guerreror/pepo: Estimate Hemiplasy and Homoplasy on a Phylogeny

P(e):P(o) implements methods to calculate the probabilities of hemiplasy (trait evolution incongruent with species tree due to incomplete lineage sorting) and homoplasy (incongruent traits due to convergent mutations). In this version, the package includes functions to estimate and plot the relative fraction of incongruency due to hemiplasy--the Hemiplasy Risk Factor (HRF)-- of all branches on a phylogeny, provided a tree is in coalescent units.

install.packages("remotes")
remotes::install_github("guerreror/pepo")