loglike.coal: loglikelihood of the species tree, i.e., Rannala and Yang...

In lliu1871/phybase: Basic functions for phylogenetic analysis

loglikelihood of the species tree, i.e., Rannala and Yang formula

Description

This function calculates the loglikelihood of a species tree from a set of gene trees using the Rannala and Yang formula

Usage

loglike.coal(gtree, sptree, taxaname,spname,species.structure,strict=T)

Arguments

gtree	a collection of gene trees
sptree	a species tree in newick format
taxaname	the names of taxa
spname	the names of species
species.structure	define which sequence belong to which species
strict	whether or not to check the result

Value

The function returns the log likelihood score.

Author(s)

Liang Liu

References

Rannala, B. and Z. Yang. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164: 1645-1656.

Examples

gtree<-"(((A:1,B:1):3,C:4):2,D:6);"
stree<-"(((A:0.5,B:0.5):1#0.1,C:1.5):1#0.1,D:2.5)#0.1;"
taxaname<-c("A","B","C","D")
spname<-taxaname
ntax<-length(taxaname)
nspecies<-length(spname)
species.structure<-matrix(0,nrow=nspecies,ncol=ntax)
diag(species.structure)<-1
loglike.coal(gtree,stree,taxaname,spname,species.structure)

lliu1871/phybase documentation built on April 21, 2024, 3:16 a.m.