Dear Jari,

Thank you a lot to your precious advices. I am alarmed because the
stressplot is indeed a bit strange. Dots are distribute along a line that
is almost parallel to X axis (Observed Dissimilarity) and at the end they
go up drawing a long pile of dots that is otherwise parallel to the Y axis
(Ordination distance). The Non-metric fit R2 is 0.99 and the linear one is
0.995.
Is I red well an accurate representation should be that dots must follor
the diagonal f unction where x=y
It is possible that is because my two datasets of samples share to few taxa
one with the other?

Thank you very much,

G.






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

>
> On 02/02/2012, at 19:43 PM, Gian Maria Niccolò Benucci wrote:
>
> > Hi Members,
> >
> > I tried to use a metaMDS to explore my two fungal communities data.
> > That's the result:
> >
> > Call:
> > metaMDS(comm = species.data_log, distance = "bray", k = 2, trymax =
> > 200,      autotransform = F)
> >
> > global Multidimensional Scaling using monoMDS
> >
> > Data:     species.data_log
> > Distance: bray
> >
> > Dimensions: 2
> > Stress:     0.0369308
> > Stress type 1, weak ties
> > Two convergent solutions found after 13 tries
> > Scaling: centring, PC rotation, halfchange scaling
> > Species: expanded scores based on Œspecies.data_log‚
> >
> > species matrix was log10() trasformed before NMDS (otherwise I got really
> > similar result with sqrt() trasfromed data)
> >
> > I wonder if the stress is too low according to dune examples and maybe
> > there is something not working in my data or code...
> >
> > thanks you for helping,
> >
>
> Not many people are worried for a low stress. NB, the stress is taken
> directly from the NMDS engine, and the current monoMDS() uses different
> stress scaling than the older isoMDS() engine: 0.037 of monoMDS corresponds
> to 3.7 of isoMDS. This is a low stress, but not directly alarming. Perhaps
> your data are easy and really two-dimensional (e.g., have some few strongly
> dominant taxa).
>
> Looking at the stressplot() graphs may help in seeing if there is
> something strange.
>
> 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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