Displaying 20 results from an estimated 4000 matches similar to: "plot hclust - canberra dist + median linkage"
2004 Oct 11
2
hclust title and paste - messed up
I use the following code to scan a (limited) parameter space of clustering
strategies ...
data <- read.table(...
dataTranspose <- t(data)
distMeth <- c("euclidean",
"maximum",
"manhattan",
"canberra",
"binary"
)
clustMeth <- c("ward",
2003 Sep 26
1
a. crossing branches with hclust, b. plot.dendrogram
Hello,
a. when I use hclust with the methods media, centroid, and mcquitty,
and plot the results, the dendrograms have lines that are crossing each
other. Is this ok?
b. My next question refers to plot.dendrogram: How can I use parameters
as "hang" or "cex" here? E.g. for
st <- as.dendrogram(subtreeshc[[x]])
I would like to have something like this, where cex and hang
2009 Dec 10
1
question about centroid-linkage (cluster analysis)
Dear R community,
I would be greatful if somebody could shed light on the following.
I have created a set of 6 points to check how centroid
agglomeration works in cluster analysis:
> Y <- data.frame(x=c(-1,1,1,-1,10,12),y=c(1,1,-1,-1,0,0))
It is quite intuitive to understand that the last clusters to be joined will be
{1,2,3,4} with {5,6}. Now, the centroid for the first cluster has
2012 Jul 04
1
Error in hclust?
Dear R users,
I have noted a difference in the merge distances given by hclust using
centroid method.
For the following data:
x<-c(1009.9,1012.5,1011.1,1011.8,1009.3,1010.6)
and using Euclidean distance, hclust using centroid method gives the
following results:
> x.dist<-dist(x)
> x.aah<-hclust(x.dist,method="centroid")
> x.aah$merge
[,1] [,2]
[1,] -3 -6
2003 Sep 16
0
hclust: median, centroid (PR#4195)
There seems to be a bug in hclust (package mva) for clustering
methods 'median' and 'centroid'.
I have written a clustering program in C and discovered that the
results for 'median' differ from those of hclust in R. I used a
third program, written by someone else in Pascal, and that
program agrees with the output of my program.
I found yet another clustering program that
2012 Nov 18
1
centroid of hclust
Dear UseRs,i want to find centroid of clusters, which i generated by hclust. Is there a way doing that? i took mean to elements in each cluster to get centroid but i am not sure if i am right?
thanks in advanceeliza
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2012 Oct 21
1
Linear discriminant function analysis based median as group centroid and nonparametric scale estimators???
Dear All,
I am using a specific approach for my master thesis. In essence, a
supervised reclassification is used as an intermediate step to find chemical
parameters which are able to reclassify defined groups. These variables will
be used in a next step where location and scale estimators of the groups are
important. Traditionally linear discriminant analysis is used for
reclassification which
2001 Nov 19
3
dist
Hi list!
I'm computing multivar. distances from a set of centroids
to a (large) set of individuals. I'm now just using rbind
to create a matrix (x) with the centroid and the individuals,
then run as.matrix(dist(x)) and finally select the appropriate columns,
as I'm not interested on the distances among individuals.
Therefore, this procedure implies a waste of computing time.
Is there
2003 Sep 17
1
plot.hclust: dendrogram too large for window (PR#4197)
plot.hclust:
Setting up a window for a dendrogram assumes the first link is
the shortest and the last is the longest. This is not always the
case when the clustering was done with hclust, method="median"
or method="centroid", and the dendrogram sometimes doesn't fit
within the window.
I propose the fix listed below.
src/main/
--- plot.c Wed Sep 17 01:03:39 2003
+++
2001 Mar 05
1
Canberra dist and double zeros
Canberra distance is defined in function `dist' (standard library `mva') as
sum(|x_i - y_i| / |x_i + y_i|)
Obviously this is undefined for cases where both x_i and y_i are zeros. Since
double zeros are common in many data sets, this is a nuisance. In our field
(from which the distance is coming), it is customary to remove double zeros:
contribution to distance is zero when both x_i
2001 Mar 05
1
Canberra dist and double zeros
Canberra distance is defined in function `dist' (standard library `mva') as
sum(|x_i - y_i| / |x_i + y_i|)
Obviously this is undefined for cases where both x_i and y_i are zeros. Since
double zeros are common in many data sets, this is a nuisance. In our field
(from which the distance is coming), it is customary to remove double zeros:
contribution to distance is zero when both x_i
2008 Jul 03
1
Otpmial initial centroid in kmeans
Helo there. I am using kmeans of base package to cluster my customers. As
the results of kmeans is dependent on the initial centroid, may I know:
1) how can we specify the centroid in the R function? (I don't want random
starting pt)
2) how to determine the optimal (if not, a good) centroid to start with? (I
am not after the fixed seed solution as it only ensure that the
2001 Jun 12
1
cophenetic matrix
Hello,
I analyse some free-sorting data so I use hierarchical
clustering.
I want to compare my proximity matrix with the tree
representation to evalute the fitting. (stress, cophenetic correlation
(pearson's correlation)...)
"The cophenetic similarity of two objects a and b is defined as the
similarity level at wich objects a and b become members of the same
cluster during the course of
2004 Dec 15
1
hclust and heatmap - slightly different dendrograms?
Good afternoon,
I ran heatmap and hclust on the same matrix x (strictly, I ran
heatmap(x), and hclust(dist(t(x))), and realized that the two
dendrograms were slightly different, in that the left-right
arrangement of one pair of subclusters (columns) was reversed in the
two functions (but all individual columns were grouped correctly).
Looking through the code for heatmap as a most definite
2011 Jul 09
1
SpatialPolygonsDataFrame holes problem
I have obtained shapefiles for Indian states from here:
http://www.maptell.com/index.php?option=com_remository&Itemid=159&func=fileinfo&filecatid=115&parent=category
Problem: I want to extract centroid coordinates for each State, but there is some coding problem with the shapefiles that prevents this.
#Code:
#After extracting the shapefiles from the india_state.zip file, then:
2008 Sep 17
1
ANOVA contrast matrix vs. TukeyHSD?
Dear Help List,
Thanks in advance for reading...I hope my questions are not too ignorant.
I have an experiment looking at evolution of wing size [centroid] in
fruitflies and the effect of 6 different experimental treatments
[treatment]. I have five replicate populations [replic] in each
treatment and have reared the flies in two different temperatures [cond]
to assay the wing size, making
2004 Oct 13
3
data(eurodist) and PCA ??
If I perform PCA on the 'eurodist' data, should I get an accurate
geographic layout of the cities with biplot?
(barring inversions, i.e. their is no way to define north.. but you get
the idea...)
I have a complex distance matrix, and I am thinking about how to cluster
it and how to visualize the quality of the resulting clusters.
If I could 'see' the clusters in space I could
2004 Nov 04
4
highly biased PCA data?
Hello, supposing that I have two or three clear categories for my data,
lets say pet preferece across fish, cat, dog. Lets say most people rate
their preference as being mostly one of the categories.
I want to do pca on the data to see three 'groups' of people, one group
for fish, one for cat and one for dog. I would like to see the odd person
who likes both or all three in the
2009 Feb 05
1
Does the "labpt" object in the Polygons-class represent the centroid of the polygon
Hello,
I need to calculate the centroids of some spatial polygons that I have
placed into a Polygons-class object. Is the labeling point in the
Polygons-class the centroid of the polygon?
Thank you for your help.
2004 Sep 10
0
hclust, centroid
Does anyone know how hclust (stats) calculates centroid linkage if only a
distance matrix can be used as the input?
...Tao