ALMaSS: OsmiaParasitoid_Population_Manager Class Reference

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#include <Osmia_Population_Manager.h>

Inheritance diagram for OsmiaParasitoid_Population_Manager:

Public Member Functions
	OsmiaParasitoid_Population_Manager (Landscape *a_landscape, int a_cellsize)

	~OsmiaParasitoid_Population_Manager ()

void	AddDispersers (int a_ref, double a_dispersers)

void	RemoveParasitoids (int a_ref, double a_dispersers)

double	GetSize (int a_ref)

double	GetSize (int a_x, int a_y)

array< double, static_cast< unsigned >TTypeOfOsmiaParasitoids::topara_foobar)>	GetParasitoidNumbers (int a_x, int a_y)
	returns an array with the parasitoid numbers in the cell at the location given by a_x, a_y More...

void	AddParasitoid (TTypeOfOsmiaParasitoids a_type, int a_x, int a_y)

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	TheAOROutputProbe ()

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 Attributes
vector< OsmiaParasitoidSubPopulation * >	m_SubPopulations
	The array storing the sub-populations of parasitoids. More...

Landscape *	m_TheLandscape
	A useful pointer to the lanscape object. More...

unsigned	m_Wide
	the number of subpopulation cells wide More...

unsigned	m_High
	the number of subpopulation cells high More...

unsigned	m_CellSize
	Width of the cell in m (they are square) More...

unsigned	m_Size
	Total cells. 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...

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...

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

virtual void	DoFirst ()

virtual void	DoBefore ()

virtual void	DoAfter ()

virtual void	DoLast ()

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

Constructor & Destructor Documentation

◆ OsmiaParasitoid_Population_Manager()

OsmiaParasitoid_Population_Manager::OsmiaParasitoid_Population_Manager	(	Landscape *	a_landscape,
		int	a_cellsize
	)

Intialises each subpopulation of Osmia parasitoids. Creates subpopulation maps and intialises each population Parasitoid populations are described by the enum TTypeOfOsmiaParasitoids

                                                                                                     : Population_Manager(L)
 {
     // Calculate the number of cells
     m_CellSize = a_cellsize;
     m_Wide = (1 + (m_TheLandscape->SupplySimAreaWidth() / m_CellSize));
     m_High = (1 + (m_TheLandscape->SupplySimAreaHeight() / m_CellSize));
     m_Size = m_Wide*m_High;
     unsigned notypes = static_cast<int>(TTypeOfOsmiaParasitoids::topara_foobar) - 1;
     std::vector<OsmiaParasitoidSubPopulation*>::size_type index = notypes * m_Size;;
     m_SubPopulations.resize(index);
     for (unsigned ps = 0; ps < notypes; ps++)
     {
         double range = cfg_OsmiaParasStartHighLow.value(2 * ps) - cfg_OsmiaParasStartHighLow.value(2 * ps + 1);
         for (unsigned int y = 0; y < m_High; y++)
             for (unsigned int x = 0; x < m_Wide; x++)
             {
                 OsmiaParasitoidSubPopulation* OPsP = new OsmiaParasitoidSubPopulation(cfg_OsmiaParasDispersal.value(ps), (g_rand_uni_fnc() * range) + cfg_OsmiaParasStartHighLow.value(2 * ps + 1), x, y, m_Wide, m_High, this);
                 index = ps* (x + y * m_Wide);
                 m_SubPopulations[index] = OPsP;
             }
         array<double, 12> morts;
         for (int m=0; m<12; m++) morts[m]= cfg_OsmiaParasDailyMort.value(ps*12+m);
         m_SubPopulations[0]->SetMortalities(morts); // This is a static member so only the one intialisation is needed, therefore outside the for y loop
     }
 }

References cfg_OsmiaParasDailyMort, cfg_OsmiaParasDispersal, cfg_OsmiaParasStartHighLow, g_rand_uni_fnc(), m_CellSize, m_High, m_Size, m_SubPopulations, m_TheLandscape, m_Wide, Landscape::SupplySimAreaHeight(), Landscape::SupplySimAreaWidth(), topara_foobar, and CfgArray_Double::value().

◆ ~OsmiaParasitoid_Population_Manager()

OsmiaParasitoid_Population_Manager::~OsmiaParasitoid_Population_Manager ( )

 {
     for (int p=0; p< int(m_SubPopulations.size()); p++)
     {
         delete m_SubPopulations[p];
     }
 }

References m_SubPopulations.

Member Function Documentation

◆ AddDispersers()

void OsmiaParasitoid_Population_Manager::AddDispersers	(	int	a_ref,
		double	a_dispersers
	)

inline

                                                        {
         m_SubPopulations[a_ref]->Add(a_dispersers);
     }

References m_SubPopulations.

Referenced by OsmiaParasitoidSubPopulation::Dispersal().

◆ AddParasitoid()

void OsmiaParasitoid_Population_Manager::AddParasitoid	(	TTypeOfOsmiaParasitoids	a_type,
		int	a_x,
		int	a_y
	)

inline

     {
         int subpop = ((a_x / m_CellSize) + (a_y / m_CellSize) * m_Wide) + (static_cast<unsigned>(a_type)-1) * m_Size;
         m_SubPopulations[subpop]->Add(1);
     }

References m_CellSize, m_Size, m_SubPopulations, and m_Wide.

◆ GetParasitoidNumbers()

array< double, static_cast< unsigned >TTypeOfOsmiaParasitoids::topara_foobar)> OsmiaParasitoid_Population_Manager::GetParasitoidNumbers	(	int	a_x,
		int	a_y
	)

returns an array with the parasitoid numbers in the cell at the location given by a_x, a_y

 {
     array<double, static_cast<unsigned>(TTypeOfOsmiaParasitoids::topara_foobar)> parasitoiddensitylist;
     // First find the right sub-population
     int subpop = (a_x / m_CellSize) + (a_y / m_CellSize) * m_Wide;
     for (unsigned ps = 1; ps < static_cast<int>(TTypeOfOsmiaParasitoids::topara_foobar); ps++)
     {
         parasitoiddensitylist[ps] = m_SubPopulations[subpop]->GetSubPopnSize();
         subpop += m_Size;
     }
     return parasitoiddensitylist;
 }

References m_CellSize, m_Size, m_SubPopulations, m_Wide, and topara_foobar.

Referenced by Osmia_Female::CalcParaistised().

◆ GetSize() [1/2]

double OsmiaParasitoid_Population_Manager::GetSize ( int a_ref )

inline

146 { return m_SubPopulations[a_ref]->GetSubPopnSize(); }

References m_SubPopulations.

◆ GetSize() [2/2]

double OsmiaParasitoid_Population_Manager::GetSize	(	int	a_x,
		int	a_y
	)

inline

147 { return m_SubPopulations[a_x+a_y*m_Wide]->GetSubPopnSize(); }

References m_SubPopulations, and m_Wide.

◆ RemoveParasitoids()

void OsmiaParasitoid_Population_Manager::RemoveParasitoids	(	int	a_ref,
		double	a_dispersers
	)

inline

                                                            {
         m_SubPopulations[a_ref]->Remove(a_dispersers);
     }

References m_SubPopulations.

Member Data Documentation

◆ m_CellSize

unsigned OsmiaParasitoid_Population_Manager::m_CellSize

protected

Width of the cell in m (they are square)

Referenced by AddParasitoid(), GetParasitoidNumbers(), and OsmiaParasitoid_Population_Manager().

◆ m_High

unsigned OsmiaParasitoid_Population_Manager::m_High

protected

the number of subpopulation cells high

Referenced by OsmiaParasitoid_Population_Manager().

◆ m_Size

unsigned OsmiaParasitoid_Population_Manager::m_Size

protected

Total cells.

Referenced by AddParasitoid(), GetParasitoidNumbers(), and OsmiaParasitoid_Population_Manager().

◆ m_SubPopulations

vector<OsmiaParasitoidSubPopulation*> OsmiaParasitoid_Population_Manager::m_SubPopulations

protected

The array storing the sub-populations of parasitoids.

Referenced by AddDispersers(), AddParasitoid(), GetParasitoidNumbers(), GetSize(), OsmiaParasitoid_Population_Manager(), RemoveParasitoids(), and ~OsmiaParasitoid_Population_Manager().

◆ m_TheLandscape

Landscape* OsmiaParasitoid_Population_Manager::m_TheLandscape

protected

A useful pointer to the lanscape object.

Referenced by OsmiaParasitoid_Population_Manager().

◆ m_Wide

unsigned OsmiaParasitoid_Population_Manager::m_Wide

protected

the number of subpopulation cells wide

Referenced by AddParasitoid(), GetParasitoidNumbers(), GetSize(), and OsmiaParasitoid_Population_Manager().

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 Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ OsmiaParasitoid_Population_Manager()

◆ ~OsmiaParasitoid_Population_Manager()

Member Function Documentation

◆ AddDispersers()

◆ AddParasitoid()

◆ GetParasitoidNumbers()

◆ GetSize() [1/2]

◆ GetSize() [2/2]

◆ RemoveParasitoids()

Member Data Documentation

◆ m_CellSize

◆ m_High

◆ m_Size

◆ m_SubPopulations

◆ m_TheLandscape

◆ m_Wide