Stores FIMS model information and creates model. Contains all objects and data pre-model construction. More...

#include <information.hpp>

Public Types
typedef std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > >::iterator	data_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >::iterator	recruitment_models_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >::iterator	recruitment_process_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > >::iterator	selectivity_models_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > >::iterator	growth_models_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > >::iterator	maturity_models_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator	fleet_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >::iterator	population_iterator

typedef std::map< uint32_t, std::shared_ptr< fims_distributions::DensityComponentBase< Type > > >::iterator	density_components_iterator

typedef std::unordered_map< uint32_t, std::shared_ptr< fims_popdy::FisheryModelBase< Type > > >::iterator	model_map_iterator

typedef std::unordered_map< uint32_t, fims::Vector< Type > * >::iterator	variable_map_iterator

Public Member Functions
void	Clear ()
	Clears all containers.

std::string	State ()
	Get a summary string of the Information object state.

void	RegisterParameter (Type &p)
	Register a parameter as estimable.

void	RegisterRandomEffect (Type &re)
	Register a random effect as estimable.

void	RegisterParameterName (std::string p_name)
	Register a parameter name.

void	RegisterRandomEffectName (std::string re_name)
	Register a random effects name.

void	SetupPriors ()
	Loop over distributions and set links to distribution x value if distribution is a prior type.

void	SetupRandomEffects ()
	Loop over distributions and set links to distribution x value if distribution is a random effects type.

void	SetupData ()
	Loop over distributions and set links to distribution expected value if distribution is a data type.

void	SetFleetLandingsData (bool &valid_model, std::shared_ptr< fims_popdy::Fleet< Type > > f)
	Set pointers to landings data in the fleet module.

void	SetFleetIndexData (bool &valid_model, std::shared_ptr< fims_popdy::Fleet< Type > > f)
	Set pointers to index data in the fleet module.

void	SetAgeCompositionData (bool &valid_model, std::shared_ptr< fims_popdy::Fleet< Type > > f)
	Set pointers to age composition data in the fleet module.

void	SetLengthCompositionData (bool &valid_model, std::shared_ptr< fims_popdy::Fleet< Type > > f)
	Set pointers to length composition data in the fleet module.

void	SetFleetSelectivityModel (bool &valid_model, std::shared_ptr< fims_popdy::Fleet< Type > > f)
	Set pointers to the selectivity module referenced in the fleet module.

void	SetRecruitment (bool &valid_model, std::shared_ptr< fims_popdy::Population< Type > > p)
	Set pointers to the recruitment module referenced in the population module.

void	SetRecruitmentProcess (bool &valid_model, std::shared_ptr< fims_popdy::Population< Type > > p)
	Set pointers to the recruitment process module referenced in the population module.

void	SetGrowth (bool &valid_model, std::shared_ptr< fims_popdy::Population< Type > > p)
	Set pointers to the growth module referenced in the population module.

void	SetMaturity (bool &valid_model, std::shared_ptr< fims_popdy::Population< Type > > p)
	Set pointers to the maturity module referenced in the population module.

void	CreateFleetObjects (bool &valid_model)
	Loop over all fleets and set pointers to fleet objects.

void	SetDataObjects (bool &valid_model)
	Loop over all density components and set pointers to data objects.

void	CreatePopulationObjects (bool &valid_model)
	Loop over all populations and set pointers to population objects.

void	CreateModelingObjects (bool &valid_model)
	Loop over all models and set pointers to population objects.

bool	CreateModel ()
	Create the generalized stock assessment model that will evaluate the objective function. Does error checking to make sure the program has all necessary components for the model and that they're in the right dimensions. This sets up pointers to all memory objects and initializes fleet and population objects.

size_t	GetNages () const
	Get the Nages object.

void	SetNages (size_t n_ages)
	Set the Nages object.

size_t	GetNyears () const
	Get the n_years object.

void	SetNyears (size_t n_years)
	Set the n_years object.

std::vector< Type * > &	GetParameters ()
	Get the Parameters object.

std::vector< Type * > &	GetFixedEffectsParameters ()
	Get the Fixed Effects Parameters object.

std::vector< Type * > &	GetRandomEffectsParameters ()
	Get the Random Effects Parameters object.

bool	CheckModel ()
	Checks to make sure all required modules are present for specified model.

Static Public Member Functions
static std::shared_ptr< Information< Type > >	GetInstance ()
	Returns a singleton Information object for type T.

