similar to: silhoutte.default bugs

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

Hello, I was wondering whether a Poisson mixture modeler/cluster analysis package is available for R. I scanned CRAN packages and couldn't find anything but I thought I'd ask. If not could anyone recommend a non-R open source package. I have found 'snob' but this program seems a bit hard to use in an automated, non interactive fashion. regards, Murad -- Murad Nayal M.D. Ph.D.

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

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

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, I am using Silhouette to estimate the number of clusters in a microarray dataset. Initially, I used the iris data to test my piece of code as follows: library(cluster) data(iris) mydata<-iris[,1:4] maxk<-15 # at most 15 clusters myindex<-rep(0,maxk) # hold the si values for each k clusters mdist<-1-cor(t(mydata)) #dissimlarity

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)

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

Dear R users, Just wondering how to extract clustered data in a file. More precisely after running any clustering algorithms, you get information about the clusterd vectors. I want to save that data after clustering is done in the same order as the clusters are produced. How can I do that After runining algorithms you get information which vectors are clustered. for example, after running pam you

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, 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),

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

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

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,

hello, i'm pete ,how can i order rows of matrix by max to min value? I have a matrix of membership degrees, with 82 (i) rows and K coloumns, K are clusters. I need first and second largest elements of the i-th row. for example 1 0.66 0.04 0.01 0.30 2 0.02 0.89 0.09 0.00 3 0.06 0.92 0.01 0.01 4 0.07 0.71 0.21 0.01 5 0.10 0.85 0.04 0.01 6 0.91 0.04 0.02 0.02 7 0.00 0.01 0.98 0.00 8 0.02

Tried several ways to connect to Internet. Perhaps R help could point me in the right direction to make this connection work. setInternet2(use = TRUE) > download.file(" + http://image.shutterstock.com/display_pic_with_logo/322090/322090,1307359665,10/stock-photo-car-silhouette-for-race-sports-design-vector-version-also-available-in-gallery-78667174.jpg + ", +

Hello everyone. I just started learning R for clustering analysis in my research project. I tried k-means method and PAM method, both of which were properly processed with my data. I have some questions about PAM graphical output. Suppose to do the commands shown below; pm<-pam(D, 6) plot(pm) I got two charts after prompted. In the first chart, 6 oval clusters are drawn together

Hello all, since we're on the topic of R-editors. I am using emacs/ess on a unix workstation (to interact with R and have been having a little problem. I usually write the R commands I need to run in a separate buffer then copy and paste them into the *R* buffer for evaluation. The problem is, if any command is spread over multiple lines emacs/R hangs when I paste it in the R buffer for