THare_Population_Manager Class Reference

The class that handles all the population lists for hares. More...

#include <hare_all.h>

Inheritance diagram for THare_Population_Manager:

Public Member Functions
	THare_Population_Manager (Landscape *L)
	This is the constructor for the hare population manager. More...
virtual	~THare_Population_Manager (void)
	THare_Population_Manager destructor. More...
virtual void	TheAOROutputProbe ()
	Output method. More...
void	CreateObjects (int ob_type, TAnimal *pvo, void *null, struct_Hare *data, int number)
	Method used to create new hares. More...
double	GetRMR (int a_age, double a_size)
	Returns the RMR given a specific age and mass. More...
int	GetHareRefNum ()
	Get the next ID number available. More...
double	GetMaxDailyGrowthEnergy (int a_age)
double	GetMaxDailyGrowthEnergyP (int a_age)
	Get the maximum daily energy needed for growth for this a_age for use in protein construction. More...
double	GetMaxDailyGrowthEnergyF (int a_age)
	Get the maximum daily energy needed for growth for this a_age for use in fat construction. More...
double	GetGrowthEfficiency (int a_age)
	Get the growth efficiency for this a_age. More...
double	GetGrowthEfficiencyP (int a_age)
	Get the growth efficiency for this a_age for creating protein. More...
double	GetGrowthEfficiencyF (int a_age)
	Get the growth efficiency for this a_age for creating fat. More...
double	GetKJperM (int a_size)
	Get the cost of moving 1m in KJ dependent upon mass (. More...
int	GetLitterSize (int noLitters)
	Returns the litter size. More...
void	AddHareDensity (int x, int y, Hare_Object a_type)
	Density function - adds one to the density in the square containing by x,y. Each square is 256x256m in size. More...
void	SubtractHareDensity (int x, int y, Hare_Object a_type)
	Density function - subtracts one from the density in the square containing by x,y. Each square is 256x256m in size. More...
int	GetInfantDensity (int x, int y)
	Density function - returns the density of infants in the square containing by x,y. Each square is 256x256m in size. More...
int	GetYoungDensity (int x, int y)
	Density function - returns the density of young in the square containing by x,y. Each square is 256x256m in size. More...
int	GetJuvenileDensity (int x, int y)
	Density function - returns the density of juveniles in the square containing by x,y. Each square is 256x256m in size. More...
int	GetMaleDensity (int x, int y)
	Density function - returns the density of males in the square containing by x,y. Each square is 256x256m in size. More...
int	GetFemaleDensity (int x, int y)
	Density function - returns the density of females in the square containing by x,y. Each square is 256x256m in size. More...
int	GetTotalDensity (int x, int y)
	Density function - returns the density of all hares in the square containing by x,y. Each square is 256x256m in size. More...
int	GetAdultDensity (int x, int y)
	Density function - returns the density of adults in the square containing by x,y. Each square is 256x256m in size. More...
int	GetDelayedAdultDensity (int x, int y)
	Density function - returns the density of adults in the square containing by x,y, but for last year at this time. Each square is 256x256m in size. More...
double	GetInterference (int h)
	Return the proportion of time used in communicating with con-specifics. More...
double	GetPolyFood (int a_poly)
	Get stored polygon food quality. More...
void	SetPolyFood (int a_poly, double a_value)
	Set polygon food quality. More...
void	BodyBurdenOut (int a_year, int a_day, double a_bb, double a_mgkg)
	BodyBurden output. More...
Public Member Functions inherited from Population_Manager
	Population_Manager (Landscape *L)
virtual	~Population_Manager (void)
void	SetNoProbes (int a_pn)
unsigned	GetLiveArraySize (int a_listindex)
	Gets the number of 'live' objects for a list index in the TheArray. More...
void	IncLiveArraySize (int a_listindex)
	Increments the number of 'live' objects for a list index in the TheArray. More...
virtual void	Catastrophe (int)
unsigned int	FarmAnimalCensus (unsigned int a_farm, unsigned int a_typeofanimal)
char *	SpeciesSpecificReporting (int a_species, int a_time)
char *	ProbeReport (int a_time)
char *	ProbeReportTimed (int a_time)
void	ImpactProbeReport (int a_Time)
bool	BeginningOfMonth ()
void	LOG (const char *fname)
int	SupplyStepSize ()
int	SupplySimW ()
int	SupplySimH ()
virtual void	Run (int NoTSteps)
virtual float	Probe (int ListIndex, probe_data *p_TheProbe)
virtual void	ImpactedProbe ()
int	SupplyListNameLength ()
TAnimal *	SupplyAnimalPtr (int a_index, int a_animal)
	Returns the pointer indexed by a_index and a_animal. Note NO RANGE CHECK. More...
unsigned	SupplyListIndexSize ()
unsigned	SupplyListSize (unsigned listindex)
bool	CheckXY (int l, int i)
	Debug method to test for out of bounds coordinates. More...
const char *	SupplyListName (int i)
bool	IsLast (unsigned listindex)
int	SupplyState (unsigned listindex, unsigned j)
virtual void	SupplyLocXY (unsigned listindex, unsigned j, int &x, int &y)
const char *	SupplyStateNames (int i)
unsigned	SupplyStateNamesLength ()
virtual void	DisplayLocations ()
int	ProbeFileInput (char *p_Filename, int p_ProbeNo)
TAnimal *	FindClosest (int x, int y, unsigned Type)
bool	OpenTheRipleysOutputProbe (string a_NWordFilename)
void	OpenTheAOROutputProbe (string a_AORFilename)
bool	OpenTheMonthlyRipleysOutputProbe ()
bool	OpenTheReallyBigProbe ()
virtual void	TheReallyBigOutputProbe ()
void	CloseTheMonthlyRipleysOutputProbe ()
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)

Public Attributes
double	m_JuvMortRate
	Input variable - Juvenile mortality rate. More...
double	m_AdultMortRate
	Input variable - Adult mortality rate. More...
double	m_YoungMortRate
	Input variable - Young mortality rate. More...
float	m_GoodYearBadYear
	Variable for adding stochasticity. More...
double	m_DMWeight [5001]
	Array for storing minimum acceptable size with age. More...
int	m_HareThresholdDD
	Input variable - Threshold density dependence level. More...
Public Attributes inherited from Population_Manager
int	IndexArrayX [5][10000]
probe_data *	TheProbe [100]
int	SimH
int	SimW
unsigned	SimHH
unsigned	SimWH
char	m_SimulationName [255]
bool	ProbesSet
Landscape *	m_TheLandscape

Protected Member Functions
void	Init ()
	Sets up data structures and calculations prior to starting simulation. More...
void	CalcLitterSize (double mean, double SD, int litter)
virtual void	DoFirst ()
	The first method called of the new time-step. More...
virtual void	DoLast ()
	The last method called before the new time-step starts. More...
virtual void	DoAlmostLast ()
	Called before clean-up of dead objects. More...
void	POMOutputs ()
	This method is called to dump the information needed for POM approaches. More...
void	MRROutputs ()
	Special probe for data to be used in mark-release-recapture simulations. More...
virtual void	TheRipleysOutputProbe (FILE *a_prb)
	Standard spatial output. More...
void	ExtraPopMort (void)
	An extra global mortality More...
void	Hunting (void)
void	HuntingGrid (void)
void	HuntingDifferentiatedBeetleBankArea (void)
virtual void	Catastrophe ()
	Annual global change in population numbers. More...
Protected Member Functions inherited from Population_Manager
virtual bool	StepFinished ()
	Overrides the population manager StepFinished - there is no chance that hunters do not finish a step behaviour. More...
virtual void	DoBefore ()
virtual void	DoAfter ()
void	EmptyTheArray ()
	Removes all objects from the TheArray by deleting them and clearing TheArray. More...
void	SortX (unsigned Type)
void	SortXIndex (unsigned Type)
void	SortY (unsigned Type)
void	SortState (unsigned Type)
void	SortStateR (unsigned Type)
unsigned	PartitionLiveDead (unsigned Type)
void	Shuffle_or_Sort (unsigned Type)
void	Shuffle (unsigned Type)

Protected Attributes
int	m_RefNums
	The last hare ID used More...
int	m_shot
	Hunting Bag. More...
double	m_MortStochast
	Stochasticity around mortality parameters More...
double	m_Interference [2500]
	Array storing density-dependence effect with density More...
int	m_DensityMap [8][200][200]
	Array storing densities measured in different ways More...
int	m_variableDD
	Used to vary the density dependence each year More...
int	m_LitterSize [12][7]
	Storage for litter size distributions (not used in default config) More...
double *	m_PolyFood
	Temporary storage More...
double	m_RMR [2][366]
	Precalculated RMR with age More...
double	m_MaxDailyGrowthEnergy [5001]
	Precalculated max growth energy requirement with size More...
double	m_GrowthEfficiency [5001]
	Precalculated growth efficiency with size More...
double	m_MaxDailyGrowthEnergyP [5001]
	Precalculated max growth energy requirement with size for protein More...
double	m_MaxDailyGrowthEnergyF [5001]
	Precalculated max growth energy requirement with size for fat More...
double	m_GrowthEfficiencyP [5001]
	Precalculated growth efficiency for protein with size More...
double	m_GrowthEfficiencyF [5001]
	Precalculated growth efficiency for fat with size More...
double	m_KJperM [7001]
	Precalculated cost of locomotion - KJ per m per kg More...
MRR_Data *	m_OurMRRData
	Data structure for MarkReleaseRecapture expts More...
FILE *	BodyBurdenPrb
Protected Attributes inherited from Population_Manager
vector< unsigned >	m_LiveArraySize
int	m_NoProbes
AOR_Probe *	m_AOR_Probe
FILE *	m_GeneticsFile
FILE *	m_AlleleFreqsFile
FILE *	m_EasyPopRes
const char *	StateNames [100]
int	m_catastrophestartyear
int	m_StepSize
vector< TListOfAnimals >	TheArray
unsigned	StateNamesLength
const char *	m_ListNames [32]
unsigned	m_ListNameLength
FILE *	TestFile
FILE *	TestFile2
unsigned	BeforeStepActions [12]
int	m_SeasonNumber
	Holds the season number. Used when running goose and hunter sims. More...
TTypesOfPopulation	m_population_type
ofstream *	AOROutputPrb
FILE *	RipleysOutputPrb
FILE *	RipleysOutputPrb1
FILE *	RipleysOutputPrb2
FILE *	RipleysOutputPrb3
FILE *	RipleysOutputPrb4
FILE *	RipleysOutputPrb5
FILE *	RipleysOutputPrb6
FILE *	RipleysOutputPrb7
FILE *	RipleysOutputPrb8
FILE *	RipleysOutputPrb9
FILE *	RipleysOutputPrb10
FILE *	RipleysOutputPrb11
FILE *	RipleysOutputPrb12
FILE *	ReallyBigOutputPrb
long int	lamdagrid [2][257][257]

Detailed Description

The class that handles all the population lists for hares.

Constructor & Destructor Documentation

THare_Population_Manager()

THare_Population_Manager::THare_Population_Manager

(

Landscape *

L

)

This is the constructor for the hare population manager.

It simply dumps unnecessary lists from the main population record (TheArray), then calls Init which initialises the variables needed before running.

 : Population_Manager(L)
{
  for (int i=0; i<5; i++)
  {
    TheArray.pop_back();
  }
  Init();
}

References Init(), and Population_Manager::TheArray.

~THare_Population_Manager()

THare_Population_Manager::~THare_Population_Manager ( void  )

virtual

THare_Population_Manager destructor.

{
    delete THare::m_vegPalatability;
    fclose(BodyBurdenPrb);
    free(m_PolyFood);
    delete m_OurMRRData;
}

References BodyBurdenPrb, m_OurMRRData, m_PolyFood, and THare::m_vegPalatability.

Member Function Documentation

AddHareDensity()

void THare_Population_Manager::AddHareDensity ( int  x, int  y, Hare_Object  a_type  )

inline

Density function - adds one to the density in the square containing by x,y. Each square is 256x256m in size.

{ m_DensityMap[a_type][x >> __DENSITYSHIFT][y >> __DENSITYSHIFT]++; }

References m_DensityMap.

Referenced by DoFirst(), and Hare_Juvenile::st_Dispersal().

BodyBurdenOut()

void THare_Population_Manager::BodyBurdenOut ( int  a_year, int  a_day, double  a_bb, double  a_mgkg  )

inline

BodyBurden output.

                                                                          {
        fprintf(BodyBurdenPrb, "%d\t%d\t%g\t%g\n", a_year, a_day, a_bb, a_mgkg);
    }

References BodyBurdenPrb.

Referenced by Hare_Male::InternalPesticideHandlingAndResponse(), and Hare_Female::InternalPesticideHandlingAndResponse().

CalcLitterSize()

void THare_Population_Manager::CalcLitterSize ( double  mean, double  SD, int  litter  )

protected

Calculates probabilities out of 10000 that a litter of a certain size is obtained.
Assumes a normal distribution around mean and SD. NB - will give problems if the SD==0.0

{
  double P;
  double Distribution[7];
  double total=0;
  // Max 6 leverets
  if (mean<=0) {
      for (int i=0; i<7; i++) {
        m_LitterSize[index][i]=10000;
      }
  } else {
      // (from Zar page 79).
      for (int i=0; i<7; i++) {
        P=(1.0/SD*sqrt(2*3.14159265) );
        P*=exp(-1*(((i-mean)*(i-mean))/(2*SD*SD)));
        Distribution[i]=P;
        total+=P;
      }
      int last=0;
      for (int i=0; i<7; i++) {
        m_LitterSize[index][i]=(int)(floor(0.5+((Distribution[i]/total)*10000)+last));
        last=m_LitterSize[index][i];
      }
  }
}

References m_LitterSize.

Referenced by Init().

Catastrophe()

void THare_Population_Manager::Catastrophe ( void  )

protectedvirtual

Annual global change in population numbers.

Remove or add hares to the population on a certain day and year - used for theoretical scenarios & testing

Reimplemented from Population_Manager.

                                                 {
    // First do we have the right day?
    int today = m_TheLandscape->SupplyDayInYear();
    if (today!=1) return;
    // First do we have the right year?
    int year = m_TheLandscape->SupplyYearNumber()-m_catastrophestartyear;
    if (year%cfg_pm_eventfrequency.value()!=0) return;
 
    THare* AH = NULL;
    // Now if the % decrease is higher or lower than 100 we need to do different things
    int esize=cfg_pm_eventsize.value();
    if (esize<100) {
        unsigned size2;
        size2 = GetLiveArraySize(hob_Juvenile);
        for ( unsigned j = 0; j < size2; j++ ) {
            if (random(100) > esize) {
                    AH = dynamic_cast < THare * > ( TheArray[hob_Juvenile] [ j ] );
                    AH->Dying(); // Kill it
            }
        }
        size2 = GetLiveArraySize(hob_Female);
        for ( unsigned j = 0; j < size2; j++ ) {
            if (random(100) > esize) {
                    AH = dynamic_cast < THare * > ( TheArray[hob_Female] [ j ] );
                    AH->Dying(); // Kill it
            }
        }
        size2 = GetLiveArraySize(hob_Male);
        for ( unsigned j = 0; j < size2; j++ ) {
            if (random(100) > esize) {
                    AH = dynamic_cast < THare * > ( TheArray[hob_Male] [ j ] );
                    AH->Dying(); // Kill it
            }
        }
    }
    else if (esize>100) {
/*
    Not implemented or needed as of yet
*/
    }
    else return; // No change so do nothing
}

References cfg_pm_eventfrequency, cfg_pm_eventsize, TAnimal::Dying(), Population_Manager::GetLiveArraySize(), hob_Female, hob_Juvenile, hob_Male, Population_Manager::m_catastrophestartyear, Population_Manager::m_TheLandscape, random(), Landscape::SupplyDayInYear(), Landscape::SupplyYearNumber(), Population_Manager::TheArray, and CfgInt::value().

CreateObjects()

void THare_Population_Manager::CreateObjects	(	int	ob_type,
		TAnimal *	pvo,
		void *	null,
		struct_Hare *	data,
		int	number
	)

Method used to create new hares.

Creates new hare objects that have just been born, or because of changes of life-stage require the creation of a new object. Input data is passed in the struct_Hare
This is a very important method - each type of population manager has its own implementation. This is the method that must be called every time a new Hare object is created.

{
    Hare_Infant*  new_Infant;
    Hare_Young*  new_Young;
    Hare_Juvenile*  new_Juvenile;
    Hare_Female*  new_Female;
    Hare_Female*  Mum;
    Hare_Male*  new_Male;
    for (int i = 0; i < number; i++)
    {
        if (unsigned(TheArray[ob_type].size()) > GetLiveArraySize(ob_type)) {
            // We need to reuse an object
            if (ob_type == 0)   // Infant
            {
                new_Infant = dynamic_cast<Hare_Infant*>(TheArray[ob_type][GetLiveArraySize(ob_type)]);
                new_Infant->ReInit((*data));
                Mum = dynamic_cast<Hare_Female*>(pvo);
                if (Mum) new_Infant->SetMum(Mum);
                new_Infant->SetWeight(data->weight);
                if (Mum) Mum->AddYoung(new_Infant);
            }
            if (ob_type == 1)   // Young
            {
                new_Young = dynamic_cast<Hare_Young*>(TheArray[ob_type][GetLiveArraySize(ob_type)]);
                new_Young->ReInit((*data));
                new_Young->SetMum(data->Mum); // NB Mum may be NULL - this is OK                                 
                THare* old_Young = (THare*)pvo;
                if (data->Mum) {
                    data->Mum->UpdateYoung(old_Young, new_Young);
                }
            }
            if (ob_type == 2)  // Juvenile
            {
                new_Juvenile = dynamic_cast<Hare_Juvenile*>(TheArray[ob_type][GetLiveArraySize(ob_type)]);
                new_Juvenile->ReInit((*data));
                new_Juvenile->SetMum(NULL);
            }
            if (ob_type == 3)   // Male
            {
                new_Male = dynamic_cast<Hare_Male*>(TheArray[ob_type][GetLiveArraySize(ob_type)]);
                new_Male->ReInit((*data));
            }
            if (ob_type == 4)  // Female
            {
                new_Female = dynamic_cast<Hare_Female*>(TheArray[ob_type][GetLiveArraySize(ob_type)]);
                new_Female->ReInit((*data));
            }
        }
        else {
 
            if (ob_type == 0)   // Infant
            {
                new_Infant = new Hare_Infant(data->x, data->y, data->L, data->HM);
                TheArray[ob_type].push_back(new_Infant);
                Mum = dynamic_cast<Hare_Female*>(pvo);
                if (Mum) new_Infant->SetMum(Mum);
                new_Infant->SetWeight(data->weight);
                if (Mum) Mum->AddYoung(new_Infant);
            }
            if (ob_type == 1)   // Young
            {
                new_Young = new Hare_Young(data->x, data->y, data->L, data->HM,
                    data->weight);
                new_Young->SetMum(data->Mum); // NB Mum may be NULL - this is OK
                // *** DeBug ***
                //new_Young->m_MyOldMum=data->oldMum;
                THare* old_Young = (THare*)pvo;
                if (data->Mum) {
                    data->Mum->UpdateYoung(old_Young, new_Young);
                }
                TheArray[ob_type].push_back(new_Young);
            }
            if (ob_type == 2)  // Juvenile
            {
                new_Juvenile = new Hare_Juvenile(data->x, data->y, data->L,
                    data->HM, data->weight);
                new_Juvenile->SetMum(NULL);
                // *** DeBug ***
                //new_Juvenile->m_MyOldMum=data->oldMum;
 
                TheArray[ob_type].push_back(new_Juvenile);
            }
            if (ob_type == 3)   // Male
            {
                new_Male = new Hare_Male(data->x, data->y, data->L, data->HM,
                    data->weight, data->age, data->RefNum);
                TheArray[ob_type].push_back(new_Male);
            }
            if (ob_type == 4)  // Female
            {
                new_Female = new Hare_Female(data->x, data->y, data->L, data->HM,
                    data->weight, data->age, data->RefNum);
                TheArray[ob_type].push_back(new_Female);
            }
        }
        IncLiveArraySize(ob_type);
    }
}

References Hare_Female::AddYoung(), struct_Hare::age, Population_Manager::GetLiveArraySize(), struct_Hare::HM, Population_Manager::IncLiveArraySize(), struct_Hare::L, struct_Hare::Mum, struct_Hare::RefNum, Hare_Infant::ReInit(), Hare_Young::ReInit(), Hare_Juvenile::ReInit(), Hare_Male::ReInit(), Hare_Female::ReInit(), THare::SetMum(), Hare_Infant::SetMum(), Hare_Infant::SetWeight(), Population_Manager::TheArray, Hare_Female::UpdateYoung(), struct_Hare::weight, struct_Hare::x, and struct_Hare::y.

