VonBertalanffySchnuteGrowthInterface Class Reference

Rcpp-facing VonBertalanffySchnute growth module. Inherits "derived observation" capability so this growth can support growth-derived outputs used by downstream age-to-length conversion/weight- at-age paths. More...

#include <rcpp_growth.hpp>

Inheritance diagram for VonBertalanffySchnuteGrowthInterface:

Public Member Functions
	VonBertalanffySchnuteGrowthInterface ()
	Construct a new VonBertalanffySchnute growth interface.
	VonBertalanffySchnuteGrowthInterface (const VonBertalanffySchnuteGrowthInterface &other)
	Copy constructor.
virtual uint32_t	get_id ()
	Get the ID for the child growth interface objects to inherit.
virtual void	finalize ()
	Extracts derived quantities back to the Rcpp interface object from the Information object.
virtual double	evaluate (double age)
	A method for each child growth interface object to inherit so each growth option can have an evaluate() function.
virtual std::string	to_json ()
	Convert the data to json representation for the output.
Public Member Functions inherited from GrowthDerivedObservationInterfaceBase
	GrowthDerivedObservationInterfaceBase (const GrowthDerivedObservationInterfaceBase &other)
	Copy constructor.
Public Member Functions inherited from GrowthInterfaceBase
	GrowthInterfaceBase ()
	The constructor.
	GrowthInterfaceBase (const GrowthInterfaceBase &other)
	Construct a new Growth Interface Base object.
virtual	~GrowthInterfaceBase ()
	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.
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
VariableVector	mean_length_young
	Expected length at the first reference age.
VariableVector	mean_length_old
	Expected length at the second reference age.
VariableVector	growth_coefficient
	Growth coefficient.
VariableVector	reference_age_for_length_young
	First reference age for the length parameterization.
VariableVector	reference_age_for_length_old
	Second reference age for the length parameterization.
VariableVector	length_weight_a
	Coefficient in the length-weight relationship, W = a * L^b.
VariableVector	length_weight_b
	Exponent in the length-weight relationship, W = a * L^b.
VariableVector	length_at_age_sd_at_reference_ages
	Natural-scale SD values at the two reference ages for the legacy interpolation path.
VariableVector	log_sd_mean_length_young
	Working-scale von Bertalanffy–Schnute variability parameter for sd(log(mean_length_young)).
VariableVector	log_sd_mean_length_old
	Working-scale von Bertalanffy–Schnute variability parameter for sd(log(mean_length_old)).
VariableVector	log_sd_growth_coefficient
	Working-scale von Bertalanffy–Schnute variability parameter for sd(log(growth_coefficient)).
VariableVector	mean_length_young_mean_length_old_logit_corr
	Working-scale von Bertalanffy–Schnute variability parameter for corr(log(mean_length_young), log(mean_length_old)).
VariableVector	mean_length_young_growth_coefficient_logit_corr
	Working-scale von Bertalanffy–Schnute variability parameter for corr(log(mean_length_young), log(growth_coefficient)).
VariableVector	mean_length_old_growth_coefficient_logit_corr
	Working-scale von Bertalanffy–Schnute variability parameter for corr(log(mean_length_old), log(growth_coefficient)).
SharedInt	n_ages = 0
	Modeled number of ages used for validation.
Public Attributes inherited from GrowthInterfaceBase
uint32_t	id
	The local id of the GrowthInterfaceBase 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 GrowthInterfaceBase
static uint32_t	id_g = 1
	The static id of the GrowthInterfaceBase object.
static std::map< uint32_t, std::shared_ptr< GrowthInterfaceBase > >	live_objects
	The map associating the IDs of GrowthInterfaceBase 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.
Protected Member Functions inherited from GrowthDerivedObservationInterfaceBase
template<typename Type >
std::shared_ptr< fims_popdy::GrowthDerivedObservationBase< Type > >	GetGrowthObservationFromInfo () const
	Look up the registered growth-derived observation object.
template<typename Type >
void	RegisterGrowthObservationInInfo (const std::shared_ptr< fims_popdy::GrowthDerivedObservationBase< Type > > &growth_observation) const
	Register a runtime growth-derived observation in Information.

Detailed Description

Rcpp-facing VonBertalanffySchnute growth module. Inherits "derived observation" capability so this growth can support growth-derived outputs used by downstream age-to-length conversion/weight- at-age paths.

Constructor & Destructor Documentation

VonBertalanffySchnuteGrowthInterface()

VonBertalanffySchnuteGrowthInterface::VonBertalanffySchnuteGrowthInterface ( const VonBertalanffySchnuteGrowthInterface &  other )

inline

Copy constructor.

Parameters

other

Source interface object.

Member Function Documentation

evaluate()

virtual double VonBertalanffySchnuteGrowthInterface::evaluate ( double  age )

inlinevirtual

A method for each child growth interface object to inherit so each growth option can have an evaluate() function.

Implements GrowthInterfaceBase.

finalize()

virtual void VonBertalanffySchnuteGrowthInterface::finalize ( )

inlinevirtual

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

Reimplemented from FIMSRcppInterfaceBase.

get_id()

virtual uint32_t VonBertalanffySchnuteGrowthInterface::get_id ( )

inlinevirtual

Get the ID for the child growth interface objects to inherit.

Implements GrowthInterfaceBase.

to_json()

virtual std::string VonBertalanffySchnuteGrowthInterface::to_json ( )

inlinevirtual

Convert the data to json representation for the output.

Reimplemented from FIMSRcppInterfaceBase.

Member Data Documentation

growth_coefficient

VariableVector VonBertalanffySchnuteGrowthInterface::growth_coefficient

Growth coefficient.

length_weight_a

VariableVector VonBertalanffySchnuteGrowthInterface::length_weight_a

Coefficient in the length-weight relationship, W = a * L^b.

length_weight_b

VariableVector VonBertalanffySchnuteGrowthInterface::length_weight_b

Exponent in the length-weight relationship, W = a * L^b.

mean_length_old

VariableVector VonBertalanffySchnuteGrowthInterface::mean_length_old

Expected length at the second reference age.

mean_length_young

VariableVector VonBertalanffySchnuteGrowthInterface::mean_length_young

Expected length at the first reference age.

reference_age_for_length_old

VariableVector VonBertalanffySchnuteGrowthInterface::reference_age_for_length_old

Second reference age for the length parameterization.

reference_age_for_length_young

VariableVector VonBertalanffySchnuteGrowthInterface::reference_age_for_length_young

First reference age for the length parameterization.

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

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