phangorn (version 2.11.1)

pml_bb: Likelihood of a tree.

Description

pml_bb for pml black box infers a phylogentic tree infers a tree using maximum likelihood (ML).

Usage

pml_bb(x, model = NULL, rearrangement = "stochastic",
  method = "unrooted", start = NULL, tip.dates = NULL, ...)

Value

pml_bb returns an object of class pml.

Arguments

x

An alignment of class (either class phyDat, DNAbin or AAbin) or an object of class modelTest.

model

A string providing model (e.g. "GTR+G(4)+I"). Not necessary if a modelTest object is supplied.

rearrangement

Type of tree tree rearrangements to perform, one of "none", "NNI", "stochastic" or "ratchet"

method

One of "unrooted", "ultrametric" or "tiplabeled".

start

A starting tree can be supplied.

tip.dates

A named vector of sampling times associated to the tips / sequences.

...

Further arguments passed to or from other methods.

Author

Klaus Schliep

Details

pml_bb is a convenience function combining pml and optim.pml. If no tree is supplied, the function will generate a starting tree. If a modelTest object is supplied the model will be chosen according to BIC.

Currently very experimental and likely to change.

tip.dates should be a named vector of sampling times, in any time unit, with time increasing toward the present. For example, this may be in units of “days since study start” or “years since 10,000 BCE”, but not “millions of yearsago”.

See Also

optim.pml, modelTest, rtt

Examples

if (FALSE) {
data(woodmouse)
tmp <- pml_bb(woodmouse)

data(Laurasiatherian)
mt <- modelTest(Laurasiatherian)
fit <- pml_bb(mt)
}