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.
std::string	value_to_string (double value)
	Report the variable 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.
VariableVector	log_M
	The natural log of the natural mortality for each year.
VariableVector	spawning_biomass_ratio
	The population spawning biomass ratio for each year.
VariableVector	log_f_multiplier
	Log of the population annual fishing mortality multiplier.
VariableVector	log_init_naa
	The natural log of the initial numbers at age.
VariableVector	proportion_female
	Proportion of females in the population.
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.
VariableVector	total_catch_weight
	Total annual catch removed from a population by all fleets in weight.
VariableVector	total_catch_numbers
	Total annual catch removed from a population by all fleets in numbers.
VariableVector	mortality_F
	Total annual fishing mortality a population is subject to.
VariableVector	mortality_M
	Total annual natural mortality a population is subject to.
VariableVector	mortality_Z
	Total annual mortality a population is subject to.
VariableVector	numbers_at_age
	Current population composition in numbers at age.
VariableVector	unfished_numbers_at_age
	Theoretical population composition in numbers at age if no fishing had occurred.
VariableVector	biomass
	Total weight of all fish in the population.
VariableVector	spawning_biomass
	Total weight of mature fish in the population.
VariableVector	unfished_biomass
	Total theoretical weight of all fish in the population if no fishing had occurred.
VariableVector	unfished_spawning_biomass
	Total theoretical weight of mature fish in the population if no fishing had occurred.
VariableVector	proportion_mature_at_age
	Fraction of all fish at a given age that are sexually mature at each age.
VariableVector	expected_recruitment
	Model-expected recruitment each year based on the stock–recruit relationship.
VariableVector	sum_selectivity
	Sum of selectivity at age across all fleets for a 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 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.

proportion_female

VariableVector PopulationInterface::proportion_female

Proportion of females in the population.

Used to calculate spawning biomass and other sex-specific derived quantities. Supplied from R as a single constant (length 1) and applied to all ages during model evaluation. Values should be in [0, 1]. Out-of-range inputs are logged as warnings.

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

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