Growth and Resource Based Mortality - Version 1.0. More...

#include <ResourceMortality.h>

Inheritance diagram for clResourceMortality:

Public Member Functions
	clResourceMortality (clSimManager *p_oSimManager)
	Constructor. More...

	~clResourceMortality ()
	Destructor. More...

void	DoShellSetup (xercesc::DOMDocument *p_oDoc)
	Performs setup for this behavior. More...

deadCode	DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
	Calculates mortality according to the growth-resource mortality equation. More...

Public Member Functions inherited from clMortalityBase
	clMortalityBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clMortalityBase ()
	Destructor. More...

void	Action ()
	Performs mortality calculations. More...

clMortalityOrg *	GetMortOrg ()
	Gets the mortality org object. More...

void	RegisterTreeDataMembers ()
	Triggers the mortality data member registrations. More...

short int	GetNewTreeInts ()
	Overridden from clBehaviorBase. More...

bool	UsesThisMortality (short int iSp, short int iTp)
	Whether or not a species/type combo uses this mortality object. More...

virtual void	PreMortCalcs (clTreePopulation *p_oPop)
	Performs calculations before any trees have been killed. More...

Public Member Functions inherited from clBehaviorBase
virtual float	GetBehaviorVersion ()
	Gets the behavior version number. More...

	clBehaviorBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clBehaviorBase ()
	Destructor. More...

virtual short int	ValidateVersionNumber (float fTestVersion)
	Makes sure that the version number of a file passed is between the minimum and current version numbers. More...

virtual void	SetSpeciesTypeCombos (short int iNumCombos, stcSpeciesTypeCombo *p_whatCombos)
	Sets the species/type combos for a behavior. More...

virtual void	SetNameData (std::string sNameString)
	Sets the string for the parameter file behavior. More...

virtual short int	GetNewTreeFloats ()
	Gets the number of new tree float data members this behavior wants to register. More...

virtual short int	GetNewTreeChars ()
	Gets the number of new tree character data members this behavior wants to register. More...

virtual short int	GetNewTreeBools ()
	Gets the number of new tree bool data members this behavior wants to register. More...

virtual short int	GetNumSpeciesTypeCombos ()
	Gets the number of species/type combos to which this behavior applies. More...

virtual short int	GetNumBehaviorSpecies ()
	Gets the number of unique tree species to which this behavior applies. More...

struct stcSpeciesTypeCombo	GetSpeciesTypeCombo (short int iIndex)
	Gets one of this behavior's type/species combos. More...

virtual short int	GetBehaviorSpecies (short int iIndex)
	Gets one of the behavior's species. More...

short int	GetBehaviorListNumber ()
	Gets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list. More...

void	SetBehaviorListNumber (short int iNumber)
	Sets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list. More...

std::string	FormatSpeciesTypeQueryString ()
	Formats the string for species/types query. More...

virtual DOMElement *	GetParentParametersElement (xercesc::DOMDocument *p_oDoc)
	This will get the correct set of parameters for this behavior based on the behavior list position number. More...

Public Member Functions inherited from clWorkerBase
	clWorkerBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clWorkerBase ()
	Destructor. More...

std::string	GetName ()
	Gets the object's namestring. More...

clSimManager *	GetSimManager ()

void	DoObjectSetup (xercesc::DOMDocument *p_oDoc, fileType iFileType)
	Triggers the setup process. More...

virtual void	TimestepCleanup ()
	Performs any necessary cleanup operations at the end of a timestep. More...

virtual void	EndOfRunCleanup ()
	Performs any necessary cleanup operations at the end of a run. More...

Protected Member Functions
void	ReadParameterFileData (xercesc::DOMDocument *p_oDoc)
	Reads in parameter file data. More...

void	GetResourceGrid ()
	Gets the "Resource" grid. More...

void	GetTreeDataMemberCodes ()
	Queries for the return codes of the "Growth", "X", and "Y" float data members of a tree. More...

Protected Member Functions inherited from clMortalityBase
void	GetData (xercesc::DOMDocument *p_oDoc)
	Triggers all mortality setup. More...

void	PopulateUsesThisMortality ()
	Declares and populates the mp_bUsesThisMortality array. More...

Protected Member Functions inherited from clWorkerBase
void	AssembleFileCode (int iFileType, int iFileVersion, char *cCode)
	Creates the proper identifying filecode for an XML file. More...

Protected Attributes
clGrid *	mp_oResourceGrid
	Grid containing the levels of the second resource. More...

short int **	mp_iGrowthCodes
	Data member codes for "Growth" member - # behavior species by total # types. More...

short int **	mp_iXCodes
	Data member codes for "X" tree data member - # behavior species by total types More...

short int **	mp_iYCodes
	Data member codes for "Y" tree data member - # behavior species by total types More...

double *	mp_fRho
	Scaling factor - ρ in equation above. More...

double *	mp_fMu
	Function mode - μ in equation above. More...

double *	mp_fDelta
	Increase in survival due to growth - δ in equation above. More...

double *	mp_fSigma
	Shape of function in low-growth conditions - σ in equation above. More...

short int *	mp_iIndexes
	For array access. More...

int	m_iNumberYearsPerTimestep
	Number of years per timestep. More...

short int	m_iResourceCode
	Index for "Resource" data member of the "Resource" grid. More...

Protected Attributes inherited from clMortalityBase
short int	m_iNumTotalSpecies
	Keep a copy for the constructor. More...

bool	m_bHooked
	Whether or not this shell object is hooked to clMortalityOrg. More...

bool **	mp_bUsesThisMortality
	2D array, species by type, of whether or not this mortality shell applies to a given species/type combo. More...

Protected Attributes inherited from clBehaviorBase
short int	m_iNumSpeciesTypeCombos
	How many type/species combos a behavior will act on. More...

short int	m_iNumBehaviorSpecies
	How many distinct species are in the combo list - important for filling species-specific values from parameter file. More...

short int *	mp_iWhatSpecies
	List of distinct species - for filling species-specific values from parameter file. More...

stcSpeciesTypeCombo *	mp_whatSpeciesTypeCombos
	Array of species/type combos that the behavior will act on. More...

short int	m_iNewTreeInts
	The number of new tree integer data members this behavior wants to add. More...

short int	m_iNewTreeFloats
	The number of new tree float data members this behavior wants to add. More...

short int	m_iNewTreeChars
	The number of new tree character data members this behavior wants to add. More...

short int	m_iNewTreeBools
	The number of new tree boolean data members this behavior wants to add. More...

short int	m_iBehaviorListNumber
	The number of this behavior in the behavior list, to differentiate between possible multiple copies of this behavior. More...

float	m_fVersionNumber
	Version number - this will be rounded to 2 digits after the decimal place. More...

std::string	m_sXMLRoot
	XML root that encloses the parameters for this behavior. More...

float	m_fMinimumVersionNumber
	Minimum version number - this behavior will run parameter data for a file marked between this number and the current version number, inclusive. More...

Protected Attributes inherited from clWorkerBase
std::string	m_sNameString
	If a behavior has registered a command line command with the sim manager, this allows it to be called. More...

clSimManager *	mp_oSimManager
	Pointer to the simulation manager object. More...

int *	mp_iAllowedFileTypes
	List of the input file types this object can handle. More...

int	m_iNumAllowedTypes
	Number of input file types this object can handle. More...

Additional Inherited Members
Static Protected Attributes inherited from clMortalityBase
static clMortalityOrg *	mp_oMortalityOrg
	clMortalityOrg object. More...

Detailed Description

Growth and Resource Based Mortality - Version 1.0.

This evaluates mortality probability as a function of growth and a second (unidentified) resource.

The probability of mortality is:

Prob = 1 - ρ * exp(-(R - μ)² / 2(δG + σ)²) where:

Prob is the probability of mortality, as a value between 0 and 1
R is the amount of some resource (whose identity is unimportant)
G is the amount of diameter growth, in cm
ρ is a scaling factor permitting to reduce survival at lower levels than 1 at the mode
μ determines the mode of the function along a gradient of the resource R (this corresponds to the optimal niche of a species, meaning where it is the top competitor, the absolute winner of competition)
δ specifies the increase in survival caused by amount of growth
σ affect the shape of the survival probability distribution in low-growth conditions

It saves some calculations to work with the probability of SURVIVAL instead of MORTALITY; remove the "1 - " part from the beginning of the above equation. To compound the survival probability over the number of years per timestep, use P^X, where P is the annual probability of survival and X is the number of years per timestep.

Once a tree's survival probability has been calculated, a random number is used to determine if the tree lives or dies.

The value of the second resource comes from a grid called "Resource", with a single float member named "Resource". This behavior doesn't create this grid, and it's considered a fatal error if it is not present at setup. This behavior will not modify the contents of this grid in any way.

This class's namestring is "resourcemortshell". Its parameter file call string is "GrowthResourceMortality".

