Climate and competition dependent neighborhood survival - Version 1.0. More...

#include <ClimateCompDepNeighborhoodSurvival.h>

Inheritance diagram for clClimateCompDepNeighborhoodSurvival:

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

	~clClimateCompDepNeighborhoodSurvival ()
	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)
	Does beginning of the time step setup. 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	ValidateData ()
	Makes sure N and D for each species does not = 0 and that the neighbor search radius >= 0. More...

void	ReadParameterFile (xercesc::DOMDocument p_oDoc, clTreePopulation p_oPop)
	Reads data from the parameter file. More...

float	GetBAT (float &fX, float &fY, clTreePopulation *p_oPop)
	Gets the total adult neighborhood basal area within the specified radius from a given point. More...

void	SetupGrid (clTreePopulation *p_oPop)
	Sets up the "Climate Comp Dep Neighborhood Survival" grid. 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_oGrid
	Grid holding survival rate for each species. More...

double *	mp_fM
	Temperature function M - sized number of species. More...

double *	mp_fN
	Temperature function N - sized number of species. More...

double *	mp_fC
	Water deficit function C - sized number of species. More...

double *	mp_fD
	Water deficit function D - sized number of species. More...

double *	mp_fA
	Crowding function A parameter - sized number of species. More...

double *	mp_fB
	Crowding function B parameter - sized number of species. More...

double *	mp_fTempFunction
	Temperature portion of the survival function - sized number of species. More...

double *	mp_fWDFunction
	Water deficit portion of the survival function - sized number of species. More...

short int *	mp_iGridSurvivalCodes
	Holds data member codes for the "survival_x" data members of the "Climate Comp Dep Neighborhood Survival" grid. More...

double	m_fRadius
	Neighborhood search radius. More...

float	m_fMinSaplingHeight
	Minimum sapling height. More...

short int	m_iBATCode
	Return code for the "BAT" grid data member. 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

Climate and competition dependent neighborhood survival - Version 1.0.

This is a mortality shell object which calculates survival as a function of climate and adult neighbor basal area.

The equation for one year's survival is:

Probability of survival = exp(-1.0*A*BAT^B)*exp(-0.5*(((X-M)/N)^2))*exp(-0.5*(((WD-C)/D)^2))

where:

A, B, M, N, C, and D are parameters
X is the plot mean annual temperature
WD is the plot water deficit
BAT is the adult neighborhood basal area within a specified radius, in square meters

Rather than calculate a survival rate for each individual tree, this calculates a survival rate for each cell in a grid called "Climate Comp Dep Neighborhood Survival". Trees then get the survival rate of the grid cell in which they are found.

Snags, seedlings, and trees that are already dead from disturbance events are never counted in the neighbor count.

For multi year time steps, the annual probability of survival is raised to the power of the number of years per time step.

The parameter file call string for this is "ClimateCompDepNeighborhoodSurvival". The namestring for this behavior is "ClimateCompDepNeighborhoodmortshell".

Author: Lora E. Murphy

Edit history:
--------------—
January 24, 2014 - Created (LEM)

Constructor & Destructor Documentation

◆ clClimateCompDepNeighborhoodSurvival()

clClimateCompDepNeighborhoodSurvival::clClimateCompDepNeighborhoodSurvival ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clClimateCompDepNeighborhoodSurvival()

clClimateCompDepNeighborhoodSurvival::~clClimateCompDepNeighborhoodSurvival ( )

Destructor.

Member Function Documentation

◆ DoMort()

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

virtual

Determines mortality for a tree.

This starts by checking the grid cell of the tree to see if survival rate has already been calculated. If so, use it. If not, calculate it for this species for this grid cell. If not already determined, get the adult neighborhood basal area for the cell and calculate the probability of survival using the equation above. Use the random number generator to decide life or death; return the result.

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 clClimateCompDepNeighborhoodSurvival::DoShellSetup ( xercesc::DOMDocument * p_oDoc )

virtual

Does setup.

ReadParameterFile() is called to read the parameter file's data.
ValidateData() is called to validate the data.
SetupGrid() is called to create the survival grid.

Parameters

p_oDoc DOM tree of parsed input tree.

Reimplemented from clMortalityBase.

◆ GetBAT()

float clClimateCompDepNeighborhoodSurvival::GetBAT	(	float &	fX,
		float &	fY,
		clTreePopulation *	p_oPop
	)

protected

Gets the total adult neighborhood basal area within the specified radius from a given point.

Neighbors must have a DBH greater than the minimum. They also cannot be dead from a disturbance event; but any trees that have a dead code of "natural" are assumed to have died in the current time step mortality cycle and thus should be counted.

Parameters

fX	X coordinate of point for which to calculate neighborhood basal area
fY	Y coordinate of point for which to calculate neighborhood basal area
p_oPop	Tree population.

Returns: Total adult basal area in square meters.

◆ PreMortCalcs()

void clClimateCompDepNeighborhoodSurvival::PreMortCalcs ( clTreePopulation * p_oPop )

virtual

Does beginning of the time step setup.

This clears all grid values and calculates the temperature portion of the survival function for each species.

Parameters

p_oPop Tree population.

Reimplemented from clMortalityBase.

◆ ReadParameterFile()

void clClimateCompDepNeighborhoodSurvival::ReadParameterFile	(	xercesc::DOMDocument *	p_oDoc,
		clTreePopulation *	p_oPop
	)

protected

Reads data from the parameter file.

Parameters

p_oDoc	DOM tree of parsed input tree.
p_oPop	Tree population.

◆ SetupGrid()

void clClimateCompDepNeighborhoodSurvival::SetupGrid ( clTreePopulation * p_oPop )

protected

Sets up the "Climate Comp Dep Neighborhood Survival" grid.

This ignores any maps.

Parameters

p_oPop Tree population object.

◆ ValidateData()

void clClimateCompDepNeighborhoodSurvival::ValidateData ( )

protected

Makes sure N and D for each species does not = 0 and that the neighbor search radius >= 0.

Exceptions

modelErr if the above conditions are not met.

Member Data Documentation

◆ m_fMinSaplingHeight

float clClimateCompDepNeighborhoodSurvival::m_fMinSaplingHeight

protected

Minimum sapling height.

For doing neighbor searches.

◆ m_fRadius

double clClimateCompDepNeighborhoodSurvival::m_fRadius

protected

Neighborhood search radius.

◆ m_iBATCode

short int clClimateCompDepNeighborhoodSurvival::m_iBATCode

protected

Return code for the "BAT" grid data member.

◆ mp_fA

double* clClimateCompDepNeighborhoodSurvival::mp_fA

protected

Crowding function A parameter - sized number of species.

◆ mp_fB

double* clClimateCompDepNeighborhoodSurvival::mp_fB

protected

Crowding function B parameter - sized number of species.

◆ mp_fC

double* clClimateCompDepNeighborhoodSurvival::mp_fC

protected

Water deficit function C - sized number of species.

◆ mp_fD

double* clClimateCompDepNeighborhoodSurvival::mp_fD

protected

Water deficit function D - sized number of species.

◆ mp_fM

double* clClimateCompDepNeighborhoodSurvival::mp_fM

protected

Temperature function M - sized number of species.

◆ mp_fN

double* clClimateCompDepNeighborhoodSurvival::mp_fN

protected

Temperature function N - sized number of species.

◆ mp_fTempFunction

double* clClimateCompDepNeighborhoodSurvival::mp_fTempFunction

protected

Temperature portion of the survival function - sized number of species.

◆ mp_fWDFunction

double* clClimateCompDepNeighborhoodSurvival::mp_fWDFunction

protected

Water deficit portion of the survival function - sized number of species.

◆ mp_iGridSurvivalCodes

short int* clClimateCompDepNeighborhoodSurvival::mp_iGridSurvivalCodes

protected

Holds data member codes for the "survival_x" data members of the "Climate Comp Dep Neighborhood Survival" grid.

Array size is total

species.

◆ mp_oGrid

clGrid* clClimateCompDepNeighborhoodSurvival::mp_oGrid

protected

Grid holding survival rate for each species.

The grid name is "Climate Comp Dep Neighborhood Survival". It has X+1 float data members, where X = the total number of species. The data member names are "survival_x", for the time step survival rate (where "x" is the species number), and "BAT" for the total adult neighborhood basal area.

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

ClimateCompDepNeighborhoodSurvival.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clClimateCompDepNeighborhoodSurvival()

◆ ~clClimateCompDepNeighborhoodSurvival()

Member Function Documentation

◆ DoMort()

◆ DoShellSetup()

◆ GetBAT()

◆ PreMortCalcs()

◆ ReadParameterFile()

◆ SetupGrid()

◆ ValidateData()

Member Data Documentation

◆ m_fMinSaplingHeight

◆ m_fRadius

◆ m_iBATCode

◆ mp_fA

◆ mp_fB

◆ mp_fC

◆ mp_fD

◆ mp_fM

◆ mp_fN

◆ mp_fTempFunction

◆ mp_fWDFunction

◆ mp_iGridSurvivalCodes

species.

◆ mp_oGrid