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clNCIMasterGrowth Class Reference

NCI growth - Version 3.0. More...

#include <NCIMasterGrowth.h>

Inheritance diagram for clNCIMasterGrowth:
clGrowthBase clNCIBehaviorBase clBehaviorBase clWorkerBase

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...
 
clGrowthOrgGetGrowthOrg ()
 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...
 
clSimManagerGetSimManager ()
 
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...
 
stcSpeciesTypeCombomp_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...
 
clSimManagermp_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 clGrowthOrgmp_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...
 
clShadingEffectBaseGetShadingEffect ()
 Get the shading effect object. More...
 
clDamageEffectBaseGetDamageEffect ()
 Get the damage effect object. More...
 
clSizeEffectBaseGetSizeEffect ()
 Get the size effect object. More...
 
clCrowdingEffectBaseGetCrowdingEffect ()
 Get the crowding effect object. More...
 
clNCITermBaseGetNCITerm ()
 Get the NCI term object. More...
 
clPrecipitationEffectBaseGetPrecipEffect ()
 Get the precipitation effect object. More...
 
clTemperatureEffectBaseGetTempEffect ()
 Get the temperature effect object. More...
 
clNitrogenEffectBaseGetNEffect ()
 Get the nitrogen effect object. More...
 
clInfectionEffectBaseGetInfectionEffect ()
 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
clShadingEffectBasemp_oShadingEffect
 The shading effect object. More...
 
clDamageEffectBasemp_oDamageEffect
 The damage effect object. More...
 
clSizeEffectBasemp_oSizeEffect
 The size effect object. More...
 
clCrowdingEffectBasemp_oCrowdingEffect
 The crowding effect object. More...
 
clNCITermBasemp_oNCITerm
 The NCI term object. More...
 
clPrecipitationEffectBasemp_oPrecipEffect
 The precipitation effect object. More...
 
clTemperatureEffectBasemp_oTempEffect
 The temperature effect object. More...
 
clNitrogenEffectBasemp_oNEffect
 The nitrogen effect object. More...
 
clInfectionEffectBasemp_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.

Copyright 2012 Charles D. Canham.

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_oSimManagerSim 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_oTreeTree to which to apply growth.
p_oPopTree population object.
fHeightGrowthAmount 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
fNumberGrowth to adjust.
iSpeciesSpecies.
Returns
Final growth.

◆ DoShellSetup()

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

Does setup.

  1. ReadParameterFile() is called to read the parameter file's data.
  2. GetTreeMemberCodes() is called to get tree data return codes.
  3. FormatQueryString() is called.
Parameters
p_oDocDOM tree of parsed input tree.
Exceptions
modelErrif 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
modelErrif 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
fNumberGrowth to adjust.
iSpeciesSpecies.
Returns
Final growth.

◆ NormalAdjust()

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

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

Parameters
fNumberGrowth to adjust.
iSpeciesSpecies.
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_oPopTree 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
sNameStringBehavior'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: