clMastingSpatialDisperse Class Reference

Spatial disperse with masting - Version 1.0. More...

#include <MastingSpatialDisperse.h>

Inheritance diagram for clMastingSpatialDisperse:

clDisperseBase clBehaviorBase clWorkerBase

List of all members.

Public Member Functions

 clMastingSpatialDisperse (clSimManager *p_oSimManager)
 Constructor.
 ~clMastingSpatialDisperse ()
 Destructor.
mastEvent GetMastEvent (int iSp)
 Get whether a given species masted this timestep.

Protected Member Functions

void DoShellSetup (xercesc::DOMDocument *p_oDoc)
 Does setup.
void CalcMastCDF (xercesc::DOMDocument *p_oDoc)
 Calculates the masting cumulative distribution function.
void CalcSeedCDF (xercesc::DOMDocument *p_oDoc, clTreePopulation *p_oPop)
 Calculates the cumulative distribution functions for seed dispersal.
void FormatQueryString (clTreePopulation *p_oPop)
 Formats the string in m_cQuery.
void DisperseOneParentSeeds (clTree *p_oTree, clTreePopulation *p_oPop, clPlot *p_oPlot, float fDbh)
 Performs dispersal of seeds for one tree.
void GetParameterFileData (xercesc::DOMDocument *p_oDoc, clTreePopulation *p_oPop)
 Extracts needed parameter file data.
void PopulateUsedTable (clTreePopulation *p_oPop)
 Declares and populates the mp_bIsUsed array.
void SetGetSeedsFunctionPointers ()
 This figures out how each species's number of seeds is calculated.
void CalculateProbabilityDistribution (float *p_fProbArray, const int &iMaxDistance, const function &iFunction, const float &fDispersalX0, const float &fThetaXb)
 Calculates the normalized probability distribution for a function for one species.
void AddSeeds ()
 Performs disperse.
void DecideMast ()
 Decides whether masting events occur for each species.
float GetNumberOfSeedsNoDraw (const float &fDbh, const short int &iSp)
 Gets the number of seeds for a tree when there does not need to be an STR draw.
float GetNumberOfSeedsDrawNormal (const float &fDbh, const short int &iSp)
 Gets the number of seeds for a tree when the tree needs a normal STR draw.
float GetNumberOfSeedsDrawLognormal (const float &fDbh, const short int &iSp)
 Gets the number of seeds for a tree when the tree needs a lognormal STR draw.

Protected Attributes

float *** mp_fSeedCDF
 For testing.
float ** mp_fStrMean
 STR mean (or STR value if deterministic).
float ** mp_fStrStdDev
 STR standard deviation.
float ** mp_fBeta
 Beta parameter.
float ** mp_fMastCDF
 Masting cumulative distribution function.
float ** mp_fFractionParticipating
 Fraction participating in disperse.
bool ** mp_bIsUsed
 Whether this behavior is used by a species/type combo.
float * mp_fFecundity
 Fecundity, if it is possible to pre-calculate it.
int * mp_iTimestepsSinceLastMast
 Number of years since the last mast for each species.
short int * mp_iIndexes
 This will speed access to the other arrays by storing each species' array index so the other arrays only have to be as big as the number of unique species for this behavior.
short int * mp_iGroup
 Group affiliation of the species.
pdfmp_iWhatPDFForSTR
 What PDF is used to draw the STR.
functionmp_iWhatFunction
 Which function is used by species.
bool * mp_bDrawSTRPerSpecies
 Whether to draw STR once per species (true) or once per tree (false).
enum mastEvent *mp_iEvent char
*m_cQuery typedef float(clMastingSpatialDisperse::* 
Ptr2GetNumberOfSeeds )(const float &, const short int &)
 Which event is occurring in the current timestep for each species.
Ptr2GetNumberOfSeedsmp_GetSeeds
 Function pointer array for the appropriate function for calculating the number of seeds.
float m_fNumYearsPerTimestep
 Number of years per timestep.
int m_iMaxDistance
 Maximum distance, in meters, a seed can disperse - which is the maximum dimension of the grid with max of 1000 m.
int m_iMaxTimesteps
 Maximum timesteps before a masting event occurs after a first masting event.

Friends

class clTestMastingSpatialDisperse


Detailed Description

Spatial disperse with masting - Version 1.0.

This class creates and disperses seeds according to the spatially-explicit model, allowing for masting events.

Masting is controlled by the cumulative distribution function: y = 1/(1 + (X / a)^b) where X is the time in years since the last mast, and a and b are parameters. The first timestep, X = 1. A random number compared to the probability distribution decides whether a mast has occurred.

The species may be organized into groups to create synchrony in masting. There can be up to N groups, where N is the number of species. If one species in a group masts, all species in the group do. Each group's mast decision is made separately, so sometimes more than one group may mast at a time.

There is a parameter for each species with the percentage of trees that participate in disperse (as a separate percentage for masting and non- masting). The set of trees, from those of above the minimum reproductive DBH, is randomly chosen each timestep.

The STR for trees can be chosen from a probability distribution function or not. It can be drawn once per species or once per tree. There are different STRs for masting and non-masting timesteps.

Once the number of seeds for a given tree has been calculated, the seeds are dispersed around the plot according to either the Weibull or Lognormal probability distribution functions.

The "seeds" are actually tallies by species in a grid. This behavior does not produce any seedlings. A separate recruitment behavior must "germinate" the seeds into seedlings according to its own rules.

The parameter file call string and namestring are both "masting spatial disperse".

Copyright 2007 Charles D. Canham.

Author:
Lora E. Murphy

Edit history:
-----------------
April 12, 2007 - Created (LEM)

Constructor & Destructor Documentation

clMastingSpatialDisperse::clMastingSpatialDisperse ( clSimManager p_oSimManager  ) 

Constructor.

Parameters:
p_oSimManager Sim Manager object.

clMastingSpatialDisperse::~clMastingSpatialDisperse (  ) 

Destructor.


Member Function Documentation

mastEvent clMastingSpatialDisperse::GetMastEvent ( int  iSp  )  [inline]

Get whether a given species masted this timestep.

Parameters:
iSp Species to check
Returns:
mast or nonmast.

void clMastingSpatialDisperse::DoShellSetup ( xercesc::DOMDocument *  p_oDoc  )  [protected, virtual]

Does setup.

This sets all values in mp_iTimestepsSinceLastMast to 1. Then it calls:

  1. GetParameterFileData
  2. CalcMastCDF
  3. CalcSeedCDF
  4. FormatQueryString
  5. PopulateUsedTable
  6. SetGetSeedsFunctionPointers

Parameters:
p_oDoc DOM tree of parsed input file.

Implements clDisperseBase.

void clMastingSpatialDisperse::CalcMastCDF ( xercesc::DOMDocument *  p_oDoc  )  [protected]

Calculates the masting cumulative distribution function.

This reads in the appropriate parameter values, finds the maximum number of years between mast events, then creates the CDF array. The parameters are thrown away because they are no longer needed.

Parameters:
p_oDoc DOM tree of parsed input file.

void clMastingSpatialDisperse::CalcSeedCDF ( xercesc::DOMDocument *  p_oDoc,
clTreePopulation p_oPop 
) [protected]

Calculates the cumulative distribution functions for seed dispersal.

This reads in the appropriate parameter values, finds the maximum seed dispersal distance, then creates the CDF array. The parameters are thrown away because they are no longer needed.

Parameters:
p_oDoc DOM tree of parsed input file.
p_oPop Tree population object.
Exceptions:
stcErr if a weibull theta value is not less than 50 (to prevent pow overflows)

void clMastingSpatialDisperse::FormatQueryString ( clTreePopulation p_oPop  )  [protected]

Formats the string in m_cQuery.

This value will be used in AddSeeds() in order to get the trees to act on.

Parameters:
p_oPop Tree Population object

void clMastingSpatialDisperse::DisperseOneParentSeeds ( clTree p_oTree,
clTreePopulation p_oPop,
clPlot p_oPlot,
float  fDbh 
) [protected]

Performs dispersal of seeds for one tree.

The number of seeds is calculated by using the pointer in mp_GetSeeds. Each seed is given a random azimuth direction from the parent. Then each seed is given a random distance from the parent that conforms to the chosen probability distribution function. This is done by comparing a random value to successive values in the cumulative probability array until the first array bucket that has a greater value than the random number. Once the seed has an azimuth direction and a distance, it is added to the species total in the appropriate grid cell.

Parameters:
p_oTree Tree for which to perform dispersal.
fDbh DBH of the tree, in cm.
p_oPlot Plot object
p_oPop Tree Population object

void clMastingSpatialDisperse::GetParameterFileData ( xercesc::DOMDocument *  p_oDoc,
clTreePopulation p_oPop 
) [protected]

Extracts needed parameter file data.

(Some parameters are extracted by other setup functions and thrown away - this gets all other, permanent parameters.)

Parameters:
p_oDoc Parsed parameter file document.
Exceptions:
stcErr if:
  • The function codes are not valid enums
  • A beta value is greater than 25 (to prevent pow overflows)
  • A value in mp_fFractionParticipating is not between 0 and 1
Parameters:
p_oPop Tree population object.

void clMastingSpatialDisperse::PopulateUsedTable ( clTreePopulation p_oPop  )  [protected]

Declares and populates the mp_bIsUsed array.

Parameters:
p_oPop Tree Population object

void clMastingSpatialDisperse::SetGetSeedsFunctionPointers (  )  [protected]

This figures out how each species's number of seeds is calculated.

