ALMaSS: Osmia_Population_Manager Class Reference

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The class to handle all Osmia bee population related matters. More...

#include <Osmia_Population_Manager.h>

Inheritance diagram for Osmia_Population_Manager:

Public Member Functions
	Osmia_Population_Manager (Landscape *L)
	Osmia_Population_Manager Constructor. More...

void	Init ()
	Used to collect data initialisation together. More...

virtual	~Osmia_Population_Manager (void)
	Osmia_Population_Manager Destructor. More...

void	TheAOROutputProbe () override
	Output method. More...

void	CreateObjects (TTypeOfOsmiaLifeStages ob_type, TAnimal pvo, struct_Osmia data, int number)
	Method for creating a new individual Osmia. More...

bool	IsEndPreWinter ()
	Returns flag to denore the end of prewintering, if ended it is set to true. More...

bool	IsOverWinterEnd ()
	Returns flag to denore the end of overwintering, if ended it is set to true. More...

bool	IsOsmiaNestPossible (int a_polyindex)
	Checks whether a nest is possible here. More...

bool	SantityCheck (int a_polyindex)
	Checks whether a nest is possible here. More...

Osmia_Nest *	CreateNest (int a_x, int a_y, int a_polyindex)
	Creates an Osmia_Nest in the polygon referenced by the index polyindex. More...

void	ReleaseOsmiaNest (int a_polyindex, Osmia_Nest *a_nest)
	Release the given nest in the given polygon. More...

int	GetForageHours ()
	Return the Osmia flying weather hours. More...

double	GetProvisioningParams (int a_age)
	Returns the values of provisioning parameters for a adult age. More...

double	GetFirstCocoonProvisioningMass (int a_age, int a_massclass)
	Return the first cocoon mass for a nest give an age and female mass. More...

double	GetSexRatioEggsAgeMass (int a_massclass, int a_age)
	Return the sex ratio for a nest give an age and female mass. More...

int	AddToDensityGrid (APoint a_loc)
	Adds a bee to the density grid at a location. More...

void	AddToDensityGrid (int a_index)
	Adds a bee to the density grid using the grid index value. More...

void	RemoveFromDensityGrid (int a_index)
	Adds a bee to the density grid using the grid index value. More...

int	GetDensity (APoint a_loc)
	Gets the number of bees at a location. More...

int	GetDensity (int a_index)
	Gets the number of bees at a location based on the grid index value. More...

void	ClearDensityGrid ()
	Empties the bee density grid. More...

double	GetPrePupalDevelDays ()
	Returns the amount of development a pre-pupal bee will get today based on temperature. More...

void	CalForageHours (void)

Public Member Functions inherited from Population_Manager
	Population_Manager (Landscape *a_l_ptr, int a_numberLifeStages=12)

virtual	~Population_Manager (void)

void	SetNoProbesAndSpeciesSpecificFunctions (int a_pn) override
	Sets up probe and species specifics. More...

void	OpenTheAOROutputProbe (const string &a_AORFilename) override
	Opens the AOR output file. More...

unsigned	GetLiveArraySize (int a_listindex) override
	Gets the number of 'live' objects for a list index in the TheArray. More...

unsigned	GetPopulationSize (int a_listindex) override
	Gets the number of species objects by default it is the same as LiveArray, however it could be different. This function should be used/overriden when we are interested in the number of the objects for presentation and not in inner maintenance of the PopulationManager and or TheArray. More...

void	IncLiveArraySize (int a_listindex)
	Increments the number of 'live' objects for a list index in the TheArray. More...

unsigned int	FarmAnimalCensus (unsigned int a_farm, unsigned int a_typeofanimal)

char *	SpeciesSpecificReporting (int a_species, int a_time) override

char *	ProbeReport (int a_time)

char *	ProbeReportTimed (int a_time)

void	ImpactProbeReport (int a_Time)

bool	BeginningOfMonth ()

void	LOG (const char *fname)

int	SupplyStepSize () const

void	Run (int NoTSteps) override

virtual unsigned	Probe (int ListIndex, Probe_Data *p_TheProbe)

virtual void	ImpactedProbe ()

virtual TAnimal *	SupplyAnimalPtr (unsigned int a_index, unsigned int a_animal)
	Returns the pointer indexed by a_index and a_animal. Note NO RANGE CHECK. More...

virtual unsigned	SupplyListIndexSize ()

unsigned	SupplyListSize (unsigned listindex) const

void	PushIndividual (const unsigned a_listindex, TAnimal *a_individual_ptr)

const char *	SupplyStateNames (int i) const

unsigned	SupplyStateNamesLength () const

virtual void	DisplayLocations ()

TAnimal *	FindIndividual (unsigned Type, TAnimal *a_me)

virtual TAnimal *	FindClosest (int x, int y, unsigned Type, TAnimal *a_me)

omp_nest_lock_t *	GetGuardMapElement (unsigned a_x_index, unsigned a_y_index)
	Return the guard map cell. More...

void	SetGuardMapElement (unsigned a_x_index, unsigned a_y_index)
	Set the given guard map cell. More...

void	UnsetGuardMapElement (unsigned a_x_index, unsigned a_y_index)
	Unset the given guard map cell. More...

void	UpdateGuardMap (int a_x, int a_y, int &a_index_x, int &a_index_y)
	Get the index of the guard map for the given location. More...

bool	OpenTheRipleysOutputProbe ()

bool	OpenTheMonthlyRipleysOutputProbe ()

bool	OpenTheReallyBigProbe ()

virtual void	TheRipleysOutputProbe (ofstream *a_prb)
	Special output functionality. More...

virtual void	TheReallyBigOutputProbe ()

void	CloseTheMonthlyRipleysOutputProbe () const

virtual void	CloseTheRipleysOutputProbe ()

virtual void	CloseTheReallyBigOutputProbe ()

TTypesOfPopulation	GetPopulationType ()

int	GetSeasonNumber ()
	Get the season number. More...

void	LamdaDeath (int x, int y)

void	LamdaBirth (int x, int y)

void	LamdaBirth (int x, int y, int z)

void	LamdaClear ()

void	LamdaDumpOutput ()

virtual int	SupplyPegPosx (int)

virtual int	SupplyPegPosy (int)

virtual int	SupplyCovPosx (int)

virtual int	SupplyCovPosy (int)

virtual bool	OpenTheFledgelingProbe ()

virtual bool	OpenTheBreedingPairsProbe ()

virtual bool	OpenTheBreedingSuccessProbe ()

virtual void	BreedingPairsOutput (int)

virtual int	TheBreedingFemalesProbe (int)

virtual int	TheFledgelingProbe ()

virtual void	BreedingSuccessProbeOutput (double, int, int, int, int, int, int, int)

virtual int	TheBreedingSuccessProbe (int &, int &, int &, int &, int &, int &)

virtual void	FledgelingProbeOutput (int, int)

virtual void	TheGeneticProbe (unsigned, int, unsigned &)

virtual void	GeneticsResultsOutput (FILE *, unsigned)

void	Debug_Shuffle (unsigned int Type)

virtual void	RunStepMethods ()

Public Member Functions inherited from Population_Manager_Base
	Population_Manager_Base (Landscape *L)
	The Population_Manager_Base constructor. More...

