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
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
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<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

id_g

template<class Type >

uint32_t fims_popdy::Fleet< Type >::id_g = 0

static

reference id for fleet object

length_bin_edges

template<class Type >

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

Resolved observation-bin edges for this fleet.

lengths

template<class Type >

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

Fleet observation-bin centers 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

is this fleet catch in weight

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

is this fleet index in weight

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

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

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