LikShiftsPP: LikShiftsPP: Calculates the likelihood of time-dependent...
In TreePar: Estimating birth and death rates based on phylogenies

Description Usage Arguments Value Author(s) References Examples

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).

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

`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).

res

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

Tanja Stadler

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.

1	# see manual of LikShifts()

Loading required package: ape
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