The Rcpp interface for Fleet to instantiate from R: fleet <- methods::new(Fleet) More...

#include <rcpp_fleet.hpp>

Inheritance diagram for FleetInterface:

Public Member Functions
	FleetInterface ()
	The constructor.

	FleetInterface (const FleetInterface &other)
	Construct a new Fleet Interface object.

virtual	~FleetInterface ()
	The destructor.

virtual uint32_t	get_id ()
	Gets the ID of the interface base object.

void	SetName (const std::string &name)
	Sets the name of the fleet.

std::string	GetName () const
	Gets the name of the fleet.

void	SetObservedAgeCompDataID (int observed_agecomp_data_id)
	Set the unique ID for the observed age-composition data object.

void	SetObservedLengthCompDataID (int observed_lengthcomp_data_id)
	Set the unique ID for the observed length-composition data object.

void	SetObservedIndexDataID (int observed_index_data_id)
	Set the unique ID for the observed index data object.

void	SetObservedLandingsDataID (int observed_landings_data_id)
	Set the unique ID for the observed landings data object.

void	SetSelectivityID (int selectivity_id)
	Set the unique ID for the selectivity object.

uint32_t	GetSelectivityID ()
	Get the unique ID for the selectivity object.

int	GetObservedAgeCompDataID ()
	Get the unique ID for the observed age-composition data object.

int	GetObservedLengthCompDataID ()
	Get the unique ID for the observed length-composition data object.

int	GetObservedIndexDataID ()
	Get the unique id for the observed index data object.

int	GetObservedLandingsDataID ()
	Get the unique id for the observed landings data object.

virtual void	finalize ()
	Extracts the derived quantities from `Information` to the Rcpp object.

Public Member Functions inherited from FleetInterfaceBase
	FleetInterfaceBase ()
	The constructor.

	FleetInterfaceBase (const FleetInterfaceBase &other)
	Construct a new Fleet Interface Base object.

virtual	~FleetInterfaceBase ()
	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.

virtual std::string	to_json ()
	Convert the data to json representation for the output.

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
SharedString	name = fims::to_string("NA")
	The name of the fleet.

SharedInt	n_ages = 0
	The number of age bins in the fleet data.

SharedInt	n_lengths = 0
	The number of length bins in the fleet data.

SharedInt	n_years = 0
	The number of years in the fleet data.

SharedString	observed_landings_units = fims::to_string("weight")
	What units are the observed landings for this fleet measured in. Options are weight or numbers, default is weight.

SharedString	observed_index_units = fims::to_string("weight")
	What units is the observed index of abundance for this fleet measured in. Options are weight or numbers, default is weight.

VariableVector	log_q
	The natural log of the index of abundance scaling parameter for this fleet.

VariableVector	log_Fmort
	The vector of the natural log of fishing mortality rates for this fleet.

VariableVector	age_to_length_conversion
	The vector of conversions to go from age to length, i.e., the age-to-length-conversion matrix.

VariableVector	landings_numbers_at_age
	Annual landings at age in numbers for a specific fleet.

VariableVector	landings_weight_at_age
	Annual landings at age in weight for a specific fleet.

VariableVector	landings_numbers_at_length
	Annual landings at length in numbers for a specific fleet.

VariableVector	landings_weight
	Total landings in weight for a specific fleet.

VariableVector	landings_numbers
	Total landings in numbers for a specific fleet.

VariableVector	landings_expected
	Total expected landings for a specific fleet, where the units of the measurement depend on the specified units for that fleet.

VariableVector	log_landings_expected
	Log total expected landings for a specific fleet, where the units of the measurement depend on the specified units for that fleet.

VariableVector	agecomp_proportion
	Proportion of total landings by age used to specify the age composition.

VariableVector	lengthcomp_proportion
	Proportion of total landings by length used to specify the length composition.

VariableVector	index_numbers_at_age
	Numbers at age for a fleet index such as survey or CPUE.

