data_ex_loci

Genetic dataset from genetic simulation on CDPOP
200 individuals, 10 populations
20 microsatellite loci (3 digits coding)
100 generations simulated

datasets

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

data_ex_loci function

An object of class 'loci' and 'data.frame' with the columns :<dl>
<dt>population</dt>
<dd>Population name</dd><dt>Other columns</dt>
<dd>20 loci columns with microsatellite data with
3 digits coding, alleles separated by "/", and missing data noted "NA/NA"</dd>
</dl>Row names correspond to individuals' ID

Format

data_ex_loci genetic dataset — data_ex_loci

An object of class 'loci' and 'data.frame' with the columns :<dl>
<dt>population</dt>
<dd>Population name</dd>

<dt>Other columns</dt>
<dd>20 loci columns with microsatellite data with
3 digits coding, alleles separated by "/", and missing data noted "NA/NA"</dd>


</dl>Row names correspond to individuals' ID

data_ex_loci: data_ex_loci genetic dataset

Description

Usage

Arguments

Format

Examples