Merge remote-tracking branch 'origin/master'

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index 75b87fae4303f161a1f75fb632e831672a80e29d..9d298fb0af7e3910857d0c6f2d6f7c9d0b2d2a41 100644 (file)
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -180,7 +180,7 @@ int CooccurrenceCommand::execute(){
         m->openOutputFile(outputFileName, out);
         outputNames.push_back(outputFileName);  outputTypes["summary"].push_back(outputFileName);
         out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-        out << "metric\tlabel\tScore\tpValue\n";
+        out << "metric\tlabel\tScore\tzScore\tstandardDeviation\n";
 
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -272,6 +272,12 @@ int CooccurrenceCommand::execute(){
 int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp, ofstream& out){
     try {
         int numOTUS = thisLookUp[0]->getNumBins();
+        
+        if(numOTUS < 2) {
+            m->mothurOut("Not enough OTUs for co-occurrence analysis, skipping"); m->mothurOutEndLine();
+            return 0;
+        }
+        
         vector< vector<int> > co_matrix; co_matrix.resize(thisLookUp[0]->getNumBins());
         for (int i = 0; i < thisLookUp[0]->getNumBins(); i++) { co_matrix[i].resize((thisLookUp.size()), 0); }
         vector<int> columntotal; columntotal.resize(thisLookUp.size(), 0);
@@ -530,12 +536,20 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         
         m->mothurOutEndLine(); m->mothurOut("average metric score: " + toString(nullMean)); m->mothurOutEndLine();
         
+        //calc_p_value is not a statistical p-value, it's just the average that are either > or < the initscore.
+        //All it does is show what is expected in a competitively structured community
+        //zscore is output so p-value can be looked up in a ztable
         double pvalue = 0.0;
         if (metric == "cscore" || metric == "checker") { pvalue = trial.calc_pvalue_greaterthan (stats, initscore); }
         else{ pvalue = trial.calc_pvalue_lessthan (stats, initscore); }
+
+        double sd = trial.getSD(runs, stats, nullMean);
+
+        double zscore = trial.get_zscore(sd, nullMean, initscore);
         
-        m->mothurOut("pvalue: " + toString(pvalue)); m->mothurOutEndLine();
-        out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << pvalue << endl;
+        m->mothurOut("zscore: " + toString(zscore)); m->mothurOutEndLine();
+        m->mothurOut("standard deviation: " + toString(sd)); m->mothurOutEndLine();
+        out << metric << '\t' << thisLookUp[0]->getLabel() << '\t' << nullMean << '\t' << zscore '\t' << sd << endl;
         
         return 0;
     }

diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index 2d25e835cbd5608bc1c4f4c6cc67397155f2c834..71c3027db2c8bbe97265cb40af839c6a81a17b33 100644 (file)
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -291,6 +291,34 @@ double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vecto
     }
 }
 /**************************************************************************************************/
+double TrialSwap2::getSD (int runs, vector<double> scorevec, double nullMean)
+{
+    try{
+        double sum = 0;
+        for(int i=0;i<runs;i++)
+            {
+                if (m->control_pressed) { return 0; }
+                sum += pow((scorevec[i] - nullMean),2);
+            }
+        return sqrt( (1/double(runs)) * sum );
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "getSD");
+        exit(1);
+    }
+}
+/**************************************************************************************************/
+double TrialSwap2::get_zscore (double sd, double nullMean, double initscore)
+{
+    try {
+        return (initscore - nullMean) / sd;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "TrialSwap2", "get_zscore");
+        exit(1);
+    }
+}
+/**************************************************************************************************/
 int TrialSwap2::print_matrix(vector<vector<int> > &matrix, int nrows, int ncols)
 {
     try {

diff --git a/trialswap2.h b/trialswap2.h
index 924938b1a16297015a3bdb14d07db0f91fc7b5bc..455221968f7d513641b0095f457a44b3778401c1 100644 (file)
--- a/trialswap2.h
+++ b/trialswap2.h
@@ -26,6 +26,8 @@ public:
     double calc_vratio (int, int, vector<int>, vector<int>);
     int calc_checker (vector<vector<int> > &, vector<int>, int, int);
     double calc_c_score (vector<vector<int> > &, vector<int>, int, int);
+    double get_zscore (double, double, double);
+    double getSD (int, vector<double>, double);
     
     
 private:
@@ -35,7 +37,7 @@ private:
     int print_matrix(vector<vector<int> > &, int, int);
     
     
-    
+        
 };
 #endif