stairs1 {treebalance} | R Documentation |
Calculation of the stairs1 value for rooted binary trees
Description
This function calculates the stairs1 value for a given rooted
binary tree
. It is a modified version of the Rogers J index and is
defined as the fraction of inner vertices whose balance
value is unequal to zero, more precisely
in which denotes the set of all inner vertices
of
, and in which
and
denote the number of leaves in the two pending subtrees that are
rooted at the direct descendants of
. The stairs1 value is an imbalance index.
Special cases: For , the function returns
and a warning.
For details on the stairs1 value, see
also Chapter 23 in "Tree balance indices: a comprehensive survey" (https://doi.org/10.1007/978-3-031-39800-1_23).
Usage
stairs1(tree)
Arguments
tree |
A rooted binary tree in phylo format. |
Value
stairs1
returns the stairs1 value of the given tree.
Author(s)
Sophie Kersting
References
M. M. Norstrom, M. C. Prosperi, R. R. Gray, A. C. Karlsson, and M. Salemi. PhyloTempo: A Set of R Scripts for Assessing and Visualizing Temporal Clustering in Genealogies Inferred from Serially Sampled Viral Sequences. Evolutionary Bioinformatics, 8:EBO.S9738, 2012. ISSN 1176-9343, 1176-9343. doi:10.4137/EBO.S9738.
Examples
tree <- ape::read.tree(text="((((,),),(,)),(((,),),(,)));")
stairs1(tree)