[R-sig-eco] Understanding NMS (non-metric multidimensional scaling) outputs

[Gavin Simpson]

On Tue, 2010-12-14 at 01:28 +0100, gian.benucci at gmail.com wrote:
> Thank you very much Roman. I will check for papers you suggested me  
> for sure. Sometimes, maybe especially for me that I am not deep inside  
> statistics yet, is simple to get outputs (with R) but is extremely  
> difficult to understand what they mean and comunicate about the  
> data... i.g. In a NMDS ordination how to comment distances of species  
> in relation to sample points?
> Thank you all for patience,

Then perhaps the "Introduction to ordination in vegan" vignette that
comes with vegan, and which you can download form CRAN [1], might be of
use?

Species points on nMDS plots in vegan are position at the weighted
averages of the site scores, with weights being the species abundance in
a given site. As such, species points will be located closer to site
points in which that species is most abundant.

HTH

G

[1] http://cran.r-project.org/web/packages/vegan/index.html

> G.
> 
> 
> 
> Il giorno 12 Dec 2010, alle ore 22:01, Roman Luštrik <roman.lustrik at gmail.co 
> m> ha scritto:
> 
> > There are a few pages about NMDS theory (for a lay person) in Zuur  
> > et al's Analysing ecological data as well as some examples with R  
> > code (I would have to check the highstats page, though). The chapter  
> > that introduces NMDS talks about stress value, too. You can also  
> > check out Clarke & Warwicks's Changes in marine communities: An  
> > approach to statistical analysis and interpretation (PRIMER-E  
> > manual). No R code, though (but can be used to understand NMDS,  
> > among other methods).
> >
> > Cheers,
> > Roman
> >
> >
> >
> > 2010/12/12 Gian Maria Niccolò Benucci <gian.benucci at gmail.com>
> > Hi everybody,
> >
> > I was wondering if exist "something" where to read about NMS  
> > outputs. In
> > particular about commenting a generated NMS ordination graph.
> > Thank you very very much in advance,
> >
> > Gian
> >
> >        [[alternative HTML version deleted]]
> >
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> >
> >
> >
> > -- 
> > In God we trust, all others bring data.
> 
> 	[[alternative HTML version deleted]]
> 
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