Thank you very much to everyone that replied. R-sig-phylo, as usual, a very
helpful and friendly community! I got everything to work now. Jonathan
Drury also replied off-list with a similar approach in function form.

Cheers,

Rafael


*--*
*Rafael Sobral Marcondes*
PhD Candidate (Systematics, Ecology and Evolution/Ornithology)

Museum of Natural Science <http://sites01.lsu.edu/wp/mns/>
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @brown_birds <https://twitter.com/brown_birds>



On Mon, Mar 12, 2018 at 12:07 PM Liam J. Revell <liam.rev...@umb.edu> wrote:

> Graham's right of course. Sorry about that.
>
> You might do something like:
>
> Si<-(Xi-matrix(1,nrow(Xi),1)%*%phyl.vcv(Xm,vcv(tree),
>         1)$alpha[,1])%*%pca$Evec
>
> I also agree with Joe that you can take the phylogeny into account
> whilst accounting for sampling error using his approach or that of Ives
> et al. In either case you will obtain a covariance matrix among traits
> the decomposition of which could be employed to compute scores for
> individuals in the original space as Joe suggests. I'm not sure whether
> or not it will make a difference. That probably depends on how much
> uncertainty in the values of species means has been ignored.
>
> All the best, Liam
>
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> & Profesor Asociado, Programa de Biología
> Universidad del Rosario
> web: http://faculty.umb.edu/liam.revell/
>
> On 3/12/2018 11:29 AM, Graham Slater wrote:
> > Hi Rafael,
> >
> > You need to mean-center your traits before multiplying by the matrix of
> > eigenvectors. Compute the vector of phylogenetic means (under BM or
> > Pagel’s lambda), subtract each value from the relevant column of Xm and
> > then compute Si. The result should be identical to the scores from your
> > phylogenetic PCA.
> >
> > Graham
> >
> > ------------------------------------------------------
> > Graham J. Slater
> > Assistant Professor
> > Department of the Geophysical Sciences
> > University of Chicago
> > 5734 S. Ellis Avenue
> > Chicago, IL 60637 USA
> >
> > Tel: (773) 702-0249
> > email: gsla...@uchicago.edu <mailto:gsla...@uchicago.edu>
> > www.fourdimensionalbiology.com <http://www.fourdimensionalbiology.com>
> >
> >
> >
> >
> >
> >
> >> On Mar 12, 2018, at 11:11 AM, Rafael S Marcondes
> >> <raf.marcon...@gmail.com <mailto:raf.marcon...@gmail.com>> wrote:
> >>
> >> Hi Liam,
> >>
> >> Thank you very much for the very fast response (as usual). To try out
> >> if I was using your approach correctly, I ran it with the
> >> species-level data, expecting that I would get the same PC scores as
> >> from phyl.PCA. That didn't happen though. Am I understanding/doing
> >> something wrong?
> >>
> >> pca<-phyl.pca(tree,Xm)
> >> Si<-Xm%*%pca$Evec
> >> Expected that Si would be identical to pca$S. But they aren't.
> >>
> >> I have attached my species-level data, individual-level data, and
> >> output of phyl.pca
> >>
> >> Thank you,
> >>
> >>
> >> *--
> >> *
> >> *Rafael Sobral Marcondes*
> >> PhD Candidate (Systematics, Ecology and Evolution/Ornithology)
> >>
> >> Museum of Natural Science <http://sites01.lsu.edu/wp/mns/>
> >> Louisiana State University
> >> 119 Foster Hall
> >> Baton Rouge, LA 70803, USA
> >>
> >> Twitter: @brown_birds <https://twitter.com/brown_birds>
> >>
> >>
> >>
> >> On Sun, Mar 11, 2018 at 5:16 PM Liam J. Revell <liam.rev...@umb.edu
> >> <mailto:liam.rev...@umb.edu>> wrote:
> >>
> >>     Hi Rafael.
> >>
> >>     So far as I know, there is currently no way to explicitly take into
> >>     account sampling error in computing principal components while also
> >>     accounting for the phylogeny. However, it is relatively
> >>     straightforward
> >>     to compute scores for individuals from a PCA conducted on species
> >>     means.
> >>
> >>     This would look as follows (in which Xm is a matrix containing
> values
> >>     for species for each trait, and Xi is a matrix with the same number
> of
> >>     columns but containing values for individuals):
> >>
> >>     pca<-phyl.pca(tree,Xm)
> >>     Si<-Xi%*%pca$Evec
> >>
> >>     Then, if you have a separate vector containing species ID as a
> factor,
> >>     you could compute means and variances for each component by species.
> >>
> >>     I hope this is some help. All the best, Liam
> >>
> >>     Liam J. Revell, Associate Professor of Biology
> >>     University of Massachusetts Boston
> >>     & Profesor Asociado, Programa de Biología
> >>     Universidad del Rosario
> >>     web: http://faculty.umb.edu/liam.revell/
> >>
> >>     On 3/11/2018 5:06 PM, Rafael S Marcondes wrote:
> >>     > Dear all,
> >>     >
> >>     > Does anyone have any advice on how to calculate measurement
> >>     error in an
> >>     > analysis using phylogenetic principal components? Or, in other
> >>     words, after
> >>     > I run a phylogenetic PCA on species-level data, how can I
> >>     "project" my
> >>     > individual-level data into the phylogenetic PCs so I can
> calculate a
> >>     > standard error? I'm running my pPCA using the lambda method and
> the
> >>     > covariance matrix.
> >>     >
> >>     > I would think this would be an usual, simple procedure, and that
> >>     there
> >>     > would be an R function for it, but I can't for the life of me find
> >>     > anything. The recent paper by Jonathan Drury et al linked below
> does
> >>     > mention doing it, but without going into any detail.
> >>     >
> >>     >
> >>
> http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2003563
> >>     >
> >>     > Thank you very much for any help,
> >>     >
> >>     >
> >>     > *--*
> >>     > *Rafael Sobral Marcondes*
> >>     > PhD Candidate (Systematics, Ecology and Evolution/Ornithology)
> >>     >
> >>     > Museum of Natural Science <http://sites01.lsu.edu/wp/mns/>
> >>     > Louisiana State University
> >>     > 119 Foster Hall
> >>     > Baton Rouge, LA 70803, USA
> >>     >
> >>     > Twitter: @brown_birds <https://twitter.com/brown_birds>
> >>     >
> >>     >       [[alternative HTML version deleted]]
> >>     >
> >>     > _______________________________________________
> >>     > R-sig-phylo mailing list - R-sig-phylo@r-project.org
> >>     <mailto:R-sig-phylo@r-project.org>
> >>     > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> >>     > Searchable archive at
> >>     http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >>     >
> >>
> >>
> <indivdata.RDS><spleveldata.RDS><pPCAresults.rds>_______________________________________________
> >> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> >> <mailto:R-sig-phylo@r-project.org>
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> >> Searchable archive at
> >> http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >
>

        [[alternative HTML version deleted]]

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

Reply via email to