#include <commons_global.h>
#include <sparsepp/spp.h>
#include <vesselcalendar.h>
#include <idtypes.h>
#include <utils/MultifieldReader.h>
#include <vector>
#include <deque>
#include <map>
#include <list>
#include <set>
#include <string>
#include <iostream>
#include <iomanip>
#include <sstream>
#include <fstream>
#include <algorithm>
#include <numeric>
#include <cmath>
#include <math.h>
#include <cstddef>
#include <pathshop.h>

Classes
struct	splitX

struct	edge

Macros
#define	__MYUTILS_H (1)

Typedefs
typedef types::NodeId::type	vertex_t

typedef int	weight_t

typedef std::map< vertex_t, std::list< edge > >	adjacency_map_t

Functions
template<double f>
double	simpson (double a, double b, int n, double S1, double S2)

template<typename T >
vector< size_t >	sort_indexes_ascending (const vector< T > &v)

template<typename T >
vector< size_t >	sort_indexes_descending (const vector< T > &v)

double COMMONSSHARED_EXPORT	trapezoidal (double a, double b, vector< double > sel)

double COMMONSSHARED_EXPORT	myintegrand (double x, double S1, double S2)

template<typename T >
void	remove_dups (vector< T > &seq)

void COMMONSSHARED_EXPORT	remove_dups (vector< int > &seq)

multimap< int, int > COMMONSSHARED_EXPORT	remove_dups (multimap< int, int > &original_map)

template<typename K , typename V >
multimap< K, V >	remove_dups (multimap< K, V > &original_map)

multimap< int, int >::const_iterator COMMONSSHARED_EXPORT	find_pair (const multimap< int, int > &map, const pair< int, int > &pair)

bool COMMONSSHARED_EXPORT	insert_if_not_present (multimap< int, int > &map, const pair< int, int > &pair)

template<typename K , typename V >
multimap< K, V >::const_iterator	find_pair (const multimap< K, V > &map, const pair< K, V > &pair)

template<typename K , typename V >
bool	insert_if_not_present (multimap< K, V > &map, const pair< K, V > &pair)

template<typename Container >
Container &	split (Container &result, const typename Container::value_type &s, const typename Container::value_type &delimiters, splitX::empties_t empties=splitX::empties_ok)

void COMMONSSHARED_EXPORT	DijkstraComputePaths (vertex_t source, adjacency_map_t &adjacency_map, spp::sparse_hash_map< vertex_t, weight_t > &min_distance, spp::sparse_hash_map< vertex_t, vertex_t > &previous, std::vector< types::NodeId > relevant_nodes)

std::list< vertex_t > COMMONSSHARED_EXPORT	DijkstraGetShortestPathTo (vertex_t target, spp::sparse_hash_map< vertex_t, vertex_t > &previous)

std::list< types::NodeId > COMMONSSHARED_EXPORT	DijkstraGetShortestPathTo (types::NodeId target, const PathShop &pathshop)

void COMMONSSHARED_EXPORT	SimplifyThePreviousMap (int source, spp::sparse_hash_map< vertex_t, vertex_t > &previous, std::vector< types::NodeId > &relevant_nodes, spp::sparse_hash_map< vertex_t, weight_t > &min_distance, string namesimu, string a_graph_name, string inputfolder)

void COMMONSSHARED_EXPORT	closeSomeNodes (std::vector< int > &nodes_to_be_closed, adjacency_map_t &adjacency_map)

vector< double > COMMONSSHARED_EXPORT	compute_distance_fgrounds (const vector< types::NodeId > &relevant_nodes, const std::vector< PathShop > &pathshops, types::NodeId from, vector< types::NodeId > grounds)

bool COMMONSSHARED_EXPORT	fill_from_coord (istream &in, vector< double > &graph_coord_x, vector< double > &graph_coord_y, vector< int > &graph_coord_harbour, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_graph (istream &in, vector< int > &graph_idx_dep, vector< int > &graph_idx_arr, vector< int > &graph_dist_km, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_code_area (istream &in, vector< int > &graph_point_code_area, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_code_marine_landscape (istream &in, vector< int > &graph_point_code_landscape, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_wind (istream &in, vector< double > &graph_point_wind, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_sst (istream &in, vector< double > &graph_point_sst, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_salinity (istream &in, vector< double > &graph_point_salinity, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_Nitrogen (istream &in, vector< double > &graph_point_Nitrogen, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_Phosphorus (istream &in, vector< double > &graph_point_Phosphorus, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_Oxygen (istream &in, vector< double > &graph_point_Oxygen, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_DissolvedCarbon (istream &in, vector< double > &graph_point_DissolvedCarbon, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_bathymetry (istream &in, vector< double > &graph_point_bathymetry, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_shippingdensity (istream &in, vector< double > &graph_point_shippingdensity, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_siltfraction (istream &in, vector< double > &graph_point_siltfraction, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_benthos_biomass (istream &in, vector< double > &graph_point_benthos_biomass, int nrow)

bool COMMONSSHARED_EXPORT	fill_from_benthos_number (istream &in, vector< double > &graph_point_benthos_number, int nrow)

bool COMMONSSHARED_EXPORT	fill_in_growth_transition (istream &in, vector< vector< double > > &growth_transition)

bool COMMONSSHARED_EXPORT	fill_in_species_interactions_mortality_proportion_matrix (istream &in, vector< vector< double > > &species_interactions_mortality_proportion_matrix)

bool COMMONSSHARED_EXPORT	fill_in_preferences_for_species_matrix (istream &in, vector< vector< double > > &preferences_for_species_matrix)

bool COMMONSSHARED_EXPORT	fill_in_selectivity_per_stock (istream &in, vector< vector< double > > &growth_transition)

bool COMMONSSHARED_EXPORT	fill_in_percent_szgroup_per_age_matrix (istream &in, vector< vector< double > > &percent_szgroup_per_age_matrix)

bool COMMONSSHARED_EXPORT	fill_in_percent_age_per_szgroup_matrix (istream &in, vector< vector< double > > &percent_age_per_szgroup_matrix)

bool COMMONSSHARED_EXPORT	fill_in_param_sr (istream &in, vector< double > &param_sr)

bool COMMONSSHARED_EXPORT	fill_in_initial_tac (istream &in, vector< double > &initial_tac)

bool COMMONSSHARED_EXPORT	fill_in_fbar_ages_min_max (istream &in, vector< double > &fbar_ages_min_max)

bool COMMONSSHARED_EXPORT	fill_from_metier_specifications (istream &in, multimap< string, double > &infos)

bool COMMONSSHARED_EXPORT	fill_from_vessels_specifications (istream &in, vector< string > &names, vector< int > &vid_is_actives, vector< int > &vid_is_part_of_ref_fleets, vector< double > &speeds, vector< double > &fuelcons, vector< double > &lengths, vector< double > &vKWs, vector< double > &carrycapacities, vector< double > &tankcapacities, vector< double > &nbfpingspertrips, vector< double > &resttime_par1s, vector< double > &resttime_par2s, vector< double > &av_trip_duration, vector< double > &mult_fuelcons_when_steaming, vector< double > &mult_fuelcons_when_fishing, vector< double > &mult_fuelcons_when_returning, vector< double > &mult_fuelcons_when_inactive, vector< int > &firm_ids, vector< VesselCalendar > &calendars)

bool COMMONSSHARED_EXPORT	fill_from_vessels_economic_specifications (istream &in, vector< double > &this_vessel_nb_crews, vector< double > &annual_other_incomes, vector< double > &landing_costs_percents, vector< double > &crewshare_and_unpaid_labour_costs_percents, vector< double > &other_variable_costs_per_unit_efforts, vector< double > &annual_insurance_costs_per_crews, vector< double > &standard_labour_hour_opportunity_costss, vector< double > &standard_annual_full_time_employement_hourss, vector< double > &other_annual_fixed_costss, vector< double > &vessel_values, vector< double > &annual_depreciation_rates, vector< double > &opportunity_interest_rates, vector< double > &annual_discount_rates)

bool COMMONSSHARED_EXPORT	fill_from_ships_specifications (istream &in, vector< string > &names, vector< double > &imos, vector< double > &yearbuilds, vector< string > &flags, vector< string > &types, vector< double > &typecodes, vector< double > &loas, vector< double > &KWs, vector< double > &breadths, vector< double > &grosstonnages, vector< double > &nbunits, vector< double > &fueluse, vector< double > &NOxEmission_gperKWh, vector< double > &SOxEmission_percentpertotalfuelmass, vector< double > &GHGEmission, vector< double > &PMEmission, vector< double > &vmaxs, vector< double > &vcruises, vector< double > &lane_ids)

bool COMMONSSHARED_EXPORT	fill_from_fishfarms_specifications (istream &in, vector< int > &fishfarms_ids, vector< string > &fishfarms_names, vector< int > &idx_nodes, vector< int > &is_actives, vector< double > &sizes, vector< double > &longs, vector< double > &lats, vector< double > &mean_SSTs, vector< double > &mean_salinities, vector< double > &mean_windspeeds, vector< double > &mean_currentspeeds, vector< double > &max_depths, vector< double > &diss_O2_mg_per_ls, vector< double > &Linf_mms, vector< double > &K_ys, vector< double > &t0_ys, vector< double > &fulton_condition_factors, vector< string > &meanw_growth_model_types, vector< int > &start_day_growings, vector< int > &end_day_harvests, vector< int > &nbyears_for_growths, vector< int > &nb_days_fallowing_periods, vector< int > &nb_fish_at_starts, vector< double > &meanw_at_starts, vector< double > &price_per_kg_at_starts, vector< double > &target_meanw_at_harvests, vector< int > &nb_fish_at_harvests, vector< double > &meanw_at_harvests, vector< double > &prop_harvest_kg_solds, vector< double > &kg_eggs_per_kgs, vector< double > &price_eggs_per_kgs, vector< double > &N_in_fish_kg_3pers, vector< double > &P_in_fish_kg_0_5pers, vector< string > &feed_types, vector< double > &feed_price_per_kgs, vector< double > &total_feed_kg, vector< double > &prop_N_in_feeds, vector< double > &prop_P_in_feeds, vector< double > &total_feed_N_kgs, vector< double > &total_feed_P_kgs, vector< string > &feed_type_vets, vector< double > &feed_vet_price_per_kgs, vector< double > &total_feed_vet_kgs, vector< double > &prop_N_in_feed_vets, vector< double > &prop_P_in_feed_vets, vector< double > &total_feed_vet_N_kgs, vector< double > &total_feed_vet_P_kgs, vector< double > &annual_discharge_N_kgs, vector< double > &annual_discharge_P_kgs, vector< double > &annual_discharge_C_kgs, vector< double > &annual_discharge_heavymetals_kgs, vector< double > &annual_discharge_medecine_kgs, vector< double > &net_harvest_kg_per_sqkm_ys, vector< double > &market_price_sold_fishs, vector< double > &operating_cost_per_days, vector< double > &annual_profits)

