create.mat: create.mat: Generates input for LikAge and...

In TreePar: Estimating birth and death rates based on phylogenies

Description

create.mat generates input for LikAge and bd.age.optim.matlab.

Usage

create.mat(x, 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).
numgridpts	Number of gridpoints to be used in the numerical likelihood calculation in LikAge or bd.age.optim.matlab.
path	Path where your MCR (Matlab Compiler Runtime) is installed (for details see ?LikAge).
matfilename	File matfilename.mat is created which contains input (speciation times) in a valid format for LikAge and bd.age.optim.matlab.

Value

res	0 is returned. The file for downstream analysis is saved as matfilename.mat.

Note

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'. This function is useful to evaluate if LikAge or bd.age.optim.matlab are called several times for one tree. Then the input for the matlab functions is created once and used in LikAge or bd.age.optim.matlab through inputformat=1 and specifying matfilename.

Author(s)

Helen Alexander, Tanja Stadler

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 containing compiled Matlab applications (see ?LikAge)
# locationMat<-"/Users/tstadler/Documents/Data/Uni/Research/R/TreeParProject/TreePar_Matlab"
##
# x<-1:20
# setwd(paste(locationMat,"/compiled",sep=""))
# out<-create.mat(x,path=path)

TreePar documentation built on May 1, 2019, 9:20 p.m.