
|
|
(description
|
|
"This package provides a collection of functions that perform operations on
|
|
time-series accelerometer data, such as identify the non-wear time, flag minutes
|
|
that are part of an activity bout, and find the maximum 10-minute average count
|
|
value. The functions are generally very flexible, allowing for a variety of
|
|
algorithms to be implemented.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-absim
|
|
(package
|
|
(name "r-absim")
|
|
(version "0.2.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "AbSim" version))
|
|
(sha256
|
|
(base32 "16ddjk8b6xw80ch4jis1y751i9561wdxh0gifbf15qiz3vjckq8m"))))
|
|
(properties `((upstream-name . "AbSim")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ape" ,r-ape)
|
|
("r-powerlaw" ,r-powerlaw)))
|
|
(home-page "https://cran.r-project.org/web/packages/AbSim/")
|
|
(synopsis "Time resolved simulations of antibody repertoires")
|
|
(description
|
|
"This package provides simulation methods for the evolution of antibody repertoires.
|
|
The heavy and light chain variable region of both human and C57BL/6 mice can
|
|
be simulated in a time-dependent fashion. Both single lineages using one set of
|
|
V-, D-, and J-genes or full repertoires can be simulated. The algorithm begins
|
|
with an initial V-D-J recombination event, starting the first phylogenetic tree.
|
|
Upon completion, the main loop of the algorithm begins, with each iteration
|
|
representing one simulated time step. Various mutation events are possible at
|
|
each time step, contributing to a diverse final repertoire.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-quic
|
|
(package
|
|
(name "r-quic")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "QUIC" version))
|
|
(sha256
|
|
(base32 "021bp9xbaih60qmss015ycblbv6d1dvb1z89y93zpqqnc2qhpv3c"))))
|
|
(properties `((upstream-name . "QUIC")))
|
|
(build-system r-build-system)
|
|
(home-page "https://www.cs.utexas.edu/users/sustik/QUIC/")
|
|
(synopsis "Regularized sparse inverse covariance matrix estimation")
|
|
(description
|
|
"This package implements the regularized Gaussian maximum likelihood
|
|
estimation of the inverse of a covariance matrix. It uses Newton's method and
|
|
coordinate descent to solve the regularized inverse covariance matrix
|
|
estimation problem.")
|
|
;; The project home page states that the release is under GPLv3 or later.
|
|
;; The CRAN page only says GPL-3.
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-abundant
|
|
(package
|
|
(name "r-abundant")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "abundant" version))
|
|
(sha256
|
|
(base32 "1m76qdmqvwpgm0sihazi2dna7cgsz9rljal18vgffb5wamwmg9k7"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-quic" ,r-quic)))
|
|
(home-page "https://cran.r-project.org/web/packages/abundant/")
|
|
(synopsis "Abundant regression and high-dimensional principal fitted components")
|
|
(description
|
|
"This package provides tools to fit and predict with the high-dimensional
|
|
principal fitted components model. This model is described by Cook, Forzani,
|
|
and Rothman (2012) @url{doi:10.1214/11-AOS962}.")
|
|
;; The DESCRIPTION file states GPL-2, but since it directly depends on a
|
|
;; GPLv3+ package (QUIC) this likely means GPLv2+.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ac3net
|
|
(package
|
|
(name "r-ac3net")
|
|
(version "1.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Ac3net" version))
|
|
(sha256
|
|
(base32 "1ns4n0xxz6p34c11bj0k7nzgmyqr9mis2b0g5nfz37dbikndyqyz"))))
|
|
(properties `((upstream-name . "Ac3net")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-data-table" ,r-data-table)))
|
|
(home-page "https://cran.r-project.org/web/packages/Ac3net/")
|
|
(synopsis "Inferring directional conservative causal core gene networks")
|
|
(description "This package infers directional Conservative causal core
|
|
(gene) networks (C3NET). This is a version of the algorithm C3NET with
|
|
directional network.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-aca
|
|
(package
|
|
(name "r-aca")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ACA" version))
|
|
(sha256
|
|
(base32 "1i3hm27nvnkvc39xlh0d1blq8q0q02czmvgi3cazmjx3jvxay0vq"))))
|
|
(properties `((upstream-name . "ACA")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/ACA/")
|
|
(synopsis "Abrupt change-point or aberration detection in point series")
|
|
(description
|
|
"This package offers an interactive function for the detection of breakpoints in
|
|
series.")
|
|
;; Any version of the GPL
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-acceptancesampling
|
|
(package
|
|
(name "r-acceptancesampling")
|
|
(version "1.0-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "AcceptanceSampling" version))
|
|
(sha256
|
|
(base32 "1z3rmln63ki2kik9kinbwr9qhr32ggbmh4mm3xqy6di119n47ca9"))))
|
|
(properties
|
|
`((upstream-name . "AcceptanceSampling")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/AcceptanceSampling/")
|
|
(synopsis "Creation and evaluation of acceptance sampling plans")
|
|
(description
|
|
"This @code{r-acceptancesampling} provides functionality for creating and evaluating
|
|
acceptance sampling plans. Acceptance sampling is a methodology commonly used
|
|
in quality control and improvement. International standards of acceptance
|
|
sampling provide sampling plans for specific circumstances. The aim of this
|
|
package is to provide an easy-to-use interface to visualize single, double or
|
|
multiple sampling plans. In addition, methods have been provided to enable the
|
|
user to assess sampling plans against pre-specified levels of performance, as
|
|
measured by the probability of acceptance for a given level of quality in the
|
|
lot.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-acclma
|
|
(package
|
|
(name "r-acclma")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ACCLMA" version))
|
|
(sha256
|
|
(base32 "1na27sp18fq12gp6vxgqw1ffsz2yi1d8xvrxbrzx5g1kqxrayy0v"))))
|
|
(properties `((upstream-name . "ACCLMA")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/ACCLMA/")
|
|
(synopsis "ACC & LMA graph plotting")
|
|
(description
|
|
"This package contains a function that imports data from a @acronym{CSV,
|
|
Comma-Separated Values} file, or uses manually entered data from the format (x,
|
|
y, weight) and plots the appropriate @acronym{ACC, Absolute Concentration
|
|
Curve} vs @acronym{LOI, Line of Independence} graph and
|
|
@acronym{LMA, @acronym{LOI} Minus @acronym{ACC}} graph. The main
|
|
function is @code{plotLMA} (source file, header) that takes a data set and plots the
|
|
appropriate @acronym{LMA} and @acronym{ACC} graphs. If no source file (a
|
|
string) was passed, a manual data entry window is opened. The header parameter
|
|
indicates by TRUE/FALSE (false by default) if the source @acronym{CSV} file has
|
|
a header row or not. The dataset should contain only one independent variable
|
|
(x) and one dependent variable (y) and can contain a weight for each
|
|
observation.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-aspi
|
|
(package
|
|
(name "r-aspi")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "aspi" version))
|
|
(sha256
|
|
(base32 "0rhvxw243vvdv3hxa6pi343gcjc2cbxq1jzqirl9k1l4i3897l87"))))
|
|
(build-system r-build-system)
|
|
(home-page
|
|
"https://cran.r-project.org/web/packages/aspi/")
|
|
(synopsis
|
|
"Analysis of symmetry of parasitic infections")
|
|
(description
|
|
"This package provides tools for the analysis and visualization of bilateral
|
|
asymmetry in parasitic infections.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-sandwich
|
|
(package
|
|
(name "r-sandwich")
|
|
(version "2.5-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sandwich" version))
|
|
(sha256
|
|
(base32
|
|
"1mk685b9wq7k566pbml52rj96i5h6b3vf215k9picgmq296nzvyv"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-zoo" ,r-zoo)))
|
|
(home-page "https://cran.r-project.org/web/packages/sandwich/")
|
|
(synopsis "Robust Covariance Matrix Estimators")
|
|
(description
|
|
"This package provides model-robust standard error estimators for
|
|
cross-sectional, time series, clustered, panel, and longitudinal data.")
|
|
;; Either version of the license.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-th-data
|
|
(package
|
|
(name "r-th-data")
|
|
(version "1.0-10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "TH.data" version))
|
|
(sha256
|
|
(base32
|
|
"0mgz7aj2d9abbmdr65zgmg1ddp3fdbs3mfj83r5xadh5ldkir2k1"))))
|
|
(properties `((upstream-name . "TH.data")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://cran.r-project.org/web/packages/TH.data/")
|
|
(synopsis "Shared data sets")
|
|
(description
|
|
"This package contains supporting data sets that are used in other
|
|
packages maintained by Torsten Hothorn.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-multcomp
|
|
(package
|
|
(name "r-multcomp")
|
|
(version "1.4-10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "multcomp" version))
|
|
(sha256
|
|
(base32
|
|
"1kzmdn9jmz5bmhf3wsfr12ljbasmwsgcsfdia52k0bi6q0swdg19"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-codetools" ,r-codetools)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-sandwich" ,r-sandwich)
|
|
("r-survival" ,r-survival)
|
|
("r-th-data" ,r-th-data)))
|
|
(home-page "https://cran.r-project.org/web/packages/multcomp/")
|
|
(synopsis "Simultaneous inference in general parametric models")
|
|
(description
|
|
"Simultaneous tests and confidence intervals for general linear
|
|
hypotheses in parametric models, including linear, generalized linear, linear
|
|
mixed effects, and survival models. The package includes demos reproducing
|
|
analyzes presented in the book \"Multiple Comparisons Using R\" (Bretz,
|
|
Hothorn, Westfall, 2010, CRC Press).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-emmeans
|
|
(package
|
|
(name "r-emmeans")
|
|
(version "1.3.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "emmeans" version))
|
|
(sha256
|
|
(base32
|
|
"0zyink60132f2a0491a94bf67hq8a0bwmw5wn19l0ms8iyiml9d2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-estimability" ,r-estimability)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-numderiv" ,r-numderiv)
|
|
("r-plyr" ,r-plyr)
|
|
("r-xtable" ,r-xtable)))
|
|
(home-page "https://github.com/rvlenth/emmeans")
|
|
(synopsis "Estimated marginal means, aka least-squares means")
|
|
(description
|
|
"This package provides tools to obtain @dfn{estimated marginal
|
|
means} (EMMs) for many linear, generalized linear, and mixed models. It can
|
|
be used to compute contrasts or linear functions of EMMs, trends, and
|
|
comparisons of slopes.")
|
|
;; Either version of the license.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-pwr
|
|
(package
|
|
(name "r-pwr")
|
|
(version "1.2-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pwr" version))
|
|
(sha256
|
|
(base32
|
|
"0r5g781lr677vp3zyhgmi7r68c87l8gd05l1s3ffnxgn5wf043sm"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr)))
|
|
(home-page "https://github.com/heliosdrm/pwr")
|
|
(synopsis "Basic functions for power analysis")
|
|
(description
|
|
"This package provides power analysis functions along the lines of
|
|
Cohen (1988).")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-libcoin
|
|
(package
|
|
(name "r-libcoin")
|
|
(version "1.0-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "libcoin" version))
|
|
(sha256
|
|
(base32
|
|
"1i893ij9vkmc4y721npw1s3prmmcs2da5vf3ajm0j8ccmfhbmp4i"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mvtnorm" ,r-mvtnorm)))
|
|
(home-page "https://cran.r-project.org/web/packages/libcoin")
|
|
(synopsis "Linear test statistics for permutation inference")
|
|
(description
|
|
"This package provides basic infrastructure for linear test statistics
|
|
and permutation inference in the framework of Strasser and Weber (1999).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-coin
|
|
(package
|
|
(name "r-coin")
|
|
(version "1.3-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "coin" version))
|
|
(sha256
|
|
(base32
|
|
"1y0yl4mjaxca0jqz53sv1gcpdg89m099rq61iszxvpx7w0vvpkmd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-libcoin" ,r-libcoin)
|
|
("r-matrixstats" ,r-matrixstats)
|
|
("r-modeltools" ,r-modeltools)
|
|
("r-multcomp" ,r-multcomp)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "http://coin.r-forge.r-project.org")
|
|
(synopsis "Conditional inference procedures in a permutation test framework")
|
|
(description
|
|
"This package provides conditional inference procedures for the general
|
|
independence problem including two-sample, K-sample (non-parametric ANOVA),
|
|
correlation, censored, ordered and multivariate problems.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-bayesplot
|
|
(package
|
|
(name "r-bayesplot")
|
|
(version "1.7.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bayesplot" version))
|
|
(sha256
|
|
(base32
|
|
"0h23sbfny2hcipvvfhq5aiwdh1vanizn7f8lpb9kffypxhcd7v7w"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("pandoc" ,ghc-pandoc)
|
|
("pandoc-citeproc" ,ghc-pandoc-citeproc)))
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-ggridges" ,r-ggridges)
|
|
("r-glue" ,r-glue)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyselect" ,r-tidyselect)))
|
|
(home-page "http://mc-stan.org/bayesplot")
|
|
(synopsis "Plotting for Bayesian models")
|
|
(description
|
|
"This package provides plotting functions for posterior analysis, model
|
|
checking, and MCMC diagnostics. The package is designed not only to provide
|
|
convenient functionality for users, but also a common set of functions that
|
|
can be easily used by developers working on a variety of R packages for
|
|
Bayesian modeling.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-tmb
|
|
(package
|
|
(name "r-tmb")
|
|
(version "1.7.15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "TMB" version))
|
|
(sha256
|
|
(base32
|
|
"1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"))))
|
|
(properties `((upstream-name . "TMB")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)
|
|
("r-rcppeigen" ,r-rcppeigen)))
|
|
(home-page "http://tmb-project.org")
|
|
(synopsis "Template model builder: a general random effect tool")
|
|
(description
|
|
"With this tool, a user should be able to quickly implement complex
|
|
random effect models through simple C++ templates. The package combines
|
|
@code{CppAD} (C++ automatic differentiation), @code{Eigen} (templated
|
|
matrix-vector library) and @code{CHOLMOD} (sparse matrix routines available
|
|
from R) to obtain an efficient implementation of the applied Laplace
|
|
approximation with exact derivatives. Key features are: Automatic sparseness
|
|
detection, parallelism through BLAS and parallel user templates.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-sjstats
|
|
(package
|
|
(name "r-sjstats")
|
|
(version "0.17.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sjstats" version))
|
|
(sha256
|
|
(base32
|
|
"1x9ybvz84vgaabmqp4z6crbv5q6kqjg6msk1spbr11zx9dbj06ca"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bayestestr" ,r-bayestestr)
|
|
("r-broom" ,r-broom)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-emmeans" ,r-emmeans)
|
|
("r-insight" ,r-insight)
|
|
("r-lme4" ,r-lme4)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-mass" ,r-mass)
|
|
("r-modelr" ,r-modelr)
|
|
("r-performance" ,r-performance)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-sjlabelled" ,r-sjlabelled)
|
|
("r-sjmisc" ,r-sjmisc)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/strengejacke/sjstats")
|
|
(synopsis "Functions for common statistical computations")
|
|
(description
|
|
"This package provides a collection of convenient functions for common
|
|
statistical computations, which are not directly provided by R's @code{base}
|
|
or @code{stats} packages. This package aims at providing, first, shortcuts
|
|
for statistical measures, which otherwise could only be calculated with
|
|
additional effort. Second, these shortcut functions are generic, and can be
|
|
applied not only to vectors, but also to other objects as well. The focus of
|
|
most functions lies on summary statistics or fit measures for regression
|
|
models, including generalized linear models, mixed effects models and Bayesian
|
|
models.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-glmmtmb
|
|
(package
|
|
(name "r-glmmtmb")
|
|
(version "0.2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "glmmTMB" version))
|
|
(sha256
|
|
(base32
|
|
"035hkywa37bz555fv6znxd4hfcs5w884365wfnwk4jx5vann4vvb"))))
|
|
(properties `((upstream-name . "glmmTMB")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lme4" ,r-lme4)
|
|
("r-matrix" ,r-matrix)
|
|
("r-nlme" ,r-nlme)
|
|
("r-rcppeigen" ,r-rcppeigen)
|
|
("r-tmb" ,r-tmb)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; for vignettes
|
|
(home-page "https://github.com/glmmTMB")
|
|
(synopsis "Generalized linear mixed models")
|
|
(description
|
|
"Fit linear and generalized linear mixed models with various extensions,
|
|
including zero-inflation. The models are fitted using maximum likelihood
|
|
estimation via the Template Model Builder. Random effects are assumed to be
|
|
Gaussian on the scale of the linear predictor and are integrated out using the
|
|
Laplace approximation. Gradients are calculated using automatic
|
|
differentiation.")
|
|
(license license:agpl3+)))
|
|
|
|
(define-public r-bayestestr
|
|
(package
|
|
(name "r-bayestestr")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bayestestR" version))
|
|
(sha256
|
|
(base32
|
|
"0729j4fdxkkvmh99nmny38dywidzgmipdjqbi2ljxygsn4jg7ysy"))))
|
|
(properties `((upstream-name . "bayestestR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-insight" ,r-insight)))
|
|
(home-page "https://github.com/easystats/bayestestR")
|
|
(synopsis "Describe Bayesian models and posterior distributions")
|
|
(description
|
|
"This package provides utilities to understand and describe posterior
|
|
distributions and Bayesian models. It includes point-estimates such as
|
|
@dfn{Maximum A Posteriori} (MAP), measures of dispersion such as @dfn{Highest
|
|
Density Interval} (HDI), and indices used for null-hypothesis testing (such as
|
|
ROPE percentage and pd).")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-performance
|
|
(package
|
|
(name "r-performance")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "performance" version))
|
|
(sha256
|
|
(base32
|
|
"1pzd6z7i1jxr2xi1shg3d0bxlbpmjl7kpmwgjnfys6syv57znd1z"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bayestestr" ,r-bayestestr)
|
|
("r-insight" ,r-insight)))
|
|
(home-page "https://easystats.github.io/performance/")
|
|
(synopsis "Assessment of regression models performance")
|
|
(description
|
|
"This package provides utilities for computing measures to assess model
|
|
quality, which are not directly provided by R's @code{base} or @code{stats}
|
|
packages. These include e.g. measures like r-squared, intraclass correlation
|
|
coefficient, root mean squared error or functions to check models for
|
|
overdispersion, singularity or zero-inflation and more. Functions apply to a
|
|
large variety of regression models, including generalized linear models, mixed
|
|
effects models and Bayesian models.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ggeffects
|
|
(package
|
|
(name "r-ggeffects")
|
|
(version "0.10.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggeffects" version))
|
|
(sha256
|
|
(base32
|
|
"0gmqzjk8k8q6j4q6asv9f3b1fv4qrw5w8xa48ha3y98shzm5np9k"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-insight" ,r-insight)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-mass" ,r-mass)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-scales" ,r-scales)
|
|
("r-sjlabelled" ,r-sjlabelled)
|
|
("r-sjmisc" ,r-sjmisc)))
|
|
(home-page "https://github.com/strengejacke/ggeffects")
|
|
(synopsis "Create tidy data frames of marginal effects for ggplot")
|
|
(description
|
|
"This package provides tools to compute marginal effects from statistical
|
|
models and return the result as tidy data frames. These data frames are ready
|
|
to use with the @code{ggplot2} package. Marginal effects can be calculated
|
|
for many different models. Interaction terms, splines and polynomial terms
|
|
are also supported. The two main functions are @code{ggpredict()} and
|
|
@code{ggeffect()}. There is a generic @code{plot()} method to plot the
|
|
results using @code{ggplot2}.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-sjplot
|
|
(package
|
|
(name "r-sjplot")
|
|
(version "2.6.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sjPlot" version))
|
|
(sha256
|
|
(base32
|
|
"0h1mkmp5mrkbf7y3zh6m4cnm737cpg1m5si0lrmal7j2ixqicwjy"))))
|
|
(properties `((upstream-name . "sjPlot")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bayestestr" ,r-bayestestr)
|
|
("r-broom" ,r-broom)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-forcats" ,r-forcats)
|
|
("r-ggeffects" ,r-ggeffects)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-glmmtmb" ,r-glmmtmb)
|
|
("r-insight" ,r-insight)
|
|
("r-knitr" ,r-knitr)
|
|
("r-lme4" ,r-lme4)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-mass" ,r-mass)
|
|
("r-modelr" ,r-modelr)
|
|
("r-nlme" ,r-nlme)
|
|
("r-performance" ,r-performance)
|
|
("r-psych" ,r-psych)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-scales" ,r-scales)
|
|
("r-sjlabelled" ,r-sjlabelled)
|
|
("r-sjmisc" ,r-sjmisc)
|
|
("r-sjstats" ,r-sjstats)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://strengejacke.github.io/sjPlot/")
|
|
(synopsis "Data visualization for statistics in social science")
|
|
(description
|
|
"This package represents a collection of plotting and table output
|
|
functions for data visualization. Results of various statistical
|
|
analyses (that are commonly used in social sciences) can be visualized using
|
|
this package, including simple and cross tabulated frequencies, histograms,
|
|
box plots, (generalized) linear models, mixed effects models, principal
|
|
component analysis and correlation matrices, cluster analyses, scatter plots,
|
|
stacked scales, effects plots of regression models (including interaction
|
|
terms) and much more. This package supports labelled data.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ini
|
|
(package
|
|
(name "r-ini")
|
|
(version "0.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ini" version))
|
|
(sha256
|
|
(base32
|
|
"04yqij344dwm0xqgara8xia42mlmij3i8711qbb5534w05a1l6bv"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/dvdscripter/ini")
|
|
(synopsis "Read and write configuration files")
|
|
(description
|
|
"This package provides tools to parse simple @code{.ini} configuration
|
|
files to an structured list. Users can manipulate this resulting list with
|
|
@code{lapply()} functions. This same structured list can be used to write
|
|
back to file after modifications.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-gh
|
|
(package
|
|
(name "r-gh")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gh" version))
|
|
(sha256
|
|
(base32
|
|
"1llinfajb0g7006jd2w1hpskxpmkjhnqarcjb71r1qvsccb2ph7k"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-httr" ,r-httr)
|
|
("r-ini" ,r-ini)
|
|
("r-jsonlite" ,r-jsonlite)))
|
|
(home-page "https://github.com/r-lib/gh#readme")
|
|
(synopsis "Access the GitHub API via R")
|
|
(description
|
|
"This package provides a minimal R client to access the GitHub API.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-fs
|
|
(package
|
|
(name "r-fs")
|
|
(version "1.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fs" version))
|
|
(sha256
|
|
(base32
|
|
"1g26rgx13dzigp2vrlld6h28q33lwbax97zvwdrq2pc3iz54v4yn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "http://fs.r-lib.org")
|
|
(synopsis "Cross-platform file system operations based on libuv")
|
|
(description
|
|
"This package provides a cross-platform interface to file system
|
|
operations, built on top of the libuv C library.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-clisymbols
|
|
(package
|
|
(name "r-clisymbols")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "clisymbols" version))
|
|
(sha256
|
|
(base32
|
|
"1q7gi2zmykhzas9v8fdnbpdq7pzdcpbhim1yxvd2062l777g4j86"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/gaborcsardi/clisymbols")
|
|
(synopsis "Unicode symbols at the R prompt")
|
|
(description
|
|
"This package provides a small subset of Unicode symbols, that are useful
|
|
when building command line applications. They fall back to alternatives on
|
|
terminals that do not support Unicode.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-usethis
|
|
(package
|
|
(name "r-usethis")
|
|
(version "1.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "usethis" version))
|
|
(sha256
|
|
(base32
|
|
"0pn6ka3726psaqlx573g6nxi90apf0rn5m4k2lz1jr66xdc19sag"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-clipr" ,r-clipr)
|
|
("r-clisymbols" ,r-clisymbols)
|
|
("r-crayon" ,r-crayon)
|
|
("r-curl" ,r-curl)
|
|
("r-desc" ,r-desc)
|
|
("r-fs" ,r-fs)
|
|
("r-gh" ,r-gh)
|
|
("r-git2r" ,r-git2r)
|
|
("r-glue" ,r-glue)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-whisker" ,r-whisker)
|
|
("r-withr" ,r-withr)
|
|
("r-yaml" ,r-yaml)))
|
|
(home-page "https://github.com/r-lib/usethis")
|
|
(synopsis "Automate R package and project setup")
|
|
(description
|
|
"This package helps you to automate R package and project setup tasks
|
|
that are otherwise performed manually. This includes setting up unit testing,
|
|
test coverage, continuous integration, Git, GitHub integration, licenses,
|
|
Rcpp, RStudio projects, and more.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-sessioninfo
|
|
(package
|
|
(name "r-sessioninfo")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sessioninfo" version))
|
|
(sha256
|
|
(base32
|
|
"0j5f3l58fynxx3v0w62vqpii7miabszgljpja36xx9s8hikh8sqn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cli" ,r-cli)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/r-lib/sessioninfo#readme")
|
|
(synopsis "R session information")
|
|
(description
|
|
"This package provides tools to query and print information about the
|
|
current R session. It is similar to @code{utils::sessionInfo()}, but includes
|
|
more information about packages, and where they were installed from.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-remotes
|
|
(package
|
|
(name "r-remotes")
|
|
(version "2.0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "remotes" version))
|
|
(sha256
|
|
(base32
|
|
"1jbn4kjimcr82zv5lnqxqa2487a96vn6jxf7wc6gnpxr6k06d61p"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/r-lib/remotes#readme")
|
|
(synopsis "R package installation from remote repositories")
|
|
(description
|
|
"Download and install R packages stored in GitHub, BitBucket, or plain
|
|
subversion or git repositories. This package is a lightweight replacement of
|
|
the @code{install_*} functions in the @code{devtools} package. Indeed most of
|
|
the code was copied over from @code{devtools}.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-xopen
|
|
(package
|
|
(name "r-xopen")
|
|
(version "1.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xopen" version))
|
|
(sha256
|
|
(base32
|
|
"1vrvgdika1d63dwygynbv2wmd87ll8dji5dy89hj576n8hw601z2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-processx" ,r-processx)))
|
|
(home-page "https://github.com/r-lib/xopen#readme")
|
|
(synopsis "Open system files, URLs, anything")
|
|
(description
|
|
"This package provides a cross-platform solution to open files,
|
|
directories or URLs with their associated programs.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-rcmdcheck
|
|
(package
|
|
(name "r-rcmdcheck")
|
|
(version "1.3.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rcmdcheck" version))
|
|
(sha256
|
|
(base32
|
|
"1d4kzgfqy72r6b7bn1j4znyksrycgypx1jjvpv9lrmvn37mpkdhs"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-callr" ,r-callr)
|
|
("r-cli" ,r-cli)
|
|
("r-crayon" ,r-crayon)
|
|
("r-desc" ,r-desc)
|
|
("r-digest" ,r-digest)
|
|
("r-pkgbuild" ,r-pkgbuild)
|
|
("r-prettyunits" ,r-prettyunits)
|
|
("r-r6" ,r-r6)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-sessioninfo" ,r-sessioninfo)
|
|
("r-withr" ,r-withr)
|
|
("r-xopen" ,r-xopen)))
|
|
(home-page "https://github.com/r-Lib/rcmdcheck#readme")
|
|
(synopsis "Run R CMD check from R and capture results")
|
|
(description
|
|
"Run @code{R CMD check} from R programmatically, and capture the results
|
|
of the individual checks.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-rapportools
|
|
(package
|
|
(name "r-rapportools")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rapportools" version))
|
|
(sha256
|
|
(base32
|
|
"1sgv4sc737i12arh5dc3263kjsz3dzg06qihfmrqyax94mv2d01b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-pander" ,r-pander)
|
|
("r-plyr" ,r-plyr)
|
|
("r-reshape" ,r-reshape)))
|
|
(home-page "https://cran.r-project.org/web/packages/rapportools/")
|
|
(synopsis "Miscellaneous helper functions with sane defaults for reporting")
|
|
(description
|
|
"This package provides helper functions that act as wrappers to more
|
|
advanced statistical methods with the advantage of having sane defaults for
|
|
quick reporting.")
