# HG changeset patch
# User mb2013
# Date 1384949899 18000
# Node ID dce35de9677e42844ff1abcbc4fbcab8c468fee1
# Parent  b9d127d6b00ed1330660735d3c348b4ab0fb8906
Uploaded

diff -r b9d127d6b00e -r dce35de9677e PCA.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PCA.R	Wed Nov 20 07:18:19 2013 -0500
@@ -0,0 +1,22 @@
+# The tool PCA creates a principle component analysis on procrustes data.
+# developer: M.Baak
+
+#commands of commandline
+args <- commandArgs(TRUE)
+#input file: procrustes coordinates
+input <- args[1]
+#output file
+output <- args[2]
+output2 <- args[3]
+
+#package geomorph
+suppressMessages(library("geomorph"))
+
+#reading of coordinates
+read <- read.csv(file <- input,header = TRUE)
+#principle componten analysis with princomp, using covariance matrix of coordinates
+pca <- princomp(x=cov(read))
+
+#output pca scores
+write.csv(pca$scores,output, row.names = FALSE)
+write.csv(pca$sdev, output2, row.names = FALSE)