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

[Terri Lacourse]

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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