CatchAtAge is a class containing a catch-at-age model, which is just one of many potential fishery models that can be used in FIMS. The CatchAtAge class inherits from the FisheryModelBase class and can be used to fit both age and length data even though it is called CatchAtAge. More...

#include <catch_at_age.hpp>

Inheritance diagram for fims_popdy::CatchAtAge< Type >:

Public Types
typedef std::map< std::string, fims::Vector< Type > >::iterator	derived_quantities_iterator
	Iterate the derived quantities.

typedef std::map< uint32_t, std::map< std::string, fims::Vector< Type > > >::iterator	fleet_derived_quantities_iterator
	Used to iterate through fleet-based derived quantities.

typedef std::map< uint32_t, std::map< std::string, fims::Vector< size_t > > >::iterator	fleet_derived_quantities_dims_iterator
	Used to iterate through fleet-based derived quantities dimensions.

typedef std::map< uint32_t, std::map< std::string, fims::Vector< Type > > >::iterator	population_derived_quantities_iterator
	Used to iterate through population-based derived quantities.

typedef std::map< uint32_t, std::map< std::string, fims::Vector< size_t > > >::iterator	population_derived_quantities_dims_iterator
	Used to iterate through population-based derived quantities dimensions.

typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator	fleet_iterator
	Iterate through fleets.

typedef std::map< std::string, fims::Vector< Type > >::iterator	dq_iterator
	Iterate through derived quantities.

Public Types inherited from fims_popdy::FisheryModelBase< Type >
typedef std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >::iterator	fleet_iterator
	Fleet-based iterator.

typedef std::map< uint32_t, std::map< std::string, fims::Vector< Type > > >	DerivedQuantitiesMap
	Type definitions for derived quantities and dimension information maps.

typedef DerivedQuantitiesMap::iterator	DerivedQuantitiesMapIterator
	Iterator for the derived quantities map.

typedef std::map< uint32_t, std::map< std::string, DimensionInfo > >	DimensionInfoMap
	Type definitions for dimension information maps.

Public Member Functions
	CatchAtAge ()

	CatchAtAge (const CatchAtAge &other)
	Copy constructor for the CatchAtAge class.

virtual	~CatchAtAge ()
	Destroy the Catch At Age object.

virtual void	Initialize ()

virtual void	Prepare ()

void	AddPopulation (uint32_t id)

std::set< uint32_t > &	GetPopulationIds ()
	Get the population ids of the model.

std::vector< std::shared_ptr< fims_popdy::Population< Type > > > &	GetPopulations ()

void	CalculateInitialNumbersAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t age)
	Calculates initial numbers at age for index and age.

void	CalculateNumbersAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t i_agem1_yearm1, size_t age)
	Calculates numbers at age for a population.

void	CalculateUnfishedNumbersAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t i_agem1_yearm1, size_t age)
	Calculates unfished numbers at age at year and age specific indices.

void	CalculateMortality (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculates total mortality for a population.

void	CalculateBiomass (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculates biomass for a population.

void	CalculateUnfishedBiomass (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculates the unfished biomass for a population.

void	CalculateSpawningBiomass (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculates spawning biomass for a population.

void	CalculateUnfishedSpawningBiomass (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculated unfished spawning biomass for a population.

void	CalculateSpawningBiomassRatio (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t year)
	Calculate the spawning biomass ratio for a population and year.

