My implementation of Berry and Berry's hierarchical Bayes algorithm for adverse events

I've been working on this for quite some time (see here for a little background), so I'm pleased that it looks close to done at least as far as the core algorithm. It uses global variables for now, and I'm sure there are a couple of other bugs lurking, but here it is, after the jump.

Working on a drug safety project

In order to move some of my personal interests along, I have been trying to implement the methodology found in Berry and Berry's article Accounting for Multiplicities in Assessing Drug Safety. This methodology uses the MedDRA hierarchy to improve the power of detecting damage to a particular organ. (The drawback, of course, is that MedDRA system organ classes do not perfectly correspond to the biology.) Apparently some other groups have already done so, but these implementations are hiding in paid software or on people's local drives, but doing my own implementation in R is a good learning experience.

I've been working on this project for some time now, off an on. Well, I've been making progress, and I'll share the results when I'm done. I'd also like to implement some of the other similar algorithms in this area, including the Poisson model that accounts for multiple occurrences of an adverse event, and a recent methodology that looks for "syndromes" (i.e. occurrences of groups of specific events all of which arise within a short time) and "constellations" (where the time restrictions are relaxed).