I am currently trying to figure out the differences between Adonis {vegan} and
Analysis of Molecular Variances AMOVA {e.g. Ade4}. I know that Adonis tests if
the position of the centroids (belonging to groups or species) are different
and that this is an approximation of compositional (beta diversity) similarity
of the sample (groups/species) to the other samples (group/species). AMOVA on
the other hand, is just an non-parametric version of ANOVA, usually applied in
population genetics but can be extended to 'ecology' in general since it works
on any distance metric. It tests the hypothesis that genetic (or whatever
distance) diversity within populations (or groups/species) is not significantly
different from that which would result from pooling the two populations
(Excoffier et al., 1992; Anderson, 2001; Martin, 2002). Both methods calculate
P-values using permutations.
So my question is; if I would use the same distance metric with the same
factor-levels, would Adonis and AMOVA produce the same or at least (extremely)
similar results?
I am also wondering the difference between Betadisper {vegan} and HOMOVA
(Homogeneity of Molecular Variance). The only difference here is that
Betadisper seems to be based on Levene's test for homogeneity of variances
while HOMOVA implements Barlett's test.
Any thoughts or comments on this would be highly appreciated, thanks!
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