Calculates an AMOVA based on the genetic distance matrix from stamppNeisD() using the amova() function from the package PEGAS for exploring within and between population variation.
stamppAmova(dist.mat, geno, perm = 100)
the matrix of genetic distances between individuals generated from stamppNeisD()
a data frame containing allele frequency data generated from stamppConvert, or a genlight object containing genotype data, individual IDs, population IDs and ploidy levels.
the number of permutations for the tests of hypotheses.
Uses the formula distance ~ populations, to calculate an AMOVA for population differentiation and within & between population variation.
This function uses the amova function from the PEGAS package.
An object of class "amova" which is a list containing a table of sum of square deviations (SSD), mean square deviations (MSD) and the number of degrees of freedom as well as the variance components
Paradis E (2010) pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics 26, 419-420. <doi:10.1093/bioinformatics/btp696>
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Loading required package: pegas Loading required package: ape Loading required package: adegenet Loading required package: ade4 /// adegenet 2.1.1 is loaded //////////// > overview: '?adegenet' > tutorials/doc/questions: 'adegenetWeb()' > bug reports/feature requests: adegenetIssues() Attaching package: 'pegas' The following object is masked from 'package:ade4': amova The following object is masked from 'package:ape': mst Analysis of Molecular Variance Call: amova(formula = dist ~ pop.names, nperm = perm) SSD MSD df pop.names 0.10701827 0.053509133 2 Error 0.01204481 0.004014937 3 Total 0.11906308 0.023812616 5 Variance components: sigma2 P.value pop.names 0.0247471 0.0792 Error 0.0040149 Phi-statistics: pop.names.in.GLOBAL 0.8604084 Variance coefficients: a 2
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