Snag mortality using Weibull function, V 1.1. More...

#include <WeibullSnagMort.h>

Inheritance diagram for clWeibullSnagMort:

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

	~clWeibullSnagMort ()
	Destructor. More...

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

deadCode	DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
	Calculates whether a snag lives or dies. 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	ReadParameterFile (xercesc::DOMDocument *p_oDoc)
	Reads required data from the parameter file. More...

void	FillDeathProbArray ()
	Declares and populates the mp_fProbabilityOfDeath array. More...

float	CalculateDeathProbability (int iSizeClass, int iSpecies, int iAge)
	Calculates a probability of death for snags of a certain age. More...

void	GetAgeCodes ()
	Gets the data member return codes for the "age" snag data member. More...

void	ValidateTypes ()
	Makes sure that this behavior has only been applied to snags. 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
float ***	mp_fProbabilityOfDeath
	Pre-calculated probabilities of death. More...

double **	mp_fAParameter
	Parameter "a" in Weibull function. More...

double **	mp_fBParameter
	Parameter "b" in Weibull function. More...

double **	mp_fSnagSizeClasses
	Upper limit of DBH in each snag size class. More...

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

short int *	mp_iAgeCodes
	Data member codes for "age" snag member for each behavior species. More...

short int *	mp_iIndexes
	For accessing arrays. More...

short int	m_iMaxPrecalcAge
	Max age, in timesteps, that the probability of death is pre-calculated. More...

short int	m_iNumSizeClasses
	Number of snag size classes for which separate parameters can be defined. 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

Snag mortality using Weibull function, V 1.1.

Snags are standing dead trees, and as such "mortality" is something of a misnomer. However, since this behavior fits in with the other mortality behaviors, we will continue to use that naming scheme.

Snag death really means that a snag falls over. The probability that this will happen to any one snag is a function of its age as a snag. The percentage standing of a snag population is:

Percent standing = 100 * e^{(-(a*Time^b))}

where Time is in years.

The rate at which snags fall over changes with snag size. This behavior allows the definition of three snag size classes. Each size class can take a different set of a and b values.

This behavior can only be applied to snags.

The namestring for this behavior is "weibsnagmortshell". The parameter file call string is "WeibullSnagMortality".

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clWeibullSnagMort()

clWeibullSnagMort::clWeibullSnagMort ( clSimManager * p_oSimManager )

Constructor.

Sets the namestring and nulls all pointers.

◆ ~clWeibullSnagMort()

clWeibullSnagMort::~clWeibullSnagMort ( )

Destructor.

Frees memory.

Member Function Documentation

◆ CalculateDeathProbability()

float clWeibullSnagMort::CalculateDeathProbability	(	int	iSizeClass,
		int	iSpecies,
		int	iAge
	)

protected

Calculates a probability of death for snags of a certain age.

The probability is calculated as since the last timestep. If F_t is the value of the function above at timestep t, then the probability P_t of mortality between timesteps t-1 and t is:

P_t = (1-(1-F_t)/(1-F_t-1))

Any probability value greater than 1 - 1.0E-5 is returned as one, and less than 1.0E-05 is returned as 0. This function will handle conversions of ages from years to timesteps.

If the age is within the first timestep, then the probability is the value of the function at time t.

Parameters

iSizeClass	Size class number, as 0, 1, or 2. THIS NUMBER IS NOT CHECKED FOR VALIDITY.
iSpecies	Species number. NOT species index, just plain old species.
iAge	Age in years.

Returns: Probability of death, between 0 and 1 inclusive.

◆ DoMort()

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

virtual

Calculates whether a snag lives or dies.

If the snag age in timesteps is less than m_iMaxPrecalcAge, then a random number is compared to the appropriate value in mp_fProbabilityOfDeath. If it is greater than that age, then its probability of death is calculated directly from the Weibull function. In each case, if the random number is less than or equal to the probability of death, then the snag dies.

Parameters

fDbh	DBH of tree being evaluated
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 clWeibullSnagMort::DoShellSetup ( xercesc::DOMDocument * p_oDoc )

virtual

Performs specific setup for this behavior.

Calls ReadParameterFile() in order to get parameter file data.
Calls CalculateDeathProbabilities().
Calls GetAgeCodes().

Parameters

p_oDoc Parsed DOM tree of parameter file.

Reimplemented from clMortalityBase.

◆ FillDeathProbArray()

void clWeibullSnagMort::FillDeathProbArray ( )

protected

Declares and populates the mp_fProbabilityOfDeath array.

For each timestep t, it calculates the probability of mortality between t and t-1 using CalculateDeathProbability().

◆ GetAgeCodes()

void clWeibullSnagMort::GetAgeCodes ( )

protected

Gets the data member return codes for the "age" snag data member.

Return codes are captured in the mp_iAgeCodes array.

◆ ReadParameterFile()

void clWeibullSnagMort::ReadParameterFile ( xercesc::DOMDocument * p_oDoc )

protected

Reads required data from the parameter file.

Parameters

p_oDoc Parsed DOM tree of parameter file.

Exceptions

modelErr

if:

any of the parameters are missing
the size classes overlap
any value for "a" is zero (this will cause a math error if true)
any value for "a" is negative, if "b" is not a whole number (this will cause a math error if true)

Because of the need for backward compatibility with version 1.0, this will accept the size class definitions as single values if they are written this way.

◆ ValidateTypes()

void clWeibullSnagMort::ValidateTypes ( )

protected

Makes sure that this behavior has only been applied to snags.

Exceptions

modelErr if any tree type besides snags has been applied to this behavior.

Member Data Documentation

◆ m_iMaxPrecalcAge

short int clWeibullSnagMort::m_iMaxPrecalcAge

protected

Max age, in timesteps, that the probability of death is pre-calculated.

◆ m_iNumSizeClasses

short int clWeibullSnagMort::m_iNumSizeClasses

protected

Number of snag size classes for which separate parameters can be defined.

◆ m_iNumYearsPerTimestep

int clWeibullSnagMort::m_iNumYearsPerTimestep

protected

Number of years per timestep.

◆ mp_fAParameter

double** clWeibullSnagMort::mp_fAParameter

protected

Parameter "a" in Weibull function.

Array size is m_iNumSizeClasses by number of behavior species.

◆ mp_fBParameter

double** clWeibullSnagMort::mp_fBParameter

protected

Parameter "b" in Weibull function.

Array size is m_iNumSizeClasses by number of behavior species.

◆ mp_fProbabilityOfDeath

float*** clWeibullSnagMort::mp_fProbabilityOfDeath

protected

Pre-calculated probabilities of death.

Array is m_iNumSizeClasses by number of behavior species by m_iMaxPrecalcAge.

◆ mp_fSnagSizeClasses

double** clWeibullSnagMort::mp_fSnagSizeClasses

protected

Upper limit of DBH in each snag size class.

This array is sized m_iNumSizeClasses by number of behavior species. The value in the third size class bucket for each species is ignored since it is always effectively infinity.

◆ mp_iAgeCodes

short int* clWeibullSnagMort::mp_iAgeCodes

protected

Data member codes for "age" snag member for each behavior species.

◆ mp_iIndexes

short int* clWeibullSnagMort::mp_iIndexes

protected

For accessing arrays.

One per species.

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

WeibullSnagMort.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clWeibullSnagMort()

◆ ~clWeibullSnagMort()

Member Function Documentation

◆ CalculateDeathProbability()

◆ DoMort()

◆ DoShellSetup()

◆ FillDeathProbArray()

◆ GetAgeCodes()

◆ ReadParameterFile()

◆ ValidateTypes()

Member Data Documentation

◆ m_iMaxPrecalcAge

◆ m_iNumSizeClasses

◆ m_iNumYearsPerTimestep

◆ mp_fAParameter

◆ mp_fBParameter

◆ mp_fProbabilityOfDeath

◆ mp_fSnagSizeClasses

◆ mp_iAgeCodes

◆ mp_iIndexes