branch_k3: Calculate branch lengths in genealogy that involves ILS

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

Description

Estimates average length of any branch in the genealogy of the sample (a,b,c), given that the species tree is ((A,B),C) and there was no coalescence of the (a,b) sample in the AB ancestral species. In other words, coalescence of the three samples (a,b,c) happens in the ABC ancestor.

Usage

branch_k3(t0 = 0, tm = Inf, branch)

Arguments

t0	Numeric. Time at start of coalescent process (i.e., constant length to be added to terminal branches; in coal units)
tm	Numberic. Maximum time to coalescence (ABC ancestor branch length)
branch	String. Branch to be returned: first ('short') or second ('long') coalescent events, mean of those two ('avg'), internal ('inter'), or ancestral branch ('anc').

Value

Numeric, the probability of at least one mutation.

Examples

branch_k3(1, 10, 'short')

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