cmdscale calculates an eigenanalysis of the dissimilarity matrix, and does not employ "stress" per se. Rather, it attempts to maximize variability along axes.
If you call the the cmdscale() function with "eig=TRUE" it returns a list object with the coordinates called "points" and the eigenvalues called "eig". Accordingly, if you have an object returned from cmdscale you can look at the dimensionality of the solution with > x <- cmdscale(dissim.matrix,eig=TRUE) > barplot(x$eig) If you really want "stress" you should use the isoMDS() function from MASS which performs nonmetric multi-dimensional scaling, and does directly employ stress. You might also want to look at functions metaMDS in package vegan, and nmds in package labdsv. There is a page at http://ecology.msu.montana.edu/labdsv/R/lab7/lab7.html and http://ecology.msu.montana.edu/labdsv/R/lab8/lab8.html that attempts to explain this. Dave R. Michelle DePrenger-Levin wrote: > 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 programs may test stress as part of the algorithm as opposed to > cmdscale() which allows us to chose the number of dimensions. Do we need > to just code in a computation of stress? > > Thanks, > Michelle > > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ David W. Roberts office 406-994-4548 Professor and Head FAX 406-994-3190 Department of Ecology email [EMAIL PROTECTED] Montana State University Bozeman, MT 59717-3460 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
