search for: silhouette

Hello, In cluster analysis with cluster, how does one colour the silhouette plots ? For example in using pam. There seems to be some problem there. Everything else can be coloured. Thanks, A. Mani Member, Cal. Math. Soc

Hi list, When I was using 'silhouette' from the 'cluster' package to calculate clustering performances, R crashed. I traced the problem to the fact that my clustering labels only have 2's and 3's. when I replaced them with 1's and 2's, the problem was solved. Is the function purposely written in this...

Hi! >library(cluster) In this lib a function called silhoutte.default is defined than on the R prompt it type >silhouette.default Error: Object "silhouette.default" not found R1.9.0 The same error are at R1.8.1 And I knew that a function silhoutte.default are present. But the same piece of code works in R1.6.2 ??? Eryk Dipl. bio-chem. Eryk Witold Wolski @ MPI-Moleculare Genetic Ihnestrasse 63-7...

Dear R users, I am mailing you about the graphical output of silhouette (cluster package) From the example of silhouette in help(silhouette): > ar <- agnes(ruspini) > si3 <- silhouette(cutree(ar, k = 5), # k = 4 gave the same as pam() above + daisy(ruspini)) > plot(si3, nmax = 80, cex.names = 0.5) from which one may conclude...

Dear all, I am trying (without much success) to use the fuction 'silhouette'. Would anyone encountered that before (or would know where I am wrong ?) Please find below the R ouput. Thanks in advance, L. > s <- silhouette(ct, as.dist(metric)) Error in "[<-"(*tmp*, iC, "sil_width", value = s.i) : number of items to replace is not a mul...

I'm fairly new to the silhouette functionality in the cluster package, so apologize if I'm asking something naive. If I run the 'agnes(ruspini)' example from the silhouette section of the cluster package vignette, and assign colours to clusters, two clusters have what appear to be incorrect colours in the silhouette...

Hi, I am using code below to get a plot that will show me on the X axis the number of clusters and on the Y axis the cluster average widths. However I am getting this error: Error in summary(silhouette(cutree(d, x), dist(iris[, -5])))$si.summary : $ operator is invalid for atomic vectors the code I am using is: avgs<-sapply(1:20,function(x) summary(silhouette(cutree(d,x), dist(iris[,-5])))$si.summary[4]) I think the problem is on the si.summary. What can I do to solve this problem? th...

On Tuesday 28 June 2005 15:30, r-help-request at stat.math.ethz.ch wrote: Re : 37. Re: A. Mani : colours in Silhouette (Mulholland, Tom) > > Message: 37 > Date: Tue, 28 Jun 2005 09:08:24 +0800 > From: "Mulholland, Tom" <Tom.Mulholland at dpi.wa.gov.au> > Subject: Re: [R] A. Mani : colours in Silhouette > To: <a_mani_sc_gs at vsnl.net>, <r-help at stat.math.ethz.ch> &...

Dear All, Is there any existing code for plotting silhouette for kmeans clustering results? Many thanks! Linda [[alternative HTML version deleted]]

Hallo Sebastian, >>>>> "SP" == Sebastian P?lsterl <sebp at k-d-w.org> >>>>> on Sun, 14 Jun 2009 14:04:52 +0200 writes: SP> Hello Martin, SP> I plotting the silhouette of a clustering and storing it as png. When I SP> try to store the image as png the bars are missing. The bars are plotted SP> when I use x11 or postscript as device. In addition, it seems to work SP> when I use a smaller matrix (e.g. ruspini). SP> Would be great if...

...I also find estrange the fact that if I set K=3 (three clusters), it gives membership for all three clusters (0.333 for all of them) and then when it gives the closest hard clustering they only belong to cluster 1 or 2, but none of them to cluster three. The plot shows only two clusters (also the silhouette plot, even if it gives in the "silhouette plot information" the silhouette width for the three clusters????????. Then, for the same data I set k=4 and surprisingly, it gives membership for the four of them (this time they are not all the same) and when it gives the closest hard clusterin...

