Im trying different linkage methods for my hierarchical clustering problem. Now I would like to evaluate which one works better. Is this as easy as just just comparing the two Dunn's index values? Or should I take other factors into consideration?
Dunn's index is the ratio of minimum inter-cluster distance to maximum cluster diameter found. As such it is a good measure to compare the two methods. The one thing to look out for with Dunn's index is if one cluster is particularly large while all others are compact, then the metric will be misleadingly low.
Other metrics to consider could be:
within clusters sum of squares
between clusters sum of squares