2 #ifndef PDSSparCC_runSparcc_h
3 #define PDSSparCC_runSparcc_h
9 // Created by Patrick Schloss on 10/31/12.
10 // Copyright (c) 2012 University of Michigan. All rights reserved.
13 /**************************************************************************************************/
16 #include "randomnumber.h"
17 #include "mothurout.h"
19 /**************************************************************************************************/
24 CalcSparcc(vector<vector<float> >, int, int, string);
25 vector<vector<float> > getRho() { return median; }
28 void addPseudoCount(vector<vector<float> >&);
29 vector<float> getLogFractions(vector<vector<float> >, string);
30 void getT_Matrix(vector<float>);
35 vector<float> getBasisVariances();
36 vector<vector<float> > getBasisCorrelations(vector<float>);
37 float getExcludedPairs(vector<vector<float> >, int&, int&);
38 void excludeValues(int, int);
39 void getMedian(vector<vector<vector<float> > >);
41 vector<float> tMatrix;
43 vector<vector<float> > dMatrix;
44 vector<float> tVector;
45 vector<vector<int> > excluded;
46 vector<vector<float> > median;
50 string normalizationMethod;
52 RandomNumberGenerator RNG;
57 /**************************************************************************************************/