meanIprime: meanIprime

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

Description

This calculates the mean of I' (Purvis and Agapow, 2012) for a phylogenetic tree. This asymmetry metric uses a weighted average of the balance of internal nodes:

mean.Iprime = \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},

where w_j = \frac{r_j+l_j-1}{r_j+l_j} if n is even and w_j = 1 if n is odd.

Usage

meanIprime(tree)

Arguments

tree	A tree of class phylo or treeshape.

Value

An object of class numeric.

References

• Purvis A, Katzourakis A, Agapow PM (2002) Evaluating phylogenetic tree shape: Two modifications to Fusco and Cronk's method. Journal of Theoretical Biology 214:99-103.

• 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]]
meanIprime(tree)

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