The class to handle all predator population related matters. More...

#include <Rabbit_Population_Manager.h>

Inheritance diagram for Rabbit_Population_Manager:

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

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

void	CreateObjects (RabbitObjectTypes ob_type, TAnimal pvo, struct_Rabbit a_data, int a_number)
	Method for creating a new individual Rabbit. More...

TTypesOfRabbitHabitat	ClassifyHabitat (TTypesOfLandscapeElement a_tole)
	Classify a landscape element type according to the rabbit habitat classification. More...

Rabbit_Warren *	FindClosestWarren (int a_x, int a_y, int a_rank)
	Finds the closest warren as the crow flies. More...

void	CheckForRabbitBreedingConditions (void)
	Determines whether it is breeding season. More...

bool	IsBreedingSeason (void)
	Get whether it is breeding season. More...

void	PesticideDeathRecord (RabbitObjectTypes ob_type)
	Records pesticide poisoning incidents. More...

unsigned	SupplyAllBigRabbits ()
	Returns the total number of rabbits. More...

double	GetGrowth (int a_age)
	Get method for the rabbit growth with age. More...

bool	GetForageDay ()
	Get method for the forage day flag. More...

void	ReproOutputRecordOutput (Rabbit_Female *a_female)
	Print reproductive record to file. More...

void	NatalDispersalRecordOutput (Rabbit_Base *a_rabbit)
	Records the natal dispersal. 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 ()

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 ()

bool	OpenTheMonthlyRipleysOutputProbe ()

bool	OpenTheReallyBigProbe ()

virtual void	TheRipleysOutputProbe (FILE *a_prb)

virtual void	TheReallyBigOutputProbe ()

void	CloseTheMonthlyRipleysOutputProbe ()

void	CloseTheRipleysOutputProbe ()

void	CloseTheReallyBigOutputProbe ()

bool	OpenTheCIPEGridOutputProbe ()

virtual void	TheCIPEGridOutputProbe ()

void	CloseTheCIPEGridOutputProbe ()

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)

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

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

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

virtual void	DoLast ()
	Things to do after the EndStep. More...

void	PreProcessWarrenLocations ()
	This pre-scans the landscape and determines all potential warren locations on start-up. More...

bool	WarrenLegalPos (int &a_x, int a_y)
	Tests the warrens list to see if this position is legal. More...

void	SaveWarrenLocations (void)
	Save warren locations. More...

void	LoadWarrenLocations (void)
	Load warren locations. More...

double	AssessPctForage (int a_x, int a_y)
	Assesses the percentage of forage for a location assuming max warren size. More...

void	CreateLocalWarrenNetworkLists (void)
	Forms the local warren network list for this warren. More...

void	WarrenOccupancyRecordOutput ()
	Print warren occupancy record to file. More...

void	PesticideDeathRecordOutput ()
	Print pesticide death record to file. More...

void	PesticideDeathRecordOutputOpen ()
	Opens pesticide death output file. More...

void	PesticideDeathRecordOutputClose ()
	Closes the pesticide death output file. More...

void	WarrenOccupancyRecordOutputOpen ()
	Opens the warren occupancy output file. More...

void	WarrenOccupancyRecordOutputClose ()
	Closes the warren occupancy output file. More...

void	WarrenOutputAnalysis ()
	Does analysis on the warren output file and saves the results to RabbitPOMSummary.txt. More...

void	LifetimeReproAnalysis ()
	Does analysis on the lifetime reproductive output file and saves the results to RabbitPOMSummary.txt. More...

void	NatalDispersalAnalysis ()
	Does analysis on the natal dispersal output file and saves the results to RabbitPOMSummary.txt. More...

void	ReproOutputRecordOutputOpen ()
	Opens the reproductive output file. More...

void	ReproOutputRecordOutputClose ()
	Closes the reproductive output file. More...

void	NatalDispersalRecordOutputOpen ()
	Opens the reproductive output file. More...

void	NatalDispersalRecordOutputClose ()
	Closes the reproductive output file. More...

void	AssignStaticVariables ()
	Assigns any static variables needing config variable assignment. More...

void	TheNWordOutputProbe ()

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	DoAlmostLast ()

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)

virtual void	Catastrophe ()

void	NWordOutput ()
	The output section for the NWord probe. . More...

Protected Attributes
int	m_warrenfixedsize
	Holds an input variable for max warren size in m. More...

int	m_warrenfixedsizediv2
	Half max warren size in m - for speed. More...

bool	m_rabbitBreedingSeason
	The breeding season flag. More...

int	m_reproswitchbuffer
	Prevents continuous breeding season switching. More...

double	m_RabbitGrowth [3650]
	Holds daily growth potential of rabbits for each day. More...

int	m_PesticideDeaths [rob_foobar]
	Holds the number of rabbits killed each day by pesticides. More...

ofstream	m_WarrenOccupancyFile
	The warren occupancy output file. More...

ofstream	m_NatalDispersalFile
	For recording the natal dispersal of adults from birth to death. More...

ofstream	m_ReproOutputFile
	For recording the lifetime reproductive success. More...

ofstream	m_PesticideDeathOFile
	The pesticide death output file. More...

bool	m_forageday
	Flag to record whether today is a possible forage day. More...

