This is the base class used to calculate the stomach content likelihood score based on the consumption of the preys in the model and the stomach content data specified in the input files. More...

#include <stomachcontent.h>

Inheritance diagram for SC:

Collaboration diagram for SC:

Public Member Functions
	SC (CommentStream &infile, const AreaClass const Area, const TimeClass const TimeInfo, Keeper const keeper, const char datafilename, const char *givenname)
	This is the SC constructor. More...

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

virtual double	calcLikelihood (const TimeClass *const TimeInfo)
	This function will calculate the likelihood score from the SC information. More...

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

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

virtual void	setPredatorsAndPreys (PredatorPtrVector &Predators, PreyPtrVector &Preys)
	This will select the predators and preys required to calculate the SC likelihood score. More...

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

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

virtual void	aggregate (int i)
	This function will aggregate consumption information for each StomachContent calculation. 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 Member Functions
virtual double	calcLikelihood ()=0
	This function will calculate the likelihood score from the SC information. More...

Protected Attributes
DoubleMatrixPtrMatrix	obsConsumption
	This is the DoubleMatrixPtrMatrix used to store stomach content (consumption) information specified in the input file. More...

DoubleMatrixPtrMatrix	modelConsumption
	This is the DoubleMatrixPtrMatrix used to store consumption (stomach content) information calculated in the model. More...

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

CharPtrVector	predatornames
	This is the CharPtrVector of the names of the predators that will be used to calculate the likelihood score. More...

CharPtrMatrix	preynames
	This is the CharPtrMatrix of the names of the preys that will be used to calculate the likelihood score. More...

CharPtrVector	areaindex
	This is the CharPtrVector of the names of the areas. More...

CharPtrVector	predindex
	This is the CharPtrVector of the names of the predator aggregation units (either age or length) that will be read in from the input file. More...

CharPtrVector	preyindex
	This is the CharPtrVector of the names of the prey aggregation units that will be read in from the input file. More...

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

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

DoubleVector	predatorlengths
	This is the DoubleVector used to store predator length information. More...

IntMatrix	predatorages
	This is the IntMatrix used to store predator age information. More...

DoubleMatrix	preylengths
	This is the DoubleMatrix used to store prey length information. More...

IntMatrix	areas
	This is the IntMatrix used to store area information. More...

int	usepredages
	This is the flag used to denote whether the predators are specified using age groups or length groups. More...

PredatorAggregator **	aggregator
	This is the PredatorAggregator used to collect information about the predation. More...

LengthGroupDivision **	preyLgrpDiv
	This is the LengthGroupDivision used to store predator length information. More...

LengthGroupDivision *	predLgrpDiv
	This is the LengthGroupDivision used to store prey length information. More...

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

ActionAtTimes	AAT
	This ActionAtTimes stores information about when the likelihood score should be calculated. More...

FormulaMatrix	digestioncoeff
	This is the FormulaMatrix used to store the digestion parameters for the various predator prey pairs. More...

DoubleMatrix	digestion
	This is the DoubleMatrix used to store the calculated digestion coefficiants for the various predator prey pairs. More...

double	epsilon
	This is the value of epsilon used when calculating the likelihood score. More...

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

Detailed Description

This is the base class used to calculate the stomach content likelihood score based on the consumption of the preys in the model and the stomach content data specified in the input files.

Note: This will always be overridden by the derived classes that actually calculate the stomach content likelihood score

Constructor & Destructor Documentation

◆ SC()

SC::SC	(	CommentStream &	infile,
		const AreaClass *const	Area,
		const TimeClass *const	TimeInfo,
		Keeper *const	keeper,
		const char *	datafilename,
		const char *	givenname
	)

This is the SC constructor.

Parameters

infile	is the CommentStream to read the SC data from
Area	is the AreaClass for the current model
TimeInfo	is the TimeClass for the current model
keeper	is the Keeper for the current model
datafilename	is the name of the file containing the SC data
givenname	is the name for the likelihood component

◆ ~SC()

SC::~SC ( )

virtual

This is the default SC destructor.

Member Function Documentation

◆ aggregate()

void SC::aggregate ( int i )

virtual

This function will aggregate consumption information for each StomachContent calculation.

Parameters

i	is the index of the prey that is being consumed

Reimplemented in SCNumbers.

◆ calcLikelihood() [1/2]

virtual double SC::calcLikelihood ( )

protectedpure virtual

This function will calculate the likelihood score from the SC information.

Returns: 0 (will be overridden in derived classes)

Implemented in SCSimple, SCRatios, SCAmounts, and SCNumbers.

◆ calcLikelihood() [2/2]

double SC::calcLikelihood ( const TimeClass *const TimeInfo )

virtual

This function will calculate the likelihood score from the SC information.

Parameters

TimeInfo is the TimeClass for the current model

Returns: likelihood score

◆ Print()

void SC::Print ( ofstream & outfile ) const

virtual

This function will print the summary SC information.

