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

[Terri Lacourse]

Hi Diogo,
I think you can also apply the Hellinger transformation to your table R data, and then use dudi.pca, no?
But, yes, the rgr::clr function is what you are after. It will give you the centered log-ratio transformation proposed by Aitchison. Or you could try rgr::ilr. But neither are suitable if your data have many zeros.

Cheers,
Terri


> On Feb 21, 2022, at 7:32 PM, Diogo B. Provete <dbprovete using gmail.com> wrote:
> 
> 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 <mailto: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 <mailto:tlacours using uvic.ca>
> ~~~~~~~~~~~~~~~~~~~
> 
> 
> 
> > On Feb 21, 2022, at 12:14 PM, Diogo B. Provete <dbprovete using gmail.com <mailto: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/ <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/ <https://ppgbioanimal.ufms.br/>>
> > __
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