Stochastic double logistic temperature dependent neighborhood disperse - Version 1.0. More...

#include <StochDoubleLogTempDepNeighDisperse.h>

Inheritance diagram for clStochDoubleLogTempDepNeighDisperse:

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

	~clStochDoubleLogTempDepNeighDisperse ()
	Destructor. 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 void	SetNameData (std::string sNameString)
	Sets the string for the parameter file 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 parameter file values. More...

void	AddSeeds ()
	Does dispersal. 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_fPA
	Colonization a - sized number of species. More...

double *	mp_fPB
	Colonization b - sized number of species. More...

double *	mp_fPM
	Colonization m - sized number of species. More...

double *	mp_fAl
	Temperature dependence of fecundity al - sized number of species. More...

double *	mp_fBl
	Temperature dependence of fecundity bl - sized number of species. More...

double *	mp_fCl
	Temperature dependence of fecundity cl - sized number of species. More...

double *	mp_fAh
	Temperature dependence of fecundity ah - sized number of species. More...

double *	mp_fBh
	Temperature dependence of fecundity bh - sized number of species. More...

double *	mp_fCh
	Temperature dependence of fecundity ch - sized number of species. More...

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

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

double	m_fRadius
	Neighborhood search radius. More...

float	m_fMinSaplingHeight
	Minimum sapling height. More...

double	m_fAnalysisPlotSize
	Original analysis plot size, square meters. More...

double	m_fAnnualizePeriod
	T, in years, to go from cumulative to annualized probability. More...

bool	m_bDeterministic
	If true, seed number is deterministic. More...

bool	m_bFecTempDep
	If true, use temperature-dependent portion of fecundity. 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

Stochastic double logistic temperature dependent neighborhood disperse - Version 1.0.

This class disperses seeds. The number of seeds is a function of the plot annual mean temperature and the basal area of conspecific adults.

If seeds are dispersed for a cell, the number of seeds per GRID CELL per year is calculated as:

Seeds = (a + fec * BAC) * corr

where

a is a parameter
BAC is the basal area of conspecific adults within a specified radius, in square meters
corr is the area of a cell divided by the analysis plot area, entered as a parameter

The "fec" term is fecundity, calculated as:

fec = fb* (al + ((1-al)/(1+(bl/X)^cl))) * (ah + ((1-ah)/(1+(X/bh)^ch)))

where X is the plot annual mean temperature IN K and fb, al, bl, cl, ah, bh, and ch are parameters. The user has the option to turn off the temperature- dependent portion of fecundity, in which case fec = fb.

The number of seeds per cell can be used as-is or used as the mean in a Poisson draw. This value is multiplied by number of years per timestep to arrive at the number of seeds per grid cell.

Colonization: The above equation for seeds includes an intercept term, which means there is the possibility for bath rain of species for which there are no adults. A species for which there are adults will always disperse. A species for which there are no adults must undergo a "colonization test". The cumulative probability of colonization (PCa) of seedlings is:

PCc = pa*(exp(-0.5*(((temp.C - pm)/pb)^2))))

where temp.C is the plot annual mean temperature in C and pac, pbc, and pmc are parameters.

This is annualized with a time period parameter t:

PCa = 1 � [(1 � PCc)^(1/t)]

If a random draw is less than or equal to PCa, then seed input is done as if there were adults present in the plot, on a quadrat by quadrat basis.

This behavior is not connected to any specific species-type combo, but is connected to specific species. There should be applyTo tags for this behavior and a unique list of species will be compiled for those tags with the type being ignored.

This behavior's namestring and parameter file call string are both "StochDoubleLogTempDepNeighDisperse".

Author: Lora E. Murphy

Edit history:
--------------—
February 20, 2014 - Created (LEM)

Constructor & Destructor Documentation

◆ clStochDoubleLogTempDepNeighDisperse()

clStochDoubleLogTempDepNeighDisperse::clStochDoubleLogTempDepNeighDisperse ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clStochDoubleLogTempDepNeighDisperse()

clStochDoubleLogTempDepNeighDisperse::~clStochDoubleLogTempDepNeighDisperse ( )

Destructor.

Member Function Documentation

◆ AddSeeds()

void clStochDoubleLogTempDepNeighDisperse::AddSeeds ( )

protectedvirtual

Does dispersal.

Implements clDisperseBase.

◆ DoShellSetup()

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

protectedvirtual

Reads in parameter file values.

Parameters

p_oDoc DOM tree of parsed parameter file.

Implements clDisperseBase.

Member Data Documentation

◆ m_bDeterministic

bool clStochDoubleLogTempDepNeighDisperse::m_bDeterministic

protected

If true, seed number is deterministic.

If false, Poisson-distributed.

◆ m_bFecTempDep

bool clStochDoubleLogTempDepNeighDisperse::m_bFecTempDep

protected

If true, use temperature-dependent portion of fecundity.

◆ m_fAnalysisPlotSize

double clStochDoubleLogTempDepNeighDisperse::m_fAnalysisPlotSize

protected

Original analysis plot size, square meters.

◆ m_fAnnualizePeriod

double clStochDoubleLogTempDepNeighDisperse::m_fAnnualizePeriod

protected

T, in years, to go from cumulative to annualized probability.

◆ m_fMinSaplingHeight

float clStochDoubleLogTempDepNeighDisperse::m_fMinSaplingHeight

protected

Minimum sapling height.

For doing neighbor searches.

◆ m_fRadius

double clStochDoubleLogTempDepNeighDisperse::m_fRadius

protected

Neighborhood search radius.

◆ mp_fA

double* clStochDoubleLogTempDepNeighDisperse::mp_fA

protected

A parameter - sized number of species.

◆ mp_fAh

double* clStochDoubleLogTempDepNeighDisperse::mp_fAh

protected

Temperature dependence of fecundity ah - sized number of species.

◆ mp_fAl

double* clStochDoubleLogTempDepNeighDisperse::mp_fAl

protected

Temperature dependence of fecundity al - sized number of species.

◆ mp_fB

double* clStochDoubleLogTempDepNeighDisperse::mp_fB

protected

B parameter - sized number of species.

◆ mp_fBh

double* clStochDoubleLogTempDepNeighDisperse::mp_fBh

protected

Temperature dependence of fecundity bh - sized number of species.

◆ mp_fBl

double* clStochDoubleLogTempDepNeighDisperse::mp_fBl

protected

Temperature dependence of fecundity bl - sized number of species.

◆ mp_fCh

double* clStochDoubleLogTempDepNeighDisperse::mp_fCh

protected

Temperature dependence of fecundity ch - sized number of species.

◆ mp_fCl

double* clStochDoubleLogTempDepNeighDisperse::mp_fCl

protected

Temperature dependence of fecundity cl - sized number of species.

◆ mp_fPA

double* clStochDoubleLogTempDepNeighDisperse::mp_fPA

protected

Colonization a - sized number of species.

◆ mp_fPB

double* clStochDoubleLogTempDepNeighDisperse::mp_fPB

protected

Colonization b - sized number of species.

◆ mp_fPM

double* clStochDoubleLogTempDepNeighDisperse::mp_fPM

protected

Colonization m - sized number of species.

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

StochDoubleLogTempDepNeighDisperse.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clStochDoubleLogTempDepNeighDisperse()

◆ ~clStochDoubleLogTempDepNeighDisperse()

Member Function Documentation

◆ AddSeeds()

◆ DoShellSetup()

Member Data Documentation

◆ m_bDeterministic

◆ m_bFecTempDep

◆ m_fAnalysisPlotSize

◆ m_fAnnualizePeriod

◆ m_fMinSaplingHeight

◆ m_fRadius

◆ mp_fA

◆ mp_fAh

◆ mp_fAl

◆ mp_fB

◆ mp_fBh

◆ mp_fBl

◆ mp_fCh

◆ mp_fCl

◆ mp_fPA

◆ mp_fPB

◆ mp_fPM