Parameters

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

◆ printLikelihood()

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

virtual

This function will print information from each StomachContent calculation.

Parameters

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

Reimplemented in SCAmounts.

◆ printSummary()

void SC::printSummary	(	ofstream &	outfile,
		double	weight
	)

virtual

This function will print summary information from each StomachContent likelihood calculation.

Parameters

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

◆ Reset()

void SC::Reset ( )

virtual

This function will reset the SC information.

◆ setPredatorsAndPreys()

void SC::setPredatorsAndPreys	(	PredatorPtrVector &	Predators,
		PreyPtrVector &	Preys
	)

virtual

This will select the predators and preys required to calculate the SC likelihood score.

Parameters

Predators	is the PredatorPtrVector of all the available predators
Preys	is the PreyPtrVector of all the available preys

Reimplemented in SCSimple, and SCRatios.

Member Data Documentation

◆ AAT

ActionAtTimes SC::AAT

protected

This ActionAtTimes stores information about when the likelihood score should be calculated.

◆ aggregator

PredatorAggregator** SC::aggregator

protected

This is the PredatorAggregator used to collect information about the predation.

◆ areaindex

CharPtrVector SC::areaindex

protected

This is the CharPtrVector of the names of the areas.

◆ areas

IntMatrix SC::areas

protected

This is the IntMatrix used to store area information.

◆ digestion

DoubleMatrix SC::digestion

protected

This is the DoubleMatrix used to store the calculated digestion coefficiants for the various predator prey pairs.

◆ digestioncoeff

FormulaMatrix SC::digestioncoeff

protected

This is the FormulaMatrix used to store the digestion parameters for the various predator prey pairs.

◆ dptr

const DoubleMatrix* SC::dptr

protected

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

◆ epsilon

double SC::epsilon

protected

This is the value of epsilon used when calculating the likelihood score.

◆ likelihoodValues

DoubleMatrix SC::likelihoodValues

protected

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

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

◆ modelConsumption

DoubleMatrixPtrMatrix SC::modelConsumption

protected

This is the DoubleMatrixPtrMatrix used to store consumption (stomach content) information calculated in the model.

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

◆ obsConsumption

DoubleMatrixPtrMatrix SC::obsConsumption

protected

This is the DoubleMatrixPtrMatrix used to store stomach content (consumption) information specified in the input file.

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

◆ predatorages

IntMatrix SC::predatorages

protected

This is the IntMatrix used to store predator age information.

◆ predatorlengths

DoubleVector SC::predatorlengths

protected

This is the DoubleVector used to store predator length information.

◆ predatornames

CharPtrVector SC::predatornames

protected

This is the CharPtrVector of the names of the predators that will be used to calculate the likelihood score.

◆ predindex

CharPtrVector SC::predindex

protected

This is the CharPtrVector of the names of the predator aggregation units (either age or length) that will be read in from the input file.

◆ predLgrpDiv

LengthGroupDivision* SC::predLgrpDiv

protected

This is the LengthGroupDivision used to store prey length information.

◆ preyindex

CharPtrVector SC::preyindex

protected

This is the CharPtrVector of the names of the prey aggregation units that will be read in from the input file.

◆ preylengths

DoubleMatrix SC::preylengths

protected

This is the DoubleMatrix used to store prey length information.

Note: The indices for this object are [prey number][prey length]

◆ preyLgrpDiv

LengthGroupDivision** SC::preyLgrpDiv

protected

This is the LengthGroupDivision used to store predator length information.

◆ preynames

CharPtrMatrix SC::preynames

protected

This is the CharPtrMatrix of the names of the preys that will be used to calculate the likelihood score.

◆ Steps

IntVector SC::Steps

protected

This is the IntVector used to store information about the steps when the likelihood score should be calculated.

◆ timeindex

int SC::timeindex

protected

This is the index of the timesteps for the likelihood component data.

◆ usepredages

int SC::usepredages

protected

This is the flag used to denote whether the predators are specified using age groups or length groups.

◆ Years

IntVector SC::Years

protected

This is the IntVector used to store information about the years when the likelihood score should be calculated.

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

src/include/stomachcontent.h
src/stomachcontent.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SC()

◆ ~SC()

Member Function Documentation

◆ aggregate()

◆ calcLikelihood() [1/2]

◆ calcLikelihood() [2/2]

◆ Print()

◆ printLikelihood()

◆ printSummary()

◆ Reset()

◆ setPredatorsAndPreys()

Member Data Documentation

◆ AAT

◆ aggregator

◆ areaindex

◆ areas

◆ digestion

◆ digestioncoeff

◆ dptr

◆ epsilon

◆ likelihoodValues

◆ modelConsumption

◆ obsConsumption

◆ predatorages

◆ predatorlengths

◆ predatornames

◆ predindex

◆ predLgrpDiv

◆ preyindex

◆ preylengths

◆ preyLgrpDiv

◆ preynames

◆ Steps

◆ timeindex

◆ usepredages

◆ Years