Rphylip (version 0.1-23)

Rrestdist: R interface for restdist

Description

This function is an R interface for restdist in the PHYLIP package (Felsenstein 2013). restdist can be used to estimate the evolutionary distances between populations based on restriction site or fragment data.

Usage

Rrestdist(X, path=NULL, ...)

Arguments

X

an object of class "rest.data" containing data for restriction sites.

path

path to the executable containing restdist. If path = NULL, the R will search several paths for restdist. See details for more information.

...

optional arguments to be passed to restdist. See details for more information.

Value

This function returns an object of class "dist".

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); method, the method for calculating the genetic distance - options are "Modified" (the default), and "Nei/Li" (Nei & Li 1979); data, the type of data - either "sites" or "fragments"; gamma alpha shape parameter of a gamma model of rate heterogeneity among sites (defaults to no gamma rate heterogeneity); kappa transition:transversion ratio (defaults to kappa = 2.0); site.length the restriction site length (defaults to site.length=6); and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

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

Nei, M., Li, W.-H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences, 76, 5269-5273.

See Also

Rdnadist, Rgendist, Rprotdist

Examples

## Not run: 
# data(restriction.data)
# D<-Rrestdist(restriction.data)
# ## End(Not run)