Thanks a lot !

At the end I found that the problem was in the data input. Once I normilized
the data input to use the chord distance as measure of dissimilarity

gaps_flor_norm<-decostand(gaps_flor, "norm"), then I run the nMDS several
times comparing them through procrustes

plot(procrustes(gap_flor_NMDS1, gap_flor_NMDS2))

Can not say more,
Thanks a lot for your response and all your work,

Cheers,


Rodrigo Vargas G.
-----------------------------------------
Silviculture Institute
Freiburg University
+49 0761 203 8621
Tennenbacher str 4 Freiburg ibr


2011/9/28 Jari Oksanen [via R] <ml-node+s789695n3850347h36@n4.nabble.com>

> rodrock <rodrigo.vargasgaete <at> gmail.com> writes:
>
>
> > I am using the envfit function over an ordination of floristic data.
> >
> > The problem is that every time that I run it changes the results.
> Sometimes
> > dramatically, selecting variables that the first time were not
> significant.
> > I do not get what could be the problem or if is normal given the
> > permutations are different.
> >
> > # the NMDS ordination
> >
> > gap_flor_NMDS_chord <- metaMDS(gaps_flor, distance = "euclid", k = 2,
> trymax
> > = 20, autotransform =TRUE,
> > noshare = 0.1, wascores = TRUE, expand = TRUE, trace = 1,
> > plot = FALSE, old.wa = FALSE, zerodist = "add")
> >
>
> > # the  Envfit calculation
> > exp_flor1 <- envfit(gap_flor_NMDS_chord, explain1, permu = 999, na.rm=T)
>
> >
>
> Rodrigo,
>
> Do you re-run your NMDS when the envfit results change? The results of NMDS
> may
> change between two runs. You should first check that the NMDS results are
> nearly
> identical. This you can do with procrustes() function in vegan:
>
> plot(procrustes(gap_flor_NMDS1, gap_flor_NMDS2))
>
> where the arguments gap_flor_NMDS1 and gap_flor_NMDS2 are two NMDS results
> that
> gave you different envfit results. Use of plot() above helps you to avoid
> looking at tiny differences in a numeric results: if you cannot see a
> difference
> in the procrustes plot, there is no difference you need to worry about.
> Only
> worry about envfit differences if the NMDS results are practically
> identical.
>
> I'm surprised if metaMDS didn't issue any warning on the combination of
> arguments you used in metaMDS: having no.share > 0 and distance = "euclid"
> sounds dubious, and I have tried to catch those cases and issue an
> informative
> warning. You could also try higher trymax to get more consistent NMDS
> results.
>
> Cheers, Jari Oksanen
>
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-----
Rodrigo Vargas G.
-----------------------------------------
Silviculture Institute
Freiburg University

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