Type	CalculateSBPR0 (std::shared_ptr< fims_popdy::Population< Type > > &population)
	Calculates equilibrium spawning biomass per recruit.

void	CalculateRecruitment (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t i_dev)
	Calculates expected recruitment for a population.

void	CalculateMaturityAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t age)
	Calculates maturity at age, in proportion, for a population.

void	CalculateCatch (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t year, size_t age)
	Calculates total catch (catch) by fleet and population for a given year by aggregating age-specific catch over ages.

void	CalculateCatchWeightAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t year, size_t age)
	Calculates weight at age of the catch for a given fleet from a population.

void	CalculateCatchNumbersAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculates numbers of fish for the catch for a given fleet from a population, year and age.

void	CalculateIndex (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculates the index for a fleet from a population.

void	CalculateIndexNumbersAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t i_age_year, size_t year, size_t age)
	Calculates the numbers for the index for a fleet from a population.

void	CalculateIndexWeightAA (std::shared_ptr< fims_popdy::Population< Type > > &population, size_t year, size_t age)
	Calculates biomass of fish for the index for a given fleet from a population.

void	evaluate_age_comp ()

Type	MeanWeightFromAgeToLengthConversionRow (const std::shared_ptr< fims_popdy::GrowthDerivedObservationBase< Type > > &growth_observation, const std::shared_ptr< fims_popdy::Fleet< Type > > &fleet, const fims::Vector< Type > &age_to_length_conversion_row)
	Compute expected fleet-specific weight-at-age from a normalized age-to-length conversion row and fleet observation-bin centers.

void	BuildAgeToLengthConversionDerivedRowOrThrow (const std::shared_ptr< fims_popdy::AgeToLengthConversionDerived< Type > > &age_to_length_conversion_derived, const std::shared_ptr< fims_popdy::Fleet< Type > > &fleet, size_t year, size_t age, fims::Vector< Type > &age_to_length_conversion_row)
	Build one fleet-specific growth-derived age-to-length conversion row or fail clearly.

Type	MeanWeightFromAgeToLengthConversionDerived (const std::shared_ptr< fims_popdy::AgeToLengthConversionDerived< Type > > &age_to_length_conversion_derived, const std::shared_ptr< fims_popdy::Fleet< Type > > &fleet, size_t year, size_t age)
	Compute fleet-specific mean weight-at-age from one growth-derived age-to-length conversion row.

void	EnsureAllFleetAgeToLengthConversion ()
	Ensure all fleets linked to this model have a usable age-to-length conversion.

void	PreparePopulationGrowthProducts ()
	Prepares cached population growth products for all populations whose growth objects expose the growth-derived observation interface.

Type	GrowthDerivedFleetMeanWeightAA (const std::shared_ptr< fims_popdy::Fleet< Type > > &fleet, size_t year, size_t age)
	Compute fleet-specific expected weight-at-age from the growth-derived age-to-length conversion path.

Type	BiologicalMeanWeightFromPreparedGrowthProducts (const std::shared_ptr< fims_popdy::Population< Type > > &population, const std::shared_ptr< fims_popdy::GrowthDerivedObservationBase< Type > > &growth_observation, size_t year, size_t age)
	Read biological mean weight-at-age directly from prepared growth products.

Type	PopulationMeanWeightAA (const std::shared_ptr< fims_popdy::Population< Type > > &population, size_t year, size_t age)
	Calculates population-level mean weight-at-age.

void	evaluate_length_comp ()

void	evaluate_index ()

void	evaluate_catch ()

virtual void	Evaluate ()
	Evaluate the model.

virtual void	Report ()

Public Member Functions inherited from fims_popdy::FisheryModelBase< Type >
	FisheryModelBase ()
	Construct a new Fishery Model Base object.

	FisheryModelBase (const FisheryModelBase &other)
	Construct a new Fishery Model Base object.

virtual	~FisheryModelBase ()
	Destroy the Fishery Model Base object.

std::map< uint32_t, std::map< std::string, DimensionInfo > > &	GetFleetDimensionInfo ()
	Get the fleet dimension information.

std::map< uint32_t, std::map< std::string, DimensionInfo > > &	GetPopulationDimensionInfo ()
	Get the population dimension information.

DerivedQuantitiesMap &	GetFleetDerivedQuantities ()
	Get the fleet derived quantities.

DerivedQuantitiesMap &	GetPopulationDerivedQuantities ()
	Get the population derived quantities.

std::map< std::string, fims::Vector< Type > > &	GetFleetDerivedQuantities (uint32_t fleet_id)
	Get the fleet derived quantities for a specified fleet.

void	InitializeFleetDerivedQuantities (uint32_t fleet_id)
	Initialize the derived quantities map for a fleet.

void	InitializePopulationDerivedQuantities (uint32_t population_id)
	Initialize the derived quantities map for a population.

std::map< std::string, fims::Vector< Type > > &	GetPopulationDerivedQuantities (uint32_t population_id)
	Get the population derived quantities for a specified population.

std::map< std::string, DimensionInfo > &	GetFleetDimensionInfo (uint32_t fleet_id)
	Get the fleet dimension information for a specified fleet.

std::map< std::string, DimensionInfo > &	GetPopulationDimensionInfo (uint32_t population_id)
	Get the population dimension information for a specified population.

virtual void	ResetVector (fims::Vector< Type > &v, Type value=0.0)
	Reset a vector from start to end with a value.

uint32_t	GetId ()
	Get the Id object.

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.

Public Attributes
std::string	name_m
	The name of the model.

std::map< std::string, fims::Vector< fims::Vector< Type > > >	report_vectors
	A map of report vectors for the object. used to populate the report_vectors map in for submodule parameters.

bool	report_age_to_length_conversion_derived_tensor = false
	Controls whether reporting materializes the full derived age-to-length tensor for fleets using the growth-derived age-to-length conversion path.

std::vector< Type >	ages

Public Attributes inherited from fims_popdy::FisheryModelBase< Type >
std::string	model_type_m
	A string specifying the model type.

std::set< uint32_t >	population_ids
	Unique identifier for the fishery model.

std::vector< std::shared_ptr< fims_popdy::Population< Type > > >	populations
	A vector of populations in the fishery model.

std::map< uint32_t, std::shared_ptr< fims_popdy::Fleet< Type > > >	fleets
	A map of fleets in the fishery model, indexed by fleet id. Unique instances to eliminate duplicate initialization.

std::shared_ptr< DerivedQuantitiesMap >	fleet_derived_quantities
	Shared pointer for the fleet derived quantities map.

std::shared_ptr< DerivedQuantitiesMap >	population_derived_quantities
	Shared pointer for the population derived quantities map.

std::shared_ptr< DimensionInfoMap >	fleet_dimension_info
	Shared pointer for the fleet dimension information map.

std::shared_ptr< DimensionInfoMap >	population_dimension_info
	Shared pointer for the population dimension information map.

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

Additional Inherited Members
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::CatchAtAge< Type >

CatchAtAge is a class containing a catch-at-age model, which is just one of many potential fishery models that can be used in FIMS. The CatchAtAge class inherits from the FisheryModelBase class and can be used to fit both age and length data even though it is called CatchAtAge.

See the Glossary for definitions of mathematical symbols used below.

Constructor & Destructor Documentation

◆ CatchAtAge() [1/2]

template<typename Type >

fims_popdy::CatchAtAge< Type >::CatchAtAge ( )

inline

Constructor for the CatchAtAge class. This constructor initializes the name of the model and sets the id of the model.

◆ CatchAtAge() [2/2]

template<typename Type >

fims_popdy::CatchAtAge< Type >::CatchAtAge ( const CatchAtAge< Type > & other )

inline

Copy constructor for the CatchAtAge class.

Parameters

other The other CatchAtAge object to copy from.

Member Function Documentation

◆ AddPopulation()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::AddPopulation ( uint32_t id )

inline

This function is used to add a population id to the set of population ids.

◆ BiologicalMeanWeightFromPreparedGrowthProducts()

template<typename Type >

Type fims_popdy::CatchAtAge< Type >::BiologicalMeanWeightFromPreparedGrowthProducts	(	const std::shared_ptr< fims_popdy::Population< Type > > &	population,
		const std::shared_ptr< fims_popdy::GrowthDerivedObservationBase< Type > > &	growth_observation,
		size_t	year,
		size_t	age
	)

inline

Read biological mean weight-at-age directly from prepared growth products.

