[R-sig-eco] Specifying contrasts for an interaction in mvabund/manyglm

[Diogo B. Provete]

Hi Kyle,
from the bottom of your message it seems that what you have is a nested
design, with Season nested within Site. If you specify your model with just
the additive effect and the interaction it doesn't take that into account.
I'm not sure if mvabund allows that kind of planned comparisons you want to
conduct. I'd try the newer package gllvm that is much more flexible and can
handle random factors.

All the best
Diogo

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