Referenced by Hare_Female::GiveBirth(), Init(), Hare_Infant::st_NextStage(), Hare_Young::st_NextStage(), and Hare_Juvenile::st_NextStage().

DoAlmostLast()

void THare_Population_Manager::DoAlmostLast ( void  )

protectedvirtual

Called before clean-up of dead objects.

In this case this only applies hunting mortality. Needs to be done before objects are tidied up at the end of the time-step.

Reimplemented from Population_Manager.

{
    if (m_TheLandscape->SupplyDayInYear()==cfg_HareHuntingDate.value()) 
    {
        if (cfg_HareHuntingType.value()==1) HuntingGrid();
          else if (cfg_HareHuntingType.value()==2) HuntingDifferentiatedBeetleBankArea();
            else Hunting();
    }
}

References cfg_HareHuntingDate, cfg_HareHuntingType, Hunting(), HuntingDifferentiatedBeetleBankArea(), HuntingGrid(), Population_Manager::m_TheLandscape, Landscape::SupplyDayInYear(), and CfgInt::value().

DoFirst()

void THare_Population_Manager::DoFirst ( void  )

protectedvirtual

The first method called of the new time-step.

Does special start of step actions here. In this case optional changes to parameter values e.g. mortality rates, data outputs e.g. POMOutputs(), and clearing the forage food array.

Reimplemented from Population_Manager.

{
#ifdef __EXTRAPOPMORT
    ExtraPopMort();
#endif
    if (m_TheLandscape->SupplyDayInYear()==1) {
 
#ifdef __VARIABLEDD
        m_variableDD=random(21);
#endif
#ifdef __YEARLYVARIABLEFOODQUALITY
        m_GoodYearBadYear = (float) (1.0 + float(random(40)-20)/100.0);
#endif
#ifdef __MORTSTOCHASTICITY
        double MortStochasticity = ((random(200)/100.0)-1.0)* m_MortStochast; // -1.0 to +1.0 * m_MortStochast
        m_YoungMortRate = cfg_hare_young_predation.value() + (cfg_hare_young_predation.value()*(MortStochasticity)); //
        m_JuvMortRate = cfg_hare_juvenile_predation.value()+ (cfg_hare_juvenile_predation.value()*(MortStochasticity)); //
        m_AdultMortRate = cfg_hare_adult_predation.value()+ (cfg_hare_adult_predation.value()*(MortStochasticity)); //
#else
        m_YoungMortRate = cfg_hare_young_predation.value();
        m_JuvMortRate=cfg_hare_juvenile_predation.value(); //
        m_AdultMortRate=cfg_hare_adult_predation.value(); //
#endif
    }
    //else if (m_TheLandscape->SupplyDayInYear()==(cfg_HareHuntingDate.value()-1)) {
  AnimalPosition HP;
  for (unsigned listindex=0; listindex<2;listindex++) {
      unsigned size = GetLiveArraySize(listindex);
    for (unsigned j=0; j<size; j++)
    {
 
      HP=TheArray[listindex][j]->SupplyPosition();
      AddHareDensity(HP.m_x, HP.m_y, (Hare_Object) listindex);
    }
  }
  for (unsigned listindex=2; listindex<TheArray.size();listindex++) {
    unsigned size= GetLiveArraySize(listindex);
    for (unsigned j=0; j<size; j++)
    {
      HP=TheArray[listindex][j]->SupplyPosition();
      int x=HP.m_x>>__DENSITYSHIFT;
      int y=HP.m_y>>__DENSITYSHIFT;
      m_DensityMap[listindex][x][y]++;
      m_DensityMap[5][x][y]++;
      m_DensityMap[7][x][y]++;
    }
  }
  if (m_TheLandscape->SupplyDayInYear()==October) {
      for (int i=0; i<100; i++) {
          for (int j=0; j<100; j++) {
              m_DensityMap[6][i][j]=m_DensityMap[7][i][j]/365;
              m_DensityMap[7][i][j]=0;
          }
      }
  }
 
  if (m_TheLandscape->SupplyDayInYear() == (270))
  {
      POMOutputs();
#ifdef __STERILITY
      unsigned size = GetLiveArraySize(hob_Female);
      for (unsigned j = 0; j<size; j++) {
          Hare_Female*  HF;
          HF = dynamic_cast<Hare_Female*>(TheArray[hob_Female][j]);
          if (HF->GetAge() < 730) {
              int test = int(g_rand_uni() * 10000);
              if (HF->GetAge() < 730) {
                  if (test<cfg_hare_firstyearsterility.value()) HF->SetSterile();
              }
              else {
                  if (test<cfg_hare_femalesterility.value()) HF->SetSterile();
              }
          }
      }
#endif
  }
 
  // Now do clear the forage food array
  for (int i=0; i<=m_TheLandscape->SupplyLargestPolyNumUsed(); i++) {
      m_PolyFood [i]=-1;
  }
}

References AddHareDensity(), cfg_hare_adult_predation, cfg_hare_femalesterility, cfg_hare_firstyearsterility, cfg_hare_juvenile_predation, cfg_hare_young_predation, ExtraPopMort(), g_rand_uni, THare::GetAge(), Population_Manager::GetLiveArraySize(), hob_Female, m_AdultMortRate, m_DensityMap, m_GoodYearBadYear, m_JuvMortRate, m_MortStochast, m_PolyFood, Population_Manager::m_TheLandscape, m_variableDD, AnimalPosition::m_x, AnimalPosition::m_y, m_YoungMortRate, October, POMOutputs(), random(), Hare_Female::SetSterile(), Landscape::SupplyDayInYear(), Landscape::SupplyLargestPolyNumUsed(), Population_Manager::TheArray, CfgInt::value(), and CfgFloat::value().

DoLast()

void THare_Population_Manager::DoLast ( void  )

protectedvirtual

The last method called before the new time-step starts.

Called after EndStep and before the landscape turns for the next time-step.
Does special end of step actions here. In this case zeroing the density maps, optional debug and mark-release-recapture outputs

Reimplemented from Population_Manager.

{
  Population_Manager::DoLast();
 
// Do our special end of time step actions here
  // Clear the old data
  for (int i=0; i<100; i++) {
    for (int j=0; j<100; j++) {
      m_DensityMap[0][i][j]=0;
      m_DensityMap[1][i][j]=0;
      m_DensityMap[2][i][j]=0;
      m_DensityMap[3][i][j]=0;
      m_DensityMap[4][i][j]=0;
      m_DensityMap[5][i][j]=0;
    }
  }
 
  //Special hare debugging test
  //if (m_TheLandscape->SupplyDayInMonth()==1) {
  /*
  if (TheArray[hob_Female].size()>0) {
        Hare_Female*  HF;
        HF = dynamic_cast<Hare_Female*>(TheArray[hob_Female][0]);
        HF->dumpEnergy();
  }
  */
  /*
    FILE* hareweights=fopen(hareweights,"HareWeights.txt","a");
      for (unsigned listindex=0; listindex<5; listindex++)
      {
        unsigned size=TheArray[listindex].size();
        if (size>0) {
            for (unsigned j=0; j<size; j++)
        {
            int age=dynamic_cast < THare * > ( TheArray[listindex][j] )->GetAge();
            double w=dynamic_cast < THare * > ( TheArray[listindex][j] )->GetWeight();
            int  weight=int (floor(0.5+w));
            fprintf(hareweights,"%i\t%i\n",age, weight);
        }
        }
  }
  fclose(hareweights);
      // End special
*/
    MRROutputs();
}

References Population_Manager::DoLast(), m_DensityMap, and MRROutputs().

ExtraPopMort()

void THare_Population_Manager::ExtraPopMort ( void  )

protected

An extra global mortality

Like Catastrophe() this just kills hares but always on Jan 1st.
Used for POM testing only.

                                                  {
    THare* AH = NULL;
    // This version simply alters populations on 1st January
    int esize= random(50);
    // First do we have the right day?
    int today = m_TheLandscape->SupplyDayInYear();
    if (today!=1) return;
    // First do we have the right year?
    // First do we have the right year?
    int year = m_TheLandscape->SupplyYearNumber();
    if (year%1!=0) return;
        unsigned size2;
        size2 = GetLiveArraySize(hob_Juvenile);
        for ( unsigned j = 0; j < size2; j++ ) {
            if (random(100) < esize) {
                    AH = dynamic_cast < THare * > ( TheArray[hob_Juvenile] [ j ] );
                    AH->Dying(); // Kill it
            }
        }
        size2 = GetLiveArraySize(hob_Male);
        for ( unsigned j = 0; j < size2; j++ ) {
            if (random(100) < esize) {
                    AH = dynamic_cast < THare * > ( TheArray[hob_Male] [ j ] );
                    AH->Dying(); // Kill it
            }
        }
        size2 = GetLiveArraySize(hob_Female);
        for ( unsigned j = 0; j < size2; j++ ) {
            if (random(100) < esize) {
                    AH = dynamic_cast < THare * > ( TheArray[hob_Female] [ j ] );
                    AH->Dying(); // Kill it
            }
        }
}

References TAnimal::Dying(), Population_Manager::GetLiveArraySize(), hob_Female, hob_Juvenile, hob_Male, Population_Manager::m_TheLandscape, random(), Landscape::SupplyDayInYear(), Landscape::SupplyYearNumber(), and Population_Manager::TheArray.

Referenced by DoFirst().

GetAdultDensity()

int THare_Population_Manager::GetAdultDensity ( int  x, int  y  )

inline

Density function - returns the density of adults in the square containing by x,y. Each square is 256x256m in size.

    { 
        return (m_DensityMap[hob_Male][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT] + m_DensityMap[hob_Female][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT]); 
    }

References hob_Female, hob_Male, and m_DensityMap.

Referenced by Hare_Juvenile::st_Dispersal(), Hare_Male::st_Foraging(), and Hare_Female::st_Foraging().

