dartR (version 1.9.9.1)

gl.amova: Performs and AMOVA using genlight data.

Description

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.

Usage

gl.amova(x, distance = NULL, permutations = 100)

Arguments

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.]

Value

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.

Examples

# NOT RUN {
#permuations should be higher, here set to 10 because of speed
gl.amova(bandicoot.gl, permutations=10)


# }