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
On Wed, 2005-04-20 at 10:35 +0200, Domenico Cozzetto wrote:> 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?I'm sorry, but I can't reproduce your problem. I have tried hard with different tricks, but sammon() always gives good numeric results, or reports on the problems with the input and refuses to continue. For a starter: which sammon did you use. I think there may be three or four implementations in R with that name alone (and some variants may be names differently). I used sammon() in MASS (Venables & Ripley), and could not get NA. You need to give more details if you want to get help. cheers, jari oksanen -- Jari Oksanen <jarioksa at sun3.oulu.fi>
On Wed, 20 Apr 2005, Domenico Cozzetto wrote:> I'm trying to get a two dimensional embedding of some data using different > meythods, among which princomp(), cmds(), sammon() and isoMDS(). I have aWhat is cmds()? There is cmdscale(), but if you have the data (needed to use PCA) then classical scaling and PCA are the same thing.> 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?We have no idea. Please read the posting guide and supply some useful information and preferably a reproducible example. One issue is which package sammon() came from. One possible hint if this is sammon() from MASS is to use a different starting configuration.> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Thanks for the attention paid to my rpoblem. Please find enclosed the matrix with my dissimilarities. This is the only case in which sammon(), from the MASS package, gives me this kind of problems. I'm using the implementation of sammon provided by the package MASS and the starting configuration is the default one. Here are the values for the other actual parameters niter = 100, trace = FALSE, magic = 0.2, tol = 1e-4 Domenico> > > -----Messaggio originale----- > > Da: Jari Oksanen [mailto:jarioksa at sun3.oulu.fi] > > Inviato: mercoled?? 20 aprile 2005 11.53 > > A: Domenico Cozzetto > > Cc: R-News > > Oggetto: Re: [R] results from sammon() > > > > > > On Wed, 2005-04-20 at 10:35 +0200, Domenico Cozzetto wrote: > > > 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? > > > > I'm sorry, but I can't reproduce your problem. I have tried hard with > > different tricks, but sammon() always gives good numeric results, or > > reports on the problems with the input and refuses to continue. For a > > starter: which sammon did you use. I think there may be three or four > > implementations in R with that name alone (and some variants may be > > names differently). I used sammon() in MASS (Venables & Ripley), and > > could not get NA. You need to give more details if you want to get help. > > > > cheers, jari oksanen > > -- > > Jari Oksanen <jarioksa at sun3.oulu.fi> > >-------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: diss.txt Url: https://stat.ethz.ch/pipermail/r-help/attachments/20050420/ddedca37/diss.txt
Dear all, I have a matrix of dissimilarities and I'd like to get a 2d embedding. I'm not an expert of these techniques, so I'm a bit confused... Furthermore I was not able to find on the web any satisfactory tutorial. So even though this may be not the most appropriate place to discuss about this issues, I'd be very grateful to those who will reply. My first question is: Do I need an initial embedding of my data before applying PCA through the methods princomp or prcomp in the stats package? What does it mean that PCA and classical scaling are equivalent? And where can I find a proof of this fact? If this is true, I should get the same results by applying the methods prcomp() or cmdscale() in stats. If it may help, use the dissimilarities in the attached "diss.tab" file. Thank you very much in advance for your attention. Domenico