Establishment with Microtopography - Version 1.0. More...

#include <MicroEstablishment.h>

Inheritance diagram for clMicroEstablishment:

Public Types
enum	substrateType { mound_scarsoil, mound_tipup, mound_freshlogs, mound_decayedlogs, mound_fflitter, mound_ffmoss, ground_scarsoil, ground_tipup, ground_freshlogs, ground_decayedlogs, ground_fflitter, ground_ffmoss, number_substrates }
	List of substrate types - be extremely careful when changing these! More...

Public Member Functions
	clMicroEstablishment (clSimManager *p_oSimManager)
	Constructor. More...

	~clMicroEstablishment ()
	Destructor. More...

void	GetData (xercesc::DOMDocument *p_oDoc)
	Performs setup. More...

void	Action ()
	Performs establishment. More...

void	TimestepCleanup ()
	Zeroes out the seed grid. More...

void	GetSubstrateProportions (float *p_fSubstrate, const float &fFromX, const float &fFromY, const float &fToX, const float &fToY)
	Produces an array of substrate proportions. More...

void	GetFreshLogProportions (float *p_fLogs, const float &fFromX, const float &fFromY, const float &fToX, const float &fToY)
	Produces an array of cumulative fresh log proportions added for m_iMaxRespiteTimesteps timesteps. More...

void	SetMoundZAndRespite (clTree *p_oSeedling)
	Sets the rooting height of a seedling in mm if it has landed on a mound substrate that is not fresh logs. More...

void	SetGroundZAndRespite (clTree *p_oSeedling)
	Sets the rooting height of a seedling in mm if it has landed on a ground substrate that is not fresh logs. 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...

clSimManager *	GetSimManager ()

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	GetParameterFileData (xercesc::DOMDocument *p_oDoc)
	Gets parameter file data. More...

void	SetupGrids ()
	Populates required grid pointers. More...

void	GetTreeDataMemberCodes ()
	Declares and populates the values in the mp_iCounterCodes and mp_iZCodes arrays, for the "lf_count" and "z" data members of seedlings, respectively. More...

void	SetFreshLogZAndRespite (clTree p_oSeedling, float p_fFreshLogProportions)
	Sets the rooting height of a tree in mm and a fern respite counter in years, if a seedling has landed on fresh logs. 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
clGrid *	mp_oSubstrateGrid
	Pointer to "Substrate" grid, created by clSubstrate. More...

clGrid *	mp_oSeedGrid
	Pointer to the "Dispersed Seeds" grid created by disperse behaviors. More...

short int *	mp_iSeedGridCode
	Data member codes for seed grid for number of seeds. More...

short int *	mp_iCounterCodes
	Holds data member codes for "lf_count" for seedlings - array size is # behavior species. More...

short int *	mp_iZCodes
	Holds data member codes for "z" for seedlings - array size is # behavior species. More...

short int *	mp_iIndexes
	Speeds access to arrays. More...

short int *	mp_iSubstrateCodes
	Array of data member codes for the "Substrate" grid. More...

double	m_fMoundProportion
	Proportion of the plot that is mound. More...

double	m_fMoundHeightMean
	Mean mound height. More...

double	m_fMoundStandardDeviation
	Mound height standard deviation. More...

double	m_fFreshLogHeightMean
	Fresh log substrate mean height. More...

double	m_fFreshLogStandardDeviation
	Fresh log height standard deviation. More...

double	m_fFreshLogA
	Fresh log alpha decay parameter; from substrate parameters. More...

double	m_fFreshLogB
	Fresh log alpha decay parameter; from substrate parameters. More...

int	m_iMaxRespiteYears
	Maximum number of years of fern respite - from parameter file. More...

int	m_iMaxRespiteTimesteps
	Maximum number of timesteps of fern respite - calculated from m_iMaxRespiteYears. More...

short int	m_iCohFreshLogCode
	Data member code - package float - dec_flog. More...

short int	m_iCohAgeCode
	Data member code - package int - age. More...

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...

stcSpeciesTypeCombo *	mp_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...

clSimManager *	mp_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...

Friends
class	clTestMicroEstablishment
	My unit tester - exists in the testing application. More...

Detailed Description

Establishment with Microtopography - Version 1.0.

This behavior germinates seeds cast by dispersal into seedlings. In addition, seeds are given a height above the ground due to microtopography.

All seeds are germinated into seedlings. A seed's substrate determines its rooting height. In order to seeds to substrates, the number of seeds is evenly divided as much as possible among the different substrate types. The clSubstrate class divides each grid cell of the "Substrate" grid into six substrate types; this further divides each substrate type in two, for mound and ground. Mound and ground are in fixed relative proportion to each other.

