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Miscellaneous R functions for phylogenetics that I use regularly

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R-functions

Miscellaneous R functions for phylogenetics that I use regularly

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  • convert.lognormal.R : converts a mean and standard deviation in real space to log space
  • geoplot.epoch.rates.R : plots outpus of get.epoch.rates against the geological timescale
  • get.epoch.rates.R : extracts mean (weighted branch length) evolutionary rates in defined epochs from phylogenetic tree samples
  • hpd.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).

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Miscellaneous R functions for phylogenetics that I use regularly

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