PopulationInterface Class Reference

Rcpp interface for a new Population to instantiate from R: population <- methods::new(population) More...

#include <rcpp_population.hpp>

Inheritance diagram for PopulationInterface:

Public Types
typedef std::set< uint32_t >::iterator	fleet_ids_iterator

Public Member Functions
	PopulationInterface ()
	The constructor.
	PopulationInterface (const PopulationInterface &other)
	Construct a new Population Interface object.
virtual	~PopulationInterface ()
	The destructor.
virtual uint32_t	get_id ()
	Gets the ID of the interface base object.
void	SetName (const std::string &name)
	Sets the name of the population.
std::string	GetName () const
	Gets the name of the population.
void	SetMaturityID (uint32_t maturity_id)
	Sets the unique ID for the Maturity object.
void	SetGrowthID (uint32_t growth_id)
	Set the unique ID for the growth object.
void	SetRecruitmentID (uint32_t recruitment_id)
	Set the unique ID for the recruitment object.
void	AddFleet (uint32_t fleet_id)
	Add a fleet id to the list of fleets operating on this population.
virtual void	finalize ()
	Extracts derived quantities back to the Rcpp interface object from the Information object.
Public Member Functions inherited from PopulationInterfaceBase
	PopulationInterfaceBase ()
	The constructor.
	PopulationInterfaceBase (const PopulationInterfaceBase &other)
	Construct a new Population Interface Base object.
virtual	~PopulationInterfaceBase ()
	The destructor.
Public Member Functions inherited from FIMSRcppInterfaceBase
virtual bool	add_to_fims_tmb ()
	A virtual method to inherit to add objects to the TMB model.
virtual std::string	to_json ()
	Convert the data to json representation for the output.
void	get_se_values (std::string name, std::map< std::string, std::vector< double > > &se_values, fims::Vector< double > &values)
	Method to extract standard error values from the se_values working map.
virtual void	set_uncertainty (std::map< std::string, std::vector< double > > &se_values)
	Set uncertainty values for the interface object.
std::string	value_to_string (double value)
	Report the parameter value as a string.
std::string	make_dimensions (uint32_t start, uint32_t end, uint32_t rep=1)
	Make a string of dimensions for the model.

Public Attributes
SharedInt	n_ages = 0
	The number of age bins.
SharedInt	n_fleets
	The number of fleets.
std::shared_ptr< std::set< uint32_t > >	fleet_ids
SharedInt	n_years
	The number of years.
SharedInt	n_lengths
	The number of length bins.
SharedInt	maturity_id
	The ID of the maturity module.
SharedInt	growth_id
	The ID of the growth module.
SharedInt	recruitment_id
	The ID of the recruitment module.
SharedInt	recruitment_err_id
	The ID of the recruitment process module.
ParameterVector	log_M
	The natural log of the natural mortality for each year.
ParameterVector	spawning_biomass_ratio
	The population spawning biomass ratio for each year.
ParameterVector	log_f_multiplier
	Log of the population annual fishing mortality multiplier.
ParameterVector	log_init_naa
	The natural log of the initial numbers at age.
RealVector	ages
	Ages that are modeled in the population, the length of this vector should equal "n_ages".
SharedString	name = fims::to_string("NA")
	The name for the population.
Public Attributes inherited from PopulationInterfaceBase
uint32_t	id
	The local id of the PopulationInterfaceBase object.
SharedBoolean	initialize_catch_at_age
	Initialize the catch at age model.
SharedBoolean	initialize_surplus_production
	Initialize the surplus production model.
Public Attributes inherited from FIMSRcppInterfaceBase
bool	finalized = false
	Is the object already finalized? The default is false.

Additional Inherited Members
Static Public Attributes inherited from PopulationInterfaceBase
static uint32_t	id_g = 1
	The static id of the PopulationInterfaceBase object.
static std::map< uint32_t, std::shared_ptr< PopulationInterfaceBase > >	live_objects
	The map associating the IDs of PopulationInterfaceBase to the objects. This is a live object, which is an object that has been created and lives in memory.
Static Public Attributes inherited from FIMSRcppInterfaceBase
static std::vector< std::shared_ptr< FIMSRcppInterfaceBase > >	fims_interface_objects
	FIMS interface object vectors.

Detailed Description

Rcpp interface for a new Population to instantiate from R: population <- methods::new(population)

Member Typedef Documentation

fleet_ids_iterator

typedef std::set<uint32_t>::iterator PopulationInterface::fleet_ids_iterator

Iterator for fleet ids.

Constructor & Destructor Documentation

PopulationInterface()

PopulationInterface::PopulationInterface ( const PopulationInterface &  other )

inline

Construct a new Population Interface object.

Parameters

other

Member Function Documentation

finalize()

virtual void PopulationInterface::finalize ( )

inlinevirtual

Extracts derived quantities back to the Rcpp interface object from the Information object.

Reimplemented from FIMSRcppInterfaceBase.

get_id()

virtual uint32_t PopulationInterface::get_id ( )

inlinevirtual

Gets the ID of the interface base object.

Returns

The ID.

Implements PopulationInterfaceBase.

GetName()

std::string PopulationInterface::GetName ( ) const

inline

Gets the name of the population.

Returns

The name.

SetGrowthID()

void PopulationInterface::SetGrowthID ( uint32_t  growth_id )

inline

Set the unique ID for the growth object.

Parameters

growth_id

Unique ID for the growth object.

SetMaturityID()

void PopulationInterface::SetMaturityID ( uint32_t  maturity_id )

inline

Sets the unique ID for the Maturity object.

Parameters

maturity_id

Unique ID for the Maturity object.

SetName()

void PopulationInterface::SetName ( const std::string &  name )

inline

Sets the name of the population.

Parameters

name	The name to set.

SetRecruitmentID()

void PopulationInterface::SetRecruitmentID ( uint32_t  recruitment_id )

inline

Set the unique ID for the recruitment object.

Parameters

recruitment_id

Unique ID for the recruitment object.

Member Data Documentation

fleet_ids

std::shared_ptr<std::set<uint32_t> > PopulationInterface::fleet_ids

list of fleets that operate on this population.

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

• inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp