[R-sig-eco] Rotations for PCoA?

[Jan Hanspach]

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?

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?

Best
Jan

Sarah Goslee wrote:
> It isn't "just like a PCA" but you can use a permutation procedure to fit
> the traits to a 2-dimensional ordination configuration using vf() in the
> ecodist package.
>
> Sarah
>
> On Mon, Oct 19, 2009 at 7:44 AM, Jan Hanspach <jan.hanspach at ufz.de> wrote:
>   
>> Dear all,
>> I have a bunch of plant species and their traits (life span, pollination
>> type, strategy type, association to human disturbance... overall 5
>> categorical and two interval scaled variables). I want to know how the
>> traits are interrelated, e.g. are annual plants predominantly ruderals
>> that grow in habitats strongly disturbed by humans.
>>
>> Therefore I calculated a Gower dissimilarity matrix on the species
>> traits (species=rows, traits=columns; using daisy(), which seems to be
>> appropriate for mixed variable types). With the dissimilartiy matrix I
>> calculate a PCoA using cmdscale and that works fine (beside some
>> negative Eigenvalues).
>>
>> Now, I want to know if  it is possible to get rotations for my traits,
>> like it is calculated for a PCA? So that I can plot my traits within the
>> ordinations space (or give the values in a table).
>> Thanks!
>> Jan
>>
>>     
>
>   

-- 
Jan Hanspach
Doktorand / Department Biozönoseforschung
PhD-Student / Department of Community Ecology

Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Helmholtz Centre for Environmental Research - UFZ
Theodor-Lieser-Str. 4 / 06120 Halle (Saale) / Germany

jan.hanspach at ufz.de / http://www.ufz.de
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