bool	fill_from_firms_specifications (istream &in, vector< int > &firm_ids, vector< string > &firm_names, vector< int > &nb_vessels, vector< double > &longs, vector< double > &lats)

bool COMMONSSHARED_EXPORT	fill_from_avai_nodes_with_pop (istream &in, map< int, double > &avai)

bool COMMONSSHARED_EXPORT	fill_from_avai_szgroup_nodes_with_pop (istream &in, multimap< types::NodeId, double > &avai)

bool COMMONSSHARED_EXPORT	fill_field_of_coeff_diffusion_this_pop (istream &in, multimap< types::NodeId, double > &coeffs)

bool COMMONSSHARED_EXPORT	fill_from_oth_land (istream &in, map< types::NodeId, double > &oth_land)

bool COMMONSSHARED_EXPORT	fill_from_overall_migration_fluxes (istream &in, multimap< int, double > &overall_migration_fluxes)

bool COMMONSSHARED_EXPORT	fill_from_relative_stability (istream &in, map< string, double > &relative_stability)

bool COMMONSSHARED_EXPORT	fill_from_nodes_in_polygons (istream &in, multimap< int, int > &nodes_in_polygons)

bool COMMONSSHARED_EXPORT	fill_multimap_from_specifications_s_i (istream &in, multimap< string, int > &infos)

bool COMMONSSHARED_EXPORT	fill_multimap_from_specifications_s_d (istream &in, multimap< string, double > &infos)

template<typename K , typename V >
bool	fill_multimap_from_specifications (istream &in, multimap< K, V > &infos)

bool COMMONSSHARED_EXPORT	fill_multimap_from_specifications_i_s (istream &in, multimap< int, string > &infos)

bool COMMONSSHARED_EXPORT	fill_multimap_from_specifications_i_d (istream &in, multimap< int, double > &infos)
	fill in the vessel attributes into a multimap <integer, double>. First line is an heading. More...

bool COMMONSSHARED_EXPORT	fill_multimap_from_specifications_i_i (istream &in, multimap< int, int > &infos)

bool COMMONSSHARED_EXPORT	fill_map_from_specifications_i_i (istream &in, map< int, int > &a_map)

bool COMMONSSHARED_EXPORT	fill_map_from_specifications_i_s (istream &in, map< int, string > &a_map)

bool COMMONSSHARED_EXPORT	fill_map_from_specifications_s_d (istream &in, map< string, double > &a_map)

template<typename DTYPE >
void	fill_map_from_specifications (istream &in, map< int, DTYPE > &map)

template<typename K , typename V >
std::vector< V >	find_entries (const std::multimap< K, V > &infos, K val)

vector< double > COMMONSSHARED_EXPORT	find_entries_s_d (multimap< string, double > &infos, string str)

vector< int > COMMONSSHARED_EXPORT	find_entries_s_i (multimap< string, int > &infos, string vid)

vector< double > COMMONSSHARED_EXPORT	find_entries_i_d (const multimap< int, double > &infos, int intg)

vector< int > COMMONSSHARED_EXPORT	find_entries_i_i (const multimap< int, int > &infos, int intg)

vector< string > COMMONSSHARED_EXPORT	find_entries_i_s (multimap< int, string > &infos, int intg)

void COMMONSSHARED_EXPORT	set_entries_d (multimap< int, double > &infos, int itr, vector< double > newval)

template<typename T , size_t N>
T *	end (T(&pArray)[N])

vector< double > COMMONSSHARED_EXPORT	scale_a_vector_to_1 (vector< double > a_vector)

bool COMMONSSHARED_EXPORT	fill_map_from_specifications_i_i (istream &in, map< int, int > &infos, string namefolderinput)

bool COMMONSSHARED_EXPORT	fill_map_from_specifications_i_s (istream &in, map< int, string > &infos, string namefolderinput)

bool COMMONSSHARED_EXPORT	fill_map_from_specifications_i_d (istream &in, map< int, double > &infos, string namefolderinput)

double COMMONSSHARED_EXPORT	decode_the_tree (string &tree, vector< string > &direction, map< string, int > &external_states, map< string, int > &internal_states)

Macro Definition Documentation

◆ __MYUTILS_H

#define __MYUTILS_H (1)

Typedef Documentation

◆ adjacency_map_t

typedef std::map<vertex_t, std::list<edge> > adjacency_map_t

◆ vertex_t

typedef types::NodeId::type vertex_t

◆ weight_t

typedef int weight_t

Function Documentation

◆ closeSomeNodes()

void COMMONSSHARED_EXPORT closeSomeNodes	(	std::vector< int > &	nodes_to_be_closed,
		adjacency_map_t &	adjacency_map
	)

◆ compute_distance_fgrounds()

vector<double> COMMONSSHARED_EXPORT compute_distance_fgrounds	(	const vector< types::NodeId > &	relevant_nodes,
		const std::vector< PathShop > &	pathshops,
		types::NodeId	from,
		vector< types::NodeId >	grounds
	)

