population.hpp

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#ifndef FIMS_POPULATION_DYNAMICS_POPULATION_HPP
#define FIMS_POPULATION_DYNAMICS_POPULATION_HPP
 
#include "../../common/model_object.hpp"
#include "../fleet/fleet.hpp"
#include "../growth/growth.hpp"
#include "../recruitment/recruitment.hpp"
#include "../../interface/interface.hpp"
#include "../maturity/maturity.hpp"
 
namespace fims_popdy {
 
template <typename Type>
struct Population : public fims_model_object::FIMSObject<Type> {
  static uint32_t id_g; 
  size_t n_years;       
  size_t n_ages;        
  size_t n_fleets;      
  // parameters are estimated; after initialize in create_model, push_back to
  // parameter list - in information.hpp (same for initial F in fleet)
  fims::Vector<Type>
      log_init_naa; 
  fims::Vector<Type>
      log_M; 
  fims::Vector<Type> proportion_female = fims::Vector<Type>(
      1, static_cast<Type>(0.5));            
  fims::Vector<Type> log_f_multiplier;       
  fims::Vector<Type> spawning_biomass_ratio; 
  // Transformed values
  fims::Vector<Type> M; 
  fims::Vector<Type> f_multiplier; 
  fims::Vector<double> ages;  
  fims::Vector<double> years; 
  int recruitment_id = -999; 
  std::shared_ptr<fims_popdy::RecruitmentBase<Type>>
      recruitment; 
  // growth
  int growth_id = -999; 
  std::shared_ptr<fims_popdy::GrowthBase<Type>>
      growth; 
  // maturity
  int maturity_id = -999; 
  std::shared_ptr<fims_popdy::MaturityBase<Type>>
      maturity; 
  // fleet
  std::set<uint32_t> fleet_ids; 
  std::vector<std::shared_ptr<fims_popdy::Fleet<Type>>>
      fleets; 
  Population() { this->id = Population::id_g++; }
 
  virtual void create_report_vectors(
      std::map<std::string, fims::Vector<fims::Vector<Type>>>& report_vectors) {
    report_vectors["log_init_naa"].emplace_back(this->log_init_naa);
    report_vectors["log_M"].emplace_back(this->log_M);
    report_vectors["log_f_multiplier"].emplace_back(this->log_f_multiplier);
    report_vectors["spawning_biomass_ratio"].emplace_back(
        this->spawning_biomass_ratio);
  }
 
  virtual void get_report_vector_count(
      std::map<std::string, size_t>& report_vector_count) {
    report_vector_count["log_init_naa"] += 1;
    report_vector_count["log_M"] += 1;
    report_vector_count["log_f_multiplier"] += 1;
    report_vector_count["spawning_biomass_ratio"] += 1;
  }
};
template <class Type>
uint32_t Population<Type>::id_g = 0;
 
}  // namespace fims_popdy
 
#endif /* FIMS_POPULATION_DYNAMICS_POPULATION_HPP */