similar to: doubts about 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

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),

I'm clustering rather large data sets and would like to cut the dendrograms to get a better view of specific components. I calculate the dissimilarity matrix using daisy() because I have a mixture of variable types: factors, ordered factors and numerical variables. If I want one dendrogram, I use agnes() for the agglomerative nesting and pltree() to draw the dendrogram. That way, I get the

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete")

Hi, this is rather a (presumed) bug report than a question because I can solve my personal statistical problem by working with hclust instead of agnes. I have done a complete linkage clustering on a dist object dm with 30 objects with agnes (R 1.8.0 on RedHat) and I want to obtain the partition that results from a cut at height=0.4. I run > cl1a <- agnes(dm, method="complete")

Hi: I have calculated the Silhouette score and Dunn score after hierarchical clustering for 3 clusters: #Distance measure d <- dist(USArrests, method = "euclidean") #Hierarchical clustering hc <- hclust(dist(USArrests), "ave") #calculating silhouette value for 3 clusters sil<- silhouette(cutree(hc, k=3), d) #calculating Dunn index for 3 clusters clus <- cutree(hc,

Hello, I had a question regarding clustering using the agnes() function from the 'cluster' package. I was wondering if anyone knew how I can identify cluster points after running the agnes function. For example, I created a dataset with points randomly scattered around (0,0), (0,1) and (1,0). After clustering, the dendrogram shows all the clustered points and I get the ordering and

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

Hi there, is there any R-function for k-nearest neighbour agglomerative hierarchical clustering? By this I mean standard agglomerative hierarchical clustering as in hclust or agnes, but with the k-nearest neighbour distance between clusters used on the higher levels where there are at least k>1 distances between two clusters (single linkage is 1-nearest neighbour clustering)? Best regards,

Dear all, I am no stat wiz and I am just trying to use the AGNES algorithm at my very modest level of statistical of understanding. I have difficulties understanding the ouput from AGNES. My question is: how to interpret the output, especially how do you I know which cluster solution is the best? In SPSS, an Agglomeration Schedule table is produced and I used to look at the biggest jump between

Hello, In the documentation for agnes in the package 'cluster', it says that NAs are allowed, and sure enough it works for a small example like : > m <- matrix(c( 1, 1, 1, 2, 1, NA, 1, 1, 1, 2, 2, 2), nrow = 3, byrow = TRUE) > agnes(m) Call: agnes(x = m) Agglomerative coefficient: 0.1614168 Order of objects: [1] 1 2 3 Height (summary): Min. 1st Qu. Median Mean 3rd

Dear R Users: I am new to R and I am trying to do a cluster analysis on a single continuous variable using the Agnes [Agglomerative Nesting (Hierarchical Clustering) ] in the Package ‘cluster’. I was able to apply this clustering method to my data: ward1 <- Agnes(balances, diss= FALSE, metric = "euclidean", stand = TRUE, method = "ward", keep.diss =TRUE, keep.data =

I think are looking for the function 'cutree' from package mva checkout its documentation: > require(mva) > ?cutree pleanty of examples to do what you want. ############################################################################# Hi R lovers! I am using the agnes function of the package cluster to compute a hierarchical clustering. I'd like to know if somebody has ever

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 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

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 List, I am trying to implement a hierarchical cluster using the hclust method agglomerative single linkage method with a small wrinkle. I would like to cluster a set of numbers on a number line only if they are within a distance of 500. I would then like to print out the members of this list. So far I can put a vector: > x<-c(2,10,200,300,600,700) into a distance matrix: >

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

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