varLeafDepI {treebalance} | R Documentation |
Calculation of the variance of leaf depths index for rooted trees
Description
This function calculates the variance of leaf depths index
for a given rooted tree
. The tree must not necessarily be binary.
is defined as
in which denotes the number of leaves of
,
denotes the set of leaves of
,
denotes the depth of
the leaf
and
denotes the average leaf depth of
.
For the function returns
and a warning.
For details on the variance of leaf depths, see
also Chapter 7 in "Tree balance indices: a comprehensive survey" (https://doi.org/10.1007/978-3-031-39800-1_7).
Usage
varLeafDepI(tree)
Arguments
tree |
A rooted tree in phylo format. |
Value
varLeafDepI
returns the variance of leaf depths index of the given tree.
Author(s)
Sophie Kersting
References
T. M. Coronado, A. Mir, F. Rossello, and L. Rotger. On Sackin's original proposal: the variance of the leaves' depths as a phylogenetic balance index. BMC Bioinformatics, 21(1), 2020. doi: 10.1186/s12859-020-3405-1. URL https://doi.org/10.1186/s12859-020-3405-1.
M. J. Sackin. "Good" and "Bad" Phenograms. Systematic Biology, 21(2):225-226, 1972. doi: 10.1093/sysbio/21.2.225.
K.-T. Shao and R. R. Sokal. Tree Balance. Systematic Zoology, 39(3):266, 1990. doi: 10.2307/2992186.
Examples
tree <- ape::read.tree(text="((((,),),(,)),(((,),),(,)));")
varLeafDepI(tree)