This is the class used to calculate the stomach content likelihood score based on a function of the amount of prey consumed, the standard deviation of this amount and the number of stomachs sampled. More...

#include <stomachcontent.h>

Inheritance diagram for SCAmounts:

Collaboration diagram for SCAmounts:

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

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

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

Public Member Functions inherited from 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. 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	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
void	readStomachAmountContent (CommentStream &infile, const TimeClass *const TimeInfo)
	This function will read the StomachContent amount data from the input file. More...

void	readStomachSampleContent (CommentStream &infile, const TimeClass *const TimeInfo)
	This function will read the StomachContent sample data from the input file. More...

virtual double	calcLikelihood ()
	This function will calculate the likelihood score from the SCAmounts information. More...

Protected Attributes
DoubleMatrixPtrMatrix	stddev
	This is the DoubleMatrixPtrMatrix used to store the standard deviation values for the consumption information specified in the input file. More...

DoubleMatrixPtrVector	number
	This is the DoubleMatrixPtrVector used to store the number of stomach samples specified in the input file. More...

Protected Attributes inherited from SC
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 class used to calculate the stomach content likelihood score based on a function of the amount of prey consumed, the standard deviation of this amount and the number of stomachs sampled.

Constructor & Destructor Documentation

◆ SCAmounts()

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

This is the SCAmounts constructor.

Parameters

infile	is the CommentStream to read the SCAmounts 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 SCAmounts data
numfilename	is the name of the file containing the SCAmounts numbers data
givenname	is the name for the likelihood component

◆ ~SCAmounts()

SCAmounts::~SCAmounts ( )

virtual

This is the default SCAmounts destructor.

Member Function Documentation

◆ calcLikelihood()

double SCAmounts::calcLikelihood ( )

protectedvirtual

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

Returns: likelihood score

Implements SC.

Reimplemented in SCRatios.

◆ printLikelihood()

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

virtual

This function will print information from each SCAmounts calculation.

Parameters

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

Reimplemented from SC.

◆ readStomachAmountContent()

void SCAmounts::readStomachAmountContent	(	CommentStream &	infile,
		const TimeClass *const	TimeInfo
	)

protected

This function will read the StomachContent amount data from the input file.

Parameters

infile	is the CommentStream to read the StomachContent data from
TimeInfo	is the TimeClass for the current model

◆ readStomachSampleContent()

void SCAmounts::readStomachSampleContent	(	CommentStream &	infile,
		const TimeClass *const	TimeInfo
	)

protected

This function will read the StomachContent sample data from the input file.

Parameters

infile	is the CommentStream to read the StomachContent data from
TimeInfo	is the TimeClass for the current model

Member Data Documentation

◆ number

DoubleMatrixPtrVector SCAmounts::number

protected

This is the DoubleMatrixPtrVector used to store the number of stomach samples specified in the input file.

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

◆ stddev

DoubleMatrixPtrMatrix SCAmounts::stddev

protected

This is the DoubleMatrixPtrMatrix used to store the standard deviation values for the consumption information specified in the input file.

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

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

◆ SCAmounts()

◆ ~SCAmounts()

Member Function Documentation

◆ calcLikelihood()

◆ printLikelihood()

◆ readStomachAmountContent()

◆ readStomachSampleContent()

Member Data Documentation

◆ number

◆ stddev