Condit's Relative Neighborhood Density Index (Omega) Calculator Version 1.0. More...

#include <ConditOmegaCalculator.h>

Inheritance diagram for clConditOmegaCalculator:

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

	~clConditOmegaCalculator ()
	Destructor. More...

void	Action ()
	Calculates Condit's Omega. More...

void	GetData (xercesc::DOMDocument *p_oDoc)
	Does setup for this behavior. 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	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	GetParameterFileData (xercesc::DOMDocument *p_oDoc)
	Reads values from the parameter file and performs setup related to the parameters. More...

void	SetupGrid ()
	Sets up the "Relative Neighborhood Density" grid and registers the data members. More...

void	GetTreeCodes (clTreePopulation *p_oPop)
	Gets the X and Y tree data codes. More...

void	SetUpSearching (clTreePopulation *p_oPop)
	Sets up the structures for searching controls. More...

void	ProcessCell (clTreePopulation p_oPop, clTree p_oFirstTree, const int &iX, const int &iY, const int &iNeighX, const int &iNeighY)
	Processes a neighboring cell's trees to find distance pairs. More...

void	ProcessOwnCell (clTree p_oFirstTree, float p_fNumTrees, const int &iX, const int &iY)
	Processes a single cell's trees to find distance pairs. 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_oGrid
	Grid holding Condit's Omega values for the plot plus each species. More...

float **	mp_fOmegaValues
	Values holding Condit's Omega for each timestep. More...

short int **	mp_iGridCodes
	Holds the codes for the "Relative Neighborhood Density" grid. More...

short int **	mp_iXCodes
	Holds codes for X data member. More...

short int **	mp_iYCodes
	Holds codes for Y data member. More...

bool **	mp_bCellsSearched
	Which cells have already been paired the current timestep. More...

float *	mp_fIncs
	Distance increment values - array size is m_iNumIncs. More...

float *	mp_fAnnulusAreas
	Area of each annulus - array size is m_iNumIncs. More...

double	m_fMaxDistance
	The max distance to which to calculate Condit's Omega. More...

double	m_fIncrement
	The distance increment used to step out to the max distance. More...

int	m_iNumIncs
	Number of increments for which to calculate Condit's Omega. More...

int	m_iNumXToSearch
	The number of cells to search in the X direction - if the plot is a rectangle and the search distance is long the distances along the two axes may be different. More...

int	m_iNumYToSearch
	The number of cells to search in the Y direction - if the plot is a rectangle and the search distance is long the distances along the two axes may be different. More...

int	m_iNumXCells
	Number of tree population grid cells in X direction. More...

int	m_iNumYCells
	Number of tree population grid cells in Y direction. More...

short int	m_iNumTotalSpecies
	Total number of species. 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...

Friends
class	clTestConditOmegaCalculator

Detailed Description

Condit's Relative Neighborhood Density Index (Omega) Calculator Version 1.0.

This behavior calculates Condit's relative neighborhood density index (omega). This index measures the aggregation of species. It is calculated for successive distances out to a maximum. The user sets the maximum distance and the increment. Omega for a species for a given distance x + Δx is calculated as:

Ω = (ΣN_x / (T * A_x))/den

where A_x is the area of the annulus described by the radii x and Δx , in square meters, N_x is the number of conspecific neighbors of trees between x and Δx , T is the total number of trees of that species in the plot, and den is the species density in the plot.

In other words, Ω is the average density of conspecific neighbors at a specific distance divided by the plot's density of that species. Saplings and adults are counted as neighbors. All other types are ignored.

Conceptually, the way to carry out this search is to take each tree, find the density of its conspecific neighbors between each pair of radii x and Δx , average those values by species, and divide by the plot density for each species. In practice I can use a quicker method. The search proceeds by tree population grid cell. For each cell, a square of cells around it is searched. A matrix is used to keep track of which cells have already been paired so they are not paired again. Each pair of conspecifics is counted into the appropriate distance bucket (twice, once for when each tree is acting as a neighbor to the other's target). Then these buckets are used to calculate Ω according to the formula above.

The statistic is calculated for all individual species.

The values are collected into a grid called "Relative Neighborhood Density".

This class's namestring and parameter file call string is "ConditsOmega". Any tree type/species assignments are ignored.

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

Constructor & Destructor Documentation

◆ clConditOmegaCalculator()

clConditOmegaCalculator::clConditOmegaCalculator ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager clSimManager object.

◆ ~clConditOmegaCalculator()

clConditOmegaCalculator::~clConditOmegaCalculator ( )

Destructor.

Member Function Documentation

◆ Action()

void clConditOmegaCalculator::Action ( )

virtual

Calculates Condit's Omega.

First, the values in the "Relative Neighborhood Density" grid are cleared. Then this moves through the grid cells looking for tree pairs. For each cell this searches cells in a circle, using ProcessCell() and ProcessOwnCell() to find pairs. Once tree pairs have been found, this finishes the Condit's Omega calculation.

Reimplemented from clBehaviorBase.

◆ GetData()

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

virtual

Does setup for this behavior.

Calls:

GetParameterFileData()
GetTreeCodes()
SetupGrid()
SetUpSearching()
Action() so that the initial conditions value will be added

Parameters

p_oDoc DOM tree of parsed input file.

Implements clWorkerBase.

◆ GetParameterFileData()

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

protected

Reads values from the parameter file and performs setup related to the parameters.

This validates the increment and distance.

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr if either the increment or the max distance are less than or equal to zero, or if the increment is less than the max distance.

◆ GetTreeCodes()

void clConditOmegaCalculator::GetTreeCodes ( clTreePopulation * p_oPop )

protected

Gets the X and Y tree data codes.

Parameters

p_oPop Tree population object

◆ ProcessCell()

void clConditOmegaCalculator::ProcessCell	(	clTreePopulation *	p_oPop,
		clTree *	p_oFirstTree,
		const int &	iX,
		const int &	iY,
		const int &	iNeighX,
		const int &	iNeighY
	)

protected

Processes a neighboring cell's trees to find distance pairs.

This finds all pairs of conspecific saplings and adults within the max distance and counts each pair into the appropriate bin in the Condit's Omega calculator array. Each pair is counted in twice (once for each tree acting as the other's neighbor).

Parameters

p_oPop	Tree population object.
p_oFirstTree	The shortest valid tree in the home cell.
iX	X coordinate of home cell.
iY	Y coordinate of home cell.
iNeighX	X coordinate of the neighbor cell to search for tree pairs.
iNeighY	Y coordinate of the neighbor cell to search for tree pairs.

◆ ProcessOwnCell()

void clConditOmegaCalculator::ProcessOwnCell	(	clTree *	p_oFirstTree,
		float *	p_fNumTrees,
		const int &	iX,
		const int &	iY
	)

protected

Processes a single cell's trees to find distance pairs.

This finds all pairs of conspecific saplings and adults within the max distance, being careful not to pair a tree with itself, and counts each pair into the appropriate bin in the Condit's Omega calculator array. Each pair is counted in twice (once for each tree acting as the other's neighbor). This also counts all the trees in the cell for the purposes of finding the plot's density.

Parameters

p_oFirstTree	The shortest valid tree in the home cell.
p_fNumTrees	The array for number of saplings and adults in the cell for each species.
iX	X coordinate of home cell.
iY	Y coordinate of home cell.

◆ SetupGrid()

void clConditOmegaCalculator::SetupGrid ( )

protected

Sets up the "Relative Neighborhood Density" grid and registers the data members.

◆ SetUpSearching()

void clConditOmegaCalculator::SetUpSearching ( clTreePopulation * p_oPop )

protected

Sets up the structures for searching controls.

This sets up the mp_bCellsSearched matrix and finds the search distances in the X and Y directions. If the search distance is more than half the plot length in either direction, then it will be limited to half the plot length. This also sets up the mp_fIncs and mp_fAnnulusAreas arrays.

Parameters

p_oPop Tree population object

Friends And Related Function Documentation

◆ clTestConditOmegaCalculator

friend class clTestConditOmegaCalculator

friend

Member Data Documentation

◆ m_fIncrement

double clConditOmegaCalculator::m_fIncrement

protected

The distance increment used to step out to the max distance.

◆ m_fMaxDistance

double clConditOmegaCalculator::m_fMaxDistance

protected

The max distance to which to calculate Condit's Omega.

◆ m_iNumIncs

int clConditOmegaCalculator::m_iNumIncs

protected

Number of increments for which to calculate Condit's Omega.

◆ m_iNumTotalSpecies

short int clConditOmegaCalculator::m_iNumTotalSpecies

protected

Total number of species.

For the destructor.

◆ m_iNumXCells

int clConditOmegaCalculator::m_iNumXCells

protected

Number of tree population grid cells in X direction.

◆ m_iNumXToSearch

int clConditOmegaCalculator::m_iNumXToSearch

protected

The number of cells to search in the X direction - if the plot is a rectangle and the search distance is long the distances along the two axes may be different.

◆ m_iNumYCells

int clConditOmegaCalculator::m_iNumYCells

protected

Number of tree population grid cells in Y direction.

◆ m_iNumYToSearch

int clConditOmegaCalculator::m_iNumYToSearch

protected

The number of cells to search in the Y direction - if the plot is a rectangle and the search distance is long the distances along the two axes may be different.

◆ mp_bCellsSearched

bool** clConditOmegaCalculator::mp_bCellsSearched

protected

Which cells have already been paired the current timestep.

The matrix size is number of total cells by number of total cells (flattening the 2D tree population cell matrix into a single array). The index for a tree population grid cell is number of X cells * X cell index + Y cell index. Since every grid cell is paired with every other, once a pair of grid cells is searched, two matrix cells must be switched to true.

◆ mp_fAnnulusAreas

float* clConditOmegaCalculator::mp_fAnnulusAreas

protected

Area of each annulus - array size is m_iNumIncs.

◆ mp_fIncs

float* clConditOmegaCalculator::mp_fIncs

protected

Distance increment values - array size is m_iNumIncs.

◆ mp_fOmegaValues

float** clConditOmegaCalculator::mp_fOmegaValues

protected

Values holding Condit's Omega for each timestep.

Array size is number of species by m_iNumIncs.

◆ mp_iGridCodes

short int** clConditOmegaCalculator::mp_iGridCodes

protected

Holds the codes for the "Relative Neighborhood Density" grid.

The first array index is number of species, with array size being m_iNumTotalSpecies. The second array index is buckets for values along the distance line, and is sized m_iNumIncs.

◆ mp_iXCodes

short int** clConditOmegaCalculator::mp_iXCodes

protected

Holds codes for X data member.

First array index is total # species, second is number types (2 - sapling, adult).

◆ mp_iYCodes

short int** clConditOmegaCalculator::mp_iYCodes

protected

Holds codes for Y data member.

First array index is total # species, second is number types (2 - sapling, adult).

◆ mp_oGrid

clGrid* clConditOmegaCalculator::mp_oGrid

protected

Grid holding Condit's Omega values for the plot plus each species.

The grid name is "Relative Neighborhood Density". It has one data member for each increment step out to the max for each species. The names are X_Y, where X is the increment step number (starting at zero) and Y is the species number (starting at zero). It also has two more for the length of distance increment ("inc") and the max distance ("dist"), to make output display easier.

This grid is always one cell per plot. Changes to grid cell resolution are ignored.

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

ConditOmegaCalculator.h

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ clConditOmegaCalculator()

◆ ~clConditOmegaCalculator()

Member Function Documentation

◆ Action()

◆ GetData()

◆ GetParameterFileData()

◆ GetTreeCodes()

◆ ProcessCell()

◆ ProcessOwnCell()

◆ SetupGrid()

◆ SetUpSearching()

Friends And Related Function Documentation

◆ clTestConditOmegaCalculator

Member Data Documentation

◆ m_fIncrement

◆ m_fMaxDistance

◆ m_iNumIncs

◆ m_iNumTotalSpecies

◆ m_iNumXCells

◆ m_iNumXToSearch

◆ m_iNumYCells

◆ m_iNumYToSearch

◆ mp_bCellsSearched

◆ mp_fAnnulusAreas

◆ mp_fIncs

◆ mp_fOmegaValues

◆ mp_iGridCodes

◆ mp_iXCodes

◆ mp_iYCodes

◆ mp_oGrid