double HomovaCommand::runHOMOVA(ofstream& HOMOVAFile, map<string, vector<int> > groupSampleMap, double alpha){
try {
map<string, vector<int> >::iterator it;
int numGroups = groupSampleMap.size();
vector<double> ssWithinOrigVector;
double bValueOrig = calcBValue(groupSampleMap, ssWithinOrigVector);
double counter = 0;
for(int i=0;i<iters;i++){
vector<double> ssWithinRandVector;
map<string, vector<int> > randomizedGroup = getRandomizedGroups(groupSampleMap);
double bValueRand = calcBValue(randomizedGroup, ssWithinRandVector);
if(bValueRand >= bValueOrig){ counter++; }
}
double pValue = (double) counter / (double) iters;
string pString = "";
if(pValue < 1/(double)iters){ pString = '<' + toString(1/(double)iters); }
else { pString = toString(pValue); }
//print homova table
it = groupSampleMap.begin();
HOMOVAFile << it->first;
m->mothurOut(it->first);
it++;
for(;it!=groupSampleMap.end();it++){
HOMOVAFile << '-' << it->first;
m->mothurOut('-' + it->first);
}
HOMOVAFile << '\t' << bValueOrig << '\t' << pString;
m->mothurOut('\t' + toString(bValueOrig) + '\t' + pString);
if(pValue < alpha){
HOMOVAFile << "*";
m->mothurOut("*");
}
for(int i=0;i<numGroups;i++){
HOMOVAFile << '\t' << ssWithinOrigVector[i];
m->mothurOut('\t' + toString(ssWithinOrigVector[i]));
}
HOMOVAFile << endl;
m->mothurOutEndLine();
return pValue;
}
catch(exception& e) {
m->errorOut(e, "HomovaCommand", "runHOMOVA");
exit(1);
}
}
double AnosimCommand::runANOSIM(ofstream& ANOSIMFile, vector<vector<double> > dMatrix, map<string, vector<int> > groupSampleMap, double alpha) {
try {
vector<vector<double> > rankMatrix = convertToRanks(dMatrix);
double RValue = calcR(rankMatrix, groupSampleMap);
int pCount = 0;
for(int i=0;i<iters;i++){
map<string, vector<int> > randGroupSampleMap = getRandomizedGroups(groupSampleMap);
double RValueRand = calcR(rankMatrix, randGroupSampleMap);
if(RValue <= RValueRand){ pCount++; }
}
double pValue = (double)pCount / (double) iters;
string pString = "";
if(pValue < 1/(double)iters){ pString = '<' + toString(1/(double)iters); }
else { pString = toString(pValue); }
map<string, vector<int> >::iterator it=groupSampleMap.begin();
m->mothurOut(it->first);
ANOSIMFile << it->first;
it++;
for(it;it!=groupSampleMap.end();it++){
m->mothurOut('-' + it->first);
ANOSIMFile << '-' << it->first;
}
m->mothurOut('\t' + toString(RValue) + '\t' + pString);
ANOSIMFile << '\t' << RValue << '\t' << pString;
if(pValue < alpha){
ANOSIMFile << "*";
m->mothurOut("*");
}
ANOSIMFile << endl;
m->mothurOutEndLine();
return pValue;
}
catch(exception& e) {
m->errorOut(e, "AnosimCommand", "calcAnisom");
exit(1);
}
}
double AmovaCommand::runAMOVA(ofstream& AMOVAFile, map<string, vector<int> > groupSampleMap, double alpha) {
try {
map<string, vector<int> >::iterator it;
int numGroups = groupSampleMap.size();
int totalNumSamples = 0;
for(it = groupSampleMap.begin();it!=groupSampleMap.end();it++){
totalNumSamples += it->second.size();
}
double ssTotalOrig = calcSSTotal(groupSampleMap);
double ssWithinOrig = calcSSWithin(groupSampleMap);
double ssAmongOrig = ssTotalOrig - ssWithinOrig;
double counter = 0;
for(int i=0;i<iters;i++){
map<string, vector<int> > randomizedGroup = getRandomizedGroups(groupSampleMap);
double ssWithinRand = calcSSWithin(randomizedGroup);
if(ssWithinRand < ssWithinOrig){ counter++; }
}
double pValue = (double)counter / (double) iters;
string pString = "";
if(pValue < 1/(double)iters){ pString = '<' + toString(1/(double)iters); }
else { pString = toString(pValue); }
//print anova table
it = groupSampleMap.begin();
AMOVAFile << it->first;
m->mothurOut(it->first);
it++;
for(it;it!=groupSampleMap.end();it++){
AMOVAFile << '-' << it->first;
m->mothurOut('-' + it->first);
}
AMOVAFile << "\tAmong\tWithin\tTotal" << endl;
m->mothurOut("\tAmong\tWithin\tTotal\n");
AMOVAFile << "SS\t" << ssAmongOrig << '\t' << ssWithinOrig << '\t' << ssTotalOrig << endl;
m->mothurOut("SS\t" + toString(ssAmongOrig) + '\t' + toString(ssWithinOrig) + '\t' + toString(ssTotalOrig) + '\n');
int dfAmong = numGroups - 1; double MSAmong = ssAmongOrig / (double) dfAmong;
int dfWithin = totalNumSamples - numGroups; double MSWithin = ssWithinOrig / (double) dfWithin;
int dfTotal = totalNumSamples - 1; double Fs = MSAmong / MSWithin;
AMOVAFile << "df\t" << dfAmong << '\t' << dfWithin << '\t' << dfTotal << endl;
m->mothurOut("df\t" + toString(dfAmong) + '\t' + toString(dfWithin) + '\t' + toString(dfTotal) + '\n');
AMOVAFile << "MS\t" << MSAmong << '\t' << MSWithin << endl << endl;
m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n\n");
AMOVAFile << "Fs:\t" << Fs << endl;
m->mothurOut("Fs:\t" + toString(Fs) + '\n');
AMOVAFile << "p-value: " << pString;
m->mothurOut("p-value: " + pString);
if(pValue < alpha){
AMOVAFile << "*";
m->mothurOut("*");
}
AMOVAFile << endl << endl;
m->mothurOutEndLine();m->mothurOutEndLine();
return pValue;
}
catch(exception& e) {
m->errorOut(e, "AmovaCommand", "runAMOVA");
exit(1);
}
}
