similar to: question on silhouette colours

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 that group 1 is composed by

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

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

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 not solve the problem. If anyone has a suggestion,

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 multiple of replacement

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 way so when I have clustering labels, "2" and

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

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),

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 @

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

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 <- length(col)) > 1) { if (lc == k) col <-

Sorry for the long message. I'm doing my best to try to explain myself. I have fitted a spline to my data, I have fitted a spline, filled in the missing data by replicating the spline coefficients 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

I have apparently found an error in the "pam" function of the "cluster" library package. Please pardon me if this error has been pointed out or if this e-mail should be directed to someone else. The problem only started occurring with R version 1.5.0, which I started using about a week ago. The problem occurs when you try to use "pam" with the input being a

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

Hello everybody: I have just started using R, specifically the clustering packages. Despite the vastness of the functionality of the system, I have found it very flexible and intuitive. It has been great fun to experiment 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

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

Hello, here is a working reproducible example which crashes R using kmeans or gives empty clusters using the nstart option with R 15.2. library(cluster) kmeans(ruspini,4) kmeans(ruspini,4,nstart=2) kmeans(ruspini,4,nstart=4) kmeans(ruspini,4,nstart=10) ?kmeans either we got empty always clusters and or, after some further commands an segfault. regards, Detlef Groth ------------ [R] Empty

I'm trying to make a R package for a work in university. It´s my first time and i made some modifications on Pam algorithm that is included on cluster package. So before run Rcmd build command i made the next things: 1- I modified pam.c and cluster.h code. I added two new arguments on pam. 2- I modified pam.q, i added there my two new arguments. 4- I create all the necessary subdirectories

Hi, I am using fanny and I have estrange results. I am wondering if someone out there can help me understand why this happens. First of all in most of my tries, it gives me a result in which each object has equal membership in all clusters. I have read that that means "the clustering is entirely fuzzy". Looking at the graphics it is really difficult to understand how objects with so

Hi dear all It's the first time for me to install a developmental version of R, I came across following errors, my system is DISTRIB_ID=Ubuntu DISTRIB_RELEASE=10.04 DISTRIB_CODENAME=lucid DISTRIB_DESCRIPTION="Ubuntu 10.04.1 LTS" I downloaded the dev version of R in cran R source, and downloaded the recommended packages by using wget as described in R manual, and run