◆ decode_the_tree()

double COMMONSSHARED_EXPORT decode_the_tree	(	string &	tree,
		vector< string > &	direction,
		map< string, int > &	external_states,
		map< string, int > &	internal_states
	)

◆ DijkstraComputePaths()

void COMMONSSHARED_EXPORT DijkstraComputePaths	(	vertex_t	source,
		adjacency_map_t &	adjacency_map,
		spp::sparse_hash_map< vertex_t, weight_t > &	min_distance,
		spp::sparse_hash_map< vertex_t, vertex_t > &	previous,
		std::vector< types::NodeId >	relevant_nodes
	)

◆ DijkstraGetShortestPathTo() [1/2]

std::list<vertex_t> COMMONSSHARED_EXPORT DijkstraGetShortestPathTo	(	vertex_t	target,
		spp::sparse_hash_map< vertex_t, vertex_t > &	previous
	)

◆ DijkstraGetShortestPathTo() [2/2]

std::list<types::NodeId> COMMONSSHARED_EXPORT DijkstraGetShortestPathTo	(	types::NodeId	target,
		const PathShop &	pathshop
	)

◆ end()

template<typename T , size_t N>

T* end ( T(&) pArray[N] )

◆ fill_field_of_coeff_diffusion_this_pop()

bool COMMONSSHARED_EXPORT fill_field_of_coeff_diffusion_this_pop	(	istream &	in,
		multimap< types::NodeId, double > &	coeffs
	)

fill in the avai attributes into a multimap

Parameters

the	avai specification file, ...

◆ fill_from_avai_nodes_with_pop()

bool COMMONSSHARED_EXPORT fill_from_avai_nodes_with_pop	(	istream &	in,
		map< int, double > &	avai
	)

fill in the avai attributes into a map

Parameters

the	vessel specification file, ...

◆ fill_from_avai_szgroup_nodes_with_pop()

bool COMMONSSHARED_EXPORT fill_from_avai_szgroup_nodes_with_pop	(	istream &	in,
		multimap< types::NodeId, double > &	avai
	)

fill in the avai attributes into a multimap

Parameters

the	avai specification file, ...

◆ fill_from_bathymetry()

bool COMMONSSHARED_EXPORT fill_from_bathymetry	(	istream &	in,
		vector< double > &	graph_point_bathymetry,
		int	nrow
	)

◆ fill_from_benthos_biomass()

bool COMMONSSHARED_EXPORT fill_from_benthos_biomass	(	istream &	in,
		vector< double > &	graph_point_benthos_biomass,
		int	nrow
	)

◆ fill_from_benthos_number()

bool COMMONSSHARED_EXPORT fill_from_benthos_number	(	istream &	in,
		vector< double > &	graph_point_benthos_number,
		int	nrow
	)

◆ fill_from_code_area()

bool COMMONSSHARED_EXPORT fill_from_code_area	(	istream &	in,
		vector< int > &	graph_point_code_area,
		int	nrow
	)

◆ fill_from_code_marine_landscape()

bool COMMONSSHARED_EXPORT fill_from_code_marine_landscape	(	istream &	in,
		vector< int > &	graph_point_code_landscape,
		int	nrow
	)

◆ fill_from_coord()

bool COMMONSSHARED_EXPORT fill_from_coord	(	istream &	in,
		vector< double > &	graph_coord_x,
		vector< double > &	graph_coord_y,
		vector< int > &	graph_coord_harbour,
		int	nrow
	)

fill in the separated vectors related to the coord object

Parameters

the	coord file, ...

◆ fill_from_DissolvedCarbon()

bool COMMONSSHARED_EXPORT fill_from_DissolvedCarbon	(	istream &	in,
		vector< double > &	graph_point_DissolvedCarbon,
		int	nrow
	)

◆ fill_from_firms_specifications()

bool fill_from_firms_specifications	(	istream &	in,
		vector< int > &	firm_ids,
		vector< string > &	firm_names,
		vector< int > &	nb_vessels,
		vector< double > &	longs,
		vector< double > &	lats
	)

fill in the firms attributes

Parameters

the	firm specification file, ...

◆ fill_from_fishfarms_specifications()

