NCI Mortality - Version 3.0. More...

#include <NCIMasterMortality.h>

Inheritance diagram for clNCIMasterMortality:

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

	~clNCIMasterMortality ()
	Destructor. More...

deadCode	DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
	Determines mortality for a tree. More...

void	DoShellSetup (xercesc::DOMDocument *p_oDoc)
	Does setup. More...

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

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	GetTreeMemberCodes ()
	Gets the return codes for needed tree data members. 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
double *	mp_fMaxPotentialValue
	Maximum survival value. More...

double	m_fMaxSurvivalPeriod
	The length of the time period of the max survival, if needed for adjustment of survival rates. More...

short int **	mp_iDeadCodes
	Return codes for the "dead" tree int data member variable. More...

short int	m_iNumTotalSpecies
	Total number of species - for the destructor. More...

std::string	m_sQuery
	For finding trees. 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...

Private Member Functions inherited from clNCIBehaviorBase
	clNCIBehaviorBase ()
	Constructor. More...

	~clNCIBehaviorBase ()
	Destructor. More...

clShadingEffectBase *	GetShadingEffect ()
	Get the shading effect object. More...

clDamageEffectBase *	GetDamageEffect ()
	Get the damage effect object. More...

clSizeEffectBase *	GetSizeEffect ()
	Get the size effect object. More...

clCrowdingEffectBase *	GetCrowdingEffect ()
	Get the crowding effect object. More...

clNCITermBase *	GetNCITerm ()
	Get the NCI term object. More...

clPrecipitationEffectBase *	GetPrecipEffect ()
	Get the precipitation effect object. More...

clTemperatureEffectBase *	GetTempEffect ()
	Get the temperature effect object. More...

clNitrogenEffectBase *	GetNEffect ()
	Get the nitrogen effect object. More...

clInfectionEffectBase *	GetInfectionEffect ()
	Get the infection effect object. More...

void	ReadParameterFile (xercesc::DOMElement p_oElement, clTreePopulation p_oPop, clBehaviorBase *p_oNCI, bool bUsingDiam)
	Reads data from the parameter file for the effects objects. More...

Private Attributes inherited from clNCIBehaviorBase
clShadingEffectBase *	mp_oShadingEffect
	The shading effect object. More...

clDamageEffectBase *	mp_oDamageEffect
	The damage effect object. More...

clSizeEffectBase *	mp_oSizeEffect
	The size effect object. More...

clCrowdingEffectBase *	mp_oCrowdingEffect
	The crowding effect object. More...

clNCITermBase *	mp_oNCITerm
	The NCI term object. More...

clPrecipitationEffectBase *	mp_oPrecipEffect
	The precipitation effect object. More...

clTemperatureEffectBase *	mp_oTempEffect
	The temperature effect object. More...

clNitrogenEffectBase *	mp_oNEffect
	The nitrogen effect object. More...

clInfectionEffectBase *	mp_oInfectionEffect
	The infection effect object. More...

Detailed Description

NCI Mortality - Version 3.0.

This is a mortality shell object which applies an NCI (neighborhood competition index) function to assess probability of survival. The basic function is a maximum rate of survival that is reduced by a set of multiplicative effects. The set of effects used is up to the user.

The annual survival probability is compounded for multi-year timesteps by taking it to the X power, where X is the number of years per timestep.

The namestring for this class is "ncimortshell". The parameter file call string is "NCIMortality".

This behavior can only be applied to saplings and adults.

Author: Lora E. Murphy

Edit history:
--------------—
June 28, 2013 - Created (LEM)
November 1, 2013: Added infection effect (LEM)

Constructor & Destructor Documentation

◆ clNCIMasterMortality()

clNCIMasterMortality::clNCIMasterMortality ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clNCIMasterMortality()

clNCIMasterMortality::~clNCIMasterMortality ( )

Destructor.

Frees memory.

Member Function Documentation

◆ DoMort()

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

virtual

Determines mortality for a tree.

Parameters

p_oTree	Tree being evaluated.
fDbh	DBH of tree being evaluated.
iSpecies	Species of tree being evaluated.

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

Implements clMortalityBase.

◆ DoShellSetup()

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

virtual

Does setup.

ReadParameterFile() is called to read the parameter file's data.
GetTreeMemberCodes() is called to get tree data return codes.
FormatQueryString() is called.

Parameters

p_oDoc DOM tree of parsed input tree.

Reimplemented from clMortalityBase.

◆ GetTreeMemberCodes()

void clNCIMasterMortality::GetTreeMemberCodes ( )

protected

Gets the return codes for needed tree data members.

Exceptions

modelErr if a light code comes back -1 for any species which uses the shading effect.

◆ PreMortCalcs()

void clNCIMasterMortality::PreMortCalcs ( clTreePopulation * p_oPop )

virtual

Performs calculations before any trees have been killed.

This finds all trees to which this behavior applies and performs their NCI calculations. Then, having done all that work, this function goes ahead and assesses the tree's mortality. Whether it lives or dies is then stashed in the "NCI Mort" bool tree data member.

Parameters

p_oPop Tree population.

Reimplemented from clMortalityBase.

Member Data Documentation

◆ m_fMaxSurvivalPeriod

double clNCIMasterMortality::m_fMaxSurvivalPeriod

protected

The length of the time period of the max survival, if needed for adjustment of survival rates.

For instance, if the max survival is for a 5-year time period, then this value is 5, and the 5th root is taken of the final survival rate to arrive at the yearly value. 1 indicates that the max rate is yearly already.

◆ m_iNumTotalSpecies

short int clNCIMasterMortality::m_iNumTotalSpecies

protected

Total number of species - for the destructor.

◆ m_sQuery

std::string clNCIMasterMortality::m_sQuery

protected

For finding trees.

◆ mp_fMaxPotentialValue

double* clNCIMasterMortality::mp_fMaxPotentialValue

protected

Maximum survival value.

Array sized number of species.

◆ mp_iDeadCodes

short int** clNCIMasterMortality::mp_iDeadCodes

protected

Return codes for the "dead" tree int data member variable.

Array size is number of species by number of tree types (even if not every species and type is represented).

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

NCIMasterMortality.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clNCIMasterMortality()

◆ ~clNCIMasterMortality()

Member Function Documentation

◆ DoMort()

◆ DoShellSetup()

◆ GetTreeMemberCodes()

◆ PreMortCalcs()

Member Data Documentation

◆ m_fMaxSurvivalPeriod

◆ m_iNumTotalSpecies

◆ m_sQuery

◆ mp_fMaxPotentialValue

◆ mp_iDeadCodes