Miscellaneous R functions for phylogenetics that I use regularly
convert.lognormal.R: converts a mean and standard deviation in real space to log spacegeoplot.epoch.rates.R: plots outpus of get.epoch.rates against the geological timescaleget.epoch.rates.R: extracts mean (weighted branch length) evolutionary rates in defined epochs from phylogenetic tree sampleshpd.R: calculates highest posterior density interval (default is 95%) from a vector of values./monophyl.multi.R: estimates the posterior probability of a group (or several groups) being monophyletic from a posterior tree sample. Includes the option to exclude rogue taxa./operators.sa.xml.R: Converts table of upper and lower age bounds for taxa into beast tip date operators for the sampled-ancestros package.tipheight.R: returns height of a taxon in the sense used by beast2 (i.e. age minus age of youngest taxon).