TreePar (version 3.3)

LikAge: LikAge: Calculates the likelihood of speciation and extinction rates for an ultrametric phylogeny under an age-dependent extinction model conditioning on the age of the tree.

Description

LikAge calculates the likelihood of speciation and extinction rates for an ultrametric phylogeny under an age-dependent extinction model conditioning on the age of the tree. Speciation rate is constant. Time to extinction is a Gamma distribution.

Usage

LikAge(x, lambda, k, theta, sampling, root=1, inputformat=0,
precision=4, numgridpts=500, path, matfilename="setup")

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).

lambda

Speciation rate.

k

Shape parameter of the Gamma distribution modelling time to extinction.

theta

Scale parameter of the Gamma distribution modelling time to extinction.

sampling

Probability to sample a present day lineage.

root

If root=1, max(x) is the crown age and the likelihood is conditioned on the crown age. If root=0, max(x) is the stem age and the likelihood is conditioned on the stem age.

inputformat

If 0, then speciation time vector 'x' is supplied. If 1, then mat-file input (obtained by create.mat) in 'matfilename' is supplied, and 'x' is not considered.

precision

Number of decimal places returned from the numerical likelihood calculation.

numgridpts

Number of gridpoints (evenly spaced time points between zero and the tree age, max(x)) used in the numerical likelihood calculation. The higher this number, the more accurate the numerical results will be.

path

Path where your MCR (Matlab Compiler Runtime) is installed (for details see ?LikAge).

matfilename

Only relevant if inputformat=1; then matfilename="setup" if input file is setup.mat.

Value

res

negative log likelihood of the parameters given the tree. The likelihood conditions on sampling of at least 1 extant tip (analog to survival=1 in other likelihood functions of TreePar).

References

H. Alexander, A. Lambert, T. Stadler. Quantifying Age-Dependent Extinction from Species Phylogenies. Submitted.

Examples

## You need MCR to run the example
## directory where MCR is installed
# path<-"/Applications/MATLAB_R2014a_node.app/"
## location of folder TreePar_Matlab
# locationMat<-"/Users/tstadler/Documents/Data/Uni/Research/R/TreeParProject/TreePar_Matlab"
#
# x<-1:20
# numgridpts<-500
# lambda<-2
# k<-1
# theta<-1
# sampling<-1
## Provide path where the folder TreePar_Matlab is available
# setwd(paste(locationMat,"/compiled",sep=""))
# LikAge(x,lambda, k, theta, sampling, path=path)
## If the shape parameter is 1, we have a constant extinction rate, 
## corresponding to the function LikShift. Then the following commands return the same result.
# LikAge(x,1, 1, 2, sampling, numgridpts=1000, path=path)
# LikShifts(x,c(0),c(1),c(1/2),c(1))