Hi and many thanks for your replies,

I have had a look at capscale() and betadisper(), but as you said, this
could only provide "residuals" in fhe form of dissimilarities, and what I
actually would like to have are true residuals, negative and positive.

I have also looked into ecodist, but I did not find anything that could
help.

Cheers,

Alicia Valdés


2014-03-18 15:06 GMT+01:00 Jari Oksanen <jari.oksanen@oulu.fi>:

>
> On 18/03/2014, at 15:23 PM, Eduard Szöcs wrote:
>
> > Dear Alicia and Jari,
> >
> > just a thought:
> > Couldn't be capscale or betadisper be used for this?
> > - To obtain the distances to the group centroid?
> >
> > But than: How to convert this from distances to abundances?
> >
> You can *almost* do this with capscale(), but not quite: for semimetric
> dissimilarities the results are not identical with capscale (they are
> identical with metric distances). The capscale() function also has fitted()
> and residuals() methods that both return dissimilarities. Now it also
> depends on what you mean with "residuals". The capscale() interpretation
> and the one I had on my mind is that
>
> 1) adonis(fitted(adonis(y ~ model)) ~ model) should give distances where
> the fitted part of adonis(y ~model) and the residual variation part should
> be null, and
>
> 2) adonis(residuals(adonis(y ~model) ~ model) should give distances where
> fit would be null and residual similar as in the original adonis(y ~ model).
>
> It would be possible to develop such functions, but not with the current
> adonis() output. You can approximate both of these with capscale() and its
> fitted() and residuals() methods, but not exactly.
>
> The ecodist package of Sarah Goslee takes a different approach, and could
> return something usable (but I do not know that package very well).
>
> What really is needed depends on what you mean with "residuals". Should
> they be dissimilarities (which cannot be negative) or straightforward
> residuals (which have an average of zero and some of which are negative).
>
> Cheers, jari Oksanen
>
>
>
>
>

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