stairs: Stairs

In phyloTop: Calculating Topological Properties of Phylogenies

Stairs

Description

Calculates the staircase-ness measure defined in Norstrom et al., Evolutionary Bioinformatics online, 8:261 (2012) doi: 10.4137/EBO.S9738.

Usage

stairs(tree)

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.

Value

Two numbers corresponding to the two staircase-ness measures for a tree. These are two related measures:

• 1: the proportion of subtrees that are imbalanced (i.e. subtrees where the left child has more tip descendants than the right child, or vice versa)

• 2: the average of all the min(l,r)/max(l,r) values of each subtree, where l and r are the number of tips in the left and right children of a subtree.

Author(s)

Michelle Kendall [e-mail]

Examples

## Find the staircase-ness measures in a random tree with 20 tips:
stairs(rtree(20))
 

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