[R-sig-eco] Relating skull shape to environmental variables

[Botta-Dukát Zoltán]

Dear Diego,

I suppose that PCA scores resulted by  geomorph::gm.prcomp are 
uncorrelated. If you use matrix of these scores as imput of dudi.pca, 
the scores in the results should be the same matrix, but in the 
requested form.

Best,

Zoltan

2020. 07. 17. 21:13 keltezéssel, Diogo B. Provete írta:
> Hi Frederico,
> thanks for replying. Also thanks Karlo for sending a separate email
> yesterday. I think I haven't made myself clear enough. Our dataset is
> derived from geometric morphometrics, we are measuring skull and jaw shape
> of bat species and we want to test the influence of land use classes on
> shape. So we have to process the data using the geomorph::gm.prcomp
> function that allows an array containing the XY landmark coordinates for
> each species (a .tps file). This function returns the PCA scores
> representing the position of each species (mean) in the shape space.
>
> ade4::dudi.pca only accepts the regular square matrix as input, that's why
> we can't use it.
>
> Best,
> Diogo
>
> Em sex., 17 de jul. de 2020 às 10:36, Frederico Faleiro <fvfaleiro using gmail.com>
> escreveu:
>
>> Hi Diogo,
>> I did not understand why you can not use the dudi.pca, but you can find
>> the tutorial from the authors here:
>> http://www.esapubs.org/archive/ecol/E095/002/ and the paper here:
>> https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/13-0196.1.
>>
>> Cheers,
>>
>> Em qua., 15 de jul. de 2020 às 15:23, Diogo B. Provete <
>> dbprovete using gmail.com> escreveu:
>>
>>> Dear list members,
>>> My PhD student Adriana Acero and I are trying to relate the mean cranial
>>> shape of species (Principal components scores) of a bat community to the
>>> land use type (% of each land use class measured from satellite data) in
>>> which species occur.
>>> Therefore, our analytical problem is more of a RLQ (relating traits to
>>> environment) that is common in community ecology. We want to use the
>>> ade4::
>>> rlq function to relate the 10 PCs representing the position of each
>>> species
>>> in the shape space (*Q*), to the environmental matrix (*R*), using the
>>> species composition matrix as *L. *
>>>
>>> The problem is that the ade4::rlq function only accepts objects of the
>>> dudi.pca class. Did anyone come across a similar issue?
>>>
>>> We tried to follow this blog post
>>> <https://www.r-bloggers.com/r-for-ecologists-rlq-analysis-semi-explained/
>>>> ,
>>> which builds the analysis step by step using custom functions and also
>>> tried to coerce our PCA object into a as.dudi class, but it didn't work.
>>>
>>> Thank you in advance,
>>> Diogo
>>>
>>>
>>> --
>>>
>>> <http://diogoprovete.weebly.com>
>>> Associate Chair (Graduate studies) in Animal Biology
>>>
>>> Skype: diogoprovete
>>>
>>> Editor: Amphibia-Reptilia
>>> <https://brill.com/view/journals/amre/amre-overview.xml?lang=en> |
>>> Journal
>>> of Herpetology <https://journalofherpetology.org> | Herpetological
>>> Journal
>>> <https://ojs.thebhs.org/index.php/HJ> | PLoS One | PeerJ
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-ecology mailing list
>>> R-sig-ecology using r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>
>>
>> --
>> Frederico Faleiro
>> Postdoctoral Researcher in the INCT-EECBio (https://www.eecbio.ufg.br/)
>> Department of Ecology | Institute of Biological Science | Federal
>> University of Goiás | Brazil
>> RG: https://www.researchgate.net/profile/Frederico_Faleiro
>> CV: http://lattes.cnpq.br/4926404840659003
>>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology