# Activate ecodist package library(ecodist) library(car) library(gclus) library(vegan) # Get working directory getwd() setwd("/Users/Tonardo/Documents/UNCG/PhD/AFLP/Analyses/MantelTESTS/toecodist/EnvPCA") getwd() # Call datasets ## Create Environmental PCAs Using ReproMonths + Dmb15 only ## package = "HSAUR" # Annual Temperature Means Env = read.csv("Env.csv") plot(Env) Env_PCA <- prcomp(Env[,], scale=TRUE) print(Env_PCA) summary(Env_PCA) a2 <- Env_PCA$rotation[,1] centera <- Env_PCA$center scalea <- Env_PCA$scale hma <- as.matrix(Env) drop(scale(hma, center = centera, scale = scalea) %*% Env_PCA$rotation[,1]) EnvPCA1 <- predict(Env_PCA)[,1] EnvPCA2 <- predict(Env_PCA)[,2] print(EnvPCA1) print(EnvPCA2) write.csv(EnvPCA1, file="EnvPCA1.csv") write.csv(EnvPCA2, file="EnvPCA2.csv")