Density Dependent Infestation. More...

#include <DensDepInfestation.h>

Inheritance diagram for clDensDepInfestation:

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

	~clDensDepInfestation ()
	Destructor. More...

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

void	Action ()
	Does insect infestation each timestep. More...

void	RegisterTreeDataMembers ()
	Registers the "YearsInfested" and "DensDepResistanceStatus" int data members. 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...

Protected Member Functions
void	ReadParFile (xercesc::DOMDocument p_oDoc, clTreePopulation p_oPop)
	Reads in parameters from the parameter file. More...

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

void	TreeInventory ()
	This traverses the tree population and does a few things: More...

void	InfestInitialConditionsTrees ()
	Assigns infestation status and length to initial conditions trees in the case that infestation starts before the beginning of the run. More...

void	DetermineCohortInfestationProbability (double fTargetRate)
	Calculates each cohort's probability of infestation for individual trees, based on the results of TreeInventory(). More...

void	EndInfestation ()
	Ends infestation. 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
short int **	mp_iYearsInfestedCodes
	Return codes for the "YearsInfested" int tree data member. More...

short int **	mp_iDensDepResistanceStatusCodes
	Return codes for the "DensDepResistanceStatus" int tree data member. More...

double *	mp_fMinDBH
	Minimum DBH for trees to be infested. More...

double *	mp_fCohortDBH
	Cohort cutoff DBH. More...

double *	mp_fProbResistant
	Probability that a tree is resistant, 0-1. More...

double *	mp_fProbConditionallySusceptible
	Probability that a tree is conditionally susceptible, 0-1. More...

double	m_fMax
	Maximum infestation rate parameter. More...

double	m_fA
	The "a" parameter. More...

double	m_fBx
	The "bx" parameter. More...

double	m_fBy
	The "by" parameter. More...

double	m_fPlotBA
	Total plot BA. More...

double	m_fPoolBA
	BA in the pool of trees to which this behavior applies (including resistant trees). More...

double	m_fSmallCohortProb
	Current probability of infestation for the smaller cohort. More...

double	m_fLargeCohortProb
	Current probability of infestation for the larger cohort. More...

long	m_iNumSmallCohortPoolTrees
	Number of trees in the pool to which this behavior applies (including resistant trees), below the cohort cutoff. More...

long	m_iNumLargeCohortPoolTrees
	Number of trees in the pool to which this behavior applies (including resistant trees), equal to or above the cohort cutoff. More...

long	m_iNumSmallCohortInfestedTrees
	Number of infested trees in the pool to which this behavior applies (including resistant trees), below the cohort cutoff. More...

long	m_iNumLargeCohortInfestedTrees
	Number of infested trees in the pool to which this behavior applies (including resistant trees), equal to or above the cohort cutoff. More...

long	m_iNumSmallInfestibleTrees
	Number of trees that can be infested (non-resistant, regardless of current infestation status), below the cohort cutoff. More...

long	m_iNumLargeInfestibleTrees
	Number of trees that can be infested (non-resistant, regardless of current infestation status), equal to or above the cohort cutoff. More...

int	m_iFirstTimestep
	Timestep to begin infestation. More...

int	m_iLastTimestep
	Timestep to end infestation. More...

int	m_iYearsOfInfestation
	Years since infestation began - 0 if there is no current infestation. More...

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

int	m_iTotalNumSpecies
	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...

Detailed Description

Density Dependent Infestation.

This behavior simulates the spread of a disease or infestation throughout a tree population.

The proportion of trees infested as a Gompertz function of time is as follows:

P = max * exp(-exp(a - b* T))

where:

P is the proportion infested
max is the maximum infestation rate
T is the time since the start of the infestation, in years
a is a parameter
b is calculated, as below

b is calculated as follows:

b = bx * BA + by

where BA is the proportion of basal area comprised of trees to which this behavior has been assigned (0 - 1).

