tree_hrf: Calculate HRF for all branches on a tree

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

Description

It assumes: no uncertainty on species tree (A,(B,C)), one sample per species, branch lengths in coalescent units.

If 'mutation' is a numeric of length 1, forward (0->1) and reverse (1->0) mutation rates are the same. If it's of length 2, the first element is the forward- and the second is the reverse mutation rate.

'mode' can be one of three: 'minimal' – Reversals are not allowed. Ancestral (ABC) time is assumed to be infinite. 'standard' – Reversals allowed. Ancestral (ABC) time is assumed to be at least 4. This is equivalent to assuming that coalescence in the ABC ancestor is very likely (most coalescence happens before this time). 'strict' – Reversals allowed. No changes to ABC time. If this time is very short, probabilities of reversals and of hemiplasy are affected. The ABC branch (where the first 0->1 would happen in a reversal scenario) and the AC branch (where the only 0->1 happens in hemiplasy) are very short, lowering the probability of events on them.

Usage

tree_hrf(edges, mutation = 0.01, mode = "standard")

Arguments

edges	a tibble (or data_frame)
mutation	numeric (forward, reverse population-wide mutation rate)
mode	character

Value

a tibble

See Also

pr_homoplasy, pr_hemiplasy, calc_hrf

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