findRates: Use diversitree to find ML speciation and extinction rates

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

Use diversitree to find ML speciation and extinction rates

Description

Makes an attempt to automatically calculate lambda and mu using diversitree given starting values for the optimization.

Usage

findRates(tree, prop.complete, ini.lambda = 1, ini.mu = 0.1, rate.estimate)

Arguments

tree	A phylogeny in ape format.
prop.complete	The proportion of all species in the tree that are currently contained in it. For instance, if a tree contains 9 species, but there should be 10 species in the tree, set sampling to 0.9.
ini.lambda	Initial speciation value for the optimization. Defaults to 1.
ini.mu	Initial extinction value for the optimization. Defaults to 0.1.
rate.estimate	Whether to use 'laser', 'ape', or 'diversitree' to calculate diversification rates. The latter is the only of those that can account for missing taxa, but in my experience returns systematically biased values.

Details

Add details.

Value

A named numeric vector with the estimated speciation and extinction rates.

References

ETM unpublished

Examples

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

tree <- multi2di(bird.families)

findRates(tree=tree, prop.complete=0.95, rate.estimate="diversitree")

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