This is the class used to calculate a likelihood score by fitting the model population to age based survey index data. More...

#include <sibyageonstep.h>

Inheritance diagram for SIByAgeOnStep:

Collaboration diagram for SIByAgeOnStep:

Public Member Functions
	SIByAgeOnStep (CommentStream &infile, const IntMatrix &areas, const IntMatrix &ages, const CharPtrVector &areaindex, const CharPtrVector &ageindex, const TimeClass const TimeInfo, const char datafilename, const char *givenname, int bio)
	This is the SIByAgeOnStep constructor. More...

virtual	~SIByAgeOnStep ()
	This is the default SIByAgeOnStep destructor. More...

virtual void	Sum (const TimeClass *const TimeInfo)
	This function will sum the survey index by age data. More...

virtual void	setFleetsAndStocks (FleetPtrVector &Fleets, StockPtrVector &Stocks)
	This will select the fleets and stocks required to calculate the survey index likelihood score. More...

virtual void	Print (ofstream &outfile) const
	This function will print the SIByAgeOnStep information. More...

Public Member Functions inherited from SIOnStep
	SIOnStep (CommentStream &infile, const char datafilename, const CharPtrVector &aindex, const TimeClass const TimeInfo, const IntMatrix &areas, const CharPtrVector &charindex, const char *givenname, int bio, SIType type)
	This is the default SIOnStep constructor. More...

virtual	~SIOnStep ()
	This is the default SIOnStep destructor. More...

virtual void	Reset ()
	This function will reset the SIOnStep information. More...

virtual void	printLikelihood (ofstream &outfile, const TimeClass *const TimeInfo)
	This function will print information from each SIOnStep regression calculation. More...

virtual void	printSummary (ofstream &outfile, const double weight)
	This function will print summary information from each SIOnStep regression calculation. More...

virtual double	calcSSE ()
	This function will calculate the SSE from the regression line. More...

FitType	getType () const
	This will return the fit type for the regression line. More...

SIType	getSIType () const
	This will return the type of survey index data to be used. More...

Public Member Functions inherited from HasName
	HasName ()
	This is the default HasName constructor. More...

virtual	~HasName ()
	This is the default HasName destructor. More...

	HasName (const char *givenname)
	This is the HasName constructor for a specified name. More...

const char *	getName () const
	This will return a null terminated text string containing the name of the object. More...

Protected Attributes
StockAggregator *	aggregator
	This is the StockAggregator used to collect information about the relevant stocks for the survey index data. More...

Protected Attributes inherited from SIOnStep
IntMatrix	Areas
	This is the IntMatrix used to store information about the areas that the survey index should be calculated on. More...

IntVector	Years
	This is the IntVector used to store information about the years when the survey index should be calculated. More...

IntVector	Steps
	This is the IntVector used to store information about the steps when the survey index should be calculated. More...

IntMatrix	Ages
	This is the IntMatrix used to store information about the ages that the survey index should be calculated on. More...

LengthGroupDivision *	LgrpDiv
	This is the LengthGroupDivision used to store information about the lengths that the survey index should be calculated on. More...

DoubleVector	likelihoodValues
	This is the DoubleVector used to store the calculated likelihood information. More...

ActionAtTimes	AAT
	This ActionAtTimes stores information about when the survey index should be calculated. More...

DoubleMatrixPtrVector	obsIndex
	This is the DoubleMatrixPtrVector used to store the survey indices specified in the input file. More...

DoubleMatrixPtrVector	modelIndex
	This is the DoubleMatrixPtrVector used to store the survey indices calculated in the model. More...

DoubleMatrixPtrVector	weightIndex
	This is the DoubleMatrixPtrVector used to store the weights specified for the regression line. More...

const AgeBandMatrixPtrVector *	alptr
	This is the AgeBandMatrixPtrVector used to temporarily store the information returned from the aggregatation function. More...

SIType	sitype
	This denotes what type of survey index data is to be used. More...

int	timeindex
	This is the index of the timesteps for the survey index data. More...

int	biomass
	This is the flag to denote whether the index should be based on the biomass or not. More...

int	useweight
	This is the flag to denote whether weighted regression line should be used when calculating the fit to the data or not. More...

Detailed Description

This is the class used to calculate a likelihood score by fitting the model population to age based survey index data.

Constructor & Destructor Documentation

◆ SIByAgeOnStep()

SIByAgeOnStep::SIByAgeOnStep	(	CommentStream &	infile,
		const IntMatrix &	areas,
		const IntMatrix &	ages,
		const CharPtrVector &	areaindex,
		const CharPtrVector &	ageindex,
		const TimeClass *const	TimeInfo,
		const char *	datafilename,
		const char *	givenname,
		int	bio
	)

This is the SIByAgeOnStep constructor.

Parameters

infile	is the CommentStream to read the survey index data from
areas	is the IntMatrix of areas that the survey index can take place on
ages	is the IntMatrix of ages from the survey index data
areaindex	is the CharPtrVector of area identifier text strings
ageindex	is the CharPtrVector of age identifier text strings
TimeInfo	is the TimeClass for the current model
datafilename	is the name of the file containing the survey index data
givenname	is the name of the SIByAgeOnStep likelihood component
bio	is the flag to denote whether the index should be based on the biomass or not

◆ ~SIByAgeOnStep()

SIByAgeOnStep::~SIByAgeOnStep ( )

virtual

This is the default SIByAgeOnStep destructor.

Member Function Documentation

◆ Print()

virtual void SIByAgeOnStep::Print ( ofstream & outfile ) const

inlinevirtual

This function will print the SIByAgeOnStep information.

Parameters

outfile is the ofstream that all the model information gets sent to

Implements SIOnStep.

◆ setFleetsAndStocks()

void SIByAgeOnStep::setFleetsAndStocks	(	FleetPtrVector &	Fleets,
		StockPtrVector &	Stocks
	)

virtual

This will select the fleets and stocks required to calculate the survey index likelihood score.

Parameters

Fleets	is the FleetPtrVector of all the available fleets
Stocks	is the StockPtrVector of all the available stocks

Implements SIOnStep.

◆ Sum()

void SIByAgeOnStep::Sum ( const TimeClass *const TimeInfo )

virtual

This function will sum the survey index by age data.

Parameters

TimeInfo is the TimeClass for the current model

Implements SIOnStep.

Member Data Documentation

◆ aggregator

StockAggregator* SIByAgeOnStep::aggregator

protected

This is the StockAggregator used to collect information about the relevant stocks for the survey index data.

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

src/include/sibyageonstep.h
src/sibyageonstep.cc

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SIByAgeOnStep()

◆ ~SIByAgeOnStep()

Member Function Documentation

◆ Print()

◆ setFleetsAndStocks()

◆ Sum()

Member Data Documentation

◆ aggregator