[R-sig-eco] how to calculate "axis variance" in metaMDS, pakage vegan?

[gabriel singer]

gian,

you may try consecutive MDS-analyses with increasing number of 
dimensions (the parameter k in the isoMDS() or metaMDS() function). then 
plot stress against the number of dimensions and judge similar to a 
scree-plot in PCA. this should tell you how many dimensions to use for 
the MDS and as such also an appropriate associate stress-value.

cheers, gabriel

Gian Maria Niccolò Benucci wrote:
> Okey, really many thanks... So having low Stress value is foundamental, as
> it is as lower as higher the model fit the data, is that right? How can I
> know if my Stress is correct? I mean, if it is enough low to asses that the
> model fit good the samples data shifts into the graph...
> Is there a treshold or something?
> I would appreciate any pdf or kind of reviews on ordination models for
> community ecology data... :)
> Thank you really much!
> Cheers,
>
> Gian
>
>
> 2009/12/1 Gian Maria Niccolò Benucci <gian.benucci at gmail.com>
>
>   
>> Hi Hi there,
>>
>> I am trying to use funcion metaMDS (vegan pakage) for Community Ecology
>> data, but I find no way to calculate the "expressed variance" of the first 2
>> axis? is there a way to do that?
>> Thanks a lot in advance,
>>
>> Gian
>>
>>
>>
>>     
>
>
>   
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-- 
Dr. Gabriel Singer
Department of Freshwater Ecology - University of Vienna
and Wassercluster Lunz Biologische Station GmbH
+43-(0)664-1266747
gabriel.singer at univie.ac.at