how to calculate "axis variance" in metaMDS, pakage vegan?
Maria Dulce Subida <mdsubida at icman.csic.es> writes:
Nevertheless you should take into account that the stress usually increases with increasing quantity of data.
I think this is the key point. The stress will always increase with increasing data, as it is harder to capture the information content of 10 variables on 2 axes than it is to capture the information content of 3 variables on 2 axes. Similarly, stress will always go down as you increase the number of axes you use, for the same reason. So I'm not convinced that any of these 'rules of thumb' (i.e., > 0.3 is a 'bad' ordination) really make much sense. Please correct me if I'm wrong! Cheers, Tyler