SORTIE Core C++ Documentation
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clWeibullClimateSurvival Class Reference

Weibull Climate survival - Version 1.0. More...

#include <WeibullClimateSurvival.h>

Inheritance diagram for clWeibullClimateSurvival:
clMortalityBase clBehaviorBase clWorkerBase

Public Member Functions

 clWeibullClimateSurvival (clSimManager *p_oSimManager)
 Constructor.
 
 ~clWeibullClimateSurvival ()
 Destructor.
 
deadCode DoMort (clTree *p_oTree, const float &fDbh, const short int &iSpecies)
 Determines mortality for a tree.
 
void DoShellSetup (xercesc::DOMDocument *p_oDoc)
 Does setup.
 
void PreMortCalcs (clTreePopulation *p_oPop)
 Calculates temperature and precipitation effects for each species for the current time step.
 
- 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.
 
int GetNumLargerNeighbors (clTree *p_oTarget)
 Counts the number of trees a target's neighborhood that have a DBH bigger than the target.
 
- 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

float * mp_fMaxRG
 Maximum potential annual survival value.
 
float * mp_fCompC
 Competition effect C.
 
float * mp_fCompD
 Competition effect D.
 
float * mp_fGamma
 Size sensitivity to crowding parameter.
 
double * mp_fSizeX0
 Size effect X0.
 
float * mp_fSizeXb
 Size effect Xb.
 
float * mp_fPrecipA
 Precipitation effect A.
 
float * mp_fPrecipB
 Precipitation effect B.
 
float * mp_fPrecipC
 Precipitation effect C.
 
float * mp_fTempA
 Temperature effect A.
 
float * mp_fTempB
 Temperature effect B.
 
float * mp_fTempC
 Temperature effect C.
 
float * mp_fTempEffect
 Temperature effect.
 
float * mp_fPrecipEffect
 Precipitation effect.
 
float * mp_fMaxCrowdingRadius
 Maximum search radius, in meters, in which to look for crowding neighbors.
 
float * mp_fMinimumNeighborDBH
 The minimum DBH, in cm, of neighbors to be included in the neighbor count.
 
float * mp_fSizeMinDBH
 Size effect minimum DBH.
 
short int * mp_iIndexes
 Speeds access to the arrays.
 
float m_fMinSaplingHeight
 Minimum sapling height.
 
short int m_iNumTotalSpecies
 Keep our own copy for the destructor.
 
- 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

Weibull Climate survival - Version 1.0.

This is a mortality shell object which calculates survival as a function of climate and neighbor density.

The equation for one year's survival is:

Probability of survival = Max Probability * Size Effect * Precipitation Effect * Climate Effect * Competition Effect

where Max Probability is the maximum annual survival possible, and the Effects are values between 0 and 1 which serve to reduce the maximum.

The equation for Size Effect is:

SE = exp(-0.5(ln(DBH/X0)/Xb)2)

where:

Size effect is subject to a minimum value for DBH, below which all trees will just get the minimum.

Precipitation Effect and Temperature Effect use the same function form. The function is: Climate Effect <- exp(-0.5*(abs(CV - C)/A)B) where:

Competition Effect is calculated as:

CE = exp(-(C * DBH γ * ndD)

where:

Snags, seedlings, and trees that are already dead from disturbance events are never counted in the neighbor count.

For multi year time steps, the annual probability of survival is raised to the power of the number of years per time step.

This cannot be applied to seedlings. An error will be thrown if seedlings are passed.

The parameter file call string for this is "WeibullClimateSurvival". The namestring for this behavior is "WeibullClimatemortshell".

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

clWeibullClimateSurvival::clWeibullClimateSurvival ( clSimManager p_oSimManager)

Constructor.

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

Destructor.

Member Function Documentation

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

Determines mortality for a tree.

For this tree, count the number of larger neighbors. Then calculate the probability of survival for each using the equations above. Use the random number generator to decide life or death.

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 clWeibullClimateSurvival::DoShellSetup ( xercesc::DOMDocument *  p_oDoc)
virtual

Does setup.

  1. ReadParameterFile() is called to read the parameter file's data.
  2. ValidateData() is called to validate the data.
Parameters
p_oDocDOM tree of parsed input tree.

Reimplemented from clMortalityBase.

int clWeibullClimateSurvival::GetNumLargerNeighbors ( clTree p_oTarget)
protected

Counts the number of trees a target's neighborhood that have a DBH bigger than the target.

Neighbors must have a DBH greater than the minimum. They also cannot be dead from a disturbance event; but any trees that have a dead code of "natural" are assumed to have died in the current time step mortality cycle and thus should be counted.

Parameters
p_oTargetTarget tree for which to count the larger neighbors.
Returns
Number of larger neighbors.
void clWeibullClimateSurvival::PreMortCalcs ( clTreePopulation p_oPop)
virtual

Calculates temperature and precipitation effects for each species for the current time step.

Parameters
p_oPopTree population.

Reimplemented from clMortalityBase.

void clWeibullClimateSurvival::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 clWeibullClimateSurvival::ValidateData ( )
protected

Makes sure all input data is valid.

The following must all be true:

  • Max radius of neighbor effects must be > 0
  • Max survival for each species must be between 0 and 1
  • Temp and precip A for each species must be > 0
  • X0 (size effect mode) for each species must be > 0
  • Xb (size effect variance) for each species must not = 0
Exceptions
modelErrif any of the above conditions are not met.

Member Data Documentation

float clWeibullClimateSurvival::m_fMinSaplingHeight
protected

Minimum sapling height.

For doing neighbor searches.

short int clWeibullClimateSurvival::m_iNumTotalSpecies
protected

Keep our own copy for the destructor.

This is the total number of tree species.

float* clWeibullClimateSurvival::mp_fCompC
protected

Competition effect C.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fCompD
protected

Competition effect D.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fGamma
protected

Size sensitivity to crowding parameter.

γ in Competition Effect equation above. Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fMaxCrowdingRadius
protected

Maximum search radius, in meters, in which to look for crowding neighbors.

For calculating the Competition Effect. Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fMaxRG
protected

Maximum potential annual survival value.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fMinimumNeighborDBH
protected

The minimum DBH, in cm, of neighbors to be included in the neighbor count.

Array is sized number of species.

float* clWeibullClimateSurvival::mp_fPrecipA
protected

Precipitation effect A.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fPrecipB
protected

Precipitation effect B.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fPrecipC
protected

Precipitation effect C.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fPrecipEffect
protected

Precipitation effect.

Keep a copy so we only have to calculate once per time step. Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fSizeMinDBH
protected

Size effect minimum DBH.

Array is sized number of species to which this behavior applies.

double* clWeibullClimateSurvival::mp_fSizeX0
protected

Size effect X0.

This must be an array of doubles in order to support very small values. Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fSizeXb
protected

Size effect Xb.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fTempA
protected

Temperature effect A.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fTempB
protected

Temperature effect B.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fTempC
protected

Temperature effect C.

Array is sized number of species to which this behavior applies.

float* clWeibullClimateSurvival::mp_fTempEffect
protected

Temperature effect.

Keep a copy so we only have to calculate once per time step. Array is sized number of species to which this behavior applies.

short int* clWeibullClimateSurvival::mp_iIndexes
protected

Speeds access to the arrays.

Array size is number of species.


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