hft.h

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// SPDX-FileCopyrightText: 2020 W. Traylor <wolfgang.traylor@senckenberg.de>
//
// SPDX-License-Identifier: LGPL-3.0-or-later
 
#ifndef FAUNA_HFT_H
#define FAUNA_HFT_H
 
#include <array>
#include <cmath>
#include <memory>
#include <set>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>
 
namespace Fauna {
 
// forward declarations
class Hft;
class Parameters;
 
 
typedef std::vector<std::shared_ptr<const Hft> > HftList;
 
 
struct AllometryParameters {
  AllometryParameters(const double coefficient, const double exponent)
      : coefficient(coefficient), exponent(exponent) {}
 
  double coefficient;
 
  double exponent;
 
  double calc(const double M) const { return coefficient * pow(M, exponent); }
};
 
 
struct GivenPointAllometry {
  double exponent;
 
  double value_male_adult;
 
 
  double extrapolate(const double bodymass_male_adult,
                     const double bodymass) const;
};
 
 
enum class ConductanceModel {
 
  BradleyDeavers1980,
 
 
  CuylerOeritsland2004
};
 
enum class DietComposer {
  PureGrazer
};
 
enum class DigestiveLimit {
  None,
 
 
  Allometric,
 
 
  FixedFraction,
 
  IlliusGordon1992
};
 
enum class ExpenditureComponent {
 
  BasalMetabolicRate,
 
 
  FieldMetabolicRate,
 
  Taylor1981,
 
  Thermoregulation,
 
  Zhu2018
};
 
enum class ForagingLimit {
 
  GeneralFunctionalResponse,
 
 
  IlliusOConnor2000
};
 
 
enum class NetEnergyModel {
  GrossEnergyFraction
};
 
enum class MortalityFactor {
 
  Background,
 
 
  Lifespan,
 
 
  StarvationIlliusOConnor2000,
 
  StarvationThreshold
};
 
enum class ReproductionModel {
  None,
  ConstantMaximum,
  Linear,
  Logistic
};
 
 
class Hft {
 public:
 
  bool is_valid(const Parameters& params, std::string& msg) const;
 
 
  bool is_valid(const Parameters& params) const;
 
  std::string name = "example";
 
 
  double body_fat_birth = 0.2;
 
 
  double body_fat_catabolism_efficiency = 0.8;
 
 
  double body_fat_deviation = 0.125;
 
 
  double body_fat_gross_energy = 39.1;
 
 
  double body_fat_maximum = 0.25;
 
 
  double body_fat_maximum_daily_gain = 0.05;
 
  int body_mass_birth = 5;
 
 
  double body_mass_empty = 0.87;
 
 
  int body_mass_female = 50;
 
 
  int body_mass_male = 70;
  int breeding_season_length = 30;
 
 
  int breeding_season_start = 121;
 
  GivenPointAllometry digestion_allometric = {-0.25, 0.05};
 
 
  double digestion_digestibility_multiplier = 1.0;
 
 
  std::array<double, 3> digestion_i_g_1992_ijk = {0.034, 3.565, 0.077};
 
 
  double digestion_fixed_fraction = 0.05;
 
  DigestiveLimit digestion_limit = DigestiveLimit::Allometric;
 
 
  double digestion_me_coefficient = 0.8;
 
 
  double digestion_k_fat = 0.5;
 
 
  double digestion_k_maintenance = 0.7;
 
  NetEnergyModel digestion_net_energy_model =
      NetEnergyModel::GrossEnergyFraction;
  std::pair<int, int> establishment_age_range = {1, 15};
 
  double establishment_density = 1.0;
 
  GivenPointAllometry expenditure_basal_rate = {0.75, 7.5};
 
  std::set<ExpenditureComponent> expenditure_components = {
      ExpenditureComponent::FieldMetabolicRate};
 
 
  double expenditure_fmr_multiplier = 2.0;
  DietComposer foraging_diet_composer = DietComposer::PureGrazer;
 
  std::set<ForagingLimit> foraging_limits = {};
 
 
  double foraging_half_max_intake_density = 20;
  int life_history_lifespan = 16;
 
  int life_history_physical_maturity_female = 3;
 
  int life_history_physical_maturity_male = 3;
 
  int life_history_sexual_maturity = 2;
  double mortality_adult_rate = 0.1;
 
  std::set<MortalityFactor> mortality_factors = {
      MortalityFactor::Background, MortalityFactor::Lifespan,
      MortalityFactor::StarvationIlliusOConnor2000};
 
  double mortality_juvenile_rate = 0.3;
 
 
  double mortality_minimum_density_threshold = 0.5;
 
 
  bool mortality_shift_body_condition_for_starvation = true;
  double reproduction_annual_maximum = 1.0;
 
  int reproduction_gestation_length = 9;
 
 
  std::array<double, 2> reproduction_logistic = {15.0, 0.3};
 
  ReproductionModel reproduction_model = ReproductionModel::ConstantMaximum;
  ConductanceModel thermoregulation_conductance =
      ConductanceModel::BradleyDeavers1980;
 
 
  double thermoregulation_core_temperature = 38;
  bool operator==(const Hft& rhs) const { return name == rhs.name; }
  bool operator!=(const Hft& rhs) const { return name != rhs.name; }
  bool operator<(const Hft& rhs) const { return name < rhs.name; }  // Comparison
 
 private:
 
  bool check_mortality_vs_reproduction(const Parameters& params,
                                       std::ostream& msg) const;
 
 
  bool check_intake_vs_expenditure(const Parameters& params,
                                   std::ostream& msg) const;
};
 
}  // namespace Fauna
#endif  // FAUNA_HFT_H