Osmia_Base Class Reference

#include <Osmia.h>

Inheritance diagram for Osmia_Base:

Public Member Functions
	Osmia_Base (struct_Osmia *data)
	Osmia constructor. More...
void	ReInit (struct_Osmia *data)
	Osmia reinitialise object methods. More...
virtual	~Osmia_Base ()
	Osmia destructor. More...
virtual void	st_Dying (void)
	Behavioural state dying. More...
virtual void	BeginStep (void)
	The BeginStep is the first 'part' of the timestep that an animal can behave in. It is called once per timestep. More...
virtual void	Step (void)
	The Step is the second 'part' of the timestep that an animal can behave in. It is called continuously until all animals report that they are 'DONE'. More...
virtual void	EndStep (void)
	The EndStep is the third 'part' of the timestep that an animal can behave in. It is called once per timestep. More...
int	GetAge ()
	A typical interface function - this one returns the age. More...
void	SetAge (int a_age)
	A typical interface function - this one returns the age. More...
double	GetMass ()
	Returns the bee's mass. More...
void	SetMass (double a_mass)
	Sets the bee's mass. More...
void	SetParasitised (TTypeOfOsmiaParasitoids a_status)
	Set the parasitised status. More...
TTypeOfOsmiaParasitoids	GetParasitised (void)
	Set the parasitised status. More...
Osmia_Nest *	GetNest ()
Public Member Functions inherited from TAnimal
	TAnimal (int x, int y, Landscape *L)
	The TAnimal constructor saving the x,y, location and the landscape pointer. More...
	TAnimal (int x, int y)
	The TAnimal constructor saving the x,y used if landscape is already set. More...
void	SetGuardMapIndex (int a_index_x, int a_index_y)
	Set the guard map index, this is used to avoid two animals operating in the same location when using multithread. More...
unsigned	SupplyFarmOwnerRef () const
	Get the current location farm ref if any. More...
AnimalPosition	SupplyPosition () const
	Returns the objects location and habitat type and veg type. More...
APoint	SupplyPoint () const
	Returns the objects location in ALMaSS coordinates. More...
int	SupplyPolygonRef () const
	Returns the polygon reference where the object is located. More...
TTypesOfLandscapeElement	SupplyPolygonType () const
	Returns the polygon type where the object is located. More...
int	Supply_m_Location_x () const
	Returns the ALMaSS x-coordinate. More...
int	Supply_m_Location_y () const
	Returns the ALMaSS y-coordinate. More...
int	SupplyGuardCellX () const
	Returns the x-index to the guard cell. More...
int	SupplyGuardCellY () const
	Returns the y-index to the guard cell. More...
int	SupplyAge () const
	Returns the animals age in days. More...
void	SetAge (int a_age)
	Sets the animals age in days. More...
virtual void	KillThis ()
	Sets all parameters ready for object destruction. More...
virtual void	CopyMyself ()
	Used to copy the object details to another in descendent classes. More...
void	SetX (const int a_x)
	Sets the x-coordinate. More...
void	SetY (const int a_y)
	Sets the y-coordinate. More...
virtual void	ReinitialiseObject (int a_x, int a_y, Landscape *a_l_ptr)
virtual void	ReinitialiseObject (int a_x, int a_y)
	Used to re-use an object - must be implemented in descendent classes. More...
virtual int	WhatState ()
	Returns the objects current state number. More...
virtual void	Dying ()
	A wrapped for KillThis - ideally should not be used. More...
void	CheckManagement ()
	Used to start a check for any management related effects at the objects current location. More...
void	CheckManagementXY (int a_x, int a_y)
	Used to start a check for any management related effects at x,y. More...
virtual bool	OnFarmEvent (FarmToDo)
	Must be reimplemented if used in descendent classes. Sets the action on a management event. More...
Public Member Functions inherited from TALMaSSObject
int	GetCurrentStateNo () const
	Returns the current state number. More...
void	SetCurrentStateNo (int a_num)
	Sets the current state number. More...
bool	GetStepDone () const
	Returns the step done indicator flag. More...
void	SetStepDone (bool a_bool)
	Sets the step done indicator flag. More...
void	ReinitialiseObjectBase ()
	Used to initialise an object. More...
	TALMaSSObject ()
	The constructor for TALMaSSObject. More...
virtual	~TALMaSSObject ()=default
	The destructor for TALMaSSObject. More...

Static Public Member Functions
static void	SetParameterValues ()
	Used to populate the static members holding mortality and development parameters. More...
static void	SetTemp (double a_temperature)
static void	SetParasitoidManager (OsmiaParasitoid_Population_Manager *a_popman)
Static Public Member Functions inherited from TAnimal
static void	SetSimulationWidth (int a_value)
	Sets the simulation width. More...
static void	SetSimulationHeight (int a_value)
	Sets the simulation height. More...
static void	SetDayInYear (int a_value)
	Sets the day in year attribute. More...
static void	SetOurLandscape (Landscape *a_value)
	Sets the landscape pointer. More...
static void	SetTempToday (double a_value)
	Sets the temperature today attribute. More...
Static Public Member Functions inherited from TALMaSSObject
static void	OnArrayBoundsError ()
	Used for debugging only, tests basic object properties. More...

Protected Attributes
TTypeOfOsmiaState	m_CurrentOState
	Variable to record current behavioural state. More...
int	m_Age
	A typical member variable - this one is the age in days. More...
Osmia_Population_Manager *	m_OurPopulationManager
	This is a time saving pointer to the correct population manager object. More...
TTypeOfOsmiaParasitoids	m_ParasitoidStatus
	Holds the parasitoid status - only one is allowed. More...
Osmia_Nest *	m_OurNest
double	m_Mass
int	m_foragehours
	A variable to hold the number of available forage hours left in a day. More...
Protected Attributes inherited from TAnimal
int	m_Location_x
	The objects ALMaSS x coordinate. More...
int	m_Location_y
	The objects ALMaSS y coordinate. More...
int	m_guard_cell_x
	The index x to the guard cell. More...
int	m_guard_cell_y
	The index y to the guard cell. More...
int	m_AgeDays {0}
	To hold the age in days. More...
PesticideToxicity	m_my_pesticide
Protected Attributes inherited from TALMaSSObject
int	m_CurrentStateNo
	The basic state number for all objects - '-1' indicates death. More...
bool	m_StepDone
	Indicates whether the iterative step code is done for this timestep. More...

