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clNCIMort Class Reference

NCI Mortality - Version 2.0. More...

#include <NCIMort.h>

Inheritance diagram for clNCIMort:
clMortalityBase clNCIBase clBehaviorBase clWorkerBase

Public Member Functions

 clNCIMort (clSimManager *p_oSimManager)
 Constructor.
 
 ~clNCIMort ()
 Destructor.
 
deadCode DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
 Determines mortality for a tree.
 
void DoShellSetup (xercesc::DOMDocument *p_oDoc)
 Performs behavior setup.
 
void PreMortCalcs (clTreePopulation *p_oPop)
 Performs calculations before any trees have been killed.
 
- Public Member Functions inherited from clMortalityBase
 clMortalityBase (clSimManager *p_oSimManager)
 Constructor.
 
virtual ~clMortalityBase ()
 Destructor.
 
void Action ()
 Performs mortality calculations.
 
clMortalityOrgGetMortOrg ()
 Gets the mortality org object.
 
void RegisterTreeDataMembers ()
 Triggers the mortality data member registrations.
 
short int GetNewTreeInts ()
 Overridden from clBehaviorBase.
 
bool UsesThisMortality (short int iSp, short int iTp)
 Whether or not a species/type combo uses this mortality object.
 
- Public Member Functions inherited from clBehaviorBase
virtual float GetBehaviorVersion ()
 Gets the behavior version number.
 
 clBehaviorBase (clSimManager *p_oSimManager)
 Constructor.
 
virtual ~clBehaviorBase ()
 Destructor.
 
virtual short int ValidateVersionNumber (float fTestVersion)
 Makes sure that the version number of a file passed is between the minimum and current version numbers.
 
virtual void SetSpeciesTypeCombos (short int iNumCombos, stcSpeciesTypeCombo *p_whatCombos)
 Sets the species/type combos for a behavior.
 
virtual void SetNameData (char *cNameString)
 Sets the string for the parameter file behavior.
 
virtual short int GetNewTreeFloats ()
 Gets the number of new tree float data members this behavior wants to register.
 
virtual short int GetNewTreeChars ()
 Gets the number of new tree character data members this behavior wants to register.
 
virtual short int GetNewTreeBools ()
 Gets the number of new tree bool data members this behavior wants to register.
 
virtual short int GetNumSpeciesTypeCombos ()
 Gets the number of species/type combos to which this behavior applies.
 
virtual short int GetNumBehaviorSpecies ()
 Gets the number of unique tree species to which this behavior applies.
 
struct stcSpeciesTypeCombo GetSpeciesTypeCombo (short int iIndex)
 Gets one of this behavior's type/species combos.
 
virtual short int GetBehaviorSpecies (short int iIndex)
 Gets one of the behavior's species.
 
short int GetBehaviorListNumber ()
 Gets the behavior list number for this behavior, which differentiates between multiple copies of the behavior in the behavior list.
 
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.
 
virtual DOMElement * GetParentParametersElement (xercesc::DOMDocument *p_oDoc)
 Formats the string for species/types query.
 
- Public Member Functions inherited from clWorkerBase
 clWorkerBase (clSimManager *p_oSimManager)
 Constructor.
 
virtual ~clWorkerBase ()
 Destructor.
 
char * GetName ()
 Gets the object's namestring.
 
void DoObjectSetup (xercesc::DOMDocument *p_oDoc, fileType iFileType)
 Triggers the setup process.
 
virtual void TimestepCleanup ()
 Performs any necessary cleanup operations at the end of a timestep.
 
virtual void EndOfRunCleanup ()
 Performs any necessary cleanup operations at the end of a run.
 
virtual void DoCommand (char *cCommand, char *cArguments)
 If a behavior has registered a command line command with the sim manager, this allows it to be called.
 

Protected Member Functions

void ValidateData ()
 Makes sure all input data is valid.
 
void ReadParameterFile (xercesc::DOMDocument *p_oDoc)
 Reads data from the parameter file.
 
void GetTreeMemberCodes ()
 Gets the return codes for needed tree data members.
 
void FormatQuery ()
 Populates m_cQuery with the query for getting NCI trees.
 
- Protected Member Functions inherited from clMortalityBase
void GetData (xercesc::DOMDocument *p_oDoc)
 Triggers all mortality setup.
 
void PopulateUsesThisMortality ()
 Declares and populates the mp_bUsesThisMortality array.
 

Protected Attributes

short int ** mp_iDeadCodes
 Return codes for the "dead" tree int data member variable.
 
float m_fNumberYearsPerTimestep
 Number of years per timestep.
 
char * m_cQuery
 Query string to get NCI trees.
 
- Protected Attributes inherited from clMortalityBase
short int m_iNumTotalSpecies
 Keep a copy for the constructor.
 
bool m_bHooked
 Whether or not this shell object is hooked to clMortalityOrg.
 
bool ** mp_bUsesThisMortality
 2D array, species by type, of whether or not this mortality shell applies to a given species/type combo.
 
- Protected Attributes inherited from clBehaviorBase
short int m_iNumSpeciesTypeCombos
 How many type/species combos a behavior will act on.
 
short int m_iNumBehaviorSpecies
 How many distinct species are in the combo list - important for filling species-specific values from parameter file.
 
short int * mp_iWhatSpecies
 List of distinct species - for filling species-specific values from parameter file.
 
stcSpeciesTypeCombomp_whatSpeciesTypeCombos
 Array of species/type combos that the behavior will act on.
 
short int m_iNewTreeInts
 The number of new tree integer data members this behavior wants to add.
 
short int m_iNewTreeFloats
 The number of new tree float data members this behavior wants to add.
 
short int m_iNewTreeChars
 The number of new tree character data members this behavior wants to add.
 
short int m_iNewTreeBools
 The number of new tree boolean data members this behavior wants to add.
 
short int m_iBehaviorListNumber
 The number of this behavior in the behavior list, to differentiate between possible multiple copies of this behavior.
 
float m_fVersionNumber
 Version number - this will be rounded to 2 digits after the decimal place.
 
std::string m_sXMLRoot
 XML root that encloses the parameters for this behavior.
 
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.
 
- Protected Attributes inherited from clWorkerBase
char m_cNameString [MAX_NAMESTRING_SIZE]
 Object's identifying namestring.
 
int * mp_iAllowedFileTypes
 List of the input file types this object can handle.
 
int m_iNumAllowedTypes
 Number of input file types this object can handle.
 

Additional Inherited Members

- Static Protected Attributes inherited from clMortalityBase
static clMortalityOrgmp_oMortalityOrg
 clMortalityOrg object.
 

Detailed Description

NCI Mortality - Version 2.0.

This is a mortality shell object which applies an NCI (neighborhood competition index) function to assess probability of survival.

The function for annual survival probability:

Survival probability = Max Probability * Damage Effect * Size Effect * Crowding Effect * Shading Effect

All NCI calculations are performed according to clNCIBase.

The annual survival probability is compounded for multi-year timesteps by taking it to the X power, where X is the number of years per timestep.

This is a generic behavior. It is expected that not all terms in the equation will be used. A user can turn off some of the terms by setting key parameters to 0 or 1. To be efficient, this behavior looks for this and has several alternate function forms to avoid extra math. It calls the correct function form through function pointers, which it sets during setup.

The namestring for this class is "ncimortshell". The parameter file call string is "NCIMortality".

This behavior adds a new boolean data member called "NCI Mort". This holds the result of the mortality calculation that happens before the main mortality process. This is so neighbors that die this timestep aren't artificially excluded from the NCI calculation.

This behavior can only be applied to saplings and adults.

If the user is using damage parameters, this behavior must be used in conjunction with the storm damage behavior. If the user is using shading, then this must be used in conjunction with a light behavior.

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

clNCIMort::clNCIMort ( clSimManager p_oSimManager)

Constructor.

Parameters
p_oSimManagerSim Manager object.
clNCIMort::~clNCIMort ( )

Destructor.

Frees memory.

Member Function Documentation

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

Determines mortality for a tree.

Parameters
p_oTreeTree being evaluated.
fDbhDBH of tree being evaluated.
iSpeciesSpecies of tree being evaluated.
Returns
natural if the tree is to die, notdead if it lives.

Implements clMortalityBase.

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

Performs behavior setup.

First, ReadParameterFile() is called to read the parameter file's data. Then ValidateData() is called to validate the data. Then GetTreeMemberCodes() is called to get tree data return codes.

Parameters
p_oDocDOM tree of parsed input tree.

Reimplemented from clMortalityBase.

void clNCIMort::FormatQuery ( )
protected

Populates m_cQuery with the query for getting NCI trees.

void clNCIMort::GetTreeMemberCodes ( )
protected

Gets the return codes for needed tree data members.

This declares and populates the mp_iDamageCodes array with the return codes for the "stm_dmg" tree int data member, and does the same for the mp_iLightCodes array and the "Light" tree float data member for any species which uses the shading effect (shading coefficient != 0).

Exceptions
modelErrif a light code comes back -1 for any species which uses the shading effect.
void clNCIMort::PreMortCalcs ( clTreePopulation p_oPop)
virtual

Performs calculations before any trees have been killed.

This finds all trees to which this behavior applies and performs their NCI calculations. Then, having done all that work, this function goes ahead and assesses the tree's mortality. Whether it lives or dies is then stashed in the "NCI Mort" bool tree data member.

Parameters
p_oPopTree population.

Reimplemented from clMortalityBase.

void clNCIMort::ReadParameterFile ( xercesc::DOMDocument *  p_oDoc)
protected

Reads data from the parameter file.

Parameters
p_oDocDOM tree of parsed input tree.
Exceptions
modelErrif this behavior has been applied to any types except sapling and adult.
void clNCIMort::ValidateData ( )
protected

Makes sure all input data is valid.

The following must all be true:

  • Max. radius of Crowding Effects must be > 0
  • Max probability of survival for each species must be 0-1
  • X0 (Size effect mode) for each species must not = 0
  • Xb (Size effect variance) for each species must not = 0
  • Eta for each species for each damage category beyond undamaged must be between 0 and 1
  • Storm Effect parameters for each species for each damage category beyond undamaged must be between 0 and 1
  • Minimum neighbor DBH must not be less than 0
Exceptions
modelErrif any of the above conditions are not met.

Member Data Documentation

char* clNCIMort::m_cQuery
protected

Query string to get NCI trees.

float clNCIMort::m_fNumberYearsPerTimestep
protected

Number of years per timestep.

From sim manager

short int** clNCIMort::mp_iDeadCodes
protected

Return codes for the "dead" tree int data member variable.

Array size is number of species by number of tree types (even if not every species and type is represented).


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