Rphylip (version 0.1-23)

opt.Rdnaml: Parameter optimizer for Rdnaml

Description

This function is an wrapper for Rdnaml that attempts to optimize gamma (the alpha shape parameter of the gamma model of rate heterogeneity among sites), kappa (the transition:transversion ratio), and bf (the base frequencies).

Usage

opt.Rdnaml(X, path=NULL, ...)

Arguments

X

an object of class "DNAbin".

path

path to the executable containing dnaml. If path = NULL, the R will search several commonly used directories for the correct executable file.

...

optional arguments. See details for more information.

Value

This function returns a list with the following components: kappa, gamma, bf (see Details), and logLik (the log-likelihood of the fitted model).

Details

Optional arguments include the following: tree fixed tree to use in optimization - if not provided, it will be estimated using Rdnaml under the default conditions; bounds a list with bounds for optimization - for kappa and gamma this should be a two-element vector, whereas for bf this should be a 4 x 2 matrix with lower bounds in column 1 and upper bounds in column 2.

More information about the dnaml program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/dnaml.html.

Obviously, use of any of the functions of this package requires that PHYLIP (Felsenstein 1989, 2013) should first be installed. Instructions for installing PHYLIP can be found on the PHYLIP webpage: http://evolution.genetics.washington.edu/phylip.html.

References

Felsenstein, J. (1981) Evolutionary trees from DNA sequences: A Maximum Likelihood approach. Journal of Molecular Evolution, 17, 368-376.

Felsenstein, J. (1989) PHYLIP--Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.

Felsenstein, J. (2013) PHYLIP (Phylogeny Inference Package) version 3.695. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

Felsenstein, J., Churchill, G. A. (1996) A Hidden Markov Model approach to variation among sites in rate of evolution. Molecular Biology and Evolution, 13, 93-104.

See Also

Rdnaml

Examples

## Not run: 
# data(primates)
# fit<-opt.Rdnaml(primates,bounds=list(kappa=c(0.1,40))
# tree<-Rdnaml(primates,kappa=fit$kappa,gamma=fit$gamma,bf=fit$bf)
# ## End(Not run)