TreePar (version 3.3)

bd.age.optim.matlab: bd.age.optim.matlab: Estimating speciation rate and age-dependent extinction rate in phylogenies.

Description

bd.age.optim.matlab estimates the maximum likelihood speciation and extinction rates in a (possibly incomplete sampled) phylogeny. Speciation rate is constant, time to extinction is assumed to be a Gamma distribution.

Usage

bd.age.optim.matlab(x, lambdainit=1, kinit=1, thetainit=2, sampling, model="G", 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).

lambdainit

Speciation rate at the initial point from which optimization starts.

kinit

Shape parameter of the Gamma distribution modelling time to extinction at the initial point from which optimization starts.

thetainit

Scale parameter of the Gamma distribution modelling time to extinction at the initial point from which optimization starts.

sampling

Probability to sample a present day lineage.

model

Model assumed for time to extinction. "G": Gamma distribution, i.e. shape parameter is estimated. "E": Exponential distribution, i.e. shape parameter is set to 1.

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

Vector of four numbers: negative log likelihood value and maximum likelihood estimate of lambda, k, theta.

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"
##
# setwd(locationMat)
# x<-read.table("branchingtimes.txt")
# numgridpts<-500
# lambda<-2
# k<-1
# theta<-1
# sampling<-1
# setwd(paste(locationMat,"/compiled",sep=""))
# LikAge(x,lambda, k, theta, sampling, path=path)
# outG <- bd.age.optim.matlab(x, lambda, k, theta, sampling, path=path)
# outE <- bd.age.optim.matlab(x, lambda, k, theta, sampling, path=path, model="E")
## compare with bd.shifts.optim for exponenetial lifetime
# outEcompare<-c(outE[1],1/(outE[2]*outE[3]),outE[2]-1/outE[3])
# outShifts <- bd.shifts.optim(x,sampling=c(1),survival=1)[[2]]