This is mothur v 1.2.0 - the April ~24, 2009 release

[mothur.git] / sharedthetayc.cpp

diff --git a/sharedthetayc.cpp b/sharedthetayc.cpp
index 1357cb611b407319de5c093ca2d0e99e14be7ead..2567110a79fde8ef9499c048927b246b49109ccd 100644 (file)
--- a/sharedthetayc.cpp
+++ b/sharedthetayc.cpp
@@ -14,10 +14,13 @@ EstOutput ThetaYC::getValues(SharedRAbundVector* shared1, SharedRAbundVector* sh
        try {   
                data.resize(1,0);
                
-               int Atotal, Btotal, tempA, tempB;
-               Atotal = 0; Btotal = 0; 
-               float thetaYC, sumSharedA, sumSharedB, a, b, d;
-               thetaYC = 0.0; sumSharedA = 0.0; sumSharedB = 0.0; a = 0.0; b = 0.0; d = 0.0;
+               int Atotal = 0;
+               int Btotal = 0;
+               float thetaYC = 0;
+               float relA = 0;
+               float relB = 0;
+               float a = 0;
+               float b = 0;
                
                //get the total values we need to calculate the theta denominator sums
                for (int i = 0; i < shared1->size(); i++) {
@@ -29,21 +32,14 @@ EstOutput ThetaYC::getValues(SharedRAbundVector* shared1, SharedRAbundVector* sh
                //calculate the theta denominator sums
                for (int j = 0; j < shared1->size(); j++) {
                        //store in temps to avoid multiple repetitive function calls
-                       tempA = shared1->getAbundance(j);
-                       tempB = shared2->getAbundance(j);
-                       
-                       //they are shared
-                       if ((tempA != 0) && (tempB != 0)) {
-                               if (Atotal != 0)        { sumSharedA = (tempA / (float)Atotal); }
-                               if (Btotal != 0)        { sumSharedB = (tempB / (float)Btotal); }
-                       
-                               a += sumSharedA * sumSharedA;
-                               b += sumSharedB * sumSharedB;
-                               d += sumSharedA * sumSharedB;
-                       }
+                       relA = shared1->getAbundance(j) / (float)Atotal;
+                       relB = shared2->getAbundance(j) / (float)Btotal;
+                                       
+                       a += relA * relB;
+                       b += pow((relA-relB),2);
                }
 
-               thetaYC = d / (float) (a + b - d);
+               thetaYC = a / (float) (b+a);
                
                if (isnan(thetaYC) || isinf(thetaYC)) { thetaYC = 0; }