This answer is based on the
adonis function in the
vegan package for R. Nesting can enter a permanova in two ways: your model and your permutation structure (the
In your model formula, nesting is simply interaction as specified in R with the forward slash or colon (
A:B:C); you are specifying that the effect of
C should differ based on the value of
A. This is like a fixed effect. Also note that forward slash differs from colon in that it includes terms for all layers in the nesting hierarchy:
strata=A:B, you limit your permutations to be between only those samples with the same levels of
B. This implicitly treats data from each
A:B interaction level as coming from the separate distributions/having disparate error structure. It is therefore somewhat similar to a random effect.
Depending on what your question is, you might include your nesting in either place or in both (see link in this answer).