R: Phylogeny inference using the least squares method

optim.phylo.ls {phytools}

R Documentation

Phylogeny inference using the least squares method

Description

This function performs phylogeny inference using least-squares.

Usage

optim.phylo.ls(D, stree=NULL, set.neg.to.zero=TRUE, fixed=FALSE,
	tol=1e-10, collapse=TRUE)

Arguments

`D`	a distance matrix.
`stree`	an optional starting tree for the optimization.
`set.neg.to.zero`	a logical value indicating whether to set negative branch lengths to zero (default `TRUE`).
`fixed`	a logical value indicating whether to estimate the topology - if `TRUE` only the branch lengths will be computed.
`tol`	a tolerance value used to assess whether the optimization has converged.
`collapse`	a logical indicating whether to collapse branches with zero length.

Details

Function uses nni from the "phangorn" package (Schliep 2011) to conduct NNIs for topology estimation. Since topology optimization is performed using NNIs, converge to the true least-squares topology is not guaranteed. It is consequently probably wise to start with a very good tree - such as a NJ tree.

Value

An objec of class "phylo" that (may be) the least-squares tree with branch lengths; also returns the sum of squares in attr(tree,"Q-score").

Author(s)

Liam Revell liam.revell@umb.edu

References

Cavalli-Sforza, L. L., and A. W. F. Edwards. (1967) Phylogenetic analysis: Modesl and estimation procedures. American Journal of Human Genetics, 19, 233-257.

Felsenstein, J. (2004) Inferring Phylogenies. Sinauer.

Paradis, E., J. Claude, and K. Strimmer. (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Schliep, K. P. (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.