g_percol

The function allows to prune a graph by removing
the links with the largest weights until the graph breaks into
two components. The returned graph is the last graph with only one
component.

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

g_percol function

<dl><dt>x</dt>
<dd>A symmetric <code>matrix</code> or a <code>dist</code> object with pairwise
distances between nodes</dd>
<dt>val_step</dt>
<dd>The number of classes to create to search for the
threshold value without testing all the possibilities. By default,
'val_step = 20'.</dd></dl>

Arguments

Author

Prune a graph using the 'percolation threshold' method — g_percol

<dl>

<dt>x</dt>
<dd>A symmetric <code>matrix</code> or a <code>dist</code> object with pairwise
distances between nodes</dd>


<dt>val_step</dt>
<dd>The number of classes to create to search for the
threshold value without testing all the possibilities. By default,
'val_step = 20'.</dd>

</dl>

g_percol: Prune a graph using the 'percolation threshold' method

Description

Usage

Value

Arguments

Author

Examples