calc_hrf: Calculate the Hemiplasy Risk Factor in a three-species clade.
In guerreror/pepo: Estimate Hemiplasy and Homoplasy on a Phylogeny

Description Usage Arguments Value See Also

HRF is the expected fraction of incongruency due to hemiplasy (vs. homoplasy). It assumes: no uncertainty on species tree (A,(B,C)), one sample per species, branch lengths in coalescent units.

Calls pr_homoplasy() and pr_hemiplasy() for the given values. The total probability of each scenario is the sum of probabilities for two incongruencies: when A and C share the derived state, and when B and C share the derived state.

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

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

1 2	calc_hrf(this_branch, descendants, ancestor, sibling, mutation_rate, model = "standard", pepo = F)

`this_branch`	Numeric. Branch length of focal internal branch.
`descendants`	Numeric vector of size 2. Lengths of branches descending from focal branch.
`ancestor`	Numeric. Length of ancestral branch (the ABC ancestor)
`sibling`	Numeric. Length of sibling branch (leading to tip node A).
`mutation_rate`	Numeric (forward, reverse population-wide mutation rate)
`model`	String. One of the three models implemented: "standard" (default), "minimal", or "strict".