GetDelayedAdultDensity()

int THare_Population_Manager::GetDelayedAdultDensity ( int  x, int  y  )

inline

Density function - returns the density of adults in the square containing by x,y, but for last year at this time. Each square is 256x256m in size.

                                                {
        return m_DensityMap[6][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT];
    }

References m_DensityMap.

Referenced by Hare_Male::st_Foraging(), and Hare_Female::st_Foraging().

GetFemaleDensity()

int THare_Population_Manager::GetFemaleDensity ( int  x, int  y  )

inline

Density function - returns the density of females in the square containing by x,y. Each square is 256x256m in size.

{ return m_DensityMap[hob_Female][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT]; }

References hob_Female, and m_DensityMap.

GetGrowthEfficiency()

double THare_Population_Manager::GetGrowthEfficiency ( int  a_age )

inline

Get the growth efficiency for this a_age.

                                         {
#ifdef __BOUNDSCHECK
       if ((a_age<0) || (a_age>5000)) {
             m_TheLandscape->Warn( "Hare GetGrowthEfficiency a_age out of bounds", NULL );
             exit( 1 );
       }
#endif
        return m_GrowthEfficiency[a_age]; }

References m_GrowthEfficiency, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Infant::st_Developing().

GetGrowthEfficiencyF()

double THare_Population_Manager::GetGrowthEfficiencyF ( int  a_age )

inline

Get the growth efficiency for this a_age for creating fat.

                                           {
#ifdef __BOUNDSCHECK
       if ((a_age<0) || (a_age>5000)) {
             m_TheLandscape->Warn( "Hare m_GrowthEfficiencyF a_age out of bounds", NULL );
             exit( 1 );
       }
#endif
        return m_GrowthEfficiencyF[a_age]; }

References m_GrowthEfficiencyF, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Juvenile::st_Developing(), Hare_Male::st_Developing(), and Hare_Female::st_Developing().

GetGrowthEfficiencyP()

double THare_Population_Manager::GetGrowthEfficiencyP ( int  a_age )

inline

Get the growth efficiency for this a_age for creating protein.

                                          {
#ifdef __BOUNDSCHECK
       if ((a_age<0) || (a_age>5000)) {
             m_TheLandscape->Warn( "Hare GetGrowthEfficiencyP a_age out of bounds", NULL );
             exit( 1 );
       }
#endif
        return m_GrowthEfficiencyP[a_age]; }

References m_GrowthEfficiencyP, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Young::st_Developing(), Hare_Juvenile::st_Developing(), Hare_Male::st_Developing(), and Hare_Female::st_Developing().

GetHareRefNum()

int THare_Population_Manager::GetHareRefNum ( )

inline

Get the next ID number available.

{ return ++m_RefNums; }

References m_RefNums.

Referenced by THare::THareInit().

GetInfantDensity()

int THare_Population_Manager::GetInfantDensity ( int  x, int  y  )

inline

Density function - returns the density of infants in the square containing by x,y. Each square is 256x256m in size.

{ return m_DensityMap[hob_Infant][x >> __DENSITYSHIFT][y >> __DENSITYSHIFT]; }

References hob_Infant, and m_DensityMap.

GetInterference()

double THare_Population_Manager::GetInterference ( int  h )

inline

Return the proportion of time used in communicating with con-specifics.

Based on:
m_Interference[i]=exp(i*cfg_HareInterferenceConstant)

                                  {
#ifdef __BOUNDSCHECK
       if ((h<0) || (h>2499)) {
             m_TheLandscape->Warn( "Hare Interference range out of bounds", NULL );
             exit( 1 );
       }
#endif
        return m_Interference[h]; //[m_variableDD];
    }

References m_Interference, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Infant::BeginStep(), Hare_Young::BeginStep(), Hare_Juvenile::BeginStep(), Hare_Juvenile::st_Dispersal(), Hare_Juvenile::st_Foraging(), Hare_Male::st_Foraging(), and Hare_Female::st_Foraging().

GetJuvenileDensity()

int THare_Population_Manager::GetJuvenileDensity ( int  x, int  y  )

inline

Density function - returns the density of juveniles in the square containing by x,y. Each square is 256x256m in size.

{ return m_DensityMap[hob_Juvenile][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT]; }

References hob_Juvenile, and m_DensityMap.

GetKJperM()

double THare_Population_Manager::GetKJperM ( int  a_size )

inline

Get the cost of moving 1m in KJ dependent upon mass (.

                                 {
#ifdef __BOUNDSCHECK
       if ((a_size<0) || (a_size>7000)) {
           char sz[255];
           _itoa(a_size,sz,10);
           m_TheLandscape->Warn( "Hare GetKJperM a_size out of bounds", sz );
           exit( 1 );
       }
#endif
        return m_KJperM[a_size]; }

References m_KJperM, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Infant::BeginStep(), Hare_Young::BeginStep(), Hare_Juvenile::BeginStep(), Hare_Male::BeginStep(), Hare_Female::BeginStep(), and Hare_Female::Init().

GetLitterSize()

int THare_Population_Manager::GetLitterSize

(

int

litter

)

Returns the litter size.

Uses a frequency distribution out of 0-9999 and 6 bins and returns one of the bins as the return based on a random number from 0-9999

{
  int testing=int(g_rand_uni()*10000);
  for (int i=0; i<7; i++) {
    if (testing<=m_LitterSize[litter][i]) return i;
  }
  // something wrong if the program gets to here
    m_TheLandscape->Warn("THare_Population_Manager::GetLitterSize - litter size error",NULL);
    exit(1);
}

References g_rand_uni, m_LitterSize, Population_Manager::m_TheLandscape, and Landscape::Warn().

GetMaleDensity()

int THare_Population_Manager::GetMaleDensity ( int  x, int  y  )

inline

Density function - returns the density of males in the square containing by x,y. Each square is 256x256m in size.

{ return m_DensityMap[hob_Male][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT]; }

References hob_Male, and m_DensityMap.

GetMaxDailyGrowthEnergy()

double THare_Population_Manager::GetMaxDailyGrowthEnergy ( int  a_age )

inline

Get the maximum daily energy needed for growth for this a_age

                                              {
#ifdef __BOUNDSCHECK
       if ((a_age<0) || (a_age>5000)) {
             m_TheLandscape->Warn( "Hare GetMaxDailyGrowthEnergy a_age out of bounds", NULL );
             exit( 1 );
       }
#endif
        return m_MaxDailyGrowthEnergy[a_age];
   }

References m_MaxDailyGrowthEnergy, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Female::DoLactation().

GetMaxDailyGrowthEnergyF()

double THare_Population_Manager::GetMaxDailyGrowthEnergyF ( int  a_age )

inline

Get the maximum daily energy needed for growth for this a_age for use in fat construction.

                                               {
#ifdef __BOUNDSCHECK
       if ((a_age<0) || (a_age>5000)) {
             m_TheLandscape->Warn( "Hare GetMaxDailyGrowthEnergyF a_age out of bounds", NULL );
             exit( 1 );
       }
#endif
        return m_MaxDailyGrowthEnergyF[a_age]; }

References m_MaxDailyGrowthEnergyF, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Juvenile::st_Developing(), Hare_Male::st_Developing(), and Hare_Female::st_Developing().

GetMaxDailyGrowthEnergyP()

double THare_Population_Manager::GetMaxDailyGrowthEnergyP ( int  a_age )

inline

Get the maximum daily energy needed for growth for this a_age for use in protein construction.

                                               {
#ifdef __BOUNDSCHECK
       if ((a_age<0) || (a_age>5000)) {
             m_TheLandscape->Warn( "Hare GetMaxDailyGrowthEnergyP a_age out of bounds", NULL );
             exit( 1 );
       }
#endif
        return m_MaxDailyGrowthEnergyP[a_age];
    }

References m_MaxDailyGrowthEnergyP, Population_Manager::m_TheLandscape, and Landscape::Warn().

Referenced by Hare_Infant::st_Developing(), Hare_Young::st_Developing(), Hare_Juvenile::st_Developing(), Hare_Male::st_Developing(), and Hare_Female::st_Developing().

GetPolyFood()

double THare_Population_Manager::GetPolyFood ( int  a_poly )

inline

Get stored polygon food quality.

{ return m_PolyFood[a_poly]; }

References m_PolyFood.

Referenced by THare::ForageSquare(), and THare::ForageSquareP().

GetRMR()

double THare_Population_Manager::GetRMR	(	int	a_age,
		double	a_size
	)

Returns the RMR given a specific age and mass.

RMR is weight dependent based on RMR=69.1*4.1868)w^0.808 (McNab 1988)
But affected by temperature. We assume that after 35days 1kg weight, that this effect is constant per kg

                                                                {
    double a_temp = m_TheLandscape->SupplyTemp();
    if (a_temp>20.0) a_temp=20.0;
    double tempdiff=18.0-a_temp;// 18 is used because this was the value where Hacklander
                                //started his expts - 20 is assumed thermoneutral point and
                                // a linear relationship between these two
    // Adjust for rainfall - assume that if we have a rainfall of >5mm then the temp diff is maximum - removing this might help add variation to juvenile survivorship!
    double rainfall = m_TheLandscape->SupplyRain();
    if (rainfall>5.0) rainfall=5.0;
    tempdiff*=1.0+(rainfall*g_RMRrainFactor);
    //tempdiff*=1.0+((rainfall*rainfall*rainfall*g_RMRrainFactor)/25); // Gives a curve sloping up
 
#ifdef __BOUNDSCHECK
       if (a_age<0)  {
             m_TheLandscape->Warn( "Hare GetRMR a_age range out of bounds", NULL );
             exit( 1 );
       }
#endif
    a_size/=1000.0;
    double RMR;
    if (a_age<37) {
        RMR=((tempdiff*m_RMR[0][a_age])+m_RMR[1][a_age])*(a_size);
    } else
    {
        a_age=36;
        RMR=(69.1*4.1868)*pow(a_size,0.808);
        RMR=RMR+(tempdiff*m_RMR[0][a_age]*a_size);
    }
    return RMR;
}

References g_RMRrainFactor, m_RMR, Population_Manager::m_TheLandscape, Landscape::SupplyRain(), Landscape::SupplyTemp(), and Landscape::Warn().

