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Population.hpp
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/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
/*
* File: Population.hpp
* Author: matthewsupernaw
*
* Created on September 14, 2016, 1:44 PM
*/
#ifndef POPULATION_HPP
#define POPULATION_HPP
#include <memory>
#include <vector>
#include <iomanip>
#include <unordered_map>
#include <unordered_set>
#include "Area.hpp"
//#include "../AutoDiff_Standalone/AutoDiff/AutoDiff.hpp"
#include "Movement.hpp"
#include "Recruitment.hpp"
#include "HarvestControlRule.hpp"
#include "MaximumSustainableYield.hpp"
#include "third_party/ATL/lib/Variable.hpp"
namespace mas {
/** @defgroup pop_dynamics Population Dynamics
*
* @{
*/
template<class REAL_T>
class Population;
/**
* Run time calculated information for a population in a specific area, by sex.
*/
template<class REAL_T>
struct Subpopulation {
typedef typename mas::VariableTrait<REAL_T>::variable variable;
int id;
int uid = -9999;
mas::FishSexType sex;
std::vector<variable> ages;
int spawning_season = 1;
/* NOTE: these values need to be defined elsewhere*/
variable spawning_season_offset = 0.0;
variable catch_season_offset = 1.0;
variable survey_season_offset = 1.0;
variable kg_to_tonnes = 1000.0; // convert kg to metric tonnes
REAL_T sex_fraction_value = 0.5;
/*==================================*/
bool males = true;
Population<REAL_T>* natal_population;
bool natal_homing = false;
std::shared_ptr<Area<REAL_T> > area;
std::shared_ptr<Area<REAL_T> > natal_area;
std::shared_ptr<GrowthBase<REAL_T> > growth_model;
std::shared_ptr<mas::NaturalMortality<REAL_T> > natural_mortality_model; // population - area specific
std::shared_ptr<mas::RecruitmentBase<REAL_T> > recruitment_model; // population - area specific
std::unordered_map<int, std::shared_ptr<mas::RecruitmentBase<REAL_T> > > seasonal_recruitment_models;
std::vector<REAL_T> maturity; // should be the same across areas, same length as ages
// these PARAMETERS can be fixed or estimated; should be in model config
#warning hard coded value initialF
variable initialF = static_cast<REAL_T> (0.0);
std::vector<variable> initialS;
std::vector<variable> M;
std::vector<variable> F; // this PARAMETER vector is shared between males and females
std::unordered_set<int> active_fleets;
std::unordered_map<int, std::vector<variable> > F_at_age; // access by fleet id these values may differ between males and females
std::unordered_map<int, std::vector<variable> > Z_at_age; // access by fleet id these values may differ between males and females
std::unordered_map<int, std::vector<variable> > SN_at_age; // access by fleet id these values may differ between males and females
// these are shared by males and females for a specific population and area
variable R0; // PARAMETER: fixed or estimated
variable S0;
variable unfished_spawning_biomass_per_recruit;
variable unfished_spawners_per_recruit;
variable fished_spawning_biomass_per_recruit;
variable fished_spawners_per_recruit;
variable fished_yield_per_recruit;
variable fished_max_yield_per_recruit;
//biological reference points
std::vector<variable> F100;
std::vector<variable> SB100;
std::vector<variable> F40;
std::vector<variable> SB40;
std::vector<variable> F35;
std::vector<variable> SB35;
std::vector<variable> F20;
std::vector<variable> S20;
std::vector<variable> SB_target;
variable avgR;
variable SB0; // derived variable, retrieve from the recruitment functor at finalize
std::vector<variable> initial_numbers;
std::vector<variable> initial_equilibrium_numbers;
std::vector<variable> initial_deviations; // PARAMETER: fixed or estimated
//
int years;
int seasons;
int forecast_years = 5;
std::vector<variable> length_at_season_start;
std::vector<variable> length_at_spawning;
std::vector<variable> length_at_catch_time;
std::vector<variable> length_at_survey_time;
std::vector<variable> weight_at_season_start;
std::vector<variable> weight_at_spawning;
std::vector<variable> weight_at_catch_time;
std::vector<variable> weight_at_survey_time;
std::vector<variable> equilibrium_to_survival_at_spawning;
std::vector<variable> fecundity_at_age;
std::vector<variable> spawning_stock_biomass;
std::vector<variable> redistributed_recruits;
std::vector<variable> immigrant_recruits;
std::vector<variable> immigrant_recruits_biomass;
std::vector<variable> emigrant_recruits;
std::vector<variable> emigrant_recruits_biomass;
std::vector<variable> imigrants;
std::vector<variable> imigrants_biomass;
std::vector<variable> emigrants;
std::vector<variable> emigrants_biomass;
std::vector<variable> growth;
std::vector<variable> recruitment;
std::vector<variable> spawning_numbers_at_age;
std::vector<variable> biomass_total;
std::vector<variable> fishing_mortality_total;
std::vector<variable> sum_selectivity;
std::vector<variable> Z;
std::vector<variable> P; //selectivity at age.
variable sum_of_Z;
std::vector<variable> S;
std::vector<variable> numbers_at_age;
std::vector<variable> biomass_at_age;
std::vector<variable> abundance;
std::vector<variable> survey_numbers_at_age; //survey numbers at age
std::vector<variable> survey_index_at_age; //survey index at age
std::vector<REAL_T> survey_biomass_total; //survey index total
std::vector<variable> catch_at_age;
std::vector<variable> catch_biomass_at_age;
std::vector<REAL_T> catch_biomass_total;
std::vector<variable> expected_N;
std::vector<variable> N_proj; // numbers-at-age in endyear + 1
static uint32_t length_weight_key_carryout;
MaximumSustainableYield<REAL_T> msy;
REAL_T MSY; // maximum sustainable yield
REAL_T Dmsy; // dead discards at MSY
REAL_T Fmsy; // fishing rate at MSY
REAL_T SSBmsy; // spawning stock biomass at msy
REAL_T Rmsy; // equilibrium recruitment at msy
REAL_T Bmsy; // total biomass (male and female) at msy
REAL_T Emsy; // exploitation rate at msy (total catch / number of fish)
REAL_T spr_msy; // spawners per recruit at msy
REAL_T SPRmsy; // spawning potential ratio (spr_msy/spr_virgin)
/**************************
* Forecasting Containers *
**************************/
std::vector<std::vector<REAL_T> > BootNumbers;
void Initialize() {
typename Area<REAL_T>::active_fleets_iterator af_it;
for (af_it = this->area->active_fleets.begin(); af_it != this->area->active_fleets.end(); ++af_it) {
(*af_it)->f_at_age[this->area->id][this->id].resize(years * seasons * ages.size());
(*af_it)->z_at_age[this->area->id][this->id].resize(years * seasons * ages.size());
if (this->sex == mas::MALE) {
(*af_it)->f_at_age_males[this->area->id][this->id].resize(years * seasons * ages.size());
(*af_it)->z_at_age_males[this->area->id][this->id].resize(years * seasons * ages.size());
} else {
(*af_it)->f_at_age_females[this->area->id][this->id].resize(years * seasons * ages.size());
(*af_it)->z_at_age_females[this->area->id][this->id].resize(years * seasons * ages.size());
}
}
length_at_season_start.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size() + 1);
length_at_spawning.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size());
length_at_catch_time.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size());
length_at_survey_time.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size());
weight_at_season_start.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size() + 1);
weight_at_spawning.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size());
weight_at_catch_time.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size());
weight_at_survey_time.resize(length_weight_key_carryout + this->years * this->seasons * this->ages.size());
equilibrium_to_survival_at_spawning.resize(years * seasons * ages.size());
fecundity_at_age.resize(years * seasons * ages.size());
spawning_numbers_at_age.resize(years * seasons * ages.size());
spawning_stock_biomass.resize(years * seasons);
recruitment.resize(years * seasons);
redistributed_recruits.resize(years * seasons);
immigrant_recruits.resize(years * seasons);
emigrant_recruits.resize(years * seasons);
abundance.resize(years * seasons);
initial_numbers.resize(this->ages.size()*3);
initial_equilibrium_numbers.resize(this->ages.size()*3);
// these are all (fixed or estimated) PARAMETERS
#warning hard coded vector initialS
initialS.resize(this->ages.size(), 1.0); //fixed
M.resize(this->ages.size()); //estimated
initial_deviations.resize(this->ages.size()); //fixed
this->sum_selectivity.resize(years * seasons * this->ages.size());
this->fishing_mortality_total.resize(years * seasons);
// F_at_age.resize(years * seasons * ages.size());
#warning needs to be more efficient, possibly allocating unused memory
std::unordered_set<int>::iterator fit;
for (fit = this->active_fleets.begin(); fit != this->active_fleets.end(); ++fit) {
F_at_age[(*fit)].resize(years * seasons * ages.size());
Z_at_age[(*fit)].resize(years * seasons * ages.size());
}
emigrants.resize(years * seasons * ages.size());
emigrants_biomass.resize(years * seasons * ages.size());
imigrants.resize(years * seasons * ages.size());
imigrants_biomass.resize(years * seasons * ages.size());
growth.resize(years * seasons * ages.size());
Z.resize(years * seasons * ages.size());
F.resize(years * seasons * ages.size());
P.resize(years * seasons * ages.size());
S.resize(years * seasons * ages.size());
biomass_total.resize(years * seasons);
survey_numbers_at_age.resize(years * seasons * ages.size());
survey_index_at_age.resize(years * seasons * ages.size());
survey_biomass_total.resize(years, seasons);
