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//
// diversityutils.hpp
// Mothur
//
// Created by Sarah Westcott on 4/11/19.
// Copyright © 2019 Schloss Lab. All rights reserved.
//
#ifndef diversityutils_hpp
#define diversityutils_hpp
#define HI_PRECISION 1.0e-12
#define LO_PRECISION 1.0e-7
#define V_MULT 25.0
#define PENALTY 1.0e20
#define SLICE 10
#include "diversitycalc.h"
/***********************************************************************/
class DiversityUtils {
public:
DiversityUtils(string met){ m = MothurOut::getInstance(); method = met; }
#ifdef USE_GSL
double logLikelihood(int n, double dAlpha, double dBeta);
double logLikelihood(int n, double dAlpha, double dBeta, double);
bool bessel(double* pdResult, int n, double dAlpha, double dBeta);
double sd(int n, double dAlpha, double dBeta);
bool bessel(double* pdResult, int n, double dAlpha, double dBeta, double);
double sd(int n, double dAlpha, double dBeta, double);
int minimiseSimplex(gsl_vector* ptX, size_t nP, void* pvData, double (*f)(const gsl_vector*, void* params), double, double, double);
vector<double> mcmc(t_Params *ptParams, t_Data *ptData, gsl_vector* ptX, void* f (void * pvInitMetro));
vector<double> outputResults(gsl_vector *ptX, t_Data *ptData, double (*f)(const gsl_vector*, void* params));
void getProposal(gsl_rng *ptGSLRNG, gsl_vector *ptXDash, gsl_vector *ptX, int* pnSDash, int nS, t_Params *ptParams);
int solveF(double x_lo, double x_hi, void* params, double tol, double *xsolve);
int solveF(double x_lo, double x_hi, double (*f)(double, void*), void* params, double tol, double *xsolve);
double logLikelihoodRampal(int n, double dMDash, double dV);
double logLikelihoodQuad(int n, double dMDash, double dV);
double logLikelihoodRampal(int n, double dMDash, double dV, double dNu);
double logLikelihoodQuad(int n, double dMDash, double dV, double dNu);
double calcMu(void *ptLNParams);
int fitSigma(vector<double>, vector<double>, int fi, t_Params *ptParams, t_Data *ptData, gsl_vector* ptX, void* f (void * pvInitMetro));
#endif
double f2X(double x, double dA, double dB, double dNDash);
double fX(double x, double dA, double dB, double dNDash);
double chao(t_Data *ptData);
double logStirlingsGamma(double dZ);
void loadAbundance(t_Data *ptData, SAbundVector* rank);
void freeAbundance(t_Data *ptData);
MothurOut* m;
private:
Utils util;
string method;
acceptRatioPos findBest(vector<double> accept);
};
/***********************************************************************/
#endif /* diversityutils_hpp */
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