VariableVector	index_weight_at_age
	Weight at age for a fleet index such as survey or CPUE.

VariableVector	index_numbers_at_length
	Numbers at length for a fleet index such as survey or CPUE.

VariableVector	index_weight
	Total weight for a fleet index such as survey or CPUE.

VariableVector	index_numbers
	Total numbers for a fleet index such as survey or CPUE.

VariableVector	index_expected
	Expected value for a fleet index, where the units of the measurement depend on the specified units for that fleet.

VariableVector	log_index_expected
	Log expected value for a fleet index, where the units of the measurement depend on the specified units for that fleet.

VariableVector	agecomp_expected
	Expected age-composition proportions for the fleet.

VariableVector	lengthcomp_expected
	Expected length-composition proportions for the fleet.

Public Attributes inherited from FleetInterfaceBase
uint32_t	id
	The local id of the FleetInterfaceBase 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 FleetInterfaceBase
static uint32_t	id_g = 1
	The static id of the FleetInterfaceBase object.

static std::map< uint32_t, std::shared_ptr< FleetInterfaceBase > >	live_objects
	The map associating the IDs of FleetInterfaceBase 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.

Detailed Description

The Rcpp interface for Fleet to instantiate from R: fleet <- methods::new(Fleet)

Constructor & Destructor Documentation

◆ FleetInterface()

FleetInterface::FleetInterface ( const FleetInterface & other )

inline

Construct a new Fleet Interface object.

Parameters

other

Member Function Documentation

◆ finalize()

virtual void FleetInterface::finalize ( )

inlinevirtual

Extracts the derived quantities from Information to the Rcpp object.

Reimplemented from FIMSRcppInterfaceBase.

◆ get_id()

virtual uint32_t FleetInterface::get_id ( )

inlinevirtual

Gets the ID of the interface base object.

Returns: The ID.

Implements FleetInterfaceBase.

◆ GetName()

std::string FleetInterface::GetName ( ) const

inline

Gets the name of the fleet.

Returns: The name.

◆ GetSelectivityID()

uint32_t FleetInterface::GetSelectivityID ( )

inline

Get the unique ID for the selectivity object.

Returns: uint32_t

◆ SetName()

void FleetInterface::SetName ( const std::string & name )

inline

Sets the name of the fleet.

Parameters

name	The name to set.

◆ SetObservedAgeCompDataID()

void FleetInterface::SetObservedAgeCompDataID ( int observed_agecomp_data_id )

inline

Set the unique ID for the observed age-composition data object.

Parameters

observed_agecomp_data_id Unique ID for the observed data object.

◆ SetObservedIndexDataID()

void FleetInterface::SetObservedIndexDataID ( int observed_index_data_id )

inline

Set the unique ID for the observed index data object.

Parameters

observed_index_data_id Unique ID for the observed data object.

◆ SetObservedLandingsDataID()

void FleetInterface::SetObservedLandingsDataID ( int observed_landings_data_id )

inline

Set the unique ID for the observed landings data object.

Parameters

observed_landings_data_id Unique ID for the observed data object.

◆ SetObservedLengthCompDataID()

void FleetInterface::SetObservedLengthCompDataID ( int observed_lengthcomp_data_id )

inline

Set the unique ID for the observed length-composition data object.

Parameters

observed_lengthcomp_data_id Unique ID for the observed data object.

◆ SetSelectivityID()

void FleetInterface::SetSelectivityID ( int selectivity_id )

inline

Set the unique ID for the selectivity object.

Parameters

selectivity_id Unique ID for the observed object.

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

inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FleetInterface()

Member Function Documentation

◆ finalize()

◆ get_id()

◆ GetName()

◆ GetSelectivityID()

◆ SetName()

◆ SetObservedAgeCompDataID()

◆ SetObservedIndexDataID()

◆ SetObservedLandingsDataID()

◆ SetObservedLengthCompDataID()

◆ SetSelectivityID()