FisheryModelBase is a base class for fishery models in FIMS. More...

#include <fishery_model_base.hpp>

Inheritance diagram for fims_popdy::FisheryModelBase< Type >:

Public Types
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator	fleet_iterator
	Fleet-based iterator.

typedef std::map< uint32_t, std::map< std::string, fims::Vector< Type > > >	DerivedQuantitiesMap
	Type definitions for derived quantities and dimension information maps.

typedef DerivedQuantitiesMap::iterator	DerivedQuantitiesMapIterator
	Iterator for the derived quantities map.

typedef std::map< uint32_t, std::map< std::string, DimensionInfo > >	DimensionInfoMap
	Type definitions for dimension information maps.

typedef std::map< uint32_t, std::map< std::string, UncertaintyReportInfo > >	UncertaintyReportInfoMap
	Type definition for the uncertainty report information map.

Public Member Functions
	FisheryModelBase ()
	Construct a new Fishery Model Base object.

	FisheryModelBase (const FisheryModelBase &other)
	Construct a new Fishery Model Base object.

virtual	~FisheryModelBase ()
	Destroy the Fishery Model Base object.

std::map< uint32_t, std::map< std::string, DimensionInfo > > &	GetFleetDimensionInfo ()
	Get the fleet dimension information.

std::map< uint32_t, std::map< std::string, DimensionInfo > > &	GetPopulationDimensionInfo ()
	Get the population dimension information.

DerivedQuantitiesMap &	GetFleetDerivedQuantities ()
	Get the fleet derived quantities.

DerivedQuantitiesMap &	GetPopulationDerivedQuantities ()
	Get the population derived quantities.

std::map< std::string, fims::Vector< Type > > &	GetFleetDerivedQuantities (uint32_t fleet_id)
	Get the fleet derived quantities for a specified fleet.

void	InitializeFleetDerivedQuantities (uint32_t fleet_id)
	Initialize the derived quantities map for a fleet.

void	InitializePopulationDerivedQuantities (uint32_t population_id)
	Initialize the derived quantities map for a population.

std::map< std::string, fims::Vector< Type > > &	GetPopulationDerivedQuantities (uint32_t population_id)
	Get the population derived quantities for a specified population.

std::map< std::string, DimensionInfo > &	GetFleetDimensionInfo (uint32_t fleet_id)
	Get the fleet dimension information for a specified fleet.

std::map< std::string, DimensionInfo > &	GetPopulationDimensionInfo (uint32_t population_id)
	Get the population dimension information for a specified population.

UncertaintyReportInfoMap &	GetFleetUncertaintyReportInfo ()
	Get the fleet uncertainty report information.

UncertaintyReportInfoMap &	GetPopulationUncertaintyReportInfo ()
	Get the population uncertainty report information.

std::map< std::string, UncertaintyReportInfo > &	GetFleetUncertaintyReportInfo (uint32_t fleet_id)
	Get the fleet uncertainty report information for a specified fleet.

std::map< std::string, UncertaintyReportInfo > &	GetPopulationUncertaintyReportInfo (uint32_t population_id)
	Get the population uncertainty report information for a specified population.

virtual void	Initialize ()
	Initialize a model.

virtual void	Prepare ()
	Prepare the model.

virtual void	ResetVector (fims::Vector< Type > &v, Type value=0.0)
	Reset a vector from start to end with a value.

virtual void	Evaluate ()
	Evaluate the model.

virtual void	Report ()
	Report the model results via TMB.

uint32_t	GetId ()
	Get the Id object.

Public Member Functions inherited from fims_model_object::FIMSObject< Type >
uint32_t	GetId () const
	Getter that returns the unique id for parameters in the model.

bool	CheckDimensions (size_t actual, size_t expected)
	Check the dimensions of an object.

virtual void	create_report_vectors (std::map< std::string, fims::Vector< fims::Vector< Type > > > &report_vectors)
	Create a map of report vectors for the object. used to populate the report_vectors map in FisheryModelBase.

virtual void	get_report_vector_count (std::map< std::string, size_t > &report_vector_count)
	Get the report vector count object. used to get the length of each report vector for populating the UncertaintyReportInfo struct in FisheryModelBase.

