[R-sig-ME] request for help with glmm

[Πίττα Eύα]

Hi,

I am a phd student in Greece. And I have some questions regarding the 
use of glmm if the data include dissimilarity values.
I do not know if this mailing list is appropriate for my questions but 
I do not know who else to turn to.
My data include islands in various archipelagos and presence-absence of 
species of 3 taxa on the them.
I estimated beta diversity as compositional dissimilarity between pairs 
of islands in the same archipelago using the Jaccard coefficient 
(proportion of common species between two islands).
For example if I have 5 islands in a given archipelago I end up with 10 
dissimilarity values.
I fitted a glmm model (using package lme4) to test for the effect of 
taxon and also the effect of inter-island distance, area and elevation 
differences between pairs of islands
on beta diversity using archipelago as a random factor.
However, dissimilarity values (and the rest) are not independent of 
each other in the same archipelago, because each island contributes to N 
- 1 of them.
I read that a glmm allows for correlation between the observations of 
the same random factor. Does this mean that a glmm takes into account 
the fact that the dissimilarity values are not independent
from each other? Or should I somehow take into account the fact that 
dissimilarity values in the same archipelago are not independent of each 
other.
I would really appreciate your help.


Thank you for your time

Eva