How can I perform Phylogenetic Principle Component Analysis (pPCA) on my data, using phylogenetic trees with branch lengths, using R? I have 22 species with their phylogenetic tree and 14 traits (variables) from these species, I wont to find the major variability axes between these traits. If someone has the R commands for conducting pPCA?
I am not familiar with exactly what goes on in a phylogenetic principal component analysis, but a quick google indicates that the R package phytools has a function for this:
http://www.phytools.org/static.help/phyl.pca.html
Phytools is an excellent R package for conducting phylogenetic analyses. It requires a phylogenetic tree and a data frame of your trait data to run a phylogenetic PCA. This will then provide you your eigenvalues and loadings.
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