X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=nmdscommand.cpp;fp=nmdscommand.cpp;h=aa1cd660b9af25b9dfdb099741b06fb6769433c1;hp=6596859c8c13f0e86b501d8ba62e9601ff4bf45a;hb=ec5c537e869028c49231dab9a37c00a9edf70723;hpb=16c6e30b7c5a9cbe35989b2aa1d6848711a86d24

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index 6596859..aa1cd66 100644
--- 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);