int run_disease_model(int *w_sday, int *w_shour, int *w_eday, int *w_ehour, int *w_duration, int *w_parms)
{
int day;
int hour;
for (day=day_first; day<=day_last; day++)
{
for (hour=0; hour<=23; hour++)
{
if ((day == day_first && hour < hour_first) ||
(day == day_last && hour > hour_last)) continue;
sporulation(day,hour);
survival(day,hour);
infection(day,hour);
calculate_warnings(day,hour);
if (model_init) model_init = FALSE;
}
}
for (day=0; day<=dmwarns; day++)
{
w_sday[day] = wrn[day].sday;
w_shour[day] = wrn[day].shour;
w_eday[day] = wrn[day].eday;
w_ehour[day] = wrn[day].ehour;
w_duration[day] = wrn[day].duration;
}
w_parms[0] = dmwarns;
w_parms[1] = c[0].els12;
w_parms[2] = c[0].primary_inf;
w_parms[3] = c[0].incubation;
return 0;
}
void WeeklyDD(const std::vector<double> &TargetedEffort, const std::vector<double> &NontargetedEffort, std::vector<double> &Biomass, const std::vector<double> &par){
// Global variables
extern int NIPY;
extern double CatchabilityScalingFactor, BiomassScalingFactor,RecruitmentScalingFactor;
extern double rho, wk, wk_1;//, M;
assert(TargetedEffort.size() == Biomass.size());
unsigned int max_timestep = TargetedEffort.size();
// Define necessary containers
std::vector< double > Rec(max_timestep, 0.0), survival(max_timestep, 0.0);
// Remember that the optimizer work on parameters of the same order of magnitude
double M = par[0];
double Targeted_catchability = par[1] * CatchabilityScalingFactor;
double Nontargeted_catchability = par[2] * CatchabilityScalingFactor;
// Initialise the vector of biomass
Biomass[0] = par[4] * BiomassScalingFactor;
Biomass[1] = par[5] * BiomassScalingFactor;
// von mises parameters
double vm_mean = par[6]; // make sure it varies between -M_PI and +M_PI
double vm_sigma = par[7]; // should be positive
// Calculate survival given the vector of effort
for(unsigned int i=0; i < max_timestep; i += 1) {
survival[i] = exp(-(M + Targeted_catchability * TargetedEffort[i] + Nontargeted_catchability * NontargetedEffort[i]));
}
// Calculate the proportion of recruitment in each week
std::vector<double> RecDist(NIPY, 0.0);
RecDist = vonMisesRecDist(vm_mean, vm_sigma);
// Create the vector of recruitment
for(unsigned int counter = 0; counter < max_timestep; counter++){
Rec[counter] = par[8 + counter / NIPY] * RecruitmentScalingFactor * RecDist[counter % NIPY];
}
// Example how to print the vector of parameters
//std::cout << "This is par[0] " << par[0] << "\n";
//std::cout << "This is par[1] " << par[1] << "\n";
//std::cout << "Number of parameters " << par.size() << "\n";
// Recursive calculation of biomass
for(unsigned int counter = 2; counter < max_timestep; counter++){
// calculate biomass
Biomass[counter] = survival[counter-1] * Biomass[counter-1] + rho * survival[counter-1] * Biomass[counter-1] - rho * survival[counter-1] *survival[counter -2] * Biomass[counter-2] - rho * survival[counter-1] * wk_1 * Rec[counter-1] + wk * Rec[counter];
if(Biomass[counter] < 0){Biomass[counter] = 0;}
}
}
