Displaying 20 results from an estimated 1500 matches similar to: "re-vertical conversion of data entries"
2010 Oct 29
1
transposing a column table
Dear R-user,
I need help on how to transpose this column of clustering vector in R with 8768 entries derived from a PAM clustering output in a vertical view to an excel file
Clustering vector:
[1] 1 1 2 2 1 2 1 2 1 1 2 2 1 2 2 2 2 1 1 1 1 2 2 1 2 2 1 2 2 2 2 2 2 2 2 1 2
[38] 2 1 1 2 2 2 2 2 1 2 1 2 2 2 2 1 2 1 2 2 1 2 2 2 2 2 2 1 2 1 2 2 2 1 1 2 2
[75] 2 1 2 2 2 2 2 2 2 1 1 2 1 2 2 2 2 2
2008 Aug 01
2
Exporting data to a text file
HI R users
With clara function I get a data frame (maybe this is not the exact word,
I'm new to R) with the following variables:
> names(myclara)
[1] "sample" "medoids" "i.med" "clustering" "objective"
[6] "clusinfo" "diss" "call" "silinfo" "data"
I want to
2009 Feb 18
0
Index-G1 error
I am using some functions from package clusterSim to evaluate the best clusters layout.
Here is the features vector I am using to cluater 12 signals:
> alpha.vec
[1] 0.8540039 0.8558350 0.8006592 0.8066406 0.8322754 0.8991699 0.8212891
[8] 0.8815918 0.9050293 0.9174194 0.8613281 0.8425293
In the following I pasted an excerpt of my program:
2008 Feb 22
2
Looping and Pasting
Hello R-community: Much of the time I want to use loops to look at graphs,
etc. For example,
I have 25 plots, for which the names are m.1$medoids, m.2$medoids, ...,
m.25$medoids.
I want to index the object number (1:25) as below (just to show concept).
for (i in 1:25){
plot(m.i$medoids)
}
I've tried the following, with negative results
for ...
2008 Dec 17
1
bug (?!) in "pam()" clustering from fpc package ?
Hello all.
I wish to run k-means with "manhattan" distance.
Since this is not supported by the function "kmeans", I turned to the "pam"
function in the "fpc" package.
Yet, when I tried to have the algorithm run with different starting points,
I found that pam ignores and keep on starting the algorithm from the same
starting-points (medoids).
For my
2009 Mar 29
1
[cluster package question] What is the "sum of the dissimilarities" in the pam command ?
Hello Martin Maechler and All,
A simple question (I hope):
How can I compute the "sum of the dissimilarities" that appears in the pam
command (from the cluster package) ?
Is it the "manhattan" distance (such as the one implemented by "dist") ?
I am asking since I am running clustering on a dataset. I found 7 medoids
with the pam command, and from it I have the
2004 Jun 29
1
give PAM my own medoids
Hello,
When using PAM (partitioning around medoids), I would like to skip the
build-step and give the fonction my own medoids.
Do you know if it is possible, and how ?
Thank you very much.
Isabel
2005 Jun 07
1
Specifying medoids in PAM?
I am using the PAM algorithm in the CLUSTER library.
When I allow PAM to seed the medoids using the default __build__
algorithm things work
well:
> pam(stats.table, metric="euclidean", stand=TRUE, k=5)
But I have some clusters from a Hierarchical analysis that I would
like to use as seeds for the PAM algorithm. I can't figure what the
mediod argument wants. When I put in the
2010 Oct 22
2
(no subject)
I am doing cluster analysis on 8768 respondents on 5 lifestyle variables and am having difficulty constructing a dissimilarity matrix which I will use for PAM. I always get an error: “cannot allocate vector of size 293.3 Mb” even if I have already increased my memory to its limit of 4000. I did it on 2GB , 32-bit OS . I tried ff and filehash and I still get the same error. Can you please
2009 Jun 29
0
Naive knn question
Dear list,
I have two dissimilarity matrices, one for a training data set which I then
clustered using PAM. The second is a diss matrix for a validation data set
(an independent field sample). I have been trying to use knn to distinguish
distances between the validation data set and the 6 mediods of the training
data defined by using PAM.
I continue to get error messages in regards to either the
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
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,
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
2006 Apr 10
2
passing known medoids to clara() in the cluster package
Greetings,
I have had good success using the clara() function to perform a simple cluster
analysis on a large dataset (1 million+ records with 9 variables).
Since the clara function is a wrapper to pam(), which will accept known medoid
data - I am wondering if this too is possible with clara() ... The
documentation does not suggest that this is possible.
Essentially I am trying to
2010 Dec 26
4
how to replace my double for loop which is little efficient!
Dear all,
My double for loop as follows, but it is little efficient, I hope all
friends can give me a "vectorized" program to replace my code. thanks
x: is a matrix 202*263, that is 202 samples, and 263 independent variables
num.compd<-nrow(x); # number of compounds
diss.all<-0
for( i in 1:num.compd)
for (j in 1:num.compd)
if (i!=j) {
S1<-sum(x[i,]*x[j,])
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
2010 Oct 22
1
Ordinal response model in depmixS4
I am running a latent class regression with 3 nominal and 2 ordinal variables using depmixS4 but the available response models do not include one for ordinal response. How do I go about this?
Penny
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2011 May 16
1
pam() clustering for large data sets
Hello everyone,
I need to do k-medoids clustering for data which consists of 50,000
observations. I have computed distances between the observations
separately and tried to use those with pam().
I got the "cannot allocate vector of length" error and I realize this
job is too memory intensive. I am at a bit of a loss on what to do at
this point.
I can't use clara(), because I
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
2002 Jan 28
1
Cluster package broken in 1.4.0?
Greetings,
I am reasonably experienced with R but I recently tried to
do some clustering using the "cluster" package, in order
to see if it would help.
I only tried this once with the 1.3.1 version and it worked
(I don't quite remember which method I used).
Now, I tried with the 1.4.0 version and no clustering function
seems to work with matrices that contain NAs, even
though