NCI growth - Version 3.0. More...

#include <NCIMasterGrowth.h>

Inheritance diagram for clNCIMasterGrowth:

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

	~clNCIMasterGrowth ()
	Destructor. More...

float	CalcDiameterGrowthValue (clTree p_oTree, clTreePopulation p_oPop, float fHeightGrowth)
	Returns the value in the tree's float data member that holds the value that was calculated by PreGrowthCalcs(). More...

void	PreGrowthCalcs (clTreePopulation *p_oPop)
	Calculates growth for all NCI trees. More...

void	DoShellSetup (xercesc::DOMDocument *p_oDoc)
	Does setup. More...

void	SetNameData (std::string sNameString)
	Captures the namestring passed to this behavior. More...

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

virtual	~clGrowthBase ()
	Destructor. More...

void	Action ()
	Performs all growth calculations if "hooked". More...

virtual float	CalcHeightGrowthValue (clTree p_oTree, clTreePopulation p_oPop, float fDiameterGrowth)
	Calculates the amount of height growth increase for a particular tree, if applicable. More...

virtual float	GetGrowthMemberValue (clTree *p_oTree, float fDiameterGrowth)
	Calculates the value to go into a tree's "Growth" data member as the amount of growth. More...

growthType	GetGrowthMethod ()
	Gets the method by which this behavior increments growth. More...

clGrowthOrg *	GetGrowthOrg ()
	Get the growth org object. More...

void	RegisterTreeDataMembers ()
	Performs data member registrations for "Growth". 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	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	GetTreeMemberCodes ()
	Gets the return codes for needed tree data members. More...

float	DeterministicAdjust (float fNumber, int iSpecies)
	Performs a deterministic adjustment of growth. More...

float	NormalAdjust (float fNumber, int iSpecies)
	Performs a stochastic adjustment of growth according to a normal distribution. More...

float	LognormalAdjust (float fNumber, int iSpecies)
	Performs a stochastic adjustment of growth according to a lognormal distribution. More...

void	SetFunctionPointer ()
	Sets the Adjust function pointer according to the value of m_iStochasticGrowthMethod. More...

Protected Member Functions inherited from clGrowthBase
void	GetData (xercesc::DOMDocument *p_oDoc)
	Triggers all growth setup if an object is hooked. 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_fMaxPotentialValue
	Maximum growth value. More...

double *	mp_fRandParameter
	Standard deviation if normal or lognormal distribution is desired. More...

short int **	mp_iGrowthCodes
	Holds return data codes for the "Growth" tree data member. More...

short int	m_iNumTotalSpecies
	Total number of species - for the destructor. More...

std::string	m_sQuery
	For finding trees. More...

pdf	m_iStochasticGrowthMethod
	What stochastic growth distribution applies to this run. More...

float(clNCIMasterGrowth::*	Adjust )(float fNumber, int iSpecies)
	Function pointer for the appropriate Adjust function. More...

Protected Attributes inherited from clGrowthBase
growthType	m_iGrowthMethod
	The method by which this object plans to update tree dimensions. More...

float	m_fConvertCmPerTSToMmPerYr
	Conversion factor from cm diameter growth per timestep to mm radial growth per year. More...

float	m_fConvertMmPerYearToCmPerTS
	Conversion factor to take amounts from mm of radial growth per year to cm of diameter growth per timestep. More...

bool	m_bHooked
	Wwhether or not this shell object is hooked to clGrowthOrg. More...

bool	m_bGoLast
	Whether or not this behavior's growth should go last when used with a complementary growth behavior. 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...

Additional Inherited Members
Public Types inherited from clGrowthBase
enum	growthType { diameter_auto, diameter_only, height_only }
	Values describing the method by which the object instance of this class plans to implement tree growth. More...

Static Protected Attributes inherited from clGrowthBase
static clGrowthOrg *	mp_oGrowthOrg
	clGrowthOrg object - this pointer is held in common by all shells More...

Private Member Functions inherited from clNCIBehaviorBase
	clNCIBehaviorBase ()
	Constructor. More...

	~clNCIBehaviorBase ()
	Destructor. More...

clShadingEffectBase *	GetShadingEffect ()
	Get the shading effect object. More...

clDamageEffectBase *	GetDamageEffect ()
	Get the damage effect object. More...

clSizeEffectBase *	GetSizeEffect ()
	Get the size effect object. More...

clCrowdingEffectBase *	GetCrowdingEffect ()
	Get the crowding effect object. More...

clNCITermBase *	GetNCITerm ()
	Get the NCI term object. More...

clPrecipitationEffectBase *	GetPrecipEffect ()
	Get the precipitation effect object. More...

clTemperatureEffectBase *	GetTempEffect ()
	Get the temperature effect object. More...

clNitrogenEffectBase *	GetNEffect ()
	Get the nitrogen effect object. More...

clInfectionEffectBase *	GetInfectionEffect ()
	Get the infection effect object. More...

void	ReadParameterFile (xercesc::DOMElement p_oElement, clTreePopulation p_oPop, clBehaviorBase *p_oNCI, bool bUsingDiam)
	Reads data from the parameter file for the effects objects. More...

Private Attributes inherited from clNCIBehaviorBase
clShadingEffectBase *	mp_oShadingEffect
	The shading effect object. More...

clDamageEffectBase *	mp_oDamageEffect
	The damage effect object. More...

clSizeEffectBase *	mp_oSizeEffect
	The size effect object. More...

clCrowdingEffectBase *	mp_oCrowdingEffect
	The crowding effect object. More...

clNCITermBase *	mp_oNCITerm
	The NCI term object. More...

clPrecipitationEffectBase *	mp_oPrecipEffect
	The precipitation effect object. More...

clTemperatureEffectBase *	mp_oTempEffect
	The temperature effect object. More...

clNitrogenEffectBase *	mp_oNEffect
	The nitrogen effect object. More...

clInfectionEffectBase *	mp_oInfectionEffect
	The infection effect object. More...

Detailed Description

NCI growth - Version 3.0.

This is a growth shell object which applies the NCI (neighborhood competition index) function. The basic function is a maximum rate of growth that is reduced by a set of multiplicative effects. The set of effects used is up to the user.

The amount of growth is in cm/year. For multi-year timesteps, the behavior will calculate total growth with a loop. Each loop iteration will increment DBH for one year. For each year, effects are recalculated with the previous year's new DBH value. All values for each year of growth are summed to get the growth for the timestep.

The final growth rate can be used as-is or as a mean to a random draw.

The parameter file call string for this to be diameter-incrementing with auto-height updating is "NCIMasterGrowth"; for diameter-only incrementing, use "NCIMasterGrowth diam only". The namestring for this behavior is "ncigrowthshell". The XML string is "NCIMasterGrowth".

Several behaviors with a prescribed set of effects were folded into this flexible system to create version 3. The trees to which this can be applied depends on the set of effects chosen.

Author: Lora E. Murphy

Edit history:
--------------—
November 27, 2012: Created (LEM)
November 1, 2013: Added infection effect (LEM)
December 23, 2013: Made child of clNCIBehaviorBase; added stochasticity (LEM)

Constructor & Destructor Documentation

◆ clNCIMasterGrowth()

clNCIMasterGrowth::clNCIMasterGrowth ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clNCIMasterGrowth()

clNCIMasterGrowth::~clNCIMasterGrowth ( )

Destructor.

Frees memory.

Member Function Documentation

◆ CalcDiameterGrowthValue()

float clNCIMasterGrowth::CalcDiameterGrowthValue	(	clTree *	p_oTree,
		clTreePopulation *	p_oPop,
		float	fHeightGrowth
	)

virtual

Returns the value in the tree's float data member that holds the value that was calculated by PreGrowthCalcs().

Parameters

p_oTree	Tree to which to apply growth.
p_oPop	Tree population object.
fHeightGrowth	Amount of height growth, in m (ignored).

Returns: Amount of diameter growth, in cm.

Reimplemented from clGrowthBase.

◆ DeterministicAdjust()

float clNCIMasterGrowth::DeterministicAdjust	(	float	fNumber,
		int	iSpecies
	)

protected

Performs a deterministic adjustment of growth.

Parameters

fNumber	Growth to adjust.
iSpecies	Species.

Returns: Final growth.

◆ DoShellSetup()

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

virtual

Does setup.

ReadParameterFile() is called to read the parameter file's data.
GetTreeMemberCodes() is called to get tree data return codes.
FormatQueryString() is called.

Parameters

p_oDoc DOM tree of parsed input tree.

Exceptions

modelErr if all values of max growth are not greater than 0.

Reimplemented from clGrowthBase.

◆ GetTreeMemberCodes()

void clNCIMasterGrowth::GetTreeMemberCodes ( )

protected

Gets the return codes for needed tree data members.

Exceptions

modelErr if a code comes back -1 for any species/type combo to which this behavior is applied.

◆ LognormalAdjust()

float clNCIMasterGrowth::LognormalAdjust	(	float	fNumber,
		int	iSpecies
	)

protected

Performs a stochastic adjustment of growth according to a lognormal distribution.

Parameters

fNumber	Growth to adjust.
iSpecies	Species.

Returns: Final growth.

◆ NormalAdjust()

float clNCIMasterGrowth::NormalAdjust	(	float	fNumber,
		int	iSpecies
	)

protected

Performs a stochastic adjustment of growth according to a normal distribution.

Parameters

fNumber	Growth to adjust.
iSpecies	Species.

Returns: Final growth.

◆ PreGrowthCalcs()

void clNCIMasterGrowth::PreGrowthCalcs ( clTreePopulation * p_oPop )

virtual

Calculates growth for all NCI trees.

Climate effects, which do not depend on individual trees, are called once; effects which do not depend on a target tree's size are called once per tree; and effects with a size component are called once per year, looping over the years in a timestep. The values are stashed in the "Growth" tree float data member for later application.

This must be called first of any growth stuff, since it uses other trees' DBHs to calculate NCI, and these must be before growth has been applied.

Growth per timestep is calculated by looping over the number of years per timestep and incrementing the DBH.

Parameters

p_oPop Tree population object.

Reimplemented from clGrowthBase.

◆ SetFunctionPointer()

void clNCIMasterGrowth::SetFunctionPointer ( )

protected

Sets the Adjust function pointer according to the value of m_iStochasticGrowthMethod.

◆ SetNameData()

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

virtual

Captures the namestring passed to this behavior.

This is overridden from clBehaviorBase so we can capture the namestring passed. Since this class can create multiple kinds of behaviors that function differently, this will capture what kind of behavior this is supposed to be.

Parameters

sNameString Behavior's namestring.

Reimplemented from clBehaviorBase.

Member Data Documentation

◆ Adjust

float(clNCIMasterGrowth::* clNCIMasterGrowth::Adjust) (float fNumber, int iSpecies)

protected

Function pointer for the appropriate Adjust function.

◆ m_iNumTotalSpecies

short int clNCIMasterGrowth::m_iNumTotalSpecies

protected

Total number of species - for the destructor.

◆ m_iStochasticGrowthMethod

pdf clNCIMasterGrowth::m_iStochasticGrowthMethod

protected

What stochastic growth distribution applies to this run.

◆ m_sQuery

std::string clNCIMasterGrowth::m_sQuery

protected

For finding trees.

◆ mp_fMaxPotentialValue

double* clNCIMasterGrowth::mp_fMaxPotentialValue

protected

Maximum growth value.

Array sized number of species.

◆ mp_fRandParameter

double* clNCIMasterGrowth::mp_fRandParameter

protected

Standard deviation if normal or lognormal distribution is desired.

One for each species.

◆ mp_iGrowthCodes

short int** clNCIMasterGrowth::mp_iGrowthCodes

protected

Holds return data codes for the "Growth" tree data member.

Array size is number of species by number of types.

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

NCIMasterGrowth.h

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clNCIMasterGrowth()

◆ ~clNCIMasterGrowth()

Member Function Documentation

◆ CalcDiameterGrowthValue()

◆ DeterministicAdjust()

◆ DoShellSetup()

◆ GetTreeMemberCodes()

◆ LognormalAdjust()

◆ NormalAdjust()

◆ PreGrowthCalcs()

◆ SetFunctionPointer()

◆ SetNameData()

Member Data Documentation

◆ Adjust

◆ m_iNumTotalSpecies

◆ m_iStochasticGrowthMethod

◆ m_sQuery

◆ mp_fMaxPotentialValue

◆ mp_fRandParameter

◆ mp_iGrowthCodes