Static Protected Attributes
static OsmiaParasitoid_Population_Manager *	m_OurParasitoidPopulationManager = NULL
	This is a time saving pointer to the parasitoid population manager object. More...
static double	m_TempToday = -9999
	The temperature today. This is static because there is only one temperature today. More...
static int	m_TempTodayInt = -9999
	The temperature today to the nearest degree. This is static because there is only one temperature today. This is mostly for use in temperature indexed arrays (if used) More...
static double	m_DailyDevelopmentMortEggs = 0
	This holds the daily mortality for eggs. More...
static double	m_DailyDevelopmentMortLarvae = 0
	This holds the daily mortality for larvae. More...
static double	m_DailyDevelopmentMortPrepupae = 0
	This holds the daily mortality for pre-pupae. More...
static double	m_DailyDevelopmentMortPupae = 0
	This holds the daily mortality for pupae. More...
static double	m_OsmiaEggDevelTotalDD = 0
	Is the number of day degrees needed for egg development to hatch. More...
static double	m_OsmiaEggDevelThreshold = 0
	Is temperature developmental threshold for egg development. More...
static double	m_OsmiaLarvaDevelTotalDD = 0
	Is the number of day degrees needed for larval hatch above the developmental threshold for larvae. More...
static double	m_OsmiaLarvaDevelThreshold = 0
	Is temperature developmental threshold for larval development. More...
static double	m_OsmiaPupaDevelTotalDD = 0
	Is the number of day degrees needed for pupal hatch above the developmental threshold for pupae. More...
static double	m_OsmiaPupaDevelThreshold = 0
	Is temperature developmental threshold for pupal development. More...
static double	m_OsmiaPrepupalDevelTotalDays = 0
	Number of days for prepupal development. More...
static double	m_OsmiaPrepupalDevelTotalDays10pct = 0
	10% of the number of days for prepupal development - just for speed More...
static double	m_OsmiaInCocoonOverwinteringTempThreshold = 0
	holds the value for the InCocoon overwintering temperature threshold More...
static double	m_OsmiaInCocoonEmergenceTempThreshold = 0
	holds the value for the InCocoon emergence temperature threshold More...
static double	m_OsmiaInCocoonPrewinteringTempThreshold = 0
	holds the value for the InCocoon prewintering temperature threshold More...
static double	m_OsmiaInCocoonWinterMortConst = 0.0
	holds the constant term value for the InCocoon winter mortality calculation More...
static double	m_OsmiaInCocoonWinterMortSlope = 0.0
	holds the coefficient value for the InCocoon winter mortality calculation More...
static double	m_OsmiaInCocoonEmergCountConst = 0.0
	holds the constant term value for the InCocoon emergence counter calculation More...
static double	m_OsmiaInCocoonEmergCountSlope = 0.0
	holds the coefficient value for the InCocoon emergence counter calculation More...
static double	m_OsmiaFemaleMassFromProvMassConst = 0.0
	holds the constant term value for the female mass calculation from provision mass More...
static double	m_OsmiaFemaleMassFromProvMassSlope = 0.0
	holds the coefficient value for the female mass calculation from provision mass More...
static double	m_MaleMinTargetProvisionMass = 0.0
	The minimum target provisioning for a male cell. More...
static double	m_MaleMaxTargetProvisionMass = 0.0
	The maximum target provisioning for a male cell. More...
static double	m_FemaleMinTargetProvisionMass = 0.0
	The minimum target provisioning for a female cell. More...
static double	m_FemaleMaxTargetProvisionMass = 0.0
	The maximum target provisioning for a female cell. More...
static double	m_FemaleMaxMass = 0.0
	The maximum female mass. More...
static double	m_FemaleMinMass = 0.0
	The minimum female mass. More...
static double	m_MaleMaxMass = 0.0
	The minimum Male mass. More...
static double	m_PollenScoreToMg = 0.0
	The conversion rate from pollen availability score to mg pollen provisioned per day. More...
static double	m_DensityDependentPollenRemovalConst = 0.0
	A parameter to link linear reduction in pollen availability to Osmia numbers per 1km2. More...
static double	m_MinimumCellConstructionTime = 0.0
	The shortest possible construction time for a cell - normally 1 day. More...
static double	m_MaximumCellConstructionTime = 0.0
	The longest possible construction time for a cell. More...
static int	m_TotalNestsPossible = 0
	The maximum number of nests possible for a bee. More...
static double	m_BombylidProbability = 0.0
	holds the probability of bombylid fly parasitism if open nest parasitoid More...
static double	m_ParasitismProbToTimeCellOpen = 0.0
	holds the ratio of open cell parasitism to time cell is open More...
static vector< double >	m_ParasitoidAttackChance = {}
	Holds the probability per capita of parasitoid attack for a subpopulation sized cell. More...
static double	m_OsmiaFemaleR50distance = 0.0
	holds the value for the female typical homing distance More...
static double	m_OsmiaFemaleR90distance = 0.0
	holds the value for the female max homing distance More...
static int	m_OsmiaFemalePrenesting = 0
	holds the value for the duration of prenesting More...
static int	m_OsmiaFemaleLifespan = 0
	holds the value for max female lifespan More...
static probability_distribution	m_generalmovementdistances = probability_distribution(cfg_OsmiaGeneralMovementProbType.value(), cfg_OsmiaGenerallMovementProbArgs.value())
	Static instance of the probability_distribution class of distance probablilties for nest searching and foraging. More...
static probability_distribution	m_dispersalmovementdistances = probability_distribution(cfg_OsmiaDispersalMovementProbType.value(), cfg_OsmiaDispersalMovementProbArgs.value())
	Static instance of the probability_distribution class of distance probablilties for dispersal. More...
static probability_distribution	m_eggspernestdistribution = probability_distribution(cfg_OsmiaEggsPerNestProbType.value(), cfg_OsmiaEggsPerNestProbArgs.value())
	Static instance of the probability_distribution class of distance probablilties for numbers of eggs per nest. More...
static probability_distribution	m_exp_ZeroToOne = probability_distribution("BETA", "1.0, 5.0")
	Static instance of the probability_distribution class of distance probablilties for approx exponential probs zero to 1.0. More...
static double	m_CocoonToProvisionMass = 0.0
	The ratio of cocoon to provision mass. More...
static double	m_ProvisionToCocoonMass = 0.0
	The ratio of provison to cocoon mass. More...
static double	m_TotalProvisioningMassLoss = 0.0
	The total provision mass loss expected first cocoon to last. More...
static double	m_TotalProvisioningMassLossRange = 0.0
	The variability around the expected total mass loss. More...
static double	m_TotalProvisioningMassLossRangeX2 = 0.0
	Twice the variability around the expected total mass loss. More...
static bool	m_UsingMechanisticParasitoids = false
	Flag for switching between ways of calculating parasitism. More...
static double	m_OsmiaFemaleBckMort = 0.0
	Holds the parameter for unspecified female daily mortality. More...
static int	m_OsmiaFemaleMinEggsPerNest = 0
	Holds the parameter for minimum planned eggs per nest. More...
static int	m_OsmiaFindNestAttemptNo = 0
	Holds the parameter for number of find nest tries. More...
static int	m_OsmiaFemaleMaxEggsPerNest = 0
	Holds the parameter for maximum planned eggs per nest. More...
static probability_distribution	m_emergenceday = probability_distribution(cfg_OsmiaEmergenceProbType.value(), cfg_OsmiaEmergenceProbArgs.value())
	Static instance of the probability_distribution class of emergence day. More...
Static Protected Attributes inherited from TAnimal
static Landscape *	m_OurLandscape = nullptr
	A pointer to the landscape object shared with all TAnimal objects. More...
static int	m_SimulationWidth = 0
	A static member for the simulation width because it is often used by descendent classes. More...
static int	m_SimulationHeight = 0
	A static member for the simulation height because it is often used by descendent classes. More...
static double	m_TemperatureToday = 0.0
	A holder for the temperature today shared with all TAnimal objects. More...
static int	m_DayInYear = 0
	A holder for the day in year shared with all TAnimal objects. More...

