fleet.hpp

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#ifndef FIMS_POPULATION_DYNAMICS_FLEET_HPP
#define FIMS_POPULATION_DYNAMICS_FLEET_HPP
 
#include "../../common/data_object.hpp"
#include "../../common/fims_vector.hpp"
#include "../../common/model_object.hpp"
#include "../../distributions/distributions.hpp"
#include "../selectivity/selectivity.hpp"
 
namespace fims_popdy {
 
template <class Type>
struct Fleet : public fims_model_object::FIMSObject<Type> {
  static uint32_t id_g; 
  size_t n_years;       
  size_t n_ages;        
  size_t n_lengths;     
  // selectivity
  int fleet_selectivity_id_m = -999; 
  std::shared_ptr<SelectivityBase<Type>>
      selectivity; 
  // landings data
  int fleet_observed_landings_data_id_m = -999; 
  std::shared_ptr<fims_data_object::DataObject<Type>>
      observed_landings_data; 
  std::string observed_landings_units; 
  // index data
  int fleet_observed_index_data_id_m = -999; 
  std::shared_ptr<fims_data_object::DataObject<Type>>
      observed_index_data; 
  std::string observed_index_units; 
  // age comp data
  int fleet_observed_agecomp_data_id_m = -999; 
  std::shared_ptr<fims_data_object::DataObject<Type>>
      observed_agecomp_data; 
  // length comp data
  int fleet_observed_lengthcomp_data_id_m = -999; 
  std::shared_ptr<fims_data_object::DataObject<Type>>
      observed_lengthcomp_data; 
  // Mortality and catchability
  fims::Vector<Type>
      log_Fmort; 
  fims::Vector<Type>
      log_q; 
  fims::Vector<Type> Fmort; 
  fims::Vector<Type>
      q; 
  fims::Vector<Type> age_to_length_conversion; 
  Fleet() { this->id = Fleet::id_g++; }
 
  virtual ~Fleet() {}
 
  void Prepare() {
    // for(size_t fleet_ = 0; fleet_ <= this->n_fleets; fleet_++) {
    // this -> Fmort[fleet_] = fims_math::exp(this -> log_Fmort[fleet_]);
 
    for (size_t i = 0; i < this->log_q.size(); i++) {
      this->q[i] = fims_math::exp(this->log_q[i]);
    }
 
    for (size_t year = 0; year < this->n_years; year++) {
      this->Fmort[year] = fims_math::exp(this->log_Fmort[year]);
    }
  }
 
  virtual void create_report_vectors(
      std::map<std::string, fims::Vector<fims::Vector<Type>>>& report_vectors) {
    report_vectors["log_Fmort"].emplace_back(this->log_Fmort.to_tmb());
    report_vectors["log_q"].emplace_back(this->log_q.to_tmb());
  }
 
  virtual void get_report_vector_count(
      std::map<std::string, size_t>& report_vector_count) {
    report_vector_count["log_Fmort"] += 1;
    report_vector_count["log_q"] += 1;
  }
};
 
// default id of the singleton fleet class
template <class Type>
uint32_t Fleet<Type>::id_g = 0;
 
}  // end namespace fims_popdy
 
#endif /* FIMS_POPULATION_DYNAMICS_FLEET_HPP */