search for: 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

I'm not sure this list is the right place for this thing. I noticed some erratic behaviour in sammon(). Running sammon on two nearly identical sets of data results in very different results. Below is an example. I create an initial configuration with cmdscale() and store it into 'vec1'. I write this to file, and read it back in again to 'vec2'. According to cor() on the three colum...

Hi list, not really a problem to solve but a strange unwanted behavior (at least I do not like it): I'm loading library(multiv) to use sammon. Later I load library(MASS) which tells me that sammon is masked now, because there is also a MASS version of sammon. Since I believe that the MASS version is at least as good as the multiv version, I would also use the MASS version, but help(sammon) still gives the help page for multiv's sam...

Hello, I am inputing a 17 x 17 symetric matrix to sammon. The matrix is a co-occurance matrix with no missing data. If this is at all relevant, running hclust on this matrix works. > samx <- sammon(q23axproduct) I receive the following error: Error in sammon(q23axproduct) : initial configuration must be complete In addition: Warning messages:...

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. 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:...

When I try to run the "sammon" function of the multiv package, I always get this error message: Error in as.vector(dist(a)) : couldn't find function "dist" It happens even with example(sammon). I am running R 1.5.0 on Win98 and I have still installed R 1.4.1 but it doesn't work on the old R version with...

Hello, I have a data set on which I run the sammon algorithm as follows: library(MASS) data = read.table('problemforr.dat') y = cmdscale(data, add=TRUE) s = sammon(data, y$points) (In case it should be relevant, I make the data available at http://idi.ntnu.no/~edsberg/problemforr.dat) With R 2.2.1 on Debian Sid I always get one of two so...

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: i...

...rking on a project that uses a SOM to generate feature maps from image data. Each image is a 100x75 pixels and RGBA, so 30,000 elements per image. I wanted to observe the structure of the pixel by pixel euclidean distance (where each image is a point in 30,000 dimensional space) of my image data. Sammon's projection seems appropriate for this, though I'm a bit concerned 400 images with 30,000 dimensions make be too large for the algo. I'm planning on only publishing B+W images, so it is possible I could throw away the colour channels to make each image 7500 dimensions. Also I'm no...

Dear members of R-mailing list, I am using Sammon's Non-Linear Mapping in R as implemented in MASS package. I have two distance matrices (attached with the mail). For the first (/5HT_MACCS_dist.dat/) /sammon()/ works fine but for the second (/5HT_TGT_dist.dat/), I get an error message "configuration has duplicates". I checked bot...

...t; > At 11:46 PM -0400 7/18/06, zubin wrote: > > >Hello, looking to draw a voronoi tessellations in R - can anyone > > >recommend a package that has tackled this? > > > > > >some background: > > > > > >i have a economic data set and created a sammons projection, like to now > > >overlay a voronoi tessellation over the sammons 2-D solution for a slick > > >visual, and potentially color each tessellation element based on a metric. > > > > > >home.u <- unique(home1) > > >home.dist <- dist(home.u)...

Hello all, I'm using R1.7.1 on Linux, generating sammon-optimized MDS plots from distance matrices. This is a calculation I run routinely, often on sample sets of up to 100 samples. This time, with three samples, the sammon function returned an error (shown below), which I tracked down to the cmdscale function it uses to find a starting configuration. I...

...6218477 0.118812936 cmdscale(test) [,1] [,2] V1 NaN NaN V2 NaN NaN V3 NaN NaN V4 NaN NaN V5 NaN NaN Warning messages: 1: some of the first 2 eigenvalues are < 0 in: cmdscale(test) 2: NaNs produced in: sqrt(ev) > isoMDS(test) Error in isoMDS(test) : NAs/Infs not allowed in d > sammon(test) Error in sammon(test) : initial configuration must be complete In addition: Warning messages: 1: some of the first 2 eigenvalues are < 0 in: cmdscale(d, k) 2: NaNs produced in: sqrt(ev) The colleagues who used the above routine are unable to tell me with certainty whether Statistica used...

...bs g77 -fPIC -g -O2 -c bea.f -o bea.o g77 -fPIC -g -O2 -c ca.f -o ca.o g77 -fPIC -g -O2 -c hc.f -o hc.o g77 -fPIC -g -O2 -c hcmovie.f -o hcmovie.o g77 -fPIC -g -O2 -c members.f -o members.o g77 -fPIC -g -O2 -c partition.f -o partition.o g77 -fPIC -g -O2 -c pca.f -o pca.o g77 -fPIC -g -O2 -c sammon.f -o sammon.o gcc -shared -o /software/R-1.0.0/library/multiv/libs/multiv.so bea.o ca.o hc.o hcmovie.o members.o partition.o pca.o sammon.o -L/usr/lib/gcc-lib/i486-linux/egcs-2.91.66 -L/usr/i486-linux/lib -lg2c -lm R help >>> Building/Updating help pages for package `multiv' F...

Dear David, you asked this question a while ago on the R mailing list and got no answer. I have the same problem and was wondering if you had found a solution Cheers Loic Loic Thibaut, PhD candidate, ARC Centre of Excellence for Coral Reef Studies, School of Marine Biology, James Cook University, Townsville, Qld, 4811, Australia. Tel + 61 747 815 735, Fax: + 61 747 251 570, email:

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 Ka...

...-file,multiv.b -s -o multiv.dll multiv.a - L../../../ gnuwin32 -lR -lf2c dlltool -k --as as --dllname multiv.dll --base-file multiv.b -- output-exp mul tiv.e --def multiv.def gcc -mdll -Wl,--base-file,multiv.b -s -o multiv.dll multiv.e multiv.a -L ../../../gnuwin32 -lR -lf2c multiv.a(sammon.o)(.text+0x495):sammon.f: undefined reference to `realpr_' make.exe[2]: *** [multiv.dll] Error 1 make.exe[2]: Leaving directory `c:/R-0.62.3/src/library/multiv/src' make.exe[1]: *** [src/multiv.dll] Error 2 make.exe[1]: Leaving directory `c:/R-0.62.3/src/library/multiv' make.exe: *** [p...

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 ! -- View this message in context: http://n4.nabble.com/math-function-MDS-method-tp1008294p1008294.html Sent from the R help mailing list archive at Nabble.com.

I am running dovecot 0.99. Everything works great; however, now I am looking at several different tools to convert mbox to Maildir. It seems the tools, mb2md.pl, perfect_maildir.pl, and others all do what they claim; however, when the messages are converted and they are stored in Maildir/cur, the email clients download these messages as new. This typically wouldn't be a problem;

...st-math -fno-strength-reduce -c partition.f -o partition.o g77 -fPIC -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c pca.f -o pca.o g77 -fPIC -O3 -fomit-frame-pointer -pipe -mcpu=pentiumpro -march=i586 -fno-fast-math -fno-strength-reduce -c sammon.f -o sammon.o gcc -shared -o multiv.so bea.o ca.o hc.o hcmovie.o members.o partition.o pca.o sammon.o -L/lib -L/lib -L/usr/local/lib -L/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.0.4 -L/usr/lib/gcc-lib/i586-mandrake-linux-gnu/3.0.4/../../.. -lreadline -ldl -lncurses -lg2c-pic -lm -L/usr/lib/R/...