Quality Vigor Classifier version 1.0 Manages tree classification based on stem vigor, species classification, and quality. More...

#include <QualityVigorClassifier.h>

Inheritance diagram for clQualityVigorClassifier:

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

	~clQualityVigorClassifier ()
	Destructor. More...

void	Action ()
	Does class management. More...

void	GetData (xercesc::DOMDocument *p_oDoc)
	Does setup by calling ReadParameterFile() and HandleInitialConditionsTrees(). More...

void	RegisterTreeDataMembers ()
	Registers the "Biomass" float data member. More...

void	AssignClass (clTreePopulation p_oPop, clTree p_oTree)
	Assigns a class to a tree based on vigor and quality. 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 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...

Private Member Functions
void	ReadParameterFile (xercesc::DOMDocument p_oDoc, clTreePopulation p_oPop)
	Reads the data from the parameter file. More...

void	HandleInitialConditionsTrees (xercesc::DOMDocument p_oDoc, clTreePopulation p_oPop)
	Handles initial conditions trees. More...

void	AssignVigorQuality (clTree *p_oTree)
	Assigns a vigor and quality to a tree based on the new adult probabilities. More...

void	EvolveVigorQuality (clTreePopulation p_oPop, clTree p_oTree)
	Evaluates possible transition in vigor and quality for a tree, then assigns the new values. More...

void	FormatQueryString (clTreePopulation *p_oPop)
	Formats the string in m_cQuery. More...

Private Attributes
char *	m_cQuery
	String to pass to clTreePopulation::Find() in order to get the trees to apply damage to. More...

double *	mp_fVigBeta0
	Beta0 for vigor transition. More...

double *	mp_fVigBeta11
	Beta1 for vigor transition, initial class 1. More...

double *	mp_fVigBeta12
	Beta1 for vigor transition, initial class 2. More...

double *	mp_fVigBeta13
	Beta1 for vigor transition, initial class 3. More...

double *	mp_fVigBeta14
	Beta1 for vigor transition, initial class 4. More...

double *	mp_fVigBeta15
	Beta1 for vigor transition, initial class 5. More...

double *	mp_fVigBeta16
	Beta1 for vigor transition, initial class 6. More...

double *	mp_fVigBeta2
	Beta2 for vigor transition. More...

double *	mp_fVigBeta3
	Beta3 for vigor transition. More...

double *	mp_fQualBeta0
	Beta0 for quality transition. More...

double *	mp_fQualBeta11
	Beta1 for quality transition, initial class 1. More...

double *	mp_fQualBeta12
	Beta1 for quality transition, initial class 2. More...

double *	mp_fQualBeta13
	Beta1 for quality transition, initial class 3. More...

double *	mp_fQualBeta14
	Beta1 for quality transition, initial class 4. More...

double *	mp_fQualBeta2
	Beta2 for quality transition. More...

double *	mp_fQualBeta3
	Beta3 for quality transition. More...

double *	mp_fNewAdultProbVigorous
	Probability of new adults being vigorous. More...

double *	mp_fNewAdultProbSawlog
	Probability of new adults being sawlog quality. More...

short int *	mp_iIndexes
	For array access. More...

short int *	mp_iVigorousInd
	Return codes for "vigorous" tree data member. More...

short int *	mp_iSawlogInd
	Return codes for "sawlog" tree data member. More...

short int *	mp_iTreeclassInd
	Return codes for "treeclass" tree data member. More...

bool *	mp_bDeciduous
	Whether or not a species is deciduous. More...

Friends
class	clTestQualityVigorClassifier

Additional Inherited Members
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 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...

Detailed Description

Quality Vigor Classifier version 1.0 Manages tree classification based on stem vigor, species classification, and quality.

Assigning a classification
The possible states of "species type" are deciduous and coniferous. The possible states of "vigor" are vigorous and not vigorous. The possible states of "quality" are sawlog potential and no sawlog potential.

Only adults can be assigned a class number.

Spp Type	Vigor	Sawlog?	DBH	Class
Deciduous	Vig	Yes	Any	1
Deciduous	Vig	No	Any	2
Deciduous	Not	Yes	> 23 cm	3
Deciduous	Not	Yes	<= 23 cm	4
Deciduous	Not	No	Any	4
Coniferous	Vig	NA	Any	5
Coniferous	Not	NA	Any	6

Assigning a vigor and quality to new adults
For each species, there is a probability that a new adult of that species is vigorous, and for deciduous species, that it is sawlog quality. A random number is compared to these values to determine the vigor and quality of a new adult tree. Classification can then proceed according to the table above.

Initial conditions
Trees may come in with a class already assigned in a tree map. If not, the user can specify the proportion of trees vigorous and sawlog in various size classes. Any trees not covered by one of the two previous assignment methods will be assigned based on the new adult proportions.

Changes in vigor and quality
The probability of transition between vigor states and quality states is calculated with the same functional form (but different parameters). The probability of being vigorous or of being of sawlog quality is:

prob= exp(βX)/(1+exp(βX)) where:

βX= β₀ + β_1init + β_2sp*DBH + β_3sp*ln(DBH)

where β_1init is a beta for the initial state.

This behavior adds three tree data members: two booleans, "vigorous" and "sawlog", and one int called "treeclass" with a possible value from 1-6.

This behavior can only be applied to adult trees.

The namestring and parameter file call string are "QualityVigorClassifier".

Author: Lora E. Murphy

Edit history:
--------------—
January 9, 2012 - Created (LEM)

Constructor & Destructor Documentation

◆ clQualityVigorClassifier()

clQualityVigorClassifier::clQualityVigorClassifier ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clQualityVigorClassifier()

clQualityVigorClassifier::~clQualityVigorClassifier ( )

Destructor.

Member Function Documentation

◆ Action()

void clQualityVigorClassifier::Action ( )

virtual

Does class management.

This gets all trees that this behavior acts on. First, vigor and quality transitions are dealt with. If a tree does not already have a class, it will get assignments based on the new adult probabilities. If it does, it will get assessed for both vigor class and quality class transition.

Reimplemented from clBehaviorBase.

◆ AssignClass()

void clQualityVigorClassifier::AssignClass	(	clTreePopulation *	p_oPop,
		clTree *	p_oTree
	)

Assigns a class to a tree based on vigor and quality.

The class value is placed in the tree's "treeclass" data member. If vigor or quality is missing, the class value assigned is 0.

Parameters

p_oPop	Tree population.
p_oTree	Tree to assign class to.

◆ AssignVigorQuality()

void clQualityVigorClassifier::AssignVigorQuality ( clTree * p_oTree )

private

Assigns a vigor and quality to a tree based on the new adult probabilities.

Parameters

p_oTree Tree to assign vigor and quality to.

◆ EvolveVigorQuality()

void clQualityVigorClassifier::EvolveVigorQuality	(	clTreePopulation *	p_oPop,
		clTree *	p_oTree
	)

private

Evaluates possible transition in vigor and quality for a tree, then assigns the new values.

Parameters

p_oPop	Tree population.
p_oTree	Tree to evaluate.

◆ FormatQueryString()

void clQualityVigorClassifier::FormatQueryString ( clTreePopulation * p_oPop )

private

Formats the string in m_cQuery.

This value will be used in Action() to pass to clTreePopulation::Find() in order to get the trees to act on.

Parameters

p_oPop Tree population object.

◆ GetData()

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

virtual

Does setup by calling ReadParameterFile() and HandleInitialConditionsTrees().

Parameters

p_oDoc DOM tree of parsed input file.

Implements clWorkerBase.

◆ HandleInitialConditionsTrees()

void clQualityVigorClassifier::HandleInitialConditionsTrees	(	xercesc::DOMDocument *	p_oDoc,
		clTreePopulation *	p_oPop
	)

private

Handles initial conditions trees.

This will look for initial conditions defined proportions of vigorous and sawlog info. If missing, or for any trees for which it is missing, the new adult probabilities will be used to assign vigorous and sawlog status, and then class.

Parameters

p_oPop	Tree population.
p_oDoc	DOM tree of parsed input file.

◆ ReadParameterFile()

void clQualityVigorClassifier::ReadParameterFile	(	xercesc::DOMDocument *	p_oDoc,
		clTreePopulation *	p_oPop
	)

private

Reads the data from the parameter file.

Parameters

p_oDoc	DOM tree of parsed input file.
p_oPop	Tree population.

◆ RegisterTreeDataMembers()

void clQualityVigorClassifier::RegisterTreeDataMembers ( )

virtual

Registers the "Biomass" float data member.

The return codes are captured in the mp_iBiomassCodes array.

Exceptions

modelErr if this behavior is being applied to any tree type except adults.

Reimplemented from clBehaviorBase.

Friends And Related Function Documentation

◆ clTestQualityVigorClassifier

friend class clTestQualityVigorClassifier

friend

Member Data Documentation

◆ m_cQuery

char* clQualityVigorClassifier::m_cQuery

private

String to pass to clTreePopulation::Find() in order to get the trees to apply damage to.

This will instigate a species/type search for all the species and types to which this behavior applies.

◆ mp_bDeciduous

bool* clQualityVigorClassifier::mp_bDeciduous

private

Whether or not a species is deciduous.

(False means coniferous.) Sized number of species assigned to this behavior.

◆ mp_fNewAdultProbSawlog

double* clQualityVigorClassifier::mp_fNewAdultProbSawlog

private

Probability of new adults being sawlog quality.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fNewAdultProbVigorous

double* clQualityVigorClassifier::mp_fNewAdultProbVigorous

private

Probability of new adults being vigorous.

Sized number of species assigned to this behavior.

◆ mp_fQualBeta0

double* clQualityVigorClassifier::mp_fQualBeta0

private

Beta0 for quality transition.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fQualBeta11

double* clQualityVigorClassifier::mp_fQualBeta11

private

Beta1 for quality transition, initial class 1.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fQualBeta12

double* clQualityVigorClassifier::mp_fQualBeta12

private

Beta1 for quality transition, initial class 2.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fQualBeta13

double* clQualityVigorClassifier::mp_fQualBeta13

private

Beta1 for quality transition, initial class 3.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fQualBeta14

double* clQualityVigorClassifier::mp_fQualBeta14

private

Beta1 for quality transition, initial class 4.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fQualBeta2

double* clQualityVigorClassifier::mp_fQualBeta2

private

Beta2 for quality transition.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fQualBeta3

double* clQualityVigorClassifier::mp_fQualBeta3

private

Beta3 for quality transition.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fVigBeta0

double* clQualityVigorClassifier::mp_fVigBeta0

private

Beta0 for vigor transition.

Sized number of species assigned to this behavior.

◆ mp_fVigBeta11

double* clQualityVigorClassifier::mp_fVigBeta11

private

Beta1 for vigor transition, initial class 1.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fVigBeta12

double* clQualityVigorClassifier::mp_fVigBeta12

private

Beta1 for vigor transition, initial class 2.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fVigBeta13

double* clQualityVigorClassifier::mp_fVigBeta13

private

Beta1 for vigor transition, initial class 3.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fVigBeta14

double* clQualityVigorClassifier::mp_fVigBeta14

private

Beta1 for vigor transition, initial class 4.

Sized number of species assigned to this behavior. If species is coniferous, this is ignored.

◆ mp_fVigBeta15

double* clQualityVigorClassifier::mp_fVigBeta15

private

Beta1 for vigor transition, initial class 5.

Sized number of species assigned to this behavior. If species is deciduous, this is ignored.

◆ mp_fVigBeta16

double* clQualityVigorClassifier::mp_fVigBeta16

private

Beta1 for vigor transition, initial class 6.

Sized number of species assigned to this behavior. If species is deciduous, this is ignored.

◆ mp_fVigBeta2

double* clQualityVigorClassifier::mp_fVigBeta2

private

Beta2 for vigor transition.

Sized number of species assigned to this behavior.

◆ mp_fVigBeta3

double* clQualityVigorClassifier::mp_fVigBeta3

private

Beta3 for vigor transition.

Sized number of species assigned to this behavior.

◆ mp_iIndexes

short int* clQualityVigorClassifier::mp_iIndexes

private

For array access.

◆ mp_iSawlogInd

short int* clQualityVigorClassifier::mp_iSawlogInd

private

Return codes for "sawlog" tree data member.

Sized number of species assigned to this behavior.

◆ mp_iTreeclassInd

short int* clQualityVigorClassifier::mp_iTreeclassInd

private

Return codes for "treeclass" tree data member.

Sized number of species assigned to this behavior.

◆ mp_iVigorousInd

short int* clQualityVigorClassifier::mp_iVigorousInd

private

Return codes for "vigorous" tree data member.

Sized number of species assigned to this behavior.

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

QualityVigorClassifier.h

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ clQualityVigorClassifier()

◆ ~clQualityVigorClassifier()

Member Function Documentation

◆ Action()

◆ AssignClass()

◆ AssignVigorQuality()

◆ EvolveVigorQuality()

◆ FormatQueryString()

◆ GetData()

◆ HandleInitialConditionsTrees()

◆ ReadParameterFile()

◆ RegisterTreeDataMembers()

Friends And Related Function Documentation

◆ clTestQualityVigorClassifier

Member Data Documentation

◆ m_cQuery

◆ mp_bDeciduous

◆ mp_fNewAdultProbSawlog

◆ mp_fNewAdultProbVigorous

◆ mp_fQualBeta0

◆ mp_fQualBeta11

◆ mp_fQualBeta12

◆ mp_fQualBeta13

◆ mp_fQualBeta14

◆ mp_fQualBeta2

◆ mp_fQualBeta3

◆ mp_fVigBeta0

◆ mp_fVigBeta11

◆ mp_fVigBeta12

◆ mp_fVigBeta13

◆ mp_fVigBeta14

◆ mp_fVigBeta15

◆ mp_fVigBeta16

◆ mp_fVigBeta2

◆ mp_fVigBeta3

◆ mp_iIndexes

◆ mp_iSawlogInd

◆ mp_iTreeclassInd

◆ mp_iVigorousInd