[Rd] kmeans

From: Gabor Grothendieck <ggrothendieck_at_gmail.com>
Date: Fri, 02 Jul 2010 18:50:28 -0400


In kmeans() in stats one gets an error message with the default clustering algorithm if centers = 1. Its often useful to calculate the sum of squares for 1 cluster, 2 clusters, etc. and this error complicates things since one has to treat 1 cluster as a special case.  A second reason is that easily getting the 1 cluster sum of squares makes it easy to calculate the between cluster sum of squares when there is more than 1 cluster.

I suggest adding the line marked ### to the source code of kmeans (the other lines shown are just ther to illustrate context). Adding this line forces kmeans to use the code for algorithm 3 if centers is 1. This is useful since unlike the code for the default algorithm, the code for algorithm 3 succeeds for centers = 1.

    if(length(centers) == 1) {

	if (centers == 1) nmeth <- 3 ###
	k <- centers

Also note that KMeans in Rcmdr produces a betweenss and a tot.withinss and it would be nice if kmeans in stats did that too:

> library(Rcmdr)
> str(KMeans(USArrests, 3))

List of 6
 $ cluster : Named int [1:50] 1 1 1 2 1 2 3 1 1 2 ...   ..- attr(*, "names")= chr [1:50] "Alabama" "Alaska" "Arizona" "Arkansas" ...  $ centers : num [1:3, 1:4] 11.81 8.21 4.27 272.56 173.29 ...

  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:3] "1" "2" "3"
  .. ..$ : chr [1:4] "Murder" "Assault" "UrbanPop" "Rape"
 $ withinss    : num [1:3] 19564 9137 19264
 $ size        : int [1:3] 16 14 20
 $ tot.withinss: num 47964  <=================
 $ betweenss   : num 307844 <=================

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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Fri 02 Jul 2010 - 22:53:09 GMT

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