This helper is for population-level quantities that should use the biological growth path without requiring fleet observation-bin mapping.

Parameters

population	Shared pointer to the population object.
growth_observation	Shared pointer to the growth-derived observation capability.
year	Year index.
age	Age index.

Returns: Biological mean weight-at-age from prepared growth products.

◆ BuildAgeToLengthConversionDerivedRowOrThrow()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::BuildAgeToLengthConversionDerivedRowOrThrow	(	const std::shared_ptr< fims_popdy::AgeToLengthConversionDerived< Type > > &	age_to_length_conversion_derived,
		const std::shared_ptr< fims_popdy::Fleet< Type > > &	fleet,
		size_t	year,
		size_t	age,
		fims::Vector< Type > &	age_to_length_conversion_row
	)

inline

Build one fleet-specific growth-derived age-to-length conversion row or fail clearly.

Parameters

age_to_length_conversion_derived	Shared pointer to the growth-derived age-to-length conversion.
fleet	Shared pointer to the fleet object.
year	Year index.
age	Age index.
age_to_length_conversion_row	Output normalized age-to-length probabilities.

◆ CalculateBiomass()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateBiomass	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculates biomass for a population.

Adds the biomass at age to the total biomass for a given year \(y\) by multiplying numbers at age \(a\) by weight at age \(w_a\):

\[ B_y \mathrel{+}= N_{a,y} \times w_a \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateCatch()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateCatch	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	year,
		size_t	age
	)

inline

Calculates total catch (catch) by fleet and population for a given year by aggregating age-specific catch over ages.

This function updates fleet-specific and total expected catch for a given year and age by accumulating age-specific catch from each fleet:

\[ CW_{f,y} \mathrel{+}= CW_{f,a,y}, \quad C_{f,y} \mathrel{+}= C_{f,a,y} \]

Parameters

population Shared pointer to the population object.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateCatchNumbersAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateCatchNumbersAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculates numbers of fish for the catch for a given fleet from a population, year and age.

This function uses the Baranov Catch Equation to calculate expected catch in numbers at age for each fleet. With F multiplier \(f_y\):

\[ C_{f,a,y} = \frac{F_{f,y} \times f_y \times S_f(a)}{Z_{a,y}} \times N_{a,y} \times \left( 1 - \exp(-Z_{a,y}) \right) \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateCatchWeightAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateCatchWeightAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	year,
		size_t	age
	)

inline

Calculates weight at age of the catch for a given fleet from a population.

This function computes the expected catch at age in weight by multiplying the expected catch numbers at age by the corresponding weight at age:

\[ CW_{f,a,y} = C_{f,a,y} \times w_a \]

Weight at age comes from the historical direct growth evaluation path unless the population growth object exposes the growth-derived observation interface, in which case the biological population mean weight-at-age path is used.

Parameters

population Shared pointer to the population object.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateIndex()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateIndex	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculates the index for a fleet from a population.

This function updates the population indices for each fleet by adding the age- and year-specific index weights and numbers to the corresponding annual totals. The updated index weight and index numbers for a given fleet and year are calculated as:

\[ IW_{f,y} \mathrel{+}= IWAA_{a,y}, \quad IN_{f,y} \mathrel{+}= INAA_{a,y} \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateIndexNumbersAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateIndexNumbersAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculates the numbers for the index for a fleet from a population.

This function calculates the expected index in numbers at age for each fleet, using catchability, selectivity, and population numbers at age:

\[ IN_{f,a,y} \mathrel{+}= q_{f,y} \times S_f(a) \times N_{a,y} \]

When timing is accounted for within FIMS the equation will include the fraction of the year when the survey was conducted \(t_y\):

\[ IN_{f,a,y} \mathrel{+}= S_{f,y}(a) \times N_{a,y} \times e^{(-t_{y}Z_{a,y})}\]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateIndexWeightAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateIndexWeightAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	year,
		size_t	age
	)

inline

Calculates biomass of fish for the index for a given fleet from a population.

