[R-sig-eco] question concerning nmds.min

[Sarah Goslee]

Are you using ecodist?

If so, you need to look at iris.nmds to get the stress and the
r2.

min(iris.nmds$stress)
iris.nmds$r2[which.min(iris.nmds$stress)]

The advantage of nmds.min() is that it lets you choose
a particular dimension solution rather than the lowest
available.

For your example, the same thing can be achieved with
iris.nmds$conf[[which.min(iris.nmds$stress)]]

Sarah

2012/2/2 Gian Maria Niccolò Benucci <gian.benucci at gmail.com>:
> Hi all,
>
> I am trying to run a nmds with function nmds()
> Once I run the following code I wonder how to look to the R2 and stress
> value of the chosen configuration.
>
> iris.nmds <- nmds(iris.md, mindim=2, maxdim=2, nits=50)
>
> iris.nmin <- nmds.min(iris.nmds)
>
>
> Which among the 50 configuration the functions chose?
> How to look to its stress and R2 values?
>
>
> If I type iris.nmin I only got the X1 and X2 coordinates...
>
>
> Thanks in advance,
>
> Gian
>

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