phangorn (version 2.12.1)

multiphyDat2pmlPart: Partition model.

Description

Model to estimate phylogenies for partitioned data.

Usage

multiphyDat2pmlPart(x, method = "unrooted", tip.dates = NULL, ...)
pmlPart2multiPhylo(x)
pmlPart(formula, object, control = pml.control(epsilon = 1e-08, maxit = 10,
  trace = 1), model = NULL, method = "unrooted", ...)

Value

kcluster returns a list with elements

logLik

log-likelihood of the fit

trees

a list of all trees during the optimization.

object

an object of class "pml" or "pmlPart"

Arguments

x

an object of class pmlPart

method

One of "unrooted", "ultrametric" or "tiplabeled". Only unrooted is properly supported right now.

tip.dates

A named vector of sampling times associated to the tips/sequences. Leave empty if not estimating tip dated phylogenies.

...

Further arguments passed to or from other methods.

formula

a formula object (see details).

object

an object of class pml or a list of objects of class pml .

control

A list of parameters for controlling the fitting process.

model

A vector containing the models containing a model for each partition.

Author

Klaus Schliep

Details

The formula object allows to specify which parameter get optimized. The formula is generally of the form edge + bf + Q ~ rate + shape + ...{}, on the left side are the parameters which get optimized over all partitions, on the right the parameter which are optimized specific to each partition. The parameters available are "nni", "bf", "Q", "inv", "shape", "edge", "rate". Each parameters can be used only once in the formula. "rate" is only available for the right side of the formula.

For partitions with different edge weights, but same topology, pmlPen can try to find more parsimonious models (see example).

pmlPart2multiPhylo is a convenience function to extract the trees out of a pmlPart object.

See Also

pml,pmlCluster,pmlMix, SH.test

Examples

data(yeast)
dm <- dist.logDet(yeast)
tree <- NJ(dm)
fit <- pml(tree,yeast)
fits <- optim.pml(fit)

weight=xtabs(~ index+genes,attr(yeast, "index"))[,1:10]

sp <- pmlPart(edge ~ rate + inv, fits, weight=weight)
sp

if (FALSE) {
sp2 <- pmlPart(~ edge + inv, fits, weight=weight)
sp2
AIC(sp2)

sp3 <- pmlPen(sp2, lambda = 2)
AIC(sp3)
}