Parameter optimizer for Rdnaml

Share:

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

1
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.

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.

Value

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

Author(s)

Liam J. Revell, Scott A. Chamberlain

Maintainer: Liam J. Revell <liam.revell@umb.edu>

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

1
2
3
4
5
6
## 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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.