[R-sig-eco] Questions about interpreting ERGM goodness of fit

[Erick LeBrun]

Hello all,

I apologize in advance as I am fairly new to networks. I have two 
networks generated in R with sample sites as nodes representing 
microbial community relatedness between sites (as bray-curtis distance 
from an OTU counts table). I am interested in looking at two categorical 
groupings as factors in network design and have built a few ERGMs to 
explore this. Everything looks good in mcmc.diagnostics() and summary() 
and the anova.ergm() looks good as well.

My problem occurs in testing goodness of fit (gof()). The degree graph 
is not too bad but the edge-wise shared partners graph for the data 
peaks far to the right of the simulated (for example simulated will peak 
at~3 and actual data has a small peak at ~3 and then a huge one at ~7.

I know that there are probably important factors missing from these 
models and I am wondering if that may be what is causing the issue(?) My 
main interest is in demonstrating importance in my categorical 
variables. Or is this indicative of some larger problem? I have looked 
through many resources explaining how to generate goodness of fit 
metrics but have not found anything to help me interpret this issue.

Thank you in advance!

Erick


(also posted in r-sig-networks)