working on pam

[mothur.git] / linearalgebra.h

diff --git a/linearalgebra.h b/linearalgebra.h
index 5819ea85d8deefba15ca1c45ccf03efd21c9321a..e4c8c1588b60c3868de7f4e06353a43112ea3037 100644 (file)
--- a/linearalgebra.h
+++ b/linearalgebra.h
@@ -20,9 +20,12 @@ public:
        ~LinearAlgebra() {}
        
        vector<vector<double> > matrix_mult(vector<vector<double> >, vector<vector<double> >);
+    vector<vector<double> >transpose(vector<vector<double> >);
        void recenter(double, vector<vector<double> >, vector<vector<double> >&);
-       int tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
+       //eigenvectors
+    int tred2(vector<vector<double> >&, vector<double>&, vector<double>&);
        int qtli(vector<double>&, vector<double>&, vector<vector<double> >&);
+    
        vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&, int); //pass in axes and number of dimensions
        vector< vector<double> > calculateEuclidianDistance(vector<vector<double> >&); //pass in axes
        vector<vector<double> > getObservedEuclideanDistance(vector<vector<double> >&);
@@ -43,8 +46,10 @@ public:
     vector<double> solveEquations(vector<vector<double> >, vector<double>);
     vector<float> solveEquations(vector<vector<float> >, vector<float>);
     vector<vector<double> > getInverse(vector<vector<double> >);
-    
-    
+    double choose(double, double);
+    double normalvariate(double mu, double sigma);
+    vector< vector<double> > lda(vector< vector<double> >& a, vector<string> groups, vector< vector<double> >& means, bool&); //Linear discriminant analysis - a is [features][valuesFromGroups] groups indicates which group each sampling comes from. For example if groups = early, late, mid, early, early. a[0][0] = value for feature0 from groupEarly.
+    int svd(vector< vector<double> >& a, vector<double>& w, vector< vector<double> >& v); //Singular value decomposition
 private:
        MothurOut* m;
        
@@ -52,11 +57,12 @@ private:
     double betacf(const double, const double, const double);
     double betai(const double, const double, const double);
     double gammln(const double);
-    double gammq(const double, const double);
+    //double gammq(const double, const double);
     double gser(double&, const double, const double, double&);
     double gcf(double&, const double, const double, double&);
     double erfcc(double);
     double gammp(const double, const double);
+    double pnorm(double x);
     
     double ran0(int&); //for testing 
     double ran1(int&); //for testing
@@ -70,7 +76,6 @@ private:
     
     void ludcmp(vector<vector<float> >&, vector<int>&, float&);
     void lubksb(vector<vector<float> >&, vector<int>&, vector<float>&);
-
     
 };