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.

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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/