mrp.supertree: Matrix representation parsimony supertree estimation

Description

This function estimates the MRP (matrix representation parsimony) supertree from a set of trees (Baum 1992; Ragan 1992).

Usage

mrp.supertree(trees, method=c("pratchet","optim.parsimony"), ...)
compute.mr(trees, type=c("phyDat","matrix"))

Arguments

trees

an object of class "multiPhylo" (i.e., a list of trees).

method

an argument specifying whether to optimize the tree using pratchet or optim.parsimony.

type

for compute.mr, the type of object to return.

...

optional arguments - mostly to be passed to pratchet or optim.parsimony.

Value

A "phylo" or "multiPhylo" object that is the MP or set of MP MRP trees. In the case of compute.mr, an object of class "phyDat" or a matrix.

Details

Function uses pratchet or optim.parsimony from the "phangorn" package (Schliep 2011) and prop.part from the "ape" package (Paradis et al. 2004). See pratchet or optim.parsimony for optional arguments, which vary slightly depending on the method. All optional arguments of these methods are available to the user with one exception. The argument tree in optim.parsimony is supplied instead as start. In addition to being an object of class "phylo", start can also be assigned the string values of "NJ" or "random", in which case either a neighbor-joining or random tree will be used as the starting tree for optimization. The function compute.mr computes the matrix-representation matrix of the input trees. It is used internally by mrp.supertree, but can also be used to export an object that can be written to file if desired.

References

Baum, B. R., (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon, 41, 3-10. Felsenstein, J. (2004) Inferring Phylogenies. Sinauer. Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290. Ragan, M. A. (1992) Phylogenetic inference based on matrix representation of trees. Molecular Phylogenetics and Evolution, 1, 53-58. Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223. Schliep, K. P. (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.