irisComparison

RandPedPCA/stuff/compareIris.R

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+
+
+# get data
+i4 <- as.matrix(iris[,1:4])
+i4cent <- scale(i4, scale = F, center = T) # traits centered
+i4tcent <- scale(t(i4), scale = F, center = T) # inds centered
+
+
+
+# Prcomp ------------------------------------------------------------------
+
+# prcompom on centered i
+
+pci4cent <- prcomp(i4cent, center = F)
+# centered by prcomp
+pci4 <- prcomp(i4cent, center = F)
+
+# identical as expected
+plot(pci4cent$x[,1:2], col=iris$Species)
+plot(pci4$x[,1:2], col=iris$Species)
+
+
+
+# Cov matrices ------------------------------------------------------------
+
+cprTrait <- crossprod(i4)
+cprTraitCent <- crossprod(i4cent)
+cprIndTraitCent <- tcrossprod(i4cent)
+cprInd <- tcrossprod(i4)
+
+
+# 1st and 2nd are 4x4 cov mats
+svdList <- lapply(list(cprTrait, cprTraitCent, cprIndTraitCent, cprInd), svd)
+
+plot((i4 %*% svdList[[1]]$v)[,1:2], col=iris$Species)
+plot((i4cent %*% svdList[[2]]$v)[,1:2], col=iris$Species)
+
+plot((svdList[[3]]$u %*% diag(svdList[[3]]$d))[,1:2], col=iris$Species)
+plot((svdList[[4]]$u %*% diag(svdList[[4]]$d))[,1:2], col=iris$Species)