descriptions

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index ab9e275279e0399182d458b7a6a64b81ba56c205..966810b1438bd7e9b4072f6a8cccd6cb2d105cee 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -544,6 +544,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector
                        vector<float> terms; 
                        float AijDenominator = 0.0;
                        vector<float> Bij;
+                       
                        //get overall abundance of each grouping
                        for (int j = 0; j < groupings.size(); j++) {
                                
@@ -554,6 +555,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector
                                        if (groupings[j][k]->getAbundance(i) != 0) { numNotZero++; }
                                }
                                
+                               //mean abundance
                                float Aij = (totalAbund / (float) groupings[j].size());
                                terms.push_back(Aij);
                                
@@ -565,7 +567,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector
                        
                        float maxIndVal = 0.0;
                        for (int j = 0; j < terms.size(); j++) { 
-                               float thisAij = (terms[j] / AijDenominator); 
+                               float thisAij = (terms[j] / AijDenominator); //relative abundance
                                float thisValue = thisAij * Bij[j] * 100.0;
                                
                                //save largest
@@ -609,7 +611,8 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >&
                                        if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
                                        
                                }
-                                       
+                               
+                               //mean abundance        
                                float Aij = (totalAbund / (float) groupings[j].size());
                                terms.push_back(Aij);
                                
@@ -621,7 +624,7 @@ vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >&
                        
                        float maxIndVal = 0.0;
                        for (int j = 0; j < terms.size(); j++) { 
-                               float thisAij = (terms[j] / AijDenominator); 
+                               float thisAij = (terms[j] / AijDenominator); //relative abundance
                                float thisValue = thisAij * Bij[j] * 100.0;
                                        
                                //save largest