varM: varM

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

Description

This calculates σ^2_M, a measure of asymmetry based on the topological distance, $M_i$, between tip $i$ and the root:

σ^2_M = \frac{1}{N} ∑_{i \in \mathcal{L}} {(M_i-M)^2} .

Usage

varM(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

• Sackin MJ (1972) Good and bad phenograms. Systematic Biology 21: 225-226.

Examples

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

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