gstud_to_genind

The function converts a file formatted to use gstudio or
popgraph package into a genind object (adegenet package)

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

gstud_to_genind function

<dl><dt>x</dt>
<dd>An object of class <code>data.frame</code> with loci columns in
format <code>locus</code> (defined in package gstudio) with as many rows as
individuals and as many columns in format <code>locus</code> as there are loci and
additional columns</dd>
<dt>pop_col</dt>
<dd>A character string indicating the name of the column with
populations' names in <code>x</code></dd>
<dt>ind_col</dt>
<dd>(optional) A character string indicating the name of the
column with individuals' ID in <code>x</code></dd></dl>

Arguments

Author

Convert a file from gstudio or popgraph into a genind object — gstud_to_genind

<dl>

<dt>x</dt>
<dd>An object of class <code>data.frame</code> with loci columns in
format <code>locus</code> (defined in package gstudio) with as many rows as
individuals and as many columns in format <code>locus</code> as there are loci and
additional columns</dd>


<dt>pop_col</dt>
<dd>A character string indicating the name of the column with
populations' names in <code>x</code></dd>


<dt>ind_col</dt>
<dd>(optional) A character string indicating the name of the
column with individuals' ID in <code>x</code></dd>

</dl>

gstud_to_genind: Convert a file from gstudio or popgraph into a genind object

Description

Usage

Value

Arguments

Author

Details

Examples