graph_plan

The function constructs a graph with a minimum planar
graph topology

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

graph_plan function

<dl><dt>crds</dt>
<dd>A <code>data.frame</code> with the spatial
coordinates of the point set (the graph nodes). It must have three columns:<ul>
<li>ID: A character string indicating the name of the points(graph nodes).</li>
<li>x: A numeric or integer indicating the longitude of the graph nodes.</li>
<li>y: A numeric or integer indicating the latitude of the graph nodes.</li>
</ul></dd>
<dt>ID</dt>
<dd>A character string indicating the name of the column
of <code>crds</code> with the point IDs</dd>
<dt>x</dt>
<dd>A character string indicating the name of the column
of <code>crds</code> with the point longitude</dd>
<dt>y</dt>
<dd>A character string indicating the name of the column
of <code>crds</code> with the point latitude</dd>
<dt>weight</dt>
<dd>A character string indicating whether the links of
the graph are weighted by Euclidean distances (TRUE)(default) or not (FALSE).
When the graph links do not have weights in Euclidean distances, each link
is given a weight of 1.</dd></dl>

Arguments

Author

Create a graph with a minimum planar graph topology — graph_plan

<dl>

<dt>crds</dt>
<dd>A <code>data.frame</code> with the spatial
coordinates of the point set (the graph nodes). It must have three columns:<ul>
<li>ID: A character string indicating the name of the points(graph nodes).</li>
<li>x: A numeric or integer indicating the longitude of the graph nodes.</li>
<li>y: A numeric or integer indicating the latitude of the graph nodes.</li>
</ul></dd>


<dt>ID</dt>
<dd>A character string indicating the name of the column
of <code>crds</code> with the point IDs</dd>


<dt>x</dt>
<dd>A character string indicating the name of the column
of <code>crds</code> with the point longitude</dd>


<dt>y</dt>
<dd>A character string indicating the name of the column
of <code>crds</code> with the point latitude</dd>


<dt>weight</dt>
<dd>A character string indicating whether the links of
the graph are weighted by Euclidean distances (TRUE)(default) or not (FALSE).
When the graph links do not have weights in Euclidean distances, each link
is given a weight of 1.</dd>

</dl>

graph_plan: Create a graph with a minimum planar graph topology

Description

Usage

Value

Arguments

Author

Details

Examples