On Mon, 2008-04-14 at 17:00 -0400, Sarah Goslee wrote: > On Mon, Apr 14, 2008 at 4:47 PM, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > > Note that the default is to produce a bray-curtis dissimilarity matrix > > from the input species data. As such, I reproduce this dissimilarity > > matrix as arg 1 to cor and then take the Euclidean distances of the > > coordinates on nMDS axes 1:2 (this example is a 2D solution but scales > > to n-dimensions) as the second argument to cor: > > > > cor(vegdist(dune), dist(sol$points))^2 > > > > In this example, the "R^2" is 0.899222 > > > > If you already have jaccard for your species data, then substitute this > > for 'vegdist(dune)' and sol for whatever your nMDS object is called. > > Good point. I forgot to clarify that you should use the same dissimilarity > metric for your original data that was used in constructing the ordination. > Euclidean distances should be used for the NMDS configuration, though.
Yes - here I use dist(sol$points) which defaults to Euclidean distances. > > > However, this assumes a linear relationship between the original > > distances and the nMDS distances. The relationship need not be linear, > > just monotonic if I recall the details correctly. > > If you (the original querent) are interested in the monotonic rather than > strictly linear relationship, you could use the "spearman" option to > cor(). I forgot about that, thanks for the reminder Sarah. This correlation (using method = "spearman") is different to the ones used in stressplot. I peeked inside the code of that function and the following should reproduce the linear fit R^2 shows on the plot produced by stressplot: ## continuing the example from my previous email require(MASS) # for Shepard() shep <- Shepard(vegdist(dune), sol$points) cor(shep$y, shep$yf)^2 The last line yields = 0.9250712. The non-metric fit is 1 - stress and this can be calculated using: 1 - (sum((shep$y - shep$yf)^2)/sum(shep$y^2)) So now you have 4 different R^2 values to choose from Stephen... HTH G > > Sarah > -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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.
