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inputs.h
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//
// Created by Jamie Cohen on 12/4/17.
//
#ifndef HPVVaccine_INPUTS_H
#define HPVVaccine_INPUTS_H
#include <cstdlib>
#include <vector>
#include <iostream>
#include <fstream>
#include <sstream>
#include <istream>
#include <cstdio>
#include <string>
#include <cmath>
#include <ctime>
#include "iniFile.h"
class Inputs{
public:
Inputs(std::string Output, std::string Data);
std::vector<int> burnin;
std::string OutputFolder;
std::string DataFolder;
std::string OutputDir;
int CohortSize;
int ModelStartAge;
int ModelStopAge;
int SimulationYears;
int BurnInYears;
int StartYear;
int Simulations;
std::string ASRMortalityFile;
std::vector< std::vector<double> > ASRMortality;
std::string CaMortalityFile;
std::vector< std::vector<double> > CaMortality;
std::string HPVIncidenceFile;
std::vector< std::vector<double> > HPVInc;
std::string HPVProgressionFile;
std::vector< std::vector<double> > HPVProgression;
std::string HPVClearanceFile;
std::vector< std::vector<double> > HPVClearance;
std::string CINProgressionFile;
std::vector< std::vector<double> > CINProgression;
std::string CINRegressionFile;
std::vector< std::vector<double> > CINRegression;
std::string VaccineEfficacyFile;
std::vector< std::vector<double> > vaccineefficacy;
std::string InitialPopulationFile;
std::vector<std::vector<double> > InitialPopulation;
std::string CostsFile;
std::vector<std::vector<double> > Costs;
std::string DisabilityFile;
std::vector<std::vector<double> > Disability;
std::string LifeExpectancyFile;
std::vector<std::vector<double> > LifeExpectancy;
int ScreenStartAge;
int ScreenStopAge;
int ScreenFrequency;
double ScreenCoverage;
double ScreenCompliance;
double AdequacyLBC;
double ColpoAvail;
double VaccineCoverage;
int VaccineDuration;
int VaccineStartAge;
int VaccineEndAge;
int VaccineStartYear;
int VaccineWaneTime;
double VaccineEfficacyPrior;
std::string MechanismofImmunity;
bool Latency;
bool WaningImmunity;
int ImmuneDuration;
int ImmuneWaneTime;
// outputs requested
bool dwelltime_output;
bool incidence_output;
bool mortality_output;
bool CEA_output;
std::string CytoSensFile;
std::vector< std::vector<double> > cytosens;
std::string CalibTargsFile;
std::vector< std::vector<double> > CalibTargs;
std::string MultipliersFile;
std::vector< std::vector<double> > Multipliers;
std::string MultipliersNamesFile;
std::string MultipliersNames;
std::string CalibTargsNamesFile;
std::string CalibTargsNames;
std::string ColpoSensFile;
std::vector< std::vector<double> > colposens;
double LLETZSuccessRateCIN;
double LLETZSuccessRateHPV;
double cPtTime;
double cPaptest;
double cReturnForResult;
double cColpoTime;
double cColpoProc;
double cCryoVisit;
double cCryoHPV;
double cCryoCIN23;
double cCryoCA;
double cStage1Ca;
double cStage2Ca;
double cStage3Ca;
double cHPVVaccine;
double disabilityCA1;
double disabilityCA2;
double disabilityCA3;
std::string VaccineType;
enum VxType { Bivalent = 0, Nonavalent = 1};
VxType vaccinetype;
double VE_1618;
double VE_high5;
enum Immunity {Degree, Factor, None};
Immunity ImmuneMechanism;
double CIN2_NL;
double CIN2_NL_allother_1;
double CIN2_NL_allother_2_4;
double CIN2_NL_allother_5;
double CIN2_NL_16_1;
double CIN2_NL_16_2_4;
double CIN2_NL_16_5;
double HPV_NL_LR_1;
double HPV_NL_LR_2_4;
double HPV_NL_LR_5;
double HPV_NL_otherHR_1;
double HPV_NL_otherHR_2_4;
double HPV_NL_otherHR_5;
double HPV_NL_high5_1;
double HPV_NL_high5_2_4;
double HPV_NL_high5_5;
double HPV_NL_16_1;
double HPV_NL_16_2_4;
double HPV_NL_16_5;
double HPV_NL_18_1;
double HPV_NL_18_2_4;
double HPV_NL_18_5;
double HPV_CIN_LR_1;
double HPV_CIN_LR_2_4;
double HPV_CIN_LR_5;
double HPV_CIN_otherHR_1;
double HPV_CIN_otherHR_2_4;
double HPV_CIN_otherHR_5;
double HPV_CIN_high5_1;
double HPV_CIN_high5_2_4;
double HPV_CIN_high5_5;
double HPV_CIN_16_1;
double HPV_CIN_16_2_4;
double HPV_CIN_16_5;