numbers_at_age.resize((years + 1) * seasons * ages.size());
biomass_at_age.resize(years * seasons * ages.size());
catch_at_age.resize(years * seasons * ages.size());
catch_biomass_at_age.resize(years * seasons * ages.size());
catch_biomass_total.resize(years * seasons);
expected_N.resize(years * seasons * ages.size());
N_proj.resize(seasons * ages.size());
}
inline void Reset() {
std::fill(this->catch_biomass_total.begin(), this->catch_biomass_total.end(), static_cast<REAL_T> (0.0));
std::fill(this->survey_biomass_total.begin(), this->survey_biomass_total.end(), static_cast<REAL_T> (0.0));
for (int i = 0; i < numbers_at_age.size(); i++) {
mas::VariableTrait<REAL_T>::SetValue(numbers_at_age[i], static_cast<REAL_T> (0.0));
}
for (int i = 0; i < survey_numbers_at_age.size(); i++) {
mas::VariableTrait<REAL_T>::SetValue(emigrants[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(emigrants_biomass[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(imigrants[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(imigrants_biomass[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(growth[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(Z[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(F[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(P[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(S[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(biomass_at_age[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(survey_numbers_at_age[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(survey_index_at_age[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(catch_at_age[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(catch_biomass_at_age[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(expected_N[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(fecundity_at_age[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(equilibrium_to_survival_at_spawning[i], static_cast<REAL_T> (0.0));
}
for (int i = 0; i < recruitment.size(); i++) {
mas::VariableTrait<REAL_T>::SetValue(recruitment[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(redistributed_recruits[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(immigrant_recruits[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(emigrant_recruits[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(abundance[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(spawning_stock_biomass[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(biomass_total[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(fishing_mortality_total[i], static_cast<REAL_T> (0.0));
}
for (int i = 0; i < this->initial_numbers.size(); i++) {
mas::VariableTrait<REAL_T>::SetValue(initial_numbers[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(initial_equilibrium_numbers[i], static_cast<REAL_T> (0.0));
}
for (int i = 0; i < this->sum_selectivity.size(); i++) {
mas::VariableTrait<REAL_T>::SetValue(this->sum_selectivity[i], static_cast<REAL_T> (0.0));
}
for (int i = 0; i < this->length_at_spawning.size(); i++) {
mas::VariableTrait<REAL_T>::SetValue(weight_at_season_start[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(length_at_season_start[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(length_at_spawning[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(length_at_catch_time[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(length_at_survey_time[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(weight_at_spawning[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(weight_at_catch_time[i], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(weight_at_survey_time[i], static_cast<REAL_T> (0.0));
}
mas::VariableTrait<REAL_T>::SetValue(weight_at_season_start[this->length_at_spawning.size()], static_cast<REAL_T> (0.0));
mas::VariableTrait<REAL_T>::SetValue(length_at_season_start[this->length_at_spawning.size()], static_cast<REAL_T> (0.0));
std::unordered_set<int>::iterator fit;
for (fit = this->active_fleets.begin(); fit != this->active_fleets.end(); ++fit) {
std::fill(F_at_age[(*fit)].begin(), F_at_age[(*fit)].end(), static_cast<REAL_T> (0.0));
std::fill(Z_at_age[(*fit)].begin(), Z_at_age[(*fit)].end(), static_cast<REAL_T> (0.0));
}
typename Area<REAL_T>::active_fleets_iterator af_it;
for (af_it = this->area->active_fleets.begin(); af_it != this->area->active_fleets.end(); ++af_it) {
std::vector<variable>& f_l = (*af_it)->f_at_age[this->area->id][this->id];
std::vector<variable>& z_l = (*af_it)->z_at_age[this->area->id][this->id];
std::fill(f_l.begin(), f_l.end(), static_cast<REAL_T> (0.0));
