I have a question regarding beta diversity analysis and PERMANOVA.
In my experimental design, I have categories with subgroups. For example: vegetation, cluster, species, plant. What I would like to do is an analysis where these groupings are considered as nested effects.
We have three wood plant species. We have three vegetation types within each species. We also have clusters, which contain a large number of different clusters (essentially the areas we sampled).
I would like to study the nesting effect of clusters within vegetation types, and vegetation types within species. Is there a way to perform this analysis?
I would also like to test the effect of the year on the plant species from which I extracted the DNA. Is this type of analysis correct?
Do you have any suggestions?