bool COMMONSSHARED_EXPORT fill_from_fishfarms_specifications	(	istream &	in,
		vector< int > &	fishfarms_ids,
		vector< string > &	fishfarms_names,
		vector< int > &	idx_nodes,
		vector< int > &	is_actives,
		vector< double > &	sizes,
		vector< double > &	longs,
		vector< double > &	lats,
		vector< double > &	mean_SSTs,
		vector< double > &	mean_salinities,
		vector< double > &	mean_windspeeds,
		vector< double > &	mean_currentspeeds,
		vector< double > &	max_depths,
		vector< double > &	diss_O2_mg_per_ls,
		vector< double > &	Linf_mms,
		vector< double > &	K_ys,
		vector< double > &	t0_ys,
		vector< double > &	fulton_condition_factors,
		vector< string > &	meanw_growth_model_types,
		vector< int > &	start_day_growings,
		vector< int > &	end_day_harvests,
		vector< int > &	nbyears_for_growths,
		vector< int > &	nb_days_fallowing_periods,
		vector< int > &	nb_fish_at_starts,
		vector< double > &	meanw_at_starts,
		vector< double > &	price_per_kg_at_starts,
		vector< double > &	target_meanw_at_harvests,
		vector< int > &	nb_fish_at_harvests,
		vector< double > &	meanw_at_harvests,
		vector< double > &	prop_harvest_kg_solds,
		vector< double > &	kg_eggs_per_kgs,
		vector< double > &	price_eggs_per_kgs,
		vector< double > &	N_in_fish_kg_3pers,
		vector< double > &	P_in_fish_kg_0_5pers,
		vector< string > &	feed_types,
		vector< double > &	feed_price_per_kgs,
		vector< double > &	total_feed_kgs,
		vector< double > &	prop_N_in_feeds,
		vector< double > &	prop_P_in_feeds,
		vector< double > &	total_feed_N_kgs,
		vector< double > &	total_feed_P_kgs,
		vector< string > &	feed_type_vets,
		vector< double > &	feed_vet_price_per_kgs,
		vector< double > &	total_feed_vet_kgs,
		vector< double > &	prop_N_in_feed_vets,
		vector< double > &	prop_P_in_feed_vets,
		vector< double > &	total_feed_vet_N_kgs,
		vector< double > &	total_feed_vet_P_kgs,
		vector< double > &	annual_discharge_N_kgs,
		vector< double > &	annual_discharge_P_kgs,
		vector< double > &	annual_discharge_C_kgs,
		vector< double > &	annual_discharge_heavymetals_kgs,
		vector< double > &	annual_discharge_medecine_kgs,
		vector< double > &	net_harvest_kg_per_sqkm_ys,
		vector< double > &	market_price_sold_fishs,
		vector< double > &	operating_cost_per_days,
		vector< double > &	annual_profits
	)

fill in the fishfarms attributes

Parameters

the	fishfarm specification file, ...

◆ fill_from_graph()

bool COMMONSSHARED_EXPORT fill_from_graph	(	istream &	in,
		vector< int > &	graph_idx_dep,
		vector< int > &	graph_idx_arr,
		vector< int > &	graph_dist_km,
		int	nrow
	)

fill in the separated vectors related to the coord object

Parameters

the	coord file, ...

◆ fill_from_metier_specifications()

bool COMMONSSHARED_EXPORT fill_from_metier_specifications	(	istream &	in,
		multimap< string, double > &	infos
	)

fill in the vessel attributes into a multimap DOUBLE

Parameters

the	vessel specification file, ...

◆ fill_from_Nitrogen()

bool COMMONSSHARED_EXPORT fill_from_Nitrogen	(	istream &	in,
		vector< double > &	graph_point_Nitrogen,
		int	nrow
	)

◆ fill_from_nodes_in_polygons()

bool COMMONSSHARED_EXPORT fill_from_nodes_in_polygons	(	istream &	in,
		multimap< int, int > &	nodes_in_polygons
	)

fill in the avai attributes into a multimap

Parameters

the	avai specification file, ...

◆ fill_from_oth_land()

bool COMMONSSHARED_EXPORT fill_from_oth_land	(	istream &	in,
		map< types::NodeId, double > &	oth_land
	)

fill in the oth_land attributes into a multimap

Parameters

the	oth_land specification file, ...

◆ fill_from_overall_migration_fluxes()

bool COMMONSSHARED_EXPORT fill_from_overall_migration_fluxes	(	istream &	in,
		multimap< int, double > &	overall_migration_fluxes
	)

fill in the overall_migration_fluxes attributes into a multimap

Parameters

the	overall_migration_fluxes specification file, ...

◆ fill_from_Oxygen()

bool COMMONSSHARED_EXPORT fill_from_Oxygen	(	istream &	in,
		vector< double > &	graph_point_Oxygen,
		int	nrow
	)

◆ fill_from_Phosphorus()

bool COMMONSSHARED_EXPORT fill_from_Phosphorus	(	istream &	in,
		vector< double > &	graph_point_Phosphorus,
		int	nrow
	)

◆ fill_from_relative_stability()

bool COMMONSSHARED_EXPORT fill_from_relative_stability	(	istream &	in,
		map< string, double > &	relative_stability
	)

fill in the attributes into a multimap

Parameters

the	specification file, ...

◆ fill_from_salinity()

bool COMMONSSHARED_EXPORT fill_from_salinity	(	istream &	in,
		vector< double > &	graph_point_salinity,
		int	nrow
	)

◆ fill_from_shippingdensity()

bool COMMONSSHARED_EXPORT fill_from_shippingdensity	(	istream &	in,
		vector< double > &	graph_point_shippingdensity,
		int	nrow
	)

◆ fill_from_ships_specifications()

bool COMMONSSHARED_EXPORT fill_from_ships_specifications	(	istream &	in,
		vector< string > &	names,
		vector< double > &	imos,
		vector< double > &	yearbuilds,
		vector< string > &	flags,
		vector< string > &	types,
		vector< double > &	typecodes,
		vector< double > &	loas,
		vector< double > &	KWs,
		vector< double > &	breadths,
		vector< double > &	grosstonnages,
		vector< double > &	nbunits,
		vector< double > &	fueluses,
		vector< double > &	NOxEmission_gperKWhs,
		vector< double > &	SOxEmission_percentpertotalfuelmasss,
		vector< double > &	GHGEmissions,
		vector< double > &	PMEmissions,
		vector< double > &	vmaxs,
		vector< double > &	vcruises,
		vector< double > &	lane_ids
	)

fill in the vessel attributes

Parameters

the	vessel specification file, ...

◆ fill_from_siltfraction()

bool COMMONSSHARED_EXPORT fill_from_siltfraction	(	istream &	in,
		vector< double > &	graph_point_siltfraction,
		int	nrow
	)

◆ fill_from_sst()

bool COMMONSSHARED_EXPORT fill_from_sst	(	istream &	in,
		vector< double > &	graph_point_sst,
		int	nrow
	)

◆ fill_from_vessels_economic_specifications()

bool COMMONSSHARED_EXPORT fill_from_vessels_economic_specifications	(	istream &	in,
		vector< double > &	this_vessel_nb_crews,
		vector< double > &	annual_other_incomes,
		vector< double > &	landing_costs_percents,
		vector< double > &	crewshare_and_unpaid_labour_costs_percents,
		vector< double > &	other_variable_costs_per_unit_efforts,
		vector< double > &	annual_insurance_costs_per_crews,
		vector< double > &	standard_labour_hour_opportunity_costss,
		vector< double > &	standard_annual_full_time_employement_hourss,
		vector< double > &	other_annual_fixed_costss,
		vector< double > &	vessel_values,
		vector< double > &	annual_depreciation_rates,
		vector< double > &	opportunity_interest_rates,
		vector< double > &	annual_discount_rates
	)

fill in the vessel attributes

Parameters

the	vessel specification file, ...

◆ fill_from_vessels_specifications()

bool COMMONSSHARED_EXPORT fill_from_vessels_specifications	(	istream &	in,
		vector< string > &	names,
		vector< int > &	vid_is_actives,
		vector< int > &	vid_is_part_of_ref_fleets,
		vector< double > &	speeds,
		vector< double > &	fuelcons,
		vector< double > &	lengths,
		vector< double > &	vKWs,
		vector< double > &	carrycapacities,
		vector< double > &	tankcapacities,
		vector< double > &	nbfpingspertrips,
		vector< double > &	resttime_par1s,
		vector< double > &	resttime_par2s,
		vector< double > &	av_trip_duration,
		vector< double > &	mult_fuelcons_when_steaming,
		vector< double > &	mult_fuelcons_when_fishing,
		vector< double > &	mult_fuelcons_when_returning,
		vector< double > &	mult_fuelcons_when_inactive,
		vector< int > &	firm_ids,
		vector< VesselCalendar > &	calendars
	)

fill in the vessel attributes

Parameters

the	vessel specification file, ...

◆ fill_from_wind()

bool COMMONSSHARED_EXPORT fill_from_wind	(	istream &	in,
		vector< double > &	graph_point_wind,
		int	nrow
	)

◆ fill_in_fbar_ages_min_max()

bool COMMONSSHARED_EXPORT fill_in_fbar_ages_min_max	(	istream &	in,
		vector< double > &	fbar_ages_min_max
	)

fill in

Parameters

the	vector file, ...

◆ fill_in_growth_transition()

bool COMMONSSHARED_EXPORT fill_in_growth_transition	(	istream &	in,
		vector< vector< double > > &	growth_transition
	)

fill in the growth transition matrix

Parameters

the	vector file, ...

◆ fill_in_initial_tac()

bool COMMONSSHARED_EXPORT fill_in_initial_tac	(	istream &	in,
		vector< double > &	initial_tac
	)

fill in

Parameters

the	vector file, ...

◆ fill_in_param_sr()

bool COMMONSSHARED_EXPORT fill_in_param_sr	(	istream &	in,
		vector< double > &	param_sr
	)

fill in

Parameters

the	vector file, ...

◆ fill_in_percent_age_per_szgroup_matrix()

bool COMMONSSHARED_EXPORT fill_in_percent_age_per_szgroup_matrix	(	istream &	in,
		vector< vector< double > > &	percent_age_per_szgroup_matrix
	)

fill in the growth transition matrix

Parameters

the	vector file, ...

◆ fill_in_percent_szgroup_per_age_matrix()

bool COMMONSSHARED_EXPORT fill_in_percent_szgroup_per_age_matrix	(	istream &	in,
		vector< vector< double > > &	percent_szgroup_per_age_matrix
	)

fill in the growth transition matrix

Parameters

the	vector file, ...

◆ fill_in_preferences_for_species_matrix()

bool COMMONSSHARED_EXPORT fill_in_preferences_for_species_matrix	(	istream &	in,
		vector< vector< double > > &	preferences_for_species_matrix
	)

fill in the preferences_for_species_matrix

Parameters

the	vector file, ...

◆ fill_in_selectivity_per_stock()

bool COMMONSSHARED_EXPORT fill_in_selectivity_per_stock	(	istream &	in,
		vector< vector< double > > &	selectivity_per_stock
	)

fill in the growth transition matrix

Parameters

the	vector file, ...

◆ fill_in_species_interactions_mortality_proportion_matrix()

bool COMMONSSHARED_EXPORT fill_in_species_interactions_mortality_proportion_matrix	(	istream &	in,
		vector< vector< double > > &	species_interactions_mortality_proportion_matrix
	)

fill in the species_interactions_mortality_proportion_matrix

Parameters

the	vector file, ...

