Hi Federico,

I red the paper you mentioned. I think NMDS is a great way to look about
differences among populations of ectomycorrhizal fungi, my research topic.
You know, the only problem is that if you want to understand statistics
completely maybe your need huge mathematics knowledge and computer skills
that often go far away from the biologist's ones. Thst' why I love
r-sig-ecology, it's a way to improve.

Thank you very much and any further comment or advice is appreciated,

Gian




On 3 February 2012 05:33, Federico Tomasetto
<federicotomasetto@hotmail.it>wrote:

>  Hi Gian,
> You may want to have a look at Clarke (1993) Non-parametric multivariate
> analyses of changes in community structure, Australian Journal of Ecology,
> 18: 117-143
> You may get a better idea of NMDS approach.
>
> Good luck
>
> Federico
>
>
> Date: Thu, 2 Feb 2012 19:30:06 +0100
> From: gian.benucci@gmail.com
> To: r-sig-ecology@r-project.org
> Subject: Re: [R-sig-eco] metaMDS result
>
> 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
> >
> >
>
> 	[[alternative HTML version deleted]]
>
>
> _______________________________________________ R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>



*----- Do not print this email unless you really need to. Save paper and
protect the environment! -----*

	[[alternative HTML version deleted]]

