get_graphab_linkset

The function gets a linkset computed in the Graphab project

Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs,	compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://igraph.org/>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.

Paul Savary

graph4lg

Build Graphs for Landscape Genetics Analysis

Gilles Vuidel

Tyler Rudolph

Alexandrine Daniel

get_graphab_linkset function

<dl><dt>proj_name</dt>
<dd>A character string indicating the Graphab project name.
The project name is also the name of the project directory in which the
file proj_name.xml is.</dd>
<dt>linkset</dt>
<dd>A character string indicating the name of the link set
whose properties are imported. The link set has been created with Graphab
or using <code>graphab_link</code> function.</dd>
<dt>proj_path</dt>
<dd>(optional) A character string indicating the path to the
directory that contains the project directory. It should be used when the
project directory is not in the current working directory. Default is NULL.
When 'proj_path = NULL', the project directory is equal to <code><a href="/link/getwd()?package=graph4lg&version=1.8.0" data-mini-rdoc="graph4lg::getwd()">getwd()</a></code>.</dd></dl>

Arguments

Author

Get linkset computed in the Graphab project — get_graphab_linkset

<dl>

<dt>proj_name</dt>
<dd>A character string indicating the Graphab project name.
The project name is also the name of the project directory in which the
file proj_name.xml is.</dd>


<dt>linkset</dt>
<dd>A character string indicating the name of the link set
whose properties are imported. The link set has been created with Graphab
or using <code>graphab_link</code> function.</dd>


<dt>proj_path</dt>
<dd>(optional) A character string indicating the path to the
directory that contains the project directory. It should be used when the
project directory is not in the current working directory. Default is NULL.
When 'proj_path = NULL', the project directory is equal to <code><a href='https://rdrr.io/r/base/getwd.html'>getwd()</a></code>.</dd>

</dl>

get_graphab_linkset: Get linkset computed in the Graphab project

Description

Usage

Value

Arguments

Author

Details

Examples