On Thu, 2009-09-03 at 04:49 -0700, swertie wrote: > Hello, I read a lot about ordination, but I am still confused... I have data > on species presence/absence for 8 different sites and I would like to > represent my species and the sites on an ordination plot to see if some > species are associated with specific sites. I used metaMDS function, which > displays both sites and species and it seems to work well. However why are > most people using CA instead of non metric multidimensional scaling? Thank > you
Inertia ;-) It's what they were taught, because that's what their supervisors were taught etc. CA has a long history within ecological circles and most people will be familiar with it. nMDS is an iterative algorithm that may nor may not converge to "the" solution. There may not be "one" solution but rather many equally good ones. It takes a lot more effort (well, if you are outside of R) to run nMDS properly and check you're not converging to a local solution. There are lots of reasons. Why are interested in this; are you concerned you've done something wrong or inappropriate with your data? HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