virtual void	Catastrophe (int)
	Must be re-implemented in descendent classes. More...

int	SupplySimW () const
	Returns landscape width in m. More...

int	SupplySimH () const
	Returns landscape height in m. More...

int	SupplySimWH () const
	Returns half the landscape width in m. More...

int	SupplySimHH () const
	Returns half the landscape height in m. More...

virtual int	ProbeFileInput (char *p_Filename, int p_ProbeNo)
	A stub to build specfic probes and functions. More...

int	SupplyListNameLength () const

const char *	SupplyListName (int a_i) const
	Get a list name from the list. More...

virtual void	SupplyLocXY (unsigned, unsigned, int &, int &)
	A stub for identifying an individual at a location. More...

virtual TAnimal *	FindClosest (int, int, unsigned)
	A stub for identifying an individual at a location. More...

std::string	SupplySimulationName ()

void	SetStepCounterInADay (int a_counter)
	Set step counter in a day. More...

int	GetStepCounterInADay (void)
	Return the sep counter in a day. More...

virtual double	GetAphidDensity (int, int)
	Return the aphid density, it is only used when aphid simulations are running. More...

Protected Member Functions
virtual void	DoFirst ()
	Things to do before anything else at the start of a timestep More...

virtual void	DoBefore ()
	Things to do before the Step. More...

virtual void	DoAfter ()
	Things to do before the EndStep. More...

virtual void	DoLast ()
	Things to do after the EndStep - here calculations related to summing global day degrees. More...

Protected Member Functions inherited from Population_Manager
virtual bool	StepFinished ()
	Methods to run the simulations. More...

virtual void	DoSpecialBetweenLifeStages (int a_life_stage)

virtual void	SortX (unsigned Type)

void	SortXIndex (unsigned Type)

virtual void	SortY (unsigned Type)

void	SortState (unsigned Type)

void	SortStateR (unsigned Type)

virtual unsigned	PartitionLiveDead (unsigned Type)

virtual void	Shuffle_or_Sort (unsigned Type)

virtual void	Shuffle (unsigned Type)

virtual void	Catastrophe ()

Protected Member Functions inherited from Population_Manager_Base
	~Population_Manager_Base ()=default

Protected Attributes
PollenMap_centroidbased *	m_ThePollenMap
	A pointer to the pollen map object. More...

int	m_FlyingWeather
	A daily value to indicate the hours the weather is OK for Osmia adult activity. More...

bool	m_PreWinteringEndFlag

bool	m_OverWinterEndFlag

Osmia_Nest_Manager	m_OurOsmiaNestManager
	This provides the interface to the Osmia_Nests linked to the polgons. More...

double	m_NestProvisioningParameters [365]
	A lookup table used to store pre-calculated nest provisioning parameters in advance since they are CPU intensive. More...

vector< eggsexratiovsagelogisticcurvedata >	m_EggSexRatioEqns
	Holds logistic equation values per age/mass of female for egg sex ratios. More...

vector< femalecocoonmassvsagelogisticcurvedata >	m_FemaleCocoonMassEqns
	Holds logistic equation values per age/mass of female for first female cocoon mass. More...

vector< int >	m_FemaleDensityGrid
	holds numbers of females per 1km2 More...

int	m_GridExtent
	holds numbers of grid cells per row More...

double	m_PollenCompetitionsReductionScaler
	An attribute used to scale the available pollen based on assumed competetion from other bee species. More...

vector< double >	m_PrePupalDevelRates
	Holds the prepupal development rates for fast access. More...

double	m_PrePupalDevelDaysToday
	Holds the prepupal development rates for today for fast access. More...

vector< OsmiaPollenNectarThresholds >	m_PN_thresholds
	Holds a list of pollen and nectar thresholds, one for each month. More...

Protected Attributes inherited from Population_Manager
vector< unsigned >	m_LiveArraySize

int	m_NoProbes = 0

std::vector< std::vector< omp_nest_lock_t * > >	m_MapGuard
	This is used to make sure animals will not behaviour at the same area - multi threads. More...

int	m_guard_cell_height_num

int	m_guard_cell_width_num

int	m_guard_cell_size

bool	m_is_paralleled
	This is used to indicate whether the species is paralleled. More...

const char *	StateNames [100] {}

int	m_StepSize {}

vector< vector< forward_list< TAnimal * > * > >	TheSubArrays
	Hold all the animal pointers. More...

vector< vector< int > >	TheSubArraysSizes
	Hold all the animal sizes in each thread. More...

vector< int >	m_LifeStageOrderVec
	The vector to store the life stage order for looping specie life stages. More...

vector< forward_list< TAnimal * >::iterator >	TheSubArraysIterators
	the iterator from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class. More...

vector< int >	TheSubArrayPreviousIndex
	the animal index number from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class. More...

vector< int >	TheSubArrayThreadIndex
	the thread index number from last time called for SupplyAnimalPtr(), this for fast loop all the animals in the derived class. More...

unsigned	StateNamesLength

FILE *	TestFile {}

FILE *	TestFile2 {}

vector< unsigned >	BeforeStepActions
	Holds the season list of possible before step actions. More...

int	m_SeasonNumber
	Holds the season number. Used when running goose and hunter sims. More...

TTypesOfPopulation	m_population_type {TOP_NoSpecies}

ofstream *	AOROutputPrb {}

ofstream *	RipleysOutputPrb {}

ofstream *	RipleysOutputPrb1 {}

ofstream *	RipleysOutputPrb2 {}

ofstream *	RipleysOutputPrb3 {}

ofstream *	RipleysOutputPrb4 {}

ofstream *	RipleysOutputPrb5 {}

ofstream *	RipleysOutputPrb6 {}

ofstream *	RipleysOutputPrb7 {}

ofstream *	RipleysOutputPrb8 {}

ofstream *	RipleysOutputPrb9 {}

ofstream *	RipleysOutputPrb10 {}

ofstream *	RipleysOutputPrb11 {}

ofstream *	RipleysOutputPrb12 {}

ofstream *	ReallyBigOutputPrb {}

AOR_Probe *	m_AOR_Probe {}
	A pointer to the AOR probe. More...

long int	lamdagrid [2][257][257] {}

Protected Attributes inherited from Population_Manager_Base
int	SimH
	stores the simulation height More...

int	SimW
	stores the simulation width More...

int	SimHH
	stores the simulation height halved More...

int	SimWH
	stores the simulation width halved More...

string	m_SimulationName
	stores the simulation name More...

Landscape *	m_TheLandscape
	holds an internal pointer to the landscape More...

int	m_ListNameLength {}
	the number of life-stages simulated in the population manager More...

const char *	m_ListNames [32] {}
	A list of life-stage names. More...

std::string	m_AORProbeFileName {"AOR_Probe.txt"}
	name of the AOR Probe file More...

std::string	m_ProbeFileName {"Probe.res"}
	name of the Probe file More...

int	m_step_counter_in_a_day
	Step counter in a day, this is used for the animals with finer step size other than one day. More...

Static Protected Attributes
static probability_distribution	m_exp_ZeroTo1 = probability_distribution("BETA", "0.75,2.5")
	Static instance of the probability_distribution class of distance probabilities for approx exponential probs zero to 1.0. More...

