This is the class used to calculate the affect of natural mortality on the stock. More...

#include <naturalm.h>

Inheritance diagram for NaturalMortality:

Collaboration diagram for NaturalMortality:

Public Member Functions
	NaturalMortality (CommentStream &infile, int minage, int numage, const char givenname, const IntVector &Areas, const TimeClass const TimeInfo, Keeper *const keeper)
	This is the NaturalMortality constructor. More...

	~NaturalMortality ()
	This is the default NaturalMortality destructor. More...

const DoubleVector &	getProportion (int area) const
	This function will return the DoubleVector of the proportion of each age group that will survive on the current timestep. More...

void	Reset (const TimeClass *const TimeInfo)
	This function will reset the NaturalMortality information. More...

void	Print (ofstream &outfile)
	This function will print the summary NaturalMortality information. 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...

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

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

	LivesOnAreas (const IntVector &Areas)
	This is the LivesOnAreas constructor for a specified vector of areas. More...

int	isInArea (int area) const
	This function will check whether the object is defined on a specified area. More...

IntVector &	getAreas ()
	This function will return the internal areas that the object is defined on. More...

int	areaNum (int area) const
	This function will return the area associated with an internal area. More...

Protected Attributes
ModelVariableVector	mortality
	This is the ModelVariableVector used to store the mortality of each age group. More...

SelectFunc *	fnMortality
	This is the SelectFunc used to calculate of the proportion of each age group of the stock that will die due to natural mortality. More...

DoubleMatrix	proportion
	This is the DoubleMatrix used to store the proportion of each age group that will survive (ie. will not die out due to natural mortality) More...

int	minStockAge
	This is the minimum age of the stock, used as an index when calculating proportion. More...

int	readoption
	This is the identifier of the function to be used to read the natural mortality data from file. More...

Protected Attributes inherited from LivesOnAreas
IntVector	areas
	This is the IntVector of internal areas that the object is defined on. More...

Additional Inherited Members
Protected Member Functions inherited from LivesOnAreas
void	storeAreas (const IntVector &Areas)
	This function will store the internal areas to be used. More...

Detailed Description

This is the class used to calculate the affect of natural mortality on the stock.

This class calculates the proportion of the stock that should be removed from the model due to natural mortality (ie. any mortality that is not due to predation, either by another stock or by a fleet). The number that is stored after this calculation contains the proportion of each area/age group that will survive (ie. is not removed due to the natural mortality).

Note: This is currently an age-based calculation, and it would be much better to replace this with a length-based calculation, by re-implementing this as a simple predator with a new suitability function to allow for higher levels of 'predation' on both the young/short fish and the old/long fish

Constructor & Destructor Documentation

◆ NaturalMortality()

NaturalMortality::NaturalMortality	(	CommentStream &	infile,
		int	minage,
		int	numage,
		const char *	givenname,
		const IntVector &	Areas,
		const TimeClass *const	TimeInfo,
		Keeper *const	keeper
	)

This is the NaturalMortality constructor.

Parameters

infile	is the CommentStream to read the NaturalMortality information from
minage	is the minimum age of the stock
numage	is the number of age groups for the stock
givenname	is the name of the stock for this NaturalMortality class
Areas	is the IntVector of the areas that the stock lives on
TimeInfo	is the TimeClass for the current model
keeper	is the Keeper for the current model

◆ ~NaturalMortality()

NaturalMortality::~NaturalMortality ( )

This is the default NaturalMortality destructor.

Member Function Documentation

◆ getProportion()

const DoubleVector& NaturalMortality::getProportion ( int area ) const

inline

This function will return the DoubleVector of the proportion of each age group that will survive on the current timestep.

Parameters

area	is the area that the natural mortality is being calculated on

Returns: proportion surviving from each age group

◆ Print()

void NaturalMortality::Print ( ofstream & outfile )

This function will print the summary NaturalMortality information.

Parameters

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

◆ Reset()

void NaturalMortality::Reset ( const TimeClass *const TimeInfo )

This function will reset the NaturalMortality information.

Parameters

TimeInfo is the TimeClass for the current model

Member Data Documentation

◆ fnMortality

SelectFunc* NaturalMortality::fnMortality

protected

This is the SelectFunc used to calculate of the proportion of each age group of the stock that will die due to natural mortality.

◆ minStockAge

int NaturalMortality::minStockAge

protected

This is the minimum age of the stock, used as an index when calculating proportion.

◆ mortality

ModelVariableVector NaturalMortality::mortality

protected

This is the ModelVariableVector used to store the mortality of each age group.

◆ proportion

DoubleMatrix NaturalMortality::proportion

protected

This is the DoubleMatrix used to store the proportion of each age group that will survive (ie. will not die out due to natural mortality)

◆ readoption

int NaturalMortality::readoption

protected

This is the identifier of the function to be used to read the natural mortality data from file.

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

src/include/naturalm.h
src/naturalm.cc

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ NaturalMortality()

◆ ~NaturalMortality()

Member Function Documentation

◆ getProportion()

◆ Print()

◆ Reset()

Member Data Documentation

◆ fnMortality

◆ minStockAge

◆ mortality

◆ proportion

◆ readoption