genepop_to_genind

The function converts a text file in the format used by GENEPOP
software into a genind object

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

genepop_to_genind function

<dl><dt>path</dt>
<dd>A character string with the path leading to the GENEPOP file
in format .txt, or alternatively the name of this file in the working
directory.</dd>
<dt>n.loci</dt>
<dd>The number of loci in the GENEPOP file (integer or numeric).</dd>
<dt>pop_names</dt>
<dd>(optional) Populations' names in the same order
as in the GENEPOP file.
Vector object (class character) of the same length as the number
of populations.
Without this parameter, populations are numbered from 1 to the number
of populations.</dd>
<dt>allele.digit.coding</dt>
<dd>Number indicating whether alleles are coded
with 3 (default) or 2 digits.</dd></dl>

Arguments

Author

Convert a GENEPOP file into a genind object — genepop_to_genind

<dl>

<dt>path</dt>
<dd>A character string with the path leading to the GENEPOP file
in format .txt, or alternatively the name of this file in the working
directory.</dd>


<dt>n.loci</dt>
<dd>The number of loci in the GENEPOP file (integer or numeric).</dd>


<dt>pop_names</dt>
<dd>(optional) Populations' names in the same order
as in the GENEPOP file.
Vector object (class character) of the same length as the number
of populations.
Without this parameter, populations are numbered from 1 to the number
of populations.</dd>


<dt>allele.digit.coding</dt>
<dd>Number indicating whether alleles are coded
with 3 (default) or 2 digits.</dd>

</dl>

genepop_to_genind: Convert a GENEPOP file into a genind object

Description

Usage

Value

Arguments

Author

Details

References

See Also

Examples