convert_from_cf: Use concordance factors as approximate branch lengths

Description Usage Arguments Value

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

1
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.