some minor changes

[mothur.git] / nmdscommand.cpp

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 6596859c8c13f0e86b501d8ba62e9601ff4bf45a..aa1cd660b9af25b9dfdb099741b06fb6769433c1 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -195,7 +195,7 @@ int NMDSCommand::execute(){
                if (axesfile != "") {  axes = readAxes(names);          }
                
                string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
-               string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "stress.nmds";
+               string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
                outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
                outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
                
@@ -208,10 +208,12 @@ int NMDSCommand::execute(){
                out.setf(ios::fixed, ios::floatfield);
                out.setf(ios::showpoint);
                
-               out2 << "Dimension\tIter\tStress\tCorr" << endl;
+               out2 << "Dimension\tIter\tStress\tRsq" << endl;
                
                double bestStress = 10000000;
+               double bestR2 = 10000000;
                vector< vector<double> > bestConfig;
+               int bestDim = 0;
                
                for (int i = mindim; i <= maxdim; i++) {
                        m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
@@ -235,21 +237,23 @@ int NMDSCommand::execute(){
                                if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
                                
                                //calc correlation between original distances and euclidean distances from this config
-                               double corr = linearCalc.calcPearson(newEuclid, matrix);
-                               corr *= corr;
+                               double rsquared = linearCalc.calcPearson(newEuclid, matrix);
+                               rsquared *= rsquared;
                                if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
                                
                                //output results
                                out << "Config" << (j+1) << '\t';
                                for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
                                out << endl;
-                               out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << corr << endl;
+                               out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << rsquared << endl;
                                
                                output(endConfig, names, out);
                                
                                //save best
                                if (stress < bestStress) {
+                                       bestDim = i;
                                        bestStress = stress;
+                                       bestR2 = rsquared;
                                        bestConfig = endConfig;
                                }
                                
@@ -263,6 +267,10 @@ int NMDSCommand::execute(){
                string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
                outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
                
+               m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
+               m->mothurOut("Lowest stress :\t" + toString(bestStress) + "\n");
+               m->mothurOut("R-squared for configuration:\t" + toString(bestR2) + "\n");
+               
                ofstream outBest;
                m->openOutputFile(BestFileName, outBest);
                outBest.setf(ios::fixed, ios::floatfield);