run_procrustes(PCA_list)

Procrustes analysis comparing PCA spaces across multiple groups or datasets.

statisticsfunctional diversity

Args:PCA_list — named list of PCA score matrices

run_procrustes <- function(PCA_list) {
  combNames <- combn(names(PCA_list), 2)
  combNames <- apply(combNames, 2, function(x) paste0(x[1], "_", x[2]))
  procrustes_table <- matrix(NA, ncol = 1, nrow = length(combNames),
                             dimnames = list(combNames, 'Birds'))
  
  for (j in 1:length(PCA_list)) {
    x <- PCA_list[[j]]$PCoA$vectors
    for (i in 1:length(PCA_list)) {
      if (i > j) {
        y <- PCA_list[[i]]$PCoA$vectors
        rownames(y) = rownames(x)
        prcTest <- ade4::procuste.rtest(as.data.frame(x), as.data.frame(y), nrepet = 999)
        cor_coef <- prcTest$obs
        p_val <- prcTest$pvalue
        signif <- ifelse(p_val < 0.001, "***", ifelse(p_val < 0.01, "**", ifelse(p_val < 0.05, "*", "ns")))
        procrustes_table[paste0(names(PCA_list)[j], "_", names(PCA_list)[i]), 1] <- 
          paste0(round(cor_coef, 3), " ", signif)
      }
    }
  }
  return(procrustes_table)
}