std::fill(z_l.begin(), z_l.end(), static_cast<REAL_T> (0.0));
if (this->sex == mas::MALE) {
std::vector<variable>& f_m_l = (*af_it)->f_at_age_males[this->area->id][this->id];
std::vector<variable>& z_m_l = (*af_it)->z_at_age_males[this->area->id][this->id];
std::fill(f_m_l.begin(), f_m_l.end(), static_cast<REAL_T> (0.0));
std::fill(z_m_l.begin(), z_m_l.end(), static_cast<REAL_T> (0.0));
} else {
std::vector<variable>& f_f_l = (*af_it)->f_at_age_females[this->area->id][this->id];
std::vector<variable>& z_f_l = (*af_it)->z_at_age_females[this->area->id][this->id];
std::fill(f_f_l.begin(), f_f_l.end(), static_cast<REAL_T> (0.0));
std::fill(z_f_l.begin(), z_f_l.end(), static_cast<REAL_T> (0.0));
}
}
}
/**
* Evaluates length at age and weight at age
*
* time of spawning, peak fishing, and survey could differ across areas for a population
*/
inline void CalculateWeightAtAge() {
std::vector<variable> length_at_season_start_temp(this->ages.size());
std::vector<variable> length_at_spawning_temp(this->ages.size());
std::vector<variable> length_at_catch_time_temp(this->ages.size());
std::vector<variable> length_at_survey_time_temp(this->ages.size());
for (int i = 0; i < ages.size(); ++i) {
variable a = ages[i];
length_at_season_start_temp[i] = this->growth_model->Evaluate(a, this->sex);
length_at_spawning_temp[i] = this->growth_model->Evaluate(a + this->spawning_season_offset, this->sex);
length_at_catch_time_temp[i] = this->growth_model->Evaluate(a + this->catch_season_offset, this->sex);
length_at_survey_time_temp[i] = this->growth_model->Evaluate(a + this->survey_season_offset, this->sex);
}
for (int y = 0; y < this->years; y++) {
for (int s = 0; s < this->seasons; s++) {
for (int a = 0; a < ages.size(); ++a) {
//dimension folded index
size_t index = y * this->seasons * this->ages.size() + s * this->ages.size() + a;
// length at age
length_at_season_start[index] = length_at_season_start_temp[a];
length_at_spawning[index] = length_at_spawning_temp[a];
length_at_catch_time[index] = length_at_catch_time_temp[a];
length_at_survey_time[index] = length_at_survey_time_temp[a];
//weight at season start
this->growth_model->GetWeight(y, s,
this->length_at_season_start[a],
ages[a].GetValue(),
this->sex, this->id, mas::MEAN_WEIGHT_AT_AGE_SEASON_START, weight_at_season_start[index]);
//weight at spawning
this->growth_model->GetWeight(y, s,
this->length_at_spawning[a],
ages[a].GetValue() + this->spawning_season_offset.GetValue(),
this->sex, this->id, mas::MEAN_WEIGHT_AT_AGE_SPAWNING, weight_at_spawning[index]);
this->fecundity_at_age[index] = this->weight_at_spawning[index] * this->maturity[a];
//weight at catch time
this->growth_model->GetWeight(y, s,
this->length_at_catch_time[a],
ages[a].GetValue() + this->catch_season_offset.GetValue(),
this->sex, this->id, mas::CATCH_MEAN_WEIGHT_AT_AGE, weight_at_catch_time[index]);
//weight at survey time
this->growth_model->GetWeight(y, s,
this->length_at_survey_time[a],
ages[a].GetValue() + this->survey_season_offset.GetValue(),
this->sex, this->id, mas::SURVEY_MEAN_WEIGHT_AT_AGE, weight_at_survey_time[index]);
}
}
}
}
inline REAL_T CalculateUnfishedSpawningBiomassPerRecruit() {
std::vector<variable > sb_per_recruit(this->years);
std::vector<variable > s_per_recruit(this->years);
for (int y = 0; y < this->years; y++) {
variable ntemp0 = 1.0;
for (int s = 0; s < this->seasons; s++) {
for (int a = 0; a < ages.size() - 1; a++) {
size_t index = y * this->seasons * this->ages.size() + (s) * this->ages.size() + a;
sb_per_recruit[y] += ntemp0 * (this->weight_at_spawning[index] * this->M[a]) *
mas::mfexp(-1.0 * this->spawning_season_offset * M[a]);
s_per_recruit[y] += ntemp0 * (this->fecundity_at_age[index] * this->M[a]) *
mas::mfexp(-1.0 * this->spawning_season_offset * M[a]);
ntemp0 *= mas::mfexp(-1.0 * this->spawning_season_offset * M[a]);
}
size_t plus_group = this->ages.size() - 1;
size_t index = y * this->seasons * this->ages.size() + (s) * this->ages.size() + plus_group;
ntemp0 /= (1.0 - mas::mfexp(-1.0 * M[plus_group]));
sb_per_recruit[y] += ntemp0 * (this->weight_at_spawning[index] * this->M[this->ages.size() - 1])
* mas::mfexp(-1.0 * this->spawning_season_offset * M[plus_group]);
s_per_recruit[y] += ntemp0 * (this->fecundity_at_age[index] * this->M[this->ages.size() - 1])
* mas::mfexp(-1.0 * this->spawning_season_offset * M[plus_group]);
}
}
this->unfished_spawning_biomass_per_recruit = (sb_per_recruit[this->years - 1]);
this->unfished_spawners_per_recruit = (s_per_recruit[this->years - 1]);
variable ret = sb_per_recruit[this->years - 1];
return ret.GetValue();
