Description Usage Arguments Value Author(s) References Examples
This function calculates the variance of leaf depths index VLD(T) for a given rooted tree T. The tree must not necessarily be binary. VLD(T) is defined as
VLD(T)=1/n * ∑_{x in V_L(T)} (δ(x)-N(T))^2
in which n denotes the number of leaves of T, V_L(T)
denotes the set of leaves of T, δ(x) denotes the depth of
the leaf x and N(T) denotes the average leaf depth of T.
For n=1 the function returns VLD(T)=0 and a warning.
1 | varLeafDepI(tree)
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tree |
A rooted tree in phylo format. |
varLeafDepI
returns the variance of leaf depths index of the given tree.
Sophie Kersting
T. M. Coronado, A. Mir, F. Rosselló, 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.
1 2 | tree <- ape::read.tree(text="((((,),),(,)),(((,),),(,)));")
varLeafDepI(tree)
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