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clStochDoubleLogTempDepNeighDisperse Class Reference

Stochastic double logistic temperature dependent neighborhood disperse - Version 1.0. More...

#include <StochDoubleLogTempDepNeighDisperse.h>

Inheritance diagram for clStochDoubleLogTempDepNeighDisperse:
clDisperseBase clBehaviorBase clWorkerBase

Public Member Functions

 clStochDoubleLogTempDepNeighDisperse (clSimManager *p_oSimManager)
 Constructor. More...
 
 ~clStochDoubleLogTempDepNeighDisperse ()
 Destructor. More...
 
- Public Member Functions inherited from clDisperseBase
 clDisperseBase (clSimManager *p_oSimManager)
 Constructor. More...
 
virtual ~clDisperseBase ()
 Destroys common objects. More...
 
void Action ()
 Performs all disperse calculations. More...
 
void TimestepCleanup ()
 Resets all values in the seed grid to 0 and sets the static m_bUpdatedGapStatus to false if this is a hooked object. 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 RegisterTreeDataMembers ()
 Registers tree data members. 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 GetNewTreeInts ()
 Gets the number of new tree integer data members this behavior wants to register. 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 EndOfRunCleanup ()
 Performs any necessary cleanup operations at the end of a run. More...
 

Protected Member Functions

void DoShellSetup (xercesc::DOMDocument *p_oDoc)
 Reads in parameter file values. More...
 
void AddSeeds ()
 Does dispersal. More...
 
- Protected Member Functions inherited from clDisperseBase
void GetData (xercesc::DOMDocument *p_oDoc)
 Triggers all disperse setup if an object is hooked. More...
 
void SetUpBase ()
 Does disperse base setup. 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...
 

Protected Attributes

double * mp_fPA
 Colonization a - sized number of species. More...
 
double * mp_fPB
 Colonization b - sized number of species. More...
 
double * mp_fPM
 Colonization m - sized number of species. More...
 
double * mp_fAl
 Temperature dependence of fecundity al - sized number of species. More...
 
double * mp_fBl
 Temperature dependence of fecundity bl - sized number of species. More...
 
double * mp_fCl
 Temperature dependence of fecundity cl - sized number of species. More...
 
double * mp_fAh
 Temperature dependence of fecundity ah - sized number of species. More...
 
double * mp_fBh
 Temperature dependence of fecundity bh - sized number of species. More...
 
double * mp_fCh
 Temperature dependence of fecundity ch - sized number of species. More...
 
double * mp_fA
 A parameter - sized number of species. More...
 
double * mp_fB
 B parameter - sized number of species. More...
 
double m_fRadius
 Neighborhood search radius. More...
 
float m_fMinSaplingHeight
 Minimum sapling height. More...
 
double m_fAnalysisPlotSize
 Original analysis plot size, square meters. More...
 
double m_fAnnualizePeriod
 T, in years, to go from cumulative to annualized probability. More...
 
bool m_bDeterministic
 If true, seed number is deterministic. More...
 
bool m_bFecTempDep
 If true, use temperature-dependent portion of fecundity. More...
 
- Protected Attributes inherited from clDisperseBase
bool m_bHooked
 
- 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 Types inherited from clDisperseBase
enum  function { weibull, lognormal }
 What PDF is used by a species. More...
 
enum  cover { gap, canopy }
 Cover status. More...
 
- Static Protected Attributes inherited from clDisperseBase
static clDisperseOrgmp_oDisperseOrg
 clDisperseOrg object - this pointer is held in common by all shells More...
 
static clGridmp_oSeedGrid
 Seed grid. More...
 
static short int * mp_iNumSeedsCode
 Data member codes for "dispersed seeds" grid for "seeds_x" data member. More...
 
static short int m_iGapCountCode
 Data member code - for counting trees for gap status. More...
 
static short int m_iIsGapCode
 Data member code for substrate grid for gap status. More...
 
static short int m_iTotalSpecies
 Total number of species. More...
 
static bool m_bUpdatedGapStatus
 A flag indicating whether or not the gap status of the seed grid has been updated this timestep. More...
 
static bool m_bIsStochastic
 Whether dispersal is stochastic (true) or deterministic (false). More...
 

Detailed Description

Stochastic double logistic temperature dependent neighborhood disperse - Version 1.0.

This class disperses seeds. The number of seeds is a function of the plot annual mean temperature and the basal area of conspecific adults.

If seeds are dispersed for a cell, the number of seeds per GRID CELL per year is calculated as:

Seeds = (a + fec * BAC) * corr

where

The "fec" term is fecundity, calculated as:

fec = fb* (al + ((1-al)/(1+(bl/X)^cl))) * (ah + ((1-ah)/(1+(X/bh)^ch)))

where X is the plot annual mean temperature IN K and fb, al, bl, cl, ah, bh, and ch are parameters. The user has the option to turn off the temperature- dependent portion of fecundity, in which case fec = fb.

The number of seeds per cell can be used as-is or used as the mean in a Poisson draw. This value is multiplied by number of years per timestep to arrive at the number of seeds per grid cell.

Colonization: The above equation for seeds includes an intercept term, which means there is the possibility for bath rain of species for which there are no adults. A species for which there are adults will always disperse. A species for which there are no adults must undergo a "colonization test". The cumulative probability of colonization (PCa) of seedlings is:

PCc = pa*(exp(-0.5*(((temp.C - pm)/pb)^2))))

where temp.C is the plot annual mean temperature in C and pac, pbc, and pmc are parameters.

This is annualized with a time period parameter t:

PCa = 1 – [(1 – PCc)^(1/t)]

If a random draw is less than or equal to PCa, then seed input is done as if there were adults present in the plot, on a quadrat by quadrat basis.

This behavior is not connected to any specific species-type combo, but is connected to specific species. There should be applyTo tags for this behavior and a unique list of species will be compiled for those tags with the type being ignored.

This behavior's namestring and parameter file call string are both "StochDoubleLogTempDepNeighDisperse".

Copyright 2014 Charles D. Canham.

Author
Lora E. Murphy


Edit history:
--------------—
February 20, 2014 - Created (LEM)

Constructor & Destructor Documentation

◆ clStochDoubleLogTempDepNeighDisperse()

clStochDoubleLogTempDepNeighDisperse::clStochDoubleLogTempDepNeighDisperse ( clSimManager p_oSimManager)

Constructor.

Parameters
p_oSimManagerSim Manager object.

◆ ~clStochDoubleLogTempDepNeighDisperse()

clStochDoubleLogTempDepNeighDisperse::~clStochDoubleLogTempDepNeighDisperse ( )

Destructor.

Member Function Documentation

◆ AddSeeds()

void clStochDoubleLogTempDepNeighDisperse::AddSeeds ( )
protectedvirtual

Does dispersal.

Implements clDisperseBase.

◆ DoShellSetup()

void clStochDoubleLogTempDepNeighDisperse::DoShellSetup ( xercesc::DOMDocument *  p_oDoc)
protectedvirtual

Reads in parameter file values.

Parameters
p_oDocDOM tree of parsed parameter file.

Implements clDisperseBase.

Member Data Documentation

◆ m_bDeterministic

bool clStochDoubleLogTempDepNeighDisperse::m_bDeterministic
protected

If true, seed number is deterministic.

If false, Poisson-distributed.

◆ m_bFecTempDep

bool clStochDoubleLogTempDepNeighDisperse::m_bFecTempDep
protected

If true, use temperature-dependent portion of fecundity.

◆ m_fAnalysisPlotSize

double clStochDoubleLogTempDepNeighDisperse::m_fAnalysisPlotSize
protected

Original analysis plot size, square meters.

◆ m_fAnnualizePeriod

double clStochDoubleLogTempDepNeighDisperse::m_fAnnualizePeriod
protected

T, in years, to go from cumulative to annualized probability.

◆ m_fMinSaplingHeight

float clStochDoubleLogTempDepNeighDisperse::m_fMinSaplingHeight
protected

Minimum sapling height.

For doing neighbor searches.

◆ m_fRadius

double clStochDoubleLogTempDepNeighDisperse::m_fRadius
protected

Neighborhood search radius.

◆ mp_fA

double* clStochDoubleLogTempDepNeighDisperse::mp_fA
protected

A parameter - sized number of species.

◆ mp_fAh

double* clStochDoubleLogTempDepNeighDisperse::mp_fAh
protected

Temperature dependence of fecundity ah - sized number of species.

◆ mp_fAl

double* clStochDoubleLogTempDepNeighDisperse::mp_fAl
protected

Temperature dependence of fecundity al - sized number of species.

◆ mp_fB

double* clStochDoubleLogTempDepNeighDisperse::mp_fB
protected

B parameter - sized number of species.

◆ mp_fBh

double* clStochDoubleLogTempDepNeighDisperse::mp_fBh
protected

Temperature dependence of fecundity bh - sized number of species.

◆ mp_fBl

double* clStochDoubleLogTempDepNeighDisperse::mp_fBl
protected

Temperature dependence of fecundity bl - sized number of species.

◆ mp_fCh

double* clStochDoubleLogTempDepNeighDisperse::mp_fCh
protected

Temperature dependence of fecundity ch - sized number of species.

◆ mp_fCl

double* clStochDoubleLogTempDepNeighDisperse::mp_fCl
protected

Temperature dependence of fecundity cl - sized number of species.

◆ mp_fPA

double* clStochDoubleLogTempDepNeighDisperse::mp_fPA
protected

Colonization a - sized number of species.

◆ mp_fPB

double* clStochDoubleLogTempDepNeighDisperse::mp_fPB
protected

Colonization b - sized number of species.

◆ mp_fPM

double* clStochDoubleLogTempDepNeighDisperse::mp_fPM
protected

Colonization m - sized number of species.


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