Displaying 20 results from an estimated 5000 matches similar to: "Problem with clusplot"
2011 Nov 04
1
How to use 'prcomp' with CLUSPLOT?
Hello,
I have a large data set that has more columns than rows (sample data below). I am trying to perform a partitioning cluster analysis and then plot that using pca. I have tried using CLUSPLOT(), but that only allows for 'princomp' where I need 'prcomp' as I do not want to reduce my columns. Is there a way to edit the CLUSPLOT() code to use 'prcomp', please?
#
2005 May 23
1
Can't reproduce clusplot princomp results.
Dear R folk:
Perhaps I'm just dense today, but I am having trouble reproducing the
principal components plotted and summarized by clusplot. Here is a brief
example using the pluton dataset. clusplot reports that the first two
principal components explain 99.7% of the variability. But this is not what
princomp is reporting. I would greatly appreciate any advice.
With best regards,
-- Tom
2008 Mar 06
2
Clustering large data matrix
Hello,
I have a large data matrix (68x13112), each row corresponding to one
observation (patients) and each column corresponding to the variables
(points within an NMR spectrum). I would like to carry out some kind of
clustering on these data to see how many clusters are there. I have
tried the function clara() from the package cluster. If I use the matrix
as is, I can perform the clara
2013 Apr 09
0
How does clusplot exactly make use of cmdscale?
Dear people,
I used clusplot to plot a partition result. The partition result was from
pamk with a distance object as input. Then I applied cmdscale on the same
distance object for coordinates to make another scatterplot.
My problem is this: the coordinates from the cmdscale calculation, though
with the same shape, were different in scale and rotation from the scatter
plot yielded by clusplot.
2009 Jan 31
1
Extracting coordinates for cluster::clusplot()
Dear Friends,
require(cluster)
x <- rbind(cbind(rnorm(10, 0, 0.5), rnorm(10, 0, 0.5)),
cbind(rnorm(15, 5, 0.5), rnorm(15, 5, 0.5)))
plot(pp <- pam(x, 2), which.plots = 1)
How can I extract the coordinates used in the plot?
_____________________________
Professor Michael Kubovy
University of Virginia
Department of Psychology
Postal Address:
P.O.Box 400400, Charlottesville, VA 22904-4400
2003 May 06
2
R vs SPSS output for princomp
Hi,
I am using R to do a principal components analysis for a class
which is generally using SPSS - so some of my question relates to
SPSS output (and this might not be the right place). I have
scoured the mailing list and the web but can't get a feel for this.
It is annoying because they will be marking to the SPSS output.
Basically I'm getting different values for the component
2002 Jan 07
3
cluster - clusplot.default (PR#1249)
The following code in clusplot.default (package cluster) is in error:
x1 <- cmdscale(x, k = 2, eig = TRUE)
var.dec <- sum(x1$eig)/sum(diag(x1$x))
if (var.dec < 0)
var.dec <- 0
if (var.dec > 1)
var.dec <- 1
x1 <- x1$points
x1 has components with names "points" and "eig", not "x", so
2005 Oct 13
2
varimax rotation difference between R and SPSS
Hi,
I am puzzeled with a differing result of princomp in R and FACTOR in
SPSS. Regarding the amount of explained Variance, the two results are
the same. However, the loadings differ substantially, in the unrotated
as well as in the rotated form.
In both cases correlation matrices are analyzed. The sums of the squared
components is one in both programs.
Maybe there is an obvious reason, but I
2009 Aug 18
0
Help with identify() points on a PAM clusplot
I created a clusplot from PAM results. It represents how signals have been classified.
Signals are identified by a numerical label.
My trial distance matrix is made up of 10 rows, one for eacjh signal.
I assigned the signals iidentifiers as rownames of the distance matrix.
rwn
[1] "1104" "1332" "2057" "2425" "2483" "2530"
1999 Oct 07
1
[Fwd: Libraries loading, but not really?] - it really IS a problem :-(
kalish at psy.uwa.edu.au wrote:
>
> I'm a newbie at R, and can't get libraries to really work.
> I did this:
> > library(help = mva)
> cancor Canonical Correlations
> cmdscale Classical (Metric) Multidimensional Scaling
> dist Distance Matrix Computation
> hclust Hierarchical Clustering
2011 Sep 23
0
Clusplot axes
I am a relative novice with R and am having some difficulty using 'clusplot'
(package Cluster).
I have performed PCA analysis (using vegan) on a large set of morphometric
measurements and revealed up to 4 principal components. To examine the
grouping of the data I have used PAM followed by clusplot to visualise the
clusters. My problem is that I would like to see the clusters plotted on
2011 Dec 28
1
Help with PCA
Dear all,
I've a correlation matrix with rows and columns headings.
I've two questions:
1) How can i import it in R, setting first row as row heading and first
column as column heading?
2) Which is the best principal component anlysis package in R?
Thanks in advance
--
View this message in context: http://r.789695.n4.nabble.com/Help-with-PCA-tp4239756p4239756.html
Sent from the R help
2007 Mar 02
2
Wishlist: Make screeplot() a generic (PR#9541)
Full_Name: Gavin Simpson
Version: 2.5.0
OS: Linux (FC5)
Submission from: (NULL) (128.40.33.76)
Screeplots are a common plot-type used to interpret the results of various
ordination methods and other techniques. A number of packages include ordination
techniques not included in a standard R installation. screeplot() works for
princomp and prcomp objects, but not for these other techniques as it
2010 Jun 30
3
Factor Loadings in Vegan's PCA
Hi all,
I am using the vegan package to run a prcincipal components analysis
on forest structural variables (tree density, basal area, average
height, regeneration density) in R.
However, I could not find out how to extract factor loadings
(correlations of each variable with each pca axis), as is straightforwar
in princomp.
Do anyone know how to do that?
Moreover, do anyone knows
2012 Feb 23
2
Advice on exploration of sub-clusters in hierarchical dendrogram
Dear R user,
I am a biochemist/bioinformatician, at the moment working on protein
clusterings by conformation similarity.
I only started seriously working with R about a couple of months ago.
I have been able so far to read my way through tutorials and set-up my
hierarchical clusterings. My problem is that I cannot find a way to obtain
information on the rooting of specific nodes, i.e. of
2007 Oct 04
0
??clusplot
Hi there,
I want to do classify some 2-dimensional points into four clusters by
pam() in the cluster package. However, I encountered some problems.
1. How can I change the "xlab" and "ylab" instead of the default
"Component 1" and "Component 2"? When I put "xlab" option in the
function, it always says "formal argument "xlab"
2003 Feb 05
1
Package: cluster -- plot.partition() change title: main=""
Dear R-list members,
I am using the cluster package and by the generation of plot.partition I ran
into the problem that an alternative title overlaps the default title.
> plot.partition(clara.14,which.plot=2,stand=TRUE, main="Silhouette plot of
14 clusters")
The manual states that all optional arguments for clusplot.default may also
be supplied to plot.partition(). Altering the
2012 Jul 05
4
Exclude missing values on only 1 variable
Hello,
I have many hundred variables in my longitudinal dataset and lots of
missings. In order to plot data I need to remove missings.
If I do
> data <- na.omit(data)
that will reduce my dataset to 2% of its original size ;)
So I only need to listwise delete missings on 3 variables (the ones I am
plotting).
data$variable1 <-na.omit(data$variable1)
does not work.
Thank you
2009 Jan 19
3
bootstrapped eigenvector method following prcomp
G'Day R users!
Following an ordination using prcomp, I'd like to test which variables
singnificantly contribute to a principal component. There is a method
suggested by Peres-Neto and al. 2003. Ecology 84:2347-2363 called
"bootstrapped eigenvector". It was asked for that in this forum in
January 2005 by J?r?me Lema?tre:
"1) Resample 1000 times with replacement entire
2004 May 10
3
Colouring hclust() trees
I have a data set with 6 variables and 251 cases.
The people who supplied me with this data set believe that it falls
naturally into three groups, and have given me a rule for determining
group number from these 6 variables.
If I do
scaled.stuff <- scale(stuff, TRUE, c(...the design ranges...))
stuff.dist <- dist(scaled.stuff)
stuff.hc <- hclust(stuff.dist)