Each observation is assigned to the closest medoid, a single observation. An observation that is between two medoids will be assigned to the closer one even if its distances to members of the other cluster are closer on average (but the medoid of that cluster is slightly farther away). If the clusters are not well separated, this can happen easily.
You could always change the cluster assignment vector to see what happens to the silhouette plot. That will affect more than just the single observation since silhouette values of all of the points in those two clusters will change slightly (very slightly if there are lots of observations in those two clusters). ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of ABABAEI, Behnam Sent: Friday, February 19, 2016 1:55 PM To: sarah.gos...@gmail.com Cc: r-help@r-project.org Subject: Re: [R] How a clustering algorithm in R can end up with negative silhouette values? Hi Sarah, Thank you for the response. But it is said in its description that after each run (sample), each observation in the whole dataset is assigned to the closest cluster. So how is it possible for one observation to be wrongly allocated, even with clara? Behnam Behnam On Fri, Feb 19, 2016 at 11:48 AM -0800, "Sarah Goslee" <sarah.gos...@gmail.com<mailto:sarah.gos...@gmail.com>> wrote: That means that points have been assigned to the wrong groups. This may readily happen with a clustering method like cluster::clara() that uses a subset of the data to cluster a dataset too large to analyze as a unit. Negative silhouette numbers strongly suggest that your clustering parameters should be changed. Sarah On Fri, Feb 19, 2016 at 6:33 AM, ABABAEI, Behnam <behnam.abab...@limagrain.com> wrote: > Hi, > > > We know that clustering methods in R assign observations to the closest > medoids. Hence, it is supposed to be the closest cluster each observation can > have. So, I wonder how it is possible to have negative values of silhouette , > while we are supposedly assign each observation to the closest cluster and > the formula in silhouette method cannot get negative? > > > Behnam. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
