I1: I1

In bdearlove/treeImbalance: Imbalance metrics for time-sampled phylogenetic trees.

Description

This calculates I1, a weighted average of the balance of internal nodes, where N is the number of tips, j is the number of nodes, and r_j and l_j represent the number of tips in the left and right subtrees respectively. Then,

I_1 = \frac{2}{(N-1)(N-2)} ∑_{j \in \mathcal{I} } {|r_j-l_j|}.

I1 is closely related to the Colless index, which can be found using colless, or by multiplying I1 by

\frac{(N-1)(N-2)}{2}.

Usage

I1(tree)

Arguments

tree	A tree of class phylo or treeshape.

Value

An object of class numeric.

References

• Pompei S, Loreto V, Tria F (2012) Phylogenetic Properties of RNA Viruses. PLoS ONE 7(9): e44849. doi:10.1371/journal.pone.0044849

• Purvis A, Agapow PM (2002) Phylogeny imbalance: Taxonomic level matters. Systematic Biology 51: 844-854.

• Fusco G, Cronk Q (1995) A new method for evaluating the shape of large phylogenies. Journal of Theoretical Biology 175: 235-243. doi: 10.1006/jtbi.1995.0136

Examples

N=30
tree<-rtreeshape(1,tip.number=N,model="pda")[[1]]
I1(tree)

bdearlove/treeImbalance documentation built on May 12, 2019, 3:39 a.m.