Referenced by THare::EnergyBalance(), THare::GetRMR(), Hare_Infant::st_Developing(), and Hare_Young::st_Foraging().

GetTotalDensity()

int THare_Population_Manager::GetTotalDensity ( int  x, int  y  )

inline

Density function - returns the density of all hares in the square containing by x,y. Each square is 256x256m in size.

{ return m_DensityMap[5][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT]; }

References m_DensityMap.

Referenced by Hare_Infant::BeginStep(), Hare_Young::BeginStep(), Hare_Juvenile::BeginStep(), Hare_Male::BeginStep(), Hare_Female::BeginStep(), and HuntingGrid().

GetYoungDensity()

int THare_Population_Manager::GetYoungDensity ( int  x, int  y  )

inline

Density function - returns the density of young in the square containing by x,y. Each square is 256x256m in size.

{ return m_DensityMap[hob_Young][x>>__DENSITYSHIFT][y>>__DENSITYSHIFT]; }

References hob_Young, and m_DensityMap.

Hunting()

void THare_Population_Manager::Hunting ( void  )

protected

Takes a fixed proportion of the population (input variable), in the middle of the hunting season.

                                             {
    m_shot=0;
    double huntpercent=cfg_HareHunting.value();
    Hare_Juvenile* AJH = NULL;
    unsigned size2;
    size2 = GetLiveArraySize(hob_Young);
    for ( unsigned j = 0; j < size2; j++ ) {
        AJH = dynamic_cast < Hare_Juvenile * > ( TheArray[ hob_Juvenile ] [ j ] );
        if ( g_rand_uni()< huntpercent) {
            // Must check if it is already dead of some other cause - is so can't kill it again
            if (AJH->GetCurrentStateNo() != -1)
            {
                AJH->ON_Dead(); // Kill it
                m_shot++;
            }
        }
    }
    Hare_Male* AH = NULL;
    size2 = GetLiveArraySize(hob_Male);
    for ( unsigned j = 0; j < size2; j++ ) {
        AH = dynamic_cast < Hare_Male * > ( TheArray[ hob_Male ] [ j ] );
        if ( g_rand_uni()< huntpercent) {
            if (AH->GetCurrentStateNo() != -1)
            {
                AH->ON_Dead(); // Kill it
                m_shot++;
            }
        }
    }
    Hare_Female* AFH = NULL;
    size2 = GetLiveArraySize(hob_Female);
    for ( unsigned j = 0; j < size2; j++ ) {
        AFH = dynamic_cast < Hare_Female * > ( TheArray[ hob_Female ] [ j ] );
        if ( g_rand_uni()< huntpercent) {
            if (AFH->GetCurrentStateNo() != -1)
            {
                AFH->ON_Dead(); // Kill it
                m_shot++;
            }
        }
    }
}

References cfg_HareHunting, g_rand_uni, TALMaSSObject::GetCurrentStateNo(), Population_Manager::GetLiveArraySize(), hob_Female, hob_Juvenile, hob_Male, hob_Young, m_shot, Hare_Juvenile::ON_Dead(), Hare_Male::ON_Dead(), Hare_Female::ON_Dead(), Population_Manager::TheArray, and CfgFloat::value().

Referenced by DoAlmostLast().

HuntingDifferentiatedBeetleBankArea()

void THare_Population_Manager::HuntingDifferentiatedBeetleBankArea ( void  )

protected

Differential hunting inside a specific area designated as beetlebank addition area. Takes a fixed proportion of the population (input variable for inside and outside), in the middle of the hunting season

                                                                         {
    m_shot=0;
    int tx1 = cfg_BeetleBankMinX.value();
    int tx2 = cfg_BeetleBankMaxX.value();
    int ty1 = cfg_BeetleBankMinY.value();
    int ty2 = cfg_BeetleBankMaxY.value();
    double huntpercent_out, huntpercent_in;
    if (!cfg_BeetleBankInvert.value())  
    {
        huntpercent_out =cfg_HareHunting.value();
        huntpercent_in =cfg_HareHuntingBeetleBankArea.value();
    }
    else
    {
        huntpercent_in =cfg_HareHunting.value();
        huntpercent_out =cfg_HareHuntingBeetleBankArea.value();
    }
    THare* AH = NULL;
    unsigned size2;
    for (int ind =hob_Juvenile; ind < hob_Foobar; ind++)
    {
        size2 = (unsigned)GetLiveArraySize(ind);
        for ( unsigned j = 0; j < size2; j++ ) 
        {
            AH = dynamic_cast < THare * > ( TheArray[ ind ] [ j ] );
            APoint xy = AH->SupplyPoint();
            if ((xy.m_x >= tx1) && (xy.m_y >= ty1) && (xy.m_x <= tx2) && (xy.m_y <= ty2)) 
            {
                if ( g_rand_uni()< huntpercent_in) 
                {
                    AH->ON_Dead(); // Kill it
                    m_shot++;
                }
            } else
            {
                if ( g_rand_uni()< huntpercent_out) 
                {
                    AH->ON_Dead(); // Kill it
                    m_shot++;
                }
            }
        }
    }
}

References cfg_BeetleBankInvert, cfg_BeetleBankMaxX, cfg_BeetleBankMaxY, cfg_BeetleBankMinX, cfg_BeetleBankMinY, cfg_HareHunting, cfg_HareHuntingBeetleBankArea, g_rand_uni, Population_Manager::GetLiveArraySize(), hob_Foobar, hob_Juvenile, m_shot, APoint::m_x, APoint::m_y, THare::ON_Dead(), TAnimal::SupplyPoint(), Population_Manager::TheArray, CfgInt::value(), CfgFloat::value(), and CfgBool::value().

Referenced by DoAlmostLast().

HuntingGrid()

void THare_Population_Manager::HuntingGrid ( void  )

protected

Hunting version based on grid squares - hunting occurs only if there are enough hares in each grid square.
Density squares are 256x256m in size, so for each ca 1 square km we need 8x8 of these squares, if total numbers is greater than a threshold then we hunt.

                                                 {
    int N;
    m_shot=0;
    for (int x=500; x<SimW; x+=1000) {
        for (int y=500; y<SimH; y+=1000) {
            // For each 1km square
            N=0;
            for (int xx=x-(256+128); xx<=x+(256+128); xx+=256) {
                for (int yy=y-(256+128); yy<=y+(256+128); yy+=256) {
                    N+=GetTotalDensity(xx,yy);
                }
            }
            if (N>cfg_HareHuntingThreshold.value()) {
                double huntpercent=cfg_HareHunting.value();
                Hare_Juvenile* AJH = NULL;
                unsigned size2;
                size2 = GetLiveArraySize(hob_Juvenile);
                for ( unsigned j = 0; j < size2; j++ ) {
                    AJH = dynamic_cast < Hare_Juvenile * > ( TheArray[ hob_Juvenile ] [ j ] );
                    if ((AJH->Supply_m_Location_x() >=x-500) &&(AJH->Supply_m_Location_x()< x+500) && (AJH->Supply_m_Location_y() >=y-500) && (AJH->Supply_m_Location_y()< y+500)) {
                        if ( g_rand_uni()< huntpercent) {
                            if (AJH->GetCurrentStateNo() != -1) {
                                AJH->ON_Dead(); // Kill it
                                m_shot++;
                            }
                        }
                    }
                }
                Hare_Male* AH = NULL;
                size2 = GetLiveArraySize(hob_Male);
                for ( unsigned j = 0; j < size2; j++ ) {
                    AH = dynamic_cast < Hare_Male * > ( TheArray[ hob_Male ] [ j ] );
                    if ((AH->Supply_m_Location_x() >=x-500) &&(AH->Supply_m_Location_x()< x+500) && (AH->Supply_m_Location_y() >=y-500) && (AH->Supply_m_Location_y()< y+500)) {
                        if ( g_rand_uni()< huntpercent) {
                            if (AH->GetCurrentStateNo() != -1) {
                                AH->ON_Dead(); // Kill it
                                m_shot++;
                            }
                        }
                    }
                }
                Hare_Female* AFH = NULL;
                size2 = GetLiveArraySize(hob_Female);
                for ( unsigned j = 0; j < size2; j++ ) {
                    AFH = dynamic_cast < Hare_Female * > ( TheArray[ hob_Female ] [ j ] );
                    if ((AFH->Supply_m_Location_x() >=x-500) && (AFH->Supply_m_Location_x()< x+500) && (AFH->Supply_m_Location_y() >=y-500) && (AFH->Supply_m_Location_y()< y+500)) {
                        if ( g_rand_uni()< huntpercent) {
                            if (AFH->GetCurrentStateNo() != -1) {
                                AFH->ON_Dead(); // Kill it
                                m_shot++;
                            }
                        }
                    }
                }
            }
        }
    }
}

References cfg_HareHunting, cfg_HareHuntingThreshold, g_rand_uni, TALMaSSObject::GetCurrentStateNo(), Population_Manager::GetLiveArraySize(), GetTotalDensity(), hob_Female, hob_Juvenile, hob_Male, m_shot, Hare_Juvenile::ON_Dead(), Hare_Male::ON_Dead(), Hare_Female::ON_Dead(), Population_Manager::SimH, Population_Manager::SimW, TAnimal::Supply_m_Location_x(), TAnimal::Supply_m_Location_y(), Population_Manager::TheArray, CfgInt::value(), and CfgFloat::value().

Referenced by DoAlmostLast().

Init()

void THare_Population_Manager::Init ( void  )

protected

Sets up data structures and calculations prior to starting simulation.

Creates some hares in semi-sensible places.

open the probe

Set up before step action sorts This determines how we handle the arrays between steps

Load State Names - these are just used to tell us what the animal is doing in the GUI

Loads a data file giving max daily growth at age together with cost of that growth per g. These are up to day 365. After 365 the cost is constant and assumes only fat is added

Calculates RMR based on Hacklander - these are the thermoneutral values

Ensure zeros in the density map!

