changeset 10:dce35de9677e draft

Uploaded
author mb2013
date Wed, 20 Nov 2013 07:18:19 -0500
parents b9d127d6b00e
children 719a2d230fa2
files PCA.R
diffstat 1 files changed, 22 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PCA.R	Wed Nov 20 07:18:19 2013 -0500
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+# 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)