Additional Inherited Members
Protected Member Functions inherited from TAnimal
void	CorrectWrapRound ()
	Corrects wrap around co-ordinate problems. More...

Constructor & Destructor Documentation

Osmia_Base()

Osmia_Base::Osmia_Base

(

struct_Osmia *

data

)

Osmia constructor.

                                         : TAnimal(data->x,data->y)
{
    ReInit(data);
    // Assign the pointer to the population manager
    m_OurPopulationManager = data->OPM;
    m_CurrentOState = toOsmias_InitialState;
    m_OurNest = data->nest;
    SetAge(data->age); // Set the age
    SetMass(data->mass);
    SetParasitised(data->parasitised);
}

References struct_Osmia::age, m_CurrentOState, m_OurNest, m_OurPopulationManager, struct_Osmia::mass, struct_Osmia::nest, struct_Osmia::OPM, struct_Osmia::parasitised, ReInit(), SetAge(), SetMass(), SetParasitised(), and toOsmias_InitialState.

~Osmia_Base()

Osmia_Base::~Osmia_Base ( void  )

virtual

Osmia destructor.

{
    ;
}

Member Function Documentation

BeginStep()

virtual void Osmia_Base::BeginStep ( void  )

inlinevirtual

The BeginStep is the first 'part' of the timestep that an animal can behave in. It is called once per timestep.

Reimplemented from TALMaSSObject.

Reimplemented in Osmia_Female.

{ ; } // NB this is not used in the Osmia_Base code

EndStep()

virtual void Osmia_Base::EndStep ( void  )

inlinevirtual

The EndStep is the third 'part' of the timestep that an animal can behave in. It is called once per timestep.

Reimplemented from TALMaSSObject.

{ ; } // NB this is not used in the Osmia_Base code

GetAge()

int Osmia_Base::GetAge ( )

inline

A typical interface function - this one returns the age.

{ return m_Age; }

References m_Age.

GetMass()

double Osmia_Base::GetMass ( )

inline

Returns the bee's mass.

{ return m_Mass; }

References m_Mass.

GetNest()

Osmia_Nest* Osmia_Base::GetNest ( )

inline

{ return m_OurNest; }

References m_OurNest.

GetParasitised()

TTypeOfOsmiaParasitoids Osmia_Base::GetParasitised ( void  )

inline

Set the parasitised status.

{ return m_ParasitoidStatus; }

References m_ParasitoidStatus.

ReInit()

void Osmia_Base::ReInit

(

struct_Osmia *

data

)

Osmia reinitialise object methods.

                                          {
    TAnimal::ReinitialiseObject(data->x, data->y);
    // Assign the pointer to the population manager
    m_OurPopulationManager = data->OPM;
    m_CurrentOState = toOsmias_InitialState;
    SetAge(data->age); // Set the age
    SetMass(data->mass);
    SetParasitised(data->parasitised);
}

References struct_Osmia::age, m_CurrentOState, m_OurPopulationManager, struct_Osmia::mass, struct_Osmia::OPM, struct_Osmia::parasitised, TAnimal::ReinitialiseObject(), SetAge(), SetMass(), SetParasitised(), toOsmias_InitialState, struct_Osmia::x, and struct_Osmia::y.

Referenced by Osmia_Base(), and Osmia_Egg::ReInit().

SetAge()

void Osmia_Base::SetAge ( int  a_age )

inline

A typical interface function - this one returns the age.

{ m_Age = a_age; }

References m_Age.

Referenced by Osmia_Base(), and ReInit().

SetMass()

void Osmia_Base::SetMass ( double  a_mass )

inline

Sets the bee's mass.

{ m_Mass = a_mass; }

References m_Mass.

Referenced by Osmia_Base(), and ReInit().

