added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow...

[mothur.git] / cooccurrencecommand.cpp

diff --git a/cooccurrencecommand.cpp b/cooccurrencecommand.cpp
index cfde0a906d7a3138160205623bd42b59f9c2918f..00de4d6ee612439732207872eba327b8a03f699e 100644 (file)
--- a/cooccurrencecommand.cpp
+++ b/cooccurrencecommand.cpp
@@ -51,6 +51,26 @@ string CooccurrenceCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string CooccurrenceCommand::getOutputFileNameTag(string type, string inputName=""){    
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "summary") {  outputFileName =  "cooccurence.summary"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "CooccurrenceCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 CooccurrenceCommand::CooccurrenceCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -176,11 +196,11 @@ int CooccurrenceCommand::execute(){
                set<string> userLabels = labels;
 
         ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "cooccurence.summary";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary");
         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 +292,12 @@ 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);
@@ -412,7 +438,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
         }
 
         //populate null matrix from probability matrix, do this a lot.
-        for(int h=0;h<runs;h++){
+        for(int k=0;k<runs;k++){
             nullmatrix.clear();
             //zero-fill the null matrix
             nullmatrix.assign(nrows, vector<int>(ncols, 0));
@@ -458,7 +484,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
                         randnum = rand() / double(RAND_MAX);
                         for(int j=0;j<ncols;j++) {
                             current = probabilityMatrix[ncols * i + j];
-                            if((randnum <= current && randnum > previous && nullmatrix[i][j] != 1) || (previous==current)){
+                            if(randnum <= current && randnum > previous && nullmatrix[i][j] != 1) {
                                 nullmatrix[i][j] = 1;
                                 count++;
                                 previous = 0.0;
@@ -494,6 +520,7 @@ int CooccurrenceCommand::getCooccurrence(vector<SharedRAbundVector*>& thisLookUp
             //swap_checkerboards takes the original matrix and swaps checkerboards
             else if(matrix == "sim9") {
                 trial.swap_checkerboards (co_matrix, ncols, nrows);
+                nullmatrix = co_matrix;
             }
             else {
                 m->mothurOut("[ERROR]: No null model selected!\n\n"); m->control_pressed = true;
@@ -529,12 +556,20 @@ 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;
     }