Software Packages
expoTree:
Calculate the likelihood of a phylogentic tree with an underlying
epidemiological model
Citation: Using an epidemiological model for phylogenetic inference
reveals densitydependence in HIV transmission.
Leventhal, Günthard, Bonhoeffer, and Stadler, 2013
(submitted)

R package: type
install.pacakges("expoTree")
or get from
CRAN.
Project page on BitBucket

The C++ code and R package are now part of the same repository on
BitBucket.
R Snippets
 Jelly Bean Plots — used in
Dünner, Leventhal & Barribeau, 2013 (in prep)
 MetropolisHastings MCMC, with
functions to estimate the Deviance Information Criterion (DIC) and the
marginal likelihood — used in
Dünner, Leventhal & Barribeau, 2013 (in prep)