Gian,
The marginal tests for one-term models had a problem in vegan 2.5-1 and vegan
2.5-2. This is fixed in vegan 2.5-3, so please upgrade. (It never occurred to
me that people would use marginal tests for one-term models where the fitted
model is compared against the empty model, and that
Thank you very much Steve,
I really appreciate you answer. I do not want to drop the main effects out
form the model, I was just trying to understand how adonis works. I was
more confused on how to use the adonis function correctly rather than on
the theory that is behind it. I have an almost
Gian,
I am bit confused by what your concern is. First, if the imbalance is not that
severe, the approach you take to analyzing a two-way permanova (type I, type
II, type III ss) is not going to matter that much. Indeed, if the design were
balanced, they would give you identical results.
