Displaying 20 results from an estimated 7000 matches similar to: "similarity measure"
2009 Oct 29
2
similarity measure for binary data
I am doing hierarchical clustering with cluster package. I couldnot find similarity measures like matching coefficient, Jaccard coefficient and sokal and sneath. Could anyone please tell package with similarity measures for binary data?
kind regards,
Ms.Karunambigai M
PhD Scholar
Dept. of Biostatistics
NIMHANS
Bangalore
India
From cricket scores to your friends. Try the Yahoo! India
2009 Nov 03
1
hierarchical clustering with Jaccard index
hi,
I want to do hierarchical clustering with Jaccord index. I tried to do with vegan package for finding index and hierarchical clustering with hclust function. While doing clustering it is showing an error message as "invalid distance method". I would be grateful if anyone tells how to rectify the error.
Thanks in advance,
kind regards,
Ms.Karunambigai M
PhD Scholar
Dept. of
2011 May 26
2
likelihood ratio test
Dear R-help,
Can anybody tell me which R package has Lo-Mendell Rubin LR test and Bootstrap
LR test to compare the model fit between k class and k+1 class model for Latent
class analysis?
Thanks in advance,
warn regards,Ms.Karunambigai M
PhD Scholar
Dept. of Biostatistics
NIMHANS
Bangalore
India
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2009 Dec 11
1
cluster size
hi r-help,
i am doing kmeans clustering in stats. i tried for five clusters clustering using:
kcl1 <- kmeans(as1[,c("contlife","somlife","agglife","sexlife",
"rellife","hordlife","doutlife","symtlife","washlife",
2009 Nov 13
1
binary data
hi,
I am trying to calculate distance matrices for binary data frame. I am using dist.binary in 'ade4' package. This is the code i run and get error message as 'missing value where True/False needed:
clss <- as.data.frame(cls)
dist.binary(clss, method = 1, diag = FALSE, upper = FALSE)
Also, if i convert the factors into numeric(i.e,1&2 in the place of 0&1 for present/absent
2011 Sep 17
0
Fw: likelihood ratio test
Ms.Karunambigai M
PhD Scholar
Dept. of Biostatistics
NIMHANS
Bangalore
India
----- Forwarded Message ----
From: karuna m <m_karuna2002@yahoo.com>
To: R-help@r-project.org
Sent: Thu, 26 May, 2011 10:55:02 AM
Subject: likelihood ratio test
Dear R-help,
Can anybody tell me which R package has Lo-Mendell Rubin LR test and Bootstrap
LR test to compare the model fit between k class and k+1
2011 Feb 02
2
clustering with finite mixture model
Dear R-help,
I am doing clustering via finite mixture model. Please suggest some packages in
R to find clusters via finite mixture model with continuous variables. And
also I wish to verify the distributional properties of the mixture distributions
by fitting the model with lognormal, gamma, exponentials etc,.
Thanks in advance,
warm regards,Ms.Karunambigai M
PhD Scholar
Dept. of Biostatistics
2001 Apr 10
5
Similarity matrix
I frequently use hclust on a similarity matrix. In R only a
distance matrix is allowed. Is there a simple reliable
transformation of a similarity matrix that will result
in a distance matrix making hclust work the same as
S-Plus with a similarity matrix? Venables & Ripley 3rd
edition implies that a simple reversal of values
will suffice. Thanks -Frank
--
Frank E Harrell Jr
2010 Jul 20
1
p-values pvclust maximum distance measure
Hi,
I am new to clustering and was wondering why pvclust using "maximum"
as distance measure nearly always results in p-values above 95%.
I wrote an example programme which demonstrates this effect. I
uploaded a PDF showing the results
Here is the code which produces the PDF file:
-------------------------------------------------------------------------------------
s <-
2010 Jun 17
1
plotting radial dendrograms
Dear list,
I am trying to plot a radial dendrogram using the ape package, which
requires my data to be of class 'phylo'. Currently I have my
dendrogram stored as an object of class 'dendrogram' which was
produced from an outside bit of C code, but was made into an object of
class 'igraph.eigenc' and converted to a dendrogram using
'as.dendrogram()' from the igraph
2013 Jul 23
1
Heat Map for species - code from Numerical Ecology with R
Hello, I am relatively new to R and I am working through the code that is provided in the book Numerical Ecology with R and I have run across an error message that I can't seem to figure out. I am using the vegan, ade4, gclus and cluster packages. The code is as follows: # Ordered community table # Species are ordered by their weighted averages on site scores or <- vegemite(spe,
2011 Sep 13
2
help with hclust and cutree
Hello,
I would like to cut a hclust tree into several groups at a specific
similarity. I assume this can be achieved by specifying the "h" argument
with the specified similarity, e.g.:
clust<-hclust(dist,"average")
cut<-cutree(clust,h=0.65)
Now, I would like to draw rectangles around the branches of the
dendrogram highlighting the corresponding clusters, as is done by
2012 Mar 29
2
hclust and plot functions work, cutree does not
Hi,
I have the distance matrix computed and I feed it to hclust function. The
plot function produces a dense dendrogram as well. But, the cutree function
applied does not produce the desired list.
Here is the code
x=data.frame(similarity_matrix)
colnames(x) = c(source_tags_vec)
rownames(x) = c(source_tags_vec)
clust_tree=hclust(as.dist(x),method="complete")
plot(clust_tree)
2012 May 24
4
Manually modifying an hclust dendrogram to remove singletons
Dear R-Help,
I have a clustering problem with hclust that I hope someone can help
me with. Consider the classic hclust example:
hc <- hclust(dist(USArrests), "ave")
plot(hc)
I would like to cut the tree up in such a way so as to avoid small
clusters, so that we get a minimum number of items in each cluster,
and therefore avoid singletons. e.g. in this example, you can see
2002 Feb 20
1
plot.hclust: strange behaviour with "manufactured" hclust object
I've been trying to get plot.hclust to work with a hclust object I
created and have not had much success. It seems that there is some
"hidden" characteristic of a hclust object that I can't see. This is
most easily seen in the following example, where plot.hclust works on
one object, but when this object is "dumped" and then re-read,
plot.hclust no longer works. Is
2011 May 17
1
simprof test using jaccard distance
Dear All,
I would like to use the simprof function (clustsig package) but the available distances do not include Jaccard distance, which is the most appropriate for pres/abs community data. Here is the core of the function:
> simprof
function (data, num.expected = 1000, num.simulated = 999, method.cluster = "average",
method.distance = "euclidean", method.transform =
2012 Oct 11
2
extracting groups from hclust() for a very large matrix
Hello,
I'm having trouble figuring out how to see resulting groups (clusters)
from my hclust() output. I have a very large matrix of 4371 plots and 29
species, so simply looking at the graph is impossible. There must be a
way to 'print' the results to a table that shows which plots were in
what group, correct?
I've attached the matrix I'm working with (the whole thing
2002 May 30
1
hclust.identify problem
Having some problems with using hclust.identify on my data, I revert to trying
it out on the example in the help manual. My result is still the same (as with
my own data):
data(iris)
hci <- hclust(dist(iris[,1:4]))
plot(hci)
testx<-identify.hclust(hci)
Error in rect.hclust(x, k = k, x = x$x, cluster = cluster[, k - 1], border
= "red") :
k must be between 2 and 0
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")