von Bertalanffy–Schnute growth model adapter implementing the generic growth-derived observation capability for catch-at-age. More...

#include <growth_model_adapter.hpp>

Inheritance diagram for fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >:

Public Types
enum class	LengthReferenceParameterization { kEstimatedReferenceLengths = 0 , kConstantLengthYoungEstimatedLengthOld , kEstimatedLengthYoungBelowConstantLengthOld , kBothConstant }
	Options for how the two reference lengths are supplied.

Public Member Functions
void	UseEstimatedReferenceMeanLengths ()
	Estimate both reference mean lengths.

void	UseConstantMeanLengthYoungWithEstimatedMeanLengthOld (Type constant_mean_length_young)
	Fix young reference length and estimate older reference mean length.

void	UseEstimatedMeanLengthYoungBelowConstantMeanLengthOld (Type constant_mean_length_old)
	Estimate young reference length below a fixed old reference length.

void	UseConstantReferenceMeanLengths (Type constant_mean_length_young, Type constant_mean_length_old)
	Fix both young and old reference mean lengths.

fims::Vector< Type > &	MeanLengthYoungVector ()
	Access the working-scale storage for the first reference-length parameter.

fims::Vector< Type > &	MeanLengthOldVector ()
	Access the log-scale length-at-reference-age-2 parameter vector.

fims::Vector< Type > &	GrowthCoefficientVector ()
	Access the log-scale VonBertalanffySchnute growth coefficient vector.

fims::Vector< Type > &	ReferenceAgeForLengthYoungVector ()
	Access the first reference-age vector.

fims::Vector< Type > &	ReferenceAgeForLengthOldVector ()
	Access the second reference-age vector.

fims::Vector< Type > &	LengthWeightAVector ()
	Access the log-scale length-weight-a vector.

fims::Vector< Type > &	LengthWeightBVector ()
	Access the log-scale length-weight-b vector.

fims::Vector< Type > &	LengthAtAgeSdAtRefAgesVector ()
	Access the log-scale length-at-age SD vector at the two reference ages.

fims::Vector< Type > &	LogSdLengthAtRefAgeYoungVector ()
	Access the log-SD vector for mean_length_young.

fims::Vector< Type > &	LogSdLengthAtRefAgeOldVector ()
	Access the log-SD vector for mean_length_old.

fims::Vector< Type > &	LogSdGrowthCoefficientVector ()
	Access the log-SD vector for growth_coefficient.

fims::Vector< Type > &	LogitCorrLengthAtRefAgeYoungLengthAtRefAgeOldVector ()
	Access the transformed correlation vector for mean_length_young and mean_length_old.

fims::Vector< Type > &	LogitCorrLengthAtRefAgeYoungKVector ()
	Access the transformed correlation vector for mean_length_young and growth_coefficient.

fims::Vector< Type > &	LogitCorrLengthAtRefAgeOldKVector ()
	Access the transformed correlation vector for mean_length_old and growth_coefficient.

void	SetAgeOffset (double min_age) override
	Set the minimum modeled age used by cached growth products.

void	Initialize (std::size_t n_years, std::size_t n_ages, std::size_t n_sexes=1) override
	Initialize the backing growth model and cache dimensions.

bool	SupportsAgeToLengthConversionDerived () const override
	Report that the adapter supports growth-derived age-to-length conversion calculations.

virtual const Type	evaluate (int year, const double &a) override
	Calculates the growth at the independent variable value.

void	PrepareGrowthProducts () override
	Prepare growth products for the current model state.

const GrowthProducts< Type > *	TryGetPreparedGrowthProducts () const override
	Return prepared growth products without triggering preparation.

Type	EvaluateWeightAtLength (const Type &length) const override
	Evaluate the length-weight relationship at a supplied length.

Public Member Functions inherited from fims_popdy::GrowthBase< Type >
	GrowthBase ()
	Constructor.

Public Member Functions inherited from fims_model_object::FIMSObject< Type >
uint32_t	GetId () const
	Getter that returns the unique id for parameters in the model.

bool	CheckDimensions (size_t actual, size_t expected)
	Check the dimensions of an object.

Public Member Functions inherited from fims_model_object::FIMSMemoryTracker
void	register_self (const uint32_t id)
	Registers a FIMSObject instance with the memory tracker.

Additional Inherited Members
Public Attributes inherited from fims_model_object::FIMSObject< Type >
uint32_t	id

std::vector< Type * >	parameters

std::vector< Type * >	random_effects_parameters

std::vector< Type * >	fixed_effects_parameters

Static Public Attributes inherited from fims_popdy::GrowthBase< Type >
static uint32_t	id_g = 0

Static Public Attributes inherited from fims_model_object::FIMSMemoryTracker
static int	total_active_objects = 0
	Total number of active FIMSObject instances currently in memory.

Detailed Description

template<typename Type>
class fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >

von Bertalanffy–Schnute growth model adapter implementing the generic growth-derived observation capability for catch-at-age.

Member Function Documentation

◆ evaluate()

template<typename Type >

virtual const Type fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::evaluate	(	int	year,
		const double &	a
	)

inlineoverridevirtual

Calculates the growth at the independent variable value.

Parameters

year	The year at which to return weight of the fish (in kg).
a	The age at which to return weight of the fish (in kg).

Implements fims_popdy::GrowthBase< Type >.

◆ EvaluateWeightAtLength()

template<typename Type >

Type fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::EvaluateWeightAtLength ( const Type & length ) const

inlineoverridevirtual

Evaluate the length-weight relationship at a supplied length.

This is used by fleet-level derived quantities that need a bin-based expectation over the same length bins used in the dynamic age-to-length conversion path.

Parameters

length Length on the natural scale.

Returns: Weight on the natural scale.

Implements fims_popdy::GrowthDerivedObservationBase< Type >.

◆ GrowthCoefficientVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::GrowthCoefficientVector ( )

inline

Access the log-scale VonBertalanffySchnute growth coefficient vector.

Returns: Mutable parameter vector.

◆ Initialize()

template<typename Type >

void fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::Initialize	(	std::size_t	n_years,
		std::size_t	n_ages,
		std::size_t	n_sexes = `1`
	)

inlineoverridevirtual

Initialize the backing growth model and cache dimensions.

Parameters

n_years	Number of modeled years.
n_ages	Number of modeled ages.
n_sexes	Number of modeled sexes.

Implements fims_popdy::GrowthDerivedObservationBase< Type >.

◆ LengthAtAgeSdAtRefAgesVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LengthAtAgeSdAtRefAgesVector ( )

inline

Access the log-scale length-at-age SD vector at the two reference ages.

Returns: Mutable parameter vector.

◆ LengthWeightAVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LengthWeightAVector ( )

inline

Access the log-scale length-weight-a vector.

Returns: Mutable parameter vector.

◆ LengthWeightBVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LengthWeightBVector ( )

inline

Access the log-scale length-weight-b vector.

Returns: Mutable parameter vector.

◆ LogitCorrLengthAtRefAgeOldKVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LogitCorrLengthAtRefAgeOldKVector ( )

inline

Access the transformed correlation vector for mean_length_old and growth_coefficient.

Returns: Mutable parameter vector.

◆ LogitCorrLengthAtRefAgeYoungKVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LogitCorrLengthAtRefAgeYoungKVector ( )

inline

Access the transformed correlation vector for mean_length_young and growth_coefficient.

Returns: Mutable parameter vector.

◆ LogitCorrLengthAtRefAgeYoungLengthAtRefAgeOldVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LogitCorrLengthAtRefAgeYoungLengthAtRefAgeOldVector ( )

inline

Access the transformed correlation vector for mean_length_young and mean_length_old.

Returns: Mutable parameter vector.

◆ LogSdGrowthCoefficientVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LogSdGrowthCoefficientVector ( )

inline

Access the log-SD vector for growth_coefficient.

Returns: Mutable parameter vector.

◆ LogSdLengthAtRefAgeOldVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LogSdLengthAtRefAgeOldVector ( )

inline

Access the log-SD vector for mean_length_old.

Returns: Mutable parameter vector.

◆ LogSdLengthAtRefAgeYoungVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::LogSdLengthAtRefAgeYoungVector ( )

inline

Access the log-SD vector for mean_length_young.

Returns: Mutable parameter vector.

◆ MeanLengthOldVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::MeanLengthOldVector ( )

inline

Access the log-scale length-at-reference-age-2 parameter vector.

Returns: Mutable parameter vector.

