[R-sig-eco] PCA for composition data followed by RLQ

[Diogo B. Provete]

Hi Terri,
thanks for the feedback. Yes, I meant exactly the transformations proposed
by Aitchison. The point is my diet data (*R*) is expressed as the
percentage of a given item found in bat faeces. So I have 5 variables
(pollen, insects, fish etc) with varying percentages whose rows sum to 100.
As for the species composition matrix (*L*), yes, certainly the Hellinger
transformation can be applied in this case, but I was more worried about
how to treat the diet data before entering them in the RLQ itself. So, how
can I calculate the log-ratios ? There's this function in  rgr::clr, but
I'm not entirely sure it's what I need.

Best,
Diogo

Em seg., 21 de fev. de 2022 às 23:11, Terri Lacourse <tlacours using uvic.ca>
escreveu:

> Dear Diogo,
>
> I don’t see a way to run a “compositional PCA” in ade4. I presume you mean
> log-ratios as proposed by Aitchison? Could you determine the log-ratios
> first and then send that to the dudi matrix?
>
> Perhaps you could use Hellinger transformation instead for your
> compositional data. That is what I do, and then I set the RLQ environment
> in this way:
>
> data1_L <- dudi.coa(data1, scannf=F, nf=2) # these are
> Hellinger-transformed compositional data like your diet data
> data2_R <- dudi.pca(data2, scannf=F, nf=2, row.w=data1_L$lw)
> data3_Q <- dudi.pca(data3, scannf=F, nf=2, row.w=data1_L$cw)
> rlq.output <- rlq(data2_R, data1_L, data3_Q, scannf=F, nf=2)
>
> Best wishes,
> -Terri
>
> ~~~~~~~~~~~~~~~~~~~
> Terri Lacourse
> Associate Professor
> Department of Biology
> University of Victoria
> Victoria, BC
> Canada V8W 2Y2
>
> tlacours using uvic.ca
> ~~~~~~~~~~~~~~~~~~~
>
>
>
> > On Feb 21, 2022, at 12:14 PM, Diogo B. Provete <dbprovete using gmail.com>
> wrote:
> >
> > Dear members,
> > I'm trying to run an RLQ analysis to test for a covariation between skull
> > shape (set of eigenvectors) and diet composition for a set of bat
> species.
> > The point is, the data for diet is expressed as percentage, with rows
> > (species) summing to 100. Therefore, it's better treated as compositional
> > data.
> >
> > I have already run a compositional PCA in the R package compositions,
> which
> > returns an object of the class princomp. However, ade4::rlq only accepts
> > dudi matrices. I don't know how to convert a princomp to a dudi object or
> > perhaps run a compositional PCA in ade4. as.dudi seems not to be called
> > directly by the user.
> >
> > Does anyone have any clue on how to do this?
> >
> > Thank you in advance,
> > Diogo
> >
> > --
> >
> > Diogo B. Provete, PhD
> >
> > Assistant Professor
> >
> > Biodiversity Synthesis lab <http://diogoprovete.weebly.com/>
> >
> > Biosciences Institute | Federal University of Mato Grosso do Sul | Brazil
> >
> >
> > Skype: diogoprovete
> >
> >
> > Director of Graduate studies in Animal Biology
> > <https://ppgbioanimal.ufms.br/>
> > __
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> >
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