Performs and AMOVA using genlight data.
This script performs an AMOVA based on the genetic distance matrix from stamppNeisD() [package StAMPP] using the amova() function from the package PEGAS for exploring within and between population variation. For detailed information use their help pages: ?pegas::amova, ?StAMPP::stamppAmova. Be aware due to a conflict of the amova functions from various packages I had to "hack" StAMPP::stamppAmova to avoid a namespace conflict.
gl.amova(x, distance = NULL, permutations = 100)
x |
– name of the genlight containing the SNP genotypes, with population information [required] |
distance |
– distance matrix between individuals (if not provided NeisD from StAMPP::stamppNeisD is calculated) |
permutations |
– number of permuations to perform for hypothesis testing [default 100]. Please note should be set to 1000 for analysis.] |
An object of class "amova" which is a list with a table of sums of square deviations (SSD), mean square deviations (MSD), and the number of degrees of freedom, and a vector of variance components.
Bernd Gruber (bugs? Post to https://groups.google.com/d/forum/dartr)
#permuations should be higher, here set to 10 because of speed gl.amova(bandicoot.gl, permutations=10)
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