Re: [R] Vegan R^2 and tau values for metaMDS

From: stephen sefick <ssefick_at_gmail.com>
Date: Mon, 14 Apr 2008 15:10:54 -0400

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

______________________________________________
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 - 22:50:34 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 - 23:30:29 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.

list of date sections of archive