X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=linearalgebra.h;h=ef9e03cde900b4e01bdd61a99083801c0d25b913;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=332101853e97ee2ff630f6792dc926c4aa9f4da4;hpb=943d3038553f82378567d3b651969146716e5862;p=mothur.git

diff --git a/linearalgebra.h b/linearalgebra.h
index 3321018..ef9e03c 100644
--- a/linearalgebra.h
+++ b/linearalgebra.h
@@ -25,14 +25,47 @@ public:
 	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> >&);
 	double calcPearson(vector<vector<double> >&, vector<vector<double> >&);
 	double calcSpearman(vector<vector<double> >&, vector<vector<double> >&);
 	double calcKendall(vector<vector<double> >&, vector<vector<double> >&);
 	
+	double calcPearson(vector<double>&, vector<double>&, double&);
+	double calcSpearman(vector<double>&, vector<double>&, double&);
+	double calcKendall(vector<double>&, vector<double>&, double&);
+    
+	double calcSpearmanSig(double, double, double, double); //length, f^3 - f where f is the number of ties in x, f^3 - f where f is the number of ties in y, sum of squared diffs in ranks. - designed to find the sif of one score.
+    double calcPearsonSig(double, double); //length, coeff.
+    double calcKendallSig(double, double); //length, coeff.
+    
+    vector<double> solveEquations(vector<vector<double> >, vector<double>);
+    vector<vector<double> > getInverse(vector<vector<double> >);
+
+    
 private:
 	MothurOut* m;
 	
 	double pythag(double, double);
+    double betacf(const double, const double, const double);
+    double betai(const double, const double, const double);
+    double gammln(const double);
+    double gammp(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 ran0(int&); //for testing 
+    double ran1(int&); //for testing
+    double ran2(int&); //for testing
+    double ran3(int&); //for testing
+    double ran4(int&); //for testing
+    void psdes(unsigned long &, unsigned long &); //for testing
+    
+    void ludcmp(vector<vector<double> >&, vector<int>&, double&);
+    void lubksb(vector<vector<double> >&, vector<int>&, vector<double>&);
+
+    
 };
 
 #endif