similar to: error in sammon (duplicates in configuration)

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 >

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

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: 1: some of the first 2 eigenvalues are

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 solutions (stress 1.74288 after 10 iterations or

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 <-

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

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 the older multiv package either. Is there a problem with the

Hello all, I'm working 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

I've ported F. Murtagh's statlib package "multiv" to R, it can be found in the usual place on CRAN. Contents: bea Bond Energy Algorithm ca Correspondence Analysis supplc Supplementary Columns in Correspondence Analysis supplr Supplementary Rows in Correspondence Analysis flou

I've ported F. Murtagh's statlib package "multiv" to R, it can be found in the usual place on CRAN. Contents: bea Bond Energy Algorithm ca Correspondence Analysis supplc Supplementary Columns in Correspondence Analysis supplr Supplementary Rows in Correspondence Analysis flou

I sent a query to R-Help about the availability of nonmetric multidimensional scaling (MDS) algorithms in R. I would like to thank Tony Rossini, Jonathan Baron, Sundar Dorai-Raj, and Brian Ripley for helpful replies. The gist of the replies is that isoMDS in the MASS library provides Kruskal's method for nonmetric MDS, sammon in the MASS library provides Sammon's nonlinear mapping method

Hi all, I'm running a multidimensional scaling model on data that are first transformed into a similarity matrix using the program daisy in the cluster package. If I already provide the similarity matrix, the plotting routine will give me the variable names on the plot itself. But, it seems that when I use the daisy program to create the similarity matrix, I can't get the program

Hi It is preferable to echo your posts to r-help, you usually get more answers and some definitelly superb to mine. It is also better to start a new mail if your question has nothing to do with original subject "Maura E Monville" <maura.monville at gmail.com> napsal dne 01.10.2007 17:44:43: > Unluckily I do not have the privilege of practising with R all day > long. I

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)

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. In short, cmdscale is returning NaN

Dear R team / R helpers / R users , I downloaded R-1.0.0 to install it but I am currently facing the following problem : Installation of packages. Here is the output I had while trying to install RmSQL : ------------- > R INSTALL -l /software/R-1.0.0/library/ /software/archive/R/RmSQL_0.2-1.tar.gz Installing package `RmSQL' ... libs RmSQL.c:7: msql.h: No such file or directory make:

Hi, Win95 version, trying to build multiv. Following error (no mention in faq etc, but someone may have mentioned it recently). Appreciate any help. ------- Building multiv.dll from multiv.a -------- echo LIBRARY multiv > multiv.def echo EXPORTS >> multiv.def nm multiv.a | sed -n "/^........ [DT] _/s/^........ [BCDRT] _/ /p" >> multiv.def gcc -mdll

Hello, I just have upgraded from Mandrake 8.1 to 8.2 and installed R 1.5.1. I now try to reinstall all the packages but get the following error (for the multiv package for instance) : /usr/bin/ld: cannot find -lreadline collect2: ld returned 1 exit status make: *** [multiv.so] Erreur 1 ERROR: compilation failed for package 'multiv' The readline library is under /lib on my system and I

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

Hello, I am trying to plot selected data points to a preexisting persp plot that satisfies a condition. I used the following statement - text(coords[,1], coords[,2], names(act[which(act > 8.75)]), cex=0.7) But I get all the points labeled, instead of the points that satisfy the condition specified. Is there any way to plot only the points I want? Also can this be done using