Dear Kevin, In the future, r-sig-eco (https://stat.ethz.ch/mailman/listinfo/r-sig-ecology) might be a better list for R-related ecological questions, although you didn't really have questions on bipartite itself (but if that's what you want to know, yes, it's the package you want to use for this kind of stuff).
Some hints: Question 1) have a look at: Nielsen, A. and J. Bascompte. 2007. Ecological networks, nestedness, and sampling effort. Journal of Ecology 95:1134-1141. and this one also discusses this sampling issue: Tylianakis, J. M., E. Laliberté, A. Nielsen, and J. Bascompte. 2010. Conservation of species interaction networks. Biological Conservation (in press; see www.elaliberte.info/publications for a PDF). Webs are often pooled in analyses. But bear in mind webs from different habitats can be more spatially / temporally variable than others, and pooling will obscure this. For example see: Laliberté, E. and J. M. Tylianakis. 2010. Deforestation homogenizes tropical parasitoid-host networks. Ecology (in press; see www.elaliberte.info/publications for a PDF). Question 2) Field constraints are always a tough call. A rule-of-thumb is that you should have at least 10 replicates per level, so maybe you could drop a few replicates. Then again, a 20m X 50m also plot seems pretty big to me. A small pilot study could help you decide how to optimize sampling effort. Question 3) Go for abundance. You can always convert back abundance to presence-absence, but not the opposite. It can be a good idea to look at differences in both binary and quantitative webs, because you can get different answers, e.g. Tylianakis, J. M., T. Tscharntke, and O. T. Lewis. 2007. Habitat modification alters the structure of tropical host-parasitoid food webs. Nature 445:202-205. or, sometimes, similar answers, such as Laliberté and Tylianakis (2010) (see above reference). Hope that helps, Etienne -- Etienne Laliberté ================================ School of Forestry University of Canterbury Private Bag 4800 Christchurch 8140, New Zealand Phone: +64 3 366 7001 ext. 8365 Fax: +64 3 364 2124 www.elaliberte.info
