From: Kathryn Iverson <kd.iverson@gmail.com>
Date: Wed, 16 May 2012 17:52:24 +0000 (-0400)
Subject: replaced p-value with zscore for lookup in ztable.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=74ee6242ea65e88074c2b1df85c0f4428b79333b;p=mothur.git

replaced p-value with zscore for lookup in ztable.
---

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index 75b87fa..6363f2a 100644
--- 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\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))) {
@@ -530,12 +530,20 @@ 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 << endl;
         
         return 0;
     }
diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index 1524890..71c3027 100644
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -293,26 +293,30 @@ double TrialSwap2::t_test (double initialscore, int runs, double nullMean, vecto
 /**************************************************************************************************/
 double TrialSwap2::getSD (int runs, vector<double> scorevec, double nullMean)
 {
-    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/runs) * sum );
+    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)
 {
-    map<double, double> ztable;
-    
-    ztable["0.00"] = 0.5;
-    
-    double z;
-    
-    z = (initscore - nullMean) / sd;
-    
-    return z;
+    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)