nConfig: Configuration sizes in a tree

In phyloTop: Calculating Topological Properties of Phylogenies

Configuration sizes in a tree

Description

Finds the sizes of configurations in the tree.

Usage

nConfig(tree, maxClade = NULL)

Arguments

tree	a tree of class phylo or phylo4. The tree should be binary and rooted; if not it will be coerced into a binary rooted tree using multi2di, if possible.
maxClade	an integer between 1 and the number of tips (the default), specifying the maximum clade size of interest.

Value

A list with 2 entries:

• cladeSizes is a vector giving the size of the clade descending at each node:tips all have the value 1, internal nodes have their number of tip descendants.

• numClades is a vector where numClades[[i]] is the number of clades of size i in the tree. All clade sizes are calculated, but the output can be restricted using maxClade to just those of size up to 'maxClade'.

Author(s)

Michelle Kendall [e-mail]

Examples

## Configuration sizes on a random tree with 10 tips:
tree <- rtree(10)
plot(tree)
nodelabels()
nConfig(tree)

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