Insect Infestation version 1.0. More...
#include <InsectInfestation.h>
Public Member Functions | |
| clInsectInfestation (clSimManager *p_oSimManager) | |
| Constructor. More... | |
| ~clInsectInfestation () | |
| 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" int data member. 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 | GetInfestationRate (long *p_iTotalTrees, long *p_iInfTrees) |
| Gets the current rate of infestation in the tree population. 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_iDataCodes |
| Return codes for the "YearsInfested" int tree data member. More... | |
| double * | mp_fIntercept |
| Intercept parameter - rate of infestation at time 1. More... | |
| double * | mp_fMax |
| Maximum infestation rate for each species. More... | |
| double * | mp_fX0 |
| The "X0" parameter for each species. More... | |
| double * | mp_fXb |
| The "Xb" parameter for each species. More... | |
| double * | mp_fMinDBH |
| Minimum DBH for trees to be infested. More... | |
| char * | m_cQuery |
| String to pass to clTreePopulation::Find() in order to get the trees to apply damage to. 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... | |
| 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
Insect Infestation version 1.0.
This behavior simulates a spreading insect infestation throughout the tree population.
The proportion of trees infested as a lognormal function of time is as follows:
P = I +((MAX-I)/(1+(T/X0)^Xb))
where:
- P is the proportion infested
- I is the function intercept, or the initial infestation rate
- MAX is the maximum infestation rate
- T is the time since the start of the infestation
- X0 is the time at which 50% of the population is infested
- Xb controls the steepness of the infestation curve
Infestation begins at a time step chosen by the user. Infestation continues until there are no more infested trees in the plot, or the ending timestep if the user indicates one.
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.
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.
An integer data member is added to trees that tracks the number of years that they have been infested. This data member is called "YearsInfested".
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 "InsectInfestation".
Copyright 2011 Charles D. Canham
Constructor & Destructor Documentation
◆ clInsectInfestation()
| clInsectInfestation::clInsectInfestation | ( | clSimManager * | p_oSimManager | ) |
Constructor.
- Parameters
-
p_oSimManager Sim Manager object.
◆ ~clInsectInfestation()
| clInsectInfestation::~clInsectInfestation | ( | ) |
Destructor.
Frees memory.
Member Function Documentation
◆ Action()
|
virtual |
Does insect infestation each timestep.
If the timestep has not yet reached the value in m_iFirstTimestep, or if the value in m_iYearsOfInfestation is 0 (indicating an infestation is over), then nothing happens.
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.
◆ 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()
|
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()
|
virtual |
Does behavior setup.
Calls the following functions:
- Parameters
-
p_oDoc DOM tree of parsed input file.
Implements clWorkerBase.
◆ GetInfestationRate()
|
protected |
Gets the current rate of infestation in the tree population.
This counts the total number of trees of each species eligible for infestation, and the number of those that are currently infested.
- Parameters
-
p_iTotalTrees Pointer to an array, sized m_iTotalNumSpecies, into which to put the total number of trees found of each species. p_iInfTrees Pointer to an array, sized m_iTotalNumSpecies, into which to put the infested number of trees found of each species.
◆ ReadParFile()
|
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 timestep to start infestation is less than 0
- The maximum infestation rate for any species is not between 0 and 1
- The infestation intercept for any species is not between 0 and 1
- The value for X0 for any species is 0
◆ RegisterTreeDataMembers()
|
virtual |
Registers the "YearsInfested" int data member.
The return codes are captured in the mp_iDataCodes array.
Reimplemented from clBehaviorBase.
Member Data Documentation
◆ 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_iFirstTimestep
|
protected |
Timestep to begin infestation.
◆ m_iLastTimestep
|
protected |
Timestep to end infestation.
◆ m_iTotalNumSpecies
|
protected |
Total number of species.
Primarily for the destructor.
◆ m_iYearsOfInfestation
|
protected |
Years since infestation began - 0 if there is no current infestation.
◆ mp_fIntercept
|
protected |
Intercept parameter - rate of infestation at time 1.
Array size is total # species.
◆ mp_fMax
|
protected |
Maximum infestation rate for each species.
Array size is total # species.
◆ mp_fMinDBH
|
protected |
Minimum DBH for trees to be infested.
Array size is total # species.
◆ mp_fX0
|
protected |
The "X0" parameter for each species.
Array size is total # species.
◆ mp_fXb
|
protected |
The "Xb" parameter for each species.
Array size is total # species.
◆ mp_iDataCodes
|
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:
