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

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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.

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.

Value

This function returns an object of class "dist".

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

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

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

## End(Not run)

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