Additional Inherited Members
Public Attributes inherited from Population_Manager
bool	ProbesSet {}

Public Attributes inherited from Population_Manager_Base
Probe_Data *	TheProbe [100] = {nullptr}
	Holds a list of pointers to standard output probes. More...

Detailed Description

The class to handle all Osmia bee population related matters.

Constructor & Destructor Documentation

◆ Osmia_Population_Manager()

Osmia_Population_Manager::Osmia_Population_Manager ( Landscape * L )

Osmia_Population_Manager Constructor.

Loads the list of Animal Classes.

                                                                : Population_Manager(L, 6)
 {
     m_ListNames[0] = "Egg";     // from egg laying to the beginning of feeding
     m_ListNames[1] = "Larva";   // larval development + cocoon spinning
     m_ListNames[2] = "Prepupa"; // the summer diapause period
     m_ListNames[3] = "Pupa";
     m_ListNames[4] = "In Cocoon";   // fully developed adults remaining within cocoons (includes overwintering period)
     m_ListNames[5] = "Female";
     m_ListNameLength = 6;
     m_SimulationName = "Osmia";
     // Init performs intialisation of the data to run the Osmia model
     Init();
     // Set up neccessary conditions for mid-lifecycle start
     m_PreWinteringEndFlag = true;
     m_OverWinterEndFlag = false;
  
  
     // Get all the polygon that is suitable for osmia nesting
     std::vector<int> suitable_polygons;
     m_OurOsmiaNestManager.UpdateOsmiaNesting();
     int num_poly = m_TheLandscape->SupplyNumberOfPolygons();
     for (int i = 0; i < num_poly; i++)
     {
         if (IsOsmiaNestPossible(i))
         {
             suitable_polygons.push_back(i);
         }
     }
     
     int num_poly_for_nesting = suitable_polygons.size();
  
     // Create some animals
     int temp_thread_num = omp_get_max_threads();
     int start_num_in_thread = (cfg_OsmiaStartNo.value() / temp_thread_num +1);
     #pragma omp parallel
     {
         for (int i = 0; i < start_num_in_thread; i++) // This will need to be an input variable (config)
         {
             struct_Osmia* sp;
             sp = new struct_Osmia;
             sp->OPM = this;
             sp->L = m_TheLandscape;
             double minmass =(cfg_OsmiaFemaleMassMin.value() - 4) / 0.25;
             double maxmass = (cfg_OsmiaFemaleMassMax.value() - 4) / 0.25;
             sp->mass = minmass + (maxmass - minmass) * g_rand_uni_fnc();
             sp->parasitised = TTypeOfOsmiaParasitoids::topara_Unparasitised;
             sp->sex = true;
  
             //first find a suitable polygon randomly
             int pindex = suitable_polygons[g_random_fnc(num_poly_for_nesting)];
             APoint temp_point = m_TheLandscape->SupplyARandomLocPoly(pindex);
             sp->x = temp_point.m_x;
             sp->y = temp_point.m_y;
             sp->nest = CreateNest(sp->x, sp->y, pindex);
             sp->overwintering_degree_days = cfg_OsmiaOverwinterDegreeDaysInitialSimu.value();
             //sp->nest->AddEgg(NULL);
             CreateObjects(TTypeOfOsmiaLifeStages::to_OsmiaInCocoon, NULL, sp, 1);
             delete sp;
         }
     }
     for (unsigned co = 0; co<unsigned(SupplyListSize(int(TTypeOfOsmiaLifeStages::to_OsmiaInCocoon))); co++)
     {
         dynamic_cast<Osmia_InCocoon*>(SupplyAnimalPtr(int(TTypeOfOsmiaLifeStages::to_OsmiaInCocoon),co))->SetAgeDegrees(2000);
     }
     // Store the competition scaler for faster access
     m_PollenCompetitionsReductionScaler = cfg_OsmiaDensityDependentPollenRemovalConst.value();
     // Store prepal development rates for faster access
     m_PrePupalDevelRates.resize(42);
     for (int i = 0; i < 42; i++) m_PrePupalDevelRates[i] = cfg_OsmiaPrepupalDevelRates.value(i);
     //PartitionLiveDead(int(TTypeOfOsmiaLifeStages::to_OsmiaInCocoon));
     m_is_paralleled = true; // Osmia is always parallel
  
     //reset the pesticide files
    #ifdef __OSMIA_PESTICIDE_STORE
    ofstream oversprayfile("osmia_overspray.txt", ios::trunc);
    oversprayfile << "Year" << '\t' << "Day" << '\t' << "Female ID" << "(application rate: "<<cfg_pest_product_amounts.value(0)<<"g/ha)"<<endl;
    oversprayfile.close();
  
    ofstream contactfile("osmia_contact.txt", ios::trunc);
    contactfile << "Year" << '\t' << "Day" << '\t' << "Female ID" << '\t' << "Pesticide(g/m2)"  << endl;
    contactfile.close();
  
    ofstream intakefile("osmia_pest_intake.txt", ios::trunc);
    intakefile << "Year" << '\t' << "Day" << '\t' << "Female ID" << '\t' << "Pesticide(g)" << '\t' << "Sugar(g)" << endl;
    intakefile.close();
  
    #endif
 }

References cfg_OsmiaDensityDependentPollenRemovalConst, cfg_OsmiaFemaleMassMax, cfg_OsmiaFemaleMassMin, cfg_OsmiaOverwinterDegreeDaysInitialSimu, cfg_OsmiaPrepupalDevelRates, cfg_OsmiaStartNo, cfg_pest_product_amounts, CreateNest(), CreateObjects(), g_rand_uni_fnc(), g_random_fnc(), Init(), IsOsmiaNestPossible(), struct_Osmia::L, Population_Manager::m_is_paralleled, Population_Manager_Base::m_ListNameLength, Population_Manager_Base::m_ListNames, m_OurOsmiaNestManager, m_OverWinterEndFlag, m_PollenCompetitionsReductionScaler, m_PrePupalDevelRates, m_PreWinteringEndFlag, Population_Manager_Base::m_SimulationName, Population_Manager_Base::m_TheLandscape, APoint::m_x, APoint::m_y, struct_Osmia::mass, struct_Osmia::nest, struct_Osmia::OPM, struct_Osmia::overwintering_degree_days, struct_Osmia::parasitised, struct_Osmia::sex, Population_Manager::SupplyAnimalPtr(), Landscape::SupplyARandomLocPoly(), Population_Manager::SupplyListSize(), Landscape::SupplyNumberOfPolygons(), to_OsmiaInCocoon, topara_Unparasitised, Osmia_Nest_Manager::UpdateOsmiaNesting(), CfgInt::value(), CfgFloat::value(), CfgArray_Double::value(), struct_Osmia::x, and struct_Osmia::y.

◆ ~Osmia_Population_Manager()

Osmia_Population_Manager::~Osmia_Population_Manager ( void )

virtual

Osmia_Population_Manager Destructor.

 {
 //  delete m_PollenNectarLists;
 #ifdef __OSMIATESTING
     delete m_female_weight_record_lock;
     m_eggsfirstnest.close();
     ofstream ofile("EggsDistributions.txt", ios::out);
     for (int i = 0; i < 30; i++)
     {
         ofile << m_egghistogram[0][i] << '\t' << m_egghistogram[1][i] << '\t' << m_egghistogram[2][i] << '\t' << m_egghistogram[3][i] << endl;
     }
     ofile.close();
 #endif // __OSMIATESTING
 }

Member Function Documentation

◆ AddToDensityGrid() [1/2]

int Osmia_Population_Manager::AddToDensityGrid ( APoint a_loc )

inline

Adds a bee to the density grid at a location.

     {
         int index = (a_loc.m_x / 1000) + (a_loc.m_y / 1000) * m_GridExtent;
         m_FemaleDensityGrid[index]++;
         return index;
     }

References m_FemaleDensityGrid, m_GridExtent, APoint::m_x, and APoint::m_y.

◆ AddToDensityGrid() [2/2]

void Osmia_Population_Manager::AddToDensityGrid ( int a_index )

inline

Adds a bee to the density grid using the grid index value.

     {
         m_FemaleDensityGrid[a_index]++;
     }

References m_FemaleDensityGrid.

◆ CalForageHours()

void Osmia_Population_Manager::CalForageHours ( void )

                                                   {
     //set it to zero first
     m_FlyingWeather = 0;
     int sunrise_time = g_date->SunRiseTime()/60;
     int sunset_time = g_date->SunSetTime()/60;
     for (int i = sunrise_time; i<=sunset_time; i++ ){
         if(g_weather->GetTempHour(i) >= cfg_OsmiaMinTempForFlying.value()){
             if(g_weather->GetWindHour(i) <= cfg_OsmiaMaxWindSpeedForFlying.value()){
                 if(g_weather->GetRainHour(i) <= cfg_OsmiaMaxPrecipForFlying.value()){
                     m_FlyingWeather += 1.0;
                 }
             }
         }
     }
 }

References cfg_OsmiaMaxPrecipForFlying, cfg_OsmiaMaxWindSpeedForFlying, cfg_OsmiaMinTempForFlying, g_date, g_weather, Weather::GetRainHour(), Weather::GetTempHour(), Weather::GetWindHour(), m_FlyingWeather, Calendar::SunRiseTime(), Calendar::SunSetTime(), and CfgFloat::value().

Referenced by DoFirst().

◆ ClearDensityGrid()

void Osmia_Population_Manager::ClearDensityGrid ( )

inline

Empties the bee density grid.

     {
         for (int i=0; i< m_FemaleDensityGrid.size(); i++) m_FemaleDensityGrid[i] = 0;
     }

References m_FemaleDensityGrid.

Referenced by DoFirst(), and Init().

◆ CreateNest()

Osmia_Nest* Osmia_Population_Manager::CreateNest	(	int	a_x,
		int	a_y,
		int	a_polyindex
	)

inline

Creates an Osmia_Nest in the polygon referenced by the index polyindex.

                                                               {
         Osmia_Nest* return_nest_ptr;
         m_TheLandscape->SetPolygonLock(a_polyindex);
         return_nest_ptr = m_OurOsmiaNestManager.CreateNest(a_x, a_y, a_polyindex); 
         m_TheLandscape->ReleasePolygonLock(a_polyindex);
         return return_nest_ptr; 
     }

References Osmia_Nest_Manager::CreateNest(), m_OurOsmiaNestManager, Population_Manager_Base::m_TheLandscape, Landscape::ReleasePolygonLock(), and Landscape::SetPolygonLock().

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

◆ CreateObjects()

void Osmia_Population_Manager::CreateObjects	(	TTypeOfOsmiaLifeStages	ob_type,
		TAnimal *	pvo,
		struct_Osmia *	data,
		int	number
	)

Method for creating a new individual Osmia.

                                                                                                                                 {
     Osmia_Egg*  new_Osmia_Egg;
     Osmia_Larva*  new_Osmia_Larva;
     Osmia_Prepupa* new_Osmia_Prepupa;
     Osmia_Pupa*  new_Osmia_Pupa;
     Osmia_InCocoon*  new_Osmia_InCocoon;
     Osmia_Female*  new_Osmia_Female;
 #ifdef __RECORDOSMIAEGGPRODUCTION
     if (os_type == TTypeOfOsmiaLifeStages::to_OsmiaEgg) RecordEggProduction(number);
 #endif
     for (int i = 0; i < number; i++) {
         switch (os_type) {
         case TTypeOfOsmiaLifeStages::to_OsmiaEgg:       
             new_Osmia_Egg = new Osmia_Egg(data);
             PushIndividual(int(os_type),new_Osmia_Egg);     
             IncLiveArraySize(int(os_type));
             data->nest->SetCellLock();
             data->nest->AddEgg(new_Osmia_Egg);
             data->nest->ReleaseCellLock();
             break;
         case TTypeOfOsmiaLifeStages::to_OsmiaLarva:
             new_Osmia_Larva = new Osmia_Larva(data);
             PushIndividual(int(os_type),new_Osmia_Larva);
             IncLiveArraySize(int(os_type));
             // Need to replace the pointer held by the nest (egg->larvae)
             data->nest->SetCellLock();
             data->nest->ReplaceNestPointer(a_caller,new_Osmia_Larva);
             data->nest->ReleaseCellLock();
             break;
         case TTypeOfOsmiaLifeStages::to_OsmiaPrepupa:
             new_Osmia_Prepupa = new Osmia_Prepupa(data);
             PushIndividual(int(os_type),new_Osmia_Prepupa);
             IncLiveArraySize(int(os_type));
             data->nest->SetCellLock();
             data->nest->ReplaceNestPointer(a_caller, new_Osmia_Prepupa);
             data->nest->ReleaseCellLock();
             break;
         case TTypeOfOsmiaLifeStages::to_OsmiaPupa:
             new_Osmia_Pupa = new Osmia_Pupa(data);
             PushIndividual(int(os_type),new_Osmia_Pupa);
             IncLiveArraySize(int(os_type));
             data->nest->SetCellLock();
             data->nest->ReplaceNestPointer(a_caller, new_Osmia_Pupa);
             data->nest->ReleaseCellLock();
             break;
         case TTypeOfOsmiaLifeStages::to_OsmiaInCocoon:
             new_Osmia_InCocoon = new Osmia_InCocoon(data);
             PushIndividual(int(os_type),new_Osmia_InCocoon);        
             IncLiveArraySize(int(os_type));
             data->nest->SetCellLock();
             //cout<<"Osmia cocoon created"<<endl;
             if(a_caller == NULL){
                 data->nest->AddCocoon(new_Osmia_InCocoon);
             }
             else{
                 data->nest->ReplaceNestPointer(a_caller, new_Osmia_InCocoon);
             }
             //cout << "Nest set created" << endl;
             data->nest->ReleaseCellLock();
             break;
         case TTypeOfOsmiaLifeStages::to_OsmiaFemale:
             new_Osmia_Female = new Osmia_Female(data);
             //code used for pestiside store
             #ifdef __OSMIA_PESTICIDE_STORE
             #pragma omp critical
             {
                 m_female_count++;
                 new_Osmia_Female->m_animal_id = m_female_count;
             }
             #endif
             PushIndividual(int(os_type),new_Osmia_Female);
             IncLiveArraySize(int(os_type));
             //data->nest->RemoveCell(a_caller);
             break;
         }
     }
 }

References Osmia_Nest::AddCocoon(), Osmia_Nest::AddEgg(), Population_Manager::IncLiveArraySize(), struct_Osmia::nest, Population_Manager::PushIndividual(), Osmia_Nest::ReleaseCellLock(), Osmia_Nest::ReplaceNestPointer(), Osmia_Nest::SetCellLock(), to_OsmiaEgg, to_OsmiaFemale, to_OsmiaInCocoon, to_OsmiaLarva, to_OsmiaPrepupa, and to_OsmiaPupa.