}
inline REAL_T CalculateFishedSpawningBiomassPerRecruit_(REAL_T F) {
std::vector<variable> faa(this->F.size());
variable z_sum;
for (int y = 0; y < this->years; y++) {
for (int s = 0; s < this->seasons; s++) {
for (int a = 0; a < ages.size() - 1; a++) {
size_t index = y * this->seasons * this->ages.size() + (s) * this->ages.size() + a;
faa[index] = P[index] * F;
z_sum = faa[index] + M[a];
}
}
}
std::vector<variable > s_per_recruit(this->years);
for (int y = 0; y < this->years; y++) {
variable ntemp0 = 1.0;
for (int s = 0; s < this->seasons; s++) {
for (int a = 0; a < ages.size() - 1; a++) {
size_t index = y * this->seasons * this->ages.size() + (s) * this->ages.size() + a;
s_per_recruit[y] += ntemp0 * (this->weight_at_spawning[index] * this->M[a]) *
mas::mfexp(-1.0 * this->spawning_season_offset * M[a]
- z_sum - P[index] * faa[index]);
ntemp0 *= mas::mfexp(-1.0 * this->spawning_season_offset * M[a]);
}//end a
//plus group
size_t plus_index = this->ages.size() - 1;
size_t index = y * this->seasons * this->ages.size() + (s) * this->ages.size() + plus_index;
ntemp0 /= (1.0 - mas::mfexp(-1.0 * M[plus_index]));
s_per_recruit[y] += ntemp0 * (this->weight_at_spawning[index] * this->M[this->ages.size() - 1])
* mas::mfexp(-1.0 * M[plus_index] -
z_sum - this->spawning_season_offset * P[index] * faa[index]);
}//end s
}//end y
this->fished_spawning_biomass_per_recruit = s_per_recruit[this->years - 1] * this->sex_fraction_value;
variable ret = s_per_recruit[this->years - 1] * this->sex_fraction_value;
return ret.GetValue();
}
inline REAL_T CalculateFishedSpawningBiomassPerRecruit(int year, int season, REAL_T F) {
for (int i = 0; i < this->ages.size(); i++) {
size_t index = year * this->seasons * this->ages.size() + season * this->ages.size() + i;
REAL_T temp = 0.0;
for (int j = 0; j < i; j++) {
size_t index2 = year * this->seasons * this->ages.size() + season * this->ages.size() + j;
temp += F * this->S[index2].GetValue() + this->M[j].GetValue();
}
}
}
inline REAL_T CalculateYieldPerRecruit(REAL_T F) {
REAL_T ret;
for (int i = 0; i < this->ages.size(); i++) {
size_t index = (this->years - 1) * this->seasons * this->ages.size() + (this->seasons - 1) * this->ages.size() + i;
ret += ((this->weight_at_catch_time[index].GetValue() * F * this->sum_selectivity[index].GetValue()) /
(F * this->sum_selectivity[index].GetValue() + this->M[i].GetValue())) * this->CalculateProbabilityOfCaptureAtAge(i, this->years - 1, this->seasons - 1, F) *
this->CalculateProbabilityOfSurvivalToAge(i, this->years - 1, this->seasons - 1, F);
std::cout << ((this->weight_at_catch_time[index].GetValue() * F * this->sum_selectivity[index].GetValue()) /
(F * this->sum_selectivity[index].GetValue() + this->M[i].GetValue())) << " * " << this->CalculateProbabilityOfCaptureAtAge(i, this->years - 1, this->seasons - 1, F) << " * " <<
this->CalculateProbabilityOfSurvivalToAge(i, this->years - 1, this->seasons - 1, F) << std::endl;
// +
// this->CalculateProbabilityOfCaptureAtAgeAOrOlder(this->ages.size() - 1, this->years - 1, this->seasons - 1, F) *
// this->CalculateProbabilityOfSurvivalToAge(i, this->years - 1, this->seasons - 1, F);
}
return ret + this->CalculateProbabilityOfCaptureAtAgeAOrOlder(this->ages.size() - 1, this->years - 1, this->seasons - 1, F) *
this->CalculateProbabilityOfSurvivalToAge(this->ages.size() - 1, this->years - 1, this->seasons - 1, F);
}
inline REAL_T CalculateProbabilityOfSurvivalToAge(int a, int year, int season, REAL_T F) {
REAL_T sum_z = 0;
for (int i = 0; i < a; i++) {
size_t index = year * this->seasons * this->ages.size() + (season) * this->ages.size() + i;
sum_z += F * this->sum_selectivity[index].GetValue() + this->M[i].GetValue();
}
return std::exp(-1.0 * sum_z);
}
inline REAL_T CalculateProbabilityOfCaptureAtAge(int a, int year, int season, REAL_T F) {
size_t index = year * this->seasons * this->ages.size() + (season) * this->ages.size() + a;
return (1.0 - std::exp(-1.0 * F * this->Z[index].GetValue()));
}
inline REAL_T CalculateProbabilityOfCaptureAtAgeAOrOlder(int a, int year, int season, REAL_T F) {
size_t index = year * this->seasons * this->ages.size() + (season) * this->ages.size() + a;
return (this->weight_at_catch_time[index].GetValue() * F * this->sum_selectivity[index].GetValue()) /
(F * this->sum_selectivity[index].GetValue() + this->M[a].GetValue());
}
inline REAL_T CalculateSPR(REAL_T F) {
variable ret = this->CalculateFishedSpawningBiomassPerRecruit(this->years - 1, this->seasons - 1, F) / this->CalculateUnfishedSpawningBiomassPerRecruit();
return ret.GetValue();
}
