patch_areas

The function extracts patch areas from a categorical raster

internal

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

patch_areas function

<dl><dt>raster</dt>
<dd>A RasterLayer object corresponding to a categorical raster layer</dd>
<dt>class</dt>
<dd>An integer value or vector with the value(s) corresponding to
the code values of the raster layer within which points will be sampled.
are computed.</dd>
<dt>edge_size</dt>
<dd>An integer value indicating the width of the edge
(in meters) of the raster layer which is ignored during the sampling
(default = 0). It prevents from sampling in the margins of the study area.</dd>
<dt>neighborhood</dt>
<dd>An integer value indicating which cells are considered
adjacent when contiguous patches are delineated (it should be 8
(default, Queen's case) or 4 (Rook's case)). This parameter is ignored
when <code>by_patch = FALSE</code>.</dd>
<dt>surf_min</dt>
<dd>An integer value indicating the minimum surface of a patch
considered for the sampling in number of raster cells. This parameter is used
whatever the <code>by_patch</code> argument is. Default is 0.</dd></dl>

Arguments

Author

Extract patch areas from a categorical raster — patch_areas

<dl>

<dt>raster</dt>
<dd>A RasterLayer object corresponding to a categorical raster layer</dd>


<dt>class</dt>
<dd>An integer value or vector with the value(s) corresponding to
the code values of the raster layer within which points will be sampled.
are computed.</dd>


<dt>edge_size</dt>
<dd>An integer value indicating the width of the edge
(in meters) of the raster layer which is ignored during the sampling
(default = 0). It prevents from sampling in the margins of the study area.</dd>


<dt>neighborhood</dt>
<dd>An integer value indicating which cells are considered
adjacent when contiguous patches are delineated (it should be 8
(default, Queen's case) or 4 (Rook's case)). This parameter is ignored
when <code>by_patch = FALSE</code>.</dd>


<dt>surf_min</dt>
<dd>An integer value indicating the minimum surface of a patch
considered for the sampling in number of raster cells. This parameter is used
whatever the <code>by_patch</code> argument is. Default is 0.</dd>

</dl>

patch_areas: Extract patch areas from a categorical raster

Description

Usage

Value

Arguments

Author