I have two dendrograms which I wish to compare to each other in order to find out how “similar” they are. But I don’t know of any method to do so (let alone a code to implement it, say, in R).
Any leads ?
UPDATE (2014-09-13):
Since asking this question, I have written an R package called dendextend, for the visualization, manipulation and comparison of dendrogram. This package is on CRAN and comes with a detailed vignette. It includes functions such as cor_cophenetic, cor_bakers_gamma and Bk / Bk_plot. As well as a tanglegram function for visually comparing two trees.
Comparing dendrograms is not quite the same as comparing hierarchical clusterings, because the former includes the lengths of branches as well as the splits, but I also think that’s a good start. I would suggest you read E. B. Fowlkes & C. L. Mallows (1983). “A Method for Comparing Two Hierarchical Clusterings”. Journal of the American Statistical Association 78 (383): 553–584 (link).
Their approach is based on cutting the trees at each level k, getting a measure Bk that compares the groupings into k clusters, and then examining the Bk vs k plots. The measure Bk is based upon looking at pairs of objects and seeing whether they fall into the same cluster or not.
I am sure that one can write code based on this method, but first we would need to know how the dendrograms are represented in R.