inline REAL_T CalculateFSPR(REAL_T fraction) {
REAL_T distance = std::numeric_limits<REAL_T>::max();
REAL_T fspr = 0.0;
for (REAL_T f = 0.0; f < 3.0; f += 0.01) {
REAL_T spr = this->CalculateSPR(f);
REAL_T dist = std::fabs(spr - fraction);
if (dist < distance) {
distance = dist;
fspr = f;
}
}
return fspr;
}
inline REAL_T CalculateFMax(const std::vector<REAL_T>& f) {
REAL_T max_yield_per_recruit = std::numeric_limits<REAL_T>::min();
REAL_T Fmax = 0.0;
for (int i = 0; i < f.size(); i++) {
REAL_T mypr = this->CalculateYieldPerRecruit(f[i]);
if (mypr > max_yield_per_recruit) {
max_yield_per_recruit = mypr;
Fmax = f[i];
}
}
return Fmax;
}
inline REAL_T CalculateEquilibriumSpawningBiomass(REAL_T F) {
REAL_T sbpr = this->CalculateFishedSpawningBiomassPerRecruit(this->years - 1, this->seasons - 1, F);
return this->recruitment_model->CalculateEquilibriumSpawningBiomass(sbpr);
}
inline REAL_T CalculateEquilibriumRecruitment(REAL_T F) {
REAL_T esb = CalculateEquilibriumSpawningBiomass(F);
return this->recruitment_model->CalculateEquilibriumRecruitment(esb);
}
inline REAL_T CalculateEquilibriumYield(REAL_T F) {
return this->CalculateEquilibriumRecruitment(F) *
this->CalculateYieldPerRecruit(F);
}
void CalculateMaximumSustainableYield(
REAL_T& msy,
REAL_T& f_msy,
REAL_T& s_msy) {
REAL_T max_yield = std::numeric_limits<REAL_T>::min();
REAL_T f_max = 0.0;
REAL_T s_max = 0.0;
for (REAL_T f = 0.0; f <= 3.0; f += 0.01) {
REAL_T equil_yield = this->CalculateEquilibriumYield(f);
if (equil_yield > max_yield) {
max_yield = equil_yield;
REAL_T esb = this->CalculateEquilibriumSpawningBiomass(f);
f_max = f;
s_max = esb;
}
}
msy = max_yield;
f_msy = f_max;
s_msy = s_max;
}
void InitializeM() {
for (int a = 0; a < this->ages.size(); a++) {
this->M[a] = this->natural_mortality_model->Evaluate(a);
}
}
void CalculateInitialNumbersEquilibrium() {
//note initial_numbers and initial_equilibrium_numbers vectors
//are both size 3*ages.size()
this->R0 = this->sex_fraction_value * mas::mfexp(this->recruitment_model->log_R0);
this->initial_equilibrium_numbers[0] = this->R0;
int a;
for (a = 1; a < this->ages.size(); a++) {
this->initial_equilibrium_numbers[a] = this->initial_equilibrium_numbers[a - 1] *
mas::exp(static_cast<REAL_T> (-1.0) * (this->M[a - 1]));
}
variable m = this->M[a - 1];
variable sum;
for (a = this->ages.size(); a < this->initial_equilibrium_numbers.size(); a++) {
this->initial_equilibrium_numbers[a] = this->initial_equilibrium_numbers[a - 1] * mas::exp(static_cast<REAL_T> (-1.0) * (m));
sum += this->initial_equilibrium_numbers[a];
}
this->initial_equilibrium_numbers[ this->ages.size() - 1] += sum +
(this->initial_equilibrium_numbers[this->initial_equilibrium_numbers.size() - 1] * mas::exp(static_cast<REAL_T> (-1.0) * (m))) /
(1.0 - mas::exp(static_cast<REAL_T> (-1.0) * (m)));
}
void CalculateInitialNumbers() {
// variable sigma_r = this->recruitment_model->sigma_r;
int a;
for (a = 0; a < this->ages.size(); a++) {
this->initial_numbers[a] = (mas::exp(static_cast<REAL_T> (-1.0) *
this->M[a] - this->initialF) * this->initial_equilibrium_numbers[a] *
mas::exp(initial_deviations[a] - static_cast<REAL_T> (0.5)
/* mas::pow(sigma_r, static_cast<REAL_T> (2.0))*/));
}
// /*
// this->initial_numbers[a] = (mas::exp(static_cast<REAL_T> (-1.0) *
// this->M[a] - this->initialF) * this->initial_equilibrium_numbers[a]/*
// mas::exp(initial_deviations[a] - static_cast<REAL_T> (0.5))*/);
// */
}
void CalculateUnfishedEquilSpawningBiomass() {
if (this->sex == FEMALE) {
this->R0 = this->sex_fraction_value * mas::mfexp(this->recruitment_model->log_R0);
this->S0 = this->unfished_spawners_per_recruit * this->R0;
variable temp;
for (int a = 0; a < this->ages.size(); a++) {
temp += this->initial_equilibrium_numbers[a] *
this->weight_at_spawning[a] * this->maturity[a] *
mas::exp(-1.0 * this->spawning_season_offset * this->M[a]);
}
this->recruitment_model->SB0[this->id][this->area->id] = temp;
this->SB0 = temp;
}
}
variable spr_unfished(int year) {
avgR = 0.0;
variable Ntmp = 1.0;
variable SBtmp;
size_t a = 0;
size_t s = 0;
for (size_t i = 0; i < year; i++) {
size_t index = year * this->seasons * this->ages.size() + s * this->ages.size() + a;
avgR += this->numbers_at_age[index];
}
avgR /= (REAL_T)this->years;
for (a = 0; a < this->ages.size(); a++) {
size_t index = year * this->seasons * this->ages.size() + s * this->ages.size() + a;
SBtmp += (Ntmp * this->maturity[a] * this->weight_at_spawning[index] * mas::exp(-1.0 * this->spawning_season_offset * this->M[a]));
Ntmp *= (mas::exp(-1.0 * this->M[a]));
}
