TreePar (version 3.3)

LikShiftsPP: LikShiftsPP: Calculates the likelihood of time-dependent birth and death rates given a phylogenetic tree.

Description

LikShiftsPP calculates the likelihood of speciation and extinction rates and shift times given a phylogenetic tree, conditioning on the age of the tree. This function uses the point process theory (Lambert and Stadler, 2013).

Usage

LikShiftsPP(x, t, lambda, mu, sampling, survival=1,root=1,n=0)

Arguments

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).

t

The time of rate shifts (t[1]=0 is required, being the present). An entry in t may not coincide with an entry in x.

lambda,mu

Vectors of the same length as t. l[i] (resp. mu[i]) specifies the speciation (resp. extinction rate) prior to t[i].

sampling

Sampling is the probability of an extant species being sampled and included into the tree.

survival

If survival = 1: The likelihood is conditioned on survival of the process (recommended). Otherwise survival = 0.

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).

n

If n != 0 the likelihood is conditioned on n extant sampled tips and tree age max(x).

Value

res

-log likelihood of the model parameters given the phylogenetic tree.

References

T. Stadler. Mammalian phylogeny reveals recent diversification rate shifts. Proc. Nat. Acad. Sci., 108(15): 6187-6192, 2011.

A. Lambert, T. Stadler. Macro-evolutionary models and coalescent point processes: the shape and probability of reconstructed phylogenies. Theo. Pop. Biol., 90: 113-128, 2013.

Examples

# see manual of LikShifts()