Neighborhood Seed Predationon - version 1.1. More...

#include <NeighborhoodSeedPredation.h>

Inheritance diagram for clNeighborhoodSeedPredation:

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

	~clNeighborhoodSeedPredation ()
	Destructor. More...

void	Action ()
	Performs neighborhood seed predation. More...

void	SetNameData (std::string sNameString)
	Captures the behavior name passed from the parameter file. 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	GetData (xercesc::DOMDocument *p_oDoc)
	Does setup. More...

void	DoStandalonePredation ()
	Performs neighborhood seed predation for the standalone version of this behavior. More...

void	DoLinkedPredation ()
	Performs neighborhood seed predation for the linked version of this behavior. More...

void	GetOfftakes (clTreePopulation p_oPop, const double p_fP0, double *p_fPn, float p_fOfftake, const int &iX, const int &iY)
	Gets the offtake (Y) values for all behavior species for a given grid cell. More...

void	SetupGrids ()
	Gets a pointer to the "Dispersed Seeds" grid, and sets up the output grid. More...

void	ReadParameterFileData (xercesc::DOMDocument *p_oDoc)
	Reads parameter file data. 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_fNonMastingP0
	Non-masting "p0" parameter. More...

double **	mp_fNonMastingPn
	Non-masting pn. More...

double *	mp_fMastingP0
	Masting "p0" parameter. More...

double *	mp_fMinNeighDBH
	Minimum neighbor DBH. More...

double **	mp_fMastingPn
	Masting pn. More...

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

short int *	mp_iStartSeedsCode
	Data member codes for the "startseeds_x" member of the output grid. More...

short int *	mp_iPropEatenCode
	Data member codes for the "propeaten_x" member of the output grid. More...

short int *	mp_iIndexes
	For accessing the other arrays. More...

bool *	mp_bCountInMast
	Whether or not a species counts when making masting decisions. More...

float	m_fPlotArea
	Area of the plot, in square meters. More...

double	m_fRadius
	Radius of neighborhoods. More...

double	m_fMastingThreshold
	Threshold of seeds per square meter for a masting timestep. More...

bool	m_bIsLinked
	Whether this is the linked (true) or standalone (false) version. More...

bool	m_bUseThresholdToDecideMast
	Whether to use a seed density threshold (true) or ask the masting disperse behaviors (false) when deciding whether this is a masting timestep. 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...

Static Protected Attributes
static clGrid *	mp_oOutputGrid
	Grid to output details of seed predation. More...

Detailed Description

Neighborhood Seed Predationon - version 1.1.

This behavior reduces the number of seeds by simulating seed predation. Rate of offtake is a function of neighborhood composition.

This can be used in two forms. In the standalone form, masting is also used to determine offtake. In the linked form, the clFuncResponseSeedPredation class determines the offtake rate, and this class figures out where seeds get eaten. In this case, masting is ignored.

In the standalone version, there are two choices for assessing masting: in the first, masting is assessed by counting the seeds to which this behavior applies and which participate in masting (two different things - the latter is controlled by a boolean parameter ) and comparing it to a density per timestep threshold. Above the threshold is masting; below is not. The second choice is to ask the masting disperse behaviors if any species has masted; if any have, then it is a masting event. (If masting disperse behaviors are not used, then masting never occurs.) The only difference between masting and non-masting timesteps is the parameters used.

For both versions, the proportion of seed removed is calculated as:

logit(Y) = p₀ + Σ p_n * RBA _n where, summing over the species from n = 1...N, p_n is the loading factor for species n, and RBA_n is the relative basal area of species n. There is a species specific minimum DBH for neighbors to include.

In the standalone version, this is used directly as the amount of seed removed. In the linked version, it is used to distribute the offtake rate from the functional response seed predation behavior. Conceptually, the local offtake rate is adjusted by a correction factor, calculated by dividing the FR offtake Z by the mean off the local offtakes, so the plot-level offtake remains the same. Mathematically it is a little more complicated:

Calculate logit(Z)
Calculate the logit(Ys) and subtract the minimum value from each (as well as the logit(Z)) so they will all be positive
Average the logit(Y)s
Divide logit(Z) by average logit(Y) to get a correction factor
Multiply each logit(Y) by the correction factor
Add back the same minimum value formerly subtracted
Backtransform logit(Y) to Y and use when removing seeds

A fatal error is thrown if a disperse behavior is not also defined for the run, and additionally if this is linked and the clFuncResponseSeedPredation class is missing.

This class's namestring is "NeighborhoodSeedPredation". If standalone, the parameter call string is "NeighborhoodSeedPredation". If linked, the parameter call string is "LinkedNeighborhoodSeedPredation".

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clNeighborhoodSeedPredation()

clNeighborhoodSeedPredation::clNeighborhoodSeedPredation ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clNeighborhoodSeedPredation()

clNeighborhoodSeedPredation::~clNeighborhoodSeedPredation ( )

Destructor.

Frees memory.

Member Function Documentation

◆ Action()

void clNeighborhoodSeedPredation::Action ( )

virtual

Performs neighborhood seed predation.

If the behavior is in linked mode, this calls DoLinkedPredation. If not, this calls DoStandalonePredation. Before the appropriate predation function is called, this copies the values from the "Dispersed Seeds" grid to the "startseeds_x" data members of the output grid; after the function is called, this calculates and posts the values of the "propeaten_x" data members.

Reimplemented from clBehaviorBase.

◆ DoLinkedPredation()

void clNeighborhoodSeedPredation::DoLinkedPredation ( )

protected

Performs neighborhood seed predation for the linked version of this behavior.

This calculates all offtakes, then adjusts them according to the offtake calculated by clFuncResponseSeedPredation. A random round is used to take care of fractional parts of seeds.

◆ DoStandalonePredation()

void clNeighborhoodSeedPredation::DoStandalonePredation ( )

protected

Performs neighborhood seed predation for the standalone version of this behavior.

First, for the whole plot, this assesses whether masting has occurred by comparing the density of seeds of species to which this behavior applies to the threshold. Then for each cell, the neighborhood relative BAs and the proportion to remove is calculated. A random round is used to take care of fractional parts of seeds. This also checks plot adult tree density; if it is zero, it is automatically not a masting time step.

◆ GetData()

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

protectedvirtual

Does setup.

This reads in values from the parameter file, gets the pointer to the dispersed seeds grid, and sets up the output grid.

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr if this is linked and there is no functional response seed predation.

Implements clWorkerBase.

◆ GetOfftakes()

void clNeighborhoodSeedPredation::GetOfftakes	(	clTreePopulation *	p_oPop,
		const double *	p_fP0,
		double **	p_fPn,
		float *	p_fOfftake,
		const int &	iX,
		const int &	iY
	)

protected

Gets the offtake (Y) values for all behavior species for a given grid cell.

Parameters

p_oPop	Tree population object.
p_fP0	p0 values to use, as an array sized m_iNumBehaviorSpecies.
p_fPn	pn values to use, as an array sized m_iNumBehaviorSpecies by the total number of species.
p_fOfftake	Place to put offtake values, as an array sized m_iNumBehaviorSpecies.
iX	Seed grid X cell number.
iY	Seed grid Y cell number.

Returns: Array of offtakes sized m_iNumBehaviorSpecies.

◆ ReadParameterFileData()

void clNeighborhoodSeedPredation::ReadParameterFileData ( xercesc::DOMDocument * p_oDoc )

protected

Reads parameter file data.

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr if any of the following are negative: neighborhood radius, min neighbor DBH, masting threshold

◆ SetNameData()

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

virtual

Captures the behavior name passed from the parameter file.

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

Parameters

sNameString Behavior name from parameter file.

Reimplemented from clBehaviorBase.

◆ SetupGrids()

void clNeighborhoodSeedPredation::SetupGrids ( )

protected

Gets a pointer to the "Dispersed Seeds" grid, and sets up the output grid.

Exceptions

modelErr if the seed grid is not found

Member Data Documentation

◆ m_bIsLinked

bool clNeighborhoodSeedPredation::m_bIsLinked

protected

Whether this is the linked (true) or standalone (false) version.

◆ m_bUseThresholdToDecideMast

bool clNeighborhoodSeedPredation::m_bUseThresholdToDecideMast

protected

Whether to use a seed density threshold (true) or ask the masting disperse behaviors (false) when deciding whether this is a masting timestep.

◆ m_fMastingThreshold

double clNeighborhoodSeedPredation::m_fMastingThreshold

protected

Threshold of seeds per square meter for a masting timestep.

This comes as an annual amount in the parameter file and is converted to a timestep amount. Only necessary if m_bUseThresholdToDecideMast is true.

◆ m_fPlotArea

float clNeighborhoodSeedPredation::m_fPlotArea

protected

Area of the plot, in square meters.

◆ m_fRadius

double clNeighborhoodSeedPredation::m_fRadius

protected

Radius of neighborhoods.

◆ mp_bCountInMast

bool* clNeighborhoodSeedPredation::mp_bCountInMast

protected

Whether or not a species counts when making masting decisions.

Only necessary if m_bUseThresholdToDecideMast is true.

◆ mp_fMastingP0

double* clNeighborhoodSeedPredation::mp_fMastingP0

protected

Masting "p0" parameter.

Array size is number of species to which this behavior applies.

◆ mp_fMastingPn

double** clNeighborhoodSeedPredation::mp_fMastingPn

protected

Masting pn.

Array size is number of behavior species by number of total species.

◆ mp_fMinNeighDBH

double* clNeighborhoodSeedPredation::mp_fMinNeighDBH

protected

Minimum neighbor DBH.

◆ mp_fNonMastingP0

double* clNeighborhoodSeedPredation::mp_fNonMastingP0

protected

Non-masting "p0" parameter.

Array size is number of species to which this behavior applies.

◆ mp_fNonMastingPn

double** clNeighborhoodSeedPredation::mp_fNonMastingPn

protected

Non-masting pn.

Array size is number of behavior species by number of total species.

◆ mp_iIndexes

short int* clNeighborhoodSeedPredation::mp_iIndexes

protected

For accessing the other arrays.

◆ mp_iPropEatenCode

short int* clNeighborhoodSeedPredation::mp_iPropEatenCode

protected

Data member codes for the "propeaten_x" member of the output grid.

Array size is total number of species.

◆ mp_iSeedGridCode

short int* clNeighborhoodSeedPredation::mp_iSeedGridCode

protected

Data member codes for seed grid for number of seeds.

Array size is number of species to which this behavior applies.

◆ mp_iStartSeedsCode

short int* clNeighborhoodSeedPredation::mp_iStartSeedsCode

protected

Data member codes for the "startseeds_x" member of the output grid.

Array size is total number of species.

◆ mp_oOutputGrid

clGrid* clNeighborhoodSeedPredation::mp_oOutputGrid

staticprotected

Grid to output details of seed predation.

The name of this grid Seed Predation Predation". Its cell size matches that of the "Dispersed Seeds" grid. For each species there are two data members: "startseeds_x" and "propeaten_x" for the pre-predation seed numbers and proportion eaten, respectively, where X is the species number. Both of the data members are float. Initial conditions maps of this grid are not respected.

◆ mp_oSeedGrid

clGrid* clNeighborhoodSeedPredation::mp_oSeedGrid

protected

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

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

NeighborhoodSeedPredation.h

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ clNeighborhoodSeedPredation()

◆ ~clNeighborhoodSeedPredation()

Member Function Documentation

◆ Action()

◆ DoLinkedPredation()

◆ DoStandalonePredation()

◆ GetData()

◆ GetOfftakes()

◆ ReadParameterFileData()

◆ SetNameData()

◆ SetupGrids()

Member Data Documentation

◆ m_bIsLinked

◆ m_bUseThresholdToDecideMast

◆ m_fMastingThreshold

◆ m_fPlotArea

◆ m_fRadius

◆ mp_bCountInMast

◆ mp_fMastingP0

◆ mp_fMastingPn

◆ mp_fMinNeighDBH

◆ mp_fNonMastingP0

◆ mp_fNonMastingPn

◆ mp_iIndexes

◆ mp_iPropEatenCode

◆ mp_iSeedGridCode

◆ mp_iStartSeedsCode

◆ mp_oOutputGrid

◆ mp_oSeedGrid