SetParameterValues()

void Osmia_Base::SetParameterValues ( )

static

Used to populate the static members holding mortality and development parameters.

                                    {
    // Mortality
    m_DailyDevelopmentMortEggs = cfg_OsmiaEggDailyMORT.value();
    m_DailyDevelopmentMortLarvae = cfg_OsmiaLarvaDailyMORT.value();
    m_DailyDevelopmentMortPrepupae = cfg_OsmiaPrepupaDailyMORT.value();
    m_DailyDevelopmentMortPupae = cfg_OsmiaPupaDailyMORT.value();
    m_OsmiaInCocoonWinterMortConst = cfg_OsmiaInCocoonWinterMortConst.value();
    m_OsmiaInCocoonWinterMortSlope = cfg_OsmiaInCocoonWinterMortSlope.value();
    // Development
    m_OsmiaEggDevelTotalDD = cfg_OsmiaEggDevelTotalDD.value();
    m_OsmiaEggDevelThreshold = cfg_OsmiaEggDevelThreshold.value();
    m_OsmiaLarvaDevelThreshold = cfg_OsmiaLarvaDevelThreshold.value();
    m_OsmiaLarvaDevelTotalDD = cfg_OsmiaLarvaDevelTotalDD.value();
    m_OsmiaPupaDevelTotalDD = cfg_OsmiaPupaDevelTotalDD.value();
    m_OsmiaPupaDevelThreshold = cfg_OsmiaPupaDevelThreshold.value();
    m_OsmiaPrepupalDevelTotalDays = cfg_OsmiaPrepupaDevelTotalDays.value();
    m_OsmiaPrepupalDevelTotalDays10pct = cfg_OsmiaPrepupaDevelTotalDays.value()*0.1;
    m_OsmiaInCocoonOverwinteringTempThreshold  = cfg_OsmiaInCocoonOverwinteringTempThreshold.value();
    m_OsmiaInCocoonEmergenceTempThreshold = cfg_OsmiaInCocoonEmergenceTempThreshold.value();
    m_OsmiaInCocoonPrewinteringTempThreshold = cfg_OsmiaInCocoonPrewinteringTempThreshold.value();
    m_OsmiaInCocoonEmergCountConst = cfg_OsmiaInCocoonEmergCountConst.value();
    m_OsmiaInCocoonEmergCountSlope = cfg_OsmiaInCocoonEmergCountSlope.value();
    // Mass
    m_OsmiaFemaleMassFromProvMassConst = cfg_OsmiaFemaleMassFromProvMassConst.value();
    m_OsmiaFemaleMassFromProvMassSlope = cfg_OsmiaFemaleMassFromProvMassSlope.value();
    m_MaleMaxMass = cfg_OsmiaMaleMassMax.value();
    m_FemaleMinMass = cfg_OsmiaFemaleMassMin.value();
    m_FemaleMaxMass = cfg_OsmiaFemaleMassMax.value();
    m_FemaleMinTargetProvisionMass = ((m_FemaleMinMass - m_OsmiaFemaleMassFromProvMassConst) / m_OsmiaFemaleMassFromProvMassSlope);
    m_FemaleMaxTargetProvisionMass = ((m_FemaleMaxMass - m_OsmiaFemaleMassFromProvMassConst) / m_OsmiaFemaleMassFromProvMassSlope);
    m_MaleMinTargetProvisionMass = m_FemaleMinTargetProvisionMass * 0.95; // This must be smaller than the female min mass
    //m_MaleMaxTargetProvisionMass = m_FemaleMaxTargetProvisionMass * 0.61; // Note here we use the female values and scale it by the literature value ratio
    m_MaleMaxTargetProvisionMass = ((m_MaleMaxMass - m_OsmiaFemaleMassFromProvMassConst) / m_OsmiaFemaleMassFromProvMassSlope);
    // Movement/dispersal
    m_OsmiaFemaleR50distance = cfg_OsmiaTypicalHomingDistance.value();
    m_OsmiaFemaleR90distance = cfg_OsmiaMaxHomingDistance.value();
 
    m_OsmiaFemalePrenesting = cfg_OsmiaFemalePrenestingDuration.value();
    m_OsmiaFemaleLifespan = cfg_OsmiaFemaleLifespan.value();
 
}

References cfg_OsmiaEggDailyMORT, cfg_OsmiaEggDevelThreshold, cfg_OsmiaEggDevelTotalDD, cfg_OsmiaFemaleLifespan, cfg_OsmiaFemaleMassFromProvMassConst, cfg_OsmiaFemaleMassFromProvMassSlope, cfg_OsmiaFemaleMassMax, cfg_OsmiaFemaleMassMin, cfg_OsmiaFemalePrenestingDuration, cfg_OsmiaInCocoonEmergCountConst, cfg_OsmiaInCocoonEmergCountSlope, cfg_OsmiaInCocoonEmergenceTempThreshold, cfg_OsmiaInCocoonOverwinteringTempThreshold, cfg_OsmiaInCocoonPrewinteringTempThreshold, cfg_OsmiaInCocoonWinterMortConst, cfg_OsmiaInCocoonWinterMortSlope, cfg_OsmiaLarvaDailyMORT, cfg_OsmiaLarvaDevelThreshold, cfg_OsmiaLarvaDevelTotalDD, cfg_OsmiaMaleMassMax, cfg_OsmiaMaxHomingDistance, cfg_OsmiaPrepupaDailyMORT, cfg_OsmiaPrepupaDevelTotalDays, cfg_OsmiaPupaDailyMORT, cfg_OsmiaPupaDevelThreshold, cfg_OsmiaPupaDevelTotalDD, cfg_OsmiaTypicalHomingDistance, m_DailyDevelopmentMortEggs, m_DailyDevelopmentMortLarvae, m_DailyDevelopmentMortPrepupae, m_DailyDevelopmentMortPupae, m_FemaleMaxMass, m_FemaleMaxTargetProvisionMass, m_FemaleMinMass, m_FemaleMinTargetProvisionMass, m_MaleMaxMass, m_MaleMaxTargetProvisionMass, m_MaleMinTargetProvisionMass, m_OsmiaEggDevelThreshold, m_OsmiaEggDevelTotalDD, m_OsmiaFemaleLifespan, m_OsmiaFemaleMassFromProvMassConst, m_OsmiaFemaleMassFromProvMassSlope, m_OsmiaFemalePrenesting, m_OsmiaFemaleR50distance, m_OsmiaFemaleR90distance, m_OsmiaInCocoonEmergCountConst, m_OsmiaInCocoonEmergCountSlope, m_OsmiaInCocoonEmergenceTempThreshold, m_OsmiaInCocoonOverwinteringTempThreshold, m_OsmiaInCocoonPrewinteringTempThreshold, m_OsmiaInCocoonWinterMortConst, m_OsmiaInCocoonWinterMortSlope, m_OsmiaLarvaDevelThreshold, m_OsmiaLarvaDevelTotalDD, m_OsmiaPrepupalDevelTotalDays, m_OsmiaPrepupalDevelTotalDays10pct, m_OsmiaPupaDevelThreshold, m_OsmiaPupaDevelTotalDD, CfgInt::value(), and CfgFloat::value().

