similar to: png() resolution problem {was "Silhouette ..."}

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 plot. library(cluster) data(ruspini) ar<- agnes(ruspini)

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

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

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 @

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

In a package I've been developing for manipulating genetic data I discovered a problem when indexing into character arrays using NA's: Create a character matrix and a numeric matrix > cmat <- matrix( letters[1:4], ncol=2, nrow=2) > nmat <- matrix( 1:4, ncol=2, nrow=2) Create an index vector containing an NA value > indvec <- c(1,2,NA) Indexing works fine for both

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 R-listers, I'm having trouble accessing "sub" objects ("attributes"?), e.g., "x$silinfo$avg.width" using the /get() /command; I'm using/ get()/ in a loop as illustrated in the following code: #FIRST MAKE CLUSTERS of VARYING k /for (i in 1:300){ assign(paste("x.",i,sep=""),pam(x,i)) #WORKS FINE }/ #NEXT, TAKE LOOK AT AVE.

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

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

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 <-

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

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 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

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

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 deleted]]