Author: Lora E. Murphy

Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)

Constructor & Destructor Documentation

◆ clResourceMortality()

clResourceMortality::clResourceMortality ( clSimManager * p_oSimManager )

Constructor.

Sets the namestring.

◆ ~clResourceMortality()

clResourceMortality::~clResourceMortality ( )

Destructor.

Member Function Documentation

◆ DoMort()

deadCode clResourceMortality::DoMort	(	clTree *	p_oTree,
		const float &	fDbh,
		const short int &	iSpecies
	)

virtual

Calculates mortality according to the growth-resource mortality equation.

The equation is listed above.

Parameters

fDbh	DBH of tree being evaluated - for seedlings will be 0
p_oTree	Tree being evaluated
iSpecies	Species of the tree being evaluated

Returns: natural if the tree is to die, notdead if it lives.

Implements clMortalityBase.

◆ DoShellSetup()

void clResourceMortality::DoShellSetup ( xercesc::DOMDocument * p_oDoc )

virtual

Performs setup for this behavior.

Calls:

ReadParameterFileData
GetTreeDataMemberCodes
GetResourceGrid

Parameters

p_oDoc Parsed DOM tree of parameter file.

Reimplemented from clMortalityBase.

◆ GetResourceGrid()

void clResourceMortality::GetResourceGrid ( )

protected

Gets the "Resource" grid.

Exceptions

modelErr if the grid named "Resource" is not present, or is not set up correctly.

◆ GetTreeDataMemberCodes()

void clResourceMortality::GetTreeDataMemberCodes ( )

protected

Queries for the return codes of the "Growth", "X", and "Y" float data members of a tree.

The "Growth" data member should have been registered by a child class of clGrowthBase.

Exceptions

modelErr if there is no code for any species/type combo which uses this behavior.

◆ ReadParameterFileData()

void clResourceMortality::ReadParameterFileData ( xercesc::DOMDocument * p_oDoc )

protected

Reads in parameter file data.

Parameters

p_oDoc Parsed DOM tree of parameter file.

Member Data Documentation

◆ m_iNumberYearsPerTimestep

int clResourceMortality::m_iNumberYearsPerTimestep

protected

Number of years per timestep.

◆ m_iResourceCode

short int clResourceMortality::m_iResourceCode

protected

Index for "Resource" data member of the "Resource" grid.

◆ mp_fDelta

double* clResourceMortality::mp_fDelta

protected

Increase in survival due to growth - δ in equation above.

Array size is number of behavior species.

◆ mp_fMu

double* clResourceMortality::mp_fMu

protected

Function mode - μ in equation above.

Array size is number of behavior species.

◆ mp_fRho

double* clResourceMortality::mp_fRho

protected

Scaling factor - ρ in equation above.

Array size is number of behavior species.

◆ mp_fSigma

double* clResourceMortality::mp_fSigma

protected

Shape of function in low-growth conditions - σ in equation above.

Array size is number of behavior species.

◆ mp_iGrowthCodes

short int** clResourceMortality::mp_iGrowthCodes

protected

Data member codes for "Growth" member - # behavior species by total # types.

◆ mp_iIndexes

short int* clResourceMortality::mp_iIndexes

protected

For array access.

◆ mp_iXCodes

short int** clResourceMortality::mp_iXCodes

protected

Data member codes for "X" tree data member - # behavior species by total

types

◆ mp_iYCodes

short int** clResourceMortality::mp_iYCodes

protected

Data member codes for "Y" tree data member - # behavior species by total

types

◆ mp_oResourceGrid

clGrid* clResourceMortality::mp_oResourceGrid

protected

Grid containing the levels of the second resource.

This is not created by this behavior; it is expected to already be available. It should be named "Resource" and have one float data member called "Resource".

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

ResourceMortality.h

Public Member Functions

Protected Member Functions

Protected Attributes

types

types

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clResourceMortality()

◆ ~clResourceMortality()

Member Function Documentation

◆ DoMort()

◆ DoShellSetup()

◆ GetResourceGrid()

◆ GetTreeDataMemberCodes()

◆ ReadParameterFileData()

Member Data Documentation

◆ m_iNumberYearsPerTimestep

◆ m_iResourceCode

◆ mp_fDelta

◆ mp_fMu

◆ mp_fRho

◆ mp_fSigma

◆ mp_iGrowthCodes

◆ mp_iIndexes

◆ mp_iXCodes

types

◆ mp_iYCodes

types

◆ mp_oResourceGrid