Displaying 20 results from an estimated 4000 matches similar to: "Problem with cluster analysis"
2002 Jan 22
1
cutree using a vector for h giving meaningless results
I try to use the routine cutree to cut a tree (created by hclust) into
several groups by specifiing the hight of the cut.
a<-1:10
cutree(tree, h=a*100)
The Matrix with group meberships returned is ok for most of the hights, but
in some cases (as for example h=800 and h=900) the results don't make sense
(group membership=0 or 58965231, it looks like the range of data allowed by
the data
1998 May 29
1
R-beta: multiv package from CRAN
Hallo Friedrich,
I have read your announcement, downloaded and installed it in R-0.61.3.
But now I have problems :)
> hc <- hierclust(dist(t(pollen)), method=3)
Error in pmatch(x, table) : argument is not of mode character
> hc <- hclust(dist(t(pollen)))
> members(hc)
Error in .Fortran("assgn", n = as.integer(n), nplus1 =
as.integer(nplus1), : C/Fortran function not in
2003 Jun 25
2
dendrograms
Hello all,
I am using libraries (mva,cluster) to produce dendrograms. With 1000
examples the dendrogram gets too crowded, and i am wondering whether there
is an option (which i cannot find) to set the number of leaf nodes, like
in matlab, and return the plot and the assignment map examples -> leaf
nodes. Any suggestion is appreciated. Thanks
Edo
2000 Jul 20
3
printing hclust with k clusters
howdy R friends,
I've searched CRAN but to no avail... I'm trying to use mva's hclust and
print out for say 10 clusters in batch. How do I do this? It's unclear if
I can use cutree.
thanks,
John Strumila
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1999 Jul 07
1
hclust
I'm using the hclust method from the package mva (pre-compiled-version
on Win NT) and would like to cut the tree in pieces.
Have someone implemented the function cutree (as in S-PLUS) in R?
Many thanks
Markus Huerzeler
--
Dr. Markus Huerzeler Phone: +41 / 61 / 686 98 83
AICOS Technologies AG Fax: +41 / 61 / 686 98 88
Efringerstrasse 32 mailto:mhuerzeler at
2003 Dec 11
1
cutree with agnes
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")
2003 Dec 11
1
cutree with agnes
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")
2013 Apr 23
1
assigning cluster id in cluster package-reg.
Well, you don't give much of an example....
I'm replying CC to the R mailing list. Please ask questions there, rather
than adressing individuals for basic help.
Here is one; does it answer your question ?
data(agriculture)
ag.ag <- agnes(agriculture)
class(ag.ag)
pltree(ag.ag) # the dendrogram, if you want to see it
## cut the dendrogram -> get cluster assignments:
(ck3 <-
2008 Jun 13
1
Output of silhouette (cluster package)
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
2005 Mar 31
2
Using kmeans given cluster centroids and data with NAs
Hello,
I have used the functions agnes and cutree to cluster my data (4977
objects x 22 variables) into 8 clusters. I would like to refine the
solution using a k-means or similar algorithm, setting the initial
cluster centres as the group means from agnes. However my data matrix
has NA's in it and the function kmeans does not appear to accept this?
> dim(centres)
[1] 8 22
> dim(data)
2015 Jun 06
2
Request: making cutree S3 in R?
Hello all,
A question/suggestion:
I was wondering if there is a chance of changing stats::cutree to be S3 and
use cutree.hclust?
For example:
cutree <- function(tree, k = NULL, h = NULL,...)
{
UseMethod("cutree")
}
cutree.hclust <- stats::cutree
# This will obviously need the actual content of stats::cutree
This would be nicer for people like me to add new methods to
2004 Jun 17
1
Re: Clustering in R
Thanks a lot, Michael!
I cc to R-help, where this question really belongs {as the
'Subject' suggests itself...} -- please drop 'bioconductor' from
CC'ing further replies.
>>>>> "michael" == michael watson (IAH-C) <michael.watson at bbsrc.ac.uk>
>>>>> on Thu, 17 Jun 2004 09:16:59 +0100 writes:
michael> OK, admittedly it
2001 Aug 22
1
cutree (PR#1067)
Full_Name: Anja von Heydebreck
Version: 1.3.0
OS: Alpha Unix
Submission from: (NULL) (141.14.19.61)
Hi,
I repeatedly obtained meaningless results from the function 'cutree'
in the 'mva' package, when the argument 'h' was greater or equal to
the maximum height occuring:
> library('mva')
> y
[,1] [,2] [,3] [,4]
[1,] 0 1 -1 1
[2,] 0 -1
2012 Dec 06
1
tool for cluster analysis
I have Windows XP Professional Version 2002 and the R-Version 2.1.1.
I did cluster analysis with the cluster package and the agnes (method =
?ward?).
The results are satisfactory.
But the dendrogram of agnes is confused to work with the results.
Is there a tool, I can get a clear arrangement of the results for the
cluster analysis.
For example a matrix with different numbers for each group.
2004 Jan 07
1
Analyzing dendrograms
Ladies and Gentlemen,
As Johan Lindberg points out, the documentation for handling dendrograms
is sparse....Does anyone know who is responsible for or working on
development of tree methods and objects? I've written a couple of scripts
for my own use to translate between parenthetical (A(B(CD))) or binary
A00 B10 C11 D11 tree formats and cluster objects in R, but as an
inexperienced
2002 Apr 29
2
cluster analyses
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
2000 Aug 31
2
Multiv / hierclust / plclust
I use hierclust (hierarchical clustering) in multiv package. In the
documentation it is said that plclust (plotting a dendrogram) is
available in S-plus. Can I find it anywhere (I have searched through
http://lib.stat.cmu.edu/S and found only quotations of plclust in
multiv) or is it only part of the S package (which I don't have)?
Thanks
---------------
Charles RAUX,
Laboratoire
2005 Feb 22
6
Run Sweave and LaTeX directly from command line
Hello!
Those of you, who use Sweave a lot, will probably find my shell script
usable. You can get it at:
http://www.bfro.uni-lj.si/MR/ggorjan/programs/shell/Sweave.sh
No warranty, however don't hesitate to contact me if you find an error or
have a patch!
--
Lep pozdrav / With regards,
Gregor GORJANC
---------------------------------------------------------------
University of
2002 Jul 10
2
incorrect URL (PR#1764)
Hi -
a tiny bug report:
the list of mirror sites given at www.r-project.org/
mentions
http://cran.mirror.aarnet.edu.au/
This domain does not exist (well, from Western Australia
netscape says the domain doesn't exist) but I found
the mirror at
http://mirror.aarnet.edu.au/pub/CRAN/
regards
Adrian Baddeley
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2002 Jul 10
2
incorrect URL (PR#1764)
Hi -
a tiny bug report:
the list of mirror sites given at www.r-project.org/
mentions
http://cran.mirror.aarnet.edu.au/
This domain does not exist (well, from Western Australia
netscape says the domain doesn't exist) but I found
the mirror at
http://mirror.aarnet.edu.au/pub/CRAN/
regards
Adrian Baddeley
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