fix_mpest_tips: Change values of branch lengths at tips

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

Description

Because estimating branch length at tips (terminal lineages) is impossible for coalescent methods, some implementations (like MP-EST) return tips of arbitrary length. These lengths don't have biological meaning but can affect the value of HRF. This function changes the values of the tips for another, equally arbitrary length. 'newval' can take a single value that is applied to all tips, a vector of equal length to the number of tips, or a phylogeny (object class 'phylo') with branch lengths in substitution rate (will be used to extrapolate coalescent branch length)

Usage

fix_mpest_tips(branches, is_tip, newval)

Arguments

branches	numeric vector
is_tip	logical vector
newval	numeric or class 'phylo'

Value

a numeric vector

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