pr_homoplasy: Probability of incongruence due to homoplasy in a...

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, observed states of binary trait were a=1, b=0, and c=1, branch lengths in coalescent units.

Roughly, it computes the product of the probabilities of events necessary for the observed incongruence. Specifically, mutations along the A and C branches (implying no mutations in other branches) or –depending on mode- mutations along the ABC ancestor and B.

See documentation of tree_hrf() for description of the three models implemented.

Usage

pr_homoplasy(this, desc_a, desc_b, sib, anc, mu_rate, mode = "standard")

Arguments

this	Numeric. Branch length of focal internal branch.
desc_a	Lengths of branches descending from focal branch.
desc_b	Lengths of branches descending from focal branch.
sib	Length of sibling branch (leading to tip node C).
anc	Length of ancestral branch (the ABC ancestor)
mu_rate	Numeric of length 2. Population-wide mutation rate (forward, reverse)
mode	String. One of the three models implemented: "standard" (default), "minimal", or "strict".

Value

Numeric, a probability

See Also

pr_hemiplasy, calc_hrf, tree_hrf

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