Aggregated mortality version 1.0. More...

#include <AggregatedMortality.h>

Inheritance diagram for clAggregatedMortality:

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

	~clAggregatedMortality ()
	Destructor. More...

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

void	PreMortCalcs (clTreePopulation *p_oPop)
	Performs mortality. More...

float	GetMortalityEpisodeProbability ()
	For testing purposes. More...

float	GetTreeMortalityProb ()
	For testing purposes. More...

deadCode	DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
	Determines mortality for a tree. 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	ReadParFile (xercesc::DOMDocument *p_oDoc)
	Reads in parameters from the parameter file. More...

void	GetDeadCodes (clTreePopulation *p_oPop)
	Gets codes for the "dead" data member for each tree type to which this behavior applies. More...

void	SetUpAppliesTo (clTreePopulation *p_oPop)
	Sets up the mp_bAppliesTo matrix. More...

bool	IsValid (clTree *p_oTree)
	Tests a tree to see whether it is eligible for killing. More...

void	KillClump (clTreePopulation p_oPop, clTree p_oTree, int iNumToKill)
	Kills a single clump of trees. 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
int **	mp_iDeadCodes
	Return codes for the "dead" bool tree data member. More...

bool **	mp_bAppliesTo
	Matrix for which tree types and species this behavior is applied. More...

double	m_fMortalityEpisodeProbability
	Per-timestep probability of a mortality episode occuring, 0 - 1. More...

double	m_fMortalityProb
	Per-timestep proportion of trees to kill, 0 - 1. More...

int	m_iNumTreesToClump
	Number of trees to kill together in a clump. More...

double	m_fClumpingParameter
	Clumping parameter for the negative binomial distribution, if applicable. More...

int	m_iTotalNumSpecies
	Total number of species. More...

bool	m_bClumpSizeDeterministic
	If true, the size of a single clump of trees to kill is deterministic. 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

Aggregated mortality version 1.0.

This behavior kills trees in a way that is clumped in both time and space.

Mortality occurs in discrete episodes, governed by a return interval specified by the user. Each timestep, the probability of a mortality episode is T/RI, where T is the number of years per timestep and RI is the return interval in years. At each timestep, a uniform random number is compared to this probability to decide whether or not an episode of mortality occurs. If not, no trees are killed by this behavior.

When a mortality episode occurs, trees are killed in clumps of a size set by the user. Each tree has an equal probability of being the first tree to die in a clump, and is evaluated individually. The probability of mortality is the total mortality probability given by the user divided by the size of the clump. This probability applies only to trees to which this behavior is applied. Other trees are not killed by this behavior, either directly or as part of a clump.

Trees are killed in clumps. The number of trees in a clump can either be deterministic, meaning the clumps are always the same size, or it can be drawn from a negative binomial probability distribution.

For each tree in the pool, the behavior uses a random number to see if it will start a clump. If it will, the behavior kills it, then its closest neighbors to which the behavior applies, until it has killed the number of trees in the clump. If the clump size is 1, then this behavior replicates the clStochasticMort method.

The mortality rate is given as per year. The per timestep amount to kill is 1-(1-AD)^X, where AD is the amount of damage and X is the number of years per timestep.

Because of the clumping thing, this chooses all its trees to kill in the PreMortCalcs function.

There could be problems if there are other mortality behaviors that come before this one. Not in a code way, but they might kill again trees this behavior has chosen to kill; so fewer than expected trees might die.

The namestring for this class is "aggregatedmortshell". The parameter file call string is "AggregatedMortality".

This behavior is only descended from clMortalityBase in order to take advantage of the registration of the "dead" tree data member.

Author: Lora E. Murphy
Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)

Constructor & Destructor Documentation

◆ clAggregatedMortality()

clAggregatedMortality::clAggregatedMortality ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clAggregatedMortality()

clAggregatedMortality::~clAggregatedMortality ( )

Destructor.

Frees memory.

Member Function Documentation

◆ DoMort()

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

virtual

Determines mortality for a tree.

This just returns the value in the "dead" bool tree data member.

Parameters

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

Implements clMortalityBase.

◆ DoShellSetup()

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

virtual

Does behavior setup.

Calls the following functions:

Then final calculations for mortality episode probability and amount of damage are made.

Parameters

p_oDoc DOM tree of parsed input file.

Reimplemented from clMortalityBase.

◆ GetDeadCodes()

void clAggregatedMortality::GetDeadCodes ( clTreePopulation * p_oPop )

protected

Gets codes for the "dead" data member for each tree type to which this behavior applies.

Parameters

p_oPop Tree population object.

Exceptions

modelErr if the codes are not available for every tree type to which this behavior is applied, or if this behavior is applied to seedlings.

◆ GetMortalityEpisodeProbability()

float clAggregatedMortality::GetMortalityEpisodeProbability ( )

inline

For testing purposes.

Returns: Probability of mortality

◆ GetTreeMortalityProb()

float clAggregatedMortality::GetTreeMortalityProb ( )

inline

For testing purposes.

Returns: Mortality probability

◆ IsValid()

bool clAggregatedMortality::IsValid ( clTree * p_oTree )

protected

Tests a tree to see whether it is eligible for killing.

It must be of a species and tree type to which this behavior is applied, and not dead.

Parameters

p_oTree Tree to test.

Returns: true if the tree is eligible; false if not.

◆ KillClump()

void clAggregatedMortality::KillClump	(	clTreePopulation *	p_oPop,
		clTree *	p_oTree,
		int	iNumToKill
	)

protected

Kills a single clump of trees.

This function gets the coordinate of the first tree in the clump. It searches a circle of an ever-widening radius until it finds enough trees to make a complete clump. It then sorts the trees it finds in distance order so that the trees closest to the target will be killed to make the clump.

Parameters

p_oPop	Tree population object.
p_oTree	First tree in the clump.
iNumToKill	Number of trees to kill.

◆ PreMortCalcs()

void clAggregatedMortality::PreMortCalcs ( clTreePopulation * p_oPop )

virtual

Performs mortality.

A random number compared to the probability of a mortality episode decides if an episode occurs. If not, this exits. If so, this goes through all the trees to which it applies. For each, if the tree is not already "dead", then a random number decides whether it begins a dead clump. To find the trees in the clump, it searches in a circle of radius 5 meters for neighbors. The trees eligible to die are killed in order of distance until the number in the clump has been reached. If not enough trees are found in 5 meters, the circle is widened in 5 meter increments until enough trees are found.

Parameters

p_oPop Tree population.

Reimplemented from clMortalityBase.

◆ ReadParFile()

void clAggregatedMortality::ReadParFile ( xercesc::DOMDocument * p_oDoc )

protected

Reads in parameters from the parameter file.

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr

if:

The value for amount to cut is not between 0 and 1
The return interval is less than 0

◆ SetUpAppliesTo()

void clAggregatedMortality::SetUpAppliesTo ( clTreePopulation * p_oPop )

protected

Sets up the mp_bAppliesTo matrix.

Parameters

p_oPop Tree population object.

Member Data Documentation

◆ m_bClumpSizeDeterministic

bool clAggregatedMortality::m_bClumpSizeDeterministic

protected

If true, the size of a single clump of trees to kill is deterministic.

If false, the size is chosen from a negative binomial probability distribution.

◆ m_fClumpingParameter

double clAggregatedMortality::m_fClumpingParameter

protected

Clumping parameter for the negative binomial distribution, if applicable.

◆ m_fMortalityEpisodeProbability

double clAggregatedMortality::m_fMortalityEpisodeProbability

protected

Per-timestep probability of a mortality episode occuring, 0 - 1.

Read from the parameter file as a return interval, then this value is calculated as T/RI, where T is the number of years per timestep and RI is the return interval in years.

◆ m_fMortalityProb

double clAggregatedMortality::m_fMortalityProb

protected

Per-timestep proportion of trees to kill, 0 - 1.

Read from the parameter file as an annual amount, then this value is calculated as (1-(1-AD)^X)/C, where AD is the amount of damage, X is the number of years per timestep, and C is the clump size.

◆ m_iNumTreesToClump

int clAggregatedMortality::m_iNumTreesToClump

protected

Number of trees to kill together in a clump.

This is either a deterministic value or the mean of the negative binomial probability distribution from which to choose a value.

◆ m_iTotalNumSpecies

int clAggregatedMortality::m_iTotalNumSpecies

protected

Total number of species.

Primarily for the destructor.

◆ mp_bAppliesTo

bool** clAggregatedMortality::mp_bAppliesTo

protected

Matrix for which tree types and species this behavior is applied.

Array index is sized total number of species by total number of life history stages.

◆ mp_iDeadCodes

int** clAggregatedMortality::mp_iDeadCodes

protected

Return codes for the "dead" bool tree data member.

Array index one is sized total number of species by total number of life history stages.

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

AggregatedMortality.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clAggregatedMortality()

◆ ~clAggregatedMortality()

Member Function Documentation

◆ DoMort()

◆ DoShellSetup()

◆ GetDeadCodes()

◆ GetMortalityEpisodeProbability()

◆ GetTreeMortalityProb()

◆ IsValid()

◆ KillClump()

◆ PreMortCalcs()

◆ ReadParFile()

◆ SetUpAppliesTo()

Member Data Documentation

◆ m_bClumpSizeDeterministic

◆ m_fClumpingParameter

◆ m_fMortalityEpisodeProbability

◆ m_fMortalityProb

◆ m_iNumTreesToClump

◆ m_iTotalNumSpecies

◆ mp_bAppliesTo

◆ mp_iDeadCodes