Density-Dependent Seed Survival - version 2.0. More...

#include <DensitySeedSurvival.h>

Inheritance diagram for clDensitySeedSurvival:

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

	~clDensitySeedSurvival ()
	Destructor. More...

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

void	SetNameData (std::string sNameString)
	Captures the namestring passed to this behavior. More...

void	Action ()
	Performs density-dependent seed survival by calling either ActionUseSeeds or ActionUseTrees. 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	RegisterTreeDataMembers ()
	Registers tree data members. More...

virtual void	SetSpeciesTypeCombos (short int iNumCombos, stcSpeciesTypeCombo *p_whatCombos)
	Sets the species/type combos for a behavior. More...

virtual short int	GetNewTreeInts ()
	Gets the number of new tree integer data members this behavior wants to register. 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	ActionUseSeeds ()
	Performs density-dependent seed survival when m_bSeeds = TRUE. More...

void	ActionUseTrees ()
	Performs density-dependent seed survival when m_bSeeds = FALSE. 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_oSeedGrid
	Pointer to the "Dispersed Seeds" grid created by disperse behaviors. More...

double *	mp_fDensDepSteepness
	Density-dependence steepness parameter. More...

double *	mp_fDensDepSlope
	Density-dependence slope parameter. More...

double *	mp_fMinHeight
	Minimum height for neighbor trees. More...

short int *	mp_iSeedGridCode
	Data member codes for seed grid for number of seeds. More...

float	m_fNormalSearchArea
	Area normally searched. More...

float	m_fXEdgeCellArea
	Area of the last row of "Dispersed Seeds" grid cells in the X direction, in square meters. More...

float	m_fYEdgeCellArea
	Area of the last row of "Dispersed Seeds" grid cells in the Y direction, in square meters. More...

float	m_fXYEdgeCellArea
	Area of the last cell of "Dispersed Seeds" grid cell in both the X and Y direction, in square meters. More...

double	m_fSearchRadius
	Radius, in meters, for which to search for conspecific trees, starting at the center of a grid cell. More...

bool	m_bSeeds
	If true, we are using the density of conspecific seeds; if false, we are using conspecific trees. 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...

Detailed Description

Density-Dependent Seed Survival - version 2.0.

This behavior reduces the number of seeds due to conspecific density-dependent effects. The "density" in question can be either other seeds, or trees in the neighborhood.

The number of seeds this behavior leaves of a given species in a particular "Dispersed Seeds" grid cell is:

R_sp = S_sp*exp(-c*Den_sp^δ)
where:

R_sp is the number of seedlings of a given species in the seed grid cell (competition is conspecific only)
S_sp is the potential number of seedlings of the species, i.e. the number of seeds dispersed to that grid cell.
Den_sp is either:
- The density of seed of the species per square meter in that grid cell; or
- The density of conspecific trees above a given height within a given radius of the cell center, stems/m2.
c is an input parameter - density-dependent slope
δ is an input parameter - density-dependent steepness

Single seeds always survive, if using seeds-only density dependence.

A fatal error is thrown if a disperse behavior is not also defined for the run.

This class's namestring is "DensityDependentSeedSurvival". In the case of conspecific seed density, the parameter file call string is also "DensityDependentSeedSurvival"; in the case of conspecific tree neighbors, it's "ConspecificTreeDensityDependentSeedSurvival".

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clDensitySeedSurvival()

clDensitySeedSurvival::clDensitySeedSurvival ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clDensitySeedSurvival()

clDensitySeedSurvival::~clDensitySeedSurvival ( )

Destructor.

Member Function Documentation

◆ Action()

void clDensitySeedSurvival::Action ( )

virtual

Performs density-dependent seed survival by calling either ActionUseSeeds or ActionUseTrees.

Reimplemented from clBehaviorBase.

◆ ActionUseSeeds()

void clDensitySeedSurvival::ActionUseSeeds ( )

protected

Performs density-dependent seed survival when m_bSeeds = TRUE.

For each grid cell in the seed grid, for each species to which this behavior applies, the number of seeds left is calculated by assessing the equation above. A random round is used to take care of fractional parts of seeds.

◆ ActionUseTrees()

void clDensitySeedSurvival::ActionUseTrees ( )

protected

Performs density-dependent seed survival when m_bSeeds = FALSE.

◆ GetData()

void clDensitySeedSurvival::GetData ( xercesc::DOMDocument * p_oDoc )

virtual

Reads in values from the parameter file.

Parameters

p_oDoc DOM tree of parsed input file.

Implements clWorkerBase.

◆ SetNameData()

void clDensitySeedSurvival::SetNameData ( std::string sNameString )

virtual

Captures the namestring passed to this behavior.

This is overridden from clBehaviorBase so we can capture the namestring passed. Since this class can create multiple kinds of behaviors that function differently, this will capture what kind of behavior this is supposed to be.

Parameters

sNameString Behavior's namestring.

Reimplemented from clBehaviorBase.

Member Data Documentation

◆ m_bSeeds

bool clDensitySeedSurvival::m_bSeeds

protected

If true, we are using the density of conspecific seeds; if false, we are using conspecific trees.

◆ m_fNormalSearchArea

float clDensitySeedSurvival::m_fNormalSearchArea

protected

Area normally searched.

If m_bSeeds = TRUE, this is the area of interior cells of the "Dispersed Seeds" grid, in square meters. If m_bSeeds = FALSE, this is the area of the circle with radius m_fSearchRadius.

◆ m_fSearchRadius

double clDensitySeedSurvival::m_fSearchRadius

protected

Radius, in meters, for which to search for conspecific trees, starting at the center of a grid cell.

Only used if m_bSeeds = FALSE.

◆ m_fXEdgeCellArea

float clDensitySeedSurvival::m_fXEdgeCellArea

protected

Area of the last row of "Dispersed Seeds" grid cells in the X direction, in square meters.

This allows for grid cells that don't divide evenly into plot lengths. Only used if m_bSeeds = TRUE.

◆ m_fXYEdgeCellArea

float clDensitySeedSurvival::m_fXYEdgeCellArea

protected

Area of the last cell of "Dispersed Seeds" grid cell in both the X and Y direction, in square meters.

This allows for grid cells that don't divide evenly into plot lengths. Only used if m_bSeeds = TRUE.

◆ m_fYEdgeCellArea

float clDensitySeedSurvival::m_fYEdgeCellArea

protected

Area of the last row of "Dispersed Seeds" grid cells in the Y direction, in square meters.

This allows for grid cells that don't divide evenly into plot lengths. Only used if m_bSeeds = TRUE.

◆ mp_fDensDepSlope

double* clDensitySeedSurvival::mp_fDensDepSlope

protected

Density-dependence slope parameter.

Array size is total number of species.

◆ mp_fDensDepSteepness

double* clDensitySeedSurvival::mp_fDensDepSteepness

protected

Density-dependence steepness parameter.

Array size is total number of species.

◆ mp_fMinHeight

double* clDensitySeedSurvival::mp_fMinHeight

protected

Minimum height for neighbor trees.

Only used if m_bSeeds = FALSE. Array size is total number of species.

◆ mp_iSeedGridCode

short int* clDensitySeedSurvival::mp_iSeedGridCode

protected

Data member codes for seed grid for number of seeds.

Array size is # total species.

◆ mp_oSeedGrid

clGrid* clDensitySeedSurvival::mp_oSeedGrid

protected

Pointer to the "Dispersed Seeds" grid created by disperse behaviors.

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

DensitySeedSurvival.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ clDensitySeedSurvival()

◆ ~clDensitySeedSurvival()

Member Function Documentation

◆ Action()

◆ ActionUseSeeds()

◆ ActionUseTrees()

◆ GetData()

◆ SetNameData()

Member Data Documentation

◆ m_bSeeds

◆ m_fNormalSearchArea

◆ m_fSearchRadius

◆ m_fXEdgeCellArea

◆ m_fXYEdgeCellArea

◆ m_fYEdgeCellArea

◆ mp_fDensDepSlope

◆ mp_fDensDepSteepness

◆ mp_fMinHeight

◆ mp_iSeedGridCode

◆ mp_oSeedGrid