[R-sig-phylo] remove phylogenetic signal from large dataset

[fran?ois RIGAL]

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

Frantz
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[Julien Clavel]

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,

Julien
________________________________
De : R-sig-phylo <r-sig-phylo-***@r-project.org> de la part de fran?ois RIGAL <***@hotmail.fr>
Envoyé : mercredi 23 mai 2018 10:25
À : r-sig-***@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

Frantz
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R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

[françois RIGAL]

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!
Frantz

Le 24 mai 2018 à 02:42, Julien Clavel <***@hotmail.fr<mailto:***@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,

Julien
________________________________
De : R-sig-phylo <r-sig-phylo-***@r-project.org<mailto:r-sig-phylo-***@r-project.org>> de la part de fran?ois RIGAL <***@hotmail.fr<mailto:***@hotmail.fr>>
Envoyé : mercredi 23 mai 2018 10:25
À : r-sig-***@r-project.org<mailto:r-sig-***@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

Frantz
_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org<mailto:R-sig-***@r-project.org>
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/
<phylo-pca-fast.txt>


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