Referenced by Osmia_Population_Manager::Init().

SetParasitised()

void Osmia_Base::SetParasitised ( TTypeOfOsmiaParasitoids  a_status )

inline

Set the parasitised status.

                                                          { 
        m_ParasitoidStatus = a_status; 
    }

References m_ParasitoidStatus.

Referenced by Osmia_Base(), and ReInit().

SetParasitoidManager()

static void Osmia_Base::SetParasitoidManager ( OsmiaParasitoid_Population_Manager *  a_popman )

inlinestatic

Set method for m_OsmiaParasitoid_Population_Manager

    { 
        m_OurParasitoidPopulationManager = a_popman; 
    }

References m_OurParasitoidPopulationManager.

Referenced by Osmia_Population_Manager::Init().

SetTemp()

static void Osmia_Base::SetTemp ( double  a_temperature )

inlinestatic

                                              { 
        m_TempToday = a_temperature;
        m_TempTodayInt = int(floor(a_temperature + 0.5)); 
    }

References m_TempToday, and m_TempTodayInt.

Referenced by Osmia_Population_Manager::DoFirst().

st_Dying()

void Osmia_Base::st_Dying ( void  )

virtual

Behavioural state dying.

Reimplemented in Osmia_Female.

{
    KillThis(); // this will kill the animal object and free up space
    m_OurNest->RemoveCell(this);
}

References TAnimal::KillThis(), m_OurNest, and Osmia_Nest::RemoveCell().

Referenced by Osmia_Population_Manager::DoBefore(), Osmia_Egg::Step(), Osmia_Larva::Step(), Osmia_Prepupa::Step(), Osmia_Pupa::Step(), and Osmia_InCocoon::Step().

Step()

virtual void Osmia_Base::Step ( void  )

inlinevirtual

The Step is the second 'part' of the timestep that an animal can behave in. It is called continuously until all animals report that they are 'DONE'.

Reimplemented from TALMaSSObject.

Reimplemented in Osmia_Female, Osmia_InCocoon, Osmia_Pupa, Osmia_Prepupa, Osmia_Larva, and Osmia_Egg.

{ ; } // NB this is not used in the Osmia_Base code

Member Data Documentation

m_Age

int Osmia_Base::m_Age

protected

A typical member variable - this one is the age in days.

Referenced by GetAge(), SetAge(), Osmia_Egg::st_Develop(), Osmia_Larva::st_Develop(), Osmia_Prepupa::st_Develop(), Osmia_Pupa::st_Develop(), Osmia_InCocoon::st_Develop(), Osmia_Pupa::st_Emerge(), Osmia_InCocoon::st_Emerge(), Osmia_Egg::st_Hatch(), Osmia_Larva::st_Prepupate(), and Osmia_Prepupa::st_Pupate().

m_BombylidProbability

double Osmia_Base::m_BombylidProbability = 0.0

staticprotected

holds the probability of bombylid fly parasitism if open nest parasitoid

Referenced by Osmia_Female::CalcParaistised(), and Osmia_Female::SetBombylidProbability().

m_CocoonToProvisionMass

double Osmia_Base::m_CocoonToProvisionMass = 0.0

staticprotected

The ratio of cocoon to provision mass.

Referenced by Osmia_Female::SetCocoonToProvisionMass().

m_CurrentOState

TTypeOfOsmiaState Osmia_Base::m_CurrentOState

protected

Variable to record current behavioural state.

A Osmia must have some simple functionality: Inititation and development And some simple characteristics, herein age. Inherits m_Location_x, m_Location_y, m_OurLandscape from TAnimal NB All areas are squares of size length X length

Referenced by Osmia_Female::BeginStep(), Osmia_Female::OnFarmEvent(), Osmia_Base(), ReInit(), Osmia_Egg::Step(), Osmia_Larva::Step(), Osmia_Prepupa::Step(), Osmia_Pupa::Step(), Osmia_InCocoon::Step(), and Osmia_Female::Step().

m_DailyDevelopmentMortEggs

double Osmia_Base::m_DailyDevelopmentMortEggs = 0

staticprotected

This holds the daily mortality for eggs.

Referenced by Osmia_Egg::DailyMortality(), and SetParameterValues().

m_DailyDevelopmentMortLarvae

double Osmia_Base::m_DailyDevelopmentMortLarvae = 0

staticprotected

This holds the daily mortality for larvae.

Referenced by Osmia_Larva::DailyMortality(), and SetParameterValues().

m_DailyDevelopmentMortPrepupae

double Osmia_Base::m_DailyDevelopmentMortPrepupae = 0

staticprotected

This holds the daily mortality for pre-pupae.

Referenced by Osmia_Prepupa::DailyMortality(), and SetParameterValues().

m_DailyDevelopmentMortPupae

double Osmia_Base::m_DailyDevelopmentMortPupae = 0

staticprotected

This holds the daily mortality for pupae.

Referenced by Osmia_Pupa::DailyMortality(), and SetParameterValues().

m_DensityDependentPollenRemovalConst

double Osmia_Base::m_DensityDependentPollenRemovalConst = 0.0

staticprotected

A parameter to link linear reduction in pollen availability to Osmia numbers per 1km2.

Referenced by Osmia_Female::SetDensityDependentPollenRemovalConst().

m_dispersalmovementdistances

probability_distribution Osmia_Base::m_dispersalmovementdistances = probability_distribution(cfg_OsmiaDispersalMovementProbType.value(), cfg_OsmiaDispersalMovementProbArgs.value())

staticprotected

Static instance of the probability_distribution class of distance probablilties for dispersal.

Referenced by Osmia_Female::st_Dispersal().

m_eggspernestdistribution

probability_distribution Osmia_Base::m_eggspernestdistribution = probability_distribution(cfg_OsmiaEggsPerNestProbType.value(), cfg_OsmiaEggsPerNestProbArgs.value())

staticprotected

Static instance of the probability_distribution class of distance probablilties for numbers of eggs per nest.

Referenced by Osmia_Female::PlanEggsPerNest().

m_emergenceday

probability_distribution Osmia_Base::m_emergenceday = probability_distribution(cfg_OsmiaEmergenceProbType.value(), cfg_OsmiaEmergenceProbArgs.value())

staticprotected

Static instance of the probability_distribution class of emergence day.

Referenced by Osmia_InCocoon::st_Develop().

m_exp_ZeroToOne

probability_distribution Osmia_Base::m_exp_ZeroToOne = probability_distribution("BETA", "1.0, 5.0")

staticprotected

Static instance of the probability_distribution class of distance probablilties for approx exponential probs zero to 1.0.

Referenced by Osmia_Female::LayEgg().

m_FemaleMaxMass

double Osmia_Base::m_FemaleMaxMass = 0.0

staticprotected

The maximum female mass.

Referenced by Osmia_Female::Init(), and SetParameterValues().

m_FemaleMaxTargetProvisionMass

double Osmia_Base::m_FemaleMaxTargetProvisionMass = 0.0

staticprotected

The maximum target provisioning for a female cell.

Referenced by Osmia_Female::LayEgg(), Osmia_Female::SetFemaleMaxTargetProvisionMass(), and SetParameterValues().

m_FemaleMinMass

double Osmia_Base::m_FemaleMinMass = 0.0

staticprotected

The minimum female mass.

Referenced by Osmia_Female::Init(), and SetParameterValues().

m_FemaleMinTargetProvisionMass

double Osmia_Base::m_FemaleMinTargetProvisionMass = 0.0

staticprotected

The minimum target provisioning for a female cell.

Referenced by Osmia_Female::LayEgg(), Osmia_Female::SetFemaleMinTargetProvisionMass(), and SetParameterValues().

m_foragehours

int Osmia_Base::m_foragehours

protected

A variable to hold the number of available forage hours left in a day.

Referenced by Osmia_Female::st_ReproductiveBehaviour().

m_generalmovementdistances

probability_distribution Osmia_Base::m_generalmovementdistances = probability_distribution(cfg_OsmiaGeneralMovementProbType.value(), cfg_OsmiaGenerallMovementProbArgs.value())

staticprotected

Static instance of the probability_distribution class of distance probablilties for nest searching and foraging.

Referenced by Osmia_Female::FindNestLocation().

m_MaleMaxMass

double Osmia_Base::m_MaleMaxMass = 0.0

staticprotected

The minimum Male mass.

Referenced by SetParameterValues().

m_MaleMaxTargetProvisionMass

double Osmia_Base::m_MaleMaxTargetProvisionMass = 0.0

staticprotected

The maximum target provisioning for a male cell.

Referenced by Osmia_Female::LayEgg(), and SetParameterValues().

m_MaleMinTargetProvisionMass

double Osmia_Base::m_MaleMinTargetProvisionMass = 0.0

staticprotected

The minimum target provisioning for a male cell.

Referenced by Osmia_Female::LayEgg(), Osmia_Female::SetMaleMinTargetProvisionMass(), SetParameterValues(), and Osmia_Female::st_ReproductiveBehaviour().

m_Mass

double Osmia_Base::m_Mass

protected

An attribute to record the mass of the bee or provisioned pollen depending on life-stage

Referenced by Osmia_Female::BeginStep(), Osmia_Female::CalculateEggLoad(), GetMass(), Osmia_Female::Init(), SetMass(), Osmia_Pupa::st_Emerge(), Osmia_InCocoon::st_Emerge(), Osmia_Egg::st_Hatch(), Osmia_Larva::st_Prepupate(), and Osmia_Prepupa::st_Pupate().

m_MaximumCellConstructionTime

double Osmia_Base::m_MaximumCellConstructionTime = 0.0

staticprotected

The longest possible construction time for a cell.

Referenced by Osmia_Female::SetMaximumCellConstructionTime(), and Osmia_Female::st_ReproductiveBehaviour().

m_MinimumCellConstructionTime

double Osmia_Base::m_MinimumCellConstructionTime = 0.0

staticprotected

The shortest possible construction time for a cell - normally 1 day.

Referenced by Osmia_Female::SetMinimumCellConstructionTime().

m_OsmiaEggDevelThreshold

double Osmia_Base::m_OsmiaEggDevelThreshold = 0

staticprotected

Is temperature developmental threshold for egg development.

Referenced by SetParameterValues(), and Osmia_Egg::st_Develop().

m_OsmiaEggDevelTotalDD

double Osmia_Base::m_OsmiaEggDevelTotalDD = 0

staticprotected

Is the number of day degrees needed for egg development to hatch.

Referenced by SetParameterValues(), and Osmia_Egg::st_Develop().

m_OsmiaFemaleBckMort

double Osmia_Base::m_OsmiaFemaleBckMort = 0.0

staticprotected

Holds the parameter for unspecified female daily mortality.

Referenced by Osmia_Female::SetDailyMort(), and Osmia_Female::st_Develop().

m_OsmiaFemaleLifespan

int Osmia_Base::m_OsmiaFemaleLifespan = 0

staticprotected

holds the value for max female lifespan

Referenced by SetParameterValues(), and Osmia_Female::st_Develop().

m_OsmiaFemaleMassFromProvMassConst

double Osmia_Base::m_OsmiaFemaleMassFromProvMassConst = 0.0

staticprotected

holds the constant term value for the female mass calculation from provision mass

Referenced by SetParameterValues(), and Osmia_InCocoon::st_Emerge().

m_OsmiaFemaleMassFromProvMassSlope

double Osmia_Base::m_OsmiaFemaleMassFromProvMassSlope = 0.0

staticprotected

holds the coefficient value for the female mass calculation from provision mass

Referenced by SetParameterValues(), and Osmia_InCocoon::st_Emerge().

m_OsmiaFemaleMaxEggsPerNest

int Osmia_Base::m_OsmiaFemaleMaxEggsPerNest = 0

staticprotected

Holds the parameter for maximum planned eggs per nest.

Referenced by Osmia_Female::PlanEggsPerNest(), and Osmia_Female::SetMaxEggsPerNest().

m_OsmiaFemaleMinEggsPerNest

int Osmia_Base::m_OsmiaFemaleMinEggsPerNest = 0

staticprotected

Holds the parameter for minimum planned eggs per nest.

Referenced by Osmia_Female::PlanEggsPerNest(), Osmia_Female::SetMinEggsPerNest(), and Osmia_Female::st_ReproductiveBehaviour().

m_OsmiaFemalePrenesting

int Osmia_Base::m_OsmiaFemalePrenesting = 0

staticprotected

holds the value for the duration of prenesting

Referenced by SetParameterValues(), and Osmia_Female::st_Develop().

m_OsmiaFemaleR50distance

double Osmia_Base::m_OsmiaFemaleR50distance = 0.0

staticprotected

holds the value for the female typical homing distance

Referenced by Osmia_Female::FindNestLocation(), and SetParameterValues().

m_OsmiaFemaleR90distance

double Osmia_Base::m_OsmiaFemaleR90distance = 0.0

staticprotected

holds the value for the female max homing distance

Referenced by SetParameterValues(), and Osmia_Female::st_Dispersal().

m_OsmiaFindNestAttemptNo

int Osmia_Base::m_OsmiaFindNestAttemptNo = 0

staticprotected

Holds the parameter for number of find nest tries.

Referenced by Osmia_Female::FindNestLocation(), and Osmia_Female::SetNestFindAttempts().

m_OsmiaInCocoonEmergCountConst

double Osmia_Base::m_OsmiaInCocoonEmergCountConst = 0.0

staticprotected

holds the constant term value for the InCocoon emergence counter calculation

Referenced by SetParameterValues(), and Osmia_InCocoon::st_Develop().

m_OsmiaInCocoonEmergCountSlope

double Osmia_Base::m_OsmiaInCocoonEmergCountSlope = 0.0

staticprotected

holds the coefficient value for the InCocoon emergence counter calculation

Referenced by SetParameterValues(), and Osmia_InCocoon::st_Develop().

m_OsmiaInCocoonEmergenceTempThreshold

double Osmia_Base::m_OsmiaInCocoonEmergenceTempThreshold = 0

staticprotected

holds the value for the InCocoon emergence temperature threshold

Referenced by SetParameterValues(), and Osmia_InCocoon::st_Develop().

m_OsmiaInCocoonOverwinteringTempThreshold

double Osmia_Base::m_OsmiaInCocoonOverwinteringTempThreshold = 0

staticprotected

holds the value for the InCocoon overwintering temperature threshold

Referenced by SetParameterValues(), and Osmia_InCocoon::st_Develop().

m_OsmiaInCocoonPrewinteringTempThreshold

double Osmia_Base::m_OsmiaInCocoonPrewinteringTempThreshold = 0

staticprotected

holds the value for the InCocoon prewintering temperature threshold

Referenced by SetParameterValues(), and Osmia_InCocoon::st_Develop().

m_OsmiaInCocoonWinterMortConst

double Osmia_Base::m_OsmiaInCocoonWinterMortConst = 0.0

staticprotected

holds the constant term value for the InCocoon winter mortality calculation

Referenced by SetParameterValues(), and Osmia_InCocoon::WinterMortality().

m_OsmiaInCocoonWinterMortSlope

double Osmia_Base::m_OsmiaInCocoonWinterMortSlope = 0.0

staticprotected

holds the coefficient value for the InCocoon winter mortality calculation

Referenced by SetParameterValues(), and Osmia_InCocoon::WinterMortality().

m_OsmiaLarvaDevelThreshold

double Osmia_Base::m_OsmiaLarvaDevelThreshold = 0

staticprotected

Is temperature developmental threshold for larval development.

Referenced by SetParameterValues(), and Osmia_Larva::st_Develop().

m_OsmiaLarvaDevelTotalDD

double Osmia_Base::m_OsmiaLarvaDevelTotalDD = 0

staticprotected

Is the number of day degrees needed for larval hatch above the developmental threshold for larvae.

Referenced by SetParameterValues(), and Osmia_Larva::st_Develop().

m_OsmiaPrepupalDevelTotalDays

double Osmia_Base::m_OsmiaPrepupalDevelTotalDays = 0

staticprotected

Number of days for prepupal development.

Referenced by Osmia_Prepupa::Osmia_Prepupa(), and SetParameterValues().

m_OsmiaPrepupalDevelTotalDays10pct

double Osmia_Base::m_OsmiaPrepupalDevelTotalDays10pct = 0

staticprotected

10% of the number of days for prepupal development - just for speed

Referenced by Osmia_Prepupa::Osmia_Prepupa(), and SetParameterValues().

m_OsmiaPupaDevelThreshold

double Osmia_Base::m_OsmiaPupaDevelThreshold = 0

staticprotected

Is temperature developmental threshold for pupal development.

Referenced by SetParameterValues(), and Osmia_Pupa::st_Develop().

m_OsmiaPupaDevelTotalDD

double Osmia_Base::m_OsmiaPupaDevelTotalDD = 0

staticprotected

Is the number of day degrees needed for pupal hatch above the developmental threshold for pupae.

