SORTIE Core C++ Documentation
Public Member Functions | Protected Attributes | List of all members
clInsectInfestationMortality Class Reference

Insect Infestation Mortality - Version 1.0. More...

#include <InsectInfestationMortality.h>

Inheritance diagram for clInsectInfestationMortality:
clMortalityBase clBehaviorBase clWorkerBase

Public Member Functions

 clInsectInfestationMortality (clSimManager *p_oSimManager)
 Constructor. More...
 
 ~clInsectInfestationMortality ()
 Destructor. More...
 
void DoShellSetup (xercesc::DOMDocument *p_oDoc)
 Reads in values from the parameter file. More...
 
deadCode DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
 Calculates mortality. More...
 
- Public Member Functions inherited from clMortalityBase
 clMortalityBase (clSimManager *p_oSimManager)
 Constructor. More...
 
virtual ~clMortalityBase ()
 Destructor. More...
 
void Action ()
 Performs mortality calculations. More...
 
clMortalityOrgGetMortOrg ()
 Gets the mortality org object. More...
 
void RegisterTreeDataMembers ()
 Triggers the mortality data member registrations. More...
 
short int GetNewTreeInts ()
 Overridden from clBehaviorBase. More...
 
bool UsesThisMortality (short int iSp, short int iTp)
 Whether or not a species/type combo uses this mortality object. More...
 
virtual void PreMortCalcs (clTreePopulation *p_oPop)
 Performs calculations before any trees have been killed. 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 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 Attributes

double ** mp_fMortProbs
 Precalculated mortality probabilities, out to m_iMaxMortTime; any infestation time beyond this can be calculated as a one-off. More...
 
double * mp_fIntercept
 Intercept - sized number of species. More...
 
double * mp_fMax
 Max mort rate - sized number of species. More...
 
double * mp_fX0
 X0 - sized number of species. More...
 
double * mp_fXb
 Xb - sized number of species. More...
 
short int ** mp_iDataCodes
 Codes for "YearsInfested" data member. More...
 
short int m_iNumSpecies
 Number of species. More...
 
short int m_iMaxMortTime
 Max number of pre-calculated mortalities. More...
 
- Protected Attributes inherited from clMortalityBase
short int m_iNumTotalSpecies
 Keep a copy for the constructor. More...
 
bool m_bHooked
 Whether or not this shell object is hooked to clMortalityOrg. More...
 
bool ** mp_bUsesThisMortality
 2D array, species by type, of whether or not this mortality shell applies to a given species/type combo. 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

- Protected Member Functions inherited from clMortalityBase
void GetData (xercesc::DOMDocument *p_oDoc)
 Triggers all mortality setup. More...
 
void PopulateUsesThisMortality ()
 Declares and populates the mp_bUsesThisMortality array. 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...
 
- Static Protected Attributes inherited from clMortalityBase
static clMortalityOrgmp_oMortalityOrg
 clMortalityOrg object. More...
 

Detailed Description

Insect Infestation Mortality - Version 1.0.

This evaluates mortality for trees that have an insect infestation.

The probability of death is a function of the number of years infested, as follows:

P = I +((MAX - I)/(1+(T/X0)^Xb))

where P is mortality probability, I is the intercept (mortality at time of infestation), MAX is max mortality probability, T is infestation time in years, X0 is time at which mortality prob = 0.5, and Xb controls steepness of the mortality increase.

A random number determines whether the trees die. Those that die have "insect" passed as the reason code.

Insect infestation is determined by the behavior of class clInsectInfestation. This class expects that behavior to be enabled and the "YearsInfested" int data member to be present for all trees to which this behavior is applied.

This class's namestring is "insect infestation mortshell". The parameter file call string is "InsectInfestationMortality".

Copyright 2011 Charles D. Canham.

Author
Lora E. Murphy


Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)

Constructor & Destructor Documentation

◆ clInsectInfestationMortality()

clInsectInfestationMortality::clInsectInfestationMortality ( clSimManager p_oSimManager)

Constructor.

Parameters
p_oSimManagerSim Manager object.

◆ ~clInsectInfestationMortality()

clInsectInfestationMortality::~clInsectInfestationMortality ( )

Destructor.

Member Function Documentation

◆ DoMort()

deadCode clInsectInfestationMortality::DoMort ( clTree p_oTree,
const float &  fDbh,
const short int &  iSpecies 
)
virtual

Calculates mortality.

This retrieves the tree's time of infestation. If it is infested, the mortality probability for that year is compared to a random number to see if the tree lives or dies. If it is uninfested, it does not die.

Parameters
p_oTreeTree being evaluated
fDbhTree's DBH
iSpeciesSpecies of the tree being evaluated
Returns
insects if the tree is to die, notdead if it lives.

Implements clMortalityBase.

◆ DoShellSetup()

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

Reads in values from the parameter file.

Parameters
p_oDocDOM tree of parsed input file.
Exceptions
modelErrif:
  • "YearsInfested" is not registered for any tree to which this behavior is applied
  • MAX is not between 0 and 1
  • Intercept is not between 0 and 1
  • X0 = 0

Reimplemented from clMortalityBase.

Member Data Documentation

◆ m_iMaxMortTime

short int clInsectInfestationMortality::m_iMaxMortTime
protected

Max number of pre-calculated mortalities.

This will be the biggest value of 2*X0.

◆ m_iNumSpecies

short int clInsectInfestationMortality::m_iNumSpecies
protected

Number of species.

For destructor.

◆ mp_fIntercept

double* clInsectInfestationMortality::mp_fIntercept
protected

Intercept - sized number of species.

◆ mp_fMax

double* clInsectInfestationMortality::mp_fMax
protected

Max mort rate - sized number of species.

◆ mp_fMortProbs

double** clInsectInfestationMortality::mp_fMortProbs
protected

Precalculated mortality probabilities, out to m_iMaxMortTime; any infestation time beyond this can be calculated as a one-off.

First index is species, second is time of infestation

◆ mp_fX0

double* clInsectInfestationMortality::mp_fX0
protected

X0 - sized number of species.

◆ mp_fXb

double* clInsectInfestationMortality::mp_fXb
protected

Xb - sized number of species.

◆ mp_iDataCodes

short int** clInsectInfestationMortality::mp_iDataCodes
protected

Codes for "YearsInfested" data member.

Array size is number of species by number of types.


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