Vegan R^2 and tau values for metaMDS

cor(x, dist(mds))^2
 Error in dist(mds) : (list) object cannot be coerced to 'double'



 On Mon, Apr 14, 2008 at 2:40 PM, Sarah Goslee <sarah.goslee at gmail.com> wrote:

 > The nmds() function in ecodist does calculate R^2, but if you're already
 >  using vegan it's easy enough to calculate for any particular NMDS
 >  result.
 >
 >  The easiest way, given original data dmat and nmds solution nmdsconf is to
 >  take
 >  cor(dmat, dist(nmdsconf))^2
 >
 >  If you try ecodist, there's a minor bug in the R^2 code, and it gives
 >  a sequence of
 >  integers at the beginning of the vector. This should be deleted, but
 >  the remaining
 >  numbers are correct. This will be fixed in the next version.
 >
 >  Sarah
 >
 >
 >
 >  On Mon, Apr 14, 2008 at 2:30 PM, stephen sefick <ssefick at gmail.com> wrote:

 >  > I am using the function metaMDS with jaccard distances to ordinate a
 >  >  set of constituent by site matrix.  I can post this data if it would
 >  >  be helpful, but it is large to include in an email.  I can also
 >  >  provide reproducable code if necessary.  I would like to get an R^2
 >  >  value for the axes of the ordination configuration that I get with
 >  >  metaMDS in the vegan package is there a way to do this- is it stored
 >  >  in some object returned by the function that I am unaware of- or is
 >  >  there another function inside of vegan or elsewhere- that I can use?
 >  >  I have seen mention of ecodist function nmds having an R^2 would this
 >  >  be the place to go?
 >  >

 >
 >
 >  --
 >  Sarah Goslee
 >  http://www.functionaldiversity.org
 >

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