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

[Diogo B. Provete]

Thank you very much to everyone who replied with their suggestions!
I could successfully run the analysis in the end.

Best,
DIogo

Em ter., 22 de fev. de 2022 às 03:09, Johannes Björk <
bjork.johannes using gmail.com> escreveu:

> What if you run
>
> clr_data= compositions::clr(data+pseudocount) #add pseducount if data
> contains a lot of zeroes. However function performs clr-transformation on
> non-zeroes (what is called robust clr).
>
> aitchison_distance = dist(clr_data, method=“euclidean”)
> pca_data = dudi.pca(data.frame(aitchison_distance))
>
> Cheers
> Johannes
>
> > On 22 Feb 2022, at 05:11, Terri Lacourse <tlacours using uvic.ca> wrote:
> >
> > 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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> >>>
> >>> Associate Editor: Austral Ecology
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> <
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> >>
> >>> | Amphibia-Reptilia
> >>> <https://brill.com/view/journals/amre/amre-overview.xml <
> https://brill.com/view/journals/amre/amre-overview.xml>> | BMC Ecology and
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> >>
> >>> | Ecology and Evolution | Frontiers in Ecology and the Environment |
> >>> Journal of Biogeography | Journal of Herpetology
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> >>
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