Rphylip (version 0.1-23)

Rconsense: R interface for consense

Description

This function is an R interface for consense in the PHYLIP package (Felsenstein 2013). consense can be used to compute the consensus tree from a set of phylogenies.

Usage

Rconsense(trees, path=NULL, ...)

Arguments

trees

an object of class "multiPhylo".

path

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

...

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

Value

This function returns an object of class "phylo". For methods other than method = "strict", tree$node.label contains the proportion of phylogenies in trees containing that subtree.

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); method which can be "extended" (extended majority rule consensus, the default), "strict" (strict consensus), or regular majority rule consensus ("majority"); "outgroup" single taxon label or vector of taxa that should be used to root all trees before analysis; rooted logical value indicated whether to treat the input trees as rooted (defaults to rooted = FALSE); and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

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

Margush, T., McMorris, F.R. (1981) Consensus n-trees. Bulletin of Mathematical Biology, 43, 239-244.

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.

Examples

## Not run: 
# trees<-rmtree(n=10,N=10)
# tree<-Rconsense(trees)
# ## End(Not run)