vonb_schnute.hpp

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#ifndef POPULATION_DYNAMICS_GROWTH_VONB_SCHNUTE_HPP
#define POPULATION_DYNAMICS_GROWTH_VONB_SCHNUTE_HPP
 
#include "../../../common/fims_math.hpp"
#include "growth_base.hpp"
 
namespace fims_popdy {
 
template <typename Type>
struct VonBertalanffySchnuteGrowth : public GrowthBase<Type> {
  Type mean_length_young = Type(0.0);
  Type mean_length_old = Type(0.0);
  Type growth_coefficient = Type(0.0);
  Type reference_age_for_length_young = Type(0.0);
  Type reference_age_for_length_old = Type(0.0);
 
  Type length_weight_a = Type(0.0);
  Type length_weight_b = Type(3.0);
 
  VonBertalanffySchnuteGrowth() : GrowthBase<Type>() {}
  virtual ~VonBertalanffySchnuteGrowth() {}
 
  Type length_at_age(const Type& age) const {
    if (reference_age_for_length_young > Type(0.0) &&
        age < reference_age_for_length_young) {
      // For early ages, avoid back-extrapolating the curved growth equation.
      // This no-seasons ramp goes from length 0 at age 0 to length young at
      // age young; seasonal growth may need a different transition in the
      // future.
      const Type age_nonnegative = age <= Type(0.0) ? Type(0.0) : age;
      return mean_length_young * age_nonnegative /
             reference_age_for_length_young;
    }
 
    const Type denom =
        Type(1.0) -
        fims_math::exp(-growth_coefficient * (reference_age_for_length_old -
                                              reference_age_for_length_young));
    // AD-safe floor to avoid divide-by-zero/NaN when denominator is tiny.
    const Type denom_safe =
        fims_math::ad_max(fims_math::ad_fabs(denom), static_cast<Type>(1e-8));
    const Type numer =
        Type(1.0) - fims_math::exp(-growth_coefficient *
                                   (age - reference_age_for_length_young));
    return mean_length_young +
           (mean_length_old - mean_length_young) * numer / denom_safe;
  }
 
  Type log_length_at_age(const Type& age) const {
    const Type length = length_at_age(age);
    const Type length_safe = fims_math::ad_max(length, static_cast<Type>(1e-8));
    return fims_math::log(length_safe);
  }
 
  void log_length_at_age_gradient(const Type& age,
                                  Type& d_log_laa_d_length_young,
                                  Type& d_log_laa_d_length_old,
                                  Type& d_log_laa_d_k) const {
    if (reference_age_for_length_young > Type(0.0) &&
        age < reference_age_for_length_young) {
      const Type age_nonnegative = age <= Type(0.0) ? Type(0.0) : age;
      const Type ratio = age_nonnegative / reference_age_for_length_young;
      const Type mean_length = mean_length_young * ratio;
      const Type mean_length_safe =
          fims_math::ad_max(mean_length, static_cast<Type>(1e-8));
 
      d_log_laa_d_length_young = ratio / mean_length_safe;
      d_log_laa_d_length_old = Type(0.0);
      d_log_laa_d_k = Type(0.0);
      return;
    }
 
    const Type age_delta_1 = age - reference_age_for_length_young;
    const Type age_delta_2 =
        reference_age_for_length_old - reference_age_for_length_young;
 
    const Type exp_num = fims_math::exp(-growth_coefficient * age_delta_1);
    const Type exp_den = fims_math::exp(-growth_coefficient * age_delta_2);
 
    const Type numer = Type(1.0) - exp_num;
    const Type denom = Type(1.0) - exp_den;
    const Type denom_safe =
        fims_math::ad_max(fims_math::ad_fabs(denom), static_cast<Type>(1e-8));
 
    const Type ratio = numer / denom_safe;
    const Type delta_length = mean_length_old - mean_length_young;
    const Type mean_length = mean_length_young + delta_length * ratio;
    const Type mean_length_safe =
        fims_math::ad_max(mean_length, static_cast<Type>(1e-8));
 
    const Type d_length_d_l1 = Type(1.0) - ratio;
    const Type d_length_d_l2 = ratio;
 
    const Type d_numer_d_k = age_delta_1 * exp_num;
    const Type d_denom_d_k = age_delta_2 * exp_den;
    const Type d_ratio_d_k = (d_numer_d_k * denom_safe - numer * d_denom_d_k) /
                             (denom_safe * denom_safe);
    const Type d_length_d_k = delta_length * d_ratio_d_k;
 
    d_log_laa_d_length_young = d_length_d_l1 / mean_length_safe;
    d_log_laa_d_length_old = d_length_d_l2 / mean_length_safe;
    d_log_laa_d_k = d_length_d_k / mean_length_safe;
  }
 
  void log_length_at_age_logscale_gradient(const Type& age,
                                           Type& d_log_laa_d_log_length_young,
                                           Type& d_log_laa_d_log_length_old,
                                           Type& d_log_laa_d_log_k) const {
    Type d_log_laa_d_length_young = Type(0.0);
    Type d_log_laa_d_length_old = Type(0.0);
    Type d_log_laa_d_k = Type(0.0);
 
    log_length_at_age_gradient(age, d_log_laa_d_length_young,
                               d_log_laa_d_length_old, d_log_laa_d_k);
 
    d_log_laa_d_log_length_young = d_log_laa_d_length_young * mean_length_young;
    d_log_laa_d_log_length_old = d_log_laa_d_length_old * mean_length_old;
    d_log_laa_d_log_k = d_log_laa_d_k * growth_coefficient;
  }
 
  Type weight_at_age(const Type& age) const {
    Type length = length_at_age(age);
    return length_weight_a * fims_math::pow(length, length_weight_b);
  }
 
  virtual const Type evaluate(int year, const double& a) override {
    (void)year;
    return weight_at_age(Type(a));
  }
};
}  // namespace fims_popdy
 
#endif  // POPULATION_DYNAMICS_GROWTH_VONB_SCHNUTE_HPP