added shen calculator

[mothur.git] / shen.cpp

diff --git a/shen.cpp b/shen.cpp
new file mode 100644 (file)
index 0000000..6bdb9b6
--- /dev/null
+++ b/shen.cpp
@@ -0,0 +1,44 @@
+/*
+ *  shen.cpp
+ *  Mothur
+ *
+ *  Created by Thomas Ryabin on 5/18/09.
+ *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *
+ */
+
+#include "shen.h"
+#include <math.h>
+
+       
+/***********************************************************************/      
+EstOutput Shen::getValues(SAbundVector* rank){
+
+       try {
+               data.resize(1,0);
+               
+               double n = (double)rank->getNumSeqs();
+               double f1 = (double)rank->get(1);
+               
+               double D_rare = 0; //I didn't know what this was. Simply replace the '0' with the appropriate expression.
+               double C_rare = 1; //I didn't know what this was. Simply replace the '1' with the appropriate expression.
+               double Y_rare = 1; //I didn't know what this was. Simply replace the '1' with the appropriate expression.
+               
+               double f0 = D_rare/C_rare + f1/C_rare * Y_rare*Y_rare - D_rare;
+               
+               data[0] = f0 * (1 - pow(1 - f1/n/f0, m));
+
+               return data;
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the Coverage class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the Coverage class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }       
+};
+
+
+/***********************************************************************/