This is the base class used to calculate a likelihood score by fitting a regression line to the model population and survey index data. More...

#include <sionstep.h>

Inheritance diagram for SIOnStep:

Collaboration diagram for SIOnStep:

Public Member Functions
	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	Sum (const TimeClass *const TimeInfo)=0
	This function will sum the survey index data. More...

virtual void	setFleetsAndStocks (FleetPtrVector &Fleets, StockPtrVector &Stocks)=0
	This will select the fleets and stocks required to calculate the regression line. More...

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

virtual void	Print (ofstream &outfile) const =0
	This function will print 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
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 base class used to calculate a likelihood score by fitting a regression line to the model population and survey index data.

Note: This will always be overridden by the derived classes that actually calculate the survey indices and the likelihood score from the regression line

Constructor & Destructor Documentation

◆ SIOnStep()

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.

Parameters

infile	is the CommentStream to read the SIOnStep data from
datafilename	is the name of the file to read the index data from
aindex	is the CharPtrVector of the names of the areas for the survey indices
TimeInfo	is the TimeClass for the current model
areas	is the IntMatrix of the areas that the survey indices are calculated on
charindex	is the CharPtrVector of the names of the column index for the survey indices
givenname	is the name for the SIOnStep component
bio	is the flag to denote whether the index should be based on the biomass or not
type	is the SIType of the SIOnStep

◆ ~SIOnStep()

SIOnStep::~SIOnStep ( )

virtual

This is the default SIOnStep destructor.

Member Function Documentation

◆ calcSSE()

double SIOnStep::calcSSE ( )

virtual

This function will calculate the SSE from the regression line.

Returns: SSE from the regession line

◆ getSIType()

SIType SIOnStep::getSIType ( ) const

inline

This will return the type of survey index data to be used.

Returns: sitype

◆ getType()

FitType SIOnStep::getType ( ) const

inline

This will return the fit type for the regression line.

Returns: fittype

◆ Print()

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

pure virtual

This function will print the SIOnStep information.

Parameters

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

Implemented in SIByLengthOnStep, SIByFleetOnStep, SIByEffortOnStep, SIByAgeOnStep, and SIByAcousticOnStep.

◆ printLikelihood()

void SIOnStep::printLikelihood	(	ofstream &	outfile,
		const TimeClass *const	TimeInfo
	)

virtual

This function will print information from each SIOnStep regression calculation.

Parameters

outfile	is the ofstream that all the model likelihood information gets sent to
TimeInfo	is the TimeClass for the current model

◆ printSummary()

void SIOnStep::printSummary	(	ofstream &	outfile,
		const double	weight
	)

virtual

This function will print summary information from each SIOnStep regression calculation.

Parameters

outfile	is the ofstream that all the model likelihood information gets sent to
weight	is the weight of the likelihood component

◆ Reset()

void SIOnStep::Reset ( )

virtual

This function will reset the SIOnStep information.

◆ setFleetsAndStocks()

virtual void SIOnStep::setFleetsAndStocks	(	FleetPtrVector &	Fleets,
		StockPtrVector &	Stocks
	)

pure virtual

This will select the fleets and stocks required to calculate the regression line.

Parameters

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

Implemented in SIByLengthOnStep, SIByFleetOnStep, SIByEffortOnStep, SIByAgeOnStep, and SIByAcousticOnStep.

◆ Sum()

virtual void SIOnStep::Sum ( const TimeClass *const TimeInfo )

pure virtual

This function will sum the survey index data.

Parameters

TimeInfo is the TimeClass for the current model

Implemented in SIByLengthOnStep, SIByFleetOnStep, SIByEffortOnStep, SIByAgeOnStep, and SIByAcousticOnStep.

Member Data Documentation

◆ AAT

ActionAtTimes SIOnStep::AAT

protected

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

◆ Ages

IntMatrix SIOnStep::Ages

protected

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

◆ alptr

const AgeBandMatrixPtrVector* SIOnStep::alptr

protected

This is the AgeBandMatrixPtrVector used to temporarily store the information returned from the aggregatation function.

◆ Areas

IntMatrix SIOnStep::Areas

protected

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

◆ biomass

int SIOnStep::biomass

protected

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

Note: The default value for this is 0, which means that the index is based on the number of the population

◆ LgrpDiv

LengthGroupDivision* SIOnStep::LgrpDiv

protected

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

◆ likelihoodValues

DoubleVector SIOnStep::likelihoodValues

protected

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

◆ modelIndex

DoubleMatrixPtrVector SIOnStep::modelIndex

protected

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

Note: The indices for this object are [time][area][index]

◆ obsIndex

DoubleMatrixPtrVector SIOnStep::obsIndex

protected

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

Note: The indices for this object are [time][area][index]

◆ sitype

SIType SIOnStep::sitype

protected

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

◆ Steps

IntVector SIOnStep::Steps

protected

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

◆ timeindex

int SIOnStep::timeindex

protected

This is the index of the timesteps for the survey index data.

◆ useweight

int SIOnStep::useweight

protected

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

Note: The default value for this is 0, which means that the regression line doesnt use weights

◆ weightIndex

DoubleMatrixPtrVector SIOnStep::weightIndex

protected

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

Note: The indices for this object are [time][area][weight]

◆ Years

IntVector SIOnStep::Years

protected

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

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

src/include/sionstep.h
src/sionstep.cc

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SIOnStep()

◆ ~SIOnStep()

Member Function Documentation

◆ calcSSE()

◆ getSIType()

◆ getType()

◆ Print()

◆ printLikelihood()

◆ printSummary()

◆ Reset()

◆ setFleetsAndStocks()

◆ Sum()

Member Data Documentation

◆ AAT

◆ Ages

◆ alptr

◆ Areas

◆ biomass

◆ LgrpDiv

◆ likelihoodValues

◆ modelIndex

◆ obsIndex

◆ sitype

◆ Steps

◆ timeindex

◆ useweight

◆ weightIndex

◆ Years