I am trying to run a population viability analysis for a single species using sets of matrices from multiple populations and I cant find the R code for this in the popbio sources.
Do you have access to the book ( assume you are referring to "Quantitative Conservation Biology")? I only know of the supplied MATLAB code at http://www.sinauer.com/quantitative-conservation-biology-theory-and-practice-of-population-viability-analysis.html but it should be pretty straitforward to translate this directly to R.