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

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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.

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.

Value

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

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

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

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

## End(Not run)

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