double HPV_CIN_18_1;
double HPV_CIN_18_2_4;
double HPV_CIN_18_5;
double CIN3_CA_high5_1_5;
double CIN3_CA_high5_6_10;
double CIN3_CA_high5_11_20;
double CIN3_CA_high5_21_30;
double CIN3_CA_high5_31_40;
double CIN3_CA_high5_41_50;
double CIN3_CA_high5_50;
double CIN3_CA_16_1_5;
double CIN3_CA_16_6_10;
double CIN3_CA_16_11_20;
double CIN3_CA_16_21_30;
double CIN3_CA_16_31_40;
double CIN3_CA_16_41_50;
double CIN3_CA_16_50;
double CIN3_CA_18_1_5;
double CIN3_CA_18_6_10;
double CIN3_CA_18_11_20;
double CIN3_CA_18_21_30;
double CIN3_CA_18_31_40;
double CIN3_CA_18_41_50;
double CIN3_CA_18_50;
double CIN3_CA_otherHR_1_5;
double CIN3_CA_otherHR_6_10;
double CIN3_CA_otherHR_11_20;
double CIN3_CA_otherHR_21_30;
double CIN3_CA_otherHR_31_40;
double CIN3_CA_otherHR_41_50;
double CIN3_CA_otherHR_50;
double NL_HPV16_17_19;
double NL_HPV16_20_24;
double NL_HPV16_25_29;
double NL_HPV16_30_34;
double NL_HPV16_35_39;
double NL_HPV16_40_44;
double NL_HPV16_45_49;
double NL_HPV16_50_54;
double NL_HPV16_55_65;
double NL_HPV18_17_19;
double NL_HPV18_20_24;
double NL_HPV18_25_29;
double NL_HPV18_30_34;
double NL_HPV18_35_39;
double NL_HPV18_40_44;
double NL_HPV18_45_49;
double NL_HPV18_50_54;
double NL_HPV18_55_65;
double NL_HPVhigh5_17_19;
double NL_HPVhigh5_20_24;
double NL_HPVhigh5_25_29;
double NL_HPVhigh5_30_34;
double NL_HPVhigh5_35_39;
double NL_HPVhigh5_40_44;
double NL_HPVhigh5_45_49;
double NL_HPVhigh5_50_54;
double NL_HPVhigh5_55_65;
double NL_HPVoHR_17_19;
double NL_HPVoHR_20_24;
double NL_HPVoHR_25_29;
double NL_HPVoHR_30_34;
double NL_HPVoHR_35_39;
double NL_HPVoHR_40_44;
double NL_HPVoHR_45_49;
double NL_HPVoHR_50_54;
double NL_HPVoHR_55_65;
double NL_HPVLR_17_19;
double NL_HPVLR_20_24;
double NL_HPVLR_25_29;
double NL_HPVLR_30_34;
double NL_HPVLR_35_39;
double NL_HPVLR_40_44;
double NL_HPVLR_45_49;
double NL_HPVLR_50_54;
double NL_HPVLR_55_65;
double ImmuneDegree;
double ImmuneDegree16;
double pRegresstoHPV;
double CIN3_NL;
double CIN2_CA;
double HPV_CIN2_16;
double HPV_CIN2_allother;
double CA1_CA1d;
double CA2_CA2d;
double CA3_CA3d;
double CA1_CA2;
double CA2_CA3;
double pHPV_LR[100];
double pHPV_otherHR[100];
double pHPV_16[100];
double pHPV_18[100];
double pHPV_31[100];
double pHPV_33[100];
double pHPV_45[100];
double pHPV_52[100];
double pHPV_58[100];
double pCIN2_CA1_16[100];
double pCIN3_CA1_16[100];
double pCIN2_CA1_18[100];
double pCIN3_CA1_18[100];
double pCIN2_CA1_oHR[100];
double pCIN3_CA1_oHR[100];
double pCIN2_CA1_31[100];
double pCIN3_CA1_31[100];
double pCIN2_CA1_33[100];
double pCIN3_CA1_33[100];
double pCIN2_CA1_45[100];
double pCIN3_CA1_45[100];
double pCIN2_CA1_52[100];
double pCIN3_CA1_52[100];
double pCIN2_CA1_58[100];
double pCIN3_CA1_58[100];
double pHPV_LR_CIN[100];
double pHPV_otherHR_CIN[100];
double pHPV_16_CIN[100];
double pHPV_18_CIN[100];
double pHPV_31_CIN[100];
double pHPV_33_CIN[100];
double pHPV_45_CIN[100];
double pHPV_52_CIN[100];
double pHPV_58_CIN[100];
double pCIN3_NL_16[100];
double pCIN3_NL_18[100];
double pCIN3_NL_LR[100];
double pCIN3_NL_oHR[100];
double pCIN3_NL_high5[100];
double pCIN2_NL_16[100];
double pCIN2_NL_18[100];
double pCIN2_NL_LR[100];
double pCIN2_NL_oHR[100];
double pCIN2_NL_high5[100];
double pHPV_LR_NL[100];
double pHPV_otherHR_NL[100];
double pHPV_16_NL[100];
double pHPV_18_NL[100];
double pHPV_31_NL[100];
double pHPV_33_NL[100];
double pHPV_45_NL[100];
double pHPV_52_NL[100];
double pHPV_58_NL[100];
double mCA1[100];
double mCA2[100];
double mCA3[100];
double mCA1d[100];
double mCA2d[100];
double mCA3d[100];
double cytosens_NL;
double cytosens_CIN;
double cytosens_Ca;
void loadData(ifstream &Infile, vector< vector<double> > &VariableName);
void loadStringData(ifstream &Infile, std::string &VariableName);
void loadRFG(std::string& RunsFileName, std::string& CurKey);
void loadVariables();
double ApplyMult(double, double);
void loadCalibParams(vector<double> calib_params);
};
#endif //HPVVaccine_INPUTS_H