This function computes the expected index weight at age by multiplying the expected index numbers at age by the corresponding weight at age:

\[ IWAA_{f,a,y} = IN_{f,a,y} \times w_a \]

Weight at age comes from the historical direct growth evaluation path unless the population growth object exposes the growth-derived observation interface, in which case the biological population mean weight-at-age path is used.

Parameters

population Shared pointer to the population object.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateInitialNumbersAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateInitialNumbersAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	age
	)

inline

Calculates initial numbers at age for index and age.

The formula used is:

\[ N_{a,0} = \exp(\log N_{a,0}) \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

age	Age index.

◆ CalculateMaturityAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateMaturityAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	age
	)

inline

Calculates maturity at age, in proportion, for a population.

This function evaluates the maturity ogive at the specified age to estimate the proportion of individuals that are mature:

\[ p_{mature,a} = \text{maturity}(a) \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

age	Age index.

◆ CalculateMortality()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateMortality	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculates total mortality for a population.

This function calculates total mortality \(Z\) for a specific age and year, combining natural mortality \(M\) and fishing mortality \(F\) from all fleets.

The fishing mortality \(F_{f,a,y}\) for each fleet \(f\) is computed using age-specific selectivity \(S_f(a)\), fleet-specific annual fishing mortality \(F_{f,y}\), and year-specific F multiplier \(f_y\):

\[ F_{f,a,y} = F_{f,y} \times f_y \times S_f(a) \]

Total fishing mortality at age \(a\) and year \(y\) is the sum over fleets:

\[ F_{a,y} = \sum_{f=1}^{N_{fleets}} F_{f,a,y} \]

Total mortality \(Z_{a,y}\) is the sum of natural and fishing mortality:

\[ Z_{a,y} = M_{a,y} + F_{a,y} \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateNumbersAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateNumbersAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	i_agem1_yearm1,
		size_t	age
	)

inline

Calculates numbers at age for a population.

This function calculates numbers at age by applying total mortality \(Z\) to individuals from the previous time step. It also handles the accumulation of a plus group.

Standard update:

\[ N_{a,y} = N_{a-1,y-1} \exp(-Z_{a-1,y-1}) \]

Plus group update (if \(a = A\)):

\[ N_{A,y} = N_{A-1,y-1} \exp(-Z_{A-1,y-1}) + N_{A,y-1} \exp(-Z_{A,y-1}) \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

i_agem1_yearm1 Dimension folded index for age-1 and year-1.

Parameters

age	Age index.

◆ CalculateRecruitment()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateRecruitment	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	i_dev
	)

inline

Calculates expected recruitment for a population.

Calculates expected recruitment as a function of spawning biomass and equilibrium spawning biomass per recruit \(\phi_0\).

The expected recruitment \(R_y\) in year \(y\) is given by:

\[ R_y = \begin{cases} f(SB_{y-1}, \phi_0), & \text{if } i_{dev} = n_{years} \\ \exp(g(y-1)), & \text{otherwise} \end{cases} \]

Where \(f()\) evaluates mean recruitment based on spawning biomass and \(\phi_0\), and \(g(y-1)\) evaluates recruitment deviations.

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

i_dev Index to log_recruit_dev of vector length n_years-1.

◆ CalculateSBPR0()

template<typename Type >

Type fims_popdy::CatchAtAge< Type >::CalculateSBPR0 ( std::shared_ptr< fims_popdy::Population< Type > > & population )

inline

Calculates equilibrium spawning biomass per recruit.