|
|
(license license:agpl3+)))
|
|
|
|
(define-public r-pander
|
|
(package
|
|
(name "r-pander")
|
|
(version "0.6.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pander" version))
|
|
(sha256
|
|
(base32
|
|
"1bd9sdghlsppmff18k5fg3i0visq9f4wc82rlhwq5m82bmgdgnyi"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://rapporter.github.io/pander")
|
|
(synopsis "Render R objects into Pandoc's markdown")
|
|
(description
|
|
"The main aim of the pander R package is to provide a minimal and easy
|
|
tool for rendering R objects into Pandoc's markdown. The package is also
|
|
capable of exporting/converting complex Pandoc documents (reports) in various
|
|
ways.")
|
|
;; This package is licensed under either the AGPLv3+ or the very rarely
|
|
;; used OSL 3.0.
|
|
(license license:agpl3+)))
|
|
|
|
(define-public r-summarytools
|
|
(package
|
|
(name "r-summarytools")
|
|
(version "0.9.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "summarytools" version))
|
|
(sha256
|
|
(base32
|
|
"1wfbkgvicaic37zgpr6zcm4a58yx43p59h0sqggdj44ncqs7147f"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-checkmate" ,r-checkmate)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-lubridate" ,r-lubridate)
|
|
("r-magick" ,r-magick)
|
|
("r-matrixstats" ,r-matrixstats)
|
|
("r-pander" ,r-pander)
|
|
("r-pryr" ,r-pryr)
|
|
("r-rapportools" ,r-rapportools)
|
|
("r-rcurl" ,r-rcurl)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/dcomtois/summarytools")
|
|
(synopsis "Tools to quickly and neatly summarize data")
|
|
(description
|
|
"This package provides tools for data frame summaries, cross-tabulations,
|
|
weight-enabled frequency tables and common univariate statistics in concise
|
|
tables available in a variety of formats (plain ASCII, Markdown and HTML). A
|
|
good point-of-entry for exploring data, both for experienced and new R
|
|
users.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-lsei
|
|
(package
|
|
(name "r-lsei")
|
|
(version "1.2-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lsei" version))
|
|
(sha256
|
|
(base32
|
|
"1xl06fb3is744pxlh42wx5hn1h0ab1k31wnmsmh0524kxzcyp0a7"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://www.stat.auckland.ac.nz/~yongwang")
|
|
(synopsis "Solve regression problems under equality/inequality constraints")
|
|
(description
|
|
"It contains functions that solve least squares linear regression
|
|
problems under linear equality/inequality constraints. Functions for solving
|
|
quadratic programming problems are also available, which transform such
|
|
problems into least squares ones first.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-npsurv
|
|
(package
|
|
(name "r-npsurv")
|
|
(version "0.4-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "npsurv" version))
|
|
(sha256
|
|
(base32
|
|
"1wq4c9yfha5azjhrn40iiqkshmvh611sa90jp3lh82n4bl9zfk20"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lsei" ,r-lsei)))
|
|
(home-page "https://www.stat.auckland.ac.nz/~yongwang")
|
|
(synopsis "Nonparametric survival analysis")
|
|
(description
|
|
"This package contains functions for non-parametric survival analysis of
|
|
exact and interval-censored observations.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-clusteval
|
|
(package
|
|
(name "r-clusteval")
|
|
(version "0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "clusteval" version))
|
|
(sha256
|
|
(base32
|
|
"1ld0bdl4fy8dsfzm3k7a37cyxc6pfc9qs31x4pxd3z5rslghz7rj"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mvtnorm" ,r-mvtnorm)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/clusteval/")
|
|
(synopsis "Evaluation of clustering algorithms")
|
|
(description
|
|
"This R package provides a suite of tools to evaluate clustering
|
|
algorithms, clusterings, and individual clusters.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-tweedie
|
|
(package
|
|
(name "r-tweedie")
|
|
(version "2.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tweedie" version))
|
|
(sha256
|
|
(base32
|
|
"10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/tweedie/")
|
|
(synopsis "Evaluation of Tweedie exponential family models")
|
|
(description
|
|
"Maximum likelihood computations for Tweedie families, including the
|
|
series expansion (Dunn and Smyth, 2005; <doi10.1007/s11222-005-4070-y>) and
|
|
the Fourier inversion (Dunn and Smyth, 2008; <doi:10.1007/s11222-007-9039-6>),
|
|
and related methods.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rcppgsl
|
|
(package
|
|
(name "r-rcppgsl")
|
|
(version "0.3.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppGSL" version))
|
|
(sha256
|
|
(base32
|
|
"16pdapq31729db53agnb48jkvdm97167n3bigy5zazc3q3isis1m"))))
|
|
(properties `((upstream-name . "RcppGSL")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("gsl" ,gsl)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; for vignettes
|
|
(home-page "https://cran.r-project.org/web/packages/RcppGSL/")
|
|
(synopsis "Rcpp integration for GSL vectors and matrices")
|
|
(description
|
|
"The GNU Scientific Library (or GSL) is a collection of numerical
|
|
routines for scientific computing. It is particularly useful for C and C++
|
|
programs as it provides a standard C interface to a wide range of mathematical
|
|
routines. There are over 1000 functions in total with an extensive test
|
|
suite. The RcppGSL package provides an easy-to-use interface between GSL data
|
|
structures and R using concepts from Rcpp which is itself a package that eases
|
|
the interfaces between R and C++.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-mvabund
|
|
(package
|
|
(name "r-mvabund")
|
|
(version "4.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mvabund" version))
|
|
(sha256
|
|
(base32
|
|
"0la935gsiryfc0zixxr1dqj0av271x96pqxbi3bp6dksbw5gm68k"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcppgsl" ,r-rcppgsl)
|
|
("r-statmod" ,r-statmod)
|
|
("r-tweedie" ,r-tweedie)))
|
|
(home-page "https://cran.r-project.org/web/packages/mvabund/")
|
|
(synopsis "Statistical methods for analysing multivariate abundance data")
|
|
(description
|
|
"This package provides a set of tools for displaying, modeling and
|
|
analysing multivariate abundance data in community ecology.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public r-afex
|
|
(package
|
|
(name "r-afex")
|
|
(version "0.23-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "afex" version))
|
|
(sha256
|
|
(base32
|
|
"0yv4s7461swn0116y4wq9v139p1br5rr6hhnq1cmkbvybmwj2vp7"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-car" ,r-car)
|
|
("r-lme4" ,r-lme4)
|
|
("r-lmertest" ,r-lmertest)
|
|
("r-pbkrtest" ,r-pbkrtest)
|
|
("r-reshape2" ,r-reshape2)))
|
|
(home-page "https://afex.singmann.science/")
|
|
(synopsis "Analysis of factorial experiments")
|
|
(description
|
|
"This package provides convenience functions for analyzing factorial
|
|
experiments using ANOVA or mixed models.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-lmertest
|
|
(package
|
|
(name "r-lmertest")
|
|
(version "3.1-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lmerTest" version))
|
|
(sha256
|
|
(base32
|
|
"1nkz8cmxa5yb8q4i65bmhnn5pd4bhwcyjplyscynb24z3f64xp9b"))))
|
|
(properties `((upstream-name . "lmerTest")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-lme4" ,r-lme4)
|
|
("r-mass" ,r-mass)
|
|
("r-numderiv" ,r-numderiv)))
|
|
(home-page "https://github.com/runehaubo/lmerTestR")
|
|
(synopsis "Tests in linear mixed effects models")
|
|
(description
|
|
"This package provides p-values in type I, II or III anova and summary
|
|
tables for @code{lmer} model fits via Satterthwaite's degrees of freedom
|
|
method. A Kenward-Roger method is also available via the @code{pbkrtest}
|
|
package. Model selection methods include step, drop1 and anova-like tables
|
|
for random effects (ranova). Methods for Least-Square means (LS-means) and
|
|
tests of linear contrasts of fixed effects are also available.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-r2glmm
|
|
(package
|
|
(name "r-r2glmm")
|
|
(version "0.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "r2glmm" version))
|
|
(sha256
|
|
(base32
|
|
"0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-afex" ,r-afex)
|
|
("r-data-table" ,r-data-table)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-lmertest" ,r-lmertest)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-pbkrtest" ,r-pbkrtest)))
|
|
(home-page "https://github.com/bcjaeger/r2glmm")
|
|
(synopsis "Compute R squared for mixed (multilevel) models")
|
|
(description
|
|
"This package computes model and semi partial R squared with confidence
|
|
limits for the linear and generalized linear mixed model (LMM and GLMM). The
|
|
R squared measure from L. J. Edwards et al. (2008) is extended to the GLMM
|
|
using @dfn{penalized quasi-likelihood} (PQL) estimation (see Jaeger et
|
|
al. (2016)).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-weights
|
|
(package
|
|
(name "r-weights")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "weights" version))
|
|
(sha256
|
|
(base32
|
|
"0186bfpkhxngrshac6bpg37alp6slwhwd43inrm8hqg0vhpfgc4c"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gdata" ,r-gdata)
|
|
("r-hmisc" ,r-hmisc)
|
|
("r-mice" ,r-mice)))
|
|
(home-page
|
|
"https://cran.r-project.org/web/packages/weights/")
|
|
(synopsis "Weighting and weighted statistics")
|
|
(description "This package Provides a variety of functions for producing
|
|
simple weighted statistics, such as weighted Pearson's correlations, partial
|
|
correlations, Chi-Squared statistics, histograms, and t-tests. Also now
|
|
includes some software for quickly recoding survey data and plotting point
|
|
estimates from interaction terms in regressions (and multiply imputed
|
|
regressions). NOTE: Weighted partial correlation calculations pulled to
|
|
address a bug.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rcppannoy
|
|
(package
|
|
(name "r-rcppannoy")
|
|
(version "0.0.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppAnnoy" version))
|
|
(sha256
|
|
(base32
|
|
"1b0fmip9c4i0my1yjrvqy8jxfiiqcggq2kms135q0b53njxnqwwg"))))
|
|
(properties `((upstream-name . "RcppAnnoy")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; for vignettes
|
|
(home-page "https://cran.r-project.org/web/packages/RcppAnnoy/")
|
|
(synopsis "Rcpp bindings for Annoy, a library for Approximate Nearest Neighbors")
|
|
(description
|
|
"Annoy is a small C++ library for Approximate Nearest Neighbors written
|
|
for efficient memory usage as well an ability to load from and save to disk.
|
|
This package provides an R interface.")
|
|
;; Annoy is released under ASL 2.0, but this wrapper is released under
|
|
;; GPLv2+.
|
|
(license (list license:gpl2+ license:asl2.0))))
|
|
|
|
(define-public r-rcpphnsw
|
|
(package
|
|
(name "r-rcpphnsw")
|
|
(version "0.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RcppHNSW" version))
|
|
(sha256
|
|
(base32
|
|
"158a069n42pbnjrlmvqsr6bm2cfp9hxpnk3nhp3dwi9qjlq4r9bm"))))
|
|
(properties `((upstream-name . "RcppHNSW")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/RcppHNSW/")
|
|
(synopsis "Rcpp bindings for hnswlib, a library for approximate nearest neighbors")
|
|
(description
|
|
"Hnswlib is a C++ library for approximate nearest neighbors. This
|
|
package provides a minimal R interface by relying on the Rcpp package.")
|
|
;; hnswlib is released under Version 2.0 of the Apache License.
|
|
(license (list license:gpl3 license:asl2.0))))
|
|
|
|
(define-public r-ncdf4
|
|
(package
|
|
(name "r-ncdf4")
|
|
(version "1.16.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ncdf4" version))
|
|
(sha256
|
|
(base32
|
|
"083sb24anyd4sw0il3x07pqn9rbx5y5ayqass6mz8x443rnjvphd"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("netcdf" ,netcdf)
|
|
("zlib" ,zlib)))
|
|
(home-page "https://cran.r-project.org/web/packages/ncdf4/index.html")
|
|
(synopsis "R interface to Unidata netCDF format data files")
|
|
(description
|
|
"This package provides a high-level R interface to data files written
|
|
using Unidata's netCDF library (version 4 or earlier), which are binary data
|
|
files that are portable across platforms and include metadata information in
|
|
addition to the data sets. Using this package, netCDF files can be opened and
|
|
data sets read in easily. It is also easy to create new netCDF dimensions,
|
|
variables, and files, in either version 3 or 4 format, and manipulate existing
|
|
netCDF files.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-biocmanager
|
|
(package
|
|
(name "r-biocmanager")
|
|
(version "1.30.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "BiocManager" version))
|
|
(sha256
|
|
(base32
|
|
"0kxs76pixk1d2lpvkyrq6nnvv1rqf55ph5f7igkadyyqirf3y2ah"))))
|
|
(properties `((upstream-name . "BiocManager")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/BiocManager/")
|
|
(synopsis "Access the Bioconductor project package repository")
|
|
(description
|
|
"This package provides a convenient tool to install and update
|
|
Bioconductor packages.")
|
|
(license license:artistic2.0)))
|
|
|
|
(define-public r-rgl
|
|
(package
|
|
(name "r-rgl")
|
|
(version "0.100.19")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rgl" version))
|
|
(sha256
|
|
(base32
|
|
"09bhvx8aq104yzysfgd7wlnq4vrvmnd4jzgj0c32whjfal10fqsh"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(inputs
|
|
`(("freetype" ,freetype)
|
|
("libpng" ,libpng)
|
|
("glu" ,glu)
|
|
("libx11" ,libx11)
|
|
("ghc-pandoc" ,ghc-pandoc)
|
|
("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-crosstalk" ,r-crosstalk)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-knitr" ,r-knitr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-manipulatewidget" ,r-manipulatewidget)
|
|
("r-shiny" ,r-shiny)))
|
|
(home-page "https://r-forge.r-project.org/projects/rgl/")
|
|
(synopsis "3D visualization using OpenGL")
|
|
(description
|
|
"This package provides medium to high level functions for 3D interactive graphics,
|
|
including functions modelled on base graphics (@code{plot3d()}, etc.) as well
|
|
as functions for constructing representations of geometric
|
|
objects (@code{cube3d()}, etc.). Output may be on screen using OpenGL, or to
|
|
various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D
|
|
image formats, including PNG, Postscript, SVG, PGF.")
|
|
;; Any version of the GPL.
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-multicool
|
|
(package
|
|
(name "r-multicool")
|
|
(version "0.1-10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "multicool" version))
|
|
(sha256
|
|
(base32
|
|
"1ybg9piya9psqg42w9i3zsnavbxhkfklfwl7cb420i5nkq6wpc2v"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/multicool/")
|
|
(synopsis "Permutations of multisets in cool-lex order")
|
|
(description
|
|
"This package provides a set of tools to permute multisets without loops
|
|
or hash tables and to generate integer partitions. Cool-lex order is similar
|
|
to colexicographical order.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-misc3d
|
|
(package
|
|
(name "r-misc3d")
|
|
(version "0.8-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "misc3d" version))
|
|
(sha256
|
|
(base32
|
|
"0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/misc3d/")
|
|
(synopsis "Miscellaneous 3D Plots")
|
|
(description
|
|
"This package provides a collection of miscellaneous 3d plots, including
|
|
isosurfaces.")
|
|
;; Any version of the GPL.
|
|
(license (list license:gpl2+ license:gpl3+))))
|
|
|
|
(define-public r-ks
|
|
(package
|
|
(name "r-ks")
|
|
(version "1.11.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ks" version))
|
|
(sha256
|
|
(base32
|
|
"06ymx244yknmpl6935l4pafqbm4gcbpnhqg7rinql6rrfr9mcrag"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-fnn" ,r-fnn)
|
|
("r-kernlab" ,r-kernlab)
|
|
("r-kernsmooth" ,r-kernsmooth)
|
|
("r-matrix" ,r-matrix)
|
|
("r-mclust" ,r-mclust)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-multicool" ,r-multicool)
|
|
("r-mvtnorm" ,r-mvtnorm)))
|
|
(home-page "http://www.mvstat.net/tduong/")
|
|
(synopsis "Kernel smoothing")
|
|
(description
|
|
"This package provides kernel smoothers for univariate and multivariate
|
|
data, including density functions, density derivatives, cumulative
|
|
distributions, modal clustering, discriminant analysis, and two-sample
|
|
hypothesis testing.")
|
|
;; Either version of the GPL.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-feature
|
|
(package
|
|
(name "r-feature")
|
|
(version "1.2.13")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "feature" version))
|
|
(sha256
|
|
(base32
|
|
"07hkw0bv38naj2hdsx4xxrm2dngi6w3rbvgr7s50bjic8hlgy1ra"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ks" ,r-ks)
|
|
("r-misc3d" ,r-misc3d)
|
|
("r-rgl" ,r-rgl)))
|
|
(home-page "http://www.mvstat.net/tduong/")
|
|
(synopsis "Inferential feature significance for kernel density estimation")
|
|
(description
|
|
"The feature package contains functions to display and compute kernel
|
|
density estimates, significant gradient and significant curvature regions.
|
|
Significant gradient and/or curvature regions often correspond to significant
|
|
features (e.g. local modes).")
|
|
;; Either version of the GPL.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-arm
|
|
(package
|
|
(name "r-arm")
|
|
(version "1.10-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "arm" version))
|
|
(sha256
|
|
(base32
|
|
"0vvp90jygajd6ydky57z66wqjq9msfbl88irj5jbsray574mh4bg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-abind" ,r-abind)
|
|
("r-coda" ,r-coda)
|
|
("r-lme4" ,r-lme4)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-nlme" ,r-nlme)))
|
|
(home-page "https://cran.r-project.org/web/packages/arm/")
|
|
(synopsis "Data analysis using regression and multilevel/hierarchical models")
|
|
(description
|
|
"This package provides functions to accompany A. Gelman and J. Hill,
|
|
Data Analysis Using Regression and Multilevel/Hierarchical Models, Cambridge
|
|
University Press, 2007.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-circular
|
|
(package
|
|
(name "r-circular")
|
|
(version "0.4-93")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "circular" version))
|
|
(sha256
|
|
(base32
|
|
"0hki85rs8wc5950pjaw28q54rly2napfbcrx3pchlfap6wwy5kkn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-boot" ,r-boot)
|
|
("r-mvtnorm" ,r-mvtnorm)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/circular/")
|
|
(synopsis "Circular statistics")
|
|
(description
|
|
"This package provides tools for circular statistics, from \"Topics in
|
|
circular Statistics\" (2001) S. Rao Jammalamadaka and A. SenGupta, World
|
|
Scientific.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-activity
|
|
(package
|
|
(name "r-activity")
|
|
(version "1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "activity" version))
|
|
(sha256
|
|
(base32
|
|
"11w2bz6p9xbzdh6773dmbbh6rws0h5dj18p8m0ivzizgq932vdzs"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-circular" ,r-circular)
|
|
("r-pbapply" ,r-pbapply)))
|
|
(home-page "https://cran.r-project.org/web/packages/activity/")
|
|
(synopsis "Animal activity statistics")
|
|
(description
|
|
"This package provides functions to fit kernel density functions to
|
|
animal activity time data; plot activity distributions; quantify overall
|
|
levels of activity; statistically compare activity metrics through
|
|
bootstrapping; and evaluate variation in linear variables with time (or other
|
|
circular variables).")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ouch
|
|
(package
|
|
(name "r-ouch")
|
|
(version "2.14-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ouch" version))
|
|
(sha256
|
|
(base32
|
|
"0ddf9bw5lhj8vb0ja78jf99i0smq4rgmm842k4a4ygap41vdyn2b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-subplex" ,r-subplex)))
|
|
(home-page "http://kingaa.github.io/ouch/")
|
|
(synopsis "Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses")
|
|
(description
|
|
"This package provides tools to fit and compare Ornstein-Uhlenbeck models
|
|
for evolution along a phylogenetic tree.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-fmsb
|
|
(package
|
|
(name "r-fmsb")
|
|
(version "0.6.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fmsb" version))
|
|
(sha256
|
|
(base32
|
|
"1n29bnyp20pvpk2lsa9fblsj5w7amp14snc74pk5w3yr5y6rj0s5"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://minato.sip21c.org/msb/")
|
|
(synopsis "Functions for medical statistics book with demographic data")
|
|
(description
|
|
"This package provides several utility functions for the book entitled
|
|
\"Practices of Medical and Health Data Analysis using R\" (Pearson Education
|
|
Japan, 2007) with Japanese demographic data and some demographic analysis
|
|
related functions.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-stabledist
|
|
(package
|
|
(name "r-stabledist")
|
|
(version "0.7-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stabledist" version))
|
|
(sha256
|
|
(base32
|
|
"0scar396wiq6wkbkvwp4qrxqc1m075y56p37i6iry5rw796p1i86"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.rmetrics.org")
|
|
(synopsis "Stable distribution functions")
|
|
(description
|
|
"This package provides density, probability and quantile functions, and
|
|
random number generation for (skew) stable distributions, using the
|
|
parametrizations of Nolan.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-gsl
|
|
(package
|
|
(name "r-gsl")
|
|
(version "2.1-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gsl" version))
|
|
(sha256
|
|
(base32
|
|
"0p4rh7npp6qbfc5sxjq86xjn7c9ivf3pd60qf1hldwckjqin7m7m"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gsl" ,gsl)))
|
|
(home-page "https://cran.r-project.org/web/packages/gsl")
|
|
(synopsis "Wrapper for the GNU Scientific Library")
|
|
(description
|
|
"This package provides an R wrapper for the special functions and quasi
|
|
random number generators of the GNU Scientific Library.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-adgoftest
|
|
(package
|
|
(name "r-adgoftest")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ADGofTest" version))
|
|
(sha256
|
|
(base32
|
|
"0ik817qzqp6kfbckjp1z7srlma0w6z2zcwykh0jdiv7nahwk3ncw"))))
|
|
(properties `((upstream-name . "ADGofTest")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/ADGofTest")
|
|
(synopsis "Anderson-Darling GoF test")
|
|
(description
|
|
"This package provides an implementation of the Anderson-Darling GoF test
|
|
with p-value calculation based on Marsaglia's 2004 paper \"Evaluating the
|
|
Anderson-Darling Distribution\".")
|
|
;; Any version of the GPL.
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-softimpute
|
|
(package
|
|
(name "r-softimpute")
|
|
(version "1.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "softImpute" version))
|
|
(sha256
|
|
(base32
|
|
"07cxbzkl08q58m1455i139952rmryjlic4s2f2hscl5zxxmfdxcq"))))
|
|
(properties `((upstream-name . "softImpute")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/softImpute")
|
|
(synopsis "Matrix completion via iterative soft-thresholded SVD")
|
|
(description
|
|
"This package provides iterative methods for matrix completion that use
|
|
nuclear-norm regularization. The package includes procedures for centering
|
|
and scaling rows, columns or both, and for computing low-rank @dfn{single
|
|
value decompositions} (SVDs) on large sparse centered matrices (i.e. principal
|
|
components).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-fftwtools
|
|
(package
|
|
(name "r-fftwtools")
|
|
(version "0.9-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fftwtools" version))
|
|
(sha256
|
|
(base32
|
|
"1nqvpzda281rxi1cmwajxxsn3sc3gz7scv8bvs5jm34kf36whha6"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("fftw" ,fftw)))
|
|
(home-page "https://github.com/krahim/fftwtools")
|
|
(synopsis "Wrapper for FFTW3")
|
|
(description
|
|
"This package provides a wrapper for several FFTW functions. It provides
|
|
access to the two-dimensional FFT, the multivariate FFT, and the
|
|
one-dimensional real to complex FFT using the FFTW3 library. The package
|
|
includes the functions @code{fftw()} and @code{mvfftw()} which are designed to
|
|
mimic the functionality of the R functions @code{fft()} and @code{mvfft()}.
|
|
The FFT functions have a parameter that allows them to not return the
|
|
redundant complex conjugate when the input is real data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-tiff
|
|
(package
|
|
(name "r-tiff")
|
|
(version "0.1-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tiff" version))
|
|
(sha256
|
|
(base32
|
|
"0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("libtiff" ,libtiff)
|
|
("libjpeg" ,libjpeg)
|
|
("zlib" ,zlib)))
|
|
(home-page "http://www.rforge.net/tiff/")
|
|
(synopsis "Read and write TIFF images")
|
|
(description
|
|
"This package provides an easy and simple way to read, write and display
|
|
bitmap images stored in the TIFF format. It can read and write both files and
|
|
in-memory raw vectors.")
|
|
;; Either of these two license versions.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-waveslim
|
|
(package
|
|
(name "r-waveslim")
|
|
(version "1.7.5.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "waveslim" version))
|
|
(sha256
|
|
(base32
|
|
"0mky0nb4xxp8rybp87mxw2f1q6k400wpxv01zr4injv7ja6028xk"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://waveslim.blogspot.com")
|
|
(synopsis "Basic wavelet routines for signal processing")
|
|
(description
|
|
"This package provides basic wavelet routines for time series (1D),
|
|
image (2D) and array (3D) analysis. The code provided here is based on
|
|
wavelet methodology developed in Percival and Walden (2000); Gencay, Selcuk
|
|
and Whitcher (2001); the dual-tree complex wavelet transform (DTCWT) from
|
|
Kingsbury (1999, 2001) as implemented by Selesnick; and Hilbert wavelet
|
|
pairs (Selesnick 2001, 2002).")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-wordcloud
|
|
(package
|
|
(name "r-wordcloud")
|
|
(version "2.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "wordcloud" version))
|
|
(sha256
|
|
(base32
|
|
"0j96yyvm6bcrrpbdx4w26piqx44a0vbsr3px9cb4zk8a8da6jwak"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/wordcloud")
|
|
(synopsis "Word clouds")
|
|
(description
|
|
"This package provides functionality to create pretty word clouds,
|
|
visualize differences and similarity between documents, and avoid
|
|
over-plotting in scatter plots with text.")
|
|
(license license:lgpl2.1)))
|
|
|
|
(define-public r-colorramps
|
|
(package
|
|
(name "r-colorramps")
|
|
(version "2.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "colorRamps" version))
|
|
(sha256
|
|
(base32
|
|
"0shbjh83x1axv4drm5r3dwgbyv70idih8z4wlzjs4hiac2qfl41z"))))
|
|
(properties `((upstream-name . "colorRamps")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/colorRamps")
|
|
(synopsis "Build color tables")
|
|
(description "This package provides features to build gradient color
|
|
maps.")
|
|
;; Any version of the GPL
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-tidytree
|
|
(package
|
|
(name "r-tidytree")
|
|
(version "0.2.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tidytree" version))
|
|
(sha256
|
|
(base32
|
|
"04bznlfs617plv258nmsyq2pywnijcnzy2pbn5b2fgjk2xqkp29w"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ape" ,r-ape)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/GuangchuangYu/tidytree")
|
|
(synopsis "Tidy tool for phylogenetic tree data manipulation")
|
|
(description
|
|
"Phylogenetic trees generally contain multiple components including nodes,
|
|
edges, branches and associated data. This package provides an approach to
|
|
convert tree objects to tidy data frames. It also provides tidy interfaces to
|
|
manipulate tree data.")
|
|
(license license:artistic2.0)))
|
|
|
|
(define-public r-rvcheck
|
|
(package
|
|
(name "r-rvcheck")
|
|
(version "0.1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rvcheck" version))
|
|
(sha256
|
|
(base32
|
|
"1i2g6gyiqyd1pn6y0h6vmlcmg1qb5pv7rym8mkw8jnyc3in9hn8b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rlang" ,r-rlang)))
|
|
(home-page "https://cran.r-project.org/web/packages/rvcheck")
|
|
(synopsis "R package version check")
|
|
(description
|
|
"This package provides tools to check the latest release version of R and
|
|
R packages (on CRAN, Bioconductor or Github).")
|
|
(license license:artistic2.0)))
|
|
|
|
(define-public r-docopt
|
|
(package
|
|
(name "r-docopt")
|
|
(version "0.6.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "docopt" version))
|
|
(sha256
|
|
(base32
|
|
"06zknnd0c5s2y0hbddzdlr3m63ib783izpck6pgz7sjbab5pd068"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/docopt/docopt.R")
|
|
(synopsis "Command-line interface specification language")
|
|
(description
|
|
"This package enables you to define a command-line interface by just
|
|
giving it a description in the specific format.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-sparsesvd
|
|
(package
|
|
(name "r-sparsesvd")
|
|
(version "0.1-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sparsesvd" version))
|
|
(sha256
|
|
(base32
|
|
"1yf373552wvdnd65r7hfcqa3v29dqn7jd4cn431mqd2acnqjrsam"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-matrix" ,r-matrix)))
|
|
(home-page "http://tedlab.mit.edu/~dr/SVDLIBC/")
|
|
(synopsis "Sparse truncated singular value decomposition")
|
|
(description
|
|
"This package provides a Wrapper around the SVDLIBC library
|
|
for (truncated) singular value decomposition of a sparse matrix. Currently,
|
|
only sparse real matrices in Matrix package format are supported.")
|
|
;; SVDLIBC is released under BSD-2. The R interface is released under
|
|
;; BSD-3.
|
|
(license (list license:bsd-3 license:bsd-2))))
|
|
|
|
(define-public r-densityclust
|
|
(package
|
|
(name "r-densityclust")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "densityClust" version))
|
|
(sha256
|
|
(base32
|
|
"1zry0vafajzmr37aylglxfvwplhdygbkb9cvzvh8cy0xgnjrnx13"))))
|
|
(properties `((upstream-name . "densityClust")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-fnn" ,r-fnn)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-ggrepel" ,r-ggrepel)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-rcolorbrewer" ,r-rcolorbrewer)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rtsne" ,r-rtsne)))
|
|
(home-page "https://cran.r-project.org/web/packages/densityClust")
|
|
(synopsis "Clustering by fast search and find of density peaks")
|
|
(description
|
|
"This package provides an improved implementation (based on k-nearest
|
|
neighbors) of the density peak clustering algorithm, originally described by
|
|
Alex Rodriguez and Alessandro Laio (Science, 2014 vol. 344). It can handle
|
|
large datasets (> 100,000 samples) very efficiently.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-combinat
|
|
(package
|
|
(name "r-combinat")
|
|
(version "0.0-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "combinat" version))
|
|
(sha256
|
|
(base32
|
|
"1h9hr88gigihc4na7lb5i7rn4az1xa7sb34zvnznaj6pdrmwy4qm"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/combinat")
|
|
(synopsis "Combinatorics utilities")
|
|
(description "This package provides assorted routines for combinatorics.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-qlcmatrix
|
|
(package
|
|
(name "r-qlcmatrix")
|
|
(version "0.9.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "qlcMatrix" version))
|
|
(sha256
|
|
(base32
|
|
"0iqkcvvy8rxlk0s83sjq57dd6fadb18p5z31lzy0gnzv1hsy1x8y"))))
|
|
(properties `((upstream-name . "qlcMatrix")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-docopt" ,r-docopt)
|
|
("r-matrix" ,r-matrix)
|
|
("r-slam" ,r-slam)
|
|
("r-sparsesvd" ,r-sparsesvd)))
|
|
(home-page "https://cran.r-project.org/web/packages/qlcMatrix")
|
|
(synopsis "Sparse matrix functions for quantitative language comparison")
|
|
(description
|
|
"This package provides an extension of the functionality of the Matrix
|
|
package for using sparse matrices. Some of the functions are very general,
|
|
while other are highly specific for the special data format used for
|
|
@dfn{quantitative language comparison} (QLC).")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ddrtree
|
|
(package
|
|
(name "r-ddrtree")
|
|
(version "0.1.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DDRTree" version))
|
|
(sha256
|
|
(base32
|
|
"16s5fjw7kwlxhrkzdny62sx32fvmg3rxjc3wrh6krd31jh1fqlfk"))))
|
|
(properties `((upstream-name . "DDRTree")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-irlba" ,r-irlba)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcppeigen" ,r-rcppeigen)))
|
|
(home-page "https://cran.r-project.org/web/packages/DDRTree")
|
|
(synopsis "Learning principal graphs with DDRTree")
|
|
(description
|
|
"This package provides an implementation of the framework of
|
|
@dfn{reversed graph embedding} (RGE) which projects data into a reduced
|
|
dimensional space while constructs a principal tree which passes through the
|
|
middle of the data simultaneously. DDRTree shows superiority to
|
|
alternatives (Wishbone, DPT) for inferring the ordering as well as the
|
|
intrinsic structure of single cell genomics data. In general, it could be
|
|
used to reconstruct the temporal progression as well as the bifurcation
|
|
structure of any data type.")
|
|
(license license:asl2.0)))
|
|
|
|
(define-public r-corpcor
|
|
(package
|
|
(name "r-corpcor")
|
|
(version "1.6.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "corpcor" version))
|
|
(sha256
|
|
(base32
|
|
"1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://strimmerlab.org/software/corpcor/")
|
|
(synopsis "Efficient estimation of covariance and (partial) correlation")
|
|
(description
|
|
"This package implements a James-Stein-type shrinkage estimator for the
|
|
covariance matrix, with separate shrinkage for variances and correlations.
|
|
Furthermore, functions are available for fast singular value decomposition,
|
|
for computing the pseudoinverse, and for checking the rank and positive
|
|
definiteness of a matrix.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-rspectra
|
|
(package
|
|
(name "r-rspectra")
|
|
(version "0.15-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RSpectra" version))
|
|
(sha256
|
|
(base32
|
|
"1ab975scdqaxdna9sayjl6l14hz991y0pc8c8ah48w000616km8s"))))
|
|
(properties `((upstream-name . "RSpectra")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcppeigen" ,r-rcppeigen)))
|
|
(home-page "https://github.com/yixuan/RSpectra")
|
|
(synopsis "Solvers for large-scale Eigenvalue and SVD problems")
|
|
(description
|
|
"This package provides an R interface to the Spectra library for
|
|
large-scale eigenvalue and SVD problems. It is typically used to compute a
|
|
few eigenvalues/vectors of an n by n matrix, e.g., the k largest eigenvalues,
|
|
which is usually more efficient than @code{eigen()} if k << n.")
|
|
;; MPL 2 or later.
|
|
(license license:mpl2.0)))
|
|
|
|
(define-public r-vbsr
|
|
(package
|
|
(name "r-vbsr")
|
|
(version "0.0.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "vbsr" version))
|
|
(sha256
|
|
(base32
|
|
"1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/vbsr")
|
|
(synopsis "Variational Bayes spike regression regularized linear models")
|
|
(description
|
|
"This package provides an efficient algorithm for solving ultra-sparse
|
|
regularized regression models using a variational Bayes algorithm with a spike
|
|
prior. The algorithm is solved on a path, with coordinate updates, and is
|
|
capable of generating very sparse models. Very general model
|
|
diagnostics for controlling type-1 errors are also provided.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-flare
|
|
(package
|
|
(name "r-flare")
|
|
(version "1.6.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "flare" version))
|
|
(sha256
|
|
(base32
|
|
"0ygif9a7a99qwv0b488wymmmncp6f5ww9yz13s4qs6p8yf37x1r1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-igraph" ,r-igraph)
|
|
("r-lattice" ,r-lattice)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)))
|
|
(home-page "https://cran.r-project.org/web/packages/flare")
|
|
(synopsis "Family of Lasso regression implementations")
|
|
(description
|
|
"This package provides implementations of a family of Lasso variants
|
|
including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating
|
|
high dimensional sparse linear models.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-lassopv
|
|
(package
|
|
(name "r-lassopv")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lassopv" version))
|
|
(sha256
|
|
(base32
|
|
"0yawnjw063jypk3riy9xab9cmliv6c9dnabi18670khd3gzb2r9z"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-lars" ,r-lars)))
|
|
(home-page "https://github.com/lingfeiwang/lassopv")
|
|
(synopsis "Non-parametric p-value estimation for predictors in Lasso")
|
|
(description
|
|
"This package enables you to estimate the p-values for predictors x
|
|
against target variable y in Lasso regression, using the regularization
|
|
strength when each predictor enters the active set of regularization path for
|
|
the first time as the statistic.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-splitstackshape
|
|
(package
|
|
(name "r-splitstackshape")
|
|
(version "1.4.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "splitstackshape" version))
|
|
(sha256
|
|
(base32
|
|
"0mpyf2kkfdl69pdc6brl1r6101vyc6pgr7z17s55ppg3y71k4q35"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-data-table" ,r-data-table)))
|
|
(home-page "https://github.com/mrdwab/splitstackshape")
|
|
(synopsis "Stack and reshape datasets after splitting concatenated values")
|
|
(description
|
|
"Online data collection tools like Google Forms often export
|
|
multiple-response questions with data concatenated in cells. The
|
|
@code{concat.split} (cSplit) family of functions provided by this package
|
|
splits such data into separate cells. This package also includes functions to
|
|
stack groups of columns and to reshape wide data, even when the data are
|
|
\"unbalanced\"---something which @code{reshape} (from base R) does not handle,
|
|
and which @code{melt} and @code{dcast} from @code{reshape2} do not easily
|
|
handle.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-tfmpvalue
|
|
(package
|
|
(name "r-tfmpvalue")
|
|
(version "0.0.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "TFMPvalue" version))
|
|
(sha256
|
|
(base32
|
|
"0h9qkl15k8v17v3g9bdnfwvh2s04ywjgg5y0xn2077dmywlja1bd"))))
|
|
(properties `((upstream-name . "TFMPvalue")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/ge11232002/TFMPvalue")
|
|
(synopsis "P-value computation for position weight matrices")
|
|
(description
|
|
"In putative @dfn{Transcription Factor Binding Sites} (TFBSs)
|
|
identification from sequence/alignments, we are interested in the significance
|
|
of certain match scores. TFMPvalue provides the accurate calculation of a
|
|
p-value with a score threshold for position weight matrices, or the score with
|
|
a given p-value. It is an interface to code originally made available by
|
|
Helene Touzet and Jean-Stephane Varre, 2007, Algorithms Mol Biol:2, 15.
|
|
Touzet and Varre (2007).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rnifti
|
|
(package
|
|
(name "r-rnifti")
|
|
(version "0.10.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RNifti" version))
|
|
(sha256
|
|
(base32
|
|
"07sfzps4yg5zdhbxh6i4rbjvbjvvf2d8i9jcf64ywbmi557sw1zv"))))
|
|
(properties `((upstream-name . "RNifti")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/jonclayden/RNifti")
|
|
(synopsis "Fast R and C++ access to NIfTI images")
|
|
(description
|
|
"This package provides very fast read and write access to images stored
|
|
in the NIfTI-1 and ANALYZE-7.5 formats, with seamless synchronisation between
|
|
compiled C and interpreted R code. It also provides a C/C++ API that can be
|
|
used by other packages.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-shades
|
|
(package
|
|
(name "r-shades")
|
|
(version "1.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shades" version))
|
|
(sha256
|
|
(base32
|
|
"0v0xp9l1zyq4iysmkrbdwk4r1rksjj8p5c1726yrcgyg55mj59nv"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/jonclayden/shades")
|
|
(synopsis "Simple color manipulation")
|
|
(description
|
|
"This package provides functions for easily manipulating colors,
|
|
creating color scales and calculating color distances.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-ore
|
|
(package
|
|
(name "r-ore")
|
|
(version "1.6.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ore" version))
|
|
(sha256
|
|
(base32
|
|
"1l1ziljgm5gwjhvjq42wi5vcwbxlaj5dl9w8bhz0wh8vx4ajj07m"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/jonclayden/ore")
|
|
(synopsis "R interface to the Onigmo regular expression library")
|
|
(description
|
|
"This package provides an alternative to R's built-in functionality for
|
|
handling regular expressions, based on the Onigmo library. It offers
|
|
first-class compiled regex objects, partial matching and function-based
|
|
substitutions, amongst other features.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-reportr
|
|
(package
|
|
(name "r-reportr")
|
|
(version "1.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reportr" version))
|
|
(sha256
|
|
(base32
|
|
"0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-ore" ,r-ore)))
|
|
(home-page "https://github.com/jonclayden/reportr")
|
|
(synopsis "General message and error reporting system")
|
|
(description
|
|
"This package provides a system for reporting messages, which offers
|
|
certain useful features over the standard R system, such as the incorporation
|
|
of output consolidation, message filtering, assertions, expression
|
|
substitution, automatic generation of stack traces for debugging, and
|
|
conditional reporting based on the current \"output level\".")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-tractor-base
|
|
(package
|
|
(name "r-tractor-base")
|
|
(version "3.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tractor.base" version))
|
|
(sha256
|
|
(base32
|
|
"0y5gm0y4chl30f5qqq8qiiw4j8g32s4i9xrvyp3cwg902kf2p86i"))))
|
|
(properties `((upstream-name . "tractor.base")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ore" ,r-ore)
|
|
("r-reportr" ,r-reportr)
|
|
("r-rnifti" ,r-rnifti)
|
|
("r-shades" ,r-shades)))
|
|
(home-page "http://www.tractor-mri.org.uk")
|
|
(synopsis "Read, manipulate and visualize magnetic resonance images")
|
|
(description
|
|
"This package provides functions for working with magnetic resonance
|
|
images. It supports reading and writing of popular file formats (DICOM,
|
|
Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive
|
|
visualization; flexible image manipulation; metadata and sparse image
|
|
handling.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-grimport
|
|
(package
|
|
(name "r-grimport")
|
|
(version "0.9-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "grImport" version))
|
|
(sha256
|
|
(base32
|
|
"0n3y6dzy8s0ifvyrgwbly6cl14lmgd54dyi74s5i984apszpsp16"))))
|
|
(properties `((upstream-name . "grImport")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("ghostscript" ,ghostscript)))
|
|
(propagated-inputs
|
|
`(("r-xml" ,r-xml)))
|
|
(home-page "https://cran.r-project.org/web/packages/grImport")
|
|
(synopsis "Convert, import, and draw PostScript pictures")
|
|
(description
|
|
"This package provides functions for converting, importing, and drawing
|
|
PostScript pictures in R plots.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-grimport2
|
|
(package
|
|
(name "r-grimport2")
|
|
(version "0.1-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "grImport2" version))
|
|
(sha256
|
|
(base32
|
|
"0dyb3nrrvxnkk9q5b136bdivcz1jj3ajx1kscm3k0kkpqjif0pls"))))
|
|
(properties `((upstream-name . "grImport2")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-jpeg" ,r-jpeg)
|
|
("r-png" ,r-png)
|
|
("r-xml" ,r-xml)))
|
|
(home-page "https://cran.r-project.org/web/packages/grImport2/")
|
|
(synopsis "Import SVG graphics")
|
|
(description
|
|
"This package provides functions for importing external vector images and
|
|
drawing them as part of R plots. This package is different from the
|
|
@code{grImport} package because, where that package imports PostScript format
|
|
images, this package imports SVG format images. Furthermore, this package
|
|
imports a specific subset of SVG, so external images must be preprocessed
|
|
using a package like @code{rsvg} to produce SVG that this package can import.
|
|
SVG features that are not supported by R graphics, such as gradient fills, can
|
|
be imported and then exported via the @code{gridSVG} package.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-kohonen
|
|
(package
|
|
(name "r-kohonen")
|
|
(version "3.0.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "kohonen" version))
|
|
(sha256
|
|
(base32
|
|
"1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/kohonen")
|
|
(synopsis "Supervised and unsupervised self-organising maps")
|
|
(description
|
|
"This package provides functions to train @dfn{self-organising
|
|
maps} (SOMs). Also interrogation of the maps and prediction using trained
|
|
maps are supported. The name of the package refers to Teuvo Kohonen, the
|
|
inventor of the SOM.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-nnls
|
|
(package
|
|
(name "r-nnls")
|
|
(version "1.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nnls" version))
|
|
(sha256
|
|
(base32
|
|
"07vcrrxvswrvfiha6f3ikn640yg0m2b4yd9lkmim1g0jmsmpfp8f"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/nnls")
|
|
(synopsis "Lawson-Hanson algorithm for non-negative least squares")
|
|
(description
|
|
"This package provides an R interface to the Lawson-Hanson implementation
|
|
of an algorithm for @dfn{non-negative least squares} (NNLS). It also allows
|
|
the combination of non-negative and non-positive constraints.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-iso
|
|
(package
|
|
(name "r-iso")
|
|
(version "0.0-18")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Iso" version))
|
|
(sha256
|
|
(base32
|
|
"014mm5b1f7i6nwlz3kyg1biph0y542kcx5bd13p68cv5a928qzid"))))
|
|
(properties `((upstream-name . "Iso")))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "http://www.stat.auckland.ac.nz/~rolf/")
|
|
(synopsis "Functions to perform isotonic regression")
|
|
(description
|
|
"This package provides support for linear order and unimodal
|
|
order (univariate) isotonic regression and bivariate isotonic regression with
|
|
linear order on both variables.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-chemometricswithr
|
|
(package
|
|
(name "r-chemometricswithr")
|
|
(version "0.1.13")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ChemometricsWithR" version))
|
|
(sha256
|
|
(base32
|
|
"166va1g3m1wv21qkmw4wpz0bsrclh3jih8smxphdc13l9pqgclpq"))))
|
|
(properties
|
|
`((upstream-name . "ChemometricsWithR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-devtools" ,r-devtools)
|
|
("r-kohonen" ,r-kohonen)
|
|
("r-mass" ,r-mass)
|
|
("r-pls" ,r-pls)))
|
|
(home-page "https://github.com/rwehrens/CWR")
|
|
(synopsis "Chemometrics with R")
|
|
(description
|
|
"This package provides functions and scripts used in the book
|
|
\"Chemometrics with R - Multivariate Data Analysis in the Natural Sciences and
|
|
Life Sciences\" by Ron Wehrens, Springer (2011).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-als
|
|
(package
|
|
(name "r-als")
|
|
(version "0.0.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ALS" version))
|
|
(sha256
|
|
(base32
|
|
"1swrn39vy50fazkpf97r7c542gkj6mlvy8gmcxllg7mf2mqx546a"))))
|
|
(properties `((upstream-name . "ALS")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-iso" ,r-iso)
|
|
("r-nnls" ,r-nnls)))
|
|
(home-page "https://cran.r-project.org/web/packages/ALS")
|
|
(synopsis "Multivariate curve resolution alternating least squares")
|
|
(description
|
|
"Alternating least squares is often used to resolve components
|
|
contributing to data with a bilinear structure; the basic technique may be
|
|
extended to alternating constrained least squares. This package provides an
|
|
implementation of @dfn{multivariate curve resolution alternating least
|
|
squares} (MCR-ALS).
|
|
|
|
Commonly applied constraints include unimodality, non-negativity, and
|
|
normalization of components. Several data matrices may be decomposed
|
|
simultaneously by assuming that one of the two matrices in the bilinear
|
|
decomposition is shared between datasets.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-strucchange
|
|
(package
|
|
(name "r-strucchange")
|
|
(version "1.5-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "strucchange" version))
|
|
(sha256
|
|
(base32
|
|
"0cdgvl6kphm2i59bmnppn1y3kv65ml111bk7yzpcx7vv8wh2w3kl"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-sandwich" ,r-sandwich)
|
|
("r-zoo" ,r-zoo)))
|
|
(home-page "https://cran.r-project.org/web/packages/strucchange")
|
|
(synopsis "Testing, monitoring, and dating structural changes")
|
|
(description
|
|
"This package provides tools for testing, monitoring and dating
|
|
structural changes in (linear) regression models. It features tests/methods
|
|
from the generalized fluctuation test framework as well as from the F
|
|
test (Chow test) framework. This includes methods to fit, plot and test
|
|
fluctuation processes (e.g., CUSUM, MOSUM, recursive/moving estimates) and F
|
|
statistics, respectively. It is possible to monitor incoming data online
|
|
using fluctuation processes. Finally, the breakpoints in regression models
|
|
with structural changes can be estimated together with confidence intervals.
|
|
Emphasis is always given to methods for visualizing the data.")
|
|
;; Either of these two GPL versions
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-pixmap
|
|
(package
|
|
(name "r-pixmap")
|
|
(version "0.4-11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pixmap" version))
|
|
(sha256
|
|
(base32
|
|
"04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/pixmap")
|
|
(synopsis "Tools for bitmap images")
|
|
(description
|
|
"This package provides functions for importing, exporting, plotting and
|
|
other manipulations of bitmapped images.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rapidjsonr
|
|
(package
|
|
(name "r-rapidjsonr")
|
|
(version "1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rapidjsonr" version))
|
|
(sha256
|
|
(base32
|
|
"0h4phjjhykbb45rg5b1xn48vqxdcvcngbm0416ds8in7j469wbwd"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rapidjsonr")
|
|
(synopsis "JSON parser")
|
|
(description
|
|
"This package provides JSON parsing capability through the Rapidjson
|
|
library.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ontologyindex
|
|
(package
|
|
(name "r-ontologyindex")
|
|
(version "2.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ontologyIndex" version))
|
|
(sha256
|
|
(base32
|
|
"127hlf0z5fmbgnq4p9h8nvn6p72d2fpcn846zzb99s213421jnry"))))
|
|
(properties `((upstream-name . "ontologyIndex")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/ontologyIndex")
|
|
(synopsis "Functions for processing ontologies in R")
|
|
(description
|
|
"This package provides functions for reading ontologies into R as lists
|
|
and manipulating sets of ontological terms.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-bigrquery
|
|
(package
|
|
(name "r-bigrquery")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bigrquery" version))
|
|
(sha256
|
|
(base32
|
|
"1if39xkr231xmjq10fx2g7bgg4jgfd3wzx1p9g3pq4hbf2s6x0is"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-bit64" ,r-bit64)
|
|
("r-curl" ,r-curl)
|
|
("r-dbi" ,r-dbi)
|
|
("r-glue" ,r-glue)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-prettyunits" ,r-prettyunits)
|
|
("r-progress" ,r-progress)
|
|
("r-rapidjsonr" ,r-rapidjsonr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/rstats-db/bigrquery")
|
|
(synopsis "R interface to Google's BigQuery API")
|
|
(description
|
|
"This package provides an R interface to Google's BigQuery database.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-gmp
|
|
(package
|
|
(name "r-gmp")
|
|
(version "0.5-13.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gmp" version))
|
|
(sha256
|
|
(base32
|
|
"042mzsl6z6s61fy5m21yf9q83l08vnyqljn4iax7kqyiycpsp0gn"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
'(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'set-CC
|
|
(lambda _ (setenv "CC" "gcc") #t)))))
|
|
(inputs `(("gmp" ,gmp)))
|
|
(home-page "https://cran.r-project.org/web/packages/gmp")
|
|
(synopsis "Multiple precision arithmetic")
|
|
(description
|
|
"This package supports multiple precision arithmetic (big integers and
|
|
rationals, prime number tests, matrix computation), \"arithmetic without
|
|
limitations\" using the GNU Multiple Precision library.")
|
|
;; Any version of the GPL.
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-rmpfr
|
|
(package
|
|
(name "r-rmpfr")
|
|
(version "0.7-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rmpfr" version))
|
|
(sha256
|
|
(base32
|
|
"1zq3as34r27v2yc729731997wdhxb6cs5ilmak4nmsljabnac7gc"))))
|
|
(properties `((upstream-name . "Rmpfr")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("mpfr" ,mpfr)))
|
|
(propagated-inputs
|
|
`(("r-gmp" ,r-gmp)))
|
|
(home-page "http://rmpfr.r-forge.r-project.org/")
|
|
(synopsis "R bindings to the MPFR library")
|
|
(description
|
|
"This package supports arithmetic (via S4 classes and methods) for
|
|
arbitrary precision floating point numbers, including transcendental
|
|
functions. To this end, the package interfaces with the @dfn{Multiple
|
|
Precision Floating-Point Reliable} (MPFR) library.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-assertive-base
|
|
(package
|
|
(name "r-assertive-base")
|
|
(version "0.0-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.base" version))
|
|
(sha256
|
|
(base32
|
|
"1xs3ysvj0z57c58jw57pckq2rynia6ks4rmjmc02alczhk54wbgh"))))
|
|
(properties
|
|
`((upstream-name . "assertive.base")))
|
|
(build-system r-build-system)
|
|
(home-page "https://bitbucket.org/richierocks/assertive.base")
|
|
(synopsis "Core of the assertive package")
|
|
(description
|
|
"This package provides a minimal set of predicates and assertions used by
|
|
the assertive package. This is mainly for use by other package developers who
|
|
want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-properties
|
|
(package
|
|
(name "r-assertive-properties")
|
|
(version "0.0-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.properties" version))
|
|
(sha256
|
|
(base32
|
|
"0sqs54acs9qk9kvm32rxzfbzxz1l8mjahpfnw7r30z2brgz661jw"))))
|
|
(properties
|
|
`((upstream-name . "assertive.properties")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.properties")
|
|
(synopsis "Assertions to check properties of variables")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of variables, such as length, names and attributes. This is
|
|
mainly for use by other package developers who want to include run-time
|
|
testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-numbers
|
|
(package
|
|
(name "r-assertive-numbers")
|
|
(version "0.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.numbers" version))
|
|
(sha256
|
|
(base32
|
|
"0jc3ss64j4m7bjydhagwwmka5n7c72vpw4kfcch0m5jvkq5qrqds"))))
|
|
(properties
|
|
`((upstream-name . "assertive.numbers")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.numbers")
|
|
(synopsis "Assertions to check properties of numbers")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of numbers. This is mainly for use by other package developers
|
|
who want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-sets
|
|
(package
|
|
(name "r-assertive-sets")
|
|
(version "0.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.sets" version))
|
|
(sha256
|
|
(base32
|
|
"1cqvh2syvh5b6d85h601zjmsdbbf3h8q98ids4dfl4frdshpasc7"))))
|
|
(properties
|
|
`((upstream-name . "assertive.sets")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.sets")
|
|
(synopsis "Assertions to check properties of sets")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of sets. This is mainly for use by other package developers
|
|
who want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-matrices
|
|
(package
|
|
(name "r-assertive-matrices")
|
|
(version "0.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.matrices" version))
|
|
(sha256
|
|
(base32
|
|
"16sykzcndv6y2d43x6v9n7m95kv76364h39kh10w4z0xw6ksfqil"))))
|
|
(properties
|
|
`((upstream-name . "assertive.matrices")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.matrices")
|
|
(synopsis "Assertions to check properties of matrices")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of matrices. This is mainly for use by other package
|
|
developers who want to include run-time testing features in their own
|
|
packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-models
|
|
(package
|
|
(name "r-assertive-models")
|
|
(version "0.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.models" version))
|
|
(sha256
|
|
(base32
|
|
"0bn4j4v5qvb2d672cgri61p8d9v258pmz35y3lvm6b9mdxwdi9mr"))))
|
|
(properties
|
|
`((upstream-name . "assertive.models")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.models")
|
|
(synopsis "Assertions to check properties of models")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of models. This is mainly for use by other package developers
|
|
who want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-reflection
|
|
(package
|
|
(name "r-assertive-reflection")
|
|
(version "0.0-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.reflection" version))
|
|
(sha256
|
|
(base32
|
|
"19zmsbn00crfqm0kwd9ys5gv87xs3gi6wmlikrz9xiwzm7hp4dhj"))))
|
|
(properties
|
|
`((upstream-name . "assertive.reflection")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.reflection")
|
|
(synopsis "Assertions for checking the state of R")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the state and capabilities of R, the operating system it is running on, and
|
|
the IDE being used. This is mainly for use by other package developers who
|
|
want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-types
|
|
(package
|
|
(name "r-assertive-types")
|
|
(version "0.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.types" version))
|
|
(sha256
|
|
(base32
|
|
"0zxq1jfrzgw95ll7alvm0xnk7aihjdksngq4ya2whyvfjbmv4vdb"))))
|
|
(properties
|
|
`((upstream-name . "assertive.types")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-properties" ,r-assertive-properties)
|
|
("r-codetools" ,r-codetools)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.types")
|
|
(synopsis "Assertions to check types of variables")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the types of variables. This is mainly for use by other package developers
|
|
who want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-files
|
|
(package
|
|
(name "r-assertive-files")
|
|
(version "0.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.files" version))
|
|
(sha256
|
|
(base32
|
|
"02pfz8j5vwcj5kl6zca46894li7lxwnlrr29j922f14ay6kdssmy"))))
|
|
(properties
|
|
`((upstream-name . "assertive.files")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-numbers" ,r-assertive-numbers)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.files")
|
|
(synopsis "Assertions to check properties of files")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of files and connections. This is mainly for use by other
|
|
package developers who want to include run-time testing features in their own
|
|
packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-code
|
|
(package
|
|
(name "r-assertive-code")
|
|
(version "0.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.code" version))
|
|
(sha256
|
|
(base32
|
|
"1qhbp668zfvhqs8avkhg9amp4zyazz6dsy4fc6kpdmw3sv8yi07g"))))
|
|
(properties
|
|
`((upstream-name . "assertive.code")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-properties" ,r-assertive-properties)
|
|
("r-assertive-types" ,r-assertive-types)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.code")
|
|
(synopsis "Assertions to check properties of code")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of code. This is mainly for use by other package developers
|
|
who want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-datetimes
|
|
(package
|
|
(name "r-assertive-datetimes")
|
|
(version "0.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.datetimes" version))
|
|
(sha256
|
|
(base32
|
|
"00a98fx8p3pr3ckayh8wmxmm4rz01s67wah9697m92yci6pv3m78"))))
|
|
(properties
|
|
`((upstream-name . "assertive.datetimes")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-types" ,r-assertive-types)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.datetimes")
|
|
(synopsis "Assertions to check properties of dates and times")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of dates and times. This is mainly for use by other package
|
|
developers who want to include run-time testing features in their own
|
|
packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-strings
|
|
(package
|
|
(name "r-assertive-strings")
|
|
(version "0.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.strings" version))
|
|
(sha256
|
|
(base32
|
|
"0n6jrk88670g4ym0r8ii40a08a90z1xadj8wcryk8h0nl04dchfm"))))
|
|
(properties
|
|
`((upstream-name . "assertive.strings")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-types" ,r-assertive-types)
|
|
("r-stringi" ,r-stringi)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.strings")
|
|
(synopsis "Assertions to check properties of strings")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of strings. This is mainly for use by other package developers
|
|
who want to include run-time testing features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-data-us
|
|
(package
|
|
(name "r-assertive-data-us")
|
|
(version "0.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.data.us" version))
|
|
(sha256
|
|
(base32
|
|
"1bgspn0sccmp9z7s7djvdvprgxlyc5vrxznp4zfjb79kwvgn83hq"))))
|
|
(properties
|
|
`((upstream-name . "assertive.data.us")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-strings" ,r-assertive-strings)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.data.us")
|
|
(synopsis "Assertions to check properties of strings")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of US-specific complex data types. This is mainly for use by
|
|
other package developers who want to include run-time testing features in
|
|
their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-data-uk
|
|
(package
|
|
(name "r-assertive-data-uk")
|
|
(version "0.0-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.data.uk" version))
|
|
(sha256
|
|
(base32
|
|
"1fzjvhwp7mwkqqix29khvs6zcrc82n6j4czvzzb473vyjyvdlj5b"))))
|
|
(properties
|
|
`((upstream-name . "assertive.data.uk")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-strings" ,r-assertive-strings)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.data.uk")
|
|
(synopsis "Assertions to check properties of strings")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of UK-specific complex data types. This is mainly for use by
|
|
other package developers who want to include run-time testing features in
|
|
their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive-data
|
|
(package
|
|
(name "r-assertive-data")
|
|
(version "0.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive.data" version))
|
|
(sha256
|
|
(base32
|
|
"00cvg2g36mdl8plrzx40m63qd55742mddqrchwy9n3c7mm4gn02s"))))
|
|
(properties
|
|
`((upstream-name . "assertive.data")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-strings" ,r-assertive-strings)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive.data")
|
|
(synopsis "Assertions to check properties of data")
|
|
(description
|
|
"This package provides a set of predicates and assertions for checking
|
|
the properties of (country independent) complex data types. This is mainly
|
|
for use by other package developers who want to include run-time testing
|
|
features in their own packages.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-assertive
|
|
(package
|
|
(name "r-assertive")
|
|
(version "0.3-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "assertive" version))
|
|
(sha256
|
|
(base32
|
|
"0blbbhlxcb5ffdxqxi62xs33ljiawh6s22a0pyvbbh79jf46rzr3"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertive-base" ,r-assertive-base)
|
|
("r-assertive-code" ,r-assertive-code)
|
|
("r-assertive-data" ,r-assertive-data)
|
|
("r-assertive-data-uk" ,r-assertive-data-uk)
|
|
("r-assertive-data-us" ,r-assertive-data-us)
|
|
("r-assertive-datetimes" ,r-assertive-datetimes)
|
|
("r-assertive-files" ,r-assertive-files)
|
|
("r-assertive-matrices" ,r-assertive-matrices)
|
|
("r-assertive-models" ,r-assertive-models)
|
|
("r-assertive-numbers" ,r-assertive-numbers)
|
|
("r-assertive-properties" ,r-assertive-properties)
|
|
("r-assertive-reflection" ,r-assertive-reflection)
|
|
("r-assertive-sets" ,r-assertive-sets)
|
|
("r-assertive-strings" ,r-assertive-strings)
|
|
("r-assertive-types" ,r-assertive-types)
|
|
("r-knitr" ,r-knitr)))
|
|
(home-page "https://bitbucket.org/richierocks/assertive")
|
|
(synopsis "Readable check functions to ensure code integrity")
|
|
(description
|
|
"This package provides lots of predicates (@code{is_*} functions) to
|
|
check the state of your variables, and assertions (@code{assert_*} functions)
|
|
to throw errors if they aren't in the right form.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-dotcall64
|
|
(package
|
|
(name "r-dotcall64")
|
|
(version "1.0-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dotCall64" version))
|
|
(sha256
|
|
(base32
|
|
"1b8p7m3w0m7bp977c6jz74xkd611cxg11j49yza59k5fp338scb9"))))
|
|
(properties `((upstream-name . "dotCall64")))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://git.math.uzh.ch/reinhard.furrer/dotCall64")
|
|
(synopsis "Enhanced foreign function interface supporting long vectors")
|
|
(description
|
|
"This package provides @code{.C64()}, an enhanced version of @code{.C()}
|
|
and @code{.Fortran()} from the R foreign function interface. @code{.C64()}
|
|
supports long vectors, arguments of type 64-bit integer, and provides a
|
|
mechanism to avoid unnecessary copies of read-only and write-only arguments.
|
|
This makes it a convenient and fast interface to C/C++ and Fortran code.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-spam
|
|
(package
|
|
(name "r-spam")
|
|
(version "2.2-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "spam" version))
|
|
(sha256
|
|
(base32
|
|
"024dgfnjfxvsiymbzrhadinamj6qy509f4sbd1zxql8ymkyxn7vi"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dotcall64" ,r-dotcall64)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://www.math.uzh.ch/pages/spam/")
|
|
(synopsis "Sparse matrix algebra")
|
|
(description
|
|
"This package provides a set of functions for sparse matrix algebra.
|
|
Differences with other sparse matrix packages are:
|
|
|
|
@enumerate
|
|
@item it only supports (essentially) one sparse matrix format;
|
|
@item it is based on transparent and simple structure(s);
|
|
@item it is tailored for MCMC calculations within G(M)RF;
|
|
@item and it is fast and scalable (with the extension package @code{spam64}).
|
|
@end enumerate\n")
|
|
;; Either of these licenses
|
|
(license (list license:bsd-3 license:lgpl2.0))))
|
|
|
|
(define-public r-fields
|
|
(package
|
|
(name "r-fields")
|
|
(version "9.8-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "fields" version))
|
|
(sha256
|
|
(base32
|
|
"1q9x68dczjym56v7x90x4x5br59vj3dww6w8v42zd3yl17h7c1h1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-maps" ,r-maps)
|
|
("r-spam" ,r-spam)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "http://www.image.ucar.edu/fields")
|
|
(synopsis "Tools for spatial data")
|
|
(description
|
|
"This is a package for curve, surface and function fitting with an
|
|
emphasis on splines, spatial data and spatial statistics. The major methods
|
|
include cubic, and thin plate splines, Kriging, and compactly supported
|
|
covariance functions for large data sets.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-spatialextremes
|
|
(package
|
|
(name "r-spatialextremes")
|
|
(version "2.0-7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "SpatialExtremes" version))
|
|
(sha256
|
|
(base32
|
|
"1y0h1pcfqp9ynxsr3yrfbihlwm25ypyb88jmm5k2g7xvm8h9g050"))))
|
|
(properties
|
|
`((upstream-name . "SpatialExtremes")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-fields" ,r-fields)
|
|
("r-maps" ,r-maps)))
|
|
(home-page "http://spatialextremes.r-forge.r-project.org/")
|
|
(synopsis "Modelling spatial extremes")
|
|
(description
|
|
"This package provides tools for the statistical modelling of spatial
|
|
extremes using max-stable processes, copula or Bayesian hierarchical models.
|
|
More precisely, this package allows (conditional) simulations from various
|
|
parametric max-stable models, analysis of the extremal spatial dependence, the
|
|
fitting of such processes using composite likelihoods or least square (simple
|
|
max-stable processes only), model checking and selection and prediction.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-drc
|
|
(package
|
|
(name "r-drc")
|
|
(version "3.0-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "drc" version))
|
|
(sha256
|
|
(base32
|
|
"0c8xn8ripzq270hy8d16fcnx02l02alddznd7fqwk3jyi6113h1y"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-car" ,r-car)
|
|
("r-gtools" ,r-gtools)
|
|
("r-mass" ,r-mass)
|
|
("r-multcomp" ,r-multcomp)
|
|
("r-plotrix" ,r-plotrix)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "https://cran.r-project.org/web/packages/drc")
|
|
(synopsis "Analysis of dose-response curves")
|
|
(description
|
|
"This package provides a suite of flexible and versatile model fitting
|
|
and after-fitting functions for the analysis of dose-response data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rmeta
|
|
(package
|
|
(name "r-rmeta")
|
|
(version "3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rmeta" version))
|
|
(sha256
|
|
(base32
|
|
"0vkbnxp579v8zmcv1isdbzj5swpr6fq17zwparxcvzswjc2x9ydr"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rmeta")
|
|
(synopsis "Tools for meta-analysis")
|
|
(description
|
|
"This package provides functions for simple fixed and random effects
|
|
meta-analysis for two-sample comparisons and cumulative meta-analyses. It
|
|
draws standard summary plots, funnel plots, and computes summaries and tests
|
|
for association and heterogeneity.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-bootstrap
|
|
(package
|
|
(name "r-bootstrap")
|
|
(version "2017.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bootstrap" version))
|
|
(sha256
|
|
(base32
|
|
"08lmsy7k8wsgv89yc904c6fidcymr1ma2ry4fl0p69p21v4iiwa4"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/bootstrap")
|
|
(synopsis "Functions for the book \"An Introduction to the Bootstrap\"")
|
|
(description
|
|
"This package provides software and data for the book \"An Introduction
|
|
to the Bootstrap\" by B. Efron and R. Tibshirani, 1993, Chapman and Hall.
|
|
This package is primarily provided for projects already based on it, and for
|
|
support of the book. New projects should preferentially use the recommended
|
|
package \"boot\".")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-survivalroc
|
|
(package
|
|
(name "r-survivalroc")
|
|
(version "1.0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "survivalROC" version))
|
|
(sha256
|
|
(base32
|
|
"0wnd65ff5w679hxa1zrpfrx9qg47q21pjxppsga6m3h4iq1yfj8l"))))
|
|
(properties `((upstream-name . "survivalROC")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/survivalROC")
|
|
(synopsis "Time-dependent ROC curve estimation from censored survival data")
|
|
(description
|
|
"Compute time-dependent ROC curve from censored survival data using
|
|
Kaplan-Meier (KM) or Nearest Neighbor Estimation (NNE) method of Heagerty,
|
|
Lumley & Pepe (Biometrics, Vol 56 No 2, 2000, PP 337-344)")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-longitudinal
|
|
(package
|
|
(name "r-longitudinal")
|
|
(version "1.1.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "longitudinal" version))
|
|
(sha256
|
|
(base32
|
|
"1d83ws28nxi3kw5lgd5n5y7865djq7ky72fw3ddi1fkkhg1r9y6l"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-corpcor" ,r-corpcor)))
|
|
(home-page "http://strimmerlab.org/software/longitudinal/")
|
|
(synopsis "Analysis of multiple time course data")
|
|
(description
|
|
"This package contains general data structures and functions for
|
|
longitudinal data with multiple variables, repeated measurements, and
|
|
irregularly spaced time points. It also implements a shrinkage estimator of
|
|
dynamical correlation and dynamical covariance.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-genenet
|
|
(package
|
|
(name "r-genenet")
|
|
(version "1.2.13")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "GeneNet" version))
|
|
(sha256
|
|
(base32
|
|
"0w52apk0nnr8nsskf26ff7ana8xiksr8wqmkjxzwhzgg7fncm61p"))))
|
|
(properties `((upstream-name . "GeneNet")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-corpcor" ,r-corpcor)
|
|
("r-fdrtool" ,r-fdrtool)
|
|
("r-longitudinal" ,r-longitudinal)))
|
|
(home-page "http://strimmerlab.org/software/genenet/")
|
|
(synopsis "Modeling and inferring gene networks")
|
|
(description
|
|
"This package analyzes gene expression (time series) data with focus on
|
|
the inference of gene networks. In particular, GeneNet implements the methods
|
|
of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
|
|
for learning large-scale gene association networks (including assignment of
|
|
putative directions).")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-rbamtools
|
|
(package
|
|
(name "r-rbamtools")
|
|
(version "2.16.11.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rbamtools" version))
|
|
(sha256
|
|
(base32
|
|
"0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj"))))
|
|
(build-system r-build-system)
|
|
(inputs `(("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-refgenome" ,r-refgenome)))
|
|
(home-page "https://cran.r-project.org/web/packages/rbamtools")
|
|
(synopsis "Read and write BAM (binary alignment) files")
|
|
(description
|
|
"This package provides an R interface to functions of the SAMtools
|
|
library.")
|
|
(license license:artistic2.0)))
|
|
|
|
(define-public r-protviz
|
|
(package
|
|
(name "r-protviz")
|
|
(version "0.4.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "protViz" version))
|
|
(sha256
|
|
(base32
|
|
"150i2q4nakz28f39kmhrchz4qsr8ax6y02512md94k8hq4hamxg1"))))
|
|
(properties `((upstream-name . "protViz")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("perl" ,perl)
|
|
("python-2" ,python-2)))
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/protViz/protViz/")
|
|
(synopsis "Visualizing and analyzing mass spectrometry data in proteomics")
|
|
(description
|
|
"This package helps with quality checks, visualizations and analysis of
|
|
mass spectrometry data, coming from proteomics experiments. The package is
|
|
developed, tested and used at the Functional Genomics Center Zurich, where it
|
|
is used mainly for prototyping, teaching, and having fun with proteomics data.
|
|
But it can also be used to do data analysis for small scale data sets.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-cmprsk
|
|
(package
|
|
(name "r-cmprsk")
|
|
(version "2.2-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cmprsk" version))
|
|
(sha256
|
|
(base32
|
|
"1nacbzx950ygaqgnj0949skhwpzar5i3xlscd44jsimk2gsppx6z"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-survival" ,r-survival)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/cmprsk")
|
|
(synopsis "Subdistribution analysis of competing risks")
|
|
(description
|
|
"This package provides tool for estimation, testing and regression
|
|
modeling of subdistribution functions in competing risks, as described in
|
|
Gray (1988), A class of K-sample tests for comparing the cumulative incidence
|
|
of a competing risk, Ann. Stat. 16:1141-1154, and Fine JP and Gray RJ (1999),
|
|
A proportional hazards model for the subdistribution of a competing risk,
|
|
JASA, 94:496-509.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-etm
|
|
(package
|
|
(name "r-etm")
|
|
(version "1.0.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "etm" version))
|
|
(sha256
|
|
(base32
|
|
"1yivbq8y0ijcl1m4nir4q9hp4pi6iphwxgjprygsdf7vp98wq677"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-data-table" ,r-data-table)
|
|
("r-lattice" ,r-lattice)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://cran.r-project.org/web/packages/etm")
|
|
(synopsis "Empirical transition matrix")
|
|
(description
|
|
"The @dfn{empirical transition matrix} (etm) package permits to estimate
|
|
the matrix of transition probabilities for any time-inhomogeneous multistate
|
|
model with finite state space using the Aalen-Johansen estimator.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-epi
|
|
(package
|
|
(name "r-epi")
|
|
(version "2.37")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Epi" version))
|
|
(sha256
|
|
(base32
|
|
"1lanr9x0c6w22406p56j7cwk6wck8njq6pscb4gzc613d68zj1lk"))))
|
|
(properties `((upstream-name . "Epi")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cmprsk" ,r-cmprsk)
|
|
("r-data-table" ,r-data-table)
|
|
("r-etm" ,r-etm)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-numderiv" ,r-numderiv)
|
|
("r-plyr" ,r-plyr)
|
|
("r-survival" ,r-survival)
|
|
("r-zoo" ,r-zoo)))
|
|
(home-page "http://BendixCarstensen.com/Epi/")
|
|
(synopsis "Statistical analysis in epidemiology")
|
|
(description
|
|
"This package provides functions for demographic and epidemiological
|
|
analysis in the Lexis diagram, i.e. register and cohort follow-up data, in
|
|
particular representation, manipulation and simulation of multistate data -
|
|
the Lexis suite of functions, which includes interfaces to the @code{mstate},
|
|
@code{etm} and @code{cmprsk} packages. It also contains functions for
|
|
Age-Period-Cohort and Lee-Carter modeling and a function for interval censored
|
|
data and some useful functions for tabulation and plotting, as well as a
|
|
number of epidemiological data sets.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ppls
|
|
(package
|
|
(name "r-ppls")
|
|
(version "1.6-1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ppls" version))
|
|
(sha256
|
|
(base32
|
|
"1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/ppls")
|
|
(synopsis "Penalized partial least squares")
|
|
(description
|
|
"This package contains linear and nonlinear regression methods based on
|
|
partial least squares and penalization techniques. Model parameters are
|
|
selected via cross-validation, and confidence intervals ans tests for the
|
|
regression coefficients can be conducted via jackknifing.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-huge
|
|
(package
|
|
(name "r-huge")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "huge" version))
|
|
(sha256
|
|
(base32
|
|
"1j93gvi1jyq3ld9jhdqhrpm2is54rk3ilmf3yw7fx6gva0y6hjqd"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-igraph" ,r-igraph)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcppeigen" ,r-rcppeigen)))
|
|
(home-page "https://cran.r-project.org/web/packages/huge")
|
|
(synopsis "High-dimensional undirected graph estimation")
|
|
(description
|
|
"This package provides a general framework for high-dimensional
|
|
undirected graph estimation. It integrates data preprocessing, neighborhood
|
|
screening, graph estimation, and model selection techniques into a pipeline.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-parcor
|
|
(package
|
|
(name "r-parcor")
|
|
(version "0.2-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "parcor" version))
|
|
(sha256
|
|
(base32
|
|
"0vgs6k92vdr0cmb8cwbv2ff6qavw30agskfd8bfh17hsskrisvx0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-epi" ,r-epi)
|
|
("r-genenet" ,r-genenet)
|
|
("r-glmnet" ,r-glmnet)
|
|
("r-mass" ,r-mass)
|
|
("r-ppls" ,r-ppls)))
|
|
(home-page "https://cran.r-project.org/web/packages/parcor")
|
|
(synopsis "Regularized estimation of partial correlation matrices")
|
|
(description
|
|
"This package estimates the matrix of partial correlations based on
|
|
different regularized regression methods: lasso, adaptive lasso, PLS, and
|
|
Ridge Regression. In addition, the package provides model selection for
|
|
lasso, adaptive lasso and Ridge regression based on cross-validation.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-mcmc
|
|
(package
|
|
(name "r-mcmc")
|
|
(version "0.9-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mcmc" version))
|
|
(sha256
|
|
(base32
|
|
"1fc6a6asn53lx7x7pnlb5mb716nv4pcmbp99f1i30y4hzygihfj4"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.stat.umn.edu/geyer/mcmc/")
|
|
(synopsis "Markov chain Monte Carlo")
|
|
(description
|
|
"This package simulates continuous distributions of random vectors using
|
|
@dfn{Markov chain Monte Carlo} (MCMC). Users specify the distribution by an R
|
|
function that evaluates the log unnormalized density. Algorithms are random
|
|
walk Metropolis algorithm (function @code{metrop}), simulated
|
|
tempering (function @code{temper}), and morphometric random walk
|
|
Metropolis (function @code{morph.metrop}), which achieves geometric ergodicity
|
|
by change of variable.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-listenv
|
|
(package
|
|
(name "r-listenv")
|
|
(version "0.7.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "listenv" version))
|
|
(sha256
|
|
(base32
|
|
"0ma5jsri2zqkrlsm9nqpikl7imbwfy1glsmk13mblw0q245h49k1"))))
|
|
(build-system r-build-system)
|
|
(native-inputs
|
|
`(("r-r-rsp" ,r-r-rsp))) ; vignette builder
|
|
(home-page "https://github.com/HenrikBengtsson/listenv")
|
|
(synopsis "Environments behaving (almost) as lists")
|
|
(description
|
|
"This package implements list environments. List environments are
|
|
environments that have list-like properties. For instance, the elements of a
|
|
list environment are ordered and can be accessed and iterated over using index
|
|
subsetting.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public r-globals
|
|
(package
|
|
(name "r-globals")
|
|
(version "0.12.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "globals" version))
|
|
(sha256
|
|
(base32
|
|
"0szyv1ayyk31bh3xqlkj43020w44xq6s4rw2bxwizyjssxm3b1br"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-codetools" ,r-codetools)))
|
|
(home-page "https://github.com/HenrikBengtsson/globals")
|
|
(synopsis "Identify global objects in R expressions")
|
|
(description
|
|
"This package provides tools to identify global (\"unknown\" or \"free\")
|
|
objects in R expressions by code inspection using various strategies, e.g.
|
|
conservative or liberal. The objective of this package is to make it as
|
|
simple as possible to identify global objects for the purpose of exporting
|
|
them in distributed compute environments.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public r-future
|
|
(package
|
|
(name "r-future")
|
|
(version "1.13.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "future" version))
|
|
(sha256
|
|
(base32
|
|
"0h8ng2a6vg4axd5f75xcb3ip9d95zi22fa048dq2bzlnncwlznjz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-globals" ,r-globals)
|
|
("r-listenv" ,r-listenv)))
|
|
(native-inputs
|
|
`(("r-r-rsp" ,r-r-rsp))) ; vignette builder
|
|
(home-page "https://github.com/HenrikBengtsson/future")
|
|
(synopsis "Unified parallel and distributed processing in R")
|
|
(description
|
|
"The purpose of this package is to provide a lightweight and unified
|
|
Future API for sequential and parallel processing of R expression via futures.
|
|
This package implements sequential, multicore, multisession, and cluster
|
|
futures. With these, R expressions can be evaluated on the local machine, in
|
|
parallel a set of local machines, or distributed on a mix of local and remote
|
|
machines. Extensions to this package implement additional backends for
|
|
processing futures via compute cluster schedulers etc. Because of its unified
|
|
API, there is no need to modify any code in order to switch from sequential on
|
|
the local machine to, say, distributed processing on a remote compute cluster.")
|
|
(license license:lgpl2.1+)))
|
|
|
|
(define-public r-future-apply
|
|
(package
|
|
(name "r-future-apply")
|
|
(version "1.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "future.apply" version))
|
|
(sha256
|
|
(base32
|
|
"00ma43ma3byrf9vfqqn9g8sn18c71ryhk7lpza5h7817f1kibw1h"))))
|
|
(properties `((upstream-name . "future.apply")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-future" ,r-future)
|
|
("r-globals" ,r-globals)))
|
|
(native-inputs
|
|
`(("r-r-rsp" ,r-r-rsp))) ; vignette builder
|
|
(home-page "https://github.com/HenrikBengtsson/future.apply")
|
|
(synopsis "Apply function to elements in parallel using futures")
|
|
(description
|
|
"This package provides implementations of @code{apply()},
|
|
@code{eapply()}, @code{lapply()}, @code{Map()}, @code{mapply()},
|
|
@code{replicate()}, @code{sapply()}, @code{tapply()}, and @code{vapply()} that
|
|
can be resolved using any future-supported backend, e.g. parallel on the local
|
|
machine or distributed on a compute cluster.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rsvd
|
|
(package
|
|
(name "r-rsvd")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rsvd" version))
|
|
(sha256
|
|
(base32
|
|
"1faskhf5j2bj9f971qljsmh182g3rnyilj1wwijz530a6skxidzz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)))
|
|
(home-page "https://github.com/erichson/rSVD")
|
|
(synopsis "Randomized singular value decomposition")
|
|
(description
|
|
"Low-rank matrix decompositions are fundamental tools and widely used for
|
|
data analysis, dimension reduction, and data compression. Classically, highly
|
|
accurate deterministic matrix algorithms are used for this task. However, the
|
|
emergence of large-scale data has severely challenged our computational
|
|
ability to analyze big data. The concept of randomness has been demonstrated
|
|
as an effective strategy to quickly produce approximate answers to familiar
|
|
problems such as the @dfn{singular value decomposition} (SVD). This package
|
|
provides several randomized matrix algorithms such as the randomized singular
|
|
value decomposition (@code{rsvd}), randomized principal component
|
|
analysis (@code{rpca}), randomized robust principal component
|
|
analysis (@code{rrpca}), randomized interpolative decomposition (@code{rid}),
|
|
and the randomized CUR decomposition (@code{rcur}). In addition several plot
|
|
functions are provided.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-sloop
|
|
(package
|
|
(name "r-sloop")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sloop" version))
|
|
(sha256
|
|
(base32
|
|
"00fk5fr5zsk2qxc1kfhmshhjxgnamm3401089sx8m2l529zd6r8j"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-codetools" ,r-codetools)
|
|
("r-crayon" ,r-crayon)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/r-lib/sloop")
|
|
(synopsis "Helpers for object-oriented programming in R")
|
|
(description
|
|
"This package provides a collection of helper functions designed to
|
|
help you to better understand object oriented programming in R, particularly
|
|
using @code{S3}.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-capushe
|
|
(package
|
|
(name "r-capushe")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "capushe" version))
|
|
(sha256
|
|
(base32
|
|
"1aa76ir1kp67hiz7dr60azyc71yzslshyc640fjh0fpw0sp5kwbc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/capushe/index.html")
|
|
(synopsis "Calibrating penalties using slope heuristics")
|
|
(description
|
|
"This package provides tools for the calibration of penalized criteria
|
|
for model selection. The calibration methods available are based on the slope
|
|
heuristics.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-dorng
|
|
(package
|
|
(name "r-dorng")
|
|
(version "1.7.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "doRNG" version))
|
|
(sha256
|
|
(base32
|
|
"1sb75aqkliprglfxc4x4wds6alqgzhvl2n812g1d32a88ra3slr7"))))
|
|
(properties `((upstream-name . "doRNG")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-foreach" ,r-foreach)
|
|
("r-iterators" ,r-iterators)
|
|
("r-pkgmaker" ,r-pkgmaker)
|
|
("r-rngtools" ,r-rngtools)))
|
|
(home-page "https://renozao.github.io/doRNG/")
|
|
(synopsis "Generic reproducible parallel backend for foreach loops")
|
|
(description
|
|
"This package provides functions to perform reproducible parallel
|
|
@code{foreach} loops, using independent random streams as generated by
|
|
L'Ecuyer's combined multiple-recursive generator. It enables to easily
|
|
convert standard @code{%dopar%} loops into fully reproducible loops,
|
|
independently of the number of workers, the task scheduling strategy, or the
|
|
chosen parallel environment and associated foreach backend.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-blockmodeling
|
|
(package
|
|
(name "r-blockmodeling")
|
|
(version "0.3.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "blockmodeling" version))
|
|
(sha256
|
|
(base32
|
|
"11v9903y9dwlzaqp8sx0fsibcg82phvappddy37r8lnxd4vchsd2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-doparallel" ,r-doparallel)
|
|
("r-dorng" ,r-dorng)
|
|
("r-foreach" ,r-foreach)
|
|
("r-matrix" ,r-matrix)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/blockmodeling")
|
|
(synopsis "Generalized and classical blockmodeling of valued networks")
|
|
(description
|
|
"This package is primarily meant as an implementation of generalized
|
|
blockmodeling for valued networks. In addition, measures of similarity or
|
|
dissimilarity based on structural equivalence and regular equivalence (REGE
|
|
algorithms) can be computed and partitioned matrices can be plotted.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-upsetr
|
|
(package
|
|
(name "r-upsetr")
|
|
(version "1.4.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "UpSetR" version))
|
|
(sha256
|
|
(base32
|
|
"007i0njnjjy7vbrxabwav7a1kk2n0hn2mkvqsdzzfk10ckp5y7im"))))
|
|
(properties `((upstream-name . "UpSetR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-plyr" ,r-plyr)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "https://github.com/hms-dbmi/UpSetR")
|
|
(synopsis "Visualize intersecting sets")
|
|
(description
|
|
"This package provides a more scalable alternative to Venn and Euler
|
|
diagrams for visualizing intersecting sets. Create visualizations of
|
|
intersecting sets using a novel matrix design, along with visualizations of
|
|
several common set, element and attribute related tasks.")
|
|
(license license:expat)))
|
|
|
|
;; This package includes a JavaScript file, which is not minified. When
|
|
;; upgrading please check that there are no new minified JavaScript files.
|
|
(define-public r-shinybs
|
|
(package
|
|
(name "r-shinybs")
|
|
(version "0.61")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinyBS" version))
|
|
(sha256
|
|
(base32
|
|
"0rhim4mbp4x9vvm7xkmpl7mhb9qd1gr96cr4dv330v863ra2kgji"))))
|
|
(properties `((upstream-name . "shinyBS")))
|
|
(build-system r-build-system)
|
|
;; The tests spawn Shiny browser apps. They cannot be run
|
|
;; non-interactively.
|
|
(arguments '(#:tests? #f))
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-shiny" ,r-shiny)))
|
|
(home-page "https://ebailey78.github.io/shinyBS/")
|
|
(synopsis "Twitter Bootstrap components for Shiny")
|
|
(description
|
|
"This package adds additional Twitter Bootstrap components to Shiny.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-outliers
|
|
(package
|
|
(name "r-outliers")
|
|
(version "0.14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "outliers" version))
|
|
(sha256
|
|
(base32
|
|
"0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/outliers/index.html")
|
|
(synopsis "Tests for outliers")
|
|
(description
|
|
"This package provides a collection of some tests commonly used for
|
|
identifying outliers.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-bayesm
|
|
(package
|
|
(name "r-bayesm")
|
|
(version "3.1-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bayesm" version))
|
|
(sha256
|
|
(base32
|
|
"0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)))
|
|
(home-page "http://www.perossi.org/home/bsm-1")
|
|
(synopsis "Bayesian inference for marketing/micro-econometrics")
|
|
(description
|
|
"This package covers many important models used in marketing and
|
|
micro-econometrics applications, including Bayes Regression (univariate or
|
|
multivariate dep var), Bayes Seemingly Unrelated Regression (SUR), Binary and
|
|
Ordinal Probit, Multinomial Logit (MNL) and Multinomial Probit (MNP),
|
|
Multivariate Probit, Negative Binomial (Poisson) Regression, Multivariate
|
|
Mixtures of Normals (including clustering), Dirichlet Process Prior Density
|
|
Estimation with normal base, Hierarchical Linear Models with normal prior and
|
|
covariates, Hierarchical Linear Models with a mixture of normals prior and
|
|
covariates, Hierarchical Multinomial Logits with a mixture of normals prior
|
|
and covariates, Hierarchical Multinomial Logits with a Dirichlet Process prior
|
|
and covariates, Hierarchical Negative Binomial Regression Models, Bayesian
|
|
analysis of choice-based conjoint data, Bayesian treatment of linear
|
|
instrumental variables models, Analysis of Multivariate Ordinal survey data
|
|
with scale usage heterogeneity, and Bayesian Analysis of Aggregate Random
|
|
Coefficient Logit Models.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-tensora
|
|
(package
|
|
(name "r-tensora")
|
|
(version "0.36.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tensorA" version))
|
|
(sha256
|
|
(base32
|
|
"176hjy3bvg3in62r97wxbhq187sjz6c1gwy9x6spaxl6k4my3zy7"))))
|
|
(properties `((upstream-name . "tensorA")))
|
|
(build-system r-build-system)
|
|
(home-page "http://www.stat.boogaart.de/tensorA")
|
|
(synopsis "Advanced tensor arithmetic with named indices")
|
|
(description
|
|
"This package provides convenience functions for advanced linear algebra
|
|
with tensors and computation with datasets of tensors on a higher level
|
|
abstraction. It includes Einstein and Riemann summing conventions, dragging,
|
|
co- and contravariate indices, and parallel computations on sequences of
|
|
tensors.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rarpack
|
|
(package
|
|
(name "r-rarpack")
|
|
(version "0.11-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rARPACK" version))
|
|
(sha256
|
|
(base32
|
|
"12h2y46xcfldhjdmm960swgn9b23zvkj5vg2bi42s9qxwgi02d63"))))
|
|
(properties `((upstream-name . "rARPACK")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rspectra" ,r-rspectra)))
|
|
(home-page "https://github.com/yixuan/rARPACK")
|
|
(synopsis "Solvers for large scale eigenvalue and SVD problems")
|
|
(description
|
|
"This package was previously an R wrapper of the ARPACK library, and now
|
|
a shell of the R package RSpectra, an R interface to the Spectra library for
|
|
solving large scale eigenvalue/vector problems. The current version of
|
|
rARPACK simply imports and exports the functions provided by RSpectra. New
|
|
users of rARPACK are advised to switch to the RSpectra package.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public r-compositions
|
|
(package
|
|
(name "r-compositions")
|
|
(version "1.40-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "compositions" version))
|
|
(sha256
|
|
(base32
|
|
"12mp05yi7jkdqg9iwh6bc9sx6sdxagcnrirznxy9hq8502p7238i"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bayesm" ,r-bayesm)
|
|
("r-energy" ,r-energy)
|
|
("r-robustbase" ,r-robustbase)
|
|
("r-tensora" ,r-tensora)))
|
|
(home-page "http://www.stat.boogaart.de/compositions")
|
|
(synopsis "Compositional data analysis")
|
|
(description
|
|
"This package provides functions for the consistent analysis of
|
|
compositional data (e.g. portions of substances) and positive
|
|
numbers (e.g. concentrations).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-cobs
|
|
(package
|
|
(name "r-cobs")
|
|
(version "1.3-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "cobs" version))
|
|
(sha256
|
|
(base32
|
|
"1pqvz7czcchri4x79g78hbwyagb3bqzdqb047zkbdinyz067c7kb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-quantreg" ,r-quantreg)
|
|
("r-sparsem" ,r-sparsem)))
|
|
(home-page "https://cran.r-project.org/web/packages/cobs")
|
|
(synopsis "Constrained B-Splines (sparse matrix based)")
|
|
(description
|
|
"This package provides qualitatively constrained (regression) smoothing
|
|
splines via linear programming and sparse matrices.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-drimpute
|
|
(package
|
|
(name "r-drimpute")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DrImpute" version))
|
|
(sha256
|
|
(base32
|
|
"1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"))))
|
|
(properties `((upstream-name . "DrImpute")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)))
|
|
(home-page "https://github.com/ikwak2/DrImpute")
|
|
(synopsis "Imputing dropout events in single-cell RNA-Seq data")
|
|
(description
|
|
"This is an R package for imputing dropout events. Many statistical
|
|
methods in cell type identification, visualization and lineage reconstruction
|
|
do not account for dropout events. DrImpute can improve the performance of
|
|
such software by imputing dropout events.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-gamlss-dist
|
|
(package
|
|
(name "r-gamlss-dist")
|
|
(version "5.1-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gamlss.dist" version))
|
|
(sha256
|
|
(base32
|
|
"0zi87lgigr83l35zqq1y1g4cdq6ssjamripzz7yis74aznh6qg1l"))))
|
|
(properties `((upstream-name . "gamlss.dist")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mass" ,r-mass)))
|
|
(home-page "http://www.gamlss.org/")
|
|
(synopsis "Distributions for Generalized Additive Models for location scale and shape")
|
|
(description
|
|
"This package provides a set of distributions which can be used for
|
|
modelling the response variables in Generalized Additive Models for Location
|
|
Scale and Shape. The distributions can be continuous, discrete or mixed
|
|
distributions. Extra distributions can be created, by transforming, any
|
|
continuous distribution defined on the real line, to a distribution defined on
|
|
ranges 0 to infinity or 0 to 1, by using a @code{log} or a @code{logit}
|
|
transformation, respectively.")
|
|
;; Either version of the GPL.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
;; This package includes JavaScript files, which are not minified. When
|
|
;; upgrading please check that there are no new minified JavaScript files.
|
|
(define-public r-shinyjs
|
|
(package
|
|
(name "r-shinyjs")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "shinyjs" version))
|
|
(sha256
|
|
(base32
|
|
"113zpijri0l80rlgrvqn6bxk0sdqgl79h7yhja2p76f9dc9i2sr8"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-shiny" ,r-shiny)))
|
|
(home-page "https://deanattali.com/shinyjs")
|
|
(synopsis "Improve the user experience of your Shiny apps")
|
|
(description
|
|
"Perform common useful JavaScript operations in Shiny apps that will
|
|
greatly improve your apps without having to know any JavaScript. Examples
|
|
include: hiding an element, disabling an input, resetting an input back to its
|
|
original value, delaying code execution by a few seconds, and many more useful
|
|
functions for both the end user and the developer. Shinyjs can also be used
|
|
to easily call your own custom JavaScript functions from R.")
|
|
(license license:agpl3+)))
|
|
|
|
;; This package includes minified JavaScript files. When upgrading please
|
|
;; check that there are no new minified JavaScript files.
|
|
(define-public r-colourpicker
|
|
(package
|
|
(name "r-colourpicker")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "colourpicker" version))
|
|
(sha256
|
|
(base32
|
|
"0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(srfi srfi-1)
|
|
(ice-9 popen))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'process-javascript
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(with-directory-excursion "inst"
|
|
(call-with-values
|
|
(lambda ()
|
|
(unzip2
|
|
`((,(assoc-ref inputs "js-salvattore")
|
|
"examples/colourInput/www/salvattore.min.js")
|
|
(,(assoc-ref inputs "js-jquery")
|
|
"htmlwidgets/lib/jquery/jquery.min.js")
|
|
("www/shared/colourpicker/js/colourpicker.js"
|
|
"www/shared/colourpicker/js/colourpicker.min.js"))))
|
|
(lambda (sources targets)
|
|
(for-each (lambda (source target)
|
|
(format #t "Processing ~a --> ~a~%"
|
|
source target)
|
|
(delete-file target)
|
|
(let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
|
|
(call-with-output-file target
|
|
(lambda (port)
|
|
(dump-port minified port)))))
|
|
sources targets))))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-miniui" ,r-miniui)
|
|
("r-shiny" ,r-shiny)
|
|
("r-shinyjs" ,r-shinyjs)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)
|
|
("js-jquery"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://code.jquery.com/jquery-3.3.1.js")
|
|
(sha256
|
|
(base32
|
|
"1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
|
|
("js-salvattore"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://raw.githubusercontent.com/rnmp/salvattore/v1.0.9/dist/salvattore.js")
|
|
(sha256
|
|
(base32
|
|
"0lfrbx7l9w5x89jpc6njmd0pk7h8fpvg537vklai2vf7b1r2nnk5"))))))
|
|
(home-page "https://github.com/daattali/colourpicker")
|
|
(synopsis "Color picker tool for Shiny and for selecting colors in plots")
|
|
(description
|
|
"This package provides a color picker that can be used as an input in
|
|
Shiny apps or Rmarkdown documents. The color picker supports alpha opacity,
|
|
custom color palettes, and many more options. A plot color helper tool is
|
|
available as an RStudio Addin, which helps you pick colors to use in your
|
|
plots. A more generic color picker RStudio Addin is also provided to let you
|
|
select colors to use in your R code.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ggextra
|
|
(package
|
|
(name "r-ggextra")
|
|
(version "0.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggExtra" version))
|
|
(sha256
|
|
(base32
|
|
"1m5zpn3l3p1y3d2692gyz50m63d58m2a3b7zb595kvcffdx2qr5b"))))
|
|
(properties `((upstream-name . "ggExtra")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-colourpicker" ,r-colourpicker)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gtable" ,r-gtable)
|
|
("r-miniui" ,r-miniui)
|
|
("r-scales" ,r-scales)
|
|
("r-shiny" ,r-shiny)
|
|
("r-shinyjs" ,r-shinyjs)))
|
|
(home-page "https://github.com/daattali/ggExtra")
|
|
(synopsis "Marginal histograms for ggplot2 and other enhancements")
|
|
(description
|
|
"This package is a collection of functions and layers to enhance ggplot2.
|
|
The flagship function is @code{ggMarginal()}, which can be used to add
|
|
marginal histograms/boxplots/density plots to ggplot2 scatterplots.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-minpack-lm
|
|
(package
|
|
(name "r-minpack-lm")
|
|
(version "1.2-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "minpack.lm" version))
|
|
(sha256
|
|
(base32
|
|
"18ym2pdql5vzngc7q5gn66d153hrfrnd8ilv8yh6vd7j7sx7vjql"))))
|
|
(properties `((upstream-name . "minpack.lm")))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/minpack.lm")
|
|
(synopsis "Levenberg-Marquardt Nonlinear Least-Squares algorithm")
|
|
(description
|
|
"The @code{nls.lm} function provides an R interface to @code{lmder} and
|
|
@code{lmdif} from the MINPACK library, for solving nonlinear least-squares
|
|
problems by a modification of the Levenberg-Marquardt algorithm, with support
|
|
for lower and upper parameter bounds. The implementation can be used via
|
|
@code{nls}-like calls using the @code{nlsLM} function.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-moments
|
|
(package
|
|
(name "r-moments")
|
|
(version "0.14")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "moments" version))
|
|
(sha256
|
|
(base32
|
|
"0f9y58w1hxcz4bqivirx25ywlmc80gbi6dfx5cnhkpdg1pk82fra"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/moments")
|
|
(synopsis "Moments, cumulants, skewness, kurtosis and related tests")
|
|
(description
|
|
"This package provides functions to calculate: moments, Pearson's
|
|
kurtosis, Geary's kurtosis and skewness; it also includes tests related to
|
|
them (Anscombe-Glynn, D'Agostino, Bonett-Seier).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-msir
|
|
(package
|
|
(name "r-msir")
|
|
(version "1.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "msir" version))
|
|
(sha256
|
|
(base32
|
|
"0pvc3q162vqq3k39nni732x05zzfz4y9y2zf56d83185ypszv9kb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mclust" ,r-mclust)))
|
|
(home-page "https://cran.r-project.org/web/packages/msir")
|
|
(synopsis "Model-based sliced inverse regression")
|
|
(description
|
|
"This is an R package for dimension reduction based on finite Gaussian
|
|
mixture modeling of inverse regression.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-pbivnorm
|
|
(package
|
|
(name "r-pbivnorm")
|
|
(version "0.6.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pbivnorm" version))
|
|
(sha256
|
|
(base32
|
|
"05jzrjqxzbcf6z245hlk7sjxiszv9paadaaimvcx5y5qgi87vhq7"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://github.com/brentonk/pbivnorm")
|
|
(synopsis "Vectorized bivariate normal CDF")
|
|
(description
|
|
"This package provides a vectorized R function for calculating
|
|
probabilities from a standard bivariate normal CDF.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-lavaan
|
|
(package
|
|
(name "r-lavaan")
|
|
(version "0.6-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lavaan" version))
|
|
(sha256
|
|
(base32
|
|
"0hw856kv11zqn6nd4216rh19i6xbnc1rh044r7jvvxkhzgbqkyxz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-mass" ,r-mass)
|
|
("r-mnormt" ,r-mnormt)
|
|
("r-numderiv" ,r-numderiv)
|
|
("r-pbivnorm" ,r-pbivnorm)))
|
|
(home-page "http://lavaan.ugent.be")
|
|
(synopsis "Latent variable analysis")
|
|
(description
|
|
"This package provides tools to fit a variety of latent variable models,
|
|
including confirmatory factor analysis, structural equation modeling and
|
|
latent growth curve models.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-nonnest2
|
|
(package
|
|
(name "r-nonnest2")
|
|
(version "0.5-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nonnest2" version))
|
|
(sha256
|
|
(base32
|
|
"1bq44qqmm59j91m0sny4xnqmxqlga4cm48qdsw8xfs3x19xwmxk6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-compquadform" ,r-compquadform)
|
|
("r-lavaan" ,r-lavaan)
|
|
("r-mvtnorm" ,r-mvtnorm)
|
|
("r-sandwich" ,r-sandwich)))
|
|
(home-page "https://cran.r-project.org/web/packages/nonnest2/")
|
|
(synopsis "Tests of non-nested models")
|
|
(description
|
|
"This package allows for testing of non-nested models. It includes tests
|
|
of model distinguishability and of model fit that can be applied to both
|
|
nested and non-nested models. The package also includes functionality to
|
|
obtain confidence intervals associated with AIC and BIC.")
|
|
;; Either version of the GPL.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-penalized
|
|
(package
|
|
(name "r-penalized")
|
|
(version "0.9-51")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "penalized" version))
|
|
(sha256
|
|
(base32
|
|
"1zcrwa93mc27qj3g4ayc2k895r6g8q0g6qb2azmvj7wqk750va7a"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-rcpparmadillo" ,r-rcpparmadillo)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://cran.r-project.org/web/packages/penalized/")
|
|
(synopsis "Penalized estimation in GLMs and in the Cox model")
|
|
(description
|
|
"This package provides tools for fitting possibly high dimensional
|
|
penalized regression models. The penalty structure can be any combination of
|
|
an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a positivity
|
|
constraint on the regression coefficients. The supported regression models
|
|
are linear, logistic and Poisson regression and the Cox Proportional Hazards
|
|
model. Cross-validation routines allow optimization of the tuning
|
|
parameters.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-zim
|
|
(package
|
|
(name "r-zim")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ZIM" version))
|
|
(sha256
|
|
(base32
|
|
"0scyfjn4ilsvha3x41c3b8bcfi31hlhwm77wn2a8hj5dsvnnmzig"))))
|
|
(properties `((upstream-name . "ZIM")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-mass" ,r-mass)))
|
|
(home-page "https://github.com/biostatstudio/ZIM")
|
|
(synopsis "Zero-inflated models (ZIM) for count time series with excess zeros")
|
|
(description
|
|
"Analyze count time series with excess zeros. Two types of statistical
|
|
models are supported: Markov regression and state-space models. They are also
|
|
known as observation-driven and parameter-driven models respectively in the
|
|
time series literature. The functions used for Markov regression or
|
|
observation-driven models can also be used to fit ordinary regression models
|
|
with independent data under the zero-inflated Poisson (ZIP) or zero-inflated
|
|
negative binomial (ZINB) assumption. The package also contains miscellaneous
|
|
functions to compute density, distribution, quantile, and generate random
|
|
numbers from ZIP and ZINB distributions.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-nor1mix
|
|
(package
|
|
(name "r-nor1mix")
|
|
(version "1.3-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "nor1mix" version))
|
|
(sha256
|
|
(base32
|
|
"1817wcvlmxs70vs4db0jkxd7i037744zz8ay3c2a9949z29fxr4w"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/nor1mix/")
|
|
(synopsis "Normal (1-d) mixture models")
|
|
(description
|
|
"This package provides S3 classes and methods for one-dimensional normal
|
|
mixture models, for, e.g., density estimation or clustering algorithms
|
|
research and teaching; it provides the widely used Marron-Wand densities. It
|
|
also provides tools for efficient random number generation and graphics.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-beanplot
|
|
(package
|
|
(name "r-beanplot")
|
|
(version "1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "beanplot" version))
|
|
(sha256
|
|
(base32
|
|
"0wmkr704fl8kdxkjwmaxw2a2h5dwzfgsgpncnk2p2wd4768jknj9"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/beanplot/")
|
|
(synopsis "Visualization via beanplots")
|
|
(description
|
|
"This package provides beanplots, an alternative to
|
|
boxplot/stripchart/violin plots. It can be used to plot univariate comparison
|
|
graphs.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-pbdzmq
|
|
(package
|
|
(name "r-pbdzmq")
|
|
(version "0.3-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pbdZMQ" version))
|
|
(sha256
|
|
(base32
|
|
"1jkfcfhspvqra7vbllrvkz3jx8j7d0ang6zzcdjgpb7200sc29mf"))))
|
|
(properties `((upstream-name . "pbdZMQ")))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("zeromq" ,zeromq)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("pkg-config" ,pkg-config)))
|
|
(home-page "https://pbdr.org/")
|
|
(synopsis "R interface to ZeroMQ")
|
|
(description
|
|
"ZeroMQ is a well-known library for high-performance asynchronous
|
|
messaging in scalable, distributed applications. This package provides high
|
|
level R wrapper functions to easily utilize ZeroMQ. The main focus is on
|
|
interactive client/server programming frameworks. A few wrapper functions
|
|
compatible with @code{rzmq} are also provided.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-repr
|
|
(package
|
|
(name "r-repr")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "repr" version))
|
|
(sha256
|
|
(base32
|
|
"0jy43g34r38fqprcdys0p9pliahrj5l64a9bbkzy206qgz0j5ppc"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-pillar" ,r-pillar)))
|
|
(home-page "https://cran.r-project.org/web/packages/repr/")
|
|
(synopsis "Serializable representations")
|
|
(description
|
|
"This package provides string and binary representations of objects for
|
|
several formats and MIME types.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-irdisplay
|
|
(package
|
|
(name "r-irdisplay")
|
|
(version "0.7.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "IRdisplay" version))
|
|
(sha256
|
|
(base32
|
|
"12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"))))
|
|
(properties `((upstream-name . "IRdisplay")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-repr" ,r-repr)))
|
|
(home-page "https://cran.r-project.org/web/packages/IRdisplay/")
|
|
(synopsis "Jupyter display machinery")
|
|
(description
|
|
"This package provides an interface to the rich display capabilities of
|
|
Jupyter front-ends (e.g. Jupyter Notebook). It is designed to be used from a
|
|
running IRkernel session.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-irkernel
|
|
(package
|
|
(name "r-irkernel")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "IRkernel" version))
|
|
(sha256
|
|
(base32
|
|
"1gij59b068qp7sbn9d0b9ghmnhfks15a9anj7bp26acv0yvdsg3s"))))
|
|
(properties `((upstream-name . "IRkernel")))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'install 'install-kernelspec
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(setenv "HOME" "/tmp")
|
|
(invoke "jupyter" "kernelspec" "install"
|
|
"--name" "ir"
|
|
"--prefix" out
|
|
(string-append out "/site-library/IRkernel/kernelspec"))
|
|
#t))))))
|
|
(inputs
|
|
`(("jupyter" ,jupyter)))
|
|
(propagated-inputs
|
|
`(("r-crayon" ,r-crayon)
|
|
("r-digest" ,r-digest)
|
|
("r-evaluate" ,r-evaluate)
|
|
("r-irdisplay" ,r-irdisplay)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-pbdzmq" ,r-pbdzmq)
|
|
("r-repr" ,r-repr)
|
|
("r-uuid" ,r-uuid)))
|
|
(home-page "https://cran.r-project.org/web/packages/IRkernel/")
|
|
(synopsis "Native R kernel for Jupyter")
|
|
(description
|
|
"The R kernel for the Jupyter environment executes R code which the
|
|
front-end (Jupyter Notebook or other front-ends) submits to the kernel via the
|
|
network.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-gmodels
|
|
(package
|
|
(name "r-gmodels")
|
|
(version "2.18.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gmodels" version))
|
|
(sha256
|
|
(base32
|
|
"0s8kd8krqk4kwv2zqxpsfy3w8qdwf5naf4b5l383vidq9sil0qb2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gdata" ,r-gdata)
|
|
("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/gmodels/")
|
|
(synopsis "Various R programming tools for model fitting")
|
|
(description
|
|
"This package provides various R programming tools for model fitting.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-apcluster
|
|
(package
|
|
(name "r-apcluster")
|
|
(version "1.4.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "apcluster" version))
|
|
(sha256
|
|
(base32
|
|
"188hdfmwjjx3aic599nwmkzjqm9j9jighi5bly6qd43c1vj6ih2s"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-matrix" ,r-matrix)
|
|
("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/apcluster/")
|
|
(synopsis "Affinity propagation clustering")
|
|
(description
|
|
"This package implements affinity propagation clustering introduced by
|
|
Frey and Dueck (2007). The package further provides leveraged affinity
|
|
propagation and an algorithm for exemplar-based agglomerative clustering that
|
|
can also be used to join clusters obtained from affinity propagation. Various
|
|
plotting functions are available for analyzing clustering results.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-valr
|
|
(package
|
|
(name "r-valr")
|
|
(version "0.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "valr" version))
|
|
(sha256
|
|
(base32
|
|
"14jhrwkiwmha3vlmm7b50n2xxyizj6ddmy89gb20mpzq7qhz1ika"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-broom" ,r-broom)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-readr" ,r-readr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "http://github.com/rnabioco/valr")
|
|
(synopsis "Genome interval arithmetic in R")
|
|
(description
|
|
"This package enables you to read and manipulate genome intervals and
|
|
signals. It provides functionality similar to command-line tool suites within
|
|
R, enabling interactive analysis and visualization of genome-scale data.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-rematch2
|
|
(package
|
|
(name "r-rematch2")
|
|
(version "2.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rematch2" version))
|
|
(sha256
|
|
(base32
|
|
"16k0i5p7fa3qfxv59ijyn638wpz8n4jrkrnilqmh5g9l8f8bn4h6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/r-lib/rematch2")
|
|
(synopsis "Tidy output from regular expression matching")
|
|
(description
|
|
"This package provides wrappers on @code{regexpr} and @code{gregexpr} to
|
|
return the match results in tidy data frames.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-picante
|
|
(package
|
|
(name "r-picante")
|
|
(version "1.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "picante" version))
|
|
(sha256
|
|
(base32
|
|
"1bcq2j7fs89c2jib68qq6la67rxyg9raryf162mwvjakpf6k19l1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ape" ,r-ape)
|
|
("r-nlme" ,r-nlme)
|
|
("r-vegan" ,r-vegan)))
|
|
(home-page "https://cran.r-project.org/web/packages/picante/")
|
|
(synopsis "Integrating phylogenies and ecology")
|
|
(description
|
|
"This package provides functions for phylocom integration, community
|
|
analyses, null-models, traits and evolution. It implements numerous
|
|
ecophylogenetic approaches including measures of community phylogenetic and
|
|
trait diversity, phylogenetic signal, estimation of trait values for
|
|
unobserved taxa, null models for community and phylogeny randomizations, and
|
|
utility functions for data input/output and phylogeny plotting. A full
|
|
description of package functionality and methods are provided by Kembel et
|
|
al. (2010).")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-reinforcelearn
|
|
(package
|
|
(name "r-reinforcelearn")
|
|
(version "0.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "reinforcelearn" version))
|
|
(sha256
|
|
(base32
|
|
"176z2q69p24i29a8sh19xxn2zl3h1z2ixdssr5i6m4yvkvdrvv3b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-checkmate" ,r-checkmate)
|
|
("r-nnet" ,r-nnet)
|
|
("r-purrr" ,r-purrr)
|
|
("r-r6" ,r-r6)))
|
|
(home-page "https://markusdumke.github.io/reinforcelearn")
|
|
(synopsis "Reinforcement learning")
|
|
(description
|
|
"This package implements reinforcement learning environments and
|
|
algorithms as described in Sutton & Barto (1998). The Q-Learning algorithm
|
|
can be used with function approximation, eligibility traces (Singh & Sutton,
|
|
1996) and experience replay (Mnih et al., 2013).")
|
|
(license license:expat)))
|
|
|
|
(define-public r-lemon
|
|
(package
|
|
(name "r-lemon")
|
|
(version "0.4.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "lemon" version))
|
|
(sha256
|
|
(base32
|
|
"0wsn5bfg10wq4dnrgpyraz2bzx9p19c7hf1pwj3h4zmpqfgsdbpw"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-gtable" ,r-gtable)
|
|
("r-knitr" ,r-knitr)
|
|
("r-lattice" ,r-lattice)
|
|
("r-plyr" ,r-plyr)
|
|
("r-scales" ,r-scales)))
|
|
(home-page "https://github.com/stefanedwards/lemon")
|
|
(synopsis "Freshen up your ggplot2 plots")
|
|
(description
|
|
"This package provides functions for working with legends and axis lines
|
|
of ggplot2, facets that repeat axis lines on all panels, and some knitr
|
|
extensions.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-wgaim
|
|
(package
|
|
(name "r-wgaim")
|
|
(version "1.4-11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "wgaim" version))
|
|
(sha256
|
|
(base32
|
|
"1jjyp100dcjjczp61xlvhmy48ynniqcys535vzbgswhr7fvijymg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lattice" ,r-lattice)
|
|
("r-qtl" ,r-qtl)))
|
|
(home-page "https://cran.r-project.org/web/packages/wgaim")
|
|
(synopsis "Whole genome average interval mapping for QTL detection")
|
|
(description
|
|
"This package integrates sophisticated mixed modelling methods with a
|
|
whole genome approach to detecting significant QTL in linkage maps.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-bedr
|
|
(package
|
|
(name "r-bedr")
|
|
(version "1.0.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bedr" version))
|
|
(sha256
|
|
(base32
|
|
"0zpqvyjgwyqawxm8qrhcv8zq2b3yxgcqkkc87br29yrl7sjb8h6j"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-data-table" ,r-data-table)
|
|
("r-r-utils" ,r-r-utils)
|
|
("r-testthat" ,r-testthat)
|
|
("r-venndiagram" ,r-venndiagram)
|
|
("r-yaml" ,r-yaml)
|
|
("bedops" ,bedops)
|
|
("bedtools" ,bedtools)
|
|
("htslib" ,htslib))) ; for tabix
|
|
(native-inputs
|
|
`(("r-knitr" ,r-knitr))) ; for vignettes
|
|
(home-page "https://cran.r-project.org/web/packages/bedr")
|
|
(synopsis "Genomic region processing")
|
|
(description
|
|
"This package is for genomic regions processing using command line tools
|
|
such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient
|
|
utilities to perform genome arithmetic e.g indexing, formatting and merging.
|
|
The bedr package's API enhances access to these tools as well as offers
|
|
additional utilities for genomic regions processing.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-partitions
|
|
(package
|
|
(name "r-partitions")
|
|
(version "1.9-19")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "partitions" version))
|
|
(sha256
|
|
(base32
|
|
"1pklfnjdc094c8nzkqcdvqzdh8v3p5n8jbg4pf9678iw648saiyx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gmp" ,r-gmp)
|
|
("r-polynom" ,r-polynom)))
|
|
(home-page "https://cran.r-project.org/web/packages/partitions")
|
|
(synopsis "Additive partitions of integers")
|
|
(description
|
|
"This package provides tools to enumerates the partitions, unequal
|
|
partitions, and restricted partitions of an integer; the three corresponding
|
|
partition functions are also given.")
|
|
;; Any version of the GPL
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-brobdingnag
|
|
(package
|
|
(name "r-brobdingnag")
|
|
(version "1.2-6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Brobdingnag" version))
|
|
(sha256
|
|
(base32
|
|
"1m3ajvcksqfck5l5hj5xiflj4ry6d896ybv4f0xxks8chgnwmv0r"))))
|
|
(properties `((upstream-name . "Brobdingnag")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/RobinHankin/Brobdingnag.git")
|
|
(synopsis "Very large numbers in R")
|
|
(description
|
|
"This package handles very large numbers in R. Real numbers are held
|
|
using their natural logarithms, plus a logical flag indicating sign. The
|
|
package includes a vignette that gives a step-by-step introduction to using S4
|
|
methods.")
|
|
;; Any version of the GPL
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-untb
|
|
(package
|
|
(name "r-untb")
|
|
(version "1.7-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "untb" version))
|
|
(sha256
|
|
(base32
|
|
"1i7m4vfslsix98dwx4jlrsldm7fhhfp25gr7aapcxqxms7ryaby6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-brobdingnag" ,r-brobdingnag)
|
|
("r-partitions" ,r-partitions)
|
|
("r-polynom" ,r-polynom)))
|
|
(home-page "https://github.com/RobinHankin/untb.git")
|
|
(synopsis "Ecological drift under the UNTB")
|
|
(description
|
|
"This package provides numerical simulations, and visualizations, of
|
|
Hubbell's @dfn{Unified Neutral Theory of Biodiversity} (UNTB).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-stepwise
|
|
(package
|
|
(name "r-stepwise")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "stepwise" version))
|
|
(sha256
|
|
(base32
|
|
"1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://stat.sfu.ca/statgen/research/stepwise.html")
|
|
(synopsis "Stepwise detection of recombination breakpoints")
|
|
(description
|
|
"This package provides a stepwise approach to identifying recombination
|
|
breakpoints in a genomic sequence alignment.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-snpmaxsel
|
|
(package
|
|
(name "r-snpmaxsel")
|
|
(version "1.0-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "SNPmaxsel" version))
|
|
(sha256
|
|
(base32
|
|
"0pjvixwqzjd3jwccc8yqq9c76afvbmfq0z1w0cwyj8bblrjpx13z"))))
|
|
(properties `((upstream-name . "SNPmaxsel")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-combinat" ,r-combinat)
|
|
("r-mvtnorm" ,r-mvtnorm)))
|
|
(home-page "https://cran.r-project.org/web/packages/SNPmaxsel/index.html")
|
|
(synopsis "Maximally selected statistics for SNP data")
|
|
(description
|
|
"This package implements asymptotic methods related to maximally selected
|
|
statistics, with applications to @dfn{single-nucleotide polymorphism} (SNP)
|
|
data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-acsnminer
|
|
(package
|
|
(name "r-acsnminer")
|
|
(version "0.16.8.25")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ACSNMineR" version))
|
|
(sha256
|
|
(base32
|
|
"0gh604s8qall6zfjlwcg2ilxjvz08dplf9k5g47idhv43scm748l"))))
|
|
(properties `((upstream-name . "ACSNMineR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)))
|
|
(home-page "https://cran.r-project.org/web/packages/ACSNMineR")
|
|
(synopsis "Gene enrichment analysis")
|
|
(description
|
|
"This package provides tools to compute and represent gene set enrichment
|
|
or depletion from your data based on pre-saved maps from the @dfn{Atlas of
|
|
Cancer Signalling Networks} (ACSN) or user imported maps. The gene set
|
|
enrichment can be run with hypergeometric test or Fisher exact test, and can
|
|
use multiple corrections. Visualization of data can be done either by
|
|
barplots or heatmaps.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-seqinr
|
|
(package
|
|
(name "r-seqinr")
|
|
(version "3.4-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "seqinr" version))
|
|
(sha256
|
|
(base32
|
|
"17zv0n5cji17izwmwg0jcbxbjl3w5rls91w15svcnlpxjms38ahn"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ade4" ,r-ade4)
|
|
("r-segmented" ,r-segmented)))
|
|
(inputs
|
|
`(("zlib" ,zlib)))
|
|
(home-page "http://seqinr.r-forge.r-project.org/")
|
|
(synopsis "Biological sequences retrieval and analysis")
|
|
(description
|
|
"This package provides tools for exploratory data analysis and data
|
|
visualization of biological sequence (DNA and protein) data. It also includes
|
|
utilities for sequence data management under the ACNUC system.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-units
|
|
(package
|
|
(name "r-units")
|
|
(version "0.6-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "units" version))
|
|
(sha256
|
|
(base32
|
|
"0kx640h60s3zzkdr302asap7diap6vri6d41scnx507yvkcqiph3"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("udunits" ,udunits)))
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/r-quantities/units/")
|
|
(synopsis "Measurement Units for R Vectors")
|
|
(description
|
|
"This package provides support for measurement units in R vectors,
|
|
matrices and arrays: automatic propagation, conversion, derivation and
|
|
simplification of units; raising errors in case of unit incompatibility. It
|
|
is compatible with the @code{POSIXct}, @code{Date} and @code{difftime}
|
|
classes.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-classint
|
|
(package
|
|
(name "r-classint")
|
|
(version "0.3-3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "classInt" version))
|
|
(sha256
|
|
(base32
|
|
"0c2z6shlxa928xa20yl956r06lx20mji3mwipdvmj3f4z5g6hgm9"))))
|
|
(properties `((upstream-name . "classInt")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-class" ,r-class)
|
|
("r-e1071" ,r-e1071)
|
|
("r-kernsmooth" ,r-kernsmooth)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://github.com/r-spatial/classInt/")
|
|
(synopsis "Choose univariate class intervals")
|
|
(description
|
|
"This package provides selected commonly used methods for choosing
|
|
univariate class intervals for mapping or other graphics purposes.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-spdata
|
|
(package
|
|
(name "r-spdata")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "spData" version))
|
|
(sha256
|
|
(base32
|
|
"162cqb331ki43jx4r8lpkjpn2l712figd896rnawg9j1jmjyl96y"))))
|
|
(properties `((upstream-name . "spData")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/Nowosad/spData")
|
|
(synopsis "Datasets for spatial analysis")
|
|
(description
|
|
"This a package containing diverse spatial datasets for demonstrating,
|
|
benchmarking and teaching spatial data analysis. It includes R data of class
|
|
@code{sf}, @code{Spatial}, and @code{nb}. It also contains data stored in a
|
|
range of file formats including GeoJSON, ESRI Shapefile and GeoPackage. Some
|
|
of the datasets are designed to illustrate specific analysis techniques.
|
|
@code{cycle_hire()} and @code{cycle_hire_osm()}, for example, are designed to
|
|
illustrate point pattern analysis techniques.")
|
|
(license license:cc0)))
|
|
|
|
(define-public r-learnbayes
|
|
(package
|
|
(name "r-learnbayes")
|
|
(version "2.15.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "LearnBayes" version))
|
|
(sha256
|
|
(base32
|
|
"0ch54v2zz2yyyk0lvn5rfikdmyz1qh9j1wk3585wl8v58mc0h4cv"))))
|
|
(properties `((upstream-name . "LearnBayes")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/LearnBayes")
|
|
(synopsis "Functions for learning Bayesian inference")
|
|
(description
|
|
"This package provides a collection of functions helpful in learning the
|
|
basic tenets of Bayesian statistical inference. It contains functions for
|
|
summarizing basic one and two parameter posterior distributions and predictive
|
|
distributions. It contains MCMC algorithms for summarizing posterior
|
|
distributions defined by the user. It also contains functions for regression
|
|
models, hierarchical models, Bayesian tests, and illustrations of Gibbs
|
|
sampling.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-deldir
|
|
(package
|
|
(name "r-deldir")
|
|
(version "0.1-21")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "deldir" version))
|
|
(sha256
|
|
(base32
|
|
"03392pl6j8rm3n32xrfkyfx866k1vm5sj87pva70yyiwh70vrnmr"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/deldir")
|
|
(synopsis "Delaunay triangulation and Dirichlet (Voronoi) tessellation")
|
|
(description
|
|
"This package provides tools for calculating the Delaunay triangulation
|
|
and the Dirichlet or Voronoi tessellation (with respect to the entire plane)
|
|
of a planar point set. It plots triangulations and tessellations in various
|
|
ways, clips tessellations to sub-windows, calculates perimeters of
|
|
tessellations, and summarizes information about the tiles of the
|
|
tessellation.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-sf
|
|
(package
|
|
(name "r-sf")
|
|
(version "0.7-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sf" version))
|
|
(sha256
|
|
(base32
|
|
"0vnyr7xyfcl928kbrb1k8l4fkd0cjrfq486g6gxpvy5j0cc2h4i1"))))
|
|
(build-system r-build-system)
|
|
(inputs
|
|
`(("gdal" ,gdal)
|
|
("geos" ,geos)
|
|
("proj" ,proj.4)
|
|
("zlib" ,zlib)))
|
|
(propagated-inputs
|
|
`(("r-classint" ,r-classint)
|
|
("r-dbi" ,r-dbi)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-units" ,r-units)))
|
|
(native-inputs `(("pkg-config" ,pkg-config)))
|
|
(home-page "https://github.com/r-spatial/sf/")
|
|
(synopsis "Simple features for R")
|
|
(description
|
|
"This package provides support for simple features, a standardized way to
|
|
encode spatial vector data. It binds to GDAL for reading and writing data, to
|
|
GEOS for geometrical operations, and to PROJ for projection conversions and
|
|
datum transformations.")
|
|
;; Either of these licenses
|
|
(license (list license:gpl2 license:expat))))
|
|
|
|
(define-public r-spdep
|
|
(package
|
|
(name "r-spdep")
|
|
(version "1.1-2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "spdep" version))
|
|
(sha256
|
|
(base32
|
|
"06mk81kc1ml2wjc8wwwgr0wasjcr4mwrxpfa8vfc373bmnha635s"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-boot" ,r-boot)
|
|
("r-coda" ,r-coda)
|
|
("r-deldir" ,r-deldir)
|
|
("r-expm" ,r-expm)
|
|
("r-gmodels" ,r-gmodels)
|
|
("r-learnbayes" ,r-learnbayes)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-nlme" ,r-nlme)
|
|
("r-sf" ,r-sf)
|
|
("r-sp" ,r-sp)
|
|
("r-spdata" ,r-spdata)))
|
|
(home-page "https://github.com/r-spatial/spdep/")
|
|
(synopsis "Spatial dependence: weighting schemes, statistics and models")
|
|
(description
|
|
"This package provides a collection of functions to create spatial
|
|
weights matrix objects from polygon contiguities, from point patterns by
|
|
distance and tessellations, for summarizing these objects, and for permitting
|
|
their use in spatial data analysis, including regional aggregation by minimum
|
|
spanning tree.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-adegenet
|
|
(package
|
|
(name "r-adegenet")
|
|
(version "2.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "adegenet" version))
|
|
(sha256
|
|
(base32
|
|
"0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ade4" ,r-ade4)
|
|
("r-ape" ,r-ape)
|
|
("r-boot" ,r-boot)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-igraph" ,r-igraph)
|
|
("r-mass" ,r-mass)
|
|
("r-reshape2" ,r-reshape2)
|
|
("r-seqinr" ,r-seqinr)
|
|
("r-shiny" ,r-shiny)
|
|
("r-spdep" ,r-spdep)
|
|
("r-vegan" ,r-vegan)))
|
|
(home-page "https://github.com/thibautjombart/adegenet")
|
|
(synopsis "Exploratory analysis of genetic and genomic data")
|
|
(description
|
|
"This package provides a toolset for the exploration of genetic and
|
|
genomic data. Adegenet provides formal (S4) classes for storing and handling
|
|
various genetic data, including genetic markers with varying ploidy and
|
|
hierarchical population structure (@code{genind} class), alleles counts by
|
|
populations (@code{genpop}), and genome-wide SNP data (@code{genlight}). It
|
|
also implements original multivariate methods (DAPC, sPCA), graphics,
|
|
statistical tests, simulation tools, distance and similarity measures, and
|
|
several spatial methods. A range of both empirical and simulated datasets is
|
|
also provided to illustrate various methods.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-pegas
|
|
(package
|
|
(name "r-pegas")
|
|
(version "0.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pegas" version))
|
|
(sha256
|
|
(base32
|
|
"0l21bapzbjcvblbvks3jh9rpy9hng1ccd7f0glhqw695lc737bpx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-adegenet" ,r-adegenet)
|
|
("r-ape" ,r-ape)))
|
|
(home-page "http://ape-package.ird.fr/pegas.html")
|
|
(synopsis "Population and evolutionary genetics analysis system")
|
|
(description
|
|
"This package provides functions for reading, writing, plotting,
|
|
analysing, and manipulating allelic and haplotypic data, including from VCF
|
|
files, and for the analysis of population nucleotide sequences and
|
|
micro-satellites including coalescent analyses, linkage disequilibrium,
|
|
population structure (Fst, Amova) and equilibrium (HWE), haplotype networks,
|
|
minimum spanning tree and network, and median-joining networks.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rmetasim
|
|
(package
|
|
(name "r-rmetasim")
|
|
(version "3.1.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rmetasim" version))
|
|
(sha256
|
|
(base32
|
|
"0sz4mdprdi6sgkfwfdvh2hr9nxiwq17sw0vggq3cvs7lzb0i6m9r"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ade4" ,r-ade4)
|
|
("r-adegenet" ,r-adegenet)
|
|
("r-gtools" ,r-gtools)
|
|
("r-pegas" ,r-pegas)))
|
|
(home-page "https://cran.r-project.org/web/packages/rmetasim")
|
|
(synopsis "Individual-based population genetic simulation environment")
|
|
(description
|
|
"This package provides an interface between R and the metasim simulation
|
|
engine. The simulation environment is documented in: Strand, A.(2002),
|
|
Metasim 1.0: an individual-based environment for simulating population
|
|
genetics of complex population dynamics.")
|
|
;; Any GPL version
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-genetics
|
|
(package
|
|
(name "r-genetics")
|
|
(version "1.3.8.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "genetics" version))
|
|
(sha256
|
|
(base32
|
|
"1v0ylnia6c44v356dsmnkx6054vcxazpzsrdh3yph5ch5vg6gjrh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-combinat" ,r-combinat)
|
|
("r-gdata" ,r-gdata)
|
|
("r-gtools" ,r-gtools)
|
|
("r-mass" ,r-mass)
|
|
("r-mvtnorm" ,r-mvtnorm)))
|
|
(home-page "https://cran.r-project.org/web/packages/genetics/")
|
|
(synopsis "Population genetics")
|
|
(description
|
|
"This package provides classes and methods for handling genetic data.
|
|
It includes classes to represent genotypes and haplotypes at single markers up
|
|
to multiple markers on multiple chromosomes. Function include allele
|
|
frequencies, flagging homo/heterozygotes, flagging carriers of certain
|
|
alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating
|
|
and testing for linkage disequilibrium, ...")
|
|
;; Any GPL version.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-snp-plotter
|
|
(package
|
|
(name "r-snp-plotter")
|
|
(version "0.5.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "snp.plotter" version))
|
|
(sha256
|
|
(base32
|
|
"16apsqvkah5l0d5qcwp3lq2jspkb6n62wzr0wskmj84jblx483vv"))))
|
|
(properties `((upstream-name . "snp.plotter")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-genetics" ,r-genetics)))
|
|
(home-page "https://cran.r-project.org/web/packages/snp.plotter/")
|
|
(synopsis "Plot p-values using single SNP and/or haplotype data")
|
|
(description
|
|
"This package helps you create plots of p-values using single SNP and/or
|
|
haplotype data. Main features of the package include options to display a
|
|
@dfn{linkage disequilibrium} (LD) plot and the ability to plot multiple
|
|
datasets simultaneously. Plots can be created using global and/or individual
|
|
haplotype p-values along with single SNP p-values. Images are created as
|
|
either PDF/EPS files.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-polspline
|
|
(package
|
|
(name "r-polspline")
|
|
(version "1.1.15")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "polspline" version))
|
|
(sha256
|
|
(base32
|
|
"19zs4kpagsrzhng1byjbz1c4jxnfk58h4rgr096ml1bjwrgamnwc"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/polspline/")
|
|
(synopsis "Polynomial spline routines")
|
|
(description
|
|
"This package provides routines for the polynomial spline fitting
|
|
routines hazard regression, hazard estimation with flexible tails, logspline,
|
|
lspec, polyclass, and polymars.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rms
|
|
(package
|
|
(name "r-rms")
|
|
(version "5.1-3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rms" version))
|
|
(sha256
|
|
(base32
|
|
"0drbr3g0x5pbxyzy50wnf92rbal8izizrcqslqhg0gsfg9adjih9"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-hmisc" ,r-hmisc)
|
|
("r-htmltable" ,r-htmltable)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-lattice" ,r-lattice)
|
|
("r-multcomp" ,r-multcomp)
|
|
("r-nlme" ,r-nlme)
|
|
("r-polspline" ,r-polspline)
|
|
("r-quantreg" ,r-quantreg)
|
|
("r-rpart" ,r-rpart)
|
|
("r-sparsem" ,r-sparsem)
|
|
("r-survival" ,r-survival)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "http://biostat.mc.vanderbilt.edu/rms")
|
|
(synopsis "Regression modeling strategies")
|
|
(description
|
|
"This is a package for regression modeling, testing, estimation,
|
|
validation, graphics, prediction, and typesetting by storing enhanced model
|
|
design attributes in the fit. The rms package is a collection of functions
|
|
that assist with and streamline modeling. It also contains functions for
|
|
binary and ordinal logistic regression models, ordinal models for continuous Y
|
|
with a variety of distribution families, and the Buckley-James multiple
|
|
regression model for right-censored responses, and implements penalized
|
|
maximum likelihood estimation for logistic and ordinary linear models. The
|
|
package works with almost any regression model, but it was especially written
|
|
to work with binary or ordinal regression models, Cox regression, accelerated
|
|
failure time models, ordinary linear models, the Buckley-James model,
|
|
generalized least squares for serially or spatially correlated observations,
|
|
generalized linear models, and quantile regression.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-haplo-stats
|
|
(package
|
|
(name "r-haplo-stats")
|
|
(version "1.7.9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "haplo.stats" version))
|
|
(sha256
|
|
(base32
|
|
"19kxascqq5qz0zdxx0w837ji207y1z2ggxkl4vmlbay03k2dw2mx"))))
|
|
(properties `((upstream-name . "haplo.stats")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rms" ,r-rms)))
|
|
(native-inputs
|
|
`(("r-r-rsp" ,r-r-rsp))) ; for vignettes
|
|
(home-page "https://www.mayo.edu/research/labs/statistical-genetics-genetic-epidemiology/software")
|
|
(synopsis "Analysis of haplotypes when linkage phase is ambiguous")
|
|
(description
|
|
"This package provides routines for the analysis of indirectly measured
|
|
haplotypes. The statistical methods assume that all subjects are unrelated
|
|
and that haplotypes are ambiguous (due to unknown linkage phase of the genetic
|
|
markers). The main functions are: @code{haplo.em()}, @code{haplo.glm()},
|
|
@code{haplo.score()}, and @code{haplo.power()}; all of which have detailed
|
|
examples in the vignette.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-bqtl
|
|
(package
|
|
(name "r-bqtl")
|
|
(version "1.0-32")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bqtl" version))
|
|
(sha256
|
|
(base32
|
|
"0jjqgsm9fmvz5nkgz608xfljjpmaf4rs4f7kxvpqn4b1l9s5lhci"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "http://famprevmed.ucsd.edu/faculty/cberry/bqtl/")
|
|
(synopsis "Bayesian QTL mapping toolkit")
|
|
(description
|
|
"This is a QTL mapping toolkit for inbred crosses and recombinant inbred
|
|
lines. It includes maximum likelihood and Bayesian tools.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ibdreg
|
|
(package
|
|
(name "r-ibdreg")
|
|
(version "0.2.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ibdreg" version))
|
|
(sha256
|
|
(base32
|
|
"1kaa5q1byi30wzr0mw4w2cv1ssxprzcwf91wrpqwkgcsdy7dkh2g"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://www.mayo.edu/research/labs/\
|
|
statistical-genetics-genetic-epidemiology/software")
|
|
(synopsis "Regression methods for IBD linkage with covariates")
|
|
(description
|
|
"This package provides a method to test genetic linkage with covariates
|
|
by regression methods with response IBD sharing for relative pairs. Account
|
|
for correlations of IBD statistics and covariates for relative pairs within
|
|
the same pedigree.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-dlmap
|
|
(package
|
|
(name "r-dlmap")
|
|
(version "1.13")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dlmap" version))
|
|
(sha256
|
|
(base32
|
|
"0s6wlkggkm3qndwyvw72xv1n0mcjb7ss3ajbq2ll6rv30splq0db"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ibdreg" ,r-ibdreg)
|
|
("r-mgcv" ,r-mgcv)
|
|
("r-nlme" ,r-nlme)
|
|
("r-qtl" ,r-qtl)
|
|
("r-wgaim" ,r-wgaim)))
|
|
(home-page "https://cran.r-project.org/web/packages/dlmap/")
|
|
(synopsis "Detection localization mapping for QTL")
|
|
(description
|
|
"This is package for QTL mapping in a mixed model framework with separate
|
|
detection and localization stages. The first stage detects the number of QTL
|
|
on each chromosome based on the genetic variation due to grouped markers on
|
|
the chromosome; the second stage uses this information to determine the most
|
|
likely QTL positions. The mixed model can accommodate general fixed and
|
|
random effects, including spatial effects in field trials and pedigree
|
|
effects. It is applicable to backcrosses, doubled haploids, recombinant
|
|
inbred lines, F2 intercrosses, and association mapping populations.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-ldheatmap
|
|
(package
|
|
(name "r-ldheatmap")
|
|
(version "0.99-5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "LDheatmap" version))
|
|
(sha256
|
|
(base32
|
|
"0il3g3n3bzv74lz7dlhyiwc2x2417v6yhx2g47pahxdzqa09kf4s"))))
|
|
(properties `((upstream-name . "LDheatmap")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-genetics" ,r-genetics)
|
|
("r-snpstats" ,r-snpstats)))
|
|
(home-page "http://stat.sfu.ca/statgen/research/ldheatmap.html")
|
|
(synopsis "Graphical display of pairwise linkage disequilibria between SNPs")
|
|
(description
|
|
"This package provides tools to produce a graphical display, as a heat
|
|
map, of measures of pairwise linkage disequilibria between SNPs. Users may
|
|
optionally include the physical locations or genetic map distances of each SNP
|
|
on the plot.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-hwde
|
|
(package
|
|
(name "r-hwde")
|
|
(version "0.67")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hwde" version))
|
|
(sha256
|
|
(base32
|
|
"0wb2f9i5qi7w77ygh8bvydfpr7j5x8dyvnnhdkajaz0wdcpkyaqy"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/hwde/")
|
|
(synopsis "Models and tests for departure from Hardy-Weinberg equilibrium")
|
|
(description
|
|
"This package fits models for genotypic disequilibria, as described in
|
|
Huttley and Wilson (2000), Weir (1996) and Weir and Wilson (1986). Contrast
|
|
terms are available that account for first order interactions between loci.
|
|
It also implements, for a single locus in a single population, a conditional
|
|
exact test for Hardy-Weinberg equilibrium.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-tdthap
|
|
(package
|
|
(name "r-tdthap")
|
|
(version "1.1-9")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tdthap" version))
|
|
(sha256
|
|
(base32
|
|
"0y01x0hcf0rw06cpn4pk17b0shf4v2c9was7vfs0zhsbq8qcwx7r"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/tdthap/")
|
|
(synopsis "TDT tests for extended haplotypes")
|
|
(description
|
|
"Functions and examples are provided for transmission/disequilibrium
|
|
tests for extended marker haplotypes, as in Clayton, D. and Jones, H. (1999)
|
|
\"Transmission/disequilibrium tests for extended marker haplotypes\".")
|
|
(license license:artistic2.0)))
|
|
|
|
(define-public r-sparql
|
|
(package
|
|
(name "r-sparql")
|
|
(version "1.16")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "SPARQL" version))
|
|
(sha256
|
|
(base32
|
|
"0gak1q06yyhdmcxb2n3v0h9gr1vqd0viqji52wpw211qp6r6dcrc"))))
|
|
(properties `((upstream-name . "SPARQL")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcurl" ,r-rcurl)
|
|
("r-xml" ,r-xml)))
|
|
(home-page "https://cran.r-project.org/web/packages/SPARQL")
|
|
(synopsis "SPARQL client for R")
|
|
(description "This package provides an interface to use SPARQL to pose
|
|
SELECT or UPDATE queries to an end-point.")
|
|
;; The only license indication is found in the DESCRIPTION file,
|
|
;; which states GPL-3. So we cannot assume GPLv3+.
