pml.fit: Internal maximum likelihood functions.

Description

These functions are internally used for the likelihood computations in pml or optim.pml.

Usage

pml.fit(tree, data, bf=rep(1/length(levels), length(levels)), shape=1, k=1, Q=rep(1, length(levels)*(length(levels)-1)/2), levels=attr(data, "levels"), inv=0, rate=1, g=NULL, w=NULL, eig=NULL, INV=NULL, ll.0=NULL, llMix=NULL,  wMix=0, ..., site=FALSE)
pml.init(data, k)
pml.free()   
edQt(Q = c(1, 1, 1, 1, 1, 1), bf = c(0.25, 0.25, 0.25, 0.25))
lli(data, tree, ...)
discrete.gamma(alpha, k)

Arguments

tree

A phylogenetic tree, object of class phylo.

data

An alignment, object of class phyDat.

Base frequencies.

shape

Shape parameter of the gamma distribution.

alpha

Shape parameter of the gamma distribution.

Number of intervals of the discrete gamma distribution.

A vector containing the lower triangular part of the rate matrix.

levels

inv

Proportion of invariable sites.

rate

Rate.

eig

Eigenvalue decomposition of Q

INV

Sparse representation of invariant sites

ll.0

llMix

wMix

...

Further arguments passed to or from other methods.

site

Value

pml.fit returns the log-likelihood.

Details

These functions are exported to be used in different packages so far only in the package coalescentMCMC, but are not intended for end user. Most of the functions call C code and are far less forgiving if the import is not what they expect than pml.

References

Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368--376.