[R-sig-eco] Use of PCoa in varipart

[Torsten Hauffe]

Hi Fernando,

using a PCoA for variation partitioning should be possible. This should
equal a distance-based redundancy analysis (plus some magic to make the
PCoA euclidean).
I don't know ade4 very well but alternatively you could use the vegan
function varpart. You can subject your Sörensen distance matrix directly to
varpart.

Cheers!

On Sun, Jun 7, 2020 at 11:32 PM Fernando Rodrigues da Silva <
fernando.ecologia using gmail.com> wrote:

> Dear R users,
>
> I would like to know if there is a possibility to perform the same analysis
> of Clappe et al. 2018 (Ecology, 1737-1747), but instead of using a
> Principal Component Analysis (PCA) in the function *varipart*, I use a
> Principal Coordinates Analysis (PCoA) based on the Simpson index of
> dissimilarity.
>
> I tried running the example of the article, but I get an error saying it is
> not yet available.
>
>
> *comp_dist <- beta.pair (mafragh$flo, index.family =
> "sorensen")pcoa.species <- dudi.pco (comp_dist$beta.sim, scannf = F)vprda
> <- varipart (pcoa.species, environment, eigenfw, type = "parametric")*
> # Error in dudi.type(Y$call) : Not yet available
> *vprdaMSR <- msr (vprda, mafragh.lw, nrepet = 999)*
>
> Does anyone know if there is any script available for this type of
> approach?
>
> All the best,
>
> *Prof. Dr. Fernando Rodrigues da Silva *
> *===========================================================**===*
> Laboratório de Ecologia Teórica: Integrando Tempo, Biologia e Espaço (
> LET.IT.BE),
> Departamento de Ciências Ambientais (DCA),
> Universidade Federal de São Carlos (UFSCar), campus Sorocaba
>
> Personal Page: *http://fernandoecologia.wix.com/fernandorodrigues
> <http://fernandoecologia.wix.com/fernandorodrigues>*
>
> *       https://orcid.org/0000-0002-0983-3207
> <https://orcid.org/0000-0002-0983-3207>    *
>
>
> *===============================================================*
>
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