BevertonHoltRecruitmentInterface Class Reference

Rcpp interface for Beverton–Holt to instantiate from R: beverton_holt <- methods::new(beverton_holt). More...

#include <rcpp_recruitment.hpp>

Inheritance diagram for BevertonHoltRecruitmentInterface:

Public Member Functions
	BevertonHoltRecruitmentInterface ()
	The constructor.
	BevertonHoltRecruitmentInterface (const BevertonHoltRecruitmentInterface &other)
	Construct a new Beverton–Holt Recruitment Interface object.
virtual	~BevertonHoltRecruitmentInterface ()
	The destructor.
virtual uint32_t	get_id ()
	Gets the ID of the interface base object.
void	SetRecruitmentProcessID (uint32_t process_id)
	Set the unique ID for the recruitment process object.
virtual double	evaluate_mean (double spawners, double ssbzero)
	Evaluate recruitment using the Beverton–Holt stock–recruitment relationship.
virtual double	evaluate_process (size_t pos)
	Evaluate recruitment process - returns 0 in this module.
virtual void	finalize ()
	Extracts derived quantities back to the Rcpp interface object from the Information object.
virtual void	set_uncertainty (std::map< std::string, std::vector< double > > &se_values)
	Sets the uncertainty values for the parameters from the standard error values passed from R.
virtual std::string	to_json ()
	Converts the data to json representation for the output.
Public Member Functions inherited from RecruitmentInterfaceBase
	RecruitmentInterfaceBase ()
	The constructor.
	RecruitmentInterfaceBase (const RecruitmentInterfaceBase &other)
	Construct a new Recruitment Interface Base object.
virtual	~RecruitmentInterfaceBase ()
	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.
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.
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_years
	The number of years.
ParameterVector	logit_steep
	The logistic transformation of steepness (h; productivity of the population), where the parameter is transformed to constrain it between 0.2 and 1.0.
ParameterVector	log_rzero
	The natural log of recruitment at unfished biomass.
ParameterVector	log_devs
	The natural log of recruitment deviations.
ParameterVector	log_r
	The recruitment random effect parameter on the natural log scale.
ParameterVector	log_expected_recruitment
	Expectation of the recruitment process.
fims_double	estimated_logit_steep
	The estimate of the logit transformation of steepness.
fims_double	estimated_log_rzero
	The estimate of the natural log of recruitment at unfished biomass.
RealVector	estimated_log_devs
	The estimates of the natural log of recruitment deviations.
Public Attributes inherited from RecruitmentInterfaceBase
uint32_t	id
	The local id of the RecruitmentInterfaceBase object.
SharedInt	process_id = -999
	The process id of the RecruitmentInterfaceBase object.
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 RecruitmentInterfaceBase
static uint32_t	id_g = 1
	The static id of the RecruitmentInterfaceBase object.
static std::map< uint32_t, std::shared_ptr< RecruitmentInterfaceBase > >	live_objects
	The map associating the IDs of RecruitmentInterfaceBase 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 Beverton–Holt to instantiate from R: beverton_holt <- methods::new(beverton_holt).

Constructor & Destructor Documentation

BevertonHoltRecruitmentInterface()

BevertonHoltRecruitmentInterface::BevertonHoltRecruitmentInterface ( const BevertonHoltRecruitmentInterface &  other )

inline

Construct a new Beverton–Holt Recruitment Interface object.

Parameters

other

The passed object to copy.

Member Function Documentation

evaluate_mean()

virtual double BevertonHoltRecruitmentInterface::evaluate_mean ( double  spawners, double  ssbzero  )

inlinevirtual

Evaluate recruitment using the Beverton–Holt stock–recruitment relationship.

Parameters

spawners	Spawning biomass per time step.
ssbzero	The biomass at unfished levels. TODO: Change to sbzero if continuing to use acronyms.

Implements RecruitmentInterfaceBase.

evaluate_process()

virtual double BevertonHoltRecruitmentInterface::evaluate_process ( size_t  pos )

inlinevirtual

Evaluate recruitment process - returns 0 in this module.

Parameters

pos	Position index, e.g., which year.

Implements RecruitmentInterfaceBase.

finalize()

virtual void BevertonHoltRecruitmentInterface::finalize ( )

inlinevirtual

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

Reimplemented from FIMSRcppInterfaceBase.

get_id()

virtual uint32_t BevertonHoltRecruitmentInterface::get_id ( )

inlinevirtual

Gets the ID of the interface base object.

Returns

The ID.

Implements RecruitmentInterfaceBase.

set_uncertainty()

virtual void BevertonHoltRecruitmentInterface::set_uncertainty ( std::map< std::string, std::vector< double > > &  se_values )

inlinevirtual

Sets the uncertainty values for the parameters from the standard error values passed from R.

Parameters

se_values

A map of parameter names and their associated standard error values.

Reimplemented from FIMSRcppInterfaceBase.

SetRecruitmentProcessID()

void BevertonHoltRecruitmentInterface::SetRecruitmentProcessID ( uint32_t  process_id )

inline

Set the unique ID for the recruitment process object.

Parameters

process_id

Unique ID for the recruitment process object.

to_json()

virtual std::string BevertonHoltRecruitmentInterface::to_json ( )

inlinevirtual

Converts the data to json representation for the output.

Returns

A string is returned specifying that the module relates to the recruitment interface with Beverton–Holt stock–recruitment relationship. It also returns the ID and the parameters. This string is formatted for a json file.

Reimplemented from FIMSRcppInterfaceBase.

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

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