SORTIE Core C++ Documentation
|
NCI Mortality - Version 2.0. More...
#include <NCIMort.h>
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. | |
![]() | |
clMortalityBase (clSimManager *p_oSimManager) | |
Constructor. | |
virtual | ~clMortalityBase () |
Destructor. | |
void | Action () |
Performs mortality calculations. | |
clMortalityOrg * | GetMortOrg () |
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. | |
![]() | |
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. | |
![]() | |
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. | |
![]() | |
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. | |
![]() | |
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. | |
![]() | |
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. | |
stcSpeciesTypeCombo * | mp_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. | |
![]() | |
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 clMortalityOrg * | mp_oMortalityOrg |
clMortalityOrg object. | |
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:
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.
Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)
clNCIMort::clNCIMort | ( | clSimManager * | p_oSimManager | ) |
Constructor.
p_oSimManager | Sim Manager object. |
clNCIMort::~clNCIMort | ( | ) |
Destructor.
Frees memory.
|
virtual |
Determines mortality for a tree.
p_oTree | Tree being evaluated. |
fDbh | DBH of tree being evaluated. |
iSpecies | Species of tree being evaluated. |
Implements clMortalityBase.
|
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.
p_oDoc | DOM tree of parsed input tree. |
Reimplemented from clMortalityBase.
|
protected |
Populates m_cQuery with the query for getting NCI trees.
|
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).
modelErr | if a light code comes back -1 for any species which uses the shading effect. |
|
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.
p_oPop | Tree population. |
Reimplemented from clMortalityBase.
|
protected |
Reads data from the parameter file.
p_oDoc | DOM tree of parsed input tree. |
modelErr | if this behavior has been applied to any types except sapling and adult. |
|
protected |
Makes sure all input data is valid.
The following must all be true:
modelErr | if any of the above conditions are not met. |
|
protected |
Query string to get NCI trees.
|
protected |
Number of years per timestep.
From sim manager
|
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).