Public Attributes
std::string	model_type_m
	A string specifying the model type.

std::set< uint32_t >	population_ids
	Unique identifier for the fishery model.

std::vector< std::shared_ptr< fims_popdy::Population< Type > > >	populations
	A vector of populations in the fishery model.

std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >	fleets
	A map of fleets in the fishery model, indexed by fleet id. Unique instances to eliminate duplicate initialization.

std::shared_ptr< DerivedQuantitiesMap >	fleet_derived_quantities
	Shared pointer for the fleet derived quantities map.

std::shared_ptr< DerivedQuantitiesMap >	population_derived_quantities
	Shared pointer for the population derived quantities map.

std::shared_ptr< DimensionInfoMap >	fleet_dimension_info
	Shared pointer for the fleet dimension information map.

std::shared_ptr< DimensionInfoMap >	population_dimension_info
	Shared pointer for the population dimension information map.

std::shared_ptr< UncertaintyReportInfoMap >	fleet_uncertainty_report_info
	Shared pointer for the uncertainty report information map.

std::shared_ptr< UncertaintyReportInfoMap >	population_uncertainty_report_info
	Shared pointer for the population uncertainty report information map.

Public Attributes inherited from fims_model_object::FIMSObject< Type >
uint32_t	id

std::vector< Type * >	parameters

std::vector< Type * >	random_effects_parameters

std::vector< Type * >	fixed_effects_parameters

Detailed Description

template<typename Type>
class fims_popdy::FisheryModelBase< Type >

FisheryModelBase is a base class for fishery models in FIMS.

Constructor & Destructor Documentation

◆ FisheryModelBase()

template<typename Type >

fims_popdy::FisheryModelBase< Type >::FisheryModelBase ( const FisheryModelBase< Type > & other )

inline

Construct a new Fishery Model Base object.

Parameters

other

Member Function Documentation

◆ Evaluate()

template<typename Type >

virtual void fims_popdy::FisheryModelBase< Type >::Evaluate ( )

inlinevirtual

Evaluate the model.

Reimplemented in fims_popdy::CatchAtAge< Type >.

◆ GetFleetDerivedQuantities() [1/2]

template<typename Type >

DerivedQuantitiesMap & fims_popdy::FisheryModelBase< Type >::GetFleetDerivedQuantities ( )

inline

Get the fleet derived quantities.

Returns: DerivedQuantitiesMap

◆ GetFleetDerivedQuantities() [2/2]

template<typename Type >

std::map< std::string, fims::Vector< Type > > & fims_popdy::FisheryModelBase< Type >::GetFleetDerivedQuantities ( uint32_t fleet_id )

inline

Get the fleet derived quantities for a specified fleet.

Parameters

fleet_id The ID of the fleet.

Returns: std::map<std::string, fims::Vector<Type>>&

◆ GetFleetDimensionInfo() [1/2]

template<typename Type >

std::map< uint32_t, std::map< std::string, DimensionInfo > > & fims_popdy::FisheryModelBase< Type >::GetFleetDimensionInfo ( )

inline

Get the fleet dimension information.

Returns: std::map<uint32_t, std::map<std::string, DimensionInfo>>

◆ GetFleetDimensionInfo() [2/2]

template<typename Type >

std::map< std::string, DimensionInfo > & fims_popdy::FisheryModelBase< Type >::GetFleetDimensionInfo ( uint32_t fleet_id )

inline

Get the fleet dimension information for a specified fleet.

Parameters

fleet_id The ID of the fleet.

Returns: std::map<std::string, DimensionInfo>

◆ GetFleetUncertaintyReportInfo()

template<typename Type >

std::map< std::string, UncertaintyReportInfo > & fims_popdy::FisheryModelBase< Type >::GetFleetUncertaintyReportInfo ( uint32_t fleet_id )

inline

Get the fleet uncertainty report information for a specified fleet.

Parameters

fleet_id The ID of the fleet.

Returns: std::map<std::string, UncertaintyReportInfo>&

◆ GetId()

template<typename Type >

uint32_t fims_popdy::FisheryModelBase< Type >::GetId ( )

inline

Get the Id object.

Returns: uint32_t

◆ GetPopulationDerivedQuantities() [1/2]

template<typename Type >

DerivedQuantitiesMap & fims_popdy::FisheryModelBase< Type >::GetPopulationDerivedQuantities ( )

inline

Get the population derived quantities.

