kmeans: Quick-TRANSfer stage steps exceeded maximum
I am running k-means clustering in R on a dataset with 636,688 rows and 7 columns using the standard stats package: kmeans(dataset, centers = 100, nstart = 25, iter.max = 20).
I get the following error: Quick-TRANSfer stage steps exceeded maximum (= 31834400), and although one can view the code at http://svn.r-project.org/R/trunk/src/library/stats/R/kmeans.R - I am unsure as to what is going wrong. I assume my problem has to do with the size of my dataset, but I would be grateful if someone could clarify once and for all what I can do to mitigate the issue.
Answer
I just had the same issue.
See the documentation of kmeans in R via ?kmeans:
The Hartigan-Wong algorithm generally does a better job than either of those, but trying several random starts (‘nstart’> 1) is often recommended. In rare cases, when some of the points (rows of ‘x’) are extremely close, the algorithm may not converge in the “Quick-Transfer” stage, signalling a warning (and returning ‘ifault = 4’). Slight rounding of the data may be advisable in that case.
In these cases, you may need to switch to the Lloyd or MacQueen algorithms.
The nasty thing about R here is that it continues with a warning that may go unnoticed. For my benchmark purposes, I consider this to be a failed run, and thus I use:
if (kms$ifault==4) { stop("Failed in Quick-Transfer"); }
Depending on your use case, you may want to do something like
if (kms$ifault==4) { kms = kmeans(X, kms$centers, algorithm="MacQueen"); }
instead, to continue with a different algorithm.
If you are benchmarking K-means, note that R uses iter.max=10 per default. It may take much more than 10 iterations to converge.