bdScaler: Generate missing speciation events

In eliotmiller/addTaxa: An R package for adding missing taxa to phylogenies

Generate missing speciation events

Description

Place speciation event in a speciation/extinction rate-informed position

Usage

bdScaler(tree, lambda, mu, min.age, max.age)

Arguments

tree	A phylogeny in ape format.
lambda	The speciation rate.
mu	The exctinction rate.
min.age	Minimum age of the missing speciation event to be inferred. Note that this is the age counting back from the tips, such that 0 is the present. Thus, min.age must always be less than max.age.
max.age	Maximum age of the missing speciation event to be inferred.

Details

This function assumes that a single species is missing, then takes the provided lambda and mu values, and the range of time over which the speciation event occurred, and generates the missing time.

Value

A missing speciation time.

References

ETM unpublished

Examples

#load a molecular tree up
data(bird.families)

bdScaler(bird.families, lambda=1, mu=0, min.age=0, max.age=10)

eliotmiller/addTaxa documentation built on Feb. 3, 2024, 12:19 a.m.