UPGMA, WPGMA and sUPGMA

UPGMA and WPGMA clustering. UPGMA and WPGMA are a wrapper function around hclust returning a phylo object. supgma perform serial sampled UPGMA similar to Drummond and Rodrigo (2000).

Usage

upgma(D, method = "average", ...)

wpgma(D, method = "mcquitty", ...)

supgma(D, tip.dates, trace = 0)

Arguments

D: A distance matrix.
method: The agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward", "single", "complete", "average", "mcquitty", "median" or "centroid". The default is "average".
...: Further arguments passed to or from other methods.
tip.dates: A named vector of sampling times associated to the tips.
trace: Show output during optimization (see details).

Value

A phylogenetic tree of class phylo.

References

Sneath, P. H., & Sokal, R. R. (1973). Numerical taxonomy. The principles and practice of numerical classification.

Sokal, R. R., & Michener, C. D. (1958). A statistical method for evaluating systematic relationships. University of Kansas Scientific Bulletin, v. 38.

Drummond, A., & Rodrigo, A. G. (2000). Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. Molecular Biology and Evolution, 17(12), 1807-1815.

Author

Klaus Schliep klaus.schliep@gmail.com

Examples


data(Laurasiatherian)
dm <- dist.ml(Laurasiatherian)
tree <- upgma(dm)
plot(tree)