--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Procrustes.R	Tue May 20 03:27:28 2014 -0400
@@ -0,0 +1,29 @@
+#Procrustes tool for performing procrustes analysis on landmark data
+#MB
+
+#commandline arguments
+args <- commandArgs(TRUE)
+#input 
+input <- args[1]
+nb_landmarks <- args[2]
+nb_dimension <- 3
+output <- args[3]
+outputcentroid <- args[4]
+
+#package geomorph
+suppressMessages(library("geomorph"))
+
+#reading input file (landmark coordinates)
+read <- read.csv(file <- input,header = FALSE)
+
+#creating good array with arrayspecs
+new_array <- arrayspecs(read,as.integer(nb_landmarks),as.integer(nb_dimension))
+
+#perform procrustes with gpagen
+output_procrustes <- gpagen(A=new_array, ShowPlot= FALSE)
+#turn array for PCA
+output_procrustes_coo <- t(two.d.array(output_procrustes$coords))
+#output procrustes coordinates
+write.csv(output_procrustes_coo,output, row.names = FALSE)
+#output procrustes centroid size
+write.csv(output_procrustes$Csize,outputcentroid, row.names = FALSE)