size_t index = year * this->seasons * this->ages.size() + s * this->ages.size() + a - 1;
Ntmp /= (mas::exp(-1.0 * this->M[a - 1]));
SBtmp += (Ntmp * this->maturity[a - 1] * this->weight_at_spawning[index] * mas::exp(-1.0 * this->spawning_season_offset * this->M[a - 1]));
return SBtmp;
}
variable spr_ratio(const variable& trial_F, int curryr) {
std::vector<variable> Ntmp(this->ages.size());
std::vector<variable> srvtmp(this->ages.size());
std::vector<variable> Ftmp(this->ages.size());
variable SBcurr;
variable SB0;
variable phi0;
size_t jj = 0;
size_t s = 0;
for (jj = 0; jj < this->ages.size(); jj++) {
size_t index = curryr * this->seasons * this->ages.size() + s * this->ages.size() + jj;
Ftmp[jj] = this->P[index] * trial_F;
srvtmp[jj] = Ftmp[jj] + this->M[jj];
}
SB0 = spr_unfished(curryr);
phi0 = SB0 / avgR;
jj = 0;
size_t index = curryr * this->seasons * this->ages.size() + s * this->ages.size() + jj;
Ntmp[jj] = avgR;
SBcurr += (Ntmp[jj] * this->maturity[jj] * this->weight_at_spawning[index] * mas::exp(-1.0 * this->spawning_season_offset * srvtmp[jj]));
for (jj = 1; jj <this->ages.size(); jj++) {
size_t index = curryr * this->seasons * this->ages.size() + s * this->ages.size() + jj;
Ntmp[jj] = Ntmp[jj - 1] * mas::exp(-1.0 * srvtmp[jj - 1]);
SBcurr += (Ntmp[jj] * this->maturity[jj] * this->weight_at_spawning[index] * mas::exp(-1.0 * this->spawning_season_offset * srvtmp[jj]));
}
size_t end_age = this->ages.size() - 1;
Ntmp[end_age] = (Ntmp[end_age - 1] * mas::exp(-srvtmp[end_age - 1]) / (1.0 - mas::exp(-1.0 * srvtmp[end_age])));
SBcurr += (Ntmp[end_age] * this->maturity[jj] * this->weight_at_spawning[index] * mas::exp(-1.0 * this->spawning_season_offset * srvtmp[end_age]));
return (SBcurr / SB0);
}
variable get_spr_rates(const variable& spr_percent, int curryr) {
REAL_T df = 1.e-3;
variable F1, F2, F3;
variable yld1, yld2, yld3;
variable dyld, dyldp;
F1 = 0.3;
for (int ii = 1; ii <= 10; ii++) // arbitrary fixed intervals
{
F2 = F1 + df;
F3 = F1 - df;
yld1 = /*-1000. */ mas::pow(mas::log(spr_percent / spr_ratio(F1, curryr)), 2.0);
yld2 = /*-1000. */ mas::pow(mas::log(spr_percent / spr_ratio(F2, curryr)), 2.0);
yld3 = /*-1000. */ mas::pow(mas::log(spr_percent / spr_ratio(F3, curryr)), 2.0);
dyld = (yld2 - yld3) / (2. * df); // First derivative (to find the root of this)
dyldp = (yld3 - (2. * yld1) + yld2) / (df * df); // Newton-Raph approximation 2nd deriv
F1 -= (dyld / dyldp);
}
return F1;
}
void BuildBootStrapNumbers() {
this->BootNumbers.resize(this->years,
std::vector<REAL_T>(this->ages.size()));
std::vector<std::vector<REAL_T> >
compressed_numbers(this->years,
std::vector<REAL_T>(this->ages.size()));
std::vector<std::vector<REAL_T> >
compressed_survivability(this->years,
std::vector<REAL_T>(this->ages.size()));
std::vector<REAL_T> NAAbsn(this->ages.size() + 1);
for (int y = 0; y < this->years; y++) {
for (int a = 0; a < this->ages.size(); a++) {
REAL_T temp_n = 0.0;
REAL_T temp_s = 0.0;
for (int s = 0; s < this->seasons; s++) {
size_t index = (y * this->seasons * this->ages.size())+
(s * this->ages.size()) + a;
temp_n += this->numbers_at_age[index].GetValue();
temp_s += this->S[index].GetValue();
}
compressed_numbers[y][a] = temp_n;
std::cout << compressed_numbers[y][a] << " ";
compressed_survivability[y][a] = temp_s;
}
std::cout << "\n";
}
REAL_T tempR = 0.0;
for (int y = 0; y < this->years; y++) {
tempR += std::log(compressed_numbers[y][0]);
}
NAAbsn[0] = std::exp(tempR / (this->years + 1.0));
//NAAbsn(iage) = NAA(nyears, iage - 1) * S(nyears, iage - 1);
std::cout << "BSN Recruitment Vector:\nSex " << this->sex << "\n";
for (int a = 1; a < this->ages.size(); a++) {
NAAbsn[a] = compressed_numbers[this->years - 1][a - 1] *
compressed_survivability[this->years - 1][a - 1];
std::cout << NAAbsn[a] << " ";
}
NAAbsn[this->ages.size()] =
compressed_numbers[this->years - 1][this->ages.size() - 1] *
compressed_survivability[this->years - 1][this->ages.size() - 1];
std::cout << NAAbsn[this->ages.size()] << " ";
std::cout << "\n\n\n";
}
inline void IncrementTime(int& y, int& s) {
if (s == this->seasons) {
y += 1;
s = 1;
} else {
s++;
}
}
inline void DecrementTime(int& y, int& s) {
if (s == 1) {
y -= 1;
s = seasons;
} else {
s--;
}
}
// /**
// * Calculate the F required to harvest the observed catch biomass
// * by 1 fleet in one time period (year) in 1 area with 1 population
// * using bisection search*/
// inline void FitInitialF(size_t max_iterations = 1000, REAL_T tolerance = 1e-5) {
// bool recording = variable::tape.recording;
// variable::tape.recording = false;
// mas::Tape<REAL_T> tape_l; //local tape
