> Yes, apparently I am having trouble reading today! I saw "Principal > Coordinates Analysis" on the MDS wikipedia page, and my brain interpreted it > as "Principal Components Analysis", and I went in the completely wrong > direction. Sorry about that.
Classical MDS is basically the same as PCA. It embeds data points in a sufficiently high-dimensional space to reproduce the distance matrix and then performs a truncated PCA to the required number of dimensions. However, iterative non-metric MDS algorithms will usually give much better results. I'm afraid I can't offer any help wrt. to the Perl/R bridge. In some of my own software, I use the Expect module to communicate interactively with Perl (which is indeed very slow). I tried Statistics::R once, but that was even slower. The RSPerl interface is much faster, but with every OS or R upgrade I had to spend several days hacking it to get it to work again, and haven't been able to do so on Mac OS X for the last three or four years. Jean, in your application the bottleneck will be to upload the distance matrix to R and (perhaps less critically) get back the MDS vectors, right? If you're willing to put in the extra work, you can speed up communication a lot by exchanging data through external files. Text files are quite fine (using scan()/write() in R), but you could also try a SQLite database, which has excellent support in both R and Perl. Best regards, Stefan Evert [ [email protected] | www.stefan-evert.de ] _______________________________________________ Perldl mailing list [email protected] http://mailman.jach.hawaii.edu/mailman/listinfo/perldl
