I have questions regarding the dendrogram and the cut-off related to hybrid hierarchical clustering performed on data, as depicted below and taken from this paper
Questions regarding Panel A (dendrogram)
The clustering itself is done using the Euclidean Distance - however the dendrogram is depicted using the squared Euclidean Distance. They don't explain why that is in the paper - is there a common reason for doing so?
In the corresponding paper, it is mentioned that the similarity and dissimilarity are calculated by comparisons on a subject-to-subject basis. Now regarding the dendrogram, I understand that I can read the y-axis as follows: For instance C1a and C1b are around 700 units apart from each other, whereas C1 and C2 are over 2000 units apart (and hence more distinct). My question however: The vertical line corresponding to C1b is longer than the vertical line corresponding to C1a. Does that mean that the subjects in C1b have a different range (bigger) of distances between each other than those in C1a? Does the distance between C1a and C1b correspond to the maximal distance found between subjects within each of the clusters?
Questions regarding Panel B (CHC criterium)
The paper states the following: "Panel (B) shows the Calinski-Harabasz criterion (..) Because the CHC did not exhibit a typical pattern (i.e. elevation at some cluster level), we defined stability (i.e. minimal change from one cluster number to the next) as our goal in deciding where to cut the dendrogram."
- I am not sure if I understand this - would you not want to chose the number of clusters which is in terms of CHC most distinct from another choice of numbers? And, maybe more importantly: Since the CHC is more and more decreasing here, does it make any sense to chose more than 2 clusters?
Many thanks - any help is greatly appreciated,