R: LikShiftsPP: Calculates the likelihood of time-dependent...
LikShiftsPP
R Documentation
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).
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.
Author(s)
Tanja Stadler
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.