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

[Jari Oksanen]

On 1/12/09 11:12 AM, "Gian Maria Niccolò Benucci" <gian.benucci at gmail.com>
wrote:

> 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,

Why nobody asks how to calculate the non-linear stress of PCA or RDA?
Non-linear stress would make just as little sense for PCA or RDA as the axis
variance makes for NMDS. The axis variance is purely a measure of PCA family
of methods (even CA family has a bit different measure), and there is no
meaningful way of calculating "expressed variance" for NMDS axes (and
indeed, a separate axis is not meaningful for NMDS: it is the configuration
spanned by all axes together that makes sense).

Cheers, Jari Oksanen