Models functional response seed predation. More...

#include <FuncResponseSeedPredation.h>

Inheritance diagram for clFuncResponseSeedPredation:

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

	~clFuncResponseSeedPredation ()
	Destructor. More...

void	Action ()
	Performs the model. More...

void	SetNameData (std::string sNameString)
	Captures the behavior name passed from the parameter file. More...

float	GetOfftakeRate ()
	Get the amount of offtake. 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 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	TimestepCleanup ()
	Performs any necessary cleanup operations at the end of a timestep. More...

virtual void	EndOfRunCleanup ()
	Performs any necessary cleanup operations at the end of a run. More...

Protected Member Functions
void	GetData (xercesc::DOMDocument *p_oDoc)
	Reads in the parameter file values. More...

void	SetPredatorInitialDensity ()
	Sets all grid cells in the predator grid with the appropriate initial density. More...

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

void	DoModel ()
	Does the model for a given value of m_fTempSeeds and m_fTempPredators. 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_oSeedGrid
	Pointer to the "Dispersed Seeds" grid created by disperse behaviors. More...

clGrid *	mp_oPredatorGrid
	Pointer to predator grid. More...

std::string	m_sOutput
	File to which to write intermediate output, if desired. More...

double *	mp_fMaxInstantaneousDeclineRate
	Max instantaneous rate at which predator abundance declines in the absense of food, number of predators per week - array index is 2 (# seasons) More...

double *	mp_fDemographicEfficiency
	Population's demographic efficiency - array size is 2 (# seasons) More...

double *	mp_fDensityDependentCoefficient
	Density-dependent coefficient - array size is 2 (# seasons) More...

double *	mp_fForagingEfficiency
	Foraging efficiency - array size is # behavior species. More...

double	m_fPredatorInitialDensity
	Predator initial density - number per square meter. More...

double *	mp_fMaxIntakeRate
	Maximum seed intake rate - number of seeds per predator per day - array size is # behavior species. More...

double	m_fProportionGerminating
	Proportion of seeds that germinate each week in the germination period - this must be a number between 0 and 1. More...

float	m_fCellArea
	Area of a seed grid grid cell in square meters - when multiplied by the density of predators, produces the number in the cell. More...

float	m_fOfftake
	Offtake rate - proportion of total seeds eaten, between 0 and 1. More...

float *	mp_fTempSeeds
	A place to stash the number of seeds, to allow easy collaborative access to this data between functions. More...

float	m_fTempPredators
	A place to stash the number of predators, to allow easy collaborative access to this data between functions. More...

int	m_iNumWeeksToModel
	Number of weeks to run the model. More...

int	m_iNumWeeksSeedFall
	Number of weeks of seed fall. More...

int	m_iWeekGerminationStarts
	Week in which germination begins. More...

int	m_iWeekSeason2Starts
	Week in which season 2 begins. More...

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

short int	m_iNumPredsCode
	Data member in the predators grid. More...

bool	m_bPreservePredatorDensities
	Whether or not to carry over mouse population densities. More...

bool	m_bIsLinked
	Whether this is the linked (true) or standalone (false) version. 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...

Detailed Description

Models functional response seed predation.

This runs as a model-within-a-model, in weekly timesteps for a year. It doesn't matter if the length of the overall model timestep is longer than a year; the amount of seeds is treated as a one-year pool, which produces the same result.

This behavior reduces the number of seeds available in the "Dispersed Seeds" grid. In each cell of that grid, there are a certain number of predators (calculated from the initial density of predators) which have the number of seeds present in that cell as a food source. Each species to which this behavior is applied has its own parameters controlling how it is predated.

Seed rain is evenly divided over a set number of timesteps (weeks). The predator population has as a food source the number of seeds added during the current week's rain (if the rain is going on) plus any leftover seeds from previous weeks which have not been consumed. Beginning at a certain week in the spring, the number of seeds available to the mice is further reduced by a certain percentage each week to simulate germination. Once germination begins, it continues until the predator model finishes running. In order to correctly calculate mouse consumption and ensure that the seeds which germinate are actually available later, this keeps track of the seeds consumed; it is this number which is subtracted from total seeds at the end.

The predator population is updated each timestep as a response to number of seeds consumed. The response parameters can be divided into two seasons.

Seed offtake for each week is calculated as

O = Σ IR_s * N where

0 = offtake
IR_s = per capita seed offtake for each species
N = number of mice

Per capita seed offtake for each species is

IR_s = c_s(1 - e^-(S*D)) * p_s

where

c_s = maximum seed intake rate per predator per day (a species-specific input parameter)
S = number of seeds per predator per day
D = foraging efficiency (a species-specific input parameter)
p_s = the proportion of the total seeds belonging to that species

The number of predators in each cell's population is calculated as

N_t = N_t-1 * e^r_t-1

where

N_t = number of predators for the current timestep
N_t-1 = number of predators in the previous timestep
r_t-1 = instantaneous rate of change in predator abundance for the previous timestep.

The instantaneous rate of change, r, can use different parameters for two user-defined seasons. r is calculated as

r = (a + d(IR) + g(N))/12

where

IR = sum of the IRs for each species
a = the maximum instantaneous rate at which predator abundance delines in the absense of food (an input parameter, season 1 or 2)
d = population's demographic efficiency (an input parameter, season 1 or 2)
g = coefficient describing the effect that density-dependent factors have on r (an input parameter, season 1 or 2)
N = number of predators per hectare
divided by 12 - to take from per quarter to per week

This behavior must be used in conjunction with a disperse behavior. If such a behavior is not present (and thus the "Dispersed Seeds" grid is not present), a fatal error will be thrown during setup.

This behavior can be used as an independent behavior where seeds are removed, or it can be linked to another behavior (i.e. the neighborhood seed predation behavior, clNeighborhoodSeedPredation) and used to calculate a whole-plot offtake amount without actually removing any seeds. It's possible to use both in a single run so separate parameters are used for each.

The namestring and parameter file call string are "FunctionalResponseSeedPredation" when used alone, or "LinkedFunctionalResponseSeedPredation" when linked with another behavior.

Author: Lora E. Murphy

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

Constructor & Destructor Documentation

◆ clFuncResponseSeedPredation()

clFuncResponseSeedPredation::clFuncResponseSeedPredation ( clSimManager * p_oSimManager )

Constructor.

Parameters

p_oSimManager Sim Manager object.

◆ ~clFuncResponseSeedPredation()

clFuncResponseSeedPredation::~clFuncResponseSeedPredation ( )

Destructor.

Frees memory.

Member Function Documentation

◆ Action()

void clFuncResponseSeedPredation::Action ( )

virtual

Performs the model.

If predator densities are not to be preserved, then the predator grid is initialized with SetPredatorInitialDensity().

Reimplemented from clBehaviorBase.

◆ DoModel()

void clFuncResponseSeedPredation::DoModel ( )

protected

Does the model for a given value of m_fTempSeeds and m_fTempPredators.

◆ GetData()

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

protectedvirtual

Reads in the parameter file values.

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr if there is no such grid called "Dispersed Seeds", or if the "Dispersed Seeds" grid does not contain a valid return code for all behavior species.

Implements clWorkerBase.

◆ GetOfftakeRate()

float clFuncResponseSeedPredation::GetOfftakeRate ( )

inline

Get the amount of offtake.

Returns: Offtake, as a proportion of seeds eaten between 0 and 1.

◆ GetParameterFileData()

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

protected

Gets the data from the parameter file.

Parameters

p_oDoc DOM tree of parsed input file.

Exceptions

modelErr

if:

Number of weeks of seedfall is less than or equal to zero
Initial predator density is less than or equal to zero
Number of weeks to run the model is less than 0 or greater than 52
Week to start germination is less than 0 or greater than 52
Proportion germinating isn't between 0 and 1

◆ SetNameData()

void clFuncResponseSeedPredation::SetNameData ( std::string sNameString )

virtual

Captures the behavior name passed from the parameter file.

This is useful since this class can produce different kinds of behaviors.

Parameters

sNameString Behavior name from parameter file.

Reimplemented from clBehaviorBase.

◆ SetPredatorInitialDensity()

void clFuncResponseSeedPredation::SetPredatorInitialDensity ( )

protected

Sets all grid cells in the predator grid with the appropriate initial density.

Member Data Documentation

◆ m_bIsLinked

bool clFuncResponseSeedPredation::m_bIsLinked

protected

Whether this is the linked (true) or standalone (false) version.

◆ m_bPreservePredatorDensities

bool clFuncResponseSeedPredation::m_bPreservePredatorDensities

protected

Whether or not to carry over mouse population densities.

◆ m_fCellArea

float clFuncResponseSeedPredation::m_fCellArea

protected

Area of a seed grid grid cell in square meters - when multiplied by the density of predators, produces the number in the cell.

◆ m_fOfftake

float clFuncResponseSeedPredation::m_fOfftake

protected

Offtake rate - proportion of total seeds eaten, between 0 and 1.

Used if this is linked.

◆ m_fPredatorInitialDensity

double clFuncResponseSeedPredation::m_fPredatorInitialDensity

protected

Predator initial density - number per square meter.

◆ m_fProportionGerminating

double clFuncResponseSeedPredation::m_fProportionGerminating

protected

Proportion of seeds that germinate each week in the germination period - this must be a number between 0 and 1.

◆ m_fTempPredators

float clFuncResponseSeedPredation::m_fTempPredators

protected

A place to stash the number of predators, to allow easy collaborative access to this data between functions.

◆ m_iNumPredsCode

short int clFuncResponseSeedPredation::m_iNumPredsCode

protected

Data member in the predators grid.

◆ m_iNumWeeksSeedFall

int clFuncResponseSeedPredation::m_iNumWeeksSeedFall

protected

Number of weeks of seed fall.

◆ m_iNumWeeksToModel

int clFuncResponseSeedPredation::m_iNumWeeksToModel

protected

Number of weeks to run the model.

◆ m_iWeekGerminationStarts

int clFuncResponseSeedPredation::m_iWeekGerminationStarts

protected

Week in which germination begins.

◆ m_iWeekSeason2Starts

int clFuncResponseSeedPredation::m_iWeekSeason2Starts

protected

Week in which season 2 begins.

◆ m_sOutput

std::string clFuncResponseSeedPredation::m_sOutput

protected

File to which to write intermediate output, if desired.

◆ mp_fDemographicEfficiency

double* clFuncResponseSeedPredation::mp_fDemographicEfficiency

protected

Population's demographic efficiency - array size is 2 (# seasons)

◆ mp_fDensityDependentCoefficient

double* clFuncResponseSeedPredation::mp_fDensityDependentCoefficient

protected

Density-dependent coefficient - array size is 2 (# seasons)

◆ mp_fForagingEfficiency

double* clFuncResponseSeedPredation::mp_fForagingEfficiency

protected

Foraging efficiency - array size is # behavior species.

◆ mp_fMaxInstantaneousDeclineRate

double* clFuncResponseSeedPredation::mp_fMaxInstantaneousDeclineRate

protected

Max instantaneous rate at which predator abundance declines in the absense of food, number of predators per week - array index is 2 (# seasons)

◆ mp_fMaxIntakeRate

double* clFuncResponseSeedPredation::mp_fMaxIntakeRate

protected

Maximum seed intake rate - number of seeds per predator per day - array size is # behavior species.

◆ mp_fTempSeeds

float* clFuncResponseSeedPredation::mp_fTempSeeds

protected

A place to stash the number of seeds, to allow easy collaborative access to this data between functions.

Array size is # behavior species.

◆ mp_iSeedGridCode

short int* clFuncResponseSeedPredation::mp_iSeedGridCode

protected

Data member codes for seed grid for number of seeds.

Array size is # behavior species.

◆ mp_oPredatorGrid

clGrid* clFuncResponseSeedPredation::mp_oPredatorGrid

protected

Pointer to predator grid.

The name of this grid is "Seed Predators". Its grid cell resolution will match that of "Dispersed Seeds". It has one float data member - "num preds". It will accept maps if m_bPreservePredatorDensities = true and if they are of the right resolution.

◆ mp_oSeedGrid

clGrid* clFuncResponseSeedPredation::mp_oSeedGrid

protected

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

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

FuncResponseSeedPredation.h

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ clFuncResponseSeedPredation()

◆ ~clFuncResponseSeedPredation()

Member Function Documentation

◆ Action()

◆ DoModel()

◆ GetData()

◆ GetOfftakeRate()

◆ GetParameterFileData()

◆ SetNameData()

◆ SetPredatorInitialDensity()

Member Data Documentation

◆ m_bIsLinked

◆ m_bPreservePredatorDensities

◆ m_fCellArea

◆ m_fOfftake

◆ m_fPredatorInitialDensity

◆ m_fProportionGerminating

◆ m_fTempPredators

◆ m_iNumPredsCode

◆ m_iNumWeeksSeedFall

◆ m_iNumWeeksToModel

◆ m_iWeekGerminationStarts

◆ m_iWeekSeason2Starts

◆ m_sOutput

◆ mp_fDemographicEfficiency

◆ mp_fDensityDependentCoefficient

◆ mp_fForagingEfficiency

◆ mp_fMaxInstantaneousDeclineRate

◆ mp_fMaxIntakeRate

◆ mp_fTempSeeds

◆ mp_iSeedGridCode

◆ mp_oPredatorGrid

◆ mp_oSeedGrid