Rphylip (version 0.1-23)

Rclique: R interface for clique

Description

This function is an R interface for clique in the PHYLIP package (Felsenstein 2013). clique can be used for phylogeny inference using the compatibility method (Le Quesne 1969; Estabrook et al. 1976).

Usage

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

Arguments

X

an object of class "phylip.data" with a set of binary characters; or a matrix.

path

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

...

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

Value

This function returns an object of class "phylo" that is the optimized tree.

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); ancestral vector of ancestral states; weights vector of weights of length equal to the number of columns in X (defaults to unweighted); minimum.clique, if specified, will cause Rclique to print out all cliques (and corresponding trees) greater than minimum.clique; outgroup outgroup if outgroup rooting of the estimated tree is desired; and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

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

Estabrook, G. F., Johnson, C. S. Jr., McMorris, F. R. (1976). A mathematical foundation for the analysis of character compatibility. Mathematical Biosciences, 23, 181-187.

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.

Le Quesne, W.J. (1969) A method of selection of characters in numerical taxonomy. Systematic Zoology, 18, 201-205.

See Also

Rdnacomp, Rmix

Examples

## Not run: 
# data(primates.bin)
# tree<-Rclique(primates.bin)
# ## End(Not run)