[R-sig-eco] Rotations for PCoA?

[Sarah Goslee]

On Mon, Oct 19, 2009 at 10:12 AM, Jan Hanspach <jan.hanspach at ufz.de> wrote:
> Dear Sarah,
> that sounds good to me, thanks!
>
> Still, I have two more questions:
>
> The variable fitting with vf() does only work when I "dummy-transform" my
> categorical variables. Are the derived correlations then still comparable to
> the Gower distance - PCoA scores where my categorical variables where
> defined as such?

I think it only makes sense with quantitative variables. There's no "direction"
to categorical variables, so how could you fit one? Usually with categorical
variables I plot the ordination with different symbols to denote the class of
the categorical variables, and look at pattern that way.

> Is it reasonable to do more than the correlations with two axes with vf(),
> i.e. after calculating the correlation for the first and the second axis
> doing the same for the third and the forth? I guess this is a very naive
> question, but shouldn't this work for the p-Values since they are calculated
> with a permutation procedure?

You're fitting the variables to that ordination diagram. It's entirely possible
 that the best fit for dimensions 3 and 4 of a four-dimensional fit are not the
same as the best fit of axis 3 and 4 by themselves. So it depends on your
question.

Alternatively, I think the vegan package has a more sophisticated vector-
fitting function.

Sarah

-- 
Sarah Goslee
http://www.functionaldiversity.org