Referenced by Osmia_Female::LayEgg(), Osmia_Population_Manager(), Osmia_Pupa::st_Emerge(), Osmia_InCocoon::st_Emerge(), Osmia_Egg::st_Hatch(), Osmia_Larva::st_Prepupate(), and Osmia_Prepupa::st_Pupate().

◆ DoAfter()

virtual void Osmia_Population_Manager::DoAfter ( )

inlineprotectedvirtual

Things to do before the EndStep.

Reimplemented from Population_Manager.

550 {}

◆ DoBefore()

void Osmia_Population_Manager::DoBefore ( )

protectedvirtual

Things to do before the Step.

Things to do before the Step

To save time we only refil the pollen map if any adults are around to care about this.

If some stages survive to winter due to slow development we kill these here

Reimplemented from Population_Manager.

 {
     int today = m_TheLandscape->SupplyDayInYear();
     if (today == 0)
     {
         unsigned size2 = (unsigned)GetLiveArraySize(int(TTypeOfOsmiaLifeStages::to_OsmiaLarva));
         for (unsigned j = 0; j < size2; j++) {
             Osmia_Larva* larva = dynamic_cast<Osmia_Larva*>(SupplyAnimalPtr(int(TTypeOfOsmiaLifeStages::to_OsmiaLarva), j));
             larva->st_Dying();
         }
         size2 = (unsigned)GetLiveArraySize(int(TTypeOfOsmiaLifeStages::to_OsmiaPrepupa));
         for (unsigned j = 0; j < size2; j++) {
             Osmia_Prepupa* prepupa = dynamic_cast<Osmia_Prepupa*>(SupplyAnimalPtr(int(TTypeOfOsmiaLifeStages::to_OsmiaPrepupa), j));
             prepupa->st_Dying();
         }
         size2 = (unsigned)GetLiveArraySize(int(TTypeOfOsmiaLifeStages::to_OsmiaPupa));
         for (unsigned j = 0; j < size2; j++) {
             Osmia_Pupa* pupa = dynamic_cast<Osmia_Pupa*>(SupplyAnimalPtr(int(TTypeOfOsmiaLifeStages::to_OsmiaPupa), j));
             pupa->st_Dying();
         }
 #ifdef __OSMIATESTING
         // Record the Osmia weights if needed
         ofstream ofile("OsmiaFemaleWeights.txt", ios::app);
         int sz = m_FemaleWeights.size();
         vector<int> histogram;
         for (int h = 0; h <= 20; h++) histogram.push_back(0);
         for (int i = 0; i < sz; i++) {
             // Create histogram values
             int col = int(m_FemaleWeights[i] / 10);
             histogram[col]++;
         }
         for (int h = 0; h <= 20; h++) {
             ofile << histogram[h] << '\t';
         }
         ofile << endl;
         ofile.close();
         m_FemaleWeights.clear();
 #endif
  
     }
     // Debug code to ensure all nests have some occupied cells.
     if (GetLiveArraySize(int(TTypeOfOsmiaLifeStages::to_OsmiaFemale)) == 0)
     {
         // Only if no females around to mess this up.
         m_OurOsmiaNestManager.CheckZeroNests();
     }
 }

References Osmia_Nest_Manager::CheckZeroNests(), Population_Manager::GetLiveArraySize(), m_OurOsmiaNestManager, Population_Manager_Base::m_TheLandscape, Osmia_Base::st_Dying(), Population_Manager::SupplyAnimalPtr(), Landscape::SupplyDayInYear(), to_OsmiaFemale, to_OsmiaLarva, to_OsmiaPrepupa, and to_OsmiaPupa.

◆ DoFirst()

void Osmia_Population_Manager::DoFirst ( void )

protectedvirtual

Things to do before anything else at the start of a timestep

Reimplemented from Population_Manager.

                                        {
     
     double temp = m_TheLandscape->SupplyTemp();
     Osmia_Base::SetTemp(temp); // Sets the static variable for temperature for all Osmia (speed optimisation)
     //if ((!g_weather->Raining()) && (temp > 10.0) && (g_weather->GetWind() < 8.0))  m_FlyingWeather = true; else m_FlyingWeather = false;
     //if (temp > 10.0 && g_weather->GetWind() < 8.0)  m_FlyingWeather = true; else m_FlyingWeather = false;
     //m_FlyingWeather = g_weather->GetFlyingHours();
     CalForageHours();
     m_OurOsmiaNestManager.UpdateOsmiaNesting(); // Updates nest status for all nests
     ClearDensityGrid(); // Clears this before all the bees get going
     int temp_i = int(floor(temp + 0.5));
     if (temp_i < 0) temp_i = 0;
     m_PrePupalDevelDaysToday = m_PrePupalDevelRates[temp_i];
  
 }

References CalForageHours(), ClearDensityGrid(), m_OurOsmiaNestManager, m_PrePupalDevelDaysToday, m_PrePupalDevelRates, Population_Manager_Base::m_TheLandscape, Osmia_Base::SetTemp(), Landscape::SupplyTemp(), and Osmia_Nest_Manager::UpdateOsmiaNesting().

◆ DoLast()

virtual void Osmia_Population_Manager::DoLast ( )

inlineprotectedvirtual

Things to do after the EndStep - here calculations related to summing global day degrees.

If the PostPreWinteringFlag is not set and its after Sept 1st then we need to test for the end of pre-wintering

Based on checking for a sustained and stable drop in autumn temperature

Reimplemented from Population_Manager.

     {
         int today = m_TheLandscape->SupplyDayInYear();
         if (today > September)
         {
             int day = g_date->OldDays() + g_date->DayInYear();
             double t0 = m_TheLandscape->SupplyTempPeriod(day, 1);
             if (!m_PreWinteringEndFlag)
             {
                 double t1 = m_TheLandscape->SupplyTempPeriod(day - 1, 1);
                 double t2 = m_TheLandscape->SupplyTempPeriod(day - 2, 1);
                 double t3 = m_TheLandscape->SupplyTempPeriod(day - 3, 1);
                 double t4 = m_TheLandscape->SupplyTempPeriod(day - 4, 1);
                 double t5 = m_TheLandscape->SupplyTempPeriod(day - 5, 1);
                 if (((t2 < 13.0) && (t1 < 13.0) && (t0 < 13.0)) && (((t5 - t4 > 1.0) && (t4 - t3 > 1.0)) || ((t3 < 13.0) && (t5 - t4 >= 3.0))))
                 {
                     m_PreWinteringEndFlag = true;
                 }
             }
         }
         if (today == March)
         {
             m_OverWinterEndFlag = true;
         }
         if (today == June)
         {
             // No emergence after April so we can safely reset this flag here.
             m_PreWinteringEndFlag = false;
             m_OverWinterEndFlag = false;
         }
 #ifdef __OSMIARECORDFORAGE
         double meanforage = 0.0;
         if (Osmia_Female::m_foragecount > 0) meanforage = Osmia_Female::m_foragesum / Osmia_Female::m_foragecount;
         cout << meanforage << endl;
         Osmia_Female::m_foragesum = 0.0;
         Osmia_Female::m_foragecount = 0.0;
 #endif
  
