From: Gavin Simpson <gavin.simpson_at_ucl.ac.uk>

Date: Mon, 14 Apr 2008 21:47:21 +0100

Date: Mon, 14 Apr 2008 21:47:21 +0100

On Mon, 2008-04-14 at 15:38 -0400, Sarah Goslee wrote:

*> Dimensionality doesn't matter. 2, 3, 14 will all work.
**>
**> What matters is that apparently vegan returns the results in some
**> format other than a straight sites x ordination coordinates matrix,
**> which is what dist expects. You'll need to convert it to one, possibly
**> with as.matrix, or extract the coordinates component from a
**> list, or whatever is appropriate for the output of that function from
*

> that package. The help file should tell you the correct approach

> for getting the nmds configuration itself.

Indeed. It returns a list of class "metaMDS", a list that contains a good deal more information than just the nMDS coordinates.

I'm not sure what you are actually trying to achieve --- is this a correlation between the original distances and the distances on the n-D nMDS axes? If so, this does what you want, using the inbuilt 'dune' data:

example(metaMDS) ## produces 'sol'

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

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. stressplot(sol) produces a Shepard diagram of the ordination. The plot shows two different R2 statistics that might be of use. See ?stressplot for details of their calculation.

**HTH
**
G

*>
**> Sarah
**>
**> On Mon, Apr 14, 2008 at 3:10 PM, stephen sefick <ssefick_at_gmail.com> wrote:
**> > the below is a three dimensional solution
**> >
**> >
**> >
**> > On Mon, Apr 14, 2008 at 3:09 PM, stephen sefick <ssefick_at_gmail.com> wrote:
**> > > cor(x, dist(mds))^2
**> > > Error in dist(mds) : (list) object cannot be coerced to 'double'
**> > >
**> > >
**> > >
**>
*

-- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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_at_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.Received on Mon 14 Apr 2008 - 20:53:28 GMT

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Mon 14 Apr 2008 - 21:30:29 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*