similar to: error running sammon

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

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

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

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

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 <-

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 >

Hello R-Masters, I have a list 's' with three elements, as shown below. I want to recode a.a, a.a2, and a.a3 to NA if the value in a.a is less than 3. I reivewed my Modern Applied Statistic Book, the online help and did some searching of R-help on the internet. I explored unlist and as.list.data.frame in an attempt to isolate the third element of the list s, but this was not helpful.

I have been wrestling with this function for quite a while, and am not making headway. 1) I want to apply a function to the following columns of a dataframe: myfunction. <- apply(ph5028[,c(83:107)],2,function(x) ... 2) Within each of the above columns there is a single numeric code, 1, 2 or 3 or an NA. 3) My goal is to determine the percent of time each person used a 2 code. So if a person

This is a "long" way; i.e., not necessarily efficient: > qs2 [1] 2 1 1 4 4 4 1 1 1 4 2 4 3 1 4 3 3 2 4 3 > qs9 [1] 4 4 1 3 4 3 1 3 1 4 1 2 3 3 4 4 1 4 2 3 > decision <- function(a, b) { + if (a == 1 || b == 1) return(1) + if (a == 2 || b == 2) return(2) + if (a == 3 || b == 3) return(3) + if (a == 4 || b == 4) return(4) + NA + } > mapply(decision,

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 R experts, The following problem outstrips my current programming knowledge. I have a dataframe with two fields that looks like the following: ID Contract 01 1 01 1 02 2 02 3 02 1 03 2 03 2 03 2 03 1 03 1 03 1 etc... I would like to end up with a dataframe with one row per ID where the value in the contract field would be the

Hello, I have spent considerable time trying to figure out that which I am about to describe. This included searching Help, consulting my various R books, and trail and (always) error. I have been assuming I would need to use a loop (looping over columns) but perhaps and apply function would do the trick. I have unsuccessfully tried both. A scaled down version of my situation is as follows:

Dear R Masters, I have searched high and low (the help archives and my various R reference material and help files) for a solution to what appears to me to be quite a simple problem. In the following syntax, variable n10 has three levels. I would like the symbols that appear in the graph for these three levels to be different colors. The best I have been able to do is to have the Key display

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 both the matrices for duplicate values using/

I will be involved with an analysis based on a file that will be roughly 25 meg. Assuming I have enough memory, is their any limitations to using R on a file this large. Thank you, Gregory L. Blevins Vice President, Partner The Market Solutions Group, Inc. gblevins at marketsolutionsgroup.com Office phone: 612 392-3163 Cell phone: 612 251-0232

Hello, In the Hmisc package, functions describe and summarize can explicitly take a weight variable. My question is can a weight variable be applied when using 'summary'? For example, using...summary(var1 ~ var2) I would like to weight the data by var 3 (same length). Is this possible? Thanks a lot. Greg Blevins The Market Solutions Group, Inc.

Hello, I have a data frame that has three fields. Resp# ActCode ProdUsed 100 3 2 100 3 2 100 4 3 100 4 3 101 3 6 102 2 1 102 3 1 103 5 1 103 5 1 103

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:

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

Okay, been working with tripack, seems the most mature package for this. Got it to work well with their test data set - data(tritest). When i tried random numbers to explore further, i am getting some results that don't reconcile. example run this: library(tripack) y <- runif(100) x <- runif(100) vm <- voronoi.mosaic(x,y) plot(vm) par(new=T) plot(x,y,col='blue') when