LikConstant: LikConstant: Calculates the likelihood of constant birth and...

In tanja819/TreePar: Estimating Birth and Death Rates Based on Phylogenies

Description

LikConstant calculates the likelihood of constant speciation and extinction rates for a given phylogenetic tree, conditioning on the age of the tree.

Usage

LikConstant(lambda,mu,sampling,x,root=1,survival=1)

Arguments

lambda,mu	Speciation and extinction rate.
sampling	Sampling is the probability of an extant species being sampled and included into the tree.
x	Vector of speciation times in the phylogeny. Time is measured increasing going into the past with the present being time 0. x can be obtained from a phylogenetic tree using getx(TREE).
root	If root = 1 then max(x) is the mrca (crown age), if root = 0 then max(x) is the age of a branch ancestral to the mrca (stem age).
survival	If survival = 1: The likelihood is conditioned on survival of the process (recommended). Otherwise survival = 0.

Value

res	-log likelihood of the birth and death rates given the tree.

Author(s)

Tanja Stadler

References

T. Stadler. On incomplete sampling under birth-death models and connections to the sampling-based coalescent. Jour. Theo. Biol. 261: 58-66, 2009.

Examples

# see manual of LikShifts()

tanja819/TreePar documentation built on May 31, 2019, 2:57 a.m.