I was trying to create a multi-color silhouette plot (each cluster a different color) from clusters created by trimkmeans. This works straighforwardly on an object created from pam however my colors are interwoven when I try the same approach on clusters from trimkmeans. I also tried sorting the silhouette object using sortSilhouette which did n...

...associated to the last node. I obtained a number of dendograms by different combination of distance and link-method by calling DIST and AGNES. The agglomerative coefficient is very high (~ 0.99) for some combinations, and is generally around 0.5 for the remaining cases. As recommended, I ran the SILHOUETTE at different cuts (CUTREE) for some of the cases. Irregardless of the AC value the highest silhouette width I get is ~ 0.4 or lower, which is too low a level of confidence for accepting any clustering structure, from what I have recently read. My first question is about the use of CUTREE and SILH...

I tried using colours in silhouette plots by specifying a vector of colours instead of the default "gray" for the col parameter. No bars are drawn, though the rest of the plot works as it did with the grey bars. On investigating cluster:::plot.silhouette, I came across this part: if (do.col.sort && (lc <- le...

Hello all, This might have been fixed in later versions (I am using R1.7.0), r-help archive contains messages reporting similar problems but no reports of codes fixes. I have encountered a couple of problems using the silhouette function. one occurs when the clustering contains clusters composed of 1 element (Martin Maechler posted code few months ago that fixes a similar problem that occurs when clusters have only 2 elements but not the case with 1 element). the other problem is due to silhouette's assumption that the...

...periment with it. Nevertheless, I am under tight time constraints to complete a cluster analysis of some data and need to come up with a "quick" solution for the following problem: When I call the plot() function with a pam.object and try to write labels for the individual objects in the silhouette plots, rather than the object number, it appears that the length of the strings allowed for the labels is limited to 5 characters. Is this an intrinsic limitation? Is there a way to work around this limitation? Thank you very much for your help and thanks for a great piece of software! Massimo Sa...

After ordering the table of membership degrees , i must get the difference between the first and second coloumns , between the first and second largest membership degree of object i. This for K=2,K=3,....to K.max=6. This difference is multiplyed by the Crisp silhouette index vector (si). Too it dependending on K=2,...,K.max=6; the result divided by the sum of these differences I need a final vector composed of the indexes for each clustering (K=2,...,K.max=6). There is a method, i think that is classe.memb, but i can't to solve problem because trasformation...

Dear List How do you change the colour settings for the banner/silhouette plot? I am trying to produce a black and white plot of publication quality. Is there a way to set black and white plots as the default for R graphics? Any help greatly appreciated. Graham Leask Economics & Strategy Group Aston University [[alternative HTML version delete...

Dear R-list members, I am using the cluster package and by the generation of plot.partition I ran into the problem that an alternative title overlaps the default title. > plot.partition(clara.14,which.plot=2,stand=TRUE, main="Silhouette plot of 14 clusters") The manual states that all optional arguments for clusplot.default may also be supplied to plot.partition(). Altering the title in clusplot() works. Question: What am I doing wrong and what would be the correct way to insert the graphic title "Silhouette plot of 14...

....INSTALL33128ce7/cluster/man/plantTraits.Rd:69: unexpected END_OF_INPUT 'Structuration de communaut ' *** installing help indices ** building package indices ... ** testing if installed package can be loaded Warning: S3 methods ‘clusplot.default’, ‘clusplot.partition’, ‘pltree.twins’, ‘silhouette.default’, ‘silhouette.clara’, ‘silhouette.partition’, ‘plot.agnes’, ‘plot.diana’, ‘plot.mona’, ‘plot.partition’, ‘plot.silhouette’, ‘print.mona’, ‘print.pam’, ‘print.summary.mona’, ‘print.summary.pam’, ‘print.summary.silhouette’, ‘summary.mona’, ‘summary.pam’, ‘summary.silhouette’ were declared in...