Suppose I have a distance matrix created by applying the weighted unifrac measure. For instance, using a
weighted_unifrac = UniFrac( physeq=ps, weighted=T, normalized=T, parallel=T, fast=T )
weighted_unifrac is now a distance matrix. Then I perform PERMANOVA using
adonis, and showing the default
permanova = adonis( formula=weighted_unifrac ~ CaseString, data=sample_data, permutations=999, method='bray' )
method doing here? I think of Bray-Curtis as a way to generate the distance matrix itself. How does
method="bray" or my choice of another
method value affect my PERMANOVA analysis?