This function calculates the spawning biomass per recruit \(\phi_0\) at equilibrium, assuming an unfished stock. The biomass is calculated as the sum of the biomass contributions from each age \(a\):

\[ \phi_0 = \sum_{a=0}^{A} N_a \times p_{female,a} \times p_{mature,a} \times w_a \]

The numbers at age \(N_a\) are calculated recursively with natural mortality:

\[ N_a = N_{a-1} \times \exp(-M_a) \quad \text{for } a = 1, \ldots, A-1 \]

Plus group update:

\[ N_A = \frac{N_{A-1} \times \exp(-M_{A-1})}{1 - \exp(-M_A)} \]

Parameters

population Shared pointer to the population object.

Returns: Type

◆ CalculateSpawningBiomass()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateSpawningBiomass	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculates spawning biomass for a population.

This function computes yearly \(y\) spawning biomass \(SB_y\) by summing the contributions from each age \(a\), accounting for proportion female, proportion mature, and weight at age \(w_a\):

\[ SB_y \mathrel{+}= N_{a,y} \times w_a \times p_{female,a} \times p_{mature,a} \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateSpawningBiomassRatio()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateSpawningBiomassRatio	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	year
	)

inline

Calculate the spawning biomass ratio for a population and year.

This method computes the ratio of spawning biomass in a given year to the spawning biomass at year zero (typically unfished), for the specified population:

\[ \text{ratio}_y = \frac{SB_y}{SB^U_0} \]

The result is stored in the population's spawning_biomass_ratio vector.

Parameters

population Shared pointer to the population object.

Parameters

year	Year index.

◆ CalculateUnfishedBiomass()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateUnfishedBiomass	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculates the unfished biomass for a population.

Updates unfished biomass \(B^U_y\) by adding the biomass of age \(a\) in year \(y\):

\[ B^U_y \mathrel{+}= N^U_{a,y} \times w_a \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ CalculateUnfishedNumbersAA()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateUnfishedNumbersAA	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	i_agem1_yearm1,
		size_t	age
	)

inline

Calculates unfished numbers at age at year and age specific indices.

This function computes unfished numbers at age by applying survival through time using only natural mortality, without any fishing pressure. It also accounts for accumulation of the plus group.

Standard update:

\[ N^U_{a,y} = N^U_{a-1,y-1} \exp(-M_{a-1,y-1}) \]

Plus group update (if \(a = A\)):

\[ N^U_{A,y} = N^U_{A-1,y-1} \exp(-M_{A-1,y-1}) + N^U_{A,y-1} \exp(-M_{A,y-1}) \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

i_agem1_yearm1 Dimension folded index for age-1 and year-1.

Parameters

age	Age index.

◆ CalculateUnfishedSpawningBiomass()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::CalculateUnfishedSpawningBiomass	(	std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	i_age_year,
		size_t	year,
		size_t	age
	)

inline

Calculated unfished spawning biomass for a population.

Updates unfished spawning biomass \(SB^U_y\) by adding the biomass of age \(a\) in year \(y\):

\[ SB^U_y \mathrel{+}= N^U_{a,y} \times w_a \times p_{female,a} \times p_{mature,a} \]

Parameters

population Shared pointer to the population object.

Parameters

i_age_year Dimension folded index for age and year.

Parameters

year	Year index.

Parameters

age	Age index.

◆ EnsureAllFleetAgeToLengthConversion()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::EnsureAllFleetAgeToLengthConversion ( )

inline

Ensure all fleets linked to this model have a usable age-to-length conversion.

Reuses each fleet's current age-to-length conversion when it matches the current population growth path and can prepare for the current model state. Otherwise rebuilds the fleet age-to-length conversion from the current population and fleet state before evaluation or reporting uses it.

◆ Evaluate()

template<typename Type >

virtual void fims_popdy::CatchAtAge< Type >::Evaluate ( )

inlinevirtual

Evaluate the model.

Reimplemented from fims_popdy::FisheryModelBase< Type >.

◆ evaluate_age_comp()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::evaluate_age_comp ( )

inline

Evaluate the proportion of catch numbers at age.

◆ evaluate_catch()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::evaluate_catch ( )

inline

Evaluate the natural log of the expected catch.

◆ evaluate_index()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::evaluate_index ( )

inline

Evaluate the natural log of the expected index.

◆ evaluate_length_comp()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::evaluate_length_comp ( )

inline

Evaluate the proportion of catch numbers at length.

◆ GetPopulations()

template<typename Type >

std::vector< std::shared_ptr< fims_popdy::Population< Type > > > & fims_popdy::CatchAtAge< Type >::GetPopulations ( )

inline

This function is used to get the populations of the model. It returns a vector of shared pointers to the populations.

Returns: std::vector<std::shared_ptr<fims_popdy::Population<Type>>>&

◆ GrowthDerivedFleetMeanWeightAA()

template<typename Type >

Type fims_popdy::CatchAtAge< Type >::GrowthDerivedFleetMeanWeightAA	(	const std::shared_ptr< fims_popdy::Fleet< Type > > &	fleet,
		size_t	year,
		size_t	age
	)

inline

Compute fleet-specific expected weight-at-age from the growth-derived age-to-length conversion path.

This helper uses the fleet-specific growth-derived path only. It first prefers the per-evaluation fleet WAA cache and then falls back to the shared age-to-length conversion-row calculation helper. If neither growth-derived path is available, the function fails rather than silently switching to a different weight-at-age meaning.

Parameters

fleet	Shared pointer to the fleet object.
year	Year index.
age	Age index.

Returns: Expected fleet-specific weight-at-age from the growth-derived path.

◆ Initialize()

template<typename Type >

virtual void fims_popdy::CatchAtAge< Type >::Initialize ( )

inlinevirtual

This function is called once at the beginning of the model run. It initializes the derived quantities for the populations and fleets.

Reimplemented from fims_popdy::FisheryModelBase< Type >.

◆ MeanWeightFromAgeToLengthConversionDerived()

template<typename Type >

Type fims_popdy::CatchAtAge< Type >::MeanWeightFromAgeToLengthConversionDerived	(	const std::shared_ptr< fims_popdy::AgeToLengthConversionDerived< Type > > &	age_to_length_conversion_derived,
		const std::shared_ptr< fims_popdy::Fleet< Type > > &	fleet,
		size_t	year,
		size_t	age
	)

inline

Compute fleet-specific mean weight-at-age from one growth-derived age-to-length conversion row.

This helper builds the fleet-specific age-to-length conversion row for the requested year and age, then converts that mapped age-to-length row into expected weight using weight-at-length evaluated at the fleet observation-bin centers.

Parameters

age_to_length_conversion_derived	Shared pointer to the growth-derived age-to-length conversion.
fleet	Shared pointer to the fleet object.
year	Year index.
age	Age index.

Returns: Expected fleet-specific mean weight-at-age.

◆ MeanWeightFromAgeToLengthConversionRow()

template<typename Type >

Type fims_popdy::CatchAtAge< Type >::MeanWeightFromAgeToLengthConversionRow	(	const std::shared_ptr< fims_popdy::GrowthDerivedObservationBase< Type > > &	growth_observation,
		const std::shared_ptr< fims_popdy::Fleet< Type > > &	fleet,
		const fims::Vector< Type > &	age_to_length_conversion_row
	)

inline

Compute expected fleet-specific weight-at-age from a normalized age-to-length conversion row and fleet observation-bin centers.

This is the bin-based downstream WAA step used with the growth-derived age-to-length conversion path. Instead of using only growth->evaluate(age), it computes expected weight as the weighted average of weight-at-length over the same fleet observation bins used in the mapped age-to-length conversion row.

Parameters

growth_observation	Shared pointer to the linked growth-derived observation capability.
fleet	Shared pointer to the fleet object.
age_to_length_conversion_row	Normalized age-to-length probabilities for one year and age.

Returns: Expected weight-at-age on the natural scale.

