similar to: enhanced multidimensional scaling?

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

Dear helpRs Does anyone have an elegant way of doing the following: For a given numeric vector, e.g. vec <- c(3,2,6,4,7) Create a series of vectors where all but 1 of the values are replaced by 0's, e.g. vec.a <- c(3,0,0,0,0) vec.b <- c(0,2,0,0,0) vec.c <- c(0,0,6,0,0) vec.d <- c(0,0,0,4,0) vec.e <- c(0,0,0,0,7) I have looked at `replace', but can't think of a

Dear R community Have just recently got back into R after a long break and have been amazed at how much it has grown, and how active the list is! Thank you so much to all those who contribute to this amazing project. My question: I am trying to calculate Mahalanobis distances for a matrix called "fgmatrix" >dim(fgmatrix) [1] 76 15 >fg.cov <- cov.wt(fgmatrix)

Hi R users Does anyone out there have a better/quicker way of adding a factor column to a data frame based on levels of another factor? I have a (large) data frame consisting of records for individual plants, each represented by a unique ID number. The species of each plant is indicated in the column "species", which is a factor column with many different levels (species). There are

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 again I'm trying to put error bars onto a barplot. I've tried something that Bill Simpson suggested a while ago, ie: x<-c(1,2,3,4,5) y<-c(1.1, 2.3, 3.0, 3.9, 5.1) ucl<-c(1.3, 2.4, 3.5, 4.1, 5.3) lcl<-c(.9, 1.8, 2.7, 3.8, 5.0) plot(x,y, ylim=range(c(lcl,ucl))) arrows(x,ucl,x,lcl,length=.05,angle=90,code=3) #or segments(x,ucl,x,lcl) but I can't get it to work on a

Hi everyone I'm trying to generate a vector of the form a <- c(1,2,3,4,1,2,3,1,2,1) where n = 5 in a general way, where n can be any positive integer. I've run out of ideas. Does anyone have any suggestions? Thanks Karen Karen Kotschy Centre for Water in the Environment University of the Witwatersrand Johannesburg Tel: 011 716-2218

Hi everyone I'm trying to generate a vector of the form a <- c(1,2,3,4,1,2,3,1,2,1) where n = 5 in a general way, where n can be any positive integer. I've run out of ideas. Does anyone have any suggestions? Thanks Karen Karen Kotschy Centre for Water in the Environment University of the Witwatersrand Johannesburg Tel: 011 716-2218

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

Another question: Is it possible to move R objects from one directory to another without copying the whole .RData and .Rhistory files? (I'm running under Linux) Thanks Karen Kotschy Centre for Water in the Environment University of the Witwatersrand Johannesburg Tel: 011 716-2218 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read

Dear help list Does anybody know if it is possible to somehow tell R to let LaTeX handle the fonts for postscript plots produced by R? It is for a thesis and I have MANY figures. These are created by R scripts dynamically as the document is compiled, using the Make system. I see that I can `manually' specify the font family each time I call the postscript device, but I am looking for a

Hi Could somebody please explain the following to me: If x is a 10x10 matrix, typing x[3] prints all 10 values of column 3, although the length of the vector =1. Why? x[,3] and x[[3]] both give all 10 values of column 3, length=10. What is the difference between these two, actually? Thanks Karen Kotschy Centre for Water in the Environment Department of Botany University of the Witwatersrand

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.

Hello, We are trying to find a function to compute "stress" in our multidimensional scaling analysis of a dissimilarity matrix. We've used "dist()" to create the matrix and "cmdscale()" for the scaling. In order to determine the number of dimensions we would like to plot stress vs. dimensions. However, we cannot find a pre-made command. It seems that other

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

Dear R users, I am using Sweave. I would like to use the width option for the graphics : \begin{figure}[h!] \centering \includegraphics[width=0.7\textwidth]{x} \end{figure} How do I get this ? Thank you very much, Randall [[alternative HTML version deleted]]

Sorry to bother you kind folks again with my questions. I am trying to learn as much as I can about all this, and I will admit that I don't have the proper background, but I hope that someone can at least point me in the correct direction. I have created a test matrix for what I want to do: s1 s2 s3 s4 s5 s1 10 5 0 8 7 s2 5 10 0 0 5 s3 0 0 10 0 0 s4 8 0 0 10 0 s5 7

Does anyone know if an R plug-in exists for the GIS package ArcView running under Windows98 or NT? I know such a plug-in is available for S-PLUS. Thanks Karen Kotschy Centre for Water in the Environment Department of Botany University of the Witwatersrand Johannesburg South Africa Tel : +2911 716-2218 Postal address: P/Bag 3 P.O Wits 2050 South Africa

Dear R developers and users! I have calculated metric MDS by cmdscale from matrix of distances (dissimilarities). I would like to ask you how can I estimate how well this new mapping represents characteristic features of my data set? Thank you for any suggestions. Best, tomek

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