Public Attributes
size_t	n_years = 0

size_t	n_ages = 0

std::vector< Type * >	parameters

std::vector< Type * >	random_effects_parameters

std::vector< Type * >	fixed_effects_parameters

std::vector< std::string >	parameter_names

std::vector< std::string >	random_effects_names

std::map< uint32_t, std::shared_ptr< fims_data_object::DataObject< Type > > >	data_objects

std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >	recruitment_models

std::map< uint32_t, std::shared_ptr< fims_popdy::RecruitmentBase< Type > > >	recruitment_process_models

std::map< uint32_t, std::shared_ptr< fims_popdy::SelectivityBase< Type > > >	selectivity_models

std::map< uint32_t, std::shared_ptr< fims_popdy::GrowthBase< Type > > >	growth_models

std::map< uint32_t, std::shared_ptr< fims_popdy::MaturityBase< Type > > >	maturity_models

std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >	fleets

std::map< uint32_t, std::shared_ptr< fims_popdy::Population< Type > > >	populations

std::map< uint32_t, std::shared_ptr< fims_distributions::DensityComponentBase< Type > > >	density_components

std::unordered_map< uint32_t, std::shared_ptr< fims_popdy::FisheryModelBase< Type > > >	models_map

std::unordered_map< uint32_t, fims::Vector< Type > * >	variable_map

Static Public Attributes
static std::shared_ptr< Information< Type > >	fims_information

Detailed Description

template<typename Type>
class fims_info::Information< Type >

Stores FIMS model information and creates model. Contains all objects and data pre-model construction.

Member Typedef Documentation

◆ data_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_data_object::DataObject<Type>>>::iterator fims_info::Information< Type >::data_iterator

iterator for the data objects

◆ density_components_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_distributions::DensityComponentBase<Type>>>::iterator fims_info::Information< Type >::density_components_iterator

iterator for distribution objects>

◆ fleet_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_popdy::Fleet<Type>>>::iterator fims_info::Information< Type >::fleet_iterator

iterator for fleet objects>

◆ growth_models_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_popdy::GrowthBase<Type>>>::iterator fims_info::Information< Type >::growth_models_iterator

iterator for growth objects>

◆ maturity_models_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_popdy::MaturityBase<Type>>>::iterator fims_info::Information< Type >::maturity_models_iterator

iterator for maturity objects>

◆ model_map_iterator

template<typename Type >

typedef std::unordered_map<uint32_t,std::shared_ptr<fims_popdy::FisheryModelBase<Type>>>::iterator fims_info::Information< Type >::model_map_iterator

iterator for variable map>

◆ population_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_popdy::Population<Type>>>::iterator fims_info::Information< Type >::population_iterator

iterator for population objects>

◆ recruitment_models_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_popdy::RecruitmentBase<Type>>>::iterator fims_info::Information< Type >::recruitment_models_iterator

iterator for recruitment objects>

◆ recruitment_process_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_popdy::RecruitmentBase<Type>>>::iterator fims_info::Information< Type >::recruitment_process_iterator

iterator for recruitment process objects>

◆ selectivity_models_iterator

template<typename Type >

typedef std::map<uint32_t,std::shared_ptr<fims_popdy::SelectivityBase<Type>>>::iterator fims_info::Information< Type >::selectivity_models_iterator

iterator for selectivity objects>

◆ variable_map_iterator

template<typename Type >

typedef std::unordered_map<uint32_t,fims::Vector<Type>*>::iterator fims_info::Information< Type >::variable_map_iterator

iterator for variable map>

Member Function Documentation

◆ CheckModel()

template<typename Type >

bool fims_info::Information< Type >::CheckModel ( )

inline

Checks to make sure all required modules are present for specified model.

Returns: True if valid model, False if invalid model, check fims.log for errors.

◆ CreateFleetObjects()

template<typename Type >

void fims_info::Information< Type >::CreateFleetObjects ( bool & valid_model )

inline

Loop over all fleets and set pointers to fleet objects.

Parameters

&valid_model reference to true/false boolean indicating whether model is valid.

◆ CreateModel()

template<typename Type >

bool fims_info::Information< Type >::CreateModel ( )

inline

Create the generalized stock assessment model that will evaluate the objective function. Does error checking to make sure the program has all necessary components for the model and that they're in the right dimensions. This sets up pointers to all memory objects and initializes fleet and population objects.

Returns: True if valid model, False if invalid model, check fims.log for errors.

◆ CreatePopulationObjects()

template<typename Type >

void fims_info::Information< Type >::CreatePopulationObjects ( bool & valid_model )

inline

Loop over all populations and set pointers to population objects.

Parameters

&valid_model reference to true/false boolean indicating whether model is valid.

◆ GetFixedEffectsParameters()

template<typename Type >

std::vector< Type * > & fims_info::Information< Type >::GetFixedEffectsParameters ( )

inline

Get the Fixed Effects Parameters object.

Returns: std::vector<Type*>&

◆ GetInstance()

template<typename Type >

static std::shared_ptr< Information< Type > > fims_info::Information< Type >::GetInstance ( )

inlinestatic

Returns a singleton Information object for type T.

Returns: singleton for type T

◆ GetNages()

template<typename Type >

size_t fims_info::Information< Type >::GetNages ( ) const

inline

Get the Nages object.

Returns: size_t

◆ GetNyears()

template<typename Type >

size_t fims_info::Information< Type >::GetNyears ( ) const

inline

Get the n_years object.

Returns: size_t

◆ GetParameters()

template<typename Type >

std::vector< Type * > & fims_info::Information< Type >::GetParameters ( )

inline

Get the Parameters object.

Returns: std::vector<Type*>&

◆ GetRandomEffectsParameters()

template<typename Type >

std::vector< Type * > & fims_info::Information< Type >::GetRandomEffectsParameters ( )

inline

Get the Random Effects Parameters object.

Returns: std::vector<Type*>&

◆ RegisterParameter()

template<typename Type >

void fims_info::Information< Type >::RegisterParameter ( Type & p )

inline

Register a parameter as estimable.

Parameters

p parameter

◆ RegisterParameterName()

template<typename Type >

void fims_info::Information< Type >::RegisterParameterName ( std::string p_name )

inline

Register a parameter name.

Parameters

p_name parameter name

◆ RegisterRandomEffect()

template<typename Type >

void fims_info::Information< Type >::RegisterRandomEffect ( Type & re )

inline

Register a random effect as estimable.

Parameters

re	random effect

◆ RegisterRandomEffectName()

template<typename Type >

void fims_info::Information< Type >::RegisterRandomEffectName ( std::string re_name )

inline

Register a random effects name.

Parameters

re_name random effects name

◆ SetAgeCompositionData()

template<typename Type >

void fims_info::Information< Type >::SetAgeCompositionData	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Fleet< Type > >	f
	)

inline

Set pointers to age composition data in the fleet module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
f	shared pointer to fleet module

◆ SetDataObjects()

template<typename Type >

void fims_info::Information< Type >::SetDataObjects ( bool & valid_model )

inline

Loop over all density components and set pointers to data objects.

Parameters

&valid_model reference to true/false boolean indicating whether model is valid.

◆ SetFleetIndexData()

template<typename Type >

void fims_info::Information< Type >::SetFleetIndexData	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Fleet< Type > >	f
	)

inline

Set pointers to index data in the fleet module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
f	shared pointer to fleet module

◆ SetFleetLandingsData()

template<typename Type >

void fims_info::Information< Type >::SetFleetLandingsData	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Fleet< Type > >	f
	)

inline

Set pointers to landings data in the fleet module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
f	shared pointer to fleet module

◆ SetFleetSelectivityModel()

template<typename Type >

void fims_info::Information< Type >::SetFleetSelectivityModel	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Fleet< Type > >	f
	)

inline

Set pointers to the selectivity module referenced in the fleet module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
f	shared pointer to fleet module

◆ SetGrowth()

template<typename Type >

void fims_info::Information< Type >::SetGrowth	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Population< Type > >	p
	)

inline

Set pointers to the growth module referenced in the population module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
p	shared pointer to population module

◆ SetLengthCompositionData()

template<typename Type >

void fims_info::Information< Type >::SetLengthCompositionData	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Fleet< Type > >	f
	)

inline

Set pointers to length composition data in the fleet module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
f	shared pointer to fleet module

◆ SetMaturity()

template<typename Type >

void fims_info::Information< Type >::SetMaturity	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Population< Type > >	p
	)

inline

Set pointers to the maturity module referenced in the population module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
p	shared pointer to population module

◆ SetNages()

template<typename Type >

void fims_info::Information< Type >::SetNages ( size_t n_ages )

inline

Set the Nages object.

Parameters

n_ages

◆ SetNyears()

template<typename Type >

void fims_info::Information< Type >::SetNyears ( size_t n_years )

inline

Set the n_years object.

Parameters

n_years

◆ SetRecruitment()

template<typename Type >

void fims_info::Information< Type >::SetRecruitment	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Population< Type > >	p
	)

inline

Set pointers to the recruitment module referenced in the population module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
p	shared pointer to population module

◆ SetRecruitmentProcess()

template<typename Type >

void fims_info::Information< Type >::SetRecruitmentProcess	(	bool &	valid_model,
		std::shared_ptr< fims_popdy::Population< Type > >	p
	)

inline

Set pointers to the recruitment process module referenced in the population module.