◆ MeanLengthYoungVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::MeanLengthYoungVector ( )

inline

Access the working-scale storage for the first reference-length parameter.

Returns: Mutable parameter vector.

◆ PrepareGrowthProducts()

template<typename Type >

void fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::PrepareGrowthProducts ( )

inlineoverridevirtual

Prepare growth products for the current model state.

Implements fims_popdy::GrowthDerivedObservationBase< Type >.

◆ ReferenceAgeForLengthOldVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::ReferenceAgeForLengthOldVector ( )

inline

Access the second reference-age vector.

Returns: Mutable parameter vector.

◆ ReferenceAgeForLengthYoungVector()

template<typename Type >

fims::Vector< Type > & fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::ReferenceAgeForLengthYoungVector ( )

inline

Access the first reference-age vector.

Returns: Mutable parameter vector.

◆ SetAgeOffset()

template<typename Type >

void fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::SetAgeOffset ( double min_age )

inlineoverridevirtual

Set the minimum modeled age used by cached growth products.

Parameters

min_age Minimum age on the natural scale.

Implements fims_popdy::GrowthDerivedObservationBase< Type >.

◆ SupportsAgeToLengthConversionDerived()

template<typename Type >

bool fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::SupportsAgeToLengthConversionDerived ( ) const

inlineoverridevirtual

Report that the adapter supports growth-derived age-to-length conversion calculations.

Returns: Always true for this adapter.

Implements fims_popdy::GrowthDerivedObservationBase< Type >.

◆ TryGetPreparedGrowthProducts()

template<typename Type >

const GrowthProducts< Type > * fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::TryGetPreparedGrowthProducts ( ) const

inlineoverridevirtual

Return prepared growth products without triggering preparation.

Returns: Pointer to prepared growth products, or nullptr if unavailable.

Implements fims_popdy::GrowthDerivedObservationBase< Type >.

◆ UseConstantMeanLengthYoungWithEstimatedMeanLengthOld()

template<typename Type >

void fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::UseConstantMeanLengthYoungWithEstimatedMeanLengthOld ( Type constant_mean_length_young )

inline

Fix young reference length and estimate older reference mean length.

Parameters

constant_mean_length_young Fixed mean length at the younger reference age.

◆ UseConstantReferenceMeanLengths()

template<typename Type >

void fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::UseConstantReferenceMeanLengths	(	Type	constant_mean_length_young,
		Type	constant_mean_length_old
	)

inline

Fix both young and old reference mean lengths.

Parameters

constant_mean_length_young	Fixed mean length at the younger reference age.
constant_mean_length_old	Fixed mean length at the older reference age.

◆ UseEstimatedMeanLengthYoungBelowConstantMeanLengthOld()

template<typename Type >

void fims_popdy::VonBertalanffySchnuteGrowthModelAdapter< Type >::UseEstimatedMeanLengthYoungBelowConstantMeanLengthOld ( Type constant_mean_length_old )

inline

Estimate young reference length below a fixed old reference length.

Parameters

constant_mean_length_old Fixed mean length at the older reference age.

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

inst/include/population_dynamics/growth/growth_model_adapter.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ evaluate()

◆ EvaluateWeightAtLength()

◆ GrowthCoefficientVector()

◆ Initialize()

◆ LengthAtAgeSdAtRefAgesVector()

◆ LengthWeightAVector()

◆ LengthWeightBVector()

◆ LogitCorrLengthAtRefAgeOldKVector()

◆ LogitCorrLengthAtRefAgeYoungKVector()

◆ LogitCorrLengthAtRefAgeYoungLengthAtRefAgeOldVector()

◆ LogSdGrowthCoefficientVector()

◆ LogSdLengthAtRefAgeOldVector()

◆ LogSdLengthAtRefAgeYoungVector()

◆ MeanLengthOldVector()

◆ MeanLengthYoungVector()

◆ PrepareGrowthProducts()

◆ ReferenceAgeForLengthOldVector()

◆ ReferenceAgeForLengthYoungVector()

◆ SetAgeOffset()

◆ SupportsAgeToLengthConversionDerived()

◆ TryGetPreparedGrowthProducts()

◆ UseConstantMeanLengthYoungWithEstimatedMeanLengthOld()

◆ UseConstantReferenceMeanLengths()

◆ UseEstimatedMeanLengthYoungBelowConstantMeanLengthOld()