Title: Install and Load the 'dartRverse' Suits of Packages
Version: 1.0.6
Date: 2025-02-17
Revision: Devious Dodo
Description: Provides a single function that supports the installation of all packages belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel' and are based on the same type of data structure ('genlight'), with additional metadata for loci and individuals (samples). For more information visit the 'GitHub' pages https://github.com/green-striped-gecko/dartRverse.
URL: https://github.com/green-striped-gecko/dartRverse
License: GPL (≥ 3)
Depends: R (≥ 3.5)
Imports: cli, rlang, devtools, RCurl, httr
Suggests: dartR.base, dartR.data, dartR.sim, dartR.captive, dartR.popgen, dartR.spatial
Encoding: UTF-8
RoxygenNote: 7.3.2
NeedsCompilation: no
Packaged: 2025-02-17 04:01:37 UTC; s425824
Maintainer: Bernd Gruber <bernd.gruber@canberra.edu.au>
Repository: CRAN
Author: Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [aut], Oliver Berry [aut]
Date/Publication: 2025-02-18 09:00:02 UTC

dartRverse-package

Description

The 'dartRverse' combines a set of packages that work together to analyse SNP and silicodart data. It is the successor of the package dartR. Due to its high number of dependencies it was necessary to break the package into several, smaller packages to reduce overall dependencies from other packages and to speed up testing. You can check which packages do exist by typing dartRverse_install().

Author(s)

Maintainer: Bernd Gruber bernd.gruber@canberra.edu.au

Authors:

See Also

Useful links:

Checks installed package and Supports installation of CRAN and Github packages of the dartRverse

Description

This functions expects the name of one (or several) dartR packages, the repository (CRAN or Github) and in the case of github the branch (main, dev, beta) to install the identified version of the pacakge. If run with no parameter the current installed packages and their versions are printed.

Usage

dartRverse_install(
  package = NULL,
  rep = "CRAN",
  branch = "main",
  verbose = TRUE
)

Arguments

package

Name of the package to install, currently [dartR.base, dartR.data, dartR.sim, dartR.spatial, dartR.popgen, dartR.sexlinked]

rep

Which repository is used ('CRAN' or 'Github').

branch

If Github is used the branch on Github needs to be specified, [either main, beta or dev] The 'main' repository on Github is identical with the latest CRAN submission. Important changes and fixes are published under 'beta' and tested there, before the are submitted to CRAN. Hence this might be the best chance to look for fixes. All 'dev' branches are 'risky' meaning they have not been tested. To get the current versions availble and which are installed run: dartRverse_install(). To get the code how to install all other packages run: dartRverse_install("all").

verbose

if set to true the current installed packages are printed.

Value

functions returns NULL

Examples

dartRverse_install("all")

dartRverse_install()

Support function to download binaries from github

Description

This functions supports the download of binaries from github. Those binaries are compiled files that allow to run dartR functions that integrate third party software such as epos (gl.run.epos), NeEstimator (gl.LDNe) or Structure (gl.run.structure). Please be aware this is just to allow for easy install and use of dartR functions seemlessly. We have explicitely asked the authors of the software for permission to include those binaries here. Understandably some authors prefer to direct users to their own websites to download the software. Here a comment is issued by the function how to do so. Please note: **The third party packages are the work of others and please make the effort to cite them accordingly**. You find the citations under the help pages of the respective functions, for example ?gl.run.epos.

Usage

gl.download.binary(
  software = NULL,
  os = NULL,
  branch = "main",
  out.dir = tempdir(),
  verbose = 2
)

Arguments

software

name of the software package to download. Currently supported are: "epos", "NeEstimator", "Stairway2" and "Gone". Please note, depending on the software several files will be downloaded

os

the operating system to download the binary for. Currently supported are: "windows", "mac" and "linux". Please be aware some binaries are not available for all operating systems.

branch

which branch to download from (leave empty for the main branch and there should not be a reason to change that)

out.dir

the path where to save the binary. If left empty the binary will be saved in the temporary directory.

verbose

.If zero, suppresses output messages. Default is zero

Value

functions returns NULL

Examples

gl.download.binary

dartRverse_install()