Mean Pairwise distance

Fast function using C++ to calculate the mean pairwise distance, using the fast algorithm by Constantinos, Sandel & Cheliotis (2012).

Usage

mean_pair_dist(phy, normalization = "none")

Arguments

phy

phylo object or ltable

normalization

"none" or "tips", in which case the obtained mean pairwise distance is normalized by the factor 2log(n), where n is the number of tips.

Value

Mean pairwise distance

References

Webb, C., D. Ackerly, M. McPeek, and M. Donoghue. 2002. Phylogenies and community ecology. Annual Review of Ecology and Systematics 33:475-505.

Tsirogiannis, Constantinos, Brody Sandel, and Dimitris Cheliotis. "Efficient computation of popular phylogenetic tree measures." Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings 12. Springer Berlin Heidelberg, 2012.