It sets the appropriate function pointers in mp_GetSeeds.

void clMastingSpatialDisperse::CalculateProbabilityDistribution ( float *  p_fProbArray,
const int &  iMaxDistance,
const function iFunction,
const float &  fDispersalX0,
const float &  fThetaXb 
) [protected]

Calculates the normalized probability distribution for a function for one species.

Parameters:
p_fProbArray The array into which to put the normalized values.
iMaxDistance The maximum distance out to which to calculate the function - which must equal the size of p_fProbArray.
iFunction Function flag.
fDispersalX0 Dispersal or X0 of the species in question, depending on the function
fThetaXb Theta or Xb of the species in question, depending on the function

void clMastingSpatialDisperse::AddSeeds (  )  [protected, virtual]

Performs disperse.

First, DecideMast() is called to determine which species mast this timestep. Then, for any species with STRs that are drawn per species, fecundity is calculated. Then this gets the group of trees to which this behavior applies. For each, a random number is compared to the appropriate value in mp_fFractionParticipating to determine whether this tree will produce seeds. That tree is passed to DisperseOneParentSeeds() for seed creation and distribution.

Implements clDisperseBase.

void clMastingSpatialDisperse::DecideMast (  )  [protected]

Decides whether masting events occur for each species.

This takes the time since last mast and compares a random number to the value for that time in the mp_fMastCDF array. It then uses that decision to set the appropriate event flag in mp_iEvent. Then the counter value for each species in m_iTimestepsSinceLastMast is set appropriately; incremented if no mast occurred, or set to 0 if it did.

If species have group affiliations, the mast decision is made for the first species. Then all other species in that group get the same value.

float clMastingSpatialDisperse::GetNumberOfSeedsNoDraw ( const float &  fDbh,
const short int &  iSp 
) [protected]

Gets the number of seeds for a tree when there does not need to be an STR draw.

seeds = fecundity * DBHβ, Fecundity should have already been calculated.

Parameters:
fDbh DBH of the tree, in cm
iSp Tree species number
Returns:
Number of seeds.

float clMastingSpatialDisperse::GetNumberOfSeedsDrawNormal ( const float &  fDbh,
const short int &  iSp 
) [protected]

Gets the number of seeds for a tree when the tree needs a normal STR draw.

seeds = STR * (DBH / 30)β

Parameters:
fDbh DBH of the tree, in cm
iSp Tree species number
Returns:
Number of seeds.

float clMastingSpatialDisperse::GetNumberOfSeedsDrawLognormal ( const float &  fDbh,
const short int &  iSp 
) [protected]

Gets the number of seeds for a tree when the tree needs a lognormal STR draw.

seeds = STR * (DBH / 30)β

Parameters:
fDbh DBH of the tree, in cm
iSp Tree species number
Returns:
Number of seeds.


Friends And Related Function Documentation

friend class clTestMastingSpatialDisperse [friend]


Member Data Documentation

For testing.

Cumulative probability array for seed dispersal. Array size is mast or non-mast by # species by max distance. The 0th bucket will never be accessed.

STR mean (or STR value if deterministic).

The array is 2D - the first index is masting or non-masting. The second index is species. This value comes from the parameter file.

STR standard deviation.

The array is 2D - the first index is masting or non-masting. The second index is species. This value comes from the parameter file.

Beta parameter.

The array is 2D - the first index is masting or non-masting. The second index is species. This value comes from the parameter file.

Masting cumulative distribution function.

Array size is number of species by m_iMaxYears.

Fraction participating in disperse.

Array is 2D. First index is masting or non-masting. The second index is species. This value comes from the parameter file.

Whether this behavior is used by a species/type combo.

First array index is species, second is type.

Fecundity, if it is possible to pre-calculate it.

Number of years since the last mast for each species.

short int* clMastingSpatialDisperse::mp_iIndexes [protected]

This will speed access to the other arrays by storing each species' array index so the other arrays only have to be as big as the number of unique species for this behavior.

short int* clMastingSpatialDisperse::mp_iGroup [protected]

Group affiliation of the species.

Any species with the same group number will always mast together. Array size is species.

What PDF is used to draw the STR.

Only deterministic, normal, and lognormal are supported.

Which function is used by species.

Whether to draw STR once per species (true) or once per tree (false).

This is from the parameter file.

enum mastEvent* mp_iEvent char* m_cQuery typedef float(clMastingSpatialDisperse::* clMastingSpatialDisperse::Ptr2GetNumberOfSeeds)(const float &, const short int &) [protected]

Which event is occurring in the current timestep for each species.

Query to perform to search for treesDefine a type for pointers to functions of the GetNumberOfSeeds type

Function pointer array for the appropriate function for calculating the number of seeds.

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

Number of years per timestep.

Maximum distance, in meters, a seed can disperse - which is the maximum dimension of the grid with max of 1000 m.

Maximum timesteps before a masting event occurs after a first masting event.

This is calculated to be the value at which all species have a prob of 0.9999, or the number of timesteps in the run, whichever is smaller.


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

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