DISPLACE
1.0
A spatial model of fisheries to help sustainable fishing and maritime spatial planning
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#include <Population.h>
Public Member Functions | |
Population (int name, string pop_name, double _avai0_beta, double _avai2_beta, double _avai3_beta, double _avai5_beta, double _avai7_beta, const vector< int > &selected_szgroups, const vector< double > &init_tot_N_at_szgroup, const vector< double > &init_prop_migrants_in_tot_N_at_szgroup, const vector< double > &init_fecundity_at_szgroup, vector< double > init_weight_at_szgroup, const vector< int > &init_comcat_at_szgroup, const vector< double > &init_maturity_at_szgroup, vector< double > init_M_at_szgroup, const vector< double > &init_proprecru_at_szgroup, const vector< double > ¶m_sr, const multimap< int, types::NodeId > &lst_idx_nodes_per_pop, const multimap< types::NodeId, double > &full_spatial_availability, const multimap< types::NodeId, double > &field_of_coeff_diffusion_this_pop, const map< types::NodeId, double > &oth_land, const multimap< int, double > &overall_migration_fluxes, const map< string, double > &relative_stability_key, const vector< vector< double > > &percent_szgroup_per_age_matrix, const vector< vector< double > > &percent_age_perszgroup_matrix, const vector< vector< double > > &growth_transition_matrix, const vector< Node * > &nodes, const vector< double > &fbar_ages_min_max, const vector< double > &init_tac, double tac_percent_simulated, double hyperstability_param, double landings_so_far, double a_calib_cpue_multiplier, double a_calib_weight_at_szgroup) | |
Population () | |
virtual | ~Population () |
int | get_name () const |
string | get_pop_name () const |
int | get_nb_szgroups () const |
int | get_nb_ages () const |
const vector< Node * > & | get_list_nodes () const |
const vector< int > & | get_selected_szgroups () const |
double | get_avai0_beta () const |
double | get_avai2_beta () const |
double | get_avai3_beta () const |
double | get_avai5_beta () const |
double | get_avai7_beta () const |
double | get_cpue_multiplier () const |
const vector< double > & | get_tot_N_at_szgroup () const |
const vector< double > & | get_tot_C_at_szgroup () const |
const vector< double > & | get_tot_D_at_szgroup () const |
const vector< double > & | get_true_tot_N_at_szgroup () const |
const vector< double > & | get_prop_migrants_in_tot_N_at_szgroup () const |
const vector< double > & | get_tot_N_at_szgroup_just_after_redistribution () const |
const vector< double > & | get_tot_N_at_szgroup_month_minus_1 () const |
const vector< double > & | get_tot_N_at_szgroup_year_minus_1 () const |
const vector< double > & | get_a_tot_N_at_szgroup_before_applying_M () const |
const vector< double > & | get_tot_N_at_age () const |
const vector< double > & | get_perceived_tot_N_at_age () const |
const vector< double > & | get_tot_N_at_age_last_quarter () const |
const vector< double > & | get_tot_F_at_age () const |
const vector< double > & | get_tot_F_at_age_running_average () const |
const vector< double > & | get_tot_F_at_age_last_quarter () const |
const vector< double > & | get_perceived_tot_F_at_age () const |
const vector< double > & | get_tot_M_at_age () const |
const vector< double > & | get_tot_W_at_age () const |
const vector< double > & | get_tot_Mat_at_age () const |
const vector< double > & | get_fbar_ages_min_max () const |
const vector< double > & | get_maturity_at_szgroup () const |
const vector< double > & | get_fecundity_at_szgroup () const |
const vector< double > & | get_weight_at_szgroup () const |
vector< int > | get_comcat_at_szgroup () const |
