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parms.h
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#ifndef PARMS_H
#define PARMS_H
#include <iostream>
#include <fstream>
#include <math.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include "seed.h"
#include "timeStep.h"
#include "functions.h"
#include "parameters.h"
using namespace std;
struct strainParms {
// strain 1 parameters
double mu1;
double kappa1;
double cR1;
double rR1;
double sigmaM11;
double sigmaM21;
double rho1;
double rhoR1;
double kR1;
double mutate1;
double eR1;
double tR1;
double gR1;
// strain 2 parameters
double mu2;
double kappa2;
double cR2;
double rR2;
double sigmaM12;
double sigmaM22;
double rho2;
double rhoR2;
double kR2;
double mutate2;
double eR2;
double tR2;
double gR2;
// MGE 1 parameters
double beta1;
double cM1;
double deltaM1;
double b1;
double M1invasion;
double f1;
double fR1;
double a1;
double mgerec1;
// MGE 2 parameters
double beta2;
double cM2;
double deltaM2;
double b2;
double M2invasion;
double f2;
double fR2;
double a2;
double mgerec2;
// non-MGE locus
double xfit;
double yfit;
double switching1;
double switching2;
// environmental parameters
double deltaX;
double deltaD;
// strain interaction terms
double interstrainTransformation;
double interstrainMGE;
double interstrainR;
double interstrainCompetition;
double interstrainKill;
int rms;
// explicit phage bias
int phageFirst;
};
#endif // PARMS_H