added get.metacommunity command.

[mothur.git] / qFinderDMM.h

diff --git a/qFinderDMM.h b/qFinderDMM.h
new file mode 100644 (file)
index 0000000..d94e6cc
--- /dev/null
+++ b/qFinderDMM.h
@@ -0,0 +1,69 @@
+//
+//  qFinderDMM.h
+//  pds_dmm
+//
+//  Created by Patrick Schloss on 11/8/12.
+//  Copyright (c) 2012 University of Michigan. All rights reserved.
+//
+
+#ifndef pds_dmm_qFinderDMM_h
+#define pds_dmm_qFinderDMM_h
+
+/**************************************************************************************************/
+
+#include "mothurout.h"
+
+/**************************************************************************************************/
+
+class qFinderDMM {
+  
+public:
+    qFinderDMM(vector<vector<int> >, int);
+    double getNLL()     {    return currNLL;        }  
+    double getAIC()     {    return aic;            }
+    double getBIC()     {    return bic;            }
+    double getLogDet()  {    return logDeterminant; }
+    double getLaplace() {    return laplace;        }
+    void printZMatrix(string, vector<string>);
+    void printRelAbund(string, vector<string>);
+
+private:
+    MothurOut* m;
+    void kMeans();
+    void optimizeLambda();
+    void calculatePiK();
+
+    double negativeLogEvidenceLambdaPi(vector<double>&);
+    void negativeLogDerivEvidenceLambdaPi(vector<double>&, vector<double>&);
+    double getNegativeLogEvidence(vector<double>&, int);
+    double getNegativeLogLikelihood();
+    vector<vector<double> > getHessian();
+    
+    int lineMinimizeFletcher(vector<double>&, vector<double>&, double, double, double, double&, double&, vector<double>&, vector<double>&);
+    int bfgs2_Solver(vector<double>&);//, double, double);
+    double cheb_eval(const double[], int, double);
+    double psi(double);
+    double psi1(double);
+
+    vector<vector<int> > countMatrix;
+    vector<vector<double> > zMatrix;
+    vector<vector<double> > lambdaMatrix;
+    vector<double> weights;
+    vector<vector<double> > error;
+    
+    int numPartitions;
+    int numSamples;
+    int numOTUs;
+    int currentPartition;
+    
+    double currNLL;
+    double aic;
+    double bic;
+    double logDeterminant;
+    double laplace;
+    
+};
+
+/**************************************************************************************************/
+
+#endif