Parameters

&valid_model	reference to true/false boolean indicating whether model is valid.
p	shared pointer to population module

◆ State()

template<typename Type >

std::string fims_info::Information< Type >::State ( )

inline

Get a summary string of the Information object state.

Returns a string containing the sizes and states of all major containers and model components in the Information object. Useful for debugging and diagnostics.

Returns: std::string summary of the Information object state.

Member Data Documentation

◆ data_objects

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > > fims_info::Information< Type >::data_objects

map that holds data objects >

◆ density_components

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_distributions::DensityComponentBase<Type> > > fims_info::Information< Type >::density_components

hash map to link each object to its shared location in memory

◆ fims_information

template<typename Type >

std::shared_ptr< Information< Type > > fims_info::Information< Type >::fims_information

static

Initial value:

=

nullptr

singleton instance >

◆ fixed_effects_parameters

template<typename Type >

std::vector<Type *> fims_info::Information< Type >::fixed_effects_parameters

list of all fixed effects parameters >

◆ fleets

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > > fims_info::Information< Type >::fleets

hash map to link each object to its shared location in memory

◆ growth_models

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > > fims_info::Information< Type >::growth_models

hash map to link each object to its shared location in memory

◆ maturity_models

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > > fims_info::Information< Type >::maturity_models

hash map to link each object to its shared location in memory

◆ models_map

template<typename Type >

std::unordered_map<uint32_t, std::shared_ptr<fims_popdy::FisheryModelBase<Type> > > fims_info::Information< Type >::models_map

hash map of fishery models, e.g., CAA, GMACS, Spatial, etc

◆ n_ages

template<typename Type >

size_t fims_info::Information< Type >::n_ages = 0

number of ages>

◆ n_years

template<typename Type >

size_t fims_info::Information< Type >::n_years = 0

number of years >

◆ parameter_names

template<typename Type >

std::vector<std::string> fims_info::Information< Type >::parameter_names

list of all parameter names estimated in the model

◆ parameters

template<typename Type >

std::vector<Type *> fims_info::Information< Type >::parameters

list of all estimated parameters >

◆ populations

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > > fims_info::Information< Type >::populations

hash map to link each object to its shared location in memory

◆ random_effects_names

template<typename Type >

std::vector<std::string> fims_info::Information< Type >::random_effects_names

list of all random effects names estimated in the model

◆ random_effects_parameters

template<typename Type >

std::vector<Type *> fims_info::Information< Type >::random_effects_parameters

list of all random effects parameters >

◆ recruitment_models

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > > fims_info::Information< Type >::recruitment_models

hash map to link each object to its shared location in memory

◆ recruitment_process_models

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > > fims_info::Information< Type >::recruitment_process_models

hash map to link each object to its shared location in memory

◆ selectivity_models

template<typename Type >

std::map<uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > > fims_info::Information< Type >::selectivity_models

hash map to link each object to its shared location in memory

◆ variable_map

template<typename Type >

std::unordered_map<uint32_t, fims::Vector<Type> *> fims_info::Information< Type >::variable_map

hash map to link a parameter, derived value, or observation to its shared location in memory

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

inst/include/common/information.hpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ data_iterator

◆ density_components_iterator

◆ fleet_iterator

◆ growth_models_iterator

◆ maturity_models_iterator

◆ model_map_iterator

◆ population_iterator

◆ recruitment_models_iterator

◆ recruitment_process_iterator

◆ selectivity_models_iterator

◆ variable_map_iterator

Member Function Documentation

◆ CheckModel()

◆ CreateFleetObjects()

◆ CreateModel()

◆ CreatePopulationObjects()

◆ GetFixedEffectsParameters()

◆ GetInstance()

◆ GetNages()

◆ GetNyears()

◆ GetParameters()

◆ GetRandomEffectsParameters()

◆ RegisterParameter()

◆ RegisterParameterName()

◆ RegisterRandomEffect()

◆ RegisterRandomEffectName()

◆ SetAgeCompositionData()

◆ SetDataObjects()

◆ SetFleetIndexData()

◆ SetFleetLandingsData()

◆ SetFleetSelectivityModel()

◆ SetGrowth()

◆ SetLengthCompositionData()

◆ SetMaturity()

◆ SetNages()

◆ SetNyears()

◆ SetRecruitment()

◆ SetRecruitmentProcess()

◆ State()

Member Data Documentation

◆ data_objects

◆ density_components

◆ fims_information

◆ fixed_effects_parameters

◆ fleets

◆ growth_models

◆ maturity_models

◆ models_map

◆ n_ages

◆ n_years

◆ parameter_names

◆ parameters

◆ populations

◆ random_effects_names

◆ random_effects_parameters

◆ recruitment_models

◆ recruitment_process_models

◆ selectivity_models

◆ variable_map