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-bookdown
|
|
(package
|
|
(name "r-bookdown")
|
|
(version "0.11")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "bookdown" version))
|
|
(sha256
|
|
(base32
|
|
"0w4fkv5fqiaqgkx44p0s161imf29zir9742126xkz1pl1j25jn1r"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-knitr" ,r-knitr)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-tinytex" ,r-tinytex)
|
|
("r-xfun" ,r-xfun)
|
|
("pandoc" ,ghc-pandoc)))
|
|
(home-page "https://github.com/rstudio/bookdown")
|
|
(synopsis "Authoring books and technical documents with R markdown")
|
|
(description "This package provides output formats and utilities for
|
|
authoring books and technical documents with R Markdown.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-optparse
|
|
(package
|
|
(name "r-optparse")
|
|
(version "1.6.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "optparse" version))
|
|
(sha256
|
|
(base32
|
|
"0zrp6jakjhawrwfri270ym83vj5a7nvjk0w6b41z41ahw2da99dm"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-getopt" ,r-getopt)))
|
|
(home-page "https://github.com/trevorld/optparse")
|
|
(synopsis "Command line option parser")
|
|
(description
|
|
"This package provides a command line parser inspired by Python's
|
|
@code{optparse} library to be used with Rscript to write shebang scripts
|
|
that accept short and long options.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-wgcna
|
|
(package
|
|
(name "r-wgcna")
|
|
(version "1.68")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "WGCNA" version))
|
|
(sha256
|
|
(base32
|
|
"1s7gy5vd7x67hpgli8r7ba2z99w3psiyv5hqmrh94zw141dg210a"))))
|
|
(properties `((upstream-name . "WGCNA")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-annotationdbi" ,r-annotationdbi)
|
|
("r-doparallel" ,r-doparallel)
|
|
("r-dynamictreecut" ,r-dynamictreecut)
|
|
("r-fastcluster" ,r-fastcluster)
|
|
("r-foreach" ,r-foreach)
|
|
("r-go-db" ,r-go-db)
|
|
("r-hmisc" ,r-hmisc)
|
|
("r-impute" ,r-impute)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-robust" ,r-robust)
|
|
("r-survival" ,r-survival)
|
|
("r-matrixstats" ,r-matrixstats)
|
|
("r-preprocesscore" ,r-preprocesscore)))
|
|
(home-page
|
|
"http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/")
|
|
(synopsis "Weighted correlation network analysis")
|
|
(description
|
|
"This package provides functions necessary to perform Weighted
|
|
Correlation Network Analysis on high-dimensional data. It includes functions
|
|
for rudimentary data cleaning, construction and summarization of correlation
|
|
networks, module identification and functions for relating both variables and
|
|
modules to sample traits. It also includes a number of utility functions for
|
|
data manipulation and visualization.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-kernlab
|
|
(package
|
|
(name "r-kernlab")
|
|
(version "0.9-27")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "kernlab" version))
|
|
(sha256
|
|
(base32
|
|
"1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/kernlab")
|
|
(synopsis "Kernel-based machine learning tools")
|
|
(description
|
|
"This package provides kernel-based machine learning methods for
|
|
classification, regression, clustering, novelty detection, quantile regression
|
|
and dimensionality reduction. Among other methods @code{kernlab} includes
|
|
Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
|
|
and a QP solver.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-hierfstat
|
|
(package
|
|
(name "r-hierfstat")
|
|
(version "0.04-22")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hierfstat" version))
|
|
(sha256
|
|
(base32
|
|
"1fav2v2996v5kb1ffa6v5wxfm921syxg6as034vd3j4jfhdibyfx"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ade4" ,r-ade4)
|
|
("r-adegenet" ,r-adegenet)
|
|
("r-gtools" ,r-gtools)))
|
|
(home-page "https://cran.r-project.org/web/packages/hierfstat/")
|
|
(synopsis "Estimation and tests of hierarchical F-statistics")
|
|
(description
|
|
"This package allows the estimation of hierarchical F-statistics from
|
|
haploid or diploid genetic data with any numbers of levels in the hierarchy,
|
|
following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions
|
|
are also given to test via randomisations the significance of each F and
|
|
variance components, using the likelihood-ratio statistics G.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-hapassoc
|
|
(package
|
|
(name "r-hapassoc")
|
|
(version "1.2-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "hapassoc" version))
|
|
(sha256
|
|
(base32
|
|
"0qs5jl0snzfchgpp6pabncwywxcmi743g91jvjiyyzw0lw85yv4s"))))
|
|
(build-system r-build-system)
|
|
(home-page "http://stat.sfu.ca/statgen/research/hapassoc.html")
|
|
(synopsis "Inference of trait associations with SNP haplotypes")
|
|
(description
|
|
"Hapassoc performs likelihood inference of trait associations with
|
|
haplotypes and other covariates in @dfn{generalized linear models} (GLMs). The
|
|
functions are developed primarily for data collected in cohort or
|
|
cross-sectional studies. They can accommodate uncertain haplotype phase and
|
|
handle missing genotypes at some SNPs.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-sampling
|
|
(package
|
|
(name "r-sampling")
|
|
(version "2.8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sampling" version))
|
|
(sha256
|
|
(base32
|
|
"06pj7dan0mknpsblmlnk7am78qrnwgnql5vvx7vmbfvib7rj6s9m"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lpsolve" ,r-lpsolve)
|
|
("r-mass" ,r-mass)))
|
|
(home-page "https://cran.r-project.org/web/packages/sampling/")
|
|
(synopsis "Survey sampling")
|
|
(description
|
|
"This package provides functions for drawing and calibrating samples.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-r2html
|
|
(package
|
|
(name "r-r2html")
|
|
(version "2.3.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "R2HTML" version))
|
|
(sha256
|
|
(base32
|
|
"00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"))))
|
|
(properties `((upstream-name . "R2HTML")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/nalimilan/R2HTML")
|
|
(synopsis "HTML export for R objects")
|
|
(description
|
|
"This package includes HTML functions and methods to write in an HTML
|
|
file. Thus, making HTML reports is easy. It includes a function that allows
|
|
redirection on the fly, which appears to be very useful for teaching purposes,
|
|
as the student can keep a copy of the produced output to keep all that they
|
|
did during the course. The package comes with a vignette describing how to
|
|
write HTML reports for statistical analysis. Finally, a driver for Sweave
|
|
allows to parse HTML flat files containing R code and to automatically write
|
|
the corresponding outputs (tables and graphs).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rjava
|
|
(package
|
|
(name "r-rjava")
|
|
(version "0.9-11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rJava" version))
|
|
(sha256
|
|
(base32
|
|
"0s9cjy1wh7snmbqwznh8f1r4ipylr7mgda4a979z963a8lqy32n2"))))
|
|
(properties `((upstream-name . "rJava")))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(ice-9 match))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'set-JAVA_HOME
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((jdk (assoc-ref inputs "jdk")))
|
|
(setenv "JAVA_HOME" jdk)
|
|
(setenv "JAVA" (which "java"))
|
|
(setenv "JAR" (which "jar"))
|
|
(setenv "JAVAC" (which "javac"))
|
|
(setenv "JAVAH" (which "javah"))
|
|
(setenv "JAVA_CPPFLAGS"
|
|
(string-append "-I" jdk "/include "
|
|
"-I" jdk "/include/linux"))
|
|
(match (find-files (string-append jdk "/jre/lib/") "libjvm.so")
|
|
((lib) (setenv "JAVA_LIBS" lib))
|
|
(_ (error "Could not find libjvm.so"))))
|
|
#t)))))
|
|
(inputs
|
|
`(("icu4c" ,icu4c)
|
|
("jdk" ,icedtea-8 "jdk")
|
|
("pcre" ,pcre)
|
|
("zlib" ,zlib)))
|
|
(home-page "http://www.rforge.net/rJava/")
|
|
(synopsis "Low-Level R to Java interface")
|
|
(description
|
|
"This package provides a low-level interface to the Java VM very much
|
|
like .C/.Call and friends. It allows the creation of objects, calling methods
|
|
and accessing fields.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-svmisc
|
|
(package
|
|
(name "r-svmisc")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "svMisc" version))
|
|
(sha256
|
|
(base32
|
|
"01r2a73wx2sh1njky961fxabx5wgddqqjqba6vjg0f3h8r3abmn2"))))
|
|
(properties `((upstream-name . "svMisc")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/SciViews/svMisc")
|
|
(synopsis "Miscellaneous functions for SciViews")
|
|
(description
|
|
"This package provides miscellaneous functions for SciViews or general
|
|
use, including tools to manage a temporary environment attached to the search
|
|
path for temporary variables you do not want to @code{save()} or
|
|
@code{load()}; test the current platform; showing progress bars, etc.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-xyz
|
|
(package
|
|
(name "r-xyz")
|
|
(version "0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xyz" version))
|
|
(sha256
|
|
(base32
|
|
"13w4sb4pvgciwr8wsz785dafj2k2kpx7znz46r5d32wx88vkycp4"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://cran.r-project.org/web/packages/xyz/")
|
|
(synopsis "Algorithm for fast interaction search in high-dimensional data")
|
|
(description
|
|
"High dimensional interaction search by brute force requires a quadratic
|
|
computational cost in the number of variables. The xyz algorithm provably
|
|
finds strong interactions in almost linear time. For details of the algorithm
|
|
see: G. Thanei, N. Meinshausen and R. Shah (2016). The xyz algorithm for fast
|
|
interaction search in high-dimensional data.")
|
|
;; Any version of the GPL.
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-rttf2pt1
|
|
(package
|
|
(name "r-rttf2pt1")
|
|
(version "1.3.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "Rttf2pt1" version))
|
|
(sha256
|
|
(base32
|
|
"12hf9r3mhjr9sawdvf7qhjf1zph2q64f77i81jwvy7awidbm0kja"))))
|
|
(properties `((upstream-name . "Rttf2pt1")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/wch/Rttf2pt1")
|
|
(synopsis "Font conversion utility")
|
|
(description
|
|
"This package contains the program @code{ttf2pt1}, for use with the
|
|
@code{extrafont} package.")
|
|
;; Most of the files are covered under the Expat license. Some files are
|
|
;; covered under BSD-3. Deviations for individual files are recorded in
|
|
;; the LICENSE file.
|
|
(license (list license:bsd-3 license:expat
|
|
(license:non-copyleft "file://LICENSE")))))
|
|
|
|
(define-public r-extrafontdb
|
|
(package
|
|
(name "r-extrafontdb")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "extrafontdb" version))
|
|
(sha256
|
|
(base32
|
|
"115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/wch/extrafontdb")
|
|
(synopsis "Database for the extrafont package")
|
|
(description
|
|
"This package holds the database for the @code{extrafont} package.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-extrafont
|
|
(package
|
|
(name "r-extrafont")
|
|
(version "0.17")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "extrafont" version))
|
|
(sha256
|
|
(base32
|
|
"0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-extrafontdb" ,r-extrafontdb)
|
|
("r-rttf2pt1" ,r-rttf2pt1)))
|
|
(home-page "https://github.com/wch/extrafont")
|
|
(synopsis "Tools for using fonts in R")
|
|
(description
|
|
"The extrafont package makes it easier to use fonts other than the basic
|
|
PostScript fonts that R uses. Fonts that are imported into extrafont can be
|
|
used with PDF or PostScript output files. There are two hurdles for using
|
|
fonts in PDF (or Postscript) output files:
|
|
|
|
@enumerate
|
|
@item Making R aware of the font and the dimensions of the characters.
|
|
@item Embedding the fonts in the PDF file so that the PDF can be displayed
|
|
properly on a device that doesn't have the font. This is usually needed if
|
|
you want to print the PDF file or share it with others.
|
|
@end enumerate
|
|
|
|
The extrafont package makes both of these things easier.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-xkcd
|
|
(package
|
|
(name "r-xkcd")
|
|
(version "0.0.6")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xkcd" version))
|
|
(sha256
|
|
(base32
|
|
"1z2y0ihn68ppay7xkglhw7djki5654g6z4bbpyy41if57z9q554f"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-extrafont" ,r-extrafont)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-hmisc" ,r-hmisc)))
|
|
(home-page "https://cran.r-project.org/web/packages/xkcd/")
|
|
(synopsis "Plot ggplot2 graphics in the XKCD style")
|
|
(description
|
|
"This package provides the means to plot ggplot2 graphs in the style of
|
|
the XKCD web comic.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-msigdbr
|
|
(package
|
|
(name "r-msigdbr")
|
|
(version "6.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "msigdbr" version))
|
|
(sha256
|
|
(base32
|
|
"1264j1hs74kq7hyh68vfynadfi6mdpq46qm1hnwzkzzhmbzpb9cg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rlang" ,r-rlang)
|
|
("r-tibble" ,r-tibble)))
|
|
(home-page "https://github.com/igordot/msigdbr")
|
|
(synopsis "MSigDB gene sets for multiple organisms")
|
|
(description
|
|
"This package provides the @dfn{Molecular Signatures Database} (MSigDB)
|
|
gene sets typically used with the @dfn{Gene Set Enrichment Analysis} (GSEA)
|
|
software in a standard R data frame with key-value pairs. Included are the
|
|
original human gene symbols and Entrez IDs as well as the equivalents for
|
|
various frequently studied model organisms such as mouse, rat, pig, fly, and
|
|
yeast.")
|
|
;; The package is covered under the Expat license, but the upstream MSigDB
|
|
;; files are made available under the Creative Commons Attribution 4.0
|
|
;; International license.
|
|
(license (list license:expat license:cc-by4.0))))
|
|
|
|
(define-public r-gridgraphics
|
|
(package
|
|
(name "r-gridgraphics")
|
|
(version "0.4-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gridGraphics" version))
|
|
(sha256
|
|
(base32
|
|
"1kr3p54bkv2q7agxrva30y9bkwkiq1k2cfl5z1kvyjv6f5xi4w5p"))))
|
|
(properties `((upstream-name . "gridGraphics")))
|
|
(build-system r-build-system)
|
|
(home-page "https://github.com/pmur002/gridgraphics")
|
|
(synopsis "Redraw base graphics using @code{grid} graphics")
|
|
(description
|
|
"This package provides functions to convert a page of plots drawn with
|
|
the @code{graphics} package into identical output drawn with the @code{grid}
|
|
package. The result looks like the original @code{graphics}-based plot, but
|
|
consists of @code{grid} grobs and viewports that can then be manipulated with
|
|
@code{grid} functions (e.g., edit grobs and revisit viewports).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-farver
|
|
(package
|
|
(name "r-farver")
|
|
(version "1.1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "farver" version))
|
|
(sha256
|
|
(base32
|
|
"1dllgx121al374gyp9pjv1m8ip4imm8zhbgyh1970dsz2c4z71i0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/thomasp85/farver")
|
|
(synopsis "Vectorized color conversion and comparison")
|
|
(description
|
|
"The encoding of color can be handled in many different ways, using
|
|
different color spaces. As different color spaces have different uses,
|
|
efficient conversion between these representations are important. This
|
|
package provides a set of functions that gives access to very fast color space
|
|
conversion and comparisons implemented in C++, and offers 100-fold speed
|
|
improvements over the @code{convertColor} function in the @code{grDevices}
|
|
package.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ggplotify
|
|
(package
|
|
(name "r-ggplotify")
|
|
(version "0.0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggplotify" version))
|
|
(sha256
|
|
(base32
|
|
"14hqlpvnaq5psz1ljcpw9isa06827rg3fm5c1dx159rsjfi56yby"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gridgraphics" ,r-gridgraphics)
|
|
("r-rvcheck" ,r-rvcheck)))
|
|
(home-page "https://github.com/GuangchuangYu/ggplotify")
|
|
(synopsis "Convert plots to @code{grob} or @code{ggplot} object")
|
|
(description
|
|
"This package provides tools to convert plot function calls (using
|
|
expression or formula) to @code{grob} or @code{ggplot} objects that are
|
|
compatible with the @code{grid} and @code{ggplot2} environment. With this
|
|
package, we are able to e.g. use @code{cowplot} to align plots produced by
|
|
@code{base} graphics, @code{grid}, @code{lattice}, @code{vcd} etc. by
|
|
converting them to @code{ggplot} objects.")
|
|
(license license:artistic2.0)))
|
|
|
|
(define-public r-triebeard
|
|
(package
|
|
(name "r-triebeard")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "triebeard" version))
|
|
(sha256
|
|
(base32
|
|
"1hqyz57gph02c9fdc07lxz113bbklif3g18sw8jan6pakhhdc7dz"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/Ironholds/triebeard/")
|
|
(synopsis "Radix trees in Rcpp")
|
|
(description
|
|
"Radix trees, or tries, are key-value data structures optimized for
|
|
efficient lookups, similar in purpose to hash tables. This package provides
|
|
an implementation of radix trees for use in R programming and in developing
|
|
packages with Rcpp.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-tweenr
|
|
(package
|
|
(name "r-tweenr")
|
|
(version "1.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "tweenr" version))
|
|
(sha256
|
|
(base32
|
|
"0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-farver" ,r-farver)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rlang" ,r-rlang)))
|
|
(home-page "https://github.com/thomasp85/tweenr")
|
|
(synopsis "Interpolate data for smooth animations")
|
|
(description
|
|
"In order to create smooth animation between states of data, tweening is
|
|
necessary. This package provides a range of functions for creating tweened
|
|
data that can be used as basis for animation. Furthermore it adds a number of
|
|
vectorized interpolaters for common R data types such as numeric, date and
|
|
color.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-polyclip
|
|
(package
|
|
(name "r-polyclip")
|
|
(version "1.10-0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "polyclip" version))
|
|
(sha256
|
|
(base32
|
|
"0jyk4maqiblvj095jd59dr76kbniyli3v3xvy0a72ljszq6vrnkl"))))
|
|
(build-system r-build-system)
|
|
(native-inputs `(("pkg-config" ,pkg-config)))
|
|
(home-page "http://www.angusj.com/delphi/clipper.php")
|
|
(synopsis "Polygon clipping")
|
|
(description
|
|
"This package provides an R port of the library Clipper. It performs
|
|
polygon clipping operations (intersection, union, set minus, set difference)
|
|
for polygonal regions of arbitrary complexity, including holes. It computes
|
|
offset polygons (spatial buffer zones, morphological dilations, Minkowski
|
|
dilations) for polygonal regions and polygonal lines. It computes the
|
|
Minkowski Sum of general polygons. There is a function for removing
|
|
self-intersections from polygon data.")
|
|
(license license:boost1.0)))
|
|
|
|
(define-public r-urltools
|
|
(package
|
|
(name "r-urltools")
|
|
(version "1.7.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "urltools" version))
|
|
(sha256
|
|
(base32
|
|
"04x3my655dd287cbsszbnf75q0swmjlxxrblcsay7a8n3df3a830"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-rcpp" ,r-rcpp)
|
|
("r-triebeard" ,r-triebeard)))
|
|
(home-page "https://github.com/Ironholds/urltools/")
|
|
(synopsis "Vectorized tools for URL handling and parsing")
|
|
(description
|
|
"This package provides a toolkit for all URL-handling needs, including
|
|
encoding and decoding, parsing, parameter extraction and modification. All
|
|
functions are designed to be both fast and entirely vectorized. It is
|
|
intended to be useful for people dealing with web-related datasets, such as
|
|
server-side logs, although may be useful for other situations involving large
|
|
sets of URLs.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-ggforce
|
|
(package
|
|
(name "r-ggforce")
|
|
(version "0.2.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggforce" version))
|
|
(sha256
|
|
(base32
|
|
"0snxx9zhcccxa7pz9pf3bjqmcmv9mz4m47v81hklnhm25jj40xg2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-gtable" ,r-gtable)
|
|
("r-mass" ,r-mass)
|
|
("r-polyclip" ,r-polyclip)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcppeigen" ,r-rcppeigen)
|
|
("r-rlang" ,r-rlang)
|
|
("r-scales" ,r-scales)
|
|
("r-tweenr" ,r-tweenr)))
|
|
(home-page "https://ggforce.data-imaginist.com")
|
|
(synopsis "Accelerating ggplot2")
|
|
(description
|
|
"The aim of the ggplot2 package is to aid in visual data investigations.
|
|
This focus has led to a lack of facilities for composing specialized plots.
|
|
Thi package aims to be a collection of mainly new statistics and geometries
|
|
that fills this gap.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-europepmc
|
|
(package
|
|
(name "r-europepmc")
|
|
(version "0.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "europepmc" version))
|
|
(sha256
|
|
(base32
|
|
"1ngqs1sqzkbwv98dd5z4cxj8bnz41wyd0g060a2vpqi3s99s4i2h"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-plyr" ,r-plyr)
|
|
("r-progress" ,r-progress)
|
|
("r-purrr" ,r-purrr)
|
|
("r-urltools" ,r-urltools)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://github.com/ropensci/europepmc/")
|
|
(synopsis "R Interface to the Europe PubMed Central RESTful Web Service")
|
|
(description
|
|
"This package provides an R Client for the
|
|
@url{https://europepmc.org/RestfulWebService,Europe PubMed Central RESTful Web
|
|
Service}. It gives access to both metadata on life science literature and
|
|
open access full texts. Europe PMC indexes all PubMed content and other
|
|
literature sources including Agricola, a bibliographic database of citations
|
|
to the agricultural literature, or Biological Patents. In addition to
|
|
bibliographic metadata, the client allows users to fetch citations and
|
|
reference lists. Links between life-science literature and other EBI
|
|
databases, including ENA, PDB or ChEMBL are also accessible.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-ggraph
|
|
(package
|
|
(name "r-ggraph")
|
|
(version "1.0.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggraph" version))
|
|
(sha256
|
|
(base32
|
|
"0fpmp326mryd1k1qvacjadksrnhbla8h960i18lmrimzrag7692c"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-ggforce" ,r-ggforce)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-ggrepel" ,r-ggrepel)
|
|
("r-gtable" ,r-gtable)
|
|
("r-igraph" ,r-igraph)
|
|
("r-mass" ,r-mass)
|
|
("r-plyr" ,r-plyr)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-scales" ,r-scales)
|
|
("r-viridis" ,r-viridis)))
|
|
(home-page "https://cran.r-project.org/web/packages/ggraph/")
|
|
(synopsis "Implementation of grammar of graphics for graphs and networks")
|
|
(description
|
|
"The grammar of graphics as implemented in ggplot2 is a poor fit for
|
|
graph and network visualizations due to its reliance on tabular data input.
