chaparral analysis script

Fitting the GeoSSE model with this script requires the R package diversitree, written by Rich FitzJohn. A snapshot of the code used for the analyses in the paper is archived by Systematic Biology as a supplemental file to the paper (diversitreeGSE_0.4-5.tar.gz) because its GPL licence is not compatible with Dryad's CC0 requirement. This package is presently undergoing rapid development, so for any new applications, please use the current, improved version of the package, available from: http://cran.r-project.org/web/packages/diversitree/ and http://www.zoology.ubc.ca/prog/diversitree/.