added a few evenness calculators and fixed a couple of bugs in filter.seqs and pre...

[mothur.git] / smithwilson.cpp

diff --git a/smithwilson.cpp b/smithwilson.cpp
new file mode 100644 (file)
index 0000000..ec04196
--- /dev/null
+++ b/smithwilson.cpp
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+/*
+ *  smithwilson.cpp
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 8/21/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "smithwilson.h"
+
+/***********************************************************************/
+
+EstOutput SmithWilson::getValues(SAbundVector* rank){
+       try {
+
+               data.resize(1,0);
+
+               double maxRank = rank->getMaxRank();
+               double sobs = rank->getNumBins();
+               
+               double innerSum = 0;
+               for(int i=1;i<=maxRank;i++){
+                       innerSum += rank->get(i) * log(i);
+               }
+               innerSum /= sobs;
+
+               double outerSum = 0;
+               for(int i=1;i<=maxRank;i++){
+                       outerSum += rank->get(i) * (log(i) - innerSum) * (log(i) - innerSum);
+               }
+               outerSum /= sobs;
+
+               if(outerSum > 0){
+                       data[0] = 1.0000 - 2.0000 / (3.14159 * atan(outerSum));
+               }
+               else{
+                       data[0] = 1.0000;
+               }
+               
+               
+               return data;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "InvSimpson", "getValues");
+               exit(1);
+       }
+}
+
+/***********************************************************************/