[R-sig-phylo] PGLS on PCA axes?
Hi, I have a quick question: I'm running a PGLS with many correlated traits and my co-author suggested to first apply PCA on the traits, then use the axes as predictors in my PGLS. I was wondering whether I need to perform a phylo PCA or if a regular PCA would do the trick? My intuition is that pPCA would be better as it takes phylogeny into account, but again it isn't being estimated jointly with the rest of the PGLS model... Also, is there any theory as to how this will impact phylogenetic signal in the residuals of the model? For some reason it feels odd to take phylogeny into account twice... Max [[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/
[R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?
I have been using the rescale function from geiger for a link prediction model I recently helped develop (https://arxiv.org/abs/1707.08354). I'm now running this model on a much larger dataset and part of the code is computing cophenetic(rescale(phy)) with 'EB' rescaling many many times. We're finding that calling cophenetic() is the rate limiting step, and if we can avoid this function we expect to speed up our code by up to 4 times. This would be very useful as our simulation has been running for over 50 days now... I was wondering if there is a way to do EB transformations on a phylogenetic distance matrix directly so as to avoid using the cophenetic function? Any help or insights would be greatly appreciated! [[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/
[R-sig-phylo] Method for calculating VIFs with a 'pgls' object?
Hello, I am interested in calculating variance inflation factors for a pgls model. Is this possible? If not, would it be statistically sound to create the same model in a glm framework to calculate VIFs? I found this post in the r-sig-phylo archive, but it isn't clear how the inflation factors were calculated: http://www.mail-archive.com/r-sig-phylo@r-project.org/msg02094.html Max [[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/
