Ic: Ic

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

Description

This calculates Ic (as defined in Pompei et al., 2012) for a phylogenetic tree. This asymmetry metric uses a weighted average of the balance of internal nodes:

I_c = \frac{1}{(N-1)} ∑_{j \in \mathcal{I}} w_j \frac{\max(r_j,l_j)-m_j}{r_j+l_j-m_j-1}.

Usage

Ic(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]]
Ic(tree)

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