similar to: R-help Digest, Vol 28, Issue 28

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

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 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,

Re: A. Mani : Avoiding loops (Petr Pikal) > Message: 9 > Date: Mon, 22 Aug 2005 06:40:45 +0200 > From: "Petr Pikal" <petr.pikal at precheza.cz> > Subject: Re: [R] A. Mani : Avoiding loops > To: "A. Mani" <a_mani_sc_gs at vsnl.net>, r-help > <r-help at stat.math.ethz.ch> > > On 20 Aug 2005 at 3:26, A. Mani wrote: > > > On

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

On Friday 19 August 2005 11:54, Sean O'Riordain wrote: > Hi, > I'm not sure what you actually want from your email (following the > posting guide is a good way of helping you explain things to the rest > of us in a way we understand - it might even answer your question! > > I'm only a beginner at R so no doubt one of our expert colleagues will > help me... >

Doing the normal build process [1] for a first time with a R 2.0.0 snapshot -- the Sep 21 version I uploaded to Debian's 'experimental' section two days ago, ended in failure. The package in question is cluster 1.9.6 which should be 2.0.0-ready. The (partial) log follows: ----------------------------------------------------------------------------- [...] g77 -mieee-fp -fPIC -g -O2

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

I need help on calling the svydesign function in the survey package (although this error appears not to be specific to svydesign). I am passing parameters incorrectly but am not sure how to correct the problem. ## Call the main function PS.sim (one of mine). The dots are parameters I omitted to simplify the question. ## y.col, str.col, clus.id, and PS.col are names of columns in the object pop.

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

> DATA [,1] [1,] -2.0314185 [2,] -0.3594015 [3,] -1.3225832 [4,] 1.5050892 [5,] -0.4535558 [6,] 3.6335036 [7,] 5.1965750 [8,] 4.2923129 [9,] 6.0913187 [10,] 4.9131070 > RESA [,1] [,2] [,3] [,4] [,5] [1,] -2.0314185 1.5050892 -1.3225832 -1.3225832 -2.0314185 [2,] -0.3594015 -0.3594015 4.2923129 -0.3594015

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

Yes and no. Given your response it appears that "Proper Case" is not a term that everyone uses. In Excel there is a function "Proper" which in essence changes "this line into something like this" into "This Line Into Something Like This." My look at casefold seesm to be that is is a wrapper of two functions to change text into either Lower or Upper case.So

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 Rhelpers I have the problem with initial values, could you please tell me how to solve it? Thank you June > p = summary(maxLik(fr,start=c(0,0,0,1,0,-25,-0.2))) Error in maxRoutine(fn = logLik, grad = grad, hess = hess, start = start, : NA in the initial gradient > p = summary(maxLik(fr,start=c(0,0,0,1,0,-25,-0.2),method="BFGS")) Error in optim(start, func, gr =

Dear WizaRds, I am trying to compute the (adjusted) Rand Index in order to comprehend the variable selection heuristic (VS-KM) according to Brusco/ Cradit 2001 (Psychometrika 66 No.2 p.249-270, 2001). Unfortunately, I am unable to correctly use cl_ensemble and cl_agreement (package: clue). Here is what I am trying to do: library(clue) ## Let p1..p4 be four partitions of the kind

Dear people, A somewhat clueless question follows: I just discovered that the lme function in contrib package nlme for R, while similar to the lme function in Splus, does not use the cluster function option. This difference does not appear to be documented in the V&R `R Complements' file. I have data which is divided into 6 groups The lme model is of the form (simplified from the actual

I am probably just looking in the wrong place. I am sure there are a number of ways to do this. If anyone could point me in the right direction it would be very much appreciated. Thanks _________________________________________________ Tom Mulholland Senior Policy Officer WA Country Health Service 189 Royal St, East Perth, WA, 6004 Tel: (08) 9222 4062 e-mail:

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