Cluster analysis in R: determine the optimal number of clusters

Question

Being a newbie in R, I\'m not very sure how to choose the best number of clusters to do a k-means analysis. After plotting a subset of below data, how many clusters will be

Answer 1

It's hard to add something too such an elaborate answer. Though I feel we should mention identify here, particularly because @Ben shows a lot of dendrogram examples.

d_dist <- dist(as.matrix(d))   # find distance matrix 
plot(hclust(d_dist)) 
clusters <- identify(hclust(d_dist))

identify lets you interactively choose clusters from an dendrogram and stores your choices to a list. Hit Esc to leave interactive mode and return to R console. Note, that the list contains the indices, not the rownames (as opposed to cutree).