gen_graph_thr

The function allows to construct a genetic graph whose
links' weights are larger or lower than a specific threshold

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

gen_graph_thr function

<dl><dt>mat_w</dt>
<dd>A symmetric (pairwise) <code>matrix</code> or a <code>dist</code> object
whose elements will be the links' weights</dd>
<dt>mat_thr</dt>
<dd>(optional) A symmetric (pairwise) distance <code>matrix</code>
or a <code>dist</code> object whose values will be used for the pruning based
on the threshold value.</dd>
<dt>thr</dt>
<dd>The threshold value (logically between min(mat_thr)
and max(mat_thr))(integer or numeric)</dd>
<dt>mode</dt>
<dd><ul>
<li>If 'mode = 'larger'' (default), all the links whose weight is larger
than 'thr' are removed.</li>
<li>If 'mode = 'lower'', all the links whose weight is lower
than 'thr' are removed.</li>
</ul></dd></dl>

Arguments

Author

Create a graph of genetic differentiation
using a link weight threshold — gen_graph_thr

<dl>

<dt>mat_w</dt>
<dd>A symmetric (pairwise) <code>matrix</code> or a <code>dist</code> object
whose elements will be the links' weights</dd>


<dt>mat_thr</dt>
<dd>(optional) A symmetric (pairwise) distance <code>matrix</code>
or a <code>dist</code> object whose values will be used for the pruning based
on the threshold value.</dd>


<dt>thr</dt>
<dd>The threshold value (logically between min(mat_thr)
and max(mat_thr))(integer or numeric)</dd>


<dt>mode</dt>
<dd><ul>
<li>If 'mode = 'larger'' (default), all the links whose weight is larger
than 'thr' are removed.</li>
<li>If 'mode = 'lower'', all the links whose weight is lower
than 'thr' are removed.</li>
</ul></dd>

</dl>

gen_graph_thr: Create a graph of genetic differentiation using a link weight threshold

Description

Usage

Value

Arguments

Author

Details

Examples