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	SetRequiresAgeLengthMapping (bool requires_age_length_mapping)
	Set whether this fleet requires age-to-length mapping.
void	SetObservedIndexDataID (int observed_index_data_id)
	Set the unique ID for the observed index data object.
void	SetObservedCatchDataID (int observed_catch_data_id)
	Set the unique ID for the observed catch 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.
bool	GetRequiresAgeLengthMapping ()
	Return whether this fleet requires age-to-length mapping.
int	GetObservedIndexDataID ()
	Get the unique id for the observed index data object.
int	GetObservedCatchDataID ()
	Get the unique id for the observed catch 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.
RealVector	lengths
	Fleet-specific observation-bin lower edges.
SharedInt	n_years = 0
	The number of years in the fleet data.
SharedString	observed_catch_units = fims::to_string("weight")
	What units are the observed catch for this fleet measured in. Options are "weight" or "number", 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 "number", 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.
RealVector	weight_at_age
	Weight at age for this fleet's catch and index weight, ordered by year and then age, with n_years x n_ages values. It is empty when the fleet uses the population weight at age. It is data, so it is never registered as a parameter.
RealVector	ageing_error
	Ageing error matrices, 1 for all years or 1 per year, with true age as rows and observed age varying fastest. It is empty when the fleet has no ageing error. It is data, so it is never registered as a parameter.
VariableVector	catch_numbers_at_age
	Annual catch at age in numbers for a specific fleet.
VariableVector	catch_weight_at_age
	Annual catch at age in weight for a specific fleet.
VariableVector	catch_numbers_at_length
	Annual catch at length in numbers for a specific fleet.
VariableVector	catch_weight
	Total catch in weight for a specific fleet.
VariableVector	catch_numbers
	Total catch in numbers for a specific fleet.
VariableVector	catch_expected
	Total expected catch for a specific fleet, where the units of the measurement depend on the specified units for that fleet.
VariableVector	log_catch_expected
	Log total expected catch for a specific fleet, where the units of the measurement depend on the specified units for that fleet.
VariableVector	agecomp_proportion
	Proportion of total catch by age used to specify the age composition.
VariableVector	lengthcomp_proportion
	Proportion of total catch 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 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.

◆ GetRequiresAgeLengthMapping()

bool FleetInterface::GetRequiresAgeLengthMapping ( )

inline

Return whether this fleet requires age-to-length mapping.

A true value indicates that the model will use an active age-to-length conversion path and the fleet's resolved length-bin observation grid. See the member documentation for details.

Returns: True when age-to-length mapping is required; otherwise false.

See also: FleetInterface::interface_requires_age_length_mapping

◆ 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.

◆ SetObservedCatchDataID()

void FleetInterface::SetObservedCatchDataID ( int observed_catch_data_id )

inline

Set the unique ID for the observed catch data object.

Parameters

observed_catch_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.

◆ 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.

◆ SetRequiresAgeLengthMapping()

void FleetInterface::SetRequiresAgeLengthMapping ( bool requires_age_length_mapping )

inline

Set whether this fleet requires age-to-length mapping.

Set this to true when an active modeled path converts quantities from age to length. See the member documentation for the effects and required length-bin inputs.

Parameters

requires_age_length_mapping True when age-to-length mapping is required; false to skip age-to-length conversion and length-bin processing.

See also: FleetInterface::interface_requires_age_length_mapping

◆ 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()

◆ GetRequiresAgeLengthMapping()

◆ GetSelectivityID()

◆ SetName()

◆ SetObservedAgeCompDataID()

◆ SetObservedCatchDataID()

◆ SetObservedIndexDataID()

◆ SetObservedLengthCompDataID()

◆ SetRequiresAgeLengthMapping()

◆ SetSelectivityID()