[R-sig-eco] simple question about nmds

[Gavin Simpson]

You can use them, but you shouldn't use them individually. Directions in
NMDS aren't like the independent (orthogonal) components of PCA or CA.
You need the distances in *both* (assuming k = 2, *all* for k > 2) NMDS
dimensions to recover the solution. Also directions across and up/down
the NMDS diagram are arbitrary - we can rotate the solution and the
solution remains the same.

What vegan does here is to use the coordinates in NMDS dimensions 1 and
2 (or 1,...,k) as predictors for a single response variable. This is a
bit silly - the models then says that the locations in the ordination
space *influence* the response variable! But if there is such a
relationship, it suggests the converse, that the response varies over
the gradients in the ordination.

G

On Mon, 2013-06-10 at 08:37 +0000, Paolo Piras wrote:
> Hi,
> actually I think you CAN use them (as predictors or response either)
> because, albeit in its unique way, NMDS **IS** a method to summarize a
> highly multidimensional phenomenon.
> best
> paolo
> ________________________________________
> Da: r-sig-ecology-bounces at r-project.org [r-sig-ecology-bounces at r-project.org] per conto di Simone Ruzza [simone.ruzza12 at gmail.com]
> Inviato: lunedì 10 giugno 2013 10.26
> A: r-sig-ecology at r-project.org
> Oggetto: Re: [R-sig-eco] simple question about nmds
> 
> Apolologies, I re-phrase what I have said before: I would be interested
> using the site scores within a multiple regression settings, but the the
> scores a response rather than predictors.
> 
> Best wishes,
> 
> Simone
> 
> 
> On Mon, Jun 10, 2013 at 9:19 AM, Simone Ruzza <simone.ruzza12 at gmail.com>wrote:
> 
> > Dear list,
> >
> > apologies for the total beginner's question. I was wondering whether
> > one can use the site scores of an NMDS ordination to do do further
> > analyses as typically done for other ordination methods, e.g. use the
> > axis scores as predictors in a multiple regression settings. I think
> > it should not be possible, because the aim of NMDS is not to summarize
> > the major patterns of variations withing a multivariate dataset. Do
> > you confirm?
> >
> > thanks in advance,
> >
> > Simone
> >
> 
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-- 
Gavin Simpson, PhD                          [t] +1 306 337 8863
Adjunct Professor, Department of Biology    [f] +1 306 337 2410
Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca
523 Research and Innovation Centre          [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada