Masting non-spatial disperse - Version 1.0. More...

#include <MastingNonSpatialDisperse.h>

Inheritance diagram for clMastingNonSpatialDisperse:

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

	~clMastingNonSpatialDisperse ()
	Destructor. More...

mastEvent	GetMastEvent (int iSp)
	Get whether a given species masted this timestep. 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	ComputeBasalArea ()
	Computes the total "basal area" of all adults for each species. 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_fInvGaussMu
	Mu parameter for inverse gaussian distribution. More...

double **	mp_fInvGaussLambda
	Lambda parameter for inverse gaussian distribution. More...

double **	mp_fNormalMean
	Mean for normal distribution. More...

double **	mp_fNormalStandardDev
	Standard deviation for normal distribution. More...

double *	mp_fBinomialP
	P parameter for binomial distribution for deciding when to mast - array size = number behavior species. More...

float *	mp_fBasalArea
	"Basal area" for each species. More...

short int *	mp_iGroup
	Group affiliation of the species. More...

enum mastEvent *	mp_iEvent
	Which event is occurring in the current timestep for each species. More...

pdf **	mp_iFunction
	PDF to use for seed draw. More...

bool	m_bGroupsUsed
	Whether or not species are put into groups. 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

Masting non-spatial disperse - Version 1.0.

This class performs non-spatial dispersal with masting. The actual dispersal is non-density dependent, or bath, dispersal. This is a constant seed rain which does not depend on the presence of parent trees in the plot. The actual disperal - just dropping a constant amount of seed everywhere - is easy. Figuring out how much seed to drop is the complicated bit.

The first decision is whether or not there will be masting. This is done by using a random draw on a binomial probability distribution. Each species gets its parameters for this distribution.

Once it is known whether masting will occur, the actual number of seeds per square meter is drawn from a random distribution. Each species can use its own probability function, and can use different functions in masting and non-masting timesteps.

Once the number of seeds per square meter is known, they are evenly distributed to the seed grid cells.

As an additional refinement, species can mast together in groups. In this case, all the species in a group are treated as one entity - masting together, and using the same parameters for seed dispersal - except that at the end, once the number of seeds per square meter is known, they are divided up according to the relative basal areas of the adults in the group across the entire plot. If there are no adults of any of the species in the plot, the seeds are divided evenly.

Apart from grouping, species operate completely independently and the masting activities of one species do not affect the others in any way.

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

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clMastingNonSpatialDisperse()

clMastingNonSpatialDisperse::clMastingNonSpatialDisperse ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clMastingNonSpatialDisperse()

clMastingNonSpatialDisperse::~clMastingNonSpatialDisperse ( )

Destructor.

Member Function Documentation

◆ AddSeeds()

void clMastingNonSpatialDisperse::AddSeeds ( )

protectedvirtual

Does dispersal.

This calculates basal area as necessary for groups; checks to see if masting is occurring or not; then uses the appropriate random draw and the appropriate parameters to pick the number of seeds to add to each grid cell.

Implements clDisperseBase.

◆ ComputeBasalArea()

void clMastingNonSpatialDisperse::ComputeBasalArea ( )

protected

Computes the total "basal area" of all adults for each species.

This will allow calculation of relative basal area for each group. Basal area is not actually basal area, since we don't need to multiply by pi to get the relative values. We'll just square the radii. Totals are placed in mp_fBasalArea.

◆ DoShellSetup()

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

protectedvirtual

Reads in parameter file values.

Parameters

p_oDoc DOM tree of parsed parameter file.

Implements clDisperseBase.

◆ GetMastEvent()

mastEvent clMastingNonSpatialDisperse::GetMastEvent ( int iSp )

Get whether a given species masted this timestep.

Parameters

iSp	Species to check

Returns: mast or nonmast.

Member Data Documentation

◆ m_bGroupsUsed

bool clMastingNonSpatialDisperse::m_bGroupsUsed

protected

Whether or not species are put into groups.

◆ mp_fBasalArea

float* clMastingNonSpatialDisperse::mp_fBasalArea

protected

"Basal area" for each species.

Since all we care about is relative proportion, this will just add up the squares of the radii. Array size = number behavior species.

◆ mp_fBinomialP

double* clMastingNonSpatialDisperse::mp_fBinomialP

protected

P parameter for binomial distribution for deciding when to mast - array size = number behavior species.

◆ mp_fInvGaussLambda

double** clMastingNonSpatialDisperse::mp_fInvGaussLambda

protected

Lambda parameter for inverse gaussian distribution.

The array is 2D - the first index is masting or non-masting. The second index is number behavior species.

◆ mp_fInvGaussMu

double** clMastingNonSpatialDisperse::mp_fInvGaussMu

protected

Mu parameter for inverse gaussian distribution.

The array is 2D - the first index is masting or non-masting. The second index is number behavior species.

◆ mp_fNormalMean

double** clMastingNonSpatialDisperse::mp_fNormalMean

protected

Mean for normal distribution.

The array is 2D - the first index is masting or non-masting. The second index is species.

◆ mp_fNormalStandardDev

double** clMastingNonSpatialDisperse::mp_fNormalStandardDev

protected

Standard deviation for normal distribution.

The array is 2D - the first index is masting or non-masting. The second index is species.

◆ mp_iEvent

enum mastEvent* clMastingNonSpatialDisperse::mp_iEvent

protected

Which event is occurring in the current timestep for each species.

◆ mp_iFunction

pdf** clMastingNonSpatialDisperse::mp_iFunction

protected

PDF to use for seed draw.

The array is 2D - the first index is masting or non-masting. The second index is number behavior species.

◆ mp_iGroup

short int* clMastingNonSpatialDisperse::mp_iGroup

protected

Group affiliation of the species.

Any species with the same group number will always mast together. Array size is number behavior species.

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

MastingNonSpatialDisperse.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clMastingNonSpatialDisperse()

◆ ~clMastingNonSpatialDisperse()

Member Function Documentation

◆ AddSeeds()

◆ ComputeBasalArea()

◆ DoShellSetup()

◆ GetMastEvent()

Member Data Documentation

◆ m_bGroupsUsed

◆ mp_fBasalArea

◆ mp_fBinomialP

◆ mp_fInvGaussLambda

◆ mp_fInvGaussMu

◆ mp_fNormalMean

◆ mp_fNormalStandardDev

◆ mp_iEvent

◆ mp_iFunction

◆ mp_iGroup