Referenced by SetParameterValues(), and Osmia_Pupa::st_Develop().

m_OurNest

Osmia_Nest* Osmia_Base::m_OurNest

protected

A useful pointer to the current nest with double use, for up to InCocoon its the nest where they are, for females its the current being provisioned

Referenced by Osmia_Female::CalcParaistised(), Osmia_Female::FindNestLocation(), GetNest(), Osmia_Female::Init(), Osmia_Female::LayEgg(), Osmia_Base(), Osmia_Egg::Osmia_Egg(), Osmia_Egg::ReInit(), Osmia_Egg::st_Develop(), Osmia_Larva::st_Develop(), Osmia_InCocoon::st_Develop(), st_Dying(), Osmia_Female::st_Dying(), Osmia_Pupa::st_Emerge(), Osmia_InCocoon::st_Emerge(), Osmia_Egg::st_Hatch(), Osmia_Larva::st_Prepupate(), Osmia_Prepupa::st_Pupate(), and Osmia_Female::st_ReproductiveBehaviour().

m_OurParasitoidPopulationManager

OsmiaParasitoid_Population_Manager * Osmia_Base::m_OurParasitoidPopulationManager = NULL

staticprotected

This is a time saving pointer to the parasitoid population manager object.

Referenced by Osmia_Female::CalcParaistised(), and SetParasitoidManager().

m_OurPopulationManager

Osmia_Population_Manager* Osmia_Base::m_OurPopulationManager

protected

This is a time saving pointer to the correct population manager object.

Referenced by Osmia_Female::BeginStep(), Osmia_Female::FindNestLocation(), Osmia_Female::Init(), Osmia_Female::LayEgg(), Osmia_Female::OnFarmEvent(), Osmia_Base(), ReInit(), Osmia_Prepupa::st_Develop(), Osmia_InCocoon::st_Develop(), Osmia_Female::st_Develop(), Osmia_Female::st_Dispersal(), Osmia_Female::st_Dying(), Osmia_Pupa::st_Emerge(), Osmia_InCocoon::st_Emerge(), Osmia_Egg::st_Hatch(), Osmia_Larva::st_Prepupate(), Osmia_Prepupa::st_Pupate(), and Osmia_Female::st_ReproductiveBehaviour().

m_ParasitismProbToTimeCellOpen

double Osmia_Base::m_ParasitismProbToTimeCellOpen = 0.0

staticprotected

holds the ratio of open cell parasitism to time cell is open

Referenced by Osmia_Female::CalcParaistised(), and Osmia_Female::SetParasitismProbToTimeCellOpen().

m_ParasitoidAttackChance

vector< double > Osmia_Base::m_ParasitoidAttackChance = {}

staticprotected

Holds the probability per capita of parasitoid attack for a subpopulation sized cell.

Referenced by Osmia_Female::CalcParaistised(), and Osmia_Female::SetParasitoidParameters().

m_ParasitoidStatus

TTypeOfOsmiaParasitoids Osmia_Base::m_ParasitoidStatus

protected

Holds the parasitoid status - only one is allowed.

Referenced by GetParasitised(), SetParasitised(), Osmia_Pupa::st_Emerge(), Osmia_InCocoon::st_Emerge(), Osmia_Egg::st_Hatch(), Osmia_Larva::st_Prepupate(), and Osmia_Prepupa::st_Pupate().

m_PollenScoreToMg

double Osmia_Base::m_PollenScoreToMg = 0.0

staticprotected

The conversion rate from pollen availability score to mg pollen provisioned per day.

Referenced by Osmia_Female::Forage(), and Osmia_Female::SetPollenScoreToMg().

m_ProvisionToCocoonMass

double Osmia_Base::m_ProvisionToCocoonMass = 0.0

staticprotected

The ratio of provison to cocoon mass.

Referenced by Osmia_Female::SetProvisionToCocoonMass().

m_TempToday

double Osmia_Base::m_TempToday = -9999

staticprotected

The temperature today. This is static because there is only one temperature today.

Referenced by SetTemp(), Osmia_Egg::st_Develop(), and Osmia_InCocoon::st_Develop().

m_TempTodayInt

int Osmia_Base::m_TempTodayInt = -9999

staticprotected

The temperature today to the nearest degree. This is static because there is only one temperature today. This is mostly for use in temperature indexed arrays (if used)

Referenced by SetTemp().

m_TotalNestsPossible

int Osmia_Base::m_TotalNestsPossible = 0

staticprotected

The maximum number of nests possible for a bee.

Referenced by Osmia_Female::CalculateEggLoad(), and Osmia_Female::SetTotalNestsPossible().

m_TotalProvisioningMassLoss

double Osmia_Base::m_TotalProvisioningMassLoss = 0.0

staticprotected

The total provision mass loss expected first cocoon to last.

Referenced by Osmia_Female::SetCocoonToProvisionMass(), and Osmia_Female::st_ReproductiveBehaviour().

m_TotalProvisioningMassLossRange

double Osmia_Base::m_TotalProvisioningMassLossRange = 0.0

staticprotected

The variability around the expected total mass loss.

Referenced by Osmia_Female::SetCocoonToProvisionMass(), and Osmia_Female::st_ReproductiveBehaviour().

m_TotalProvisioningMassLossRangeX2

double Osmia_Base::m_TotalProvisioningMassLossRangeX2 = 0.0

staticprotected

Twice the variability around the expected total mass loss.

Referenced by Osmia_Female::SetCocoonToProvisionMass(), and Osmia_Female::st_ReproductiveBehaviour().

m_UsingMechanisticParasitoids

bool Osmia_Base::m_UsingMechanisticParasitoids = false

staticprotected

Flag for switching between ways of calculating parasitism.

Referenced by Osmia_Female::CalcParaistised(), and Osmia_Female::SetUsingMechanisticParasitoids().

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

• /builds/ALMaSS/ALMaSS_MIDox/Osmia/Osmia.h
• /builds/ALMaSS/ALMaSS_MIDox/Osmia/Osmia.cpp
• /builds/ALMaSS/ALMaSS_MIDox/Osmia/Osmia_Population_Manager.cpp