 #ifdef __OSMIATESTING       
         if (today == 364) {
             ofstream file1("OsmiaStageLengths.txt", ios::app);
             file1 << "Year: " << g_date->GetYear() << endl;
             file1 << "Mean egg stage days is:" << '\t'  << m_EggStageLength.get_meanvalue() << endl;
             file1 << "Mean larval stage days is:" << '\t' << m_LarvalStageLength.get_meanvalue() << endl;
             file1 << "Mean prepupal stage days is:" << '\t' << m_PrePupaStageLength.get_meanvalue() << endl;
             file1 << "Mean pupal stage days is:" << '\t' << m_PupaStageLength.get_meanvalue() << endl;
             file1 << "Mean incocoon stage days is:" << '\t' << m_InCocoonStageLength.get_meanvalue() << endl;
             m_EggStageLength.ClearData();
             m_LarvalStageLength.ClearData();
             m_PrePupaStageLength.ClearData();
             m_PupaStageLength.ClearData();
             m_InCocoonStageLength.ClearData();
             file1.close();
         }
 #endif
     }

References SimpleStatistics::ClearData(), Calendar::DayInYear(), g_date, SimpleStatistics::get_meanvalue(), Calendar::GetYear(), June, m_OverWinterEndFlag, m_PreWinteringEndFlag, Population_Manager_Base::m_TheLandscape, March, Calendar::OldDays(), September, Landscape::SupplyDayInYear(), and Landscape::SupplyTempPeriod().

◆ GetDensity() [1/2]

int Osmia_Population_Manager::GetDensity ( APoint a_loc )

inline

Gets the number of bees at a location.

     {
         int index = (a_loc.m_x / 1000) + (a_loc.m_y / 1000) * m_GridExtent;
         return m_FemaleDensityGrid[index];
     }

References m_FemaleDensityGrid, m_GridExtent, APoint::m_x, and APoint::m_y.

◆ GetDensity() [2/2]

int Osmia_Population_Manager::GetDensity ( int a_index )

inline

Gets the number of bees at a location based on the grid index value.

     {
         return m_FemaleDensityGrid[a_index];
     }

References m_FemaleDensityGrid.

◆ GetFirstCocoonProvisioningMass()

double Osmia_Population_Manager::GetFirstCocoonProvisioningMass	(	int	a_age,
		int	a_massclass
	)

inline

Return the first cocoon mass for a nest give an age and female mass.

     {
         return m_FemaleCocoonMassEqns[a_massclass][a_age]-(m_exp_ZeroTo1.Get() * m_FemaleCocoonMassEqns[a_massclass][a_age] * 0.6);
     }

References probability_distribution::Get(), m_exp_ZeroTo1, and m_FemaleCocoonMassEqns.

Referenced by Osmia_Female::st_ReproductiveBehaviour().

◆ GetForageHours()

int Osmia_Population_Manager::GetForageHours ( )

inline

Return the Osmia flying weather hours.

432 { return m_FlyingWeather; }

References m_FlyingWeather.

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

◆ GetPrePupalDevelDays()

double Osmia_Population_Manager::GetPrePupalDevelDays ( )

inline

Returns the amount of development a pre-pupal bee will get today based on temperature.

                                   {
         return m_PrePupalDevelDaysToday;
     }

References m_PrePupalDevelDaysToday.

Referenced by Osmia_Prepupa::st_Develop().

◆ GetProvisioningParams()

double Osmia_Population_Manager::GetProvisioningParams ( int a_age )

inline

Returns the values of provisioning parameters for a adult age.

                                             {
         return m_NestProvisioningParameters[a_age];
     }

References m_NestProvisioningParameters.

◆ GetSexRatioEggsAgeMass()

double Osmia_Population_Manager::GetSexRatioEggsAgeMass	(	int	a_massclass,
		int	a_age
	)

inline

Return the sex ratio for a nest give an age and female mass.

     {
         return m_EggSexRatioEqns[a_massclass][a_age];
     }

References m_EggSexRatioEqns.

Referenced by Osmia_Female::st_ReproductiveBehaviour().

◆ Init()

void Osmia_Population_Manager::Init ( )

Used to collect data initialisation together.

Initiates the Osmia nests on each landscape element The temperature related mortality needs to be calculated for in nest development and stored in the static variable in the Osmia_Base

Calculate number of hours needed for provisioning of one cell depending on Osmia age [based on Seidelmann 2006]

Sets the parasitoid parameters for per capitata likelihood of parasitism

Creates the data structures to hold Osmia density measures

Calculate the foraging efficiency with age mg/hr

Resets the OsmiaStageLengths output file.

 {
     // struct_Osmia o_data;
     // o_data.age = 0;
     // o_data.L = m_TheLandscape;
     // o_data.OPM = this;
     // o_data.x = 0;
     // o_data.y = 0;
     // o_data.nest = NULL;
     // o_data.parasitised = TTypeOfOsmiaParasitoids::topara_Unparasitised;
     // o_data.mass = 100;
     // o_data.sex = true;
     m_PreWinteringEndFlag = true;
     #ifdef __OSMIATESTING
         m_female_weight_record_lock = new omp_nest_lock_t;
         omp_init_nest_lock(m_female_weight_record_lock);
  
         for (int i = 0; i < 30; i++)
         {
             m_egghistogram[0][i] = 0;
             m_egghistogram[1][i] = 0;
             m_egghistogram[2][i] = 0;
             m_egghistogram[3][i] = 0;
         }
         m_eggsfirstnest.open("eggsfirstnest.txt", ios_base::out);
         ofstream ofile("OsmiaFemaleWeights.txt", ios::out);
     #endif
     m_OurOsmiaNestManager.InitOsmiaBeeNesting();
     // Set the values of egg/base static variables
  
     Osmia_Egg::SetParameterValues();
     /*temporarily uses .get()'ed version of GetPopulation to get the raw pointer, will move to smart pointers: issue opened*/
     Osmia_Egg::SetParasitoidManager(static_cast<OsmiaParasitoid_Population_Manager*>(this->m_TheLandscape->SupplyThePopManagerList()->GetPopulation(TOP_OsmiaParasitoids)));
     // Set the values of InCocoon static variables
     Osmia_InCocoon::SetOverwinteringTempThreshold(cfg_OsmiaInCocoonOverwinteringTempThreshold.value());
  
     // Set the values of female static variables
     Osmia_Female::SetDailyMort(cfg_OsmiaFemaleBckMort.value());
     Osmia_Female::SetMinEggsPerNest(cfg_OsmiaMinNoEggsInNest.value());
     Osmia_Female::SetMaxEggsPerNest(cfg_OsmiaMaxNoEggsInNest.value());
     Osmia_Female::SetCocoonToProvisionMass(cfg_OsmiaProvMassFromCocoonMass.value());// Also sets some other derived static members
     Osmia_Female::SetProvisionToCocoonMass(cfg_OsmiaCocoonMassFromProvMass.value());
     Osmia_Female::SetPollenScoreToMg(cfg_PollenScoreToMg.value());
     Osmia_Female::SetMinimumCellConstructionTime(cfg_MinimumCellConstructionTime.value());
     Osmia_Female::SetMaximumCellConstructionTime(cfg_MaximumCellConstructionTime.value());
     Osmia_Female::SetTotalNestsPossible(cfg_TotalNestsPossible.value());
     Osmia_Female::SetBombylidProbability(cfg_OsmiaBombylidProb.value());
     Osmia_Female::SetParasitismProbToTimeCellOpen(cfg_OsmiaParasitismProbToTimeCellOpen.value());
     Osmia_Female::SetUsingMechanisticParasitoids(cfg_UsingMechanisticParasitoids.value());
     Osmia_Female::SetNestFindAttempts(cfg_OsmiaFemaleFindNestAttemptNo.value());
     Osmia_Female::SetForageSteps(cfg_OsmiaForageSteps.value());
     Osmia_Female::SetForageMaskDetailed(cfg_OsmiaDetailedMaskStep.value(), cfg_OsmiaTypicalHomingDistance.value());
     Osmia_Female::SetPollenGiveUpThreshold(cfg_OsmiaPollenGiveUpThreshold.value());
     Osmia_Female::SetPollenGiveUpReturn(cfg_OsmiaPollenGiveUpReturn.value());
 #ifdef __OSMIARECORDFORAGE
     Osmia_Female::m_foragesum = 0.0;
     Osmia_Female::m_foragecount = 0;
 #endif
 #ifdef __OSMIA_PESTICIDE
     Osmia_Female::m_OsmiaPPPEffectProb = cfg_OsmiaPesticideProbability.value();
     Osmia_Female::m_OsmiaPPPThreshold = cfg_OsmiaPesticideThreshold.value();
 #endif
  
     // Read the pollen and nectar thresholds
     OsmiaPollenNectarThresholds pnt;
     for (int m = 0; m < 12; m++)
     {
         pnt.m_pollenTquan = cfg_OsmiaPollenThresholds.value(m);
         pnt.m_pollenTqual = cfg_OsmiaPollenThresholds.value(m + 12);
         pnt.m_nectarTquan = cfg_OsmiaNectarThresholds.value(m);
         pnt.m_nectarTqual = cfg_OsmiaNectarThresholds.value(m + 12);
         m_PN_thresholds.push_back(pnt);
     }
  
     // Calculates sexratio for egg lookups
  
     // Create a data curve for 0 to 59 days for the sex ratio
     // Logistic(x | x0, min, max, k) = min + (max - min) / (1 + exp(-k * (x - x0)))
     vector<double> params_logistic, params_lin, params_logistic2, params_lin2; // these are X0,min,max,k, and linear a,b respectively
     params_logistic = cfg_OsmiaSexRatioVsMotherAgeLogistic.value();
     params_lin = cfg_OsmiaSexRatioVsMotherMassLinear.value();
     eggsexratiovsagelogisticcurvedata curve1;
     params_lin2 = Cfg_OsmiaFemaleCocoonMassVsMotherMassLinear.value();
     params_logistic2 = Cfg_OsmiaFemaleCocoonMassVsMotherAgeLogistic.value();
     femalecocoonmassvsagelogisticcurvedata curve2;
     for (double mass = cfg_OsmiaFemaleMassMin.value(); mass <= cfg_OsmiaFemaleMassMax.value(); mass += cfg_OsmiaAdultMassCategoryStep.value())
     {
         for (unsigned age = 0; age <= 60; age++)
         {
             // Calculate the data for the egg sex ration curve
             double adjustedmax = params_lin[0] * mass + params_lin[1];
             curve1.push_back(params_logistic[1] + (adjustedmax - params_logistic[1]) / (1 + exp(-params_logistic[3] * (age - params_logistic[0]))));
             // Calculate the data for the cocoon mass vs female mass curve
             double avg_female_cocoon_mass = params_lin2[0] * mass + params_lin2[1];
             double first_female_cocoon_mass = avg_female_cocoon_mass + cfg_Osmia_LifetimeCocoonMassLoss.value() / 2.0; // this lifetime cocoon mass loss nedds to have +/- 5 mg
             // NB this is calculated as provisioning mass
             curve2.push_back( 40.0+ (cfg_OsmiaProvMassFromCocoonMass.value() * (params_logistic2[1] + (first_female_cocoon_mass - params_logistic2[1]) / (1 + exp(-params_logistic2[3] * (age - params_logistic2[0]))))));
         }
         m_EggSexRatioEqns.push_back(curve1);
         m_FemaleCocoonMassEqns.push_back(curve2);
         curve1.clear();
         curve2.clear();
     }
     // Calculate nest provisioning time parameters
     for (int d = 0; d < 365; d++) //here max 60 is needed because then bee will die anyway
     {
         /***CJT** Changed from daily to hours */
         double eff = 21.643 / (1 + pow(exp(1.0), (log(d) - log(18.888)) * 3.571)); // provisioning efficiency [mg/h]
         double constructime = (2.576 * eff + 56.17) / eff;   // cell construction time [h]
         m_NestProvisioningParameters[d] = int(constructime );   // days needed for 1 cell construction
     }
     Osmia_Female::SetParasitoidParameters(cfg_OsmiaPerCapitaParasationChance.value());
     m_GridExtent = SimW / 1000;
     int GEy = SimH / 1000;
     m_FemaleDensityGrid.resize(m_GridExtent * GEy);
     ClearDensityGrid();
  
     Osmia_Female::AddForageEfficiency(0);
     for (int i = 1; i <= 100; i++) Osmia_Female::AddForageEfficiency(21.643 / (1 + exp((log(i) - log(18.888)) * 3.571)));
     #ifdef __OSMIATESTING
     ofstream file1("OsmiaStageLengths.txt", ios::out);
     file1.close();
     #endif
  
 }

Referenced by Osmia_Population_Manager().

◆ IsEndPreWinter()

bool Osmia_Population_Manager::IsEndPreWinter ( )

inline

Returns flag to denore the end of prewintering, if ended it is set to true.

410 { return m_PreWinteringEndFlag; }

References m_PreWinteringEndFlag.

Referenced by Osmia_InCocoon::st_Develop().

◆ IsOsmiaNestPossible()

bool Osmia_Population_Manager::IsOsmiaNestPossible ( int a_polyindex )

inline

Checks whether a nest is possible here.

414 { return m_OurOsmiaNestManager.IsOsmiaNestPossible(a_polyindex); }

References Osmia_Nest_Manager::IsOsmiaNestPossible(), and m_OurOsmiaNestManager.

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

◆ IsOverWinterEnd()

bool Osmia_Population_Manager::IsOverWinterEnd ( )

inline

Returns flag to denore the end of overwintering, if ended it is set to true.

412 { return m_OverWinterEndFlag; }

References m_OverWinterEndFlag.

Referenced by Osmia_InCocoon::st_Develop().

◆ ReleaseOsmiaNest()

void Osmia_Population_Manager::ReleaseOsmiaNest	(	int	a_polyindex,
		Osmia_Nest *	a_nest
	)

inline

Release the given nest in the given polygon.

                                                                {
         m_TheLandscape->SetPolygonLock(a_polyindex);
         m_OurOsmiaNestManager.ReleaseOsmiaNest(a_polyindex, a_nest);
         m_TheLandscape->ReleasePolygonLock(a_polyindex);
     }

References m_OurOsmiaNestManager, Population_Manager_Base::m_TheLandscape, Osmia_Nest_Manager::ReleaseOsmiaNest(), Landscape::ReleasePolygonLock(), and Landscape::SetPolygonLock().

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

◆ RemoveFromDensityGrid()

void Osmia_Population_Manager::RemoveFromDensityGrid ( int a_index )

inline

Adds a bee to the density grid using the grid index value.

     {
         m_FemaleDensityGrid[a_index]--;
     }

References m_FemaleDensityGrid.

◆ SantityCheck()

bool Osmia_Population_Manager::SantityCheck ( int a_polyindex )

inline

Checks whether a nest is possible here.

416 { return m_OurOsmiaNestManager.SanityCheck(a_polyindex); }

References m_OurOsmiaNestManager, and Osmia_Nest_Manager::SanityCheck().

◆ TheAOROutputProbe()

void Osmia_Population_Manager::TheAOROutputProbe ( )

overridevirtual

Output method.

Reimplemented from Population_Manager.

489 { m_AOR_Probe->DoProbe(int(TTypeOfOsmiaLifeStages::to_OsmiaFemale)); }

References AOR_Probe::DoProbe(), Population_Manager::m_AOR_Probe, and to_OsmiaFemale.

Member Data Documentation

◆ m_EggSexRatioEqns

vector<eggsexratiovsagelogisticcurvedata> Osmia_Population_Manager::m_EggSexRatioEqns

protected

Holds logistic equation values per age/mass of female for egg sex ratios.

Referenced by GetSexRatioEggsAgeMass(), and Init().

◆ m_exp_ZeroTo1

probability_distribution Osmia_Population_Manager::m_exp_ZeroTo1 = probability_distribution("BETA", "0.75,2.5")

staticprotected

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

A distribution to create an exponential decay from zero to one.

Referenced by GetFirstCocoonProvisioningMass().

◆ m_FemaleCocoonMassEqns

vector<femalecocoonmassvsagelogisticcurvedata> Osmia_Population_Manager::m_FemaleCocoonMassEqns

protected

Holds logistic equation values per age/mass of female for first female cocoon mass.

Referenced by GetFirstCocoonProvisioningMass(), and Init().

◆ m_FemaleDensityGrid

vector<int> Osmia_Population_Manager::m_FemaleDensityGrid

protected

holds numbers of females per 1km2

Referenced by AddToDensityGrid(), ClearDensityGrid(), GetDensity(), Init(), and RemoveFromDensityGrid().

◆ m_FlyingWeather

int Osmia_Population_Manager::m_FlyingWeather

protected

A daily value to indicate the hours the weather is OK for Osmia adult activity.

Referenced by CalForageHours(), and GetForageHours().

◆ m_GridExtent

int Osmia_Population_Manager::m_GridExtent

protected

holds numbers of grid cells per row

Referenced by AddToDensityGrid(), GetDensity(), and Init().

◆ m_NestProvisioningParameters

double Osmia_Population_Manager::m_NestProvisioningParameters[365]

protected

A lookup table used to store pre-calculated nest provisioning parameters in advance since they are CPU intensive.

Referenced by GetProvisioningParams(), and Init().

◆ m_OurOsmiaNestManager

Osmia_Nest_Manager Osmia_Population_Manager::m_OurOsmiaNestManager

protected

This provides the interface to the Osmia_Nests linked to the polgons.

it duplicates some functionality of the Landscape but is held here to prevent bloating of landscape code/footprint for other models

Referenced by CreateNest(), DoBefore(), DoFirst(), Init(), IsOsmiaNestPossible(), Osmia_Population_Manager(), ReleaseOsmiaNest(), and SantityCheck().

◆ m_OverWinterEndFlag

bool Osmia_Population_Manager::m_OverWinterEndFlag

protected

A flag to signal the period between onset of wintering and March 1st

Referenced by DoLast(), IsOverWinterEnd(), and Osmia_Population_Manager().

◆ m_PN_thresholds

vector< OsmiaPollenNectarThresholds> Osmia_Population_Manager::m_PN_thresholds

protected

Holds a list of pollen and nectar thresholds, one for each month.

Referenced by Init().

◆ m_PollenCompetitionsReductionScaler

double Osmia_Population_Manager::m_PollenCompetitionsReductionScaler

protected

An attribute used to scale the available pollen based on assumed competetion from other bee species.

Referenced by Osmia_Population_Manager().

◆ m_PrePupalDevelDaysToday

double Osmia_Population_Manager::m_PrePupalDevelDaysToday

protected

Holds the prepupal development rates for today for fast access.

Referenced by DoFirst(), and GetPrePupalDevelDays().

◆ m_PrePupalDevelRates

vector<double> Osmia_Population_Manager::m_PrePupalDevelRates

protected

Holds the prepupal development rates for fast access.

Referenced by DoFirst(), and Osmia_Population_Manager().

◆ m_PreWinteringEndFlag

bool Osmia_Population_Manager::m_PreWinteringEndFlag

protected

A flag to signal the prewinter phase is over

Referenced by DoLast(), Init(), IsEndPreWinter(), and Osmia_Population_Manager().

◆ m_ThePollenMap

PollenMap_centroidbased* Osmia_Population_Manager::m_ThePollenMap

protected

A pointer to the pollen map object.

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Osmia_Population_Manager()

◆ ~Osmia_Population_Manager()

Member Function Documentation

◆ AddToDensityGrid() [1/2]

◆ AddToDensityGrid() [2/2]

◆ CalForageHours()

◆ ClearDensityGrid()

◆ CreateNest()

◆ CreateObjects()

◆ DoAfter()

◆ DoBefore()

◆ DoFirst()

◆ DoLast()

◆ GetDensity() [1/2]

◆ GetDensity() [2/2]

◆ GetFirstCocoonProvisioningMass()

◆ GetForageHours()

◆ GetPrePupalDevelDays()

◆ GetProvisioningParams()

◆ GetSexRatioEggsAgeMass()

◆ Init()

◆ IsEndPreWinter()

◆ IsOsmiaNestPossible()

◆ IsOverWinterEnd()

◆ ReleaseOsmiaNest()

◆ RemoveFromDensityGrid()

◆ SantityCheck()

◆ TheAOROutputProbe()

Member Data Documentation

◆ m_EggSexRatioEqns

◆ m_exp_ZeroTo1

◆ m_FemaleCocoonMassEqns

◆ m_FemaleDensityGrid

◆ m_FlyingWeather

◆ m_GridExtent

◆ m_NestProvisioningParameters

◆ m_OurOsmiaNestManager

◆ m_OverWinterEndFlag

◆ m_PN_thresholds

◆ m_PollenCompetitionsReductionScaler

◆ m_PrePupalDevelDaysToday

◆ m_PrePupalDevelRates

◆ m_PreWinteringEndFlag

◆ m_ThePollenMap