Rphylip (version 0.1-23)

Rdollop: R interface for dollop

Description

This function is an R interface for dollop in the PHYLIP package (Felsenstein 2013). dollop can be used for Dollo (Le Quesne 1974; Farris 1977) and polymorphism (Inger 1967; Farris 1978; Felsenstein 1979) parsimony tree inference.

Usage

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

Arguments

X

an object of class "phylip.data" with a set of binary characters; or a matrix. Data should be "0" and "1". The states "P" (or "B"), for polymorphism, and "?" are also permitted.

path

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

...

optional arguments to be passed to dollop. 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); tree object of class "phylo" - if supplied, then the Dollo or polymorphism parsimony score will be computed on a fixed input topology; method indicating whether Dollo (method="dollo", the default) or polymorphism (method="polymorphism") should be used; random.order add taxa to tree in random order (defaults to random.order = TRUE); random.addition number of random addition replicates for random.order = TRUE (defaults to random.addition = 10); threshold threshold value for threshold parsimony (defaults to ordinary parsimony); ancestral vector of ancestral states, which allows for the unordered Dollo parsimony method of Felsenstein (1984); weights vector of weights of length equal to the number of columns in X (defaults to unweighted); and cleanup remove PHYLIP input & output files after the analysis is completed (defaults to cleanup = TRUE).

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

Farris, J.S. (1977) Phylogenetic analysis under Dollo's Law. Systematic Zoology, 26, 77-88.

Farris, J.S. (1978) Inferring phylogenetic trees from chromosome inversion data. Systematic Zoology, 27, 275-284.

Felsenstein, J. (1979) Alternative methods of phylogenetic inference and their interrelationship. Systematic Zoology, 28, 49-62.

Felsenstein, J. (1984) The statistical approach to inferring evolutionary trees and what it tells us about parsimony and compatibility. pp. 169-191 in: Cladistics: Perspectives in the Reconstruction of Evolutionary History, edited by T. Duncan and T. F. Stuessy. Columbia University Press, New York.

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.

Inger, R.F. (1967) The development of a phylogeny of frogs. Evolution, 21, 369-384.

Le Quesne, W.J. (1974) The uniquely evolved character concept and its cladistic application. Systematic Zoology, 23, 513-517.

See Also

Rpars, Rdnapars

Examples

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