Displaying 20 results from an estimated 1200 matches similar to: "Cluster package broken in 1.4.0?"
2004 Jun 29
1
PAM clustering: using my own dissimilarity matrix
Hello,
I would like to use my own dissimilarity matrix in a PAM clustering with
method "pam" (cluster package) instead of a dissimilarity matrix created
by daisy.
I read data from a file containing the dissimilarity values using
"read.csv". This creates a matrix (alternatively: an array or vector)
which is not accepted by "pam": A call
2017 Aug 17
2
PAM Clustering
Dear Germano,
Thank you for your fast reply,
In the above code, *MYData *is the actual data set.
Do not we need to convert *MYData to *the dissimilarity matrix using
*pam(as.dist(**MYData**), k = 10, diss = TRUE*)* code line?*
*Regards.*
On Thu, Aug 17, 2017 at 2:58 PM, Germano Rossi <germano.rossi at gmail.com>
wrote:
> try this
>
> MYdata <-
2007 Nov 28
2
Clustering
Hello all!
I am performingsome clustering analysis on microarray data using
agnes{cluster} and I have created my own dissimilarity matrix according to a
distance measure different from "euclidean" or "manhattan" etc. My question
is, if I choose for example method="complete", how are the distances
between the elements calculated? Are they taken form the dissimilarity
2008 Sep 02
2
cluster a distance(analogue)-object using agnes(cluster)
I try to perform a clustering using an existing dissimilarity matrix that I
calculated using distance (analogue)
I tried two different things. One of them worked and one not and I don`t
understand why.
Here the code:
not working example
library(cluster)
library(analogue)
iris2<-as.data.frame(iris)
str(iris2)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7
2011 Jun 27
3
New to R, trying to use agnes, but can't load my ditance matrix
Hi,
I'm mighty new to R. I'm using it on Windows. I'm trying to cluster using a
distance matrix I created from the data on my own and called it D10.dist. I
loaded the cluster package. Then tried the following command...
> agnes("E:D10.dist", diss = TRUE, metric = "euclidean", stand = FALSE,
> method = "average", par.method, keep.diss = n < 1000,
2006 Apr 07
1
fuzzy classification and dissimilarity matrix
Hello,
I want to make a fuzzy classification from a dissimilarity matrix
(calculated with daisy from package 'cluster'). I have tried to use
fanny (package cluster) but I have the same problems than described in a
previous message
(http://tolstoy.newcastle.edu.au/R/help/05/05/4546.html) i.e. it always
gives me two clusters in the results (even if k is different from 2)
with the same
2017 Aug 17
0
PAM Clustering
Sorry, I never use pam. In the help, you can see that pam require a
dataframe OR a dissimilarity matrix. If diss=FALSE then "euclidean" was use.So,
I interpret that a matrix of dissimilarity is generated automatically.
Problems may be in your data. Indeed
pam(ruspini, 4)$diss
write a dissimilaty matrix
while
pam(MYdata,10)$diss
wite NULL
2017-08-17 16:03 GMT+02:00 Sema Atasever
2001 Jan 09
2
PAM clustering (using triangular matrix)
Hi,
I'm trying to use a similarity matrix (triangular) as input for pam() or
fanny() clustering algorithms.
The problem is that this algorithms can only accept a dissimilarity
matrix, normally generated by daisy().
However, daisy only accept 'data matrix or dataframe. Dissimilarities
will be computed between the rows of x'.
Is there any way to say to that your data are already a
2005 May 30
2
"FANNY" function in R package "cluster"
Dear All,
I am attempting to use the FANNY fuzzy clustering function in R
(Kaufman & Rousseeuw, 1990), found in the "cluster" package. I have
run into a variety of difficulties; the two most crucial difficulties
are enumerated below.
1. Where is the 'm' parameter in FANNY?
In _Finding Groups in Data: An Introduction to Cluster Analysis_
(1990) by Kaufman & Rousseeuw,
2005 May 30
2
How to access to sum of dissimilarities in CLARA
Dear All ,
Since dissimilarity is one of quality measures in clustering , I'm trying to access to the sum of dissimilarity as a whole measure. But after running my data using CLARA I obtain :
1128 dissimilarities, summarized :
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.033155 0.934630 2.257000 2.941600 4.876600 8.943700
But I can not find the sum of dissimilarity.How can i
2009 Jun 17
1
Predict Fanny Membership
Hello List,
My question is an elementary one. I have run a fuzzy kmeans cluster using
FANNY to group freshwater fish assemblages. I then went in the field to
validate that classification and have retrieved new assemblage data for a
new suite of streams. Therefore I would like to use Predict to determine how
well the original clustering fits the new data. However I have not figured
out a
2011 Jan 27
3
agnes clustering and NAs
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
2007 Nov 27
2
exporting clustering results to table
Hello list,
the following approach did not work:
clustersA <- pam(distances, nkA, diss=TRUE);
gc();
filenameclu = paste("filenameclu", ".txt");
write.table(clustersA , file=filenameclu,sep=",");
although it worked with
clustersA <- hclust(distances, method="ward");
and a consecutive
kclassA <- cutree(clustersA, k=nkA);
filename =
2006 Apr 05
1
"partitioning cluster function"
Hi All,
For the function "bclust"(e1071), the argument "base.method" is
explained as "must be the name of a partitioning cluster function
returning a list with the same components as the return value of
'kmeans'.
In my understanding, there are three partitioning cluster functions in
R, which are "clara, pam, fanny". Then I check each of them to
2003 Feb 28
1
Pam and Fanny vector length problems
I have "small" problem ...
with the cluster library each time I try to use
the "agnes","pam","fanny" functions with more than 20000 elements
I get the following error:
>Error in vector("double", length) : negative length vectors are not allowed
>In addition: Warning message:
>NAs introduced by coercion
But with the clara
2009 Aug 18
15
dlm stress test hangs OCFS2
This email is also sent to cluster-devel at redhat.com. Since this issue is about
both dlm and ocfs2, I send the email here to look for help from upstream.
This is an already known issue.
on ocfs2 with user space cluster stack, run the test script from
http://people.redhat.com/~teigland/make_panic on the mounted ocfs2 volume from 2
nodes simultaneously, the access to ocfs2 volume on both nodes
2011 Jul 14
1
recursive function - finding connections
Dear all,
I'm having some problems getting my recursive function to work. At first I though that maybe my data was too big and I increase option(expressions=50000). Then I thought that I would try it on some smaller data. Still not working. :(
I would have thought there should be a function for this already, so any suggestions are welcomed for other methods. I did try igraph but couldn't
2002 May 20
1
R bug in cluster package (PR#1580)
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
2007 Jun 28
2
restructuring matrix
Hi all,
let's say I have matrix
People Desc Value
Mary Height 50
Mary Weight 100
Fanny Height 60
Fanny Height 200
Is there a quick way to form the following matrix?
People Height Weight
Mary 50 100
Fanny 60 200
(Assuming I don't know the length of people/desc and let's say these are
characters matrix.. I tried
2006 Apr 07
3
Pointer position on keypress event?
Hi.
Is there any straightforward way to tell pointer position (x, y)
upon keypress? In original wxWidgets, wxKeyEvent supports GetX()
and GetY() methods, but wxRuby''s KeyEvent object does not have
one. I also checked with event.methods and event.instance_variables.
Do I need to keep track of pointer position by evt_motion?
--
Taisuke Yamada <tyamadajp@spam.rakugaki.org>,