R interface for treedist

Description

This function is an R interface for treedist in the PHYLIP package (Felsenstein 2013). treedist can be used to compute the distance between trees by two different methods.

Usage

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Rtreedist(trees, method=c("branch.score","symmetric"), path=NULL, ...)

Arguments

trees

an object of class "multiPhylo". (Or, under rare circumstances, an object of class "phylo". See below.)

method

method to compute the distance between trees. method="branch.score" is the branch score method of Kuhner & Felsenstein (1994). method="symmetric" is the symmetric distance or Robinson-Foulds distance (Bourque 1978; Robinson & Foulds 1981).

path

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

...

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

Details

Optional arguments include the following: quiet suppress some output to R console (defaults to quiet = FALSE); trees2 object of class "multiPhylo" or "phylo" - if two sets of trees are to be compared; rooted logical value indicating whether trees should be treated as rooted (defaults to rooted = FALSE); distances argument telling treedist which distances to compute - could be "all" (all pairwise in trees), "all.1to2" (all in trees by all in trees2), "adjacent" (adjacent species in trees only), and "corresponding" (all corresponding trees in trees and trees2); and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

More information about the treedist program in PHYLIP can be found here http://evolution.genetics.washington.edu/phylip/doc/treedist.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 a matrix of pairwise distances for distances = "all" and distances = "all.1to2", or a named vector for distances = "adjacent" and distances = "corresponding".

Author(s)

Liam J. Revell, Scott A. Chamberlain

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

References

Bourque, M. (1978) Arbres de Steiner et reseaux dont certains sommets sont a localisation variable. Ph.D. Dissertation, Universite de Montreal, Montreal, Quebec.

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.

Kuhner, M.K., Felsenstein, J. (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution, 11, 459-468.

Robinson, D.F., Foulds, L.R. (1981) Comparison of phylogenetic trees. Mathematical Biosciences, 53, 131-147.

Examples

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## Not run: 
trees<-rmtree(n=10,N=10)
D<-Rtreedist(trees,method="symmetric")

## End(Not run)

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