R help - Apr 2008 - Vegan R^2 and tau values for metaMDS

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?

-- 
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.

	-K. Mullis

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'
>
>
>
>  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
>  >
>
>
>
>
>
> --
>  Let's not spend our time and resources thinking about things that are
>  so little or so large that all they really do for us is puff us up and
>  make us feel like gods. We are mammals, and have not exhausted the
>  annoying little problems of being mammals.
>
>         -K. Mullis
>


-- 
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.

	-K. Mullis