◆ fill_map_from_specifications()

template<typename DTYPE >

void fill_map_from_specifications	(	istream &	in,
		map< int, DTYPE > &	map
	)

◆ fill_map_from_specifications_i_d()

bool COMMONSSHARED_EXPORT fill_map_from_specifications_i_d	(	istream &	in,
		map< int, double > &	infos,
		string	namefolderinput
	)

fill in the vessel attributes into a map <int, int>

Parameters

e.g.	the vessel specification file, ...

◆ fill_map_from_specifications_i_i() [1/2]

bool COMMONSSHARED_EXPORT fill_map_from_specifications_i_i	(	istream &	in,
		map< int, int > &	a_map
	)

fill in the avai attributes into a multimap

Parameters

the	avai specification file, ...

◆ fill_map_from_specifications_i_i() [2/2]

bool COMMONSSHARED_EXPORT fill_map_from_specifications_i_i	(	istream &	in,
		map< int, int > &	infos,
		string	namefolderinput
	)

fill in the vessel attributes into a map <int, int>

Parameters

e.g.	the vessel specification file, ...

◆ fill_map_from_specifications_i_s() [1/2]

bool COMMONSSHARED_EXPORT fill_map_from_specifications_i_s	(	istream &	in,
		map< int, string > &	a_map
	)

fill in the avai attributes into a multimap

Parameters

the	avai specification file, ...

◆ fill_map_from_specifications_i_s() [2/2]

bool COMMONSSHARED_EXPORT fill_map_from_specifications_i_s	(	istream &	in,
		map< int, string > &	infos,
		string	namefolderinput
	)

fill in the vessel attributes into a map <int, int>

Parameters

e.g.	the vessel specification file, ...

◆ fill_map_from_specifications_s_d()

bool COMMONSSHARED_EXPORT fill_map_from_specifications_s_d	(	istream &	in,
		map< string, double > &	infos
	)

fill in the vessel attributes into a map <int, int>

Parameters

e.g.	the vessel specification file, ...

◆ fill_multimap_from_specifications()

template<typename K , typename V >

bool fill_multimap_from_specifications	(	istream &	in,
		multimap< K, V > &	infos
	)

◆ fill_multimap_from_specifications_i_d()

bool COMMONSSHARED_EXPORT fill_multimap_from_specifications_i_d	(	istream &	in,
		multimap< int, double > &	infos
	)

fill in the vessel attributes into a multimap <integer, double>. First line is an heading.

Parameters

e.g.	the vessel specification file, ...

◆ fill_multimap_from_specifications_i_i()

bool COMMONSSHARED_EXPORT fill_multimap_from_specifications_i_i	(	istream &	in,
		multimap< int, int > &	infos
	)

fill in the vessel attributes into a multimap <int, int>

Parameters

e.g.	the vessel specification file, ...

◆ fill_multimap_from_specifications_i_s()

bool COMMONSSHARED_EXPORT fill_multimap_from_specifications_i_s	(	istream &	in,
		multimap< int, string > &	infos
	)

fill in the vessel attributes into a multimap <int, string>

Parameters

e.g.	the vessel specification file, ...

◆ fill_multimap_from_specifications_s_d()

bool COMMONSSHARED_EXPORT fill_multimap_from_specifications_s_d	(	istream &	in,
		multimap< string, double > &	infos
	)

fill in the vessel attributes into a multimap <string, double>

Parameters

e.g.	the vessel specification file, ...

◆ fill_multimap_from_specifications_s_i()

bool COMMONSSHARED_EXPORT fill_multimap_from_specifications_s_i	(	istream &	in,
		multimap< string, int > &	infos
	)

fill in the vessel attributes into a multimap <string, integer>

Parameters

e.g.	the vessel specification file, ...

◆ find_entries()

template<typename K , typename V >

std::vector<V> find_entries	(	const std::multimap< K, V > &	infos,
		K	val
	)

◆ find_entries_i_d()

vector<double> COMMONSSHARED_EXPORT find_entries_i_d	(	const multimap< int, double > &	infos,
		int	intg
	)

◆ find_entries_i_i()

vector<int> COMMONSSHARED_EXPORT find_entries_i_i	(	const multimap< int, int > &	infos,
		int	intg
	)

◆ find_entries_i_s()

vector<string> COMMONSSHARED_EXPORT find_entries_i_s	(	multimap< int, string > &	infos,
		int	intg
	)

◆ find_entries_s_d()

vector<double> COMMONSSHARED_EXPORT find_entries_s_d	(	multimap< string, double > &	infos,
		string	str
	)

◆ find_entries_s_i()

vector<int> COMMONSSHARED_EXPORT find_entries_s_i	(	multimap< string, int > &	infos,
		string	vid
	)

◆ find_pair() [1/2]

multimap<int,int>::const_iterator COMMONSSHARED_EXPORT find_pair	(	const multimap< int, int > &	map,
		const pair< int, int > &	pair
	)

◆ find_pair() [2/2]

template<typename K , typename V >

multimap<K,V>::const_iterator find_pair	(	const multimap< K, V > &	map,
		const pair< K, V > &	pair
	)

◆ insert_if_not_present() [1/2]

bool COMMONSSHARED_EXPORT insert_if_not_present	(	multimap< int, int > &	map,
		const pair< int, int > &	pair
	)

◆ insert_if_not_present() [2/2]

template<typename K , typename V >

bool insert_if_not_present	(	multimap< K, V > &	map,
		const pair< K, V > &	pair
	)