This behavior allows for the possibility that there are various levels of resistance in the tree population. Users can assign a percentage of trees that are "resistant" or "conditionally susceptible". This behavior will not infest "resistant" trees but otherwise does nothing with this information - other behaviors are planned that take advantage of this.

All species are treated as a common pool and there are no species-specific parameters for infestation. There are species-specific parameters for the rates of resistance and conditional susceptibility.

The proportion of trees infested at time T does not depend on additions to or subtractions from the tree population. The number of trees of a species at that time is counted and the number of trees that are newly infested is the number required to cause the appropriate proportion to be infested. If for some reason there are more trees infested than there should be at that time, no additional trees are infested.

Susceptible individuals come in two size classes, with the cutoff DBH set as a parameter. All the individuals above this DBH are infected before any below the cutoff are. Note that when max < 1, it is possible that no individuals below the DBH cutoff will ever be infected.

There is no spatial component to the selection of trees for infestation. It is assumed that all trees have an equal chance of becoming infested no matter where they are in the plot. The number of trees that should be infested for a given time step minus the number that actually are gives the probability that an uninfested tree will become infested this time step. A random number is used against this probability for each uninfested tree to determine whether or not it will become infested.

Infestation begins at a year specified by the user. This can be negative, indicating that the infestation began before the beginning of the run. In this case, the behavior setup before the run will include the step of determining the number of infested initial conditions trees and their length of infestation.

Two integer data member is added to trees. The first is called "YearsInfested" and tracks the number of years that a tree has been infested. The second is called "DensDepResistanceStatus" and equals a value in the enum densDepResistanceStatus in DataTypes.h.

This behavior will not infest trees below a minimum DBH set by the user. Because of the need for DBH, obviously seedlings are ignored.

This behavior's call string and name string are both "DensDepInfestation".

Author: Lora E. Murphy
Edit history:
--------------—
August 5, 2013 - Created (LEM)
July 27, 2015 - Added infection end date (LEM)

Constructor & Destructor Documentation

◆ clDensDepInfestation()

clDensDepInfestation::clDensDepInfestation ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clDensDepInfestation()

clDensDepInfestation::~clDensDepInfestation ( )

Destructor.

Member Function Documentation

◆ Action()

void clDensDepInfestation::Action ( )

virtual

Does insect infestation each timestep.

TreeInventory() collects data about the tree population. This is used to calculate first the b parameter and then the proportion of trees infested.

The counter in m_iYearsOfInfestation is incremented and the target level of infestation is calculated for each species according to the function above. GetInfestationRate() calculates the actual current rate. The difference between the target and actual rates gives the probability of an uninfested tree becoming infested. Then for each tree to which this behavior is applied, if the tree is not infested, a random number compared to the infestation probability determines if it will become infested. If so, a value of 1 is entered into the "YearsInfested" data member. If the tree was already infested, the data member value is incremented.

Reimplemented from clBehaviorBase.

◆ DetermineCohortInfestationProbability()

void clDensDepInfestation::DetermineCohortInfestationProbability ( double fTargetRate )

protected

Calculates each cohort's probability of infestation for individual trees, based on the results of TreeInventory().

First, the desired number of new trees to infest is calculated. If it is 0, both probabilities are also 0. If there are enough infestible trees in the larger cohort to satisfy the new number, then the smaller cohort's probability is set to 0 and the larger cohort's probability is the number of new trees to infest divided by the number of non-infested trees. If there are not enough trees in the larger cohort, its probability is set to 1, and the smaller cohort's probability is set to the number of new trees to infest minus infestible trees in the larger cohort divided by number of non-infested small cohort trees.

Results are placed in m_fSmallCohortProb and m_fLargeCohortProb.

Parameters

fTargetRate Total current proportion of trees to be infested.

◆ EndInfestation()

void clDensDepInfestation::EndInfestation ( )

protected

Ends infestation.

All flags are reset to 0 and m_iYearsOfInfestation is set to 0 which will make sure no trees are infected in the future.

◆ FormatQueryString()

void clDensDepInfestation::FormatQueryString ( clTreePopulation * p_oPop )

protected

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 clDensDepInfestation::GetData ( xercesc::DOMDocument * p_oDoc )

virtual

Does behavior setup.

Parameters

p_oDoc DOM tree of parsed input file.

Implements clWorkerBase.

◆ InfestInitialConditionsTrees()

void clDensDepInfestation::InfestInitialConditionsTrees ( )

protected

Assigns infestation status and length to initial conditions trees in the case that infestation starts before the beginning of the run.

◆ ReadParFile()

void clDensDepInfestation::ReadParFile	(	xercesc::DOMDocument *	p_oDoc,
		clTreePopulation *	p_oPop
	)

protected

Reads in parameters from the parameter file.

Parameters

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

Exceptions

modelErr

if:

A value in the minimum DBH is less than 0
The maximum infestation rate is not between 0 and 1
A value in the cohort cutoff DBH is less than 0
The probability of resistance is not between 0 and 1
The probability of conditional susceptibility is not between 0 and 1

◆ RegisterTreeDataMembers()

void clDensDepInfestation::RegisterTreeDataMembers ( )

virtual

Registers the "YearsInfested" and "DensDepResistanceStatus" int data members.

Reimplemented from clBehaviorBase.

◆ TreeInventory()

void clDensDepInfestation::TreeInventory ( )

protected

This traverses the tree population and does a few things:

Gets the total plot BA and puts it in m_fPlotBA
Gets the BA of the pool of trees to which this behavior applies (all trees above minimum infestible DBH, regardless of resistance status) and puts it in m_fPoolBA
Counts the number of trees in the pool to which this behavior applies and puts it in m_iNumSmallCohortPoolTrees and m_iNumLargeCohortPoolTrees
Checks for new trees with no current infestation status, and assigns them a status
Counts currently infested trees and puts it in m_iNumSmallCohortInfestedTrees and m_iNumLargeCohortInfestedTrees
Counts the number of infestible trees (not resistant), regardless of infestation status, and puts it in m_iNumSmallInfestibleTrees and m_iNumLargeInfestibleTrees

Member Data Documentation

◆ m_cQuery

char* clDensDepInfestation::m_cQuery

protected

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.

◆ m_fA

double clDensDepInfestation::m_fA

protected

The "a" parameter.

◆ m_fBx

double clDensDepInfestation::m_fBx

protected

The "bx" parameter.

◆ m_fBy

double clDensDepInfestation::m_fBy

protected

The "by" parameter.

◆ m_fLargeCohortProb

double clDensDepInfestation::m_fLargeCohortProb

protected

Current probability of infestation for the larger cohort.

◆ m_fMax

double clDensDepInfestation::m_fMax

protected

Maximum infestation rate parameter.

◆ m_fPlotBA

double clDensDepInfestation::m_fPlotBA

protected

Total plot BA.

◆ m_fPoolBA

double clDensDepInfestation::m_fPoolBA

protected

BA in the pool of trees to which this behavior applies (including resistant trees).

◆ m_fSmallCohortProb

double clDensDepInfestation::m_fSmallCohortProb

protected

Current probability of infestation for the smaller cohort.

◆ m_iFirstTimestep

int clDensDepInfestation::m_iFirstTimestep

protected

Timestep to begin infestation.

◆ m_iLastTimestep

int clDensDepInfestation::m_iLastTimestep

protected

Timestep to end infestation.

◆ m_iNumLargeCohortInfestedTrees

long clDensDepInfestation::m_iNumLargeCohortInfestedTrees

protected

Number of infested trees in the pool to which this behavior applies (including resistant trees), equal to or above the cohort cutoff.

◆ m_iNumLargeCohortPoolTrees

long clDensDepInfestation::m_iNumLargeCohortPoolTrees

protected

Number of trees in the pool to which this behavior applies (including resistant trees), equal to or above the cohort cutoff.

◆ m_iNumLargeInfestibleTrees

long clDensDepInfestation::m_iNumLargeInfestibleTrees

protected

Number of trees that can be infested (non-resistant, regardless of current infestation status), equal to or above the cohort cutoff.

◆ m_iNumSmallCohortInfestedTrees

long clDensDepInfestation::m_iNumSmallCohortInfestedTrees

protected

Number of infested trees in the pool to which this behavior applies (including resistant trees), below the cohort cutoff.

◆ m_iNumSmallCohortPoolTrees

long clDensDepInfestation::m_iNumSmallCohortPoolTrees

protected

Number of trees in the pool to which this behavior applies (including resistant trees), below the cohort cutoff.

◆ m_iNumSmallInfestibleTrees

long clDensDepInfestation::m_iNumSmallInfestibleTrees

protected

Number of trees that can be infested (non-resistant, regardless of current infestation status), below the cohort cutoff.

◆ m_iTotalNumSpecies

int clDensDepInfestation::m_iTotalNumSpecies

protected

Total number of species.

Primarily for the destructor.

◆ m_iYearsOfInfestation

int clDensDepInfestation::m_iYearsOfInfestation

protected

Years since infestation began - 0 if there is no current infestation.

◆ mp_fCohortDBH

double* clDensDepInfestation::mp_fCohortDBH

protected

Cohort cutoff DBH.

Trees above this size are infested before trees below it. Array size is total # species.

◆ mp_fMinDBH

double* clDensDepInfestation::mp_fMinDBH

protected

Minimum DBH for trees to be infested.

Array size is total # species.

◆ mp_fProbConditionallySusceptible

double* clDensDepInfestation::mp_fProbConditionallySusceptible

protected

Probability that a tree is conditionally susceptible, 0-1.

Array size is total # species.

◆ mp_fProbResistant

double* clDensDepInfestation::mp_fProbResistant

protected

Probability that a tree is resistant, 0-1.

Array size is total # species.

◆ mp_iDensDepResistanceStatusCodes

short int** clDensDepInfestation::mp_iDensDepResistanceStatusCodes

protected

Return codes for the "DensDepResistanceStatus" int tree data member.

Array index one is sized m_iTotalNumSpecies; array index two is sized number of total types.

◆ mp_iYearsInfestedCodes

short int** clDensDepInfestation::mp_iYearsInfestedCodes

protected

Return codes for the "YearsInfested" int tree data member.

Array index one is sized m_iTotalNumSpecies; array index two is sized number of total types.

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

DensDepInfestation.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ clDensDepInfestation()

◆ ~clDensDepInfestation()

Member Function Documentation

◆ Action()

◆ DetermineCohortInfestationProbability()

◆ EndInfestation()

◆ FormatQueryString()

◆ GetData()

◆ InfestInitialConditionsTrees()

◆ ReadParFile()

◆ RegisterTreeDataMembers()

◆ TreeInventory()

Member Data Documentation

◆ m_cQuery

◆ m_fA

◆ m_fBx

◆ m_fBy

◆ m_fLargeCohortProb

◆ m_fMax

◆ m_fPlotBA

◆ m_fPoolBA

◆ m_fSmallCohortProb

◆ m_iFirstTimestep

◆ m_iLastTimestep

◆ m_iNumLargeCohortInfestedTrees

◆ m_iNumLargeCohortPoolTrees

◆ m_iNumLargeInfestibleTrees

◆ m_iNumSmallCohortInfestedTrees

◆ m_iNumSmallCohortPoolTrees

◆ m_iNumSmallInfestibleTrees

◆ m_iTotalNumSpecies

◆ m_iYearsOfInfestation

◆ mp_fCohortDBH

◆ mp_fMinDBH

◆ mp_fProbConditionallySusceptible

◆ mp_fProbResistant

◆ mp_iDensDepResistanceStatusCodes

◆ mp_iYearsInfestedCodes