Spatial dispersal - Version 1.0. More...

#include <SpatialDisperse.h>

Inheritance diagram for clSpatialDispersal:

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

	~clSpatialDispersal ()
	Destructor. More...

void	SetNameData (std::string sNameString)
	Captures the behavior name passed from the parameter file. More...

Public Member Functions inherited from clDisperseBase
	clDisperseBase (clSimManager *p_oSimManager)
	Constructor. More...

virtual	~clDisperseBase ()
	Destroys common objects. More...

void	Action ()
	Performs all disperse calculations. More...

void	TimestepCleanup ()
	Resets all values in the seed grid to 0 and sets the static m_bUpdatedGapStatus to false if this is a hooked 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	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	EndOfRunCleanup ()
	Performs any necessary cleanup operations at the end of a run. More...

Protected Member Functions
void	DoShellSetup (xercesc::DOMDocument *p_oDoc)
	Reads in values from the parameter file. More...

float	CalculateFunctionValue (float fDistance, int iSpecies, function iFunction, cover iCover)
	Calculates the function value at a particular point. More...

void	DeclareArrays ()
	Declares the arrays. More...

void	SpatialDisperse (clTree p_oTree, clTreePopulation p_oPop, clPlot *p_oPlot, float fDbh)
	Performs dispersal of seeds for one tree according to gap disperse. More...

void	NonSpatialDisperse (clTree p_oTree, clTreePopulation p_oPop, clPlot *p_oPlot, float fDbh)
	Performs dispersal of seeds for one tree according to non-gap disperse. More...

void	GetParameterFileData (xercesc::DOMDocument *p_oDoc)
	Extracts needed parameter file data. More...

void	CalcFecAndFunctions ()
	Calculates fecundity and the probability distribution functions. More...

void	PopulateUsedTable (clTreePopulation *p_oPop)
	Declares and populates the mp_bIsUsed array. More...

void	CalculateGapStatus (clTreePopulation *p_oPop)
	Updates the gap status of the seed grid, if this is "GapDisperse". More...

void	CalculateProbabilityDistribution (double *p_fProbArray, int iMaxDistance, int iSpecies, function iFunction, cover iCover)
	Calculates the normalized probability distribution for a function for one species. More...

void	AddSeeds ()
	Performs dispersal. More...

float	GetNumberOfSeeds (float fDbh, short int iSp, int iCover, int iFunc)
	Gets the number of seeds to disperse for a tree, corrected for the number of years per timestep. More...

Protected Member Functions inherited from clDisperseBase
void	GetData (xercesc::DOMDocument *p_oDoc)
	Triggers all disperse setup if an object is hooked. More...

void	SetUpBase ()
	Does disperse base setup. 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_fDispersalX0
	For testing. More...

double ***	mp_fThetaXb
	Theta (weibull) or Xb (lognormal) parameter. More...

double ***	mp_fStr
	STR parameter. More...

double ***	mp_fBeta
	Beta parameter. More...

double ***	mp_fFecundity
	Fecundity for 30 cm dbh tree for each species. More...

double *	mp_fStumpBeta
	Beta parameter for stumps. More...

double *	mp_fStumpStr
	STR parameter for stumps. More...

double *	mp_fStumpFecundity
	Fecundity for stumps. More...

double *	mp_fDbhForReproduction
	Array of species with each one's dbh for reproduction. More...

double ****	mp_fCumProb
	Cumulative probability array for gap and canopy cover. More...

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

int	m_iMaxDistance
	Maximum distance, in meters, a seed can disperse. More...

int	m_iMaxGapDensity
	Maximum number of reproductively mature trees allowed in a grid cell for the grid cell to retain gap status. More...

short int *	mp_iIndexes
	This will speed access to the other arrays by storing each species' array index so the other arrays only have to be as big as the number of unique species for this behavior. More...

short int	m_iNumFunctions
	How many functions there are - 2. More...

short int	m_iNumCovers
	How many cover types there are - 2. More...

function **	mp_iWhatFunction
	Which function is used - array indexes are cover by species. More...

char *	m_cQuery
	Query to perform to search for trees. More...

bool **	mp_bIsUsed
	Whether this behavior is used by a species/type combo. More...

bool	m_bIsGap
	True if this is gap disperse; false if not. More...

bool	m_bStumps
	True if this behavior applies to stumps. More...

Protected Attributes inherited from clDisperseBase
bool	m_bHooked

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
Protected Types inherited from clDisperseBase
enum	function { weibull, lognormal }
	What PDF is used by a species. More...

enum	cover { gap, canopy }
	Cover status. More...

Static Protected Attributes inherited from clDisperseBase
static clDisperseOrg *	mp_oDisperseOrg
	clDisperseOrg object - this pointer is held in common by all shells More...

static clGrid *	mp_oSeedGrid
	Seed grid. More...

static short int *	mp_iNumSeedsCode
	Data member codes for "dispersed seeds" grid for "seeds_x" data member. More...

static short int	m_iGapCountCode
	Data member code - for counting trees for gap status. More...

static short int	m_iIsGapCode
	Data member code for substrate grid for gap status. More...

static short int	m_iTotalSpecies
	Total number of species. More...

static bool	m_bUpdatedGapStatus
	A flag indicating whether or not the gap status of the seed grid has been updated this timestep. More...

static bool	m_bIsStochastic
	Whether dispersal is stochastic (true) or deterministic (false). More...

Detailed Description

Spatial dispersal - Version 1.0.

This class creates and disperses seeds according to the spatially-explicit model. Parent trees of greater than the minimum reproductive DBH have the number of seeds calculated. The seeds are dispersed around the plot according to either the Weibull or Lognormal probability distribution functions.

Forest cover can be taken into account during seed distribution (gap) or ignored (non-gap).

This behavior can also be used for suckering of stumps. If this is desired, apply this to the species which sucker, tree type stump. If this is gap disperse, stumps reproduce pretending they're always in gap conditions. They use the probability distribution function of their species' gap function. If this is non-gap disperse, they reproduce like other adults of their species.

The "seeds" are actually tallies by species in a grid. This behavior does not produce any seedlings. A separate recruitment behavior must "germinate" the seeds into seedlings according to its own rules.

To call this as gap disperse in the parameter file, use the string "GapDisperse". To call this as non-gap disperse, use the string "NonGapDisperse". There is a place in the parameters for indicating which probability distribution function should be used under each cover type. The namestring for this class is "SpatialDisperse".

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clSpatialDispersal()

clSpatialDispersal::clSpatialDispersal ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clSpatialDispersal()

clSpatialDispersal::~clSpatialDispersal ( )

Destructor.

Member Function Documentation

◆ AddSeeds()

void clSpatialDispersal::AddSeeds ( )

protectedvirtual

Performs dispersal.

This searches for all types to which it is applied. For trees which are of the appropriate species/type combo, either SpatialDisperse() or NonSpatialDisperse() is called.

Implements clDisperseBase.

◆ CalcFecAndFunctions()

void clSpatialDispersal::CalcFecAndFunctions ( )

protected

Calculates fecundity and the probability distribution functions.

Fecundity is calculated as

fec = STR/30^beta

◆ CalculateFunctionValue()

float clSpatialDispersal::CalculateFunctionValue	(	float	fDistance,
		int	iSpecies,
		function	iFunction,
		cover	iCover
	)

protected

Calculates the function value at a particular point.

Parameters

fDistance	Distance at which to calculate function value.
iSpecies	Species for which to calculate function value.
iFunction	Which function to calculate (weibull or lognormal).
iCover	Cover for which to calculate function value.

Returns: Value of function.

◆ CalculateGapStatus()

void clSpatialDispersal::CalculateGapStatus ( clTreePopulation * p_oPop )

protected

Updates the gap status of the seed grid, if this is "GapDisperse".

It counts all parent trees present in each grid cell (those that have a DBH of at least the minimum reproductive age for their species). The counts are placed in each grid cell and when the count is higher than the cutoff for gap status, the grid is under canopy; otherwise, it is under gap.

This counts all species, not just the ones to which this behavior applies. However, for those species that do not use this behavior, their minimum adult DBH will be used as the cutoff for counting, even if they have a minimum reproductive DBH listed. That's because I haven't bothered with the logistics of figuring out if a species uses another disperse behavior.

Parameters

p_oPop Tree population object.

◆ CalculateProbabilityDistribution()

void clSpatialDispersal::CalculateProbabilityDistribution	(	double *	p_fProbArray,
		int	iMaxDistance,
		int	iSpecies,
		function	iFunction,
		cover	iCover
	)

protected

Calculates the normalized probability distribution for a function for one species.

Parameters

p_fProbArray	The array into which to put the normalized values.
iMaxDistance	The maximum distance out to which to calculate the function - which must equal the size of p_fProbArray.
iSpecies	Species for which we're calculating.
iFunction	Function flag.
iCover	Cover flag.

◆ DeclareArrays()

void clSpatialDispersal::DeclareArrays ( )

protected

Declares the arrays.

◆ DoShellSetup()

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

protectedvirtual

Reads in values from the parameter file.

