likelihood function

Negative Log Likelihood Ratio

This function calculates log likelihood ratio value.

likelihood(thetast, fobs, merge2)

Arguments

• thetast: a starting values for the parameter we need to estimate
• fobs: the $4^K$ joint distribution array for K edge tree
• merge2: a (K-1) x 2 matrix describing the tree topology

Details

This function calculates the log likelihood ratio value for F(t). It needs a vector of starting values for the parameters estimate, $4^K$ observed divergence array and merge matrix describing the tree topology.

Returns

The value of the log likelihood ratio

References

Faisal Ababneh, Lars S Jermiin, Chunsheng Ma, John Robinson (2006). Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22(10), 1225-1231.

See Also

gn, gn2

Examples

merge2<-matrix(c(-1,-4,-3,2,-2,-5,1,3), 4, 2)
theta<-c(rep(.25,3), rep(.25,3), rep(.25,3), c(.2,.35,.79,.01,.93,.47),3,.1,.5,.8)
F1<-gn(theta, merge2)
lh<-likelihood(theta, F1, merge2)
lh