select_linkage: Cluster algorithm selection and validation

In phyloregion: Biogeographic Regionalization and Macroecology

Cluster algorithm selection and validation

Description

This function contrasts different hierarchical clustering algorithms on the phylogenetic beta diversity matrix for degree of data distortion using Sokal & Rohlf’s (1962) cophenetic correlation coefficient.

Usage

select_linkage(x)

Arguments

x	a numeric matrix, data frame or "dist" object.

Value

• A numeric value corresponding to the good clustering algorithm for the distance matrix

• If plot = TRUE, a barplot of cophenetic correlation for all the clustering algorithms is drawn.

References

Sokal, R.R. & Rohlf, F.J. (1962) The comparison of dendrograms by objective methods. Taxon 11: 33–40.

Examples

data(africa)
tree <- africa$phylo
bc <- beta_diss(africa$comm)
y <- select_linkage(bc[[1]])
barplot(y, horiz = TRUE, las = 1)

phyloregion documentation built on Aug. 15, 2023, 9:07 a.m.