|
|
The ggraph package is an extension of the ggplot2 API tailored to graph
|
|
visualizations and provides the same flexible approach to building up plots
|
|
layer by layer.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-varselrf
|
|
(package
|
|
(name "r-varselrf")
|
|
(version "0.7-8")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "varSelRF" version))
|
|
(sha256
|
|
(base32
|
|
"0h49rl1j13yfh97rsfsyh9s2c4wajny4rzms2qw77d0cavxqg53i"))))
|
|
(properties `((upstream-name . "varSelRF")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-randomforest" ,r-randomforest)))
|
|
(home-page "http://ligarto.org/rdiaz/Software/Software.html")
|
|
(synopsis "Variable selection using random forests")
|
|
(description
|
|
"This package provides tools for the variable selection from random
|
|
forests using both backwards variable elimination (for the selection of small
|
|
sets of non-redundant variables) and selection based on the importance
|
|
spectrum (somewhat similar to scree plots; for the selection of large,
|
|
potentially highly-correlated variables). The main applications are in
|
|
high-dimensional data (e.g., microarray data, and other genomics and
|
|
proteomics applications).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-pamr
|
|
(package
|
|
(name "r-pamr")
|
|
(version "1.56.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "pamr" version))
|
|
(sha256
|
|
(base32
|
|
"0ycpgkk23y3zzkb42n2skcyl35ps1n7jmyzfj7pbxr3f6gr2grfh"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-cluster" ,r-cluster)
|
|
("r-survival" ,r-survival)))
|
|
(native-inputs `(("gfortran" ,gfortran)))
|
|
(home-page "https://cran.r-project.org/web/packages/pamr/")
|
|
(synopsis "Prediction Analysis for Microarrays")
|
|
(description
|
|
"This package provides some functions for sample classification in
|
|
microarrays.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rda
|
|
(package
|
|
(name "r-rda")
|
|
(version "1.0.2-2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rda" version))
|
|
(sha256
|
|
(base32
|
|
"1y4fawslr3i6crjaxhsdb47kfsqkyszdx6avq3r5far5a4pvc639"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/rda/")
|
|
(synopsis "Shrunken centroids regularized discriminant analysis")
|
|
(description
|
|
"This package provides tools for shrunken centroids regularized
|
|
discriminant analysis for the purpose of classifying high dimensional data.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-ggvis
|
|
(package
|
|
(name "r-ggvis")
|
|
(version "0.4.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggvis" version))
|
|
(sha256
|
|
(base32
|
|
"1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-dplyr" ,r-dplyr)
|
|
("r-htmltools" ,r-htmltools)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-lazyeval" ,r-lazyeval)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-shiny" ,r-shiny)))
|
|
(home-page "https://ggvis.rstudio.com/")
|
|
(synopsis "Interactive grammar of graphics")
|
|
(description
|
|
"This package is a data visualization package for R providing an
|
|
implementation of an interactive grammar of graphics, taking the best parts of
|
|
ggplot2, combining them with the reactive framework of Shiny and drawing web
|
|
graphics using Vega.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-gbm
|
|
(package
|
|
(name "r-gbm")
|
|
(version "2.1.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "gbm" version))
|
|
(sha256
|
|
(base32
|
|
"0vs6ljaqhwwpgr8wlbhmm4v147rd82kl16rpaijqiylxcc8dxyq6"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-gridextra" ,r-gridextra)
|
|
("r-lattice" ,r-lattice)
|
|
("r-survival" ,r-survival)))
|
|
(home-page "https://github.com/gbm-developers/gbm")
|
|
(synopsis "Generalized boosted regression models")
|
|
(description
|
|
"This package is an implementation of extensions to Freund and Schapire's
|
|
AdaBoost algorithm and Friedman's gradient boosting machine. It includes
|
|
regression methods for least squares, absolute loss, t-distribution loss,
|
|
quantile regression, logistic, multinomial logistic, Poisson, Cox proportional
|
|
hazards partial likelihood, AdaBoost exponential loss, Huberized hinge loss,
|
|
and Learning to Rank measures (LambdaMart).")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-threejs
|
|
(package
|
|
(name "r-threejs")
|
|
(version "0.3.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "threejs" version))
|
|
(sha256
|
|
(base32
|
|
"1s3rdlzy7man6177ycayg6xsh6k8y1r9rdj9yzn3b93j2rs0nxbi"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(srfi srfi-1)
|
|
(ice-9 popen))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'process-javascript
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(with-directory-excursion "inst"
|
|
(call-with-values
|
|
(lambda ()
|
|
(unzip2
|
|
`((,(assoc-ref inputs "js-jquery")
|
|
"htmlwidgets/lib/jquery/jquery.min.js")
|
|
(,(assoc-ref inputs "js-threejs-85")
|
|
"htmlwidgets/lib/threejs-85/three.min.js"))))
|
|
(lambda (sources targets)
|
|
(for-each (lambda (source target)
|
|
(format #t "Processing ~a --> ~a~%"
|
|
source target)
|
|
(delete-file target)
|
|
(let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
|
|
(call-with-output-file target
|
|
(lambda (port)
|
|
(dump-port minified port)))))
|
|
sources targets))))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-base64enc" ,r-base64enc)
|
|
("r-crosstalk" ,r-crosstalk)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-igraph" ,r-igraph)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)
|
|
("js-jquery"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://code.jquery.com/jquery-3.3.1.js")
|
|
(sha256
|
|
(base32
|
|
"1b8zxrp6xwzpw25apn8j4qws0f6sr7qr7h2va5h1mjyfqvn29anq"))))
|
|
("js-threejs-85"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://raw.githubusercontent.com/mrdoob/three.js/r85/build/three.js")
|
|
(sha256
|
|
(base32
|
|
"17khh3dmijdjw4qb9qih1rqhxgrmm3pc6w8lzdx6rf6a3mrc9xnl"))))))
|
|
(home-page "https://bwlewis.github.io/rthreejs")
|
|
(synopsis "Interactive 3D scatter plots, networks and globes")
|
|
(description
|
|
"Create interactive 3D scatter plots, network plots, and globes in R
|
|
using the three.js visualization library.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-mlbench
|
|
(package
|
|
(name "r-mlbench")
|
|
(version "2.1-1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mlbench" version))
|
|
(sha256
|
|
(base32
|
|
"1rp035qxfgh5ail92zjh9jh57dj0b8babw3wsg29v8ricpal30bl"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/mlbench/")
|
|
(synopsis "Machine learning benchmark problems")
|
|
(description
|
|
"This package provides a collection of artificial and real-world machine
|
|
learning benchmark problems, including, e.g., several data sets from the UCI
|
|
repository.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-mpm
|
|
(package
|
|
(name "r-mpm")
|
|
(version "1.0-22")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mpm" version))
|
|
(sha256
|
|
(base32
|
|
"0wijw8v0wmbfrda5564cmnp788qmlkk21yn5cp5qk8aprm9l1fnk"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-kernsmooth" ,r-kernsmooth)
|
|
("r-mass" ,r-mass)))
|
|
(home-page "http://mpm.r-forge.r-project.org")
|
|
(synopsis "Multivariate projection methods")
|
|
(description
|
|
"This is a package for exploratory graphical analysis of multivariate
|
|
data, specifically gene expression data with different projection methods:
|
|
principal component analysis, correspondence analysis, spectral map
|
|
analysis.")
|
|
(license license:gpl2+)))
|
|
|
|
(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)
|
|
("zlib" ,zlib)))
|
|
(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.")
|
|
;; Any of these GPL versions.
|
|
(license (list license:gpl2 license:gpl3))))
|
|
|
|
(define-public r-ggcorrplot
|
|
(package
|
|
(name "r-ggcorrplot")
|
|
(version "0.1.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggcorrplot" version))
|
|
(sha256
|
|
(base32
|
|
"0hi9lz121ya1l2lbm7rqlxg6fs6bvxck396dngnidrhl5fvqb41b"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-ggplot2" ,r-ggplot2)
|
|
("r-reshape2" ,r-reshape2)))
|
|
(home-page "http://www.sthda.com/english/wiki/ggcorrplot")
|
|
(synopsis "Visualization of a correlation matrix using ggplot2")
|
|
(description
|
|
"The ggcorrplot package can be used to visualize easily a correlation
|
|
matrix using ggplot2. It provides a solution for reordering the correlation
|
|
matrix and displays the significance level on the plot. It also includes a
|
|
function for computing a matrix of correlation p-values.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-flexdashboard
|
|
(package
|
|
(name "r-flexdashboard")
|
|
(version "0.5.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "flexdashboard" version))
|
|
(sha256
|
|
(base32
|
|
"0fy3nbrr67zqgd44r2mc850s5sp0hzfcw3zqs15m8kxzj1aw067x"))))
|
|
(build-system r-build-system)
|
|
(arguments
|
|
`(#:modules ((guix build utils)
|
|
(guix build r-build-system)
|
|
(srfi srfi-1)
|
|
(srfi srfi-26)
|
|
(ice-9 popen)
|
|
(ice-9 textual-ports))
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'process-javascript
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(with-directory-excursion "inst"
|
|
;; Concatenate all components of prism.js
|
|
(let ((contents (string-join
|
|
(map (lambda (name)
|
|
(call-with-input-file
|
|
(assoc-ref inputs name)
|
|
get-string-all))
|
|
(list "js-prism"
|
|
"js-prism-r"
|
|
"js-prism-line-numbers"))
|
|
"\n")))
|
|
(call-with-output-file "prism-src.js"
|
|
(cut display contents <>)))
|
|
(call-with-values
|
|
(lambda ()
|
|
(unzip2
|
|
`(("www/stickytableheaders/jquery.stickytableheaders.js"
|
|
"www/stickytableheaders/jquery.stickytableheaders.min.js")
|
|
("www/sly/sly.js"
|
|
"www/sly/sly.min.js")
|
|
("prism-src.js"
|
|
"www/prism/prism.js")
|
|
(,(assoc-ref inputs "js-raphael")
|
|
"htmlwidgets/lib/raphael/raphael-2.1.4.min.js")
|
|
(,(assoc-ref inputs "js-featherlight")
|
|
"www/featherlight/featherlight.min.js"))))
|
|
(lambda (sources targets)
|
|
(for-each (lambda (source target)
|
|
(format #t "Processing ~a --> ~a~%"
|
|
source target)
|
|
(delete-file target)
|
|
(let ((minified (open-pipe* OPEN_READ "uglify-js" source)))
|
|
(call-with-output-file target
|
|
(lambda (port)
|
|
(dump-port minified port)))))
|
|
sources targets))))
|
|
#t)))))
|
|
(propagated-inputs
|
|
`(("r-htmltools" ,r-htmltools)
|
|
("r-htmlwidgets" ,r-htmlwidgets)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-knitr" ,r-knitr)
|
|
("r-rmarkdown" ,r-rmarkdown)
|
|
("r-shiny" ,r-shiny)))
|
|
(native-inputs
|
|
`(("uglify-js" ,uglify-js)
|
|
("js-raphael"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://raw.githubusercontent.com/DmitryBaranovskiy/raphael/v2.1.4/raphael.js")
|
|
(sha256
|
|
(base32
|
|
"1h4c4akrgcj7wra9j1z1rv2406j0yf68y9c0wg8v7w9ibw2iwf1x"))))
|
|
("js-prism"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/prism.js")
|
|
(sha256
|
|
(base32
|
|
"0gqa9irbp9k8p5r3d98cszajzhjnssnl43nrsc5aiy7ki52z500c"))))
|
|
("js-prism-r"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/components/prism-r.js")
|
|
(sha256
|
|
(base32
|
|
"1x31glci7wdgr2305njy0bm2lncb0jyn0j1s2g72rqi29xid9aki"))))
|
|
("js-prism-line-numbers"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://raw.githubusercontent.com/PrismJS/prism/v1.16.0/plugins/line-numbers/prism-line-numbers.js")
|
|
(sha256
|
|
(base32
|
|
"1543wgf3iynrilyb27jq8px3h5gvfz5xmdib5ik2ki400c1sl991"))))
|
|
("js-featherlight"
|
|
,(origin
|
|
(method url-fetch)
|
|
(uri "https://raw.githubusercontent.com/noelboss/featherlight/1.3.4/src/featherlight.js")
|
|
(sha256
|
|
(base32
|
|
"14kkhwzvp8rxq2mrck5i0xcm8v5rqwqhwnmncbng8h4qq42zx3sb"))))))
|
|
(home-page "https://rmarkdown.rstudio.com/flexdashboard")
|
|
(synopsis "R Markdown format for flexible dashboards")
|
|
(description
|
|
"This package provides an R Markdown format for converting an R Markdown
|
|
document to a grid-oriented dashboard. The dashboard flexibly adapts the size
|
|
of its components to the containing web page.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-preseqr
|
|
(package
|
|
(name "r-preseqr")
|
|
(version "4.0.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "preseqR" version))
|
|
(sha256
|
|
(base32
|
|
"1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"))))
|
|
(properties `((upstream-name . "preseqR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-polynom" ,r-polynom)))
|
|
(home-page "https://cran.r-project.org/web/packages/preseqR/")
|
|
(synopsis "Predicting species accumulation curves")
|
|
(description
|
|
"This package can be used to predict the r-species accumulation
|
|
curve (r-SAC), which is the number of species represented at least r times as
|
|
a function of the sampling effort. When r = 1, the curve is known as the
|
|
species accumulation curve, or the library complexity curve in high-throughput
|
|
genomic sequencing. The package includes both parametric and nonparametric
|
|
methods, as described by Deng C, et al. (2018).")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-mapplots
|
|
(package
|
|
(name "r-mapplots")
|
|
(version "1.5.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "mapplots" version))
|
|
(sha256
|
|
(base32
|
|
"18s2y66f8vi8g2r8a25zbgp2xm079r8v8qxv0w71h8krycs6vs9p"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/mapplots/")
|
|
(synopsis "Data visualization on maps")
|
|
(description
|
|
"This package helps you create simple maps; add sub-plots like pie plots
|
|
to a map or any other plot; format, plot and export gridded data. The package
|
|
was developed for displaying fisheries data but most functions can be used for
|
|
more generic data visualisation.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-pmcmr
|
|
(package
|
|
(name "r-pmcmr")
|
|
(version "4.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "PMCMR" version))
|
|
(sha256
|
|
(base32
|
|
"09bvdj2h1086r2cgy3myrhlylplxxlliv8nwx09c8kb1vn02i2ij"))))
|
|
(properties `((upstream-name . "PMCMR")))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/PMCMR/")
|
|
(synopsis "Calculate pairwise multiple comparisons of mean rank sums")
|
|
(description
|
|
"This is a deprecated package for calculating pairwise multiple
|
|
comparisons of mean rank sums. This package is superseded by the novel
|
|
PMCMRplus package. The PMCMR package is no longer maintained, but kept for
|
|
compatibility of reverse depending packages for some time.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-downloader
|
|
(package
|
|
(name "r-downloader")
|
|
(version "0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "downloader" version))
|
|
(sha256
|
|
(base32
|
|
"1axggnsc27zzgr7snf41j3zd1vp3nfpmq4zj4d01axc709dyg40q"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-digest" ,r-digest)))
|
|
(home-page "https://github.com/wch/downloader")
|
|
(synopsis "Download files over HTTP and HTTPS")
|
|
(description
|
|
"This package provides a wrapper for the @code{download.file} function,
|
|
making it possible to download files over HTTPS across platforms. The
|
|
@code{RCurl} package provides this functionality (and much more) but has
|
|
external dependencies. This package has is implemented purely in R.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-rex
|
|
(package
|
|
(name "r-rex")
|
|
(version "1.1.2")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "rex" version))
|
|
(sha256
|
|
(base32
|
|
"0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-lazyeval" ,r-lazyeval)
|
|
("r-magrittr" ,r-magrittr)))
|
|
(home-page "https://github.com/kevinushey/rex")
|
|
(synopsis "Friendly regular expressions")
|
|
(description
|
|
"This package provides a friendly interface for the construction of
|
|
regular expressions. Regular expressions are a very powerful feature, however
|
|
they are often difficult to interpret. Rex allows you to build complex
|
|
regular expressions from human readable expressions")
|
|
(license license:expat)))
|
|
|
|
(define-public r-sctransform
|
|
(package
|
|
(name "r-sctransform")
|
|
(version "0.2.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sctransform" version))
|
|
(sha256
|
|
(base32
|
|
"1r5kiqqs318q59h2i8m7c6nhghp9w6q26ss2y5a390lkhsawgx6p"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-future" ,r-future)
|
|
("r-future-apply" ,r-future-apply)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-mass" ,r-mass)
|
|
("r-matrix" ,r-matrix)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-rcppeigen" ,r-rcppeigen)
|
|
("r-reshape2" ,r-reshape2)))
|
|
(home-page "https://github.com/ChristophH/sctransform")
|
|
(synopsis "Variance stabilizing transformations for Single Cell UMI Data")
|
|
(description
|
|
"This package provides a normalization method for single-cell UMI count
|
|
data using a variance stabilizing transformation. The transformation is based
|
|
on a negative binomial regression model with regularized parameters. As part
|
|
of the same regression framework, this package also provides functions for
|
|
batch correction, and data correction.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-styler
|
|
(package
|
|
(name "r-styler")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "styler" version))
|
|
(sha256
|
|
(base32
|
|
"1k660lpjvd64gnf6bndcb1cq3qxsvik928kcn6271zmkhja5rgyb"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)
|
|
("r-cli" ,r-cli)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-purrr" ,r-purrr)
|
|
("r-rematch2" ,r-rematch2)
|
|
("r-rlang" ,r-rlang)
|
|
("r-rprojroot" ,r-rprojroot)
|
|
("r-tibble" ,r-tibble)
|
|
("r-withr" ,r-withr)
|
|
("r-xfun" ,r-xfun)))
|
|
(home-page "https://github.com/r-lib/styler")
|
|
(synopsis "Non-invasive pretty printing of R code")
|
|
(description
|
|
"This is a package for pretty-printing R code without changing the user's
|
|
formatting intent.")
|
|
(license license:gpl3)))
|
|
|
|
(define-public r-scrime
|
|
(package
|
|
(name "r-scrime")
|
|
(version "1.3.5")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "scrime" version))
|
|
(sha256
|
|
(base32
|
|
"0y2mh9fsffjf3i15bafpasa17z99c1s75r8g6h4hgcwfgpjx75sx"))))
|
|
(build-system r-build-system)
|
|
(home-page "https://cran.r-project.org/web/packages/scrime/")
|
|
(synopsis "Analysis of high-dimensional categorical data such as SNP data")
|
|
(description
|
|
"This package provides tools for the analysis of high-dimensional data
|
|
developed/implemented at the group \"Statistical Complexity Reduction In
|
|
Molecular Epidemiology\" (SCRIME). The main focus is on SNP data, but most of
|
|
the functions can also be applied to other types of categorical data.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-blme
|
|
(package
|
|
(name "r-blme")
|
|
(version "1.0-4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "blme" version))
|
|
(sha256
|
|
(base32
|
|
"1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-lme4" ,r-lme4)))
|
|
(home-page "https://github.com/vdorie/blme")
|
|
(synopsis "Bayesian linear mixed-effects models")
|
|
(description
|
|
"This package provides tools for maximum a posteriori estimation for
|
|
linear and generalized linear mixed-effects models in a Bayesian setting. It
|
|
extends the lme4 package.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-batchtools
|
|
(package
|
|
(name "r-batchtools")
|
|
(version "0.9.11")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "batchtools" version))
|
|
(sha256
|
|
(base32
|
|
"02mj21ypcjv5fs7ajf63p6bq0cyvihdl55hlpqx6kmsfjin1cr0v"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-backports" ,r-backports)
|
|
("r-base64url" ,r-base64url)
|
|
("r-brew" ,r-brew)
|
|
("r-checkmate" ,r-checkmate)
|
|
("r-data-table" ,r-data-table)
|
|
("r-digest" ,r-digest)
|
|
("r-fs" ,r-fs)
|
|
("r-progress" ,r-progress)
|
|
("r-r6" ,r-r6)
|
|
("r-rappdirs" ,r-rappdirs)
|
|
("r-stringi" ,r-stringi)
|
|
("r-withr" ,r-withr)))
|
|
(home-page "https://github.com/mllg/batchtools")
|
|
(synopsis "Tools for computation on batch systems")
|
|
(description
|
|
"As a successor of the packages BatchJobs and BatchExperiments, this
|
|
package provides a parallel implementation of the Map function for high
|
|
performance computing systems managed by various schedulers. A multicore and
|
|
socket mode allow the parallelization on a local machines, and multiple
|
|
machines can be hooked up via SSH to create a makeshift cluster. Moreover,
|
|
the package provides an abstraction mechanism to define large-scale computer
|
|
experiments in a well-organized and reproducible way.")
|
|
(license license:lgpl3)))
|
|
|
|
(define-public r-clue
|
|
(package
|
|
(name "r-clue")
|
|
(version "0.3-57")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "clue" version))
|
|
(sha256
|
|
(base32
|
|
"05rdcahawxlxci3fjxihjvvh33wqpxw50sx015165ab4nh3rsdkf"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-cluster" ,r-cluster)))
|
|
(home-page "https://cran.r-project.org/web/packages/clue/")
|
|
(synopsis "Tools for analyzing cluster ensembles")
|
|
(description "Cluster ensembles are collections of individual solutions to
|
|
a given clustering problem which are useful or necessary to consider in a wide
|
|
range of applications. This R package provides an extensible computational
|
|
environment for creating and analyzing cluster ensembles, with basic data
|
|
structures for representing partitions and hierarchies, and facilities for
|
|
computing on them, including methods for measuring proximity and obtaining
|
|
consensus and secondary clusterings.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-sitmo
|
|
(package
|
|
(name "r-sitmo")
|
|
(version "2.0.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "sitmo" version))
|
|
(sha256
|
|
(base32
|
|
"0apdhwy3kxs39agsbvx5vn3xsgb22bf3jrwmr2cmqk9kmxbx740c"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-rcpp" ,r-rcpp)))
|
|
(home-page "https://github.com/coatless/sitmo/")
|
|
(synopsis "Parallel pseudo random number generator header files")
|
|
(description
|
|
"This package provides two high quality and fast PPRNGs that may be used
|
|
in an OpenMP parallel environment. In addition, there is a generator for one
|
|
dimensional low-discrepancy sequence.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-dqrng
|
|
(package
|
|
(name "r-dqrng")
|
|
(version "0.2.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "dqrng" version))
|
|
(sha256
|
|
(base32
|
|
"0rp8q5zijlvaqmpnkwr314w9w40sj4fz7sqsdgsffcfvn42w2jg1"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bh" ,r-bh)
|
|
("r-rcpp" ,r-rcpp)
|
|
("r-sitmo" ,r-sitmo)))
|
|
(home-page "https://www.daqana.org/dqrng")
|
|
(synopsis "Fast pseudo random number generators")
|
|
(description
|
|
"Several fast random number generators are provided as C++ header-only
|
|
libraries: the PCG family as well as Xoroshiro128+ and Xoshiro256+.
|
|
Additionally, fast functions for generating random numbers according to a
|
|
uniform, normal and exponential distribution are included. The latter two use
|
|
the Ziggurat algorithm originally proposed by Marsaglia and Tsang. These
|
|
functions are exported to R and as a C++ interface and are enabled for use
|
|
with the default 64 bit generator from the PCG family, Xoroshiro128+ and
|
|
Xoshiro256+ as well as the 64 bit version of the 20 rounds Threefry
|
|
engine (Salmon et al., 2011) as provided by the package @code{sitmo}.")
|
|
;; This package includes code under CC0 and Apache 2.0 or Expat, but as a
|
|
;; whole is distributed under the terms of the AGPL 3.
|
|
(license license:agpl3)))
|
|
|
|
(define-public r-dalex
|
|
(package
|
|
(name "r-dalex")
|
|
(version "0.4")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "DALEX" version))
|
|
(sha256
|
|
(base32
|
|
"1mr8lqq8s4aacmh7xdhmkmv8vsjqjczlqlaw27xnsljgj2kgq87a"))))
|
|
(properties `((upstream-name . "DALEX")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-ggplot2" ,r-ggplot2)))
|
|
(home-page "https://pbiecek.github.io/DALEX/")
|
|
(synopsis "Descriptive machine learning explanations")
|
|
(description
|
|
"Machine Learning models are widely used and have various applications in
|
|
classification or regression. Models created with boosting, bagging, stacking
|
|
or similar techniques are often used due to their high performance, but such
|
|
black-box models usually lack interpretability. The DALEX package contains
|
|
various explainers that help to understand the link between input variables
|
|
and model output.")
|
|
;; Any version of the GPL
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-enrichr
|
|
(package
|
|
(name "r-enrichr")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "enrichR" version))
|
|
(sha256
|
|
(base32
|
|
"0lfdr45sdyqhvgz8q4qdbk12mpv86d6id665kq6aaslgr8jggfmn"))))
|
|
(properties `((upstream-name . "enrichR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-httr" ,r-httr)
|
|
("r-rjson" ,r-rjson)))
|
|
(home-page "https://cran.r-project.org/web/packages/enrichR/")
|
|
(synopsis "R Interface to Enrichr database for analyzing gene sets")
|
|
(description
|
|
"This package provides an R interface to all Enrichr databases, a
|
|
web-based tool for analyzing gene sets and returns any enrichment of common
|
|
annotated biological functions.")
|
|
(license license:gpl2+)))
|
|
|
|
(define-public r-plot3d
|
|
(package
|
|
(name "r-plot3d")
|
|
(version "1.1.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "plot3D" version))
|
|
(sha256
|
|
(base32
|
|
"0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"))))
|
|
(properties `((upstream-name . "plot3D")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs `(("r-misc3d" ,r-misc3d)))
|
|
(home-page "https://cran.r-project.org/web/packages/plot3D")
|
|
(synopsis "Plot multi-dimensional data")
|
|
(description
|
|
"This package provides functions for viewing 2D and 3D data, including
|
|
perspective plots, slice plots, surface plots, scatter plots, etc. It
|
|
includes data sets from oceanography.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public r-ggfortify
|
|
(package
|
|
(name "r-ggfortify")
|
|
(version "0.4.7")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "ggfortify" version))
|
|
(sha256
|
|
(base32
|
|
"1wk9j0xg5hj9i1vf62qjiphv8cbsgq7y6baay3pfl3wyb2dwgci0"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-dplyr" ,r-dplyr)
|
|
("r-ggplot2" ,r-ggplot2)
|
|
("r-gridextra" ,r-gridextra)
|
|
("r-scales" ,r-scales)
|
|
("r-stringr" ,r-stringr)
|
|
("r-tibble" ,r-tibble)
|
|
("r-tidyr" ,r-tidyr)))
|
|
(home-page "https://github.com/sinhrks/ggfortify")
|
|
(synopsis "Data visualization tools for statistical analysis results")
|
|
(description
|
|
"This package provides unified plotting tools for statistics commonly
|
|
used, such as GLM, time series, PCA families, clustering and survival
|
|
analysis. The package offers a single plotting interface for these analysis
|
|
results and plots in a unified style using the @code{ggplot2} package.")
|
|
(license license:gpl2)))
|
|
|
|
(define-public r-refmanager
|
|
(package
|
|
(name "r-refmanager")
|
|
(version "1.2.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "RefManageR" version))
|
|
(sha256
|
|
(base32
|
|
"1hfxa1qacfryk36mpaqdhdgws5jwxiyy489ikd3wa18bp1wz8dkp"))))
|
|
(properties `((upstream-name . "RefManageR")))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-bibtex" ,r-bibtex)
|
|
("r-httr" ,r-httr)
|
|
("r-jsonlite" ,r-jsonlite)
|
|
("r-lubridate" ,r-lubridate)
|
|
("r-plyr" ,r-plyr)
|
|
("r-stringr" ,r-stringr)
|
|
("r-xml2" ,r-xml2)))
|
|
(home-page "https://github.com/ropensci/RefManageR/")
|
|
(synopsis "Straightforward BibTeX and BibLaTeX bibliography management")
|
|
(description
|
|
"This package provides tools for importing and working with bibliographic
|
|
references. It greatly enhances the @code{bibentry} class by providing a
|
|
class @code{BibEntry} which stores BibTeX and BibLaTeX references, supports
|
|
UTF-8 encoding, and can be easily searched by any field, by date ranges, and
|
|
by various formats for name lists (author by last names, translator by full
|
|
names, etc.). Entries can be updated, combined, sorted, printed in a number
|
|
of styles, and exported. BibTeX and BibLaTeX @code{.bib} files can be read
|
|
into R and converted to @code{BibEntry} objects.")
|
|
;; Any of these licenses may be picked.
|
|
(license (list license:gpl2 license:gpl3 license:bsd-3))))
|
|
|
|
(define-public r-citr
|
|
(package
|
|
(name "r-citr")
|
|
(version "0.3.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "citr" version))
|
|
(sha256
|
|
(base32
|
|
"0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-assertthat" ,r-assertthat)
|
|
("r-bibtex" ,r-bibtex)
|
|
("r-curl" ,r-curl)
|
|
("r-httr" ,r-httr)
|
|
("r-miniui" ,r-miniui)
|
|
("r-refmanager" ,r-refmanager)
|
|
("r-rstudioapi" ,r-rstudioapi)
|
|
("r-shiny" ,r-shiny)
|
|
("r-shinyjs" ,r-shinyjs)
|
|
("r-yaml" ,r-yaml)))
|
|
(home-page "https://github.com/crsh/citr")
|
|
(synopsis "RStudio add-in to insert Markdown citations")
|
|
(description
|
|
"This package provides functions and an RStudio add-in that search a
|
|
BibTeX or BibLaTeX file to create and insert formatted Markdown citations into
|
|
the current document.")
|
|
(license license:expat)))
|
|
|
|
(define-public r-xgboost
|
|
(package
|
|
(name "r-xgboost")
|
|
(version "0.82.1")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (cran-uri "xgboost" version))
|
|
(sha256
|
|
(base32
|
|
"0plhx63wcm4syslzmjfv6bdgaqn96fnav048hrj0vxk4dzgfp8sq"))))
|
|
(build-system r-build-system)
|
|
(propagated-inputs
|
|
`(("r-data-table" ,r-data-table)
|
|
("r-magrittr" ,r-magrittr)
|
|
("r-matrix" ,r-matrix)
|
|
("r-stringi" ,r-stringi)))
|
|
(home-page "https://github.com/dmlc/xgboost")
|
|
(synopsis "Extreme gradient boosting")
|
|
(description
|
|
"This package provides an R interface to Extreme Gradient Boosting, which
|
|
is an efficient implementation of the gradient boosting framework from Chen
|
|
and Guestrin (2016). The package includes efficient linear model solver and
|
|
tree learning algorithms. The package can automatically do parallel
|
|
computation on a single machine. It supports various objective functions,
|
|
including regression, classification and ranking. The package is made to be
|
|
extensible, so that users are also allowed to define their own objectives
|
|
easily.")
|
|
(license license:asl2.0)))
|