◆ PopulationMeanWeightAA()

template<typename Type >

Type fims_popdy::CatchAtAge< Type >::PopulationMeanWeightAA	(	const std::shared_ptr< fims_popdy::Population< Type > > &	population,
		size_t	year,
		size_t	age
	)

inline

Calculates population-level mean weight-at-age.

This function returns the biological mean weight at age for a population. If the growth object does not support the growth-derived observation interface, it uses the historical direct growth evaluation path. If the growth object does support that interface, it reads biological mean weight-at-age directly from the prepared growth products and does not require any fleet observation-bin mapping.

Parameters

population	Shared pointer to the population object.
year	Year index.
age	Age index.

Returns: Mean weight-at-age on the natural scale.

◆ Prepare()

template<typename Type >

virtual void fims_popdy::CatchAtAge< Type >::Prepare ( )

inlinevirtual

This function is used to reset the derived quantities of a population or fleet to a given value.

Reimplemented from fims_popdy::FisheryModelBase< Type >.

◆ PreparePopulationGrowthProducts()

template<typename Type >

void fims_popdy::CatchAtAge< Type >::PreparePopulationGrowthProducts ( )

inline

Prepares cached population growth products for all populations whose growth objects expose the growth-derived observation interface.

This helper makes sure growth-derived-capable populations prepare their cached growth products before catch-at-age evaluation so code that uses those prepared values can access them consistently.

◆ Report()

template<typename Type >

virtual void fims_popdy::CatchAtAge< Type >::Report ( )

inlinevirtual

This method is used to generate TMB reports from the population dynamics model.

Reimplemented from fims_popdy::FisheryModelBase< Type >.

Member Data Documentation

◆ ages

template<typename Type >

std::vector<Type> fims_popdy::CatchAtAge< Type >::ages

vector of the ages for referencing

◆ report_age_to_length_conversion_derived_tensor

template<typename Type >

bool fims_popdy::CatchAtAge< Type >::report_age_to_length_conversion_derived_tensor = false

Controls whether reporting materializes the full derived age-to-length tensor for fleets using the growth-derived age-to-length conversion path.

Default is false to avoid large report-side allocations.

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

inst/include/models/functors/catch_at_age.hpp

Public Types

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CatchAtAge() [1/2]

◆ CatchAtAge() [2/2]

Member Function Documentation

◆ AddPopulation()

◆ BiologicalMeanWeightFromPreparedGrowthProducts()

◆ BuildAgeToLengthConversionDerivedRowOrThrow()

◆ CalculateBiomass()

◆ CalculateCatch()

◆ CalculateCatchNumbersAA()

◆ CalculateCatchWeightAA()

◆ CalculateIndex()

◆ CalculateIndexNumbersAA()

◆ CalculateIndexWeightAA()

◆ CalculateInitialNumbersAA()

◆ CalculateMaturityAA()

◆ CalculateMortality()

◆ CalculateNumbersAA()

◆ CalculateRecruitment()

◆ CalculateSBPR0()

◆ CalculateSpawningBiomass()

◆ CalculateSpawningBiomassRatio()

◆ CalculateUnfishedBiomass()

◆ CalculateUnfishedNumbersAA()

◆ CalculateUnfishedSpawningBiomass()

◆ EnsureAllFleetAgeToLengthConversion()

◆ Evaluate()

◆ evaluate_age_comp()

◆ evaluate_catch()

◆ evaluate_index()

◆ evaluate_length_comp()

◆ GetPopulations()

◆ GrowthDerivedFleetMeanWeightAA()

◆ Initialize()

◆ MeanWeightFromAgeToLengthConversionDerived()

◆ MeanWeightFromAgeToLengthConversionRow()

◆ PopulationMeanWeightAA()

◆ Prepare()

◆ PreparePopulationGrowthProducts()

◆ Report()

Member Data Documentation

◆ ages

◆ report_age_to_length_conversion_derived_tensor