The definition of seedling rooting height comes from the clLightFilter class. Since this class makes no sense without that, that behavior is required to be in the run (as marked by the presence of the tree data members "lf_count" and "z").

Ground substrates (except fresh log) give a seed a rooting height of 0. Fresh log and mound substrates give rooting heights that are randomly drawn on normal distributions, the shape of which are controlled by means and standard deviations provided by the user.

If the seed lands on a log substrate, it also gets a respite from fern shading. The number of years of respite is set in the "lf_count" data member. The number of years is determined by the age of the log substrate on which the seedling landed (which is determined by dividing the fresh logs pool up by age and doing a random draw to determine which it is), and that age is subtracted from the maximum respite time.

Requirements for using an object of this class in a run:

A disperse behavior is used
Substrate (clSubstrate) is used
Light filter (clLightFilter) is used

The namestring and parameter file call string for this class are both "MicroEstablishment". Apply this behavior to the desired species; use any type, since type will be ignored.

Author: Lora E. Murphy

Edit history:
--------------—
October 20, 2011 - Wiped the slate clean for SORTIE 7.0 (LEM)

Member Enumeration Documentation

◆ substrateType

enum clMicroEstablishment::substrateType

List of substrate types - be extremely careful when changing these!

Enumerator
mound_scarsoil	Scarified soil on mound.
mound_tipup	Tipup on mound.
mound_freshlogs	Fresh logs on mound.
mound_decayedlogs	Decayed logs on mound.
mound_fflitter	Forest floor litter on mound.
mound_ffmoss	Forest floor moss on mound.
ground_scarsoil	Scarified soil on ground.
ground_tipup	Tipup on ground.
ground_freshlogs	Fresh logs on ground.
ground_decayedlogs	Decayed logs on ground.
ground_fflitter	Forest floor litter on ground.
ground_ffmoss	Forest floor moss on ground.
number_substrates	This is now shorthand for the total number of substrates.

Constructor & Destructor Documentation

◆ clMicroEstablishment()

clMicroEstablishment::clMicroEstablishment ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clMicroEstablishment()

clMicroEstablishment::~clMicroEstablishment ( )

Destructor.

Member Function Documentation

◆ Action()

void clMicroEstablishment::Action ( )

virtual

Performs establishment.

Steps for each grid cell in Dispersed Seeds:

The proportions of each of the substrate types are calculated for the grid cell by calling GetSubstrateProportions().
The seeds are divided up among the substrate types according to their relative proportions.
A seedling is created for each seed.
The seedling then gets a rooting height and a fern light respite counter, depending on the type of substrate upon which it landed. If it landed on fresh logs, it's passed to SetFreshLogZAndRespite(). If it landed on a mound substrate, it's passed to SetMoundZAndRespite(). If it landed on a ground substrate, it's passed to SetGroundZAndRespite().

Reimplemented from clBehaviorBase.

◆ GetData()

void clMicroEstablishment::GetData ( xercesc::DOMDocument * p_oDoc )

virtual

Performs setup.

Calls:

GetParameterFileData()
SetupGrids()
DoLightSetup(), if m_bUsesLight is true

Parameters

p_oDoc DOM tree of parsed input file.

Implements clWorkerBase.

◆ GetFreshLogProportions()

void clMicroEstablishment::GetFreshLogProportions	(	float *	p_fLogs,
		const float &	fFromX,
		const float &	fFromY,
		const float &	fToX,
		const float &	fToY
	)

Produces an array of cumulative fresh log proportions added for m_iMaxRespiteTimesteps timesteps.

First, the amount of fresh log substrate for each timestep is placed in the appropriate array bucket. This value comes from substrate cohort packages. We have to decay the amount of fresh log by the age of the cohort; here's how:

FL' = FL * exp( a * T^b )

where FL' is the amount of fresh logs left, FL is the amount of original fresh logs (the amount in the "freshlog" package data member), a is the fresh log decay alpha substrate parameter, T is the cohort's age in years, and b is the fresh log beta substrate decay parameter.

Then the values are converted to proportion of total fresh log by dividing each array bucket by the total in all buckets. Then, to each array value, the total value of all previous buckets is added so that the fresh log proportions are cumulative.

Note:This also used to collect fresh log mean DBHs. This has been commented out as not currently needed.

Areas are averaged over grid cells if seed grid cell sizes are bigger than substrate grid cell sizes.