Intitialise the Pattern Oriented Modelling output file

{
    g_VegHeightForageReduction = cfg_VegHeightForageReduction.value();
    g_FarmIntensiveness = cfg_FarmIntensiveness.value();
    g_FarmIntensivenessH = cfg_FarmIntensivenessH.value();
    g_RMRrainFactor = cfg_RMRrainFactor.value();
    m_RefNums=0;
    m_MortStochast = cfg_HareMortStochasticity.value();
    m_HareThresholdDD = cfg_HareThresholdDD.value();
  if ( cfg_RipleysOutput_used.value() ) {
     OpenTheRipleysOutputProbe("");
  }
  if ( cfg_ReallyBigOutput_used.value() ) {
    OpenTheReallyBigProbe();
  } else ReallyBigOutputPrb=0;
  BodyBurdenPrb = fopen("HareBodyBurden.txt", "w");
  if (!BodyBurdenPrb) {
          g_msg->Warn(WARN_FILE, "Population_Manager::OpenBodyBurdenProbe(): ""Unable to open probe file", "HareBodyBurden.txt");
          exit(1);
  }
  //-----------------------------------------------------------------------------
  // Initialisation code for the hare population manager
  strcpy(m_SimulationName,"Hare");
  // Load List of Hare Classes
  m_ListNames[0]="Infant";
  m_ListNames[1]="Young";
  m_ListNames[2]="Juvenile";
  m_ListNames[3]="Male";
  m_ListNames[4]="Female";
  m_ListNameLength = 5;
  m_population_type = TOP_Hare;
  // Create an instance of THare to set static members
  THare* thare = new THare( 0, 0, m_TheLandscape, this );
  thare->loadVegPalatability();
  delete thare;
  BeforeStepActions[0]=0; // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = do nothing
  BeforeStepActions[1]=0; // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = do nothing
  BeforeStepActions[2]=0; // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = do nothing
  BeforeStepActions[3]=0; // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = do nothing
  BeforeStepActions[4]=0; // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = do nothing
 
  StateNames[tohs_InitialState] = "Initial State";
  StateNames[  tohs_NextStage ] = "Next Stage";
  StateNames[  tohs_Developing ] = "Development";
  StateNames[  tohs_Dispersal ] = "Dispersal";
  StateNames[  tohs_Foraging ] = "Foraging";
  StateNames[  tohs_Resting ] = "Resting";
  StateNames[  tohs_Running ] = "Running";
  StateNames[  tohs_ReproBehaviour ] = "ReprodBehaviour";
  StateNames[  tohs_Dying ] = "Dying";
 
  // Deal with peg global
  g_hare_peg_inertia=cfg_hare_peg_inertia.value();
  // Create some hares
  // This is only used when the simulation starts and puts a starting number of
  // hares in the landscape at random positions
  //
  struct_Hare* sp;
  sp = new struct_Hare;
  sp->HM = this;
  sp->L = m_TheLandscape;
  sp->age=365;
  sp->weight=3800/3;
  sp->RefNum=0;
  bool b;
  for (int i=0; i<cfg_hare_StartingNo.value(); i++)
    {
        do {
            sp->x = random(SimW);
            sp->y = random(SimH);
            TTypesOfLandscapeElement te=m_TheLandscape->SupplyElementType(sp->x,sp->y);
        switch (te)
        {
        case tole_Building:
        case tole_Freshwater:
        case tole_FishFarm:
        case tole_Pond:
        case tole_River:
        case tole_Saltwater:
        case tole_Coast:
        case tole_BareRock:
        case tole_AmenityGrass:
        case tole_Parkland:
        case tole_UrbanNoVeg:
        case tole_UrbanPark:
        case tole_BuiltUpWithParkland:
        case tole_SandDune:
        case tole_Copse:
        case tole_MetalledPath:
        case tole_Carpark:
        case tole_Churchyard:
        case tole_Stream:
        case tole_HeritageSite:
            b=false;
            break;
        default:
            b=true;
        }
        }
        while (!b);
        CreateObjects(3,NULL,NULL,sp,1); // 3 = Males
  }
  for (int i=0; i<cfg_hare_StartingNo.value(); i++)
  {
        do {
            sp->x = random(SimW);
            sp->y = random(SimH);
            TTypesOfLandscapeElement te=m_TheLandscape->SupplyElementType(sp->x,sp->y);
        switch (te)
        {
        case tole_Building:
        case tole_Pond:
        case tole_Freshwater:
        case tole_FishFarm:
        case tole_River:
        case tole_Saltwater:
        case tole_Coast:
        case tole_BareRock:
        case tole_AmenityGrass:
        case tole_Parkland:
        case tole_UrbanNoVeg:
        case tole_UrbanPark:
        case tole_BuiltUpWithParkland:
        case tole_SandDune:
        case tole_Copse:
        case tole_MetalledPath:
        case tole_Carpark:
        case tole_Churchyard:
        case tole_Stream:
        case tole_HeritageSite:
            b=false;
            break;
        default:
            b=true;
        }
        }
        while (!b);
        CreateObjects(4,NULL,NULL,sp,1); // 4 = Females
  }
  delete sp;
  double weightDM, rmr, f0, f1,f2,protcost,fatcost, totalgrowthcost;
  ifstream* HareDataFile = new ifstream("Hare_GrowthALMaSS_Input.txt", ios::in);
  if (!HareDataFile->is_open()) {
      // This is an error since we are running hares - so say so.
      m_TheLandscape->Warn("THare_Population_Manager::Init - Hare_GrowthALMaSS_Input.txt is missing or in use", "");
      exit(1);
  }
  else {
      // File format: "Age" "Ing-free dmBW (g,dm)"  "Protein W-gain (g,dm)" "Fat W-gain (g,dm)"
      // "KJcost prot"  "KJ cost fat"   "Energy cost (kJ) to achieve BW gain    " "resting energy kJ"
      for (int i = 0; i<5000; i++) {
          (*HareDataFile) >> f0 >> weightDM >> f1 >> f2 >> protcost >> fatcost >> totalgrowthcost >> rmr;
          // These arrays are little wasteful of space because many are only really used for the first 36 days, but
          // if this is a problem it can be fixed later CJT 12-09-2006
          m_MaxDailyGrowthEnergyP[i] = protcost; // How much energy for protein growth max at age i
          if (protcost>0) m_GrowthEfficiencyP[i] = f1 / protcost; // KJ per g protein at age i
          else m_GrowthEfficiencyP[i] = 0;
          m_MaxDailyGrowthEnergyF[i] = fatcost; // How much energy for fat growth max at age i
          if (fatcost>0) m_GrowthEfficiencyF[i] = f2 / fatcost; // KJ per g fat at age i
          else m_GrowthEfficiencyF[i] = 0;
          // No 366 is in fact the value for day 366 and rest of life and is about adding only fat
          m_MaxDailyGrowthEnergy[i] = totalgrowthcost;
          m_GrowthEfficiency[i] = (f1 + f2) / totalgrowthcost;
          m_DMWeight[i] = weightDM*cfg_min_growth_attain.value(); // Used to test for falling behind in growth
      }
      HareDataFile->close();
  }
 
  m_RMR[0][0]=0;
  m_RMR[1][0]=0;
  /* OLD CODE
  for (int i=1; i<7001; i++) {
    m_RMR[i]=((3.8*pow((double(i)/(0.88*0.33)),-0.27))*20.1*24)*((double(i)/(0.88*0.33))/1000.0); // KJ/day See energetics notes
  }
  */
    for (int i=1; i<=37; i++) {
        m_RMR[0][i]=(-1.5658*i + 58.487); // Slope KJ/day/degree See energetics notes
        m_RMR[1][i]=1525.4*pow(i,-0.3997); // KJ/day See energetics notes
    }
 
 
  // Energy for walking dependent upon weight KJ per m
  for (int i=1; i<7001; i++) {
      //m_KJperM[i]=(9.08*pow(((double (i)/(0.88*0.33))/1000.0),0.77344))*0.001; // KJ/M for each weight
      double fi=3.75*i/1000.0; // Corrected for dw to ww + ingesta
      // m_KJperM[i]=(10.7*pow(fi,-0.316)*fi)/1000.0;
      m_KJperM[i] = (10.7*pow(fi, cfg_HareWalkingPowerConst.value())*fi) / 1000.0;
  }
 m_KJperM[0]=0.0;
 
  double mean=cfg_littersize_mean1.value();
  double SD=cfg_littersize_SD1.value();
  CalcLitterSize(mean,SD,0);
 
  mean=cfg_littersize_mean2.value();
  SD=cfg_littersize_SD2.value();
  CalcLitterSize(mean,SD,1);
 
  mean=cfg_littersize_mean3.value();
  SD=cfg_littersize_SD3.value();
  CalcLitterSize(mean,SD,2);
 
  mean=cfg_littersize_mean4.value();
  SD=cfg_littersize_SD4.value();
  CalcLitterSize(mean,SD,3);
 
  mean=cfg_littersize_mean5.value();
  SD=cfg_littersize_SD5.value();
  CalcLitterSize(mean,SD,4);
 
  mean=cfg_littersize_mean6.value();
  SD=cfg_littersize_SD6.value();
  CalcLitterSize(mean,SD,5);
 
  mean=cfg_littersize_mean7.value();
  SD=cfg_littersize_SD7.value();
  CalcLitterSize(mean,SD,6);
 
  mean=cfg_littersize_mean8.value();
  SD=cfg_littersize_SD8.value();
  CalcLitterSize(mean,SD,7);
 
  mean=cfg_littersize_mean9.value();
  SD=cfg_littersize_SD9.value();
  CalcLitterSize(mean,SD,8);
 
  mean=cfg_littersize_mean10.value();
  SD=cfg_littersize_SD10.value();
  CalcLitterSize(mean,SD,9);
 
  mean=cfg_littersize_mean11.value();
  SD=cfg_littersize_SD11.value();
  CalcLitterSize(mean,SD,10);
 
  mean=cfg_littersize_mean12.value();
  SD=cfg_littersize_SD12.value();
  CalcLitterSize(mean,SD,11);
 
  for (int i=1; i<2500; i++) {
        m_Interference[i]=exp(i*cfg_HareInterferenceConstant.value());
    }
    m_Interference[0]=1.0;
 
  for (int i=0; i<200; i++) {
    for (int j=0; j<200; j++) {
      m_DensityMap[0][i][j]=0;
      m_DensityMap[1][i][j]=0;
      m_DensityMap[2][i][j]=0;
      m_DensityMap[3][i][j]=0;
      m_DensityMap[4][i][j]=0;
      m_DensityMap[5][i][j]=0;
      m_DensityMap[6][i][j]=0;
      m_DensityMap[7][i][j]=0;
    }
  }
  m_PolyFood = (double*)malloc(sizeof(double)* (1+m_TheLandscape->SupplyLargestPolyNumUsed()) );
  if ( m_PolyFood == NULL ) {
      g_msg->Warn( WARN_FILE, "HarePopulationManager::Init: Out of memory!", "" );
    exit( 1 );
  }
  FILE* fp;
  fp=fopen("LitterProduction.txt","w");
  fclose(fp);
  fp=fopen("EnergyCheck.txt","w");
  fclose(fp);
  fp=fopen("POM_Hare.txt","w");
    fprintf(fp,"1) Timestep,\n");
    fprintf(fp,"2-6) Population Size of add stages,\n");
    fprintf(fp,"7) Females < 365 days old,\n");
    fprintf(fp,"8) Females >=1 & < 2 yrs old,\n");
    fprintf(fp,"9) Females >=2 & < 3 yrs old,\n");
    fprintf(fp,"10) Females >=3 & < 4 yrs old,\n");
    fprintf(fp,"11) Females >=4 & < 5 yrs old,\n");
    fprintf(fp,"12) Females >=4 yrs old,\n");
    fprintf(fp,"13) Mean bodyweight of females (dw),\n");
    fprintf(fp,"14) variance in bodyweight,\n");
  fclose(fp);
  fp=fopen("POM_FemaleHareWeights.txt","w");
  fclose(fp);
  // Mortality variables
  m_variableDD=10;
  // MRR
  m_OurMRRData = new MRR_Data;
}

References struct_Hare::age, Population_Manager::BeforeStepActions, BodyBurdenPrb, CalcLitterSize(), cfg_FarmIntensiveness, cfg_FarmIntensivenessH, cfg_hare_peg_inertia, cfg_hare_StartingNo, cfg_HareInterferenceConstant, cfg_HareMortStochasticity, cfg_HareThresholdDD, cfg_HareWalkingPowerConst, cfg_littersize_mean1, cfg_littersize_mean10, cfg_littersize_mean11, cfg_littersize_mean12, cfg_littersize_mean2, cfg_littersize_mean3, cfg_littersize_mean4, cfg_littersize_mean5, cfg_littersize_mean6, cfg_littersize_mean7, cfg_littersize_mean8, cfg_littersize_mean9, cfg_littersize_SD1, cfg_littersize_SD10, cfg_littersize_SD11, cfg_littersize_SD12, cfg_littersize_SD2, cfg_littersize_SD3, cfg_littersize_SD4, cfg_littersize_SD5, cfg_littersize_SD6, cfg_littersize_SD7, cfg_littersize_SD8, cfg_littersize_SD9, cfg_min_growth_attain, cfg_ReallyBigOutput_used, cfg_RipleysOutput_used, cfg_RMRrainFactor, cfg_VegHeightForageReduction, CreateObjects(), g_FarmIntensiveness, g_FarmIntensivenessH, g_hare_peg_inertia, g_msg, g_RMRrainFactor, g_VegHeightForageReduction, struct_Hare::HM, struct_Hare::L, THare::loadVegPalatability(), m_DensityMap, m_DMWeight, m_GrowthEfficiency, m_GrowthEfficiencyF, m_GrowthEfficiencyP, m_HareThresholdDD, m_Interference, m_KJperM, Population_Manager::m_ListNameLength, Population_Manager::m_ListNames, m_MaxDailyGrowthEnergy, m_MaxDailyGrowthEnergyF, m_MaxDailyGrowthEnergyP, m_MortStochast, m_OurMRRData, m_PolyFood, Population_Manager::m_population_type, m_RefNums, m_RMR, Population_Manager::m_SimulationName, Population_Manager::m_TheLandscape, m_variableDD, Population_Manager::OpenTheReallyBigProbe(), Population_Manager::OpenTheRipleysOutputProbe(), random(), Population_Manager::ReallyBigOutputPrb, struct_Hare::RefNum, Population_Manager::SimH, Population_Manager::SimW, Population_Manager::StateNames, Landscape::SupplyElementType(), Landscape::SupplyLargestPolyNumUsed(), tohs_Developing, tohs_Dispersal, tohs_Dying, tohs_Foraging, tohs_InitialState, tohs_NextStage, tohs_ReproBehaviour, tohs_Resting, tohs_Running, tole_AmenityGrass, tole_BareRock, tole_Building, tole_BuiltUpWithParkland, tole_Carpark, tole_Churchyard, tole_Coast, tole_Copse, tole_FishFarm, tole_Freshwater, tole_HeritageSite, tole_MetalledPath, tole_Parkland, tole_Pond, tole_River, tole_Saltwater, tole_SandDune, tole_Stream, tole_UrbanNoVeg, tole_UrbanPark, TOP_Hare, CfgInt::value(), CfgFloat::value(), CfgBool::value(), MapErrorMsg::Warn(), Landscape::Warn(), WARN_FILE, struct_Hare::weight, struct_Hare::x, and struct_Hare::y.

Referenced by THare_Population_Manager().

MRROutputs()

void THare_Population_Manager::MRROutputs ( )

protected

Special probe for data to be used in mark-release-recapture simulations.

What this has to do is to print to the MMR file the occurence if any of each animal that ever existed between two dates.
If that animal has been counted before then add to that animals line, otherwise create a new line.
Requires that each hare has a unique ID number.
NB this counts the population with zero error.

                                          {
    //
    // Step one - do we count today?
    if ((m_TheLandscape->SupplyYearNumber()<cfg_MRR_FirstYear.value())||(m_TheLandscape->SupplyYearNumber()>cfg_MRR_LastYear.value())) return;
    int day=m_TheLandscape->SupplyDayInYear();
    if ((day!=cfg_MRR1.value()) && (day!=cfg_MRR2.value()) && (day!=cfg_MRR3.value()) && (day!=cfg_MRR4.value()) && (day!=cfg_MRR5.value())) return;
    // We want to count today
    // Loop through all Juvenile and Adult hares and put their details in the MRR data array
    unsigned size = GetLiveArraySize(hob_Juvenile);
    for (unsigned j=0; j<size; j++) { // Every other one, so assume 50% males
        Hare_Juvenile*  HJ;
        HJ = dynamic_cast<Hare_Juvenile*>(TheArray[hob_Juvenile][j]);
        m_OurMRRData->AddEntry(HJ->GetRefNum());
    }
    size = GetLiveArraySize(hob_Female);
    for (unsigned j=0; j<size; j++) {
        Hare_Female*  HF;
        HF = dynamic_cast<Hare_Female*>(TheArray[hob_Female][j]);
        m_OurMRRData->AddEntry(HF->GetRefNum());
    }
    size= GetLiveArraySize(hob_Male);
    for (unsigned j=0; j<size; j++) {
        Hare_Male*  HM;
        HM = dynamic_cast<Hare_Male*>(TheArray[hob_Male][j]);
        m_OurMRRData->AddEntry(HM->GetRefNum());
    }
 
    // If we need to dump the results this time do this
    if ((day==cfg_MRR5.value() && (m_TheLandscape->SupplyYearNumber()==cfg_MRR_LastYear.value()))) m_OurMRRData->OutputToFile();
    m_OurMRRData->IncTrapping();
}

References MRR_Data::AddEntry(), cfg_MRR1, cfg_MRR2, cfg_MRR3, cfg_MRR4, cfg_MRR5, cfg_MRR_FirstYear, cfg_MRR_LastYear, Population_Manager::GetLiveArraySize(), THare::GetRefNum(), hob_Female, hob_Juvenile, hob_Male, MRR_Data::IncTrapping(), m_OurMRRData, Population_Manager::m_TheLandscape, MRR_Data::OutputToFile(), Landscape::SupplyDayInYear(), Landscape::SupplyYearNumber(), Population_Manager::TheArray, and CfgInt::value().

Referenced by DoLast().

POMOutputs()

void THare_Population_Manager::POMOutputs ( )

protected

This method is called to dump the information needed for POM approaches.

The data dumped is variable dependent upon what is needed at the time. Contents vary from version to version.

                                          {
    //
    // Outputs are:
    // 1) Timestep
    // 2-6) Population Size of add stages
    // 7) Females < 2 yrs old
    // 8) Females >=2 & < 3 yrs old
    // 9) Females >=3 & < 4 yrs old
    // 10) Females >=4 & < 5 yrs old
    // 11) Females >=5 yrs old
    // 12) Mean bodyweight of females (dw)
    // 13) variance in bodyweight
    // 14) Mean yearlings
    // 14) Var yearlings
    // 16) m_shot
 
    int age0 = 0;
    int age1 = 0;
    int age2 = 0;
    int age3 = 0;
    int age4 = 0;
    int age5 = 0;
    int age6 = 0;
    int age7 = 0;
    double totweight = 0.0;
    double totweight2 = 0.0;
    double yearlingstotweight = 0.0;
    double yearlingstotweight2 = 0.0;
    FILE* POMOut = fopen("POM_Hare.txt", "a");
    FILE* POMOut2 = fopen("POM_FemaleHareWeights.txt", "a");
    if (!POMOut) {
        // something wrong if the program gets to here
        m_TheLandscape->Warn("THare_Population_Manager::POMOutputs - POM_Output.txt can't be opened", NULL);
        exit(1);
    }
    // Now sort out the data for the females
    int yearlingssize = 0;
    unsigned size = GetLiveArraySize(hob_Juvenile);
    for (unsigned j = 0; j<size; j += 2) { // Every other one, so assume 50% males
        Hare_Juvenile*  HJ;
        HJ = dynamic_cast<Hare_Juvenile*>(TheArray[hob_Juvenile][j]);
        double bw = HJ->GetTotalWeight();
        if (bw>1000) {
            yearlingstotweight += bw; // This removes hares that are still almost leverets
            yearlingstotweight2 += (bw*bw);
            yearlingssize++;
            fprintf(POMOut2, "0\t%g\n", (float)bw);
        }
    }
    size = GetLiveArraySize(hob_Female);
    for (unsigned j = 0; j < size; j++) {
        Hare_Female*  HF;
        HF = dynamic_cast<Hare_Female*>(TheArray[hob_Female][j]);
        double bw = HF->GetTotalWeight();
        if (HF->GetAge() < 365) {
            age0++;
            if (bw>333) {
                yearlingstotweight += bw; // This removes hares that are still almost leverets
                yearlingstotweight2 += (bw*bw);
                yearlingssize++;
            }
            fprintf(POMOut2, "0\t%g\n", (float)bw);
        }
        else {
            totweight += bw;
            totweight2 += (bw*bw);
            if (HF->GetAge() < 730) {
                age1++;
                fprintf(POMOut2, "1\t%g\n", (float)bw);
            }
            else if (HF->GetAge() < 1095) {
                age2++;
                fprintf(POMOut2, "2\t%g\n", (float)bw);
            }
            else if (HF->GetAge() < 1460) {
                age3++;
                fprintf(POMOut2, "3\t%g\n", (float)bw);
            }
            else if (HF->GetAge() < 1825) {
                age4++;
                fprintf(POMOut2, "4\t%g\n", (float)bw);
            }
            else if (HF->GetAge() < 2190) {
                age5++;
                fprintf(POMOut2, "5\t%g\n", (float)bw);
            }
            else if (HF->GetAge() < 2555) {
                age6++;
                fprintf(POMOut2, "6\t%g\n", (float)bw);
            }
            else {
                age7++;
                fprintf(POMOut2, "7\t%g\n", (float)bw);
            }
        }
        // Do the bodyweight stuff
    }
    double yearlingsvar = (yearlingstotweight2 - ((yearlingstotweight*yearlingstotweight) / double(yearlingssize))) / double(yearlingssize);
    double yearlingsmean = yearlingstotweight / double(yearlingssize);
    double var = (totweight2 - ((totweight*totweight) / double(size))) / double(size);
    double mean = totweight / double(size);
    float meanf = (float)mean;
    float varf = (float)var;
    float meany = (float)yearlingsmean;
    float vary = (float)yearlingsvar;
    /*
    // Lets test the density grid
    int den = 0;
    for (int i = 0; i < 200; i++)
    for (int j = 0; j < 200; j++)
    {
    for (int l = 0; l < hob_Foobar; l++)
    den += m_DensityMap[l][i][j];
    }
    */
    fprintf(POMOut, "%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%d\t%g\t%g\t%g\t%g\t%d\n", (int)m_TheLandscape->SupplyDayInYear(), GetLiveArraySize(hob_Infant), GetLiveArraySize(hob_Young), GetLiveArraySize(hob_Juvenile), GetLiveArraySize(hob_Male), GetLiveArraySize(hob_Female), age0, age1, age2, age3, age4, age5, age6, age7, meanf, varf, meany, vary, m_shot);
    fclose(POMOut);
    fclose(POMOut2);
}

References THare::GetAge(), Population_Manager::GetLiveArraySize(), THare::GetTotalWeight(), hob_Female, hob_Infant, hob_Juvenile, hob_Male, hob_Young, m_shot, Population_Manager::m_TheLandscape, Landscape::SupplyDayInYear(), Population_Manager::TheArray, and Landscape::Warn().

Referenced by DoFirst().

SetPolyFood()

void THare_Population_Manager::SetPolyFood ( int  a_poly, double  a_value  )

inline

Set polygon food quality.

{ m_PolyFood[a_poly]=a_value; }

References m_PolyFood.

Referenced by THare::ForageSquare(), and THare::ForageSquareP().

SubtractHareDensity()

void THare_Population_Manager::SubtractHareDensity ( int  x, int  y, Hare_Object  a_type  )

inline

Density function - subtracts one from the density in the square containing by x,y. Each square is 256x256m in size.

{ m_DensityMap[a_type][x >> __DENSITYSHIFT][y >> __DENSITYSHIFT]--; }

References m_DensityMap.

Referenced by Hare_Juvenile::st_Dispersal().

TheAOROutputProbe()

void THare_Population_Manager::TheAOROutputProbe ( )

virtual

Output method.

Reimplemented from Population_Manager.

                                                 {
    m_AOR_Probe->DoProbe(hob_Female);
}

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

TheRipleysOutputProbe()

void THare_Population_Manager::TheRipleysOutputProbe ( FILE *  a_prb )

protectedvirtual

Standard spatial output.

Special probe for data to be used in spatial statistics

Reimplemented from Population_Manager.

                                                                  {
  // Currently just counts females
    Hare_Female* FH;
    unsigned totalF= GetLiveArraySize(hob_Female);
    int x,y;
    int w = m_TheLandscape->SupplySimAreaWidth();
    int h = m_TheLandscape->SupplySimAreaHeight();
    fprintf(a_prb,"%d %d %d %d %d\n", 0,w ,0, h, totalF);
    for (unsigned j=0; j<totalF; j++)      //adult females
    {
        FH=dynamic_cast<Hare_Female*>(TheArray[hob_Female][j]);
        x=FH->Supply_m_Location_x();
        y=FH->Supply_m_Location_y();
        fprintf(a_prb,"%d\t%d\n", x,y);
    }
    fflush(a_prb);
}

References Population_Manager::GetLiveArraySize(), hob_Female, Population_Manager::m_TheLandscape, TAnimal::Supply_m_Location_x(), TAnimal::Supply_m_Location_y(), Landscape::SupplySimAreaHeight(), Landscape::SupplySimAreaWidth(), and Population_Manager::TheArray.

Member Data Documentation

BodyBurdenPrb

FILE* THare_Population_Manager::BodyBurdenPrb

protected

Probe for pestidcide output/testing

Referenced by BodyBurdenOut(), Init(), and ~THare_Population_Manager().

m_AdultMortRate

double THare_Population_Manager::m_AdultMortRate

Input variable - Adult mortality rate.

Referenced by DoFirst(), and THare::WasPredated().

m_DensityMap

int THare_Population_Manager::m_DensityMap[8][200][200]

protected

Array storing densities measured in different ways

Referenced by AddHareDensity(), DoFirst(), DoLast(), GetAdultDensity(), GetDelayedAdultDensity(), GetFemaleDensity(), GetInfantDensity(), GetJuvenileDensity(), GetMaleDensity(), GetTotalDensity(), GetYoungDensity(), Init(), and SubtractHareDensity().

m_DMWeight

double THare_Population_Manager::m_DMWeight[5001]

Array for storing minimum acceptable size with age.

Referenced by Init().

m_GoodYearBadYear

float THare_Population_Manager::m_GoodYearBadYear

Variable for adding stochasticity.

Referenced by DoFirst().

m_GrowthEfficiency

double THare_Population_Manager::m_GrowthEfficiency[5001]

protected

Precalculated growth efficiency with size

Referenced by GetGrowthEfficiency(), and Init().

m_GrowthEfficiencyF

double THare_Population_Manager::m_GrowthEfficiencyF[5001]

protected

Precalculated growth efficiency for fat with size

Referenced by GetGrowthEfficiencyF(), and Init().

m_GrowthEfficiencyP

double THare_Population_Manager::m_GrowthEfficiencyP[5001]

protected

Precalculated growth efficiency for protein with size

Referenced by GetGrowthEfficiencyP(), and Init().

m_HareThresholdDD

int THare_Population_Manager::m_HareThresholdDD

Input variable - Threshold density dependence level.

Referenced by Hare_Young::BeginStep(), Hare_Juvenile::BeginStep(), Init(), Hare_Juvenile::st_Foraging(), Hare_Male::st_Foraging(), and Hare_Female::st_Foraging().

m_Interference

double THare_Population_Manager::m_Interference[2500]

protected

Array storing density-dependence effect with density

Referenced by GetInterference(), and Init().

m_JuvMortRate

double THare_Population_Manager::m_JuvMortRate

Input variable - Juvenile mortality rate.

Referenced by Hare_Juvenile::BeginStep(), DoFirst(), and Hare_Juvenile::WasPredated().

m_KJperM

double THare_Population_Manager::m_KJperM[7001]

protected

Precalculated cost of locomotion - KJ per m per kg

Referenced by GetKJperM(), and Init().

m_LitterSize

int THare_Population_Manager::m_LitterSize[12][7]

protected

Storage for litter size distributions (not used in default config)

Referenced by CalcLitterSize(), and GetLitterSize().

m_MaxDailyGrowthEnergy

double THare_Population_Manager::m_MaxDailyGrowthEnergy[5001]

protected

Precalculated max growth energy requirement with size

Referenced by GetMaxDailyGrowthEnergy(), and Init().

m_MaxDailyGrowthEnergyF

double THare_Population_Manager::m_MaxDailyGrowthEnergyF[5001]

protected

Precalculated max growth energy requirement with size for fat

Referenced by GetMaxDailyGrowthEnergyF(), and Init().

m_MaxDailyGrowthEnergyP

double THare_Population_Manager::m_MaxDailyGrowthEnergyP[5001]

protected

Precalculated max growth energy requirement with size for protein

Referenced by GetMaxDailyGrowthEnergyP(), and Init().

m_MortStochast

double THare_Population_Manager::m_MortStochast

protected

Stochasticity around mortality parameters

Referenced by DoFirst(), and Init().

m_OurMRRData

MRR_Data* THare_Population_Manager::m_OurMRRData

protected

Data structure for MarkReleaseRecapture expts

Referenced by Init(), MRROutputs(), and ~THare_Population_Manager().

m_PolyFood

double* THare_Population_Manager::m_PolyFood

protected

Temporary storage

Referenced by DoFirst(), GetPolyFood(), Init(), SetPolyFood(), and ~THare_Population_Manager().

m_RefNums

int THare_Population_Manager::m_RefNums

protected

The last hare ID used

Referenced by GetHareRefNum(), and Init().

m_RMR

double THare_Population_Manager::m_RMR[2][366]

protected

Precalculated RMR with age

Referenced by GetRMR(), and Init().

m_shot

int THare_Population_Manager::m_shot

protected

Hunting Bag.

Referenced by Hunting(), HuntingDifferentiatedBeetleBankArea(), HuntingGrid(), and POMOutputs().

m_variableDD

int THare_Population_Manager::m_variableDD

protected

Used to vary the density dependence each year

Referenced by DoFirst(), and Init().

m_YoungMortRate

double THare_Population_Manager::m_YoungMortRate

Input variable - Young mortality rate.

Referenced by Hare_Infant::BeginStep(), Hare_Young::BeginStep(), and DoFirst().

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

• /builds/a1mass/almass_stable_oddox/Hare/hare_all.h
• /builds/a1mass/almass_stable_oddox/Hare/Hare_all.cpp