◆ myintegrand()

double COMMONSSHARED_EXPORT myintegrand	(	double	x,
		double	S1,
		double	S2
	)

◆ remove_dups() [1/4]

template<typename T >

void remove_dups ( vector< T > & seq )

◆ remove_dups() [2/4]

void COMMONSSHARED_EXPORT remove_dups ( vector< int > & seq )

◆ remove_dups() [3/4]

multimap<int,int> COMMONSSHARED_EXPORT remove_dups ( multimap< int, int > & original_map )

◆ remove_dups() [4/4]

template<typename K , typename V >

multimap<K,V> remove_dups ( multimap< K, V > & original_map )

◆ scale_a_vector_to_1()

vector<double> COMMONSSHARED_EXPORT scale_a_vector_to_1 ( vector< double > a_vector )

◆ set_entries_d()

void COMMONSSHARED_EXPORT set_entries_d	(	multimap< int, double > &	infos,
		int	itr,
		vector< double >	newval
	)

◆ SimplifyThePreviousMap()

void COMMONSSHARED_EXPORT SimplifyThePreviousMap	(	int	source,
		spp::sparse_hash_map< vertex_t, vertex_t > &	previous,
		std::vector< types::NodeId > &	relevant_nodes,
		spp::sparse_hash_map< vertex_t, weight_t > &	min_distance,
		string	namesimu,
		string	a_graph_name,
		string	inputfolder
	)

◆ simpson()

template<double f>

double simpson	(	double	a,
		double	b,
		int	n,
		double	S1,
		double	S2
	)

◆ sort_indexes_ascending()

template<typename T >

vector<size_t> sort_indexes_ascending ( const vector< T > & v )

◆ sort_indexes_descending()

template<typename T >

vector<size_t> sort_indexes_descending ( const vector< T > & v )

◆ split()

template<typename Container >

Container& split	(	Container &	result,
		const typename Container::value_type &	s,
		const typename Container::value_type &	delimiters,
		splitX::empties_t	empties = `splitX::empties_ok`
	)

◆ trapezoidal()

double COMMONSSHARED_EXPORT trapezoidal	(	double	a,
		double	b,
		vector< double >	sel
	)

Classes

Macros

Typedefs

Functions

Macro Definition Documentation

◆ __MYUTILS_H

Typedef Documentation

◆ adjacency_map_t

◆ vertex_t

◆ weight_t

Function Documentation

◆ closeSomeNodes()

◆ compute_distance_fgrounds()

◆ decode_the_tree()

◆ DijkstraComputePaths()

◆ DijkstraGetShortestPathTo() [1/2]

◆ DijkstraGetShortestPathTo() [2/2]

◆ end()

◆ fill_field_of_coeff_diffusion_this_pop()

◆ fill_from_avai_nodes_with_pop()

◆ fill_from_avai_szgroup_nodes_with_pop()

◆ fill_from_bathymetry()

◆ fill_from_benthos_biomass()

◆ fill_from_benthos_number()

◆ fill_from_code_area()

◆ fill_from_code_marine_landscape()

◆ fill_from_coord()

◆ fill_from_DissolvedCarbon()

◆ fill_from_firms_specifications()

◆ fill_from_fishfarms_specifications()

◆ fill_from_graph()

◆ fill_from_metier_specifications()

◆ fill_from_Nitrogen()

◆ fill_from_nodes_in_polygons()

◆ fill_from_oth_land()

◆ fill_from_overall_migration_fluxes()

◆ fill_from_Oxygen()

◆ fill_from_Phosphorus()

◆ fill_from_relative_stability()

◆ fill_from_salinity()

◆ fill_from_shippingdensity()

◆ fill_from_ships_specifications()

◆ fill_from_siltfraction()

◆ fill_from_sst()

◆ fill_from_vessels_economic_specifications()

◆ fill_from_vessels_specifications()

◆ fill_from_wind()

◆ fill_in_fbar_ages_min_max()

◆ fill_in_growth_transition()

◆ fill_in_initial_tac()

◆ fill_in_param_sr()

◆ fill_in_percent_age_per_szgroup_matrix()

◆ fill_in_percent_szgroup_per_age_matrix()

◆ fill_in_preferences_for_species_matrix()

◆ fill_in_selectivity_per_stock()

◆ fill_in_species_interactions_mortality_proportion_matrix()

◆ fill_map_from_specifications()

◆ fill_map_from_specifications_i_d()

◆ fill_map_from_specifications_i_i() [1/2]

◆ fill_map_from_specifications_i_i() [2/2]

◆ fill_map_from_specifications_i_s() [1/2]

◆ fill_map_from_specifications_i_s() [2/2]

◆ fill_map_from_specifications_s_d()

◆ fill_multimap_from_specifications()

◆ fill_multimap_from_specifications_i_d()

◆ fill_multimap_from_specifications_i_i()

◆ fill_multimap_from_specifications_i_s()

◆ fill_multimap_from_specifications_s_d()

◆ fill_multimap_from_specifications_s_i()

◆ find_entries()

◆ find_entries_i_d()

◆ find_entries_i_i()

◆ find_entries_i_s()

◆ find_entries_s_d()

◆ find_entries_s_i()

◆ find_pair() [1/2]

◆ find_pair() [2/2]

◆ insert_if_not_present() [1/2]

◆ insert_if_not_present() [2/2]

◆ myintegrand()