// tape_l.derivative_trace_level = atl::SECOND_ORDER_REVERSE;
// atl::Variable<REAL_T> f_l;
// atl::Variable<REAL_T> c_biomass;
// atl::Variable<REAL_T> sum;
// this->initialF.SetValue(static_cast<REAL_T> (0.0));
// tape_l.recording = true;
// REAL_T previous = 0;
// for (size_t iter = 0; iter < max_iterations; iter++) {
// f_l.SetValue(0.0);
// c_biomass.SetValue(0.0);
// sum.SetValue(0.0);
// std::vector< std::shared_ptr<mas::Fleet<REAL_T> > >& fleets = this->area->seasonal_fleet_operations[1];
// for (int f = 0; f < fleets.size(); f++) {
// for (int a = 0; a < this->ages.size(); a++) {
// // variable length_at_catch = this->growth_model->Evaluate(this->ages[a].GetValue() + this->catch_season_offset, this->sex);
// // variable wct = this->weight_at_catch_time[a];
//
// c_biomass.Assign(tape_l, c_biomass + this->weight_at_catch_time[a] *
// fleets[f]->season_area_selectivity[1][this->area->id]->Evaluate(this->ages[a]) *
// this->initialF * this->initial_equilibrium_numbers[a] *
// (1.0 - atl::exp(-this->M[a] - this->initialF)) /
// (this->M[a] + this->initialF), tape_l.NextIndex());
//
// }
// REAL_T C_B = fleets[f]->catch_biomass_data->get(0, 0); //*1000.0;
//
// f_l.Assign(tape_l, f_l + ((C_B) - (c_biomass))*((C_B) - (c_biomass)));
// }
// std::cout << tape_l.Value(this->initialF.info->id) << " " << tape_l.stack_current << "---->\n";
// tape_l.AccumulateSecondOrder();
// REAL_T deltaX = tape_l.Value(this->initialF.info->id) / tape_l.Value(this->initialF.info->id, this->initialF.info->id);
// if (std::fabs(tape_l.Value(this->initialF.info->id)) <= tolerance ||
// deltaX != deltaX) {
// tape_l.Reset();
// break;
// }
// this->initialF.SetValue(this->initialF.GetValue() - deltaX);
// if (iter) {
// if (std::fabs(previous - this->initialF.GetValue()) < 1e-5) {
// tape_l.Reset();
// break;
// }
// }
// previous = this->initialF.GetValue();
// tape_l.Reset();
// }
// variable::tape.recording = recording;
// }
/**
* Calculate the F required to harvest the observed catch biomass
* by 1 fleet in one time period (year) in 1 area with 1 population
* using bisection search*/
inline void FCalc() {
// if (this->initialF.GetValue() == 0.0) {
bool recording = variable::tape.recording;
variable::tape.recording = false;
// this->InitialNumbersEquilibrium();
this->initialF = static_cast<REAL_T> (0.0);
std::vector< std::shared_ptr<Fleet<REAL_T> > >& fleets = this->area->seasonal_fleet_operations[1];
variable wct, wct2;
for (int f = 0; f < fleets.size(); f++) {
if (fleets[f]->catch_biomass_data.get() != NULL) {
// std::shared_ptr<mas::FishingMortality<REAL_T> >& fm =
// fleets[f]->season_area_fishing_mortality[1][this->area->id];
REAL_T Epsilon = 0.0001;
REAL_T LowerBound = 0.0;
REAL_T UpperBound = 10.0;
REAL_T HasConverged = 0;
int Iteration = 0;
int amax = this->ages.size();
while (HasConverged == 0) {
REAL_T MidPoint = (LowerBound + UpperBound) / 2.0;
Iteration = Iteration + 1;
if ((UpperBound - MidPoint) < Epsilon) {
HasConverged = 1;
this->initialF += MidPoint;
break;
}
REAL_T tmp1 = 0.0;
for (int a = 0; a < amax; a++) {
// variable length_at_catch = this->growth_model->Evaluate(this->ages[a].GetValue() + this->catch_fraction_of_year, this->sex);
REAL_T N_ = this->initial_equilibrium_numbers[a].GetValue();
tmp1 = tmp1 + this->weight_at_catch_time[a].GetValue()/*this->weight_at_catch_time[a].GetValue()*/ *
fleets[f]->season_area_selectivity[1][this->area->id]->Evaluate(this->ages[a]).GetValue() *
MidPoint * N_ *
(1.0 - std::exp(-this->natural_mortality_model->Evaluate(a).GetValue() - MidPoint)) /
(this->natural_mortality_model->Evaluate(a).GetValue() + MidPoint);
}
#warning switch to observed catch biomass
//data is in MT
REAL_T C_B = fleets[f]->catch_biomass_data->get(0, 0); //this->C_Biomass[y * this->seasons + s].GetValue();//observed catch biomass
tmp1 = tmp1 - C_B;
REAL_T tmp2 = 0.0;
for (int a = 0; a < amax; a++) {
REAL_T N_ = this->initial_equilibrium_numbers[a].GetValue();
tmp2 = tmp2 + this->weight_at_catch_time[a].GetValue()/*this->weight_at_catch_time[a].GetValue()*/ *
fleets[f]->season_area_selectivity[1][this->area->id]->Evaluate(this->ages[a]).GetValue() *
UpperBound * N_ *
(1.0 - std::exp(-this->natural_mortality_model->Evaluate(a).GetValue() - UpperBound)) /
(this->natural_mortality_model->Evaluate(a).GetValue() + UpperBound);
}
tmp2 = tmp2 - C_B;
if (tmp1 * tmp2 <= 0.0) {
LowerBound = MidPoint;
} else {
UpperBound = MidPoint;
}
}
}
}
variable::tape.recording = recording;
// }
}
/**
* Evaluates mortality for all ages in a year and season.
* @param year
* @param season
*/