Hi Jari,

I indeed used isoMDS() of MASS but I also tried with monoMDS() of vegan and
the diagrams I got were almost the same. The stress instead were different,
but I think is correct as you suggested me in the past, these function
calculated stress in different ways.
Thank you very much,

-- 
Gian



2012/3/2 Jari Oksanen <jari.oksanen@oulu.fi>

>
> On 02/03/2012, at 12:08 PM, Gian Maria Niccolò Benucci wrote:
>
> > Hi everyone,
> >
> > I am doing a metaMDS in a sqrt() dataset of 24 samples. The NMDS diagram
> is
> > ok but when I try to see the Shepard diagram I have this result:
> >
> >> stressplot(metaMDS3)
> > Using step-across dissimilarities:
> > Too long or NA distances: 147 out of 276 (53.3%)
> > Stepping across 276 dissimilarities...
> > Connectivity of distance matrix with threshold dissimilarity 1
> > Data are connected
> >
> > Do it means that some data exceed the max dissimilarity (1)? Perhaps
> > because I have some singletons?
> > Thank you very much for helping,
> >
> It looks really much like you used isoMDS engine in metaMDS: isoMDS does
> not save the dissimilarities used in the analysis, and stressplot tries
> reconstruct them. For some reason stressplot() now assumes that you used
> stepacross() also in metaMDS/isoMDS and tries to do the same. If this was
> the only message you did, stressplot() was correct: stressplot should stop
> with error if the reconstructed dissimilarities do not match with your
> ordination result.
>
> If you don't want to use stressplot, you should turn off them already in
> metaMDS. However, I don't recommend you do so if you use isoMDS.
>
> Cheers, Jari Oksanen
> --
> Jari Oksanen, Dept Biology, Univ Oulu, 90014 Finland
> jari.oksanen@oulu.fi, Ph. +358 400 408593, http://cc.oulu.fi/~jarioksa
>
>
>
>

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