stairs2 {treebalance} | R Documentation |
Calculation of the stairs2 value for rooted binary trees
Description
This function calculates the stairs2 value st2(T)
for a given rooted
binary tree T
. It is defined as the mean ratio between the leaf
numbers of the smaller and larger pending subtree over all inner vertices, more precisely
st2(T)=\frac{1}{n-1}\cdot\sum_{u \in V_{in}(T)} \frac{n_{u_a}}{n_{u_b}}
in which V_{in}(T)
denotes the set of all inner vertices
of T
, and in which n_{u_a}\geq n_{u_b}
denote the number of leaves
in the two pending subtrees that are
rooted at the direct descendants of u
. The stairs2 value is an imbalance index.
Special cases: For n=1
, the function returns st2(T)=0
and a warning.
For details on the stairs2 value, see
also Chapter 23 in "Tree balance indices: a comprehensive survey" (https://doi.org/10.1007/978-3-031-39800-1_23).
Usage
stairs2(tree)
Arguments
tree |
A rooted binary tree in phylo format. |
Value
stairs2
returns the stairs2 value of the given tree.
Author(s)
Sophie Kersting
References
C. Colijn, J. Gardy. Phylogenetic tree shapes resolve disease transmission patterns. Evolution, Medicine, and Public Health, 2014(1):96-108, 2014. ISSN 2050-6201. doi: 10.1093/emph/eou018.
Examples
tree <- ape::read.tree(text="((((,),),(,)),(((,),),(,)));")
stairs2(tree)