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 "population_dynamics/selectivity/selectivity.hpp"
#include "population_dynamics/age_to_length_conversion/functors/base.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; 
  fims::Vector<double>
      lengths; 
  fims::Vector<double>
      length_bin_edges; 
  // selectivity
  int fleet_selectivity_id_m = -999; 
  std::shared_ptr<SelectivityBase<Type>>
      selectivity; 
  // age-to-length conversion model
  std::shared_ptr<AgeToLengthConversionBase<Type>>
      age_to_length_conversion_model; 
  bool requires_age_length_mapping =
      false; 
  // catch data
  int fleet_observed_catch_data_id_m = -999; 
  std::shared_ptr<fims_data_object::DataObject<Type>>
      observed_catch_data; 
  std::string observed_catch_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++;
    this->register_self(this->id);
  }
  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]);
    }
  }
};
 
// 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 */