mrp.supertree: Matrix representation parsimony supertree estimation

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Matrix representation parsimony supertree estimation

Description

This function estimates the MRP (matrix representation parsimony) supertree from a set of input 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" that consists of a list of phylogenetic trees.
method	an argument specifying whether to optimize the tree using the phangorn parsimony optimizer pratchet or optim.parsimony.
type	for compute.mr, the type of object to return (e.g., "phyDat" or "matrix").
...	optional arguments - mostly to be passed to pratchet or optim.parsimony.

Details

mrp.supertree uses pratchet or optim.parsimony from the phangorn package (Schliep, 2011) for optimization, and prop.part from 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.

Value

An object of class "phylo" or "multiPhylo" that is the MP or set of MP MRP trees.

In the case of compute.mr, an object of class "phyDat" or a matrix.

Author(s)

Liam Revell [e-mail]

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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

Schliep, K. P. (2011) phangorn: phylogenetic analysis in R. Bioinformatics, 27, 592-593.

See Also

exhaustiveMP, optim.parsimony, pratchet

phytools documentation built on June 22, 2024, 10:39 a.m.