I have a data frame of multivariate abundances (species) that have been measured from sites under two different treatments. These same sites have been repeatedly measured over multiple years.
I am modelling the change in species abundances between treatments over time using the
mvabund package in R. My model is
However, because the same sites have been sampled repeatedly they are repeated measures and thus are not independent between years. I want to account for this in my model by restricting the permutations using the
However, I am struggling to conceptually understand how I need to restrict the permutations to account for this non-independence.