MultiTreeDistance: Multiple tree distances

In graemetlloyd/metatree: Generating Meta-Analytical Phylogenies

Description

Given a set of input trees, calculates all pairwise tree distances.

Usage

MultiTreeDistance(trees, distance = "contradiction", rescale = TRUE)

Arguments

trees	An object of class 'multi.phylo'.
distance	The type of disatnce to use, must be one of "RF" (RObinson-Foulds) or "contradiction" (tree contradiction).
rescale	Whether or not to rescale the distance (zero to one).

Details

This function is an incomplete attempt to generalise the MultiTreeContradiction function to incorporate not just contradiction differences (Bapst et al. 2018), but also the Robinson-Foulds distance metric (Robinson and Foulds 1981).

It is not yet ready for general use.

Value

A symmetric matrix of pairwise tree distances.

Author(s)

Graeme T. Lloyd [e-mail]

References

Bapst, D. W., H. A. Schreiber, and S. J. Carlson. 2018. Combined analysis of extant Rhynchonellida (Brachiopoda) using morphological and molecular data. Systematic Biology, 67, 32-48.

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

See Also

paleotree::treeContradiction and phytools::multiRF.

Examples

# Generate three example trees (with tips labelled A-D):
ExampleTrees <- read.tree(text = c("(A,B,C,D);", "(A,(B,(C,D)));",
  "((A,B),C,D);"))

# Calculate rescaled RF distances matrix:
MultiTreeDistance(ExampleTrees, distance = "RF")

graemetlloyd/metatree documentation built on April 29, 2021, 2:32 a.m.