Insect Infestation Mortality - Version 1.0. More...

#include <InsectInfestationMortality.h>

Inheritance diagram for clInsectInfestationMortality:

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

	~clInsectInfestationMortality ()
	Destructor. More...

void	DoShellSetup (xercesc::DOMDocument *p_oDoc)
	Reads in values from the parameter file. More...

deadCode	DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
	Calculates mortality. 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 Attributes
double **	mp_fMortProbs
	Precalculated mortality probabilities, out to m_iMaxMortTime; any infestation time beyond this can be calculated as a one-off. More...

double *	mp_fIntercept
	Intercept - sized number of species. More...

double *	mp_fMax
	Max mort rate - sized number of species. More...

double *	mp_fX0
	X0 - sized number of species. More...

double *	mp_fXb
	Xb - sized number of species. More...

short int **	mp_iDataCodes
	Codes for "YearsInfested" data member. More...

short int	m_iNumSpecies
	Number of species. More...

short int	m_iMaxMortTime
	Max number of pre-calculated mortalities. 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
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...

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

Detailed Description

Insect Infestation Mortality - Version 1.0.

This evaluates mortality for trees that have an insect infestation.

The probability of death is a function of the number of years infested, as follows:

P = I +((MAX - I)/(1+(T/X0)^Xb))

where P is mortality probability, I is the intercept (mortality at time of infestation), MAX is max mortality probability, T is infestation time in years, X0 is time at which mortality prob = 0.5, and Xb controls steepness of the mortality increase.

A random number determines whether the trees die. Those that die have "insect" passed as the reason code.

Insect infestation is determined by the behavior of class clInsectInfestation. This class expects that behavior to be enabled and the "YearsInfested" int data member to be present for all trees to which this behavior is applied.

This class's namestring is "insect infestation mortshell". The parameter file call string is "InsectInfestationMortality".

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clInsectInfestationMortality()

clInsectInfestationMortality::clInsectInfestationMortality ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clInsectInfestationMortality()

clInsectInfestationMortality::~clInsectInfestationMortality ( )

Destructor.

Member Function Documentation

◆ DoMort()

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

virtual

Calculates mortality.

This retrieves the tree's time of infestation. If it is infested, the mortality probability for that year is compared to a random number to see if the tree lives or dies. If it is uninfested, it does not die.

Parameters

p_oTree	Tree being evaluated
fDbh	Tree's DBH
iSpecies	Species of the tree being evaluated

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

Implements clMortalityBase.

◆ DoShellSetup()

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

virtual

Reads in values from the parameter file.

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr

if:

"YearsInfested" is not registered for any tree to which this behavior is applied
MAX is not between 0 and 1
Intercept is not between 0 and 1
X0 = 0

Reimplemented from clMortalityBase.

Member Data Documentation

◆ m_iMaxMortTime

short int clInsectInfestationMortality::m_iMaxMortTime

protected

Max number of pre-calculated mortalities.

This will be the biggest value of 2*X0.

◆ m_iNumSpecies

short int clInsectInfestationMortality::m_iNumSpecies

protected

Number of species.

For destructor.

◆ mp_fIntercept

double* clInsectInfestationMortality::mp_fIntercept

protected

Intercept - sized number of species.

◆ mp_fMax

double* clInsectInfestationMortality::mp_fMax

protected

Max mort rate - sized number of species.

◆ mp_fMortProbs

double** clInsectInfestationMortality::mp_fMortProbs

protected

Precalculated mortality probabilities, out to m_iMaxMortTime; any infestation time beyond this can be calculated as a one-off.

First index is species, second is time of infestation

◆ mp_fX0

double* clInsectInfestationMortality::mp_fX0

protected

X0 - sized number of species.

◆ mp_fXb

double* clInsectInfestationMortality::mp_fXb

protected

Xb - sized number of species.

◆ mp_iDataCodes

short int** clInsectInfestationMortality::mp_iDataCodes

protected

Codes for "YearsInfested" data member.

Array size is number of species by number of types.

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

InsectInfestationMortality.h

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clInsectInfestationMortality()

◆ ~clInsectInfestationMortality()

Member Function Documentation

◆ DoMort()

◆ DoShellSetup()

Member Data Documentation

◆ m_iMaxMortTime

◆ m_iNumSpecies

◆ mp_fIntercept

◆ mp_fMax

◆ mp_fMortProbs

◆ mp_fX0

◆ mp_fXb

◆ mp_iDataCodes