Hi Julien
Many thanks for your reply and for the R code. This is really fast! Yes I see 
your point with the use of comparative methods on these new pPC axes. It seems 
to be the common approach in the literature.
Thanks again!

Le 24 mai 2018 à 02:42, Julien Clavel 
<julien.cla...@hotmail.fr<mailto:julien.cla...@hotmail.fr>> a écrit :

Hi Frantz,

The attached code can run the phylogenetic PCA (computes the scores) in few 
seconds on a species tree with more than 5000 tips. Note however that the 
phylogenetic pca is not exactly "removing" the phylo signal. It is a rigid 
rotation of what you obtain with the conventional PCA. You may still have to 
use comparative methods on these axes

Best wishes,

De : R-sig-phylo 
de la part de fran?ois RIGAL 
Envoyé : mercredi 23 mai 2018 10:25
À : r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>
Objet : [R-sig-phylo] remove phylogenetic signal from large dataset

Dear colleagues

I am struggling to find a way to remove phylogenetic signal from quantitative 
traits for a very large dataset (more than 5000 species. I already tried to 
implement a pPCA (function phyl.pca in the phytools package) but the function 
ran for more than a week and I decide to abort it. I also checked for the 
phylogenetic eigenvector approach but again I am not sure it makes senses for a 
so large phylogeny. (Too much PCoA axes and problem of selection of those 
axes). Thereofore, I would to ask if someone knows about a method to remove 
phylogeneitic signal for such large dataset, or, simply if it make sense to 
even try to remove phylo signal from such big data.

Many thanks

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