Protected Attributes inherited from Population_Manager
vector< unsigned >	m_LiveArraySize

int	m_NoProbes

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 [10]

unsigned	m_ListNameLength

FILE *	TestFile

FILE *	TestFile2

unsigned	BeforeStepActions [10]

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

TTypesOfPopulation	m_population_type

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 *	CIPEGridOutputPrb

FILE *	CIPEGridOutputPrbB

FILE *	ReallyBigOutputPrb

FILE *	NWordOutputPrb

int *	m_cgridcount

int *	m_gridcount [4]

int	m_cgridcountwidth

int	m_gridcountwidth [4]

int	m_cipegridsize

int	m_gridcountsize [4]

long int	lamdagrid [2][257][257]

Additional Inherited Members
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

Detailed Description

The class to handle all predator population related matters.

Definition at line 89 of file Rabbit_Population_Manager.h.

Constructor & Destructor Documentation

Rabbit_Population_Manager::Rabbit_Population_Manager ( Landscape * L )

Rabbit_Population_Manager Constructor.

Loads the list of Animal Classes.

Initialises global parameters/variables.

Creates some rabbits by introducing a number of male and female rabbits aged 100 to 365 days old. The number is defined by the input configuration variable cfg_StartNoRabbits.

The population manager needs to pre-process the landscape map for potential warren locations. This is very time consuming and so it is possible to read in a pre-processed list of locations. However, if this is done then it needs to be made very certain that the list being read in is the correct one for that landscape. No auto checking is possible.

Definition at line 118 of file Rabbit_Population_Manager.cpp.

References AssignStaticVariables(), cfg_rabbitdailygrowthparam1, cfg_rabbitdailygrowthparam2, cfg_rabbitdailygrowthparam3, cfg_RabbitStartNos, cfg_RabbitUseNatalDispersalRecord, cfg_RabbitUseReproOutput, cfg_warrenfixedsize, cfg_warrenreadlocations, CreateLocalWarrenNetworkLists(), CreateObjects(), g_land_width, LoadWarrenLocations(), struct_Rabbit::m_age, Rabbit_Base::m_dispersalmortperm, struct_Rabbit::m_L, Population_Manager::m_ListNameLength, Population_Manager::m_ListNames, Rabbit_Warren::m_maxForageHeight, struct_Rabbit::m_NPM, m_rabbitBreedingSeason, m_RabbitGrowth, m_reproswitchbuffer, Population_Manager::m_SimulationName, Population_Manager::m_TheLandscape, struct_Rabbit::m_Warren, m_warrenfixedsize, m_warrenfixedsizediv2, struct_Rabbit::m_weightage, struct_Rabbit::m_x, struct_Rabbit::m_x2, struct_Rabbit::m_y, struct_Rabbit::m_y2, NatalDispersalRecordOutputOpen(), Population_Manager::OpenTheRipleysOutputProbe(), PesticideDeathRecordOutputOpen(), PreProcessWarrenLocations(), ReproOutputRecordOutputOpen(), rob_Female, rob_Male, SaveWarrenLocations(), Population_Manager::SimH, Population_Manager::SimW, Landscape::SupplySimAreaWidth(), CfgInt::value(), CfgFloat::value(), CfgBool::value(), and WarrenOccupancyRecordOutputOpen().

                                                                  : Population_Manager(L)
 {
     m_ListNames[0] = "Young";
     m_ListNames[1] = "Juvenile";
     m_ListNames[2] = "Male";
     m_ListNames[3] = "Female";
     m_ListNames[4] = "Possible Warrens";
     m_ListNameLength = 5;
     g_land_width = m_TheLandscape->SupplySimAreaWidth(); // Needs the landscape to be square!!!
 
     strcpy( m_SimulationName, "Rabbit Simulation" );
     struct_Rabbit* sp = new struct_Rabbit;
     sp->m_NPM = this;
     sp->m_L = m_TheLandscape;
     sp->m_age = 100+random(265);
     sp->m_Warren = NULL;
     sp->m_x2 = -1;
     sp->m_y2 = -1;
     sp->m_weightage = 300; // Should not be weak animals to start with
 
     for (int i = 0; i< cfg_RabbitStartNos.value(); i++)
     {
         sp->m_x = random(SimW);
         sp->m_y = random(SimH);
         CreateObjects(rob_Male,NULL,sp,1); // 
     }
     for (int i=0; i< cfg_RabbitStartNos.value(); i++) 
     {
         sp->m_x = random(SimW);
         sp->m_y = random(SimH);
         CreateObjects(rob_Female,NULL,sp,1); // 
     }
     delete sp;
     // Load parameters
     Rabbit_Warren::m_maxForageHeight = cfg_maxForageHeight.value();
     Rabbit_Base::m_dispersalmortperm = cfg_dispersalmortperm.value();
     m_warrenfixedsize = cfg_warrenfixedsize.value();
     m_warrenfixedsizediv2 = m_warrenfixedsize / 2;
     m_reproswitchbuffer = 30;
     m_rabbitBreedingSeason = false;
 
     if (cfg_warrenreadlocations.value())
     {
         LoadWarrenLocations();
     }
     else
     {   
         PreProcessWarrenLocations();
         SaveWarrenLocations();
     }
     CreateLocalWarrenNetworkLists();
     // Open output files
     if (cfg_RipleysOutput_used.value()) {
         OpenTheRipleysOutputProbe();
     }
     PesticideDeathRecordOutputOpen();
     if (cfg_RabbitUseReproOutput.value()) ReproOutputRecordOutputOpen();
     if (cfg_RabbitUseNatalDispersalRecord.value()) NatalDispersalRecordOutputOpen();
     WarrenOccupancyRecordOutputOpen();
     // Assign static variable
     AssignStaticVariables();
     // Create the rabbit growth rate lookup data
     for (int i = 1; i < 300; i++) {
         m_RabbitGrowth[i] = cfg_rabbitdailygrowthparam1.value() - (cfg_rabbitdailygrowthparam1.value()*exp(cfg_rabbitdailygrowthparam2.value()*i)) + cfg_rabbitdailygrowthparam3.value();
     }
     // Now fill this in for up to 10 years (no rabbit should ever live that long )
     for (int i = 300; i < 3350; i++) {
         m_RabbitGrowth[ i ] = cfg_rabbitdailygrowthparam1.value() - (cfg_rabbitdailygrowthparam1.value()*exp( cfg_rabbitdailygrowthparam2.value()*300 )) + cfg_rabbitdailygrowthparam3.value();
     }
 
 }

Rabbit_Population_Manager::~Rabbit_Population_Manager ( void )

virtual

Rabbit_Population_Manager Destructor.

Closes the output files created specially for rabbit output. Calls post run analysis routines and then empties any active rabbits from the TheArray deleting the respective rabbit objects.

Definition at line 223 of file Rabbit_Population_Manager.cpp.

References cfg_RabbitUseNatalDispersalRecord, cfg_RabbitUseReproOutput, LifetimeReproAnalysis(), NatalDispersalAnalysis(), NatalDispersalRecordOutputClose(), PesticideDeathRecordOutputClose(), ReproOutputRecordOutputClose(), Population_Manager::TheArray, CfgBool::value(), WarrenOccupancyRecordOutputClose(), and WarrenOutputAnalysis().

 {
     PesticideDeathRecordOutputClose();
     WarrenOccupancyRecordOutputClose();
     if (cfg_RabbitUseReproOutput.value()) {
         ReproOutputRecordOutputClose();
         LifetimeReproAnalysis();
     }
     if (cfg_RabbitUseNatalDispersalRecord.value()) {
         NatalDispersalRecordOutputClose();
         NatalDispersalAnalysis();
     }
     WarrenOutputAnalysis();
     for (unsigned i = 0; i < TheArray.size(); i++) {
     for ( unsigned j = 0; j < TheArray[ i ].size(); j++ ) {
         // This just stops a DEBUG error
         TheArray[ i ] [ j ]->KillThis();
     }
   }
 }

Member Function Documentation

double Rabbit_Population_Manager::AssessPctForage	(	int	a_x,
		int	a_y
	)

protected

Assesses the percentage of forage for a location assuming max warren size.

/**

Parameters

[in]	a_x	the x coordinate for the TL corner of the warren.
[in]	a_y	the y coordinate for the TL corner of the warren.

Returns: The % of are covered by permanent forage.

Loops through the potential warren area and find all the forage and sums this. Then calculate the percentage.

This is done by getting the polygon references and checking if we had this one already. If not save it with an area of 1 otherwise increment the correct record by 1.

Returns the total forage area divided by the total warren area.

Definition at line 549 of file Rabbit_Population_Manager.cpp.

Referenced by PreProcessWarrenLocations().

{

void Rabbit_Population_Manager::AssignStaticVariables ( void )

protected

Assigns any static variables needing config variable assignment.

This is just needed to make the C++ work. Default variables are assigned to static members at start-up, but any that we actually want to get configuration variable values have to be dealt with here

Definition at line 201 of file Rabbit_Population_Manager.cpp.

References struct_Rabbit::m_age, Rabbit_Base::m_dispersalmortperm, struct_Rabbit::m_L, Rabbit_Warren::m_maxForageHeight, Rabbit_Warren::m_minForageDigestability, struct_Rabbit::m_NPM, Rabbit_Base::m_pesticidedegradationrate, Population_Manager::m_TheLandscape, struct_Rabbit::m_Warren, Rabbit_Female::SetMaxKits(), Rabbit_Female::SetMinKits(), and CfgFloat::value().

Referenced by Rabbit_Population_Manager().

 {
     struct_Rabbit* sp = new struct_Rabbit;
     sp->m_NPM = this;
     sp->m_L = m_TheLandscape;
     sp->m_age = 100 + random(265);
     sp->m_Warren = NULL;
     Rabbit_Female* rf = new Rabbit_Female(0,0,-1,-1,m_TheLandscape,this,0, 300,NULL);
     Rabbit_Warren* rw = new Rabbit_Warren(0, 0, m_TheLandscape, this, 0, NULL);
     rw->m_maxForageHeight = cfg_maxForageHeight.value();
     rw->m_minForageDigestability = cfg_minForageDigestability.value();
     rf->m_dispersalmortperm = cfg_dispersalmortperm.value();
     rf->SetMinKits(cfg_rabbitminkits.value());
     rf->SetMaxKits(cfg_rabbitmaxkits.value() - cfg_rabbitminkits.value()); // Here we actually use the difference to calculate range
     rf->m_pesticidedegradationrate = cfg_rabbit_pesticidedegradationrate.value(); // default of 0.0 will remove all body burden pesticide at the end of each day
     delete rw;
     delete rf;
 }

void Rabbit_Population_Manager::CheckForRabbitBreedingConditions ( void )

Determines whether it is breeding season.

Definition at line 732 of file Rabbit_Population_Manager.cpp.

Referenced by DoFirst().

 {
     /*
     * Once the temperature comes up over a certain trigger the breeding seasons starts. Rapid switching is prevented by not making the test again for 120 days.
     * When the temperature in the future drops down again then the breeding season stops
     */
     if (--m_reproswitchbuffer > 0) return;
 
     if (!m_rabbitBreedingSeason)
     {
         if (m_TheLandscape->SupplyTempPeriod(g_date->Date()+60,60) > cfg_rabbitminbreedingtemp.value())
         {
             m_reproswitchbuffer = 120;
             m_rabbitBreedingSeason = true;
 #ifdef __RABBITBREEDINGSEASONCHECK
             cout << g_date->GetYearNumber() << " " << g_date->DayInYear() << " " << m_TheLandscape->SupplyTempPeriod( g_date->Date()+60, 60 ) << " - " << "Started" << endl;
 #endif
         }
     }
     else
     {
 if (m_TheLandscape->SupplyTempPeriod(g_date->Date()+60,60) < cfg_rabbitminbreedingtemp.value() ) 
         {
             m_reproswitchbuffer = 90;
             m_rabbitBreedingSeason = false;
 #ifdef __RABBITBREEDINGSEASONCHECK
             cout << g_date->GetYearNumber() << " " << g_date->DayInYear() << " " << m_TheLandscape->SupplyTempPeriod( g_date->Date()+30, 90 ) << " - " << "Stopped" << endl;
 #endif
         }
     }
 }

TTypesOfRabbitHabitat Rabbit_Population_Manager::ClassifyHabitat ( TTypesOfLandscapeElement a_tole )

Classify a landscape element type according to the rabbit habitat classification.

Parameters

[in] a_tole The type of landscape element

Returns: The type of rabbit habitat represented by the landscape element type.

This is basically a translation function from the element type from the landscape map to the type of habitat it represents for the rabbit. This makes no assessment of the vegetation on the element though.

Definition at line 455 of file Rabbit_Population_Manager.cpp.

References Population_Manager::m_TheLandscape, tole_ActivePit, tole_AmenityGrass, tole_BareRock, tole_BeetleBank, tole_Building, tole_BuiltUpWithParkland, tole_Carpark, tole_Churchyard, tole_Coast, tole_ConiferousForest, tole_Copse, tole_DeciduousForest, tole_Field, tole_FieldBoundary, tole_FishFarm, tole_Freshwater, tole_Garden, tole_Heath, tole_HedgeBank, tole_Hedges, tole_HeritageSite, tole_IndividualTree, tole_LargeRoad, tole_Marsh, tole_MetalledPath, tole_MixedForest, tole_MownGrass, tole_NaturalGrassDry, tole_NaturalGrassWet, tole_Orchard, tole_OrchardBand, tole_Parkland, tole_PermanentSetaside, tole_PermPasture, tole_PermPastureLowYield, tole_PermPastureTussocky, tole_PermPastureTussockyWet, tole_PitDisused, tole_PlantNursery, tole_Pond, tole_Pylon, tole_Railway, tole_River, tole_RiversidePlants, tole_RiversideTrees, tole_RoadsideSlope, tole_RoadsideVerge, tole_Saltmarsh, tole_Saltwater, tole_SandDune, tole_Scrub, tole_SmallRoad, tole_StoneWall, tole_Stream, tole_Track, tole_UnknownGrass, tole_UnsprayedFieldMargin, tole_UrbanNoVeg, tole_UrbanPark, tole_Vildtager, tole_Wasteland, tole_WindTurbine, tole_WoodlandMargin, tole_WoodyEnergyCrop, tole_YoungForest, torh_Cover, torh_Forage, torh_Other, torh_TemporaryForage, and Landscape::Warn().

Referenced by Rabbit_Warren::InitEvaluation(), and WarrenLegalPos().

 {
     static char error_num[ 20 ];
     switch (a_tole)
     {
         case tole_UnsprayedFieldMargin://31
         case tole_Field://20&30
         case tole_RoadsideVerge://13
         case tole_BeetleBank://141
             return torh_TemporaryForage;
             break;
         case tole_Railway://118
         case tole_FieldBoundary://160
         case tole_PermPastureLowYield://26
         case tole_PermPastureTussocky://27
         case tole_PermanentSetaside://33
         case tole_PermPasture://35
         case tole_NaturalGrassDry://110//case tole11
         case tole_PitDisused://75
         case tole_YoungForest://55
         case tole_HedgeBank://140
         case tole_Heath://94
         case tole_Parkland://14
         case tole_SandDune://101
         case tole_Orchard://56
         case tole_RoadsideSlope:  //201
         case tole_HeritageSite:  //208
         case tole_UnknownGrass:
         case  tole_Vildtager:
         case tole_MownGrass:
         case tole_Wasteland:
             return torh_Forage;
             break;
         case tole_Hedges://130
         case tole_Copse://41
         case tole_Scrub://70
         case tole_RiversideTrees://97
         case tole_DeciduousForest://40
         case tole_MixedForest://60
         case tole_ConiferousForest://50
         case tole_WoodlandMargin:
         case tole_WoodyEnergyCrop:
             return torh_Cover;
             break;
         case tole_UrbanPark:  //17
         case tole_NaturalGrassWet:
         case tole_Churchyard: //204
         case tole_Saltmarsh:  //206
         case tole_Stream:  //207
         case tole_Carpark:  //203
         case tole_IndividualTree:  //42
         case tole_MetalledPath:  //202
         case tole_StoneWall://15
         case tole_Garden://11//case tole20
         case tole_Track://123
         case tole_SmallRoad://122
         case tole_LargeRoad://121
         case tole_Building://5
         case tole_ActivePit://115
         case tole_Pond:
         case tole_Freshwater://90
         case tole_FishFarm:
         case tole_River://96
         case tole_Saltwater://80
         case tole_Coast://100
         case tole_UrbanNoVeg://6
         case tole_BuiltUpWithParkland://16
         case tole_AmenityGrass://12
         case tole_OrchardBand://57
         case tole_BareRock://59
         case tole_Marsh://95
         case tole_RiversidePlants://98
         case tole_PlantNursery:
         case tole_Pylon:
         case tole_WindTurbine:
         case  tole_PermPastureTussockyWet:
             return torh_Other;
             break;
         default:
             sprintf( error_num, "%d", a_tole );
             m_TheLandscape->Warn("Rabbit_Warren::InitEvaluation Unknown tole type: ", error_num);
             exit(1);
             break;
     }
 }

void Rabbit_Population_Manager::CreateLocalWarrenNetworkLists ( void )

protected

Forms the local warren network list for this warren.

Loops through all warrens in a double loop and checks if any warrens are within maxWarrenNetworkDist of each other. If so then they are added to the warren local network for that warren. If no warrens are close, then the nearest one is added, so that the list is not empty. This is not optimised because it is only called once - of course it could be done faster.

Definition at line 637 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Population_Manager().

 {
     int sz = (int) TheArray[rob_Warren].size();
     for (int i=0; i< sz; i++) 
     {
         int closest = -1;
         int dist = SimH;
         int mDist = SimH;
         int ourX = TheArray[rob_Warren][i]->Supply_m_Location_x();
         int ourY = TheArray[rob_Warren][i]->Supply_m_Location_y();
         for (int j=0; j< sz; j++) 
         {
             if (i!=j) // Don't add ourselves
             {
                 int theirX = TheArray[rob_Warren][j]->Supply_m_Location_x();
                 int theirY = TheArray[rob_Warren][j]->Supply_m_Location_y();
                 dist = (int) sqrt( (double)(((theirX-ourX)*(theirX-ourX)) + ((theirY-ourY)*(theirY - ourY))) );
                 if (dist < cfg_maxWarrenNetworkDist.value()) 
                 {
                     // Add to the network for this warren
                     LocalWarrenNewtorkEntry LWNE;
                     LWNE.m_aWarren = dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][j]);
                     LWNE.m_dist = dist;
                     dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][i])->AddNetworkConnection( LWNE );
                 }
                 if (dist < mDist) 
                 { 
                     mDist = dist; 
                     closest = j; 
                 }
             }
         }
         if (dist > cfg_maxWarrenNetworkDist.value())
         {
             // Add the closest warren since there are no others
             LocalWarrenNewtorkEntry LWNE;
             LWNE.m_aWarren = dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][closest]);
             LWNE.m_dist = dist;
             dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][i])->AddNetworkConnection( LWNE );
         }
     }
     for (int i=0; i< sz; i++) 
     {
         dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][i])->NetworkEvaluation();
     }
 }

void Rabbit_Population_Manager::CreateObjects	(	RabbitObjectTypes	ob_type,
		TAnimal *	pvo,
		struct_Rabbit *	a_data,
		int	a_number
	)

Method for creating a new individual Rabbit.

Parameters

[in]	ob_type	The type of rabbit to create.
[in]	pvo	unused unless a young is created in which case this points to the mother.
[in]	a_data	A data structure containing the information needed to create the rabbit object.
[in]	a_number	The number of objects to create using a_data.

Creates a_number of new rabbit objects of type ob_type using the information about the rabbit passed in a_data. All rabbit objects created are added to the appropriate rabbit lists held in TheArray. Note that rabbit warrens are also created here to take advantage of the code in TAnimal and population manager handling - I know they are not actually rabbits themselves :)

Warren size is assumed to be 4x the fixed area, this is because low fixed area means low change of less than 100% forage, and rabbits forage quite a distance from the burrow

Definition at line 248 of file Rabbit_Population_Manager.cpp.

References Rabbit_Warren::GetCarryingCapacity(), struct_Rabbit::m_age, struct_Rabbit::m_L, struct_Rabbit::m_NPM, struct_Rabbit::m_soil, struct_Rabbit::m_Warren, m_warrenfixedsize, struct_Rabbit::m_weightage, struct_Rabbit::m_x, struct_Rabbit::m_x2, struct_Rabbit::m_y, struct_Rabbit::m_y2, rob_Female, rob_Juvenile, rob_Male, rob_Warren, rob_Young, and Population_Manager::TheArray.

Referenced by DoFirst(), PreProcessWarrenLocations(), Rabbit_Population_Manager(), Rabbit_Juvenile::st_BecomeAdult(), Rabbit_Young::st_BecomeJuvenile(), and Rabbit_Female::st_GiveBirth().

 {
     switch (ob_type)
     {
     case rob_Young:
        Rabbit_Young*  new_RabbitY;
        for (int i=0; i<a_number; i++)
        {
            new_RabbitY = new Rabbit_Young(a_data->m_x, a_data->m_y, a_data->m_x2, a_data->m_y2, dynamic_cast<Rabbit_Female*>(pvo), a_data->m_L, a_data->m_NPM, a_data->m_Warren);
            TheArray[ob_type].push_back(new_RabbitY);
            dynamic_cast<Rabbit_Female*>(pvo)->AddYoung(new_RabbitY);
        }
        break;
     case rob_Juvenile:
        Rabbit_Juvenile*  new_RabbitJ;
        for (int i=0; i<a_number; i++)
        {
            new_RabbitJ = new Rabbit_Juvenile(a_data->m_x, a_data->m_y, a_data->m_x2, a_data->m_y2, dynamic_cast<Rabbit_Female*>(pvo), a_data->m_L, a_data->m_NPM, a_data->m_age, a_data->m_weightage, a_data->m_Warren);
            TheArray[ob_type].push_back(new_RabbitJ);
        }
        break;
     case rob_Male:
        Rabbit_Male*  new_RabbitM;
        for (int i=0; i<a_number; i++)
        {
            new_RabbitM = new Rabbit_Male(a_data->m_x, a_data->m_y, a_data->m_x2, a_data->m_y2, a_data->m_L, a_data->m_NPM, a_data->m_age, a_data->m_weightage, a_data->m_Warren);
            TheArray[ob_type].push_back(new_RabbitM);
        }
        break;
     case rob_Female:
        Rabbit_Female*  new_RabbitF;
        for (int i=0; i<a_number; i++)
        {
            new_RabbitF = new Rabbit_Female(a_data->m_x, a_data->m_y, a_data->m_x2, a_data->m_y2, a_data->m_L, a_data->m_NPM, a_data->m_age, a_data->m_weightage, a_data->m_Warren);
            TheArray[ob_type].push_back(new_RabbitF);
        }
        break;
     case rob_Warren:
        Rabbit_Warren*  new_RabbitW;
        for (int i=0; i<a_number; i++)
        {
            new_RabbitW = new Rabbit_Warren(a_data->m_x, a_data->m_y, a_data->m_L, a_data->m_NPM, m_warrenfixedsize, a_data->m_soil); 
            if (new_RabbitW->GetCarryingCapacity()>0)   TheArray[ob_type].push_back(new_RabbitW);
            else delete new_RabbitW;
        }
        break;
     }
 }

virtual void Rabbit_Population_Manager::DoAfter ( )

inlineprotectedvirtual

Things to do before the EndStep.

Reimplemented from Population_Manager.

Definition at line 156 of file Rabbit_Population_Manager.h.

156 {}

virtual void Rabbit_Population_Manager::DoBefore ( )

inlineprotectedvirtual

Things to do before the Step.

Reimplemented from Population_Manager.

Definition at line 154 of file Rabbit_Population_Manager.h.

154 {}

void Rabbit_Population_Manager::DoFirst ( )

protectedvirtual

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

Reimplemented from Population_Manager.

Definition at line 310 of file Rabbit_Population_Manager.cpp.

References cfg_rabbitdiseasedensitydependencedelay, cfg_rabbitmaxforagerainfall, cfg_rabbitminimumforagetemp, CheckForRabbitBreedingConditions(), CreateObjects(), struct_Rabbit::m_age, m_forageday, struct_Rabbit::m_L, struct_Rabbit::m_NPM, m_PesticideDeaths, Population_Manager::m_TheLandscape, struct_Rabbit::m_Warren, struct_Rabbit::m_weightage, struct_Rabbit::m_x, struct_Rabbit::m_x2, struct_Rabbit::m_y, struct_Rabbit::m_y2, rob_Female, rob_foobar, rob_Male, rob_Warren, rob_Young, Population_Manager::SimH, Population_Manager::SimW, Landscape::SupplyDayInYear(), Landscape::SupplyRain(), Landscape::SupplyTemp(), Landscape::SupplyYearNumber(), Population_Manager::TheArray, CfgInt::value(), and CfgFloat::value().

 {
 #ifdef __RABBITDEBUG2
     if (m_TheLandscape->SupplyYearNumber()== 1000)
         if (m_TheLandscape->SupplyDayInYear() == 1) {
             struct_Rabbit* sp = new struct_Rabbit;
             sp->m_NPM = this;
             sp->m_L = m_TheLandscape;
             sp->m_age = 100 + random( 265 );
             sp->m_Warren = NULL;
             sp->m_x2 = -1;
             sp->m_y2 = -1;
             sp->m_weightage = 300; // Should not be weak animals to start with
 
             for (int i = 0; i< 500; i++) {
                 sp->m_x = random( SimW );
                 sp->m_y = random( SimH );
                 CreateObjects( rob_Male, NULL, sp, 1 ); // 
             }
             for (int i = 0; i< 500; i++) {
                 sp->m_x = random( SimW );
                 sp->m_y = random( SimH );
                 CreateObjects( rob_Female, NULL, sp, 1 ); // 
             }
             delete sp;
         }
 #endif
     CheckForRabbitBreedingConditions(); 
     for (int r = (int)rob_Young; r < (int)rob_foobar; r++)
     {
         m_PesticideDeaths[r] = 0;
     }
     // Manage warren disease
     if (m_TheLandscape->SupplyDayInYear() % cfg_rabbitdiseasedensitydependencedelay.value() == 0)
     {
         for (unsigned i = 0; i < TheArray[rob_Warren].size(); i++) dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][i])->CalcDisease();
     }
     // Determine whether today is forage day
     double rainfall = m_TheLandscape->SupplyRain();
     double temp = m_TheLandscape->SupplyTemp();
     if ((temp<cfg_rabbitminimumforagetemp.value()) || (rainfall>cfg_rabbitmaxforagerainfall.value())) m_forageday = false; else m_forageday = true;
 }

void Rabbit_Population_Manager::DoLast ( )

protectedvirtual

Things to do after the EndStep.

For POM testing the following records have been added to the output:

The mean number of litters per female
Natal dispersal% for each sex
Lifetime reproductive success (no kits and mean litter size) (on death of rabbit)

Reimplemented from Population_Manager.

Definition at line 358 of file Rabbit_Population_Manager.cpp.

References cfg_warrenoccupancyrecordday, Population_Manager::m_TheLandscape, PesticideDeathRecordOutput(), Landscape::SupplyDayInYear(), CfgInt::value(), and WarrenOccupancyRecordOutput().

 {
     int today = m_TheLandscape->SupplyDayInYear();
     // Do the output jobs
     // Pesticide deaths
     PesticideDeathRecordOutput(); 
     // Warren occupancy
     if (today == cfg_warrenoccupancyrecordday.value()) WarrenOccupancyRecordOutput();
 }

Rabbit_Warren * Rabbit_Population_Manager::FindClosestWarren	(	int	a_x,
		int	a_y,
		int	a_rank
	)

Finds the closest warren as the crow flies.

Parameters

[in]	a_x	the x coordinate for the TL corner of the warren.
[in]	a_y	the y coordinate for the TL corner of the warren.
[in]	a_rank	the nth rank closest warren to return

Returns: a pointer to the nth rank closest warren. If none returns NULL.

Loops through all warrens and calculates the distance to a_x, a_y. Returns the one ranked 'a_rank' closest as the crow flies. Can handle up to 10 ranks - it will cause an error to ask for more. This is used for the occaisions where the closest warren is one the rabbit knows already, so don't ask for that one.

Definition at line 689 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Male::st_EvaluateTerritory(), and Rabbit_Female::st_EvaluateTerritory().

 {
     int results[10];
     int dist;
     TAnimal* ptrs[10];
     for (int r = 0; r < 10; r++) {
         results[ r ] = SimH*SimW;
         ptrs[ r ] = NULL;
     }
     int sz = (int) TheArray[rob_Warren].size();
     for (int i=0; i< sz; i++) 
     {
         int X = TheArray[rob_Warren][i]->Supply_m_Location_x();
         int Y = TheArray[rob_Warren][i]->Supply_m_Location_y();
         dist = (int)sqrt( ((double( X - a_x )*double( X - a_x )) + (double( Y - a_y )*double( Y - a_y ))) );
         for (int r=0; r<10; r++)
         {
             if (dist<=results[r])
             {
                 for (int t=r+1; t<10; t++)
                 {
                     results[t]=results[t-1];
                     ptrs[t]=ptrs[t-1];
                 }
                 results[r]=dist;
                 ptrs[r]=TheArray[rob_Warren][i];
                 break;
             }
         }
     }
     Rabbit_Warren*  rw = dynamic_cast<Rabbit_Warren*>(ptrs[ a_rank ]);
     return rw;
 }

bool Rabbit_Population_Manager::GetForageDay ( )

inline

Get method for the forage day flag.

Definition at line 123 of file Rabbit_Population_Manager.h.

Referenced by Rabbit_Adult::EndStep(), Rabbit_Young::st_Develop(), Rabbit_Juvenile::st_Develop(), and Rabbit_Warren::st_WarrenBeing().

                         {
        return m_forageday;
    }

double Rabbit_Population_Manager::GetGrowth ( int a_age )

inline

Get method for the rabbit growth with age.

Definition at line 116 of file Rabbit_Population_Manager.h.

Referenced by Rabbit_Adult::EndStep(), Rabbit_Adult::Rabbit_Adult(), Rabbit_Juvenile::Rabbit_Juvenile(), Rabbit_Young::st_Develop(), and Rabbit_Juvenile::st_Develop().

                                  {
 //     if ((a_age < 0) || (a_age >= 3650)) {
 //         int rubbish = 1;
 //     }
        return m_RabbitGrowth[ a_age ];
    }

bool Rabbit_Population_Manager::IsBreedingSeason ( void )

inline

Get whether it is breeding season.

Definition at line 106 of file Rabbit_Population_Manager.h.

Referenced by Rabbit_Female::st_GiveBirth(), Rabbit_Female::st_UpdateBreedingStatus(), and Rabbit_Warren::st_WarrenBeing().

106 { return m_rabbitBreedingSeason; }

Rabbit_Population_Manager::m_rabbitBreedingSeason

bool m_rabbitBreedingSeason

The breeding season flag.

Definition: Rabbit_Population_Manager.h:133

void Rabbit_Population_Manager::LifetimeReproAnalysis ( )

protected

Does analysis on the lifetime reproductive output file and saves the results to RabbitPOMSummary.txt.

Definition at line 1058 of file Rabbit_Population_Manager.cpp.

Referenced by ~Rabbit_Population_Manager().

                                                       {
     /*
     % Success   0.66
     Average litters( of reproducers )   4.39
     Av.Total Offspring  21.13
     Mean Repro Age  348.26
     Max Repro Age   2069.00
     */
     int Year, Day, Age, Offspring, Litter;
     double NoSuccessfulReproducers = 0;
     double NoOffspring = 0;
     double TotalAdults = 0;
     double ZeroLitters = 0;
     double TotalLitters = 0;
     double AvNoYoungLitter = 0;
     double AvLittersPerFemale = 0;
     double AvTotalOffspring = 0;
     double pctSuccess = 0;
     double MeanReproAge = 0;
     double SumReproAge = 0;
     double MaxReproAge = 0;
     double sumunderage = 0;
     double sumunderageoffspring = 0;
 
     ifstream ReproFile( "RabbitLifetimeReproRecord.txt", ios::in );
     // Read the header line
     char st[ 2000 ];
     ReproFile.getline( st, 2000 );
     ReproFile >> Year >> Day >> Age >> Offspring >> Litter;
     while (!ReproFile.eof()) {
         if (Year > 2000) {
             if (Age >= 304) {
                 TotalAdults++;
                 SumReproAge += Age - 304;
                 if (Litter > 0) {
                     TotalLitters += Litter;
                     NoSuccessfulReproducers++;
                     if (MaxReproAge < Age - 304) MaxReproAge = Age - 304;
                 }
                 else ZeroLitters++;
                 NoOffspring += Offspring;
             }
             else if (Litter > 0) {
                 sumunderage++;
                 sumunderageoffspring += Offspring;
             }
         }
         ReproFile >> Year >> Day >> Age >> Offspring >> Litter;
     }
     if (TotalLitters > 0) AvNoYoungLitter = NoOffspring / TotalLitters;
     if (TotalAdults > 0) {
         MeanReproAge = SumReproAge / TotalAdults;
         pctSuccess = NoSuccessfulReproducers / TotalAdults;
         AvLittersPerFemale = TotalLitters / NoSuccessfulReproducers;
     }
     AvTotalOffspring = AvLittersPerFemale * AvNoYoungLitter;
     ofstream ofile( "RabbitPOMSummary.txt", ios::app );
     ofile << NoSuccessfulReproducers
         << '\t' << TotalLitters
         << '\t' << NoOffspring
         << '\t' << pctSuccess
         << '\t' << AvTotalOffspring
         << '\t' << AvNoYoungLitter
         << '\t' << AvLittersPerFemale
         << '\t' << MeanReproAge
         << '\t' << MaxReproAge
         << '\t' << sumunderage
         << '\t' << sumunderageoffspring << '\t';
     ofile.close();
 }

void Rabbit_Population_Manager::LoadWarrenLocations ( void )

protected

Load warren locations.

If warren locations are not to be calculated then they are loaded from a standard file called "RabbitWarrenLocations.txt". If the wrong file is used there is no error checking and the result is usually a mysterious crash or strange results. Great care must be taken to ensure this does not happen.

Definition at line 607 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Population_Manager().

 {
     ifstream ifile(cfg_warrenlocationsfile.value());
     if ( !ifile.is_open() ) 
     {
         g_msg->Warn("Rabbit_Population_Manager::LoadWarrenLocations() Cannot open file: ", cfg_warrenlocationsfile.value());
       exit( 1 );
     }
     int sz;
     ifile >> sz;
     for (int i=0; i< sz; i++) 
     {
         int x,y,s;
         ifile >> x >> y >> s;
         struct_Rabbit sR;
         sR.m_NPM = this;
         sR.m_L = m_TheLandscape;
         sR.m_x = x;
         sR.m_y = y;
         sR.m_soil = s;
         CreateObjects(rob_Warren,NULL,&sR,1); 
     }
     ifile.close();
 }

void Rabbit_Population_Manager::NatalDispersalAnalysis ( )

protected

Does analysis on the natal dispersal output file and saves the results to RabbitPOMSummary.txt.

Definition at line 1130 of file Rabbit_Population_Manager.cpp.

Referenced by ~Rabbit_Population_Manager().

                                                        {
     int year, day, bornx, borny, newx, newy, sex;
     int sedmales = 0;
     int sedfemales = 0;
     int dispmales = 0;
     int dispfemales = 0;
     double malenataldisp = 0;
     double femalenataldisp = 0;
     ifstream DispFile( "RabbitNatalDispersalRecord.txt", ios::in );
     // Read the header line
     char st[ 2000 ];
     DispFile.getline( st, 2000 );
     DispFile >> year >> day >> bornx >> borny >> newx >> newy >> sex;
     while (!DispFile.eof()) {
         if (year > 2000) {
             if ((bornx != newx) || (borny != newy)) {
                 if (sex == 2) dispmales++; else dispfemales++;
             }
             else if (sex == 2) sedmales++; else sedfemales++;
         }
         DispFile >> year >> day >> bornx >> borny >> newx >> newy >> sex;
     }
     if ((dispmales + sedmales)>0) malenataldisp = dispmales / double( dispmales + sedmales );
     if ((dispfemales + sedfemales)>0) femalenataldisp = dispfemales / double( dispfemales + sedfemales );
     ofstream ofile( "RabