SORTIE Core C++ Documentation
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Weibull Climate survival - Version 1.0. More...
#include <WeibullClimateSurvival.h>
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. | |
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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. | |
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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. | |
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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. | |
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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. | |
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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. | |
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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. | |
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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 | |
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static clMortalityOrg * | mp_oMortalityOrg |
clMortalityOrg object. | |
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:
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:
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:
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.
Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)
clWeibullClimateSurvival::clWeibullClimateSurvival | ( | clSimManager * | p_oSimManager | ) |
Constructor.
p_oSimManager | Sim Manager object. |
clWeibullClimateSurvival::~clWeibullClimateSurvival | ( | ) |
Destructor.
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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.
p_oTree | Tree being evaluated. |
fDbh | DBH of tree being evaluated. |
iSpecies | Species of tree being evaluated. |
Implements clMortalityBase.
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virtual |
Does setup.
p_oDoc | DOM tree of parsed input tree. |
Reimplemented from clMortalityBase.
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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.
p_oTarget | Target tree for which to count the larger neighbors. |
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virtual |
Calculates temperature and precipitation effects for each species for the current time step.
p_oPop | Tree population. |
Reimplemented from clMortalityBase.
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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. |
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protected |
Makes sure all input data is valid.
The following must all be true:
modelErr | if any of the above conditions are not met. |
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protected |
Minimum sapling height.
For doing neighbor searches.
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protected |
Keep our own copy for the destructor.
This is the total number of tree species.
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protected |
Competition effect C.
Array is sized number of species to which this behavior applies.
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protected |
Competition effect D.
Array is sized number of species to which this behavior applies.
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protected |
Size sensitivity to crowding parameter.
γ in Competition Effect equation above. Array is sized number of species to which this behavior applies.
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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.
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protected |
Maximum potential annual survival value.
Array is sized number of species to which this behavior applies.
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protected |
The minimum DBH, in cm, of neighbors to be included in the neighbor count.
Array is sized number of species.
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protected |
Precipitation effect A.
Array is sized number of species to which this behavior applies.
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protected |
Precipitation effect B.
Array is sized number of species to which this behavior applies.
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protected |
Precipitation effect C.
Array is sized number of species to which this behavior applies.
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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.
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protected |
Size effect minimum DBH.
Array is sized number of species to which this behavior applies.
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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.
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protected |
Size effect Xb.
Array is sized number of species to which this behavior applies.
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protected |
Temperature effect A.
Array is sized number of species to which this behavior applies.
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protected |
Temperature effect B.
Array is sized number of species to which this behavior applies.
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protected |
Temperature effect C.
Array is sized number of species to which this behavior applies.
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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.
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protected |
Speeds access to the arrays.
Array size is number of species.