FleetInterface Class Reference

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.
void	get_se_values (std::string name, std::map< std::string, std::vector< double > > &se_values, fims::Vector< double > &values)
	Method to extract standard error values from the se_values working map.
virtual void	set_uncertainty (std::map< std::string, std::vector< double > > &se_values)
	Set uncertainty values for the interface object.
std::string	value_to_string (double value)
	Report the parameter 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.
ParameterVector	log_q
	The natural log of the index of abundance scaling parameter for this fleet.
ParameterVector	log_Fmort
	The vector of the natural log of fishing mortality rates for this fleet.
ParameterVector	log_landings_expected
	The vector of natural log of the expected total landings for the fleet.
ParameterVector	log_index_expected
	The vector of natural log of the expected index of abundance for the fleet.
ParameterVector	agecomp_expected
	The vector of expected landings-at-age in numbers for the fleet.
ParameterVector	lengthcomp_expected
	The vector of expected landings-at-length in numbers for the fleet.
ParameterVector	agecomp_proportion
	The vector of expected landings-at-age in numbers for the fleet.
ParameterVector	lengthcomp_proportion
	The vector of expected landings-at-length in numbers for the fleet.
ParameterVector	age_to_length_conversion
	The vector of conversions to go from age to length, i.e., the age-to-length-conversion matrix.
Rcpp::NumericVector	derived_landings_naa
	Derived landings-at-age in numbers.
Rcpp::NumericVector	derived_landings_nal
	Derived landings-at-length in numbers.
Rcpp::NumericVector	derived_landings_waa
	Derived landings-at-age in weight (mt).
Rcpp::NumericVector	derived_landings_expected
	Derived landings in observed units.
Rcpp::NumericVector	derived_landings_w
	Derived landings in weight.
Rcpp::NumericVector	derived_landings_n
	Derived landings in numbers.
Rcpp::NumericVector	derived_index_naa
	Derived landings-at-age in numbers.
Rcpp::NumericVector	derived_index_nal
	Derived landings-at-length in numbers.
Rcpp::NumericVector	derived_index_waa
	Derived landings-at-age in weight (mt).
Rcpp::NumericVector	derived_index_expected
	Derived index in observed units.
Rcpp::NumericVector	derived_index_w
	Derived index in weight.
Rcpp::NumericVector	derived_index_n
	Derived index in numbers.
Rcpp::NumericVector	derived_agecomp_proportion
	Derived age composition proportions.
Rcpp::NumericVector	derived_lengthcomp_proportion
	Derived length composition proportions.
Rcpp::NumericVector	derived_agecomp_expected
	Derived age compositions.
Rcpp::NumericVector	derived_lengthcomp_expected
	Derived length compositions.
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.

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

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