Displaying 20 results from an estimated 400 matches similar to: "Fwd: MDS problems [ajtee@ajtee.uklinux.net]"
2005 Jun 28
2
enhanced MDS
Hi again
Sorry, in looking again at sammon and isoMDS I see that they seem to do
exactly what I want, except that they are non-metric, which means, as I
understand it, that they relate the rank orders of the variables rather than
the actual distances.
Could I use these non-metric MDS packages even if my distances are metric?
Thanks
Karen
--
Karen Kotschy
Centre for Water in the Environment
2010 Jan 06
1
math function - MDS method
Hi,
I need math function which is used in: isoMDS, Sammon and metaMDS method.
Anybody know where I may find it? Any manual or webside?
I would be very happy
Thanks a lot !
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2008 Feb 20
1
Stress with MDS
Hi,
I am looking for the best multidimensional configuration for my data (47*47
distance matrix).
I ve tried classical metric (cmdscale) and non metric MDS (isoMDS, nmds)
but it is now difficult to choose the best solution because of the
uncertainties in the definitions of the "stress" function.
So, same problem, several questions :
1. Statistical consideration : With
2006 Jun 15
3
MDS with missing data?
Hello
I will be applying MDS (actually Isomap) to make a
psychological
"concept map" of the similarities between N concepts.
I would like to scale to a large number of concepts,
however, the
resulting N*(N-1) pairwise similarities is prohibitive
for a user survey.
I'm thinking of giving people random subsets of the
pairwise
similarities.
Does anyone have recommendations for this
2009 Apr 15
3
Kruskal's MDS results
Dear List,
I'm trying to interpret the results of the Kruskal's Non-metric Multidimensional Scaling algorithm (isoMDS, MASS package).
The 'goodness of fit' is reported as "The final stress achieved (in percent)".
What does this mean exactly? I've tried to google for an answer but I've not come up with a definitive answer.
Regards,
Dieter
--
Dieter Vanderelst
2005 Mar 08
1
Multidimensional Scaling (MDS) in R
Hi;
I am working with the similarity matrix below and I would like to plot
a two-dimensional MDS solution such as each point in the plot has a
label.
This is what I did:
data <- read.table('c:/multivariate/mds/colour.txt',header=FALSE)
similarity <- as.dist(data)
distance <- 1-similarity
result.nmds <- nmds(distance)
plot(result.nmds)
(nmds and plot.nmds as defined at
2011 Apr 02
3
Plotting MDS (multidimensional scaling)
Hi,
I just encountered what I thought was strange behavior in MDS. However, it
turned out that the mistake was mine. The lesson learned from my mistake is
that one should plot on a square pane when plotting results of an MDS. Not
doing so can be very misleading. Follow the example of an equilateral
triangle below to see what I mean. I hope this helps others to avoid this
kind of headache.
2005 Jun 22
2
PCA and MDS
Dear All,
I am not familar with R. I want to use PCA (principal components
analysis) and MDS (multidimensional scaling). Can someone tell me
which R package I should use for PCA and MDS? I appreciate your help
in advance.
Ray
2007 Jun 21
1
MDS size limitations
What are the limitations on size of matrix for MDS functions?
steve
--
Steve Antos
Priva-Technologies
847-640-9020 x3114
cell (540)409-1231
[[alternative HTML version deleted]]
2007 Jan 07
3
MDS in 3D
Hi,
I have tried to develop multidimensional scaling for 3D space using PCA without success, yet;-) Is there some application ready in R?
Cheers,
Atte
2001 Oct 12
1
MASS: isoMDS and sammon
If tbl is an object of class 'dist', you can do this:
a <- sammon(tbl, k=3)
But you can't do this:
b <- isoMDS(tbl, k=3)
Wouldn't it be sensible to have identical interfaces to sammon()
and isoMDS() ?
I think all that would be needed is to change this:
isoMDS <- function(d, y=cmdscale(d, 2), maxit=50, trace=TRUE)
{
...into this:
isoMDS <-
2007 Feb 13
4
isoMDS vs. other non-metric non-R routines
Dear useRs,
last week I asked you about a problem related to isoMDS. It turned
out that in my case isoMDS was trapped. Nonetheless, I still have
some problems with other data sets. Therefore I would like to know if
anyone here has experience with how well isoMDS performs in
comparison to other non-metric MDS routines, like Minissa.
I have the feeling that for large data sets with a high
2005 Mar 21
1
How to do such MDS in R
i know cmdscale and isoMDS inR can do classical and non-metric MDS.but i want to konw if there is packages can carry on "individual differences scaling" and "multidimensional analysis og preference"?both method are important one,but i can not find any clue on how to do it using R.
anyone can help?
thank you!
2005 Apr 20
4
results from sammon()
Dear all,
I'm trying to get a two dimensional embedding of some data using different
meythods, among which princomp(), cmds(), sammon() and isoMDS(). I have a
problem with sammon() because the coordinates I get are all equal to NA.
What does it mean? Why the method fails in finding the coordinates? Can I do
anything to get some meaningful results?
Thank you very much
Domenico
2004 Feb 26
2
Multidimensional scaling and distance matrices
Dear All,
I am in the somewhat unfortunate position of having to reproduce the
results previously obtained from (non-metric?) MDS on a "kinship" matrix
using Statistica. A kinship matrix measures affinity between groups, and
has its maximum values on the diagonal.
Apparently, starting with a nxn kinship matrix, all it was needed to do
was to feed it to Statistica flagging that the
2008 Sep 03
1
how to reduce stress value in isoMDS?
I apply isoMDS to my data, but the result turns out to be bad as the stress
value stays around 31! Yeah, 31 ,not 3.1... I don't know if I ignore
something before recall isoMDS.
My code as follow:
m <- read.table("e:/tsdata.txt",header=T,sep=",")
article_number <- ts(m, start = 2004,end=2008, frequency = 1
,names=colnames(m))
2004 Sep 08
8
isoMDS
Dear List:
I have a question regarding an MDS procedure that I am accustomed to
using. I have searched around the archives a bit and the help doc and
still need a little assistance. The package isoMDS is what I need to
perform the non-metric scaling, but I am working with similarity
matrices, not dissimilarities. The question may end up being resolved
simply.
Here is a bit of substantive
2006 Apr 19
3
isoMDS and 0 distances
Hi,
I'm trying to do a non-metric multidimensional scaling using isoMDS.
However, I have some '0' distances in my data, and I'm not sure how to
deal with them. I'd rather not drop rows from the original data, as I am
comparing several datasets (morphology and molecular data) for the same
individuals, and it's interesting to see how much morphological
variation can be
2002 Apr 19
4
Multidimensional scaling
A student of mine wants to use R to do some nonmetric multidimensional
scaling. According to the R FAQ, there's a package called pcurve that
computes multidimensional scaling solutions, but I was not able to locate
it the contrib page (I am a Windows user with R version 1.4.1). Can
anyone tell me whether it is possible to do nonmetric multidimensional
scaling with R, and if so, how?
John
2000 Aug 22
2
various ordinations
Colleagues,
I'm developing a library of functions for community ecology analyses and
have a couple of questions that I've not been able to answer via faqs or
docs.
1) Are there existing functions for:
a) Bray-Curtis (polar) ordination?
b) non-metric multidimensional scaling (NMDS)?
c) canonical correlation analyses (CCA and DCA)?
d) TWINSPAN (doubtful...)?
2) If not,