Parameters

fFromX	Origin X coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
fFromY	Origin Y coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
fToX	End X coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
fToY	End Y coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
p_fLogs	Pointer to an array, sized m_iMaxRespiteTimesteps + 1, in which to put the fresh log proportions. Each bucket will hold the cumulative proportion of fresh log of the array index's age in timesteps. The last bucket is always 1.

◆ GetParameterFileData()

void clMicroEstablishment::GetParameterFileData ( xercesc::DOMDocument * p_oDoc )

protected

Gets parameter file data.

Parameters

p_oDoc Parsed parameter file.

Exceptions

modelErr if m_fMoundProportion is not between 0 and 1, inclusive.

◆ GetSubstrateProportions()

void clMicroEstablishment::GetSubstrateProportions	(	float *	p_fSubstrate,
		const float &	fFromX,
		const float &	fFromY,
		const float &	fToX,
		const float &	fToY
	)

Produces an array of substrate proportions.

First, the amount of substrate for each substrate type is placed in the appropriate array bucket. Then mound substrates are multiplied by the proportion of the total area that is mound; ground substrates are multipled by 1 - that proportion. Areas are averaged over grid cells if seed grid cell sizes are bigger than substrate grid cell sizes.

Parameters

fFromX	Origin X coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
fFromY	Origin Y coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
fToX	End X coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
fToY	End Y coordinate of the grid cell of "Dispersed Seeds" for which to get substrate proportions.
p_fSubstrate	Pointer to an array, sized number_substrates, in which to put the substrate proportion for each value in substrateTypes.

◆ GetTreeDataMemberCodes()

void clMicroEstablishment::GetTreeDataMemberCodes ( )

protected

Declares and populates the values in the mp_iCounterCodes and mp_iZCodes arrays, for the "lf_count" and "z" data members of seedlings, respectively.

Exceptions

ModelErr if there is no code for any species which uses establishment.

◆ SetFreshLogZAndRespite()

void clMicroEstablishment::SetFreshLogZAndRespite	(	clTree *	p_oSeedling,
		float *	p_fFreshLogProportions
	)

protected

Sets the rooting height of a tree in mm and a fern respite counter in years, if a seedling has landed on fresh logs.

A random number is compared to successive values in p_fFreshLogProportions until an array value is greater than the random value. That bucket represents the age of the fresh logs, in timesteps, onto which the seed has landed. The respite counter is m_iMaxRespite minus the age of the fresh log cohort in years.

The rooting height is a normally-distributed random number using the fresh log mean height and standard deviation from the parameter file. (Fresh logs overlie and obliterate the effects of mounds.)

Parameters

p_oSeedling	The seedling for which to set rooting height and fern respite.
p_fFreshLogProportions	An array holding the cumulative proportion of fresh logs x timesteps ago, up to m_iMaxRespiteTimesteps.

◆ SetGroundZAndRespite()

void clMicroEstablishment::SetGroundZAndRespite ( clTree * p_oSeedling )

Sets the rooting height of a seedling in mm if it has landed on a ground substrate that is not fresh logs.

The rooting height and fern respite counters are always 0.

Parameters

p_oSeedling The seedling for which to set rooting height and fern respite.

◆ SetMoundZAndRespite()

void clMicroEstablishment::SetMoundZAndRespite ( clTree * p_oSeedling )

Sets the rooting height of a seedling in mm if it has landed on a mound substrate that is not fresh logs.

The rooting height is a random normally-distributed value using the mound mean height (in m_fMoundHeightMean) and mound standard deviation (in m_fMoundStandardDeviation). In this non-fresh-log case, the fern respite counter is always 0.

Parameters

p_oSeedling The seedling for which to set rooting height and fern respite.

◆ SetupGrids()

void clMicroEstablishment::SetupGrids ( )

protected

Populates required grid pointers.

This gets a pointer to the "Substrate" grid and all its data members, and gets a pointer to the "Dispersed Seeds" grid and all its data members.

Exceptions

modelErr if either the "Substrate" or "Dispersed Seeds" grid does not exist.

◆ TimestepCleanup()

void clMicroEstablishment::TimestepCleanup ( )

virtual

Zeroes out the seed grid.

Reimplemented from clWorkerBase.

Friends And Related Function Documentation

◆ clTestMicroEstablishment

friend class clTestMicroEstablishment

friend

My unit tester - exists in the testing application.

I didn't want to have to do this but I couldn't figure out a way to effectively unit test any other way.