Parameters

p_oDoc DOM tree of parsed input file.

Implements clDisperseBase.

◆ GetNumberOfSeeds()

float clSpatialDispersal::GetNumberOfSeeds	(	float	fDbh,
		short int	iSp,
		int	iCover,
		int	iFunc
	)

protected

Gets the number of seeds to disperse for a tree, corrected for the number of years per timestep.

The equation is seeds = fecundity * DBH^β, where all parameters are appropriate for forest cover if this is gap disperse.

Parameters

fDbh	DBH of the tree, in cm
iSp	Tree species number
iCover	Forest cover
iFunc	Disperse function used

Returns: Number of seeds.

◆ GetParameterFileData()

void clSpatialDispersal::GetParameterFileData ( xercesc::DOMDocument * p_oDoc )

protected

Extracts needed parameter file data.

This function takes into account whether or not this is gap.

The minimum reproductive DBH array is pre-loaded with the minimum adult DBH values, so if there is a species that is not used by this behavior, CalculateGapStatus() still has something to use.

Parameters

p_oDoc Parsed parameter file document.

Exceptions

stcErr

if:

A weibull theta value is not less than 50 (to prevent pow overflows)
The function codes are not valid enums
A beta value is greater than 25 (to prevent pow overflows)

◆ NonSpatialDisperse()

void clSpatialDispersal::NonSpatialDisperse	(	clTree *	p_oTree,
		clTreePopulation *	p_oPop,
		clPlot *	p_oPlot,
		float	fDbh
	)

protected

Performs dispersal of seeds for one tree according to non-gap disperse.

The number of seeds is calculated. Each seed is given a random azimuth direction from the parent. Then each seed is given a random distance from the parent that conforms to the chosen probability distribution function. This is done by comparing a random value to successive values in the cumulative probability array until the first array bucket that has a greater value than the random number. Once the seed has an azimuth direction and a distance, it is added to the species total in the appropriate grid cell.

Parameters

p_oTree	Tree for which to perform dispersal.
fDbh	DBH of the tree, in cm.
p_oPlot	Plot object
p_oPop	Tree Population object

◆ PopulateUsedTable()

void clSpatialDispersal::PopulateUsedTable ( clTreePopulation * p_oPop )

protected

Declares and populates the mp_bIsUsed array.

Parameters

p_oPop Tree Population object

◆ SetNameData()

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

virtual

Captures the behavior name passed from the parameter file.

This is useful since this class can produce a few different kinds of behaviors.

Parameters

sNameString Behavior name from parameter file.

Reimplemented from clBehaviorBase.

◆ SpatialDisperse()

void clSpatialDispersal::SpatialDisperse	(	clTree *	p_oTree,
		clTreePopulation *	p_oPop,
		clPlot *	p_oPlot,
		float	fDbh
	)

protected

Performs dispersal of seeds for one tree according to gap disperse.

The number of seeds for a tree is calculated with the higher of gap or canopy STR.

Each seed is given a random azimuth angle. It is then given a random distance that conforms to the probability distribution function of the current forest cover of the parent. (This distance is gotten by comparing a random value to successive values in the appropriate cumulative probability array until the first array bucket that has a greater value than the random number.) Once the seed has an azimuth and a distance, the function determines which grid cell it should drop in.

Once the seed has a target grid cell, that cell's cover is checked. Then the seed's survival is evaluated. If the seed is in the cover type with the higher STR, it automatically survives. Otherwise, a random number is compared to the ratio of the lower STR to the higher STR to determine if it survives.

If the seed survives, it may need to be repositioned. If both parent and seed are under closed canopy, the seed is dropped where it is. If the parent is in gap and seedling is in canopy, a new distance is calculated as though the parent was also in canopy. The shortest of the two distances is used to determine where the seed lands. If the seed lands in a gap cell, the function "walks out" the line of the seed's path from parent to target landing cell, checking each intermediate grid cell's cover along the way. If any of the grid cells in the line are under canopy cover, the seed drops in the first canopy cell it reaches.

Parameters

p_oTree	Tree for which to perform dispersal.
fDbh	DBH of the tree, in cm.
p_oPlot	Plot object
p_oPop	Tree Population object

Member Data Documentation

◆ m_bIsGap

bool clSpatialDispersal::m_bIsGap

protected

True if this is gap disperse; false if not.

◆ m_bStumps

bool clSpatialDispersal::m_bStumps

protected

True if this behavior applies to stumps.

◆ m_cQuery

char* clSpatialDispersal::m_cQuery

protected

Query to perform to search for trees.

◆ m_iMaxDistance

int clSpatialDispersal::m_iMaxDistance

protected

Maximum distance, in meters, a seed can disperse.

◆ m_iMaxGapDensity

int clSpatialDispersal::m_iMaxGapDensity

protected

Maximum number of reproductively mature trees allowed in a grid cell for the grid cell to retain gap status.

◆ m_iNumCovers

short int clSpatialDispersal::m_iNumCovers

protected

How many cover types there are - 2.

◆ m_iNumFunctions

short int clSpatialDispersal::m_iNumFunctions

protected

How many functions there are - 2.

◆ m_iNumYearsPerTimestep

int clSpatialDispersal::m_iNumYearsPerTimestep

protected

Number of years per timestep.

◆ mp_bIsUsed

bool** clSpatialDispersal::mp_bIsUsed

protected

Whether this behavior is used by a species/type combo.

First array index is species, second is type.

◆ mp_fBeta

double*** clSpatialDispersal::mp_fBeta

protected

Beta parameter.

The array is 3D - first index is which disperse function is used. The second index is cover. The third index is species. This value comes from the parameter file.

◆ mp_fCumProb

double**** clSpatialDispersal::mp_fCumProb

protected

Cumulative probability array for gap and canopy cover.

Array size is

functions by # covers by # species by max distance.

◆ mp_fDbhForReproduction

double* clSpatialDispersal::mp_fDbhForReproduction

protected

Array of species with each one's dbh for reproduction.

◆ mp_fDispersalX0

double*** clSpatialDispersal::mp_fDispersalX0

protected

For testing.

Dispersal (weibull) or X0 (lognormal) parameter. The array is 3D - first index is which disperse function is used. The second index is cover. The third index is species. This value comes from the parameter file.

◆ mp_fFecundity

double*** clSpatialDispersal::mp_fFecundity

protected

Fecundity for 30 cm dbh tree for each species.

The array is 3D - first index is which disperse function is used. The second index is cover. The third index is species.

◆ mp_fStr

double*** clSpatialDispersal::mp_fStr

protected

STR parameter.

The array is 3D - first index is which disperse function is used. The second index is cover. The third index is species. This value comes from the parameter file.

◆ mp_fStumpBeta

double* clSpatialDispersal::mp_fStumpBeta

protected

Beta parameter for stumps.

This matches the beta parameter for live trees for this species.

◆ mp_fStumpFecundity

double* clSpatialDispersal::mp_fStumpFecundity

protected

Fecundity for stumps.

◆ mp_fStumpStr

double* clSpatialDispersal::mp_fStumpStr

protected

STR parameter for stumps.

This matches the STR parameter for live trees for this species.

◆ mp_fThetaXb

double*** clSpatialDispersal::mp_fThetaXb

protected

Theta (weibull) or Xb (lognormal) parameter.

If this is theta, this value must be less than 50 to protect against pow overflows. The array is 3D - first index is which disperse function is used. The second index is cover. The third index is species. This value comes from the parameter file.

◆ mp_iIndexes

short int* clSpatialDispersal::mp_iIndexes

protected

This will speed access to the other arrays by storing each species' array index so the other arrays only have to be as big as the number of unique species for this behavior.

◆ mp_iWhatFunction

function** clSpatialDispersal::mp_iWhatFunction

protected

Which function is used - array indexes are cover by species.

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

SpatialDisperse.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clSpatialDispersal()

◆ ~clSpatialDispersal()

Member Function Documentation

◆ AddSeeds()

◆ CalcFecAndFunctions()

◆ CalculateFunctionValue()

◆ CalculateGapStatus()

◆ CalculateProbabilityDistribution()

◆ DeclareArrays()

◆ DoShellSetup()

◆ GetNumberOfSeeds()

◆ GetParameterFileData()

◆ NonSpatialDisperse()

◆ PopulateUsedTable()

◆ SetNameData()

◆ SpatialDisperse()

Member Data Documentation

◆ m_bIsGap

◆ m_bStumps

◆ m_cQuery

◆ m_iMaxDistance

◆ m_iMaxGapDensity

◆ m_iNumCovers

◆ m_iNumFunctions

◆ m_iNumYearsPerTimestep

◆ mp_bIsUsed

◆ mp_fBeta

◆ mp_fCumProb

functions by # covers by # species by max distance.

◆ mp_fDbhForReproduction

◆ mp_fDispersalX0

◆ mp_fFecundity

◆ mp_fStr

◆ mp_fStumpBeta

◆ mp_fStumpFecundity

◆ mp_fStumpStr

◆ mp_fThetaXb

◆ mp_iIndexes

◆ mp_iWhatFunction