convert_from_cf: Use concordance factors as approximate branch lengths

In guerreror/pepo: Estimate Hemiplasy and Homoplasy on a Phylogeny

Description

Under the assumption that all gene tree discordance is due to incomplete lineage sorting, this function estimates length for internal branches of a tree by taking the proportion of discordant trees (i.e. 1 minus the concordance factor) and solving for branch length t = -ln(3⁄2* (1-CF)). It will return 0 for CF < 1/3, and Infinite for CF == 1 (which isn't realistic but essentially eliminates the possibility of hemiplasy)

Usage

convert_from_cf(tree, concordance_factors)

Arguments

tree	a phylogeny of class 'phylo'
concordance_factors	string or numeric vector of length equal to number of branches in tree

Value

numeric vector of estimated branches

guerreror/pepo documentation built on May 23, 2019, 9:01 p.m.