fims_popdy::Fleet< Type > Struct Template Reference

Base class for all fleets. More...

#include <fleet.hpp>

Inheritance diagram for fims_popdy::Fleet< Type >:

Public Member Functions
	Fleet ()
	Constructor.
virtual	~Fleet ()
	Destructor.
void	Prepare ()
	Prepare to run the fleet module. Called at each model iteration, and used to exponentiate the natural log of q and Fmort parameters prior to evaluation.
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
size_t	n_years
size_t	n_ages
size_t	n_lengths
fims::Vector< double >	lengths
fims::Vector< double >	length_bin_edges
int	fleet_selectivity_id_m = -999
std::shared_ptr< SelectivityBase< Type > >	selectivity
std::shared_ptr< AgeToLengthConversionBase< Type > >	age_to_length_conversion_model
bool	requires_age_length_mapping
int	fleet_observed_catch_data_id_m = -999
std::shared_ptr< fims_data_object::DataObject< Type > >	observed_catch_data
std::string	observed_catch_units
int	fleet_observed_index_data_id_m = -999
std::shared_ptr< fims_data_object::DataObject< Type > >	observed_index_data
std::string	observed_index_units
int	fleet_observed_agecomp_data_id_m = -999
std::shared_ptr< fims_data_object::DataObject< Type > >	observed_agecomp_data
int	fleet_observed_lengthcomp_data_id_m = -999
std::shared_ptr< fims_data_object::DataObject< Type > >	observed_lengthcomp_data
fims::Vector< Type >	log_Fmort
fims::Vector< Type >	log_q
fims::Vector< Type >	Fmort
fims::Vector< Type >	q
fims::Vector< Type >	age_to_length_conversion
fims::Vector< Type >	ageing_error
	Ageing error matrices, 1 for all years or 1 per year, with true age as rows and observed age varying fastest. When it is empty, the fleet has no ageing error.
fims::Vector< Type >	weight_at_age
	Weight at age for this fleet's catch and index weight, ordered by year and then age. When it is empty, the population weight at age is used, e.g., when the fleet has no weight-at-age data of its own.
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<class Type>
struct fims_popdy::Fleet< Type >

Base class for all fleets.

Template Parameters

Type	The type of the fleet object.

Member Data Documentation

age_to_length_conversion

template<class Type>

fims::Vector<Type> fims_popdy::Fleet< Type >::age_to_length_conversion

derived quantity age to length conversion matrix

age_to_length_conversion_model

template<class Type>

std::shared_ptr<AgeToLengthConversionBase<Type> > fims_popdy::Fleet< Type >::age_to_length_conversion_model

fleet-specific age-to-length conversion model

fleet_observed_agecomp_data_id_m

template<class Type>

int fims_popdy::Fleet< Type >::fleet_observed_agecomp_data_id_m = -999

id of age comp data

fleet_observed_catch_data_id_m

template<class Type>

int fims_popdy::Fleet< Type >::fleet_observed_catch_data_id_m = -999

id of catch data

fleet_observed_index_data_id_m

template<class Type>

int fims_popdy::Fleet< Type >::fleet_observed_index_data_id_m = -999

id of index data

fleet_observed_lengthcomp_data_id_m

template<class Type>

int fims_popdy::Fleet< Type >::fleet_observed_lengthcomp_data_id_m = -999

id of length comp data

fleet_selectivity_id_m

template<class Type>

int fims_popdy::Fleet< Type >::fleet_selectivity_id_m = -999

id of selectivity component

Fmort

template<class Type>

fims::Vector<Type> fims_popdy::Fleet< Type >::Fmort

transformed parameter: Fishing mortality

length_bin_edges

template<class Type>

fims::Vector<double> fims_popdy::Fleet< Type >::length_bin_edges

Bin lower edges plus the last bin's upper edge.

lengths

template<class Type>

fims::Vector<double> fims_popdy::Fleet< Type >::lengths

Fleet observation-bin lower edges for this fleet.

log_Fmort

template<class Type>

fims::Vector<Type> fims_popdy::Fleet< Type >::log_Fmort

estimated parameter: log Fishing mortality

log_q

template<class Type>

fims::Vector<Type> fims_popdy::Fleet< Type >::log_q

estimated parameter: catchability of the fleet

n_ages

template<class Type>

size_t fims_popdy::Fleet< Type >::n_ages

the number of ages in the model

n_lengths

template<class Type>

size_t fims_popdy::Fleet< Type >::n_lengths

the number of fleet observation bins for this fleet

n_years

template<class Type>

size_t fims_popdy::Fleet< Type >::n_years

the number of years in the model

observed_agecomp_data

template<class Type>

std::shared_ptr<fims_data_object::DataObject<Type> > fims_popdy::Fleet< Type >::observed_agecomp_data

observed agecomp data

observed_catch_data

template<class Type>

std::shared_ptr<fims_data_object::DataObject<Type> > fims_popdy::Fleet< Type >::observed_catch_data

observed catch data

observed_catch_units

template<class Type>

std::string fims_popdy::Fleet< Type >::observed_catch_units

"weight" or "number"

observed_index_data

template<class Type>

std::shared_ptr<fims_data_object::DataObject<Type> > fims_popdy::Fleet< Type >::observed_index_data

observed index data

observed_index_units

template<class Type>

std::string fims_popdy::Fleet< Type >::observed_index_units

"weight" or "number"

observed_lengthcomp_data

template<class Type>

std::shared_ptr<fims_data_object::DataObject<Type> > fims_popdy::Fleet< Type >::observed_lengthcomp_data

observed lengthcomp data

q

template<class Type>

fims::Vector<Type> fims_popdy::Fleet< Type >::q

transformed parameter: the catchability of the fleet

requires_age_length_mapping

template<class Type>

bool fims_popdy::Fleet< Type >::requires_age_length_mapping

Initial value:

=
      false

whether an active modeled path requires age-to-length conversion-based mapping

selectivity

template<class Type>

std::shared_ptr<SelectivityBase<Type> > fims_popdy::Fleet< Type >::selectivity

selectivity component

---

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

• inst/include/population_dynamics/fleet/fleet.hpp