select_linkage function

Cluster algorithm selection and validation

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.

select_linkage(x)

Arguments

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

Returns

• 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.

Examples

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

References

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