Returns: DerivedQuantitiesMap

◆ GetPopulationDerivedQuantities() [2/2]

template<typename Type >

std::map< std::string, fims::Vector< Type > > & fims_popdy::FisheryModelBase< Type >::GetPopulationDerivedQuantities ( uint32_t population_id )

inline

Get the population derived quantities for a specified population.

Parameters

population_id The ID of the population.

Returns: std::map<std::string, fims::Vector<Type>>&

◆ GetPopulationDimensionInfo() [1/2]

template<typename Type >

std::map< uint32_t, std::map< std::string, DimensionInfo > > & fims_popdy::FisheryModelBase< Type >::GetPopulationDimensionInfo ( )

inline

Get the population dimension information.

Returns: std::map<uint32_t, std::map<std::string, DimensionInfo>>

◆ GetPopulationDimensionInfo() [2/2]

template<typename Type >

std::map< std::string, DimensionInfo > & fims_popdy::FisheryModelBase< Type >::GetPopulationDimensionInfo ( uint32_t population_id )

inline

Get the population dimension information for a specified population.

Parameters

population_id The ID of the population.

Returns: std::map<std::string, DimensionInfo>

◆ GetPopulationUncertaintyReportInfo()

template<typename Type >

std::map< std::string, UncertaintyReportInfo > & fims_popdy::FisheryModelBase< Type >::GetPopulationUncertaintyReportInfo ( uint32_t population_id )

inline

Get the population uncertainty report information for a specified population.

Parameters

population_id The ID of the population.

Returns: std::map<std::string, UncertaintyReportInfo>&

◆ Initialize()

template<typename Type >

virtual void fims_popdy::FisheryModelBase< Type >::Initialize ( )

inlinevirtual

Initialize a model.

Reimplemented in fims_popdy::CatchAtAge< Type >.

◆ InitializeFleetDerivedQuantities()

template<typename Type >

void fims_popdy::FisheryModelBase< Type >::InitializeFleetDerivedQuantities ( uint32_t fleet_id )

inline

Initialize the derived quantities map for a fleet.

Ensures the derived quantities map for the specified fleet exists. If not, creates an empty map for the fleet ID.

Parameters

fleet_id The ID of the fleet to initialize.

◆ InitializePopulationDerivedQuantities()

template<typename Type >

void fims_popdy::FisheryModelBase< Type >::InitializePopulationDerivedQuantities ( uint32_t population_id )

inline

Initialize the derived quantities map for a population.

Ensures the derived quantities map for the specified population exists. If not, creates an empty map for the population ID.

Parameters

population_id The ID of the population to initialize.

◆ Prepare()

template<typename Type >

virtual void fims_popdy::FisheryModelBase< Type >::Prepare ( )

inlinevirtual

Prepare the model.

Reimplemented in fims_popdy::CatchAtAge< Type >.

◆ Report()

template<typename Type >

virtual void fims_popdy::FisheryModelBase< Type >::Report ( )

inlinevirtual

Report the model results via TMB.

Reimplemented in fims_popdy::CatchAtAge< Type >.

◆ ResetVector()

template<typename Type >

virtual void fims_popdy::FisheryModelBase< Type >::ResetVector	(	fims::Vector< Type > &	v,
		Type	value = `0.0`
	)

inlinevirtual

Reset a vector from start to end with a value.

Parameters

v	A vector to reset.
value	The value you want to use for all elements in the vector. The default is 0.0.

The documentation for this class was generated from the following file:

inst/include/models/functors/fishery_model_base.hpp

Public Types

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FisheryModelBase()

Member Function Documentation

◆ Evaluate()

◆ GetFleetDerivedQuantities() [1/2]

◆ GetFleetDerivedQuantities() [2/2]

◆ GetFleetDimensionInfo() [1/2]

◆ GetFleetDimensionInfo() [2/2]

◆ GetFleetUncertaintyReportInfo()

◆ GetId()

◆ GetPopulationDerivedQuantities() [1/2]

◆ GetPopulationDerivedQuantities() [2/2]

◆ GetPopulationDimensionInfo() [1/2]

◆ GetPopulationDimensionInfo() [2/2]

◆ GetPopulationUncertaintyReportInfo()

◆ Initialize()

◆ InitializeFleetDerivedQuantities()

◆ InitializePopulationDerivedQuantities()

◆ Prepare()

◆ Report()

◆ ResetVector()