R interface for consense

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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

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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.

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.

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.

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

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

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

## End(Not run)

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