(This article was first published on Recology, and kindly contributed to R-bloggers)
Earlier, I posted about generating networks from abundance distributions that you specify. If this post was interesting, check out Jeff Kilpatrick's website, where he provides code he produced in R and Octave to compare real bipartite networks to ones generated based on ecological variables measured in the field (in our case it was abundance, body size, and nectar production). We used that code for a paper we published. Code was modified from code produced by Diego P. Vazquez.
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Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).