[R-sig-eco] Intepreting a plot from a "constrained" NMDS

[Jari Oksanen]

On 8 Dec 2008, at 2:53, stephen sefick wrote:

> A way that may work is use the axis scores as y in a regression- this
> seems like it would let you interpret how the communities are
> distributed in species space.  Just a thought
>

NEVER do this! The rotation is not determined in NMDS. If you rotate  
the NMDS solution you will always have the very same solutios, but the  
correlations with the "axis scores" will change. The whole point of  
having envfit/vectorfit in vegan is that you don't need to calculate  
the correlations with the axes.

The axis rotation is determined in eigenvector ordination, but that  
does not mean that the direction is meaningful. You can see this with  
envfit/vectorfit in unconstrained eigenvector ordination, but also in  
constrained ordination: very rarely the fitted vectors or biplot  
arrows are parallel to axes. Only if axes are parallel to axes (and go  
along the axes), then it would be meaningful to look a the  
relationship of axis and something else.

And indeed, there is no constrained NMDS in vegan. It is unconstrained  
with an interpretation through vector fitting.

cheers, jari oksanen
> Stephen Sefick
>
> On Sat, Dec 6, 2008 at 11:58 AM, Manuel Spínola  
> <mspinola10 at gmail.com> wrote:
>> Dear list members,
>>
>> Is there any reference or document on how to interpret a  
>> "constrained"
>> non-metrical multidimensional scaling using ecological data?  By
>> "constrained" I mean after fitting environmental covariables,  
>> using, for
>> example, the "envfit" function in the vegan package.  Is it  
>> possible to
>> interpret the resulting plot in the same way that a constrained  
>> ordination,
>> for example CCA?
>> Thank you very much in advance.
>> Best,
>>
>> Manuel
>>
>> --
>> Manuel Spínola, Ph.D.
>> Instituto Internacional en Conservación y Manejo de Vida Silvestre
>> Universidad Nacional
>> Apartado 1350-3000
>> Heredia
>> COSTA RICA
>> mspinola at una.ac.cr
>> mspinola10 at gamil.com
>> Teléfono: (506) 2277-3598
>> Fax: (506) 2237-7036
>>
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>
>
>
> -- 
> Stephen Sefick
>
> Let's not spend our time and resources thinking about things that are
> so little or so large that all they really do for us is puff us up and
> make us feel like gods.  We are mammals, and have not exhausted the
> annoying little problems of being mammals.
>
> 								-K. Mullis
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