some minor changes

[mothur.git] / homovacommand.cpp

diff --git a/homovacommand.cpp b/homovacommand.cpp
index 52456b4ddedcd7b1db62a4fa8d03c5082eedf932..defccd3beeddb28da8d22a092a2ec43343e5add0 100644 (file)
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -216,8 +216,8 @@ int HomovaCommand::execute(){
                m->openOutputFile(HOMOVAFileName, HOMOVAFile);
                outputNames.push_back(HOMOVAFileName); outputTypes["homova"].push_back(HOMOVAFileName);
                
-               HOMOVAFile << "HOMOVA\tBValue\tP-value\tSSwithin_values" << endl;
-               m->mothurOut("HOMOVA\tBValue\tP-value\tSSwithin_values\n");
+               HOMOVAFile << "HOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values" << endl;
+               m->mothurOut("HOMOVA\tBValue\tP-value\tSSwithin/(Ni-1)_values\n");
                
                double fullHOMOVAPValue = runHOMOVA(HOMOVAFile, origGroupSampleMap, experimentwiseAlpha);
 
@@ -231,8 +231,7 @@ int HomovaCommand::execute(){
                        
                        for(itA=origGroupSampleMap.begin();itA!=origGroupSampleMap.end();itA++){
                                itB = itA;itB++;
-                               for(itB;itB!=origGroupSampleMap.end();itB++){
-                                       
+                               for(;itB!=origGroupSampleMap.end();itB++){
                                        map<string, vector<int> > pairwiseGroupSampleMap;
                                        pairwiseGroupSampleMap[itA->first] = itA->second;
                                        pairwiseGroupSampleMap[itB->first] = itB->second;
@@ -296,7 +295,7 @@ double HomovaCommand::runHOMOVA(ofstream& HOMOVAFile, map<string, vector<int> >
                HOMOVAFile << it->first;
                m->mothurOut(it->first);
                it++;
-               for(it;it!=groupSampleMap.end();it++){
+               for(;it!=groupSampleMap.end();it++){
                        HOMOVAFile << '-' << it->first;
                        m->mothurOut('-' + it->first);
                }
@@ -379,6 +378,8 @@ double HomovaCommand::calcBValue(map<string, vector<int> > groupSampleMap, vecto
                        
                        secondTermSum += (numSamplesInGroup - 1) * log(ssWithinVector[index] / (double)(numSamplesInGroup - 1));
                        inverseOneMinusSum += 1.0 / (double)(numSamplesInGroup - 1);
+                       
+                       ssWithinVector[index] /= (double)(numSamplesInGroup - 1); //this line is only for output purposes to scale SSw by the number of samples in the group
                        index++;
                }