PERMANOVA and PERMDISP and pairwise

[colinbrislawn (Colin J Brislawn)]

Got it. Let's start with Justine's explanation of beta diversity permdisp vs permanova

@jwdebelius

You want to combine permanova and permdisp, since they test different hypothesis. Permanova asks if there is a difference in either within or between group distance for any of my groups. Permdisp tests the hypothesis that there is a significant difference in within group variance.

So, my hope is that I see a large signal in permanova and a small one in permdisp, because that suggests that my difference is driven by differences between communities compared to differences within one of my communities.

Theres more discussion of beta diversity stat testing here (best of the forums!).

For omnibus ANOVA vs pairwise, what to do about conflicting results has been discussed in a variety of contexts:

Why use ANOVA at all instead of jumping straight into post-hoc or planned comparisons tests?

Do we need a global test before post hoc tests?