Thank you very much. I am just concerned because I wonder if I used the best method. I have presence/absence data. With isoMDS I can specify "Bray-Curtis" distance method, which is adequate, but I was not sure of the method used by metaMDS. I think that it is Euclidian distance. Can I use it for presence/absence data?
Gavin Simpson wrote: > > 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 > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > ______________________________________________ > [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 > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/Confusion-metaMDS-and-CA-tp25274426p25292096.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ [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 and provide commented, minimal, self-contained, reproducible code.
