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.