Member Data Documentation

◆ m_fFreshLogA

double clMicroEstablishment::m_fFreshLogA

protected

Fresh log alpha decay parameter; from substrate parameters.

This lets this class calculate fresh log ages.

◆ m_fFreshLogB

double clMicroEstablishment::m_fFreshLogB

protected

Fresh log alpha decay parameter; from substrate parameters.

This lets this class calculate fresh log ages.

◆ m_fFreshLogHeightMean

double clMicroEstablishment::m_fFreshLogHeightMean

protected

Fresh log substrate mean height.

Read in in meters, then converted to mm

◆ m_fFreshLogStandardDeviation

double clMicroEstablishment::m_fFreshLogStandardDeviation

protected

Fresh log height standard deviation.

Read in in meters, then converted to mm

◆ m_fMoundHeightMean

double clMicroEstablishment::m_fMoundHeightMean

protected

Mean mound height.

Read in in meters, then converted to mm

◆ m_fMoundProportion

double clMicroEstablishment::m_fMoundProportion

protected

Proportion of the plot that is mound.

◆ m_fMoundStandardDeviation

double clMicroEstablishment::m_fMoundStandardDeviation

protected

Mound height standard deviation.

Read in in meters, then converted to mm

◆ m_iCohAgeCode

short int clMicroEstablishment::m_iCohAgeCode

protected

Data member code - package int - age.

◆ m_iCohFreshLogCode

short int clMicroEstablishment::m_iCohFreshLogCode

protected

Data member code - package float - dec_flog.

◆ m_iMaxRespiteTimesteps

int clMicroEstablishment::m_iMaxRespiteTimesteps

protected

Maximum number of timesteps of fern respite - calculated from m_iMaxRespiteYears.

◆ m_iMaxRespiteYears

int clMicroEstablishment::m_iMaxRespiteYears

protected

Maximum number of years of fern respite - from parameter file.

◆ mp_iCounterCodes

short int* clMicroEstablishment::mp_iCounterCodes

protected

Holds data member codes for "lf_count" for seedlings - array size is # behavior species.

◆ mp_iIndexes

short int* clMicroEstablishment::mp_iIndexes

protected

Speeds access to arrays.

◆ mp_iSeedGridCode

short int* clMicroEstablishment::mp_iSeedGridCode

protected

Data member codes for seed grid for number of seeds.

Array size is

behavior species.

◆ mp_iSubstrateCodes

short int* clMicroEstablishment::mp_iSubstrateCodes

protected

Array of data member codes for the "Substrate" grid.

It's sized number_substrates; repeat substrates get the same code (i.e. mound and ground fresh logs

◆ mp_iZCodes

short int* clMicroEstablishment::mp_iZCodes

protected

Holds data member codes for "z" for seedlings - array size is # behavior species.

◆ mp_oSeedGrid

clGrid* clMicroEstablishment::mp_oSeedGrid

protected

Pointer to the "Dispersed Seeds" grid created by disperse behaviors.

◆ mp_oSubstrateGrid

clGrid* clMicroEstablishment::mp_oSubstrateGrid

protected

Pointer to "Substrate" grid, created by clSubstrate.

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

MicroEstablishment.h

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Member Enumeration Documentation

◆ substrateType

Constructor & Destructor Documentation

◆ clMicroEstablishment()

◆ ~clMicroEstablishment()

Member Function Documentation

◆ Action()

◆ GetData()

◆ GetFreshLogProportions()

◆ GetParameterFileData()

◆ GetSubstrateProportions()

◆ GetTreeDataMemberCodes()

◆ SetFreshLogZAndRespite()

◆ SetGroundZAndRespite()

◆ SetMoundZAndRespite()

◆ SetupGrids()

◆ TimestepCleanup()

Friends And Related Function Documentation

◆ clTestMicroEstablishment

Member Data Documentation

◆ m_fFreshLogA

◆ m_fFreshLogB

◆ m_fFreshLogHeightMean

◆ m_fFreshLogStandardDeviation

◆ m_fMoundHeightMean

◆ m_fMoundProportion

◆ m_fMoundStandardDeviation

◆ m_iCohAgeCode

◆ m_iCohFreshLogCode

◆ m_iMaxRespiteTimesteps

◆ m_iMaxRespiteYears

◆ mp_iCounterCodes

◆ mp_iIndexes

◆ mp_iSeedGridCode

behavior species.

◆ mp_iSubstrateCodes

◆ mp_iZCodes

◆ mp_oSeedGrid

◆ mp_oSubstrateGrid