##get packages
> library(phytools)
> library(strap)
##read in data 
>Theropod.matrix <- read.table(“S10_Data.txt")
## make calibrated tree file
>Theropod.ages <- read.table(“S9Ages.txt")
>Theropod.tree <- read.nexus(“S8phylogeny.tre")
>Theropod.ts.tree <- DatePhylo(Theropod.tree, Theropod.ages, 2, "equal")
##run phylogenetic PCA
> Theropod.PPCA <- phyl.pca(Theropod.ts.tree, Theropod.matrix, method = "BM", mode = "cov")
##plot results
>biplot(Theropod.PPCA,choices=c(2,3))
##output pPCA scores for plotting in PAST
>Theropod.PPCA $S