phyloTop: phyloTop: topological properties of phylogenies

In phyloTop: Calculating Topological Properties of Phylogenies

phyloTop: topological properties of phylogenies

Description

Calculate a range of topological properties for one or more phylogenetic trees.

Usage

phyloTop(treeList, funcs = "all", normalise = FALSE)

Arguments

treeList	a list or multiPhylo object, or a single tree of class phylo or phylo4. All trees should be binary and rooted; if not they will be coerced into binary rooted trees using multi2di, if possible.
funcs	a list of functions. The default is to apply all of the topological functions from the package, but a subset can be specified instead. The functions available are: avgLadder cherries colless.phylo ILnumber maxHeight pitchforks sackin.phylo stairs (note that this adds two columns to the output, "stairs1" and "stairs2")
normalise	option to normalise the results of functions where possible. Default is FALSE

Value

A matrix where rows correspond to trees and columns correspond to topological properties.

Author(s)

Michelle Kendall [e-mail]

See Also

avgLadder, cherries, colless.phylo, ILnumber, maxHeight, pitchforks, sackin.phylo, stairs

Examples

## Apply all of the functions to a list of 10 random trees, each with 50 tips:
phyloTop(rmtree(10,50))
## Normalising the results where possible:
phyloTop(rmtree(10,50), normalise=TRUE)

phyloTop documentation built on Feb. 16, 2023, 5:55 p.m.