bd.age.optim.matlab: bd.age.optim.matlab: Estimating speciation rate and...
In TreePar: Estimating birth and death rates based on phylogenies

Description Usage Arguments Value Note Author(s) References Examples

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.

1 2	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")

`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.

res

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

This function relies on compiled Matlab applications that need to be downloaded. For setting up the environment to run the function, please refer to 'Notes' in function 'LikAge'.

Helen Alexander, Tanja Stadler

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

## 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]]

Loading required package: ape
Loading required package: Matrix
Loading required package: subplex
Loading required package: TreeSim
Loading required package: geiger
Loading required package: deSolve