const vector< double > & | get_M_at_szgroup () const |
const vector< double > & | get_proprecru_at_szgroup () const |
const vector< double > & | get_SSB_at_szgroup () const |
double | get_SSB () const |
double | get_fbar () const |
double | get_proportion_mature_fish () const |
const vector< double > & | get_FFmsy () const |
const vector< double > & | get_param_sr () const |
vector< vector< double > > | get_growth_transition_matrix () const |
vector< vector< double > > | get_percent_szgroup_per_age_matrix () const |
vector< vector< double > > | get_percent_age_per_szgroup_matrix () const |
multimap< types::NodeId, double > | get_full_spatial_availability () const |
multimap< types::NodeId, double > | get_field_of_coeff_diffusion_this_pop () const |
multimap< int, double > | get_overall_migration_fluxes () const |
map< types::NodeId, double > | get_oth_land () const |
double | get_hyperstability_param () const |
double | get_oth_land_multiplier () const |
Tac * | get_tac () const |
double | get_quota () const |
double | get_quota_uptake () const |
int | get_is_choking_fisheries () const |
double | get_landings_so_far () const |
double | get_tot_N_at_age0 () const |
const vector< double > & | get_landings_at_end_of_years () const |
void | set_quota (double _quota) |
void | set_quota_uptake (double _quota_uptake) |
void | set_selected_szgroups (vector< int > selected_szgroups) |
void | set_avai0_beta (double _avai0_beta) |
void | set_avai2_beta (double _avai2_beta) |
void | set_avai3_beta (double _avai3_beta) |
void | set_avai5_beta (double _avai5_beta) |
void | set_avai7_beta (double _avai7_beta) |
void | set_cpue_multiplier (double _cpue_multiplier) |
void | set_hyperstability_param (double _hyperstability_param) |
void | set_tot_N_at_szgroup (const vector< double > &_N_at_szgroup) |
void | set_tot_C_at_szgroup (const vector< double > &_C_at_szgroup) |
void | set_tot_D_at_szgroup (const vector< double > &_D_at_szgroup) |
void | set_true_tot_N_at_szgroup (const vector< double > &_true_tot_N_at_szgroup) |
void | set_prop_migrants_in_tot_N_at_szgroup (const vector< double > &_prop_migrants_at_szgroup) |
void | set_tot_N_at_szgroup_just_after_redistribution (const vector< double > &_N_at_szgroup_just_after_redistribution) |
void | set_tot_N_at_szgroup_month_minus_1 (const vector< double > &_N_at_szgroup_month_minus_1) |
void | set_tot_N_at_szgroup_year_minus_1 (const vector< double > &_N_at_szgroup_year_minus_1) |
void | set_a_tot_N_at_szgroup_before_applying_M (const vector< double > &_a_tot_N_at_szgroup_before_applying_M) |
void | set_tot_N_at_age (const vector< double > &_N_at_age) |
void | set_perceived_tot_N_at_age (const vector< double > &_perceived_N_at_age) |
void | set_tot_N_at_age_last_quarter (const vector< double > &_N_at_age_last_quarter) |
void | set_tot_F_at_age (const vector< double > &_F_at_age) |
void | set_tot_F_at_age_running_average (const vector< double > &_tot_F_at_age_running_average) |
void | set_perceived_tot_F_at_age (const vector< double > &_perceived_F_at_age) |
void | set_tot_F_at_age_last_quarter (const vector< double > &_tot_F_at_age_last_quarter) |
void | set_tot_M_at_age (const vector< double > &_M_at_age) |
void | set_tot_W_at_age (const vector< double > &_W_at_age) |
void | set_tot_Mat_at_age (const vector< double > &_Mat_at_age) |
void | set_adults_diet_preference_per_stock (const vector< double > &_adults_diet_preference_per_stock) |
void | set_juveniles_diet_preference_per_stock (const vector< double > &_juveniles_diet_preference_per_stock) |
void | set_maturity_at_szgroup (const vector< double > &_maturity_at_szgroup) |
void | set_fecundity_at_szgroup (const vector< double > &_fecundity_at_szgroup) |
void | set_weight_at_szgroup (const vector< double > &_weight_at_szgroup) |
void | set_comcat_at_szgroup (vector< int > _comcat_at_szgroup) |
void | set_M_at_szgroup (const vector< double > &_M_at_szgroup) |
void | set_proprecru_at_szgroup (const vector< double > &_proprecru_at_szgroup) |
void | set_SSB_at_szgroup (const vector< double > &_SSB_at_szgroup) |
void | set_SSB (double _SSB) |
void | set_fbar (double _fbar) |
void | set_FFmsy (const vector< double > &_FFmsy) |
void | set_is_choking_fisheries (int is_choking_fisheries) |
void | set_proportion_mature_fish (double _proportion_mature_fish) |
void | set_landings_so_far (double _landings_so_far) |
void | add_to_landings_at_end_of_years (double value) |
void | set_param_sr (const vector< double > &_param_sr) |
void | set_full_spatial_availability (multimap< types::NodeId, double > _full_spatial_availability) |
void | set_field_of_coeff_diffusion_this_pop (multimap< types::NodeId, double > _field_of_coeff_diffusion_this_pop) |
void | set_overall_migration_fluxes (multimap< int, double > _overall_migration_fluxes) |
void | set_oth_land (map< types::NodeId, double > _oth_land) |
void | set_oth_land_multiplier (double _a_multiplier) |
void | set_list_nodes (vector< Node * > _list_nodes) |
void | distribute_N () |
void | aggregate_N () |
void | diffuse_N_from_field (adjacency_map_t &adjacency_map) |
void | compute_tot_N_and_F_and_W_at_age (int a_month_i) |
void | compute_tot_M_at_age () |
double | compute_fbar () |
vector< double > | compute_SSB () |
double | compute_proportion_mature_fish () |
void | clear_tot_F_at_age () |
void | clear_tot_M_at_age () |
void | clear_tot_C_at_szgroup () |
void | clear_tot_D_at_szgroup () |
void | do_growth () |
void | apply_overall_migration_fluxes (vector< Population * > &populations) |
void | add_recruits_from_eggs () |
void | add_recruits_from_SR () |
void | add_recruits_from_a_fixed_number () |
void | apply_natural_mortality () |
void | export_popdyn_N (ofstream &popdyn_N, int tstep) |
void | export_popdyn_F (ofstream &popdyn_F, int tstep) |
void | export_popdyn_SSB (ofstream &popdyn_SSB, int tstep) |
void | export_popdyn_annual_indic (ofstream &popdyn_annual_indic, int tstep, const DynAllocOptions &dyn_alloc_sce) |
Population::Population | ( | int | name, |
string | pop_name, | ||
double | _avai0_beta, | ||
double | _avai2_beta, | ||
double | _avai3_beta, | ||
double | _avai5_beta, | ||
double | _avai7_beta, | ||
const vector< int > & | selected_szgroups, | ||
const vector< double > & | init_tot_N_at_szgroup, | ||
const vector< double > & | init_prop_migrants_in_tot_N_at_szgroup, | ||
const vector< double > & | init_fecundity_at_szgroup, | ||
vector< double > | init_weight_at_szgroup, | ||
const vector< int > & | init_comcat_at_szgroup, | ||
const vector< double > & | init_maturity_at_szgroup, | ||
vector< double > | init_M_at_szgroup, | ||
const vector< double > & | init_proprecru_at_szgroup, | ||
const vector< double > & | param_sr, | ||
const multimap< int, types::NodeId > & | lst_idx_nodes_per_pop, | ||
const multimap< types::NodeId, double > & | full_spatial_availability, | ||
const multimap< types::NodeId, double > & | field_of_coeff_diffusion_this_pop, | ||
const map< types::NodeId, double > & | oth_land, | ||
const multimap< int, double > & | overall_migration_fluxes, | ||
const map< string, double > & | relative_stability_key, | ||
const vector< vector< double > > & | percent_szgroup_per_age_matrix, | ||
const vector< vector< double > > & | percent_age_perszgroup_matrix, | ||
const vector< vector< double > > & | growth_transition_matrix, | ||
const vector< Node * > & | nodes, | ||
const vector< double > & | fbar_ages_min_max, | ||
const vector< double > & | init_tac, | ||
double | tac_percent_simulated, | ||
double | hyperstability_param, | ||
double | landings_so_far, | ||
double | a_calib_cpue_multiplier, | ||
double | a_calib_weight_at_szgroup | ||
) |
Population::Population | ( | ) |
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virtual |
void Population::add_recruits_from_a_fixed_number | ( | ) |
void Population::add_recruits_from_eggs | ( | ) |
void Population::add_recruits_from_SR | ( | ) |
void Population::add_to_landings_at_end_of_years | ( | double | value | ) |
void Population::aggregate_N | ( | ) |
void Population::apply_natural_mortality | ( | ) |
void Population::apply_overall_migration_fluxes | ( | vector< Population * > & | populations | ) |
void Population::clear_tot_C_at_szgroup | ( | ) |
void Population::clear_tot_D_at_szgroup | ( | ) |
void Population::clear_tot_F_at_age | ( | ) |
void Population::clear_tot_M_at_age | ( | ) |
double Population::compute_fbar | ( | ) |
double Population::compute_proportion_mature_fish | ( | ) |
vector< double > Population::compute_SSB | ( | ) |
void Population::compute_tot_M_at_age | ( | ) |
void Population::compute_tot_N_and_F_and_W_at_age | ( | int | a_month_i | ) |
void Population::diffuse_N_from_field | ( | adjacency_map_t & | adjacency_map | ) |
void Population::distribute_N | ( | ) |
void Population::do_growth | ( | ) |
void Population::export_popdyn_annual_indic | ( | ofstream & | popdyn_annual_indic, |
int | tstep, | ||
const DynAllocOptions & | dyn_alloc_sce | ||
) |
void Population::export_popdyn_F | ( | ofstream & | popdyn_F, |
int | tstep | ||
) |
void Population::export_popdyn_N | ( | ofstream & | popdyn_N, |
int | tstep | ||
) |
void Population::export_popdyn_SSB | ( | ofstream & | popdyn_SSB, |
int | tstep | ||
) |
const vector< double > & Population::get_a_tot_N_at_szgroup_before_applying_M | ( | ) | const |
double Population::get_avai0_beta | ( | ) | const |
double Population::get_avai2_beta | ( | ) | const |
double Population::get_avai3_beta | ( | ) | const |
double Population::get_avai5_beta | ( | ) | const |
double Population::get_avai7_beta | ( | ) | const |
vector< int > Population::get_comcat_at_szgroup | ( | ) | const |
double Population::get_cpue_multiplier | ( | ) | const |
double Population::get_fbar | ( | ) | const |
const vector< double > & Population::get_fbar_ages_min_max | ( | ) | const |
const vector< double > & Population::get_fecundity_at_szgroup | ( | ) | const |
const vector< double > & Population::get_FFmsy | ( | ) | const |
multimap< types::NodeId, double > Population::get_field_of_coeff_diffusion_this_pop | ( | ) | const |
multimap< types::NodeId, double > Population::get_full_spatial_availability | ( | ) | const |
vector< vector< double > > Population::get_growth_transition_matrix | ( | ) | const |
double Population::get_hyperstability_param | ( | ) | const |
int Population::get_is_choking_fisheries | ( | ) | const |
const vector< double > & Population::get_landings_at_end_of_years | ( | ) | const |
double Population::get_landings_so_far | ( | ) | const |
const vector< Node * > & Population::get_list_nodes | ( | ) | const |
const vector< double > & Population::get_M_at_szgroup | ( | ) | const |
const vector< double > & Population::get_maturity_at_szgroup | ( | ) | const |
int Population::get_name | ( | ) | const |
int Population::get_nb_ages | ( | ) | const |
int Population::get_nb_szgroups | ( | ) | const |
map< types::NodeId, double > Population::get_oth_land | ( | ) | const |
double Population::get_oth_land_multiplier | ( | ) | const |
multimap< int, double > Population::get_overall_migration_fluxes | ( | ) | const |
const vector< double > & Population::get_param_sr | ( | ) | const |
const vector< double > & Population::get_perceived_tot_F_at_age | ( | ) | const |
const vector< double > & Population::get_perceived_tot_N_at_age | ( | ) | const |
vector< vector< double > > Population::get_percent_age_per_szgroup_matrix | ( | ) | const |
vector< vector< double > > Population::get_percent_szgroup_per_age_matrix | ( | ) | const |
string Population::get_pop_name | ( | ) | const |
const vector< double > & Population::get_prop_migrants_in_tot_N_at_szgroup | ( | ) | const |
double Population::get_proportion_mature_fish | ( | ) | const |
const vector< double > & Population::get_proprecru_at_szgroup | ( | ) | const |
double Population::get_quota | ( | ) | const |
double Population::get_quota_uptake | ( | ) | const |
const vector< int > & Population::get_selected_szgroups | ( | ) | const |
double Population::get_SSB | ( | ) | const |
const vector< double > & Population::get_SSB_at_szgroup | ( | ) | const |
Tac * Population::get_tac | ( | ) | const |
const vector< double > & Population::get_tot_C_at_szgroup | ( | ) | const |
const vector< double > & Population::get_tot_D_at_szgroup | ( | ) | const |
const vector< double > & Population::get_tot_F_at_age | ( | ) | const |
const vector< double > & Population::get_tot_F_at_age_last_quarter | ( | ) | const |
const vector< double > & Population::get_tot_F_at_age_running_average | ( | ) | const |
const vector< double > & Population::get_tot_M_at_age | ( | ) | const |
const vector< double > & Population::get_tot_Mat_at_age | ( | ) | const |
const vector< double > & Population::get_tot_N_at_age | ( | ) | const |
double Population::get_tot_N_at_age0 | ( | ) | const |
const vector<double>& Population::get_tot_N_at_age_last_quarter | ( | ) | const |
const vector< double > & Population::get_tot_N_at_szgroup | ( | ) | const |
const vector< double > & Population::get_tot_N_at_szgroup_just_after_redistribution | ( | ) | const |
const vector< double > & Population::get_tot_N_at_szgroup_month_minus_1 | ( | ) | const |
const vector< double > & Population::get_tot_N_at_szgroup_year_minus_1 | ( | ) | const |
const vector< double > & Population::get_tot_W_at_age | ( | ) | const |
const vector< double > & Population::get_true_tot_N_at_szgroup | ( | ) | const |
const vector< double > & Population::get_weight_at_szgroup | ( | ) | const |
void Population::set_a_tot_N_at_szgroup_before_applying_M | ( | const vector< double > & | _a_tot_N_at_szgroup_before_applying_M | ) |
void Population::set_adults_diet_preference_per_stock | ( | const vector< double > & | _adults_diet_preference_per_stock | ) |
void Population::set_avai0_beta | ( | double | _avai0_beta | ) |
void Population::set_avai2_beta | ( | double | _avai2_beta | ) |
void Population::set_avai3_beta | ( | double | _avai3_beta | ) |
void Population::set_avai5_beta | ( | double | _avai5_beta | ) |
void Population::set_avai7_beta | ( | double | _avai7_beta | ) |
void Population::set_comcat_at_szgroup | ( | vector< int > | _comcat_at_szgroup | ) |
void Population::set_cpue_multiplier | ( | double | _cpue_multiplier | ) |
void Population::set_fbar | ( | double | _fbar | ) |
void Population::set_fecundity_at_szgroup | ( | const vector< double > & | _fecundity_at_szgroup | ) |
void Population::set_FFmsy | ( | const vector< double > & | _FFmsy | ) |
void Population::set_field_of_coeff_diffusion_this_pop | ( | multimap< types::NodeId, double > | _field_of_coeff_diffusion_this_pop | ) |
void Population::set_full_spatial_availability | ( | multimap< types::NodeId, double > | _full_spatial_availability | ) |
void Population::set_hyperstability_param | ( | double | _hyperstability_param | ) |
void Population::set_is_choking_fisheries | ( | int | is_choking_fisheries | ) |
void Population::set_juveniles_diet_preference_per_stock | ( | const vector< double > & | _juveniles_diet_preference_per_stock | ) |
void Population::set_landings_so_far | ( | double | _landings_so_far | ) |
void Population::set_list_nodes | ( | vector< Node * > | _list_nodes | ) |
void Population::set_M_at_szgroup | ( | const vector< double > & | _M_at_szgroup | ) |
void Population::set_maturity_at_szgroup | ( | const vector< double > & | _maturity_at_szgroup | ) |
void Population::set_oth_land | ( | map< types::NodeId, double > | _oth_land | ) |
void Population::set_oth_land_multiplier | ( | double | _a_multiplier | ) |
void Population::set_overall_migration_fluxes | ( | multimap< int, double > | _overall_migration_fluxes | ) |
void Population::set_param_sr | ( | const vector< double > & | _param_sr | ) |
void Population::set_perceived_tot_F_at_age | ( | const vector< double > & | _perceived_F_at_age | ) |
void Population::set_perceived_tot_N_at_age | ( | const vector< double > & | _perceived_N_at_age | ) |
void Population::set_prop_migrants_in_tot_N_at_szgroup | ( | const vector< double > & | _prop_migrants_at_szgroup | ) |
void Population::set_proportion_mature_fish | ( | double | _proportion_mature_fish | ) |
void Population::set_proprecru_at_szgroup | ( | const vector< double > & | _proprecru_at_szgroup | ) |
void Population::set_quota | ( | double | _quota | ) |
void Population::set_quota_uptake | ( | double | _quota_uptake | ) |
void Population::set_selected_szgroups | ( | vector< int > | selected_szgroups | ) |
void Population::set_SSB | ( | double | _SSB | ) |
void Population::set_SSB_at_szgroup | ( | const vector< double > & | _SSB_at_szgroup | ) |
void Population::set_tot_C_at_szgroup | ( | const vector< double > & | _C_at_szgroup | ) |
void Population::set_tot_D_at_szgroup | ( | const vector< double > & | _D_at_szgroup | ) |
void Population::set_tot_F_at_age | ( | const vector< double > & | _F_at_age | ) |
void Population::set_tot_F_at_age_last_quarter | ( | const vector< double > & | _tot_F_at_age_last_quarter | ) |
void Population::set_tot_F_at_age_running_average | ( | const vector< double > & | _tot_F_at_age_running_average | ) |
void Population::set_tot_M_at_age | ( | const vector< double > & | _M_at_age | ) |
void Population::set_tot_Mat_at_age | ( | const vector< double > & | _Mat_at_age | ) |
void Population::set_tot_N_at_age | ( | const vector< double > & | _N_at_age | ) |
void Population::set_tot_N_at_age_last_quarter | ( | const vector< double > & | _N_at_age_last_quarter | ) |
void Population::set_tot_N_at_szgroup | ( | const vector< double > & | _N_at_szgroup | ) |
void Population::set_tot_N_at_szgroup_just_after_redistribution | ( | const vector< double > & | _N_at_szgroup_just_after_redistribution | ) |
void Population::set_tot_N_at_szgroup_month_minus_1 | ( | const vector< double > & | _N_at_szgroup_month_minus_1 | ) |
void Population::set_tot_N_at_szgroup_year_minus_1 | ( | const vector< double > & | _N_at_szgroup_year_minus_1 | ) |
void Population::set_tot_W_at_age | ( | const vector< double > & | _W_at_age | ) |
void Population::set_true_tot_N_at_szgroup | ( | const vector< double > & | _true_tot_N_at_szgroup | ) |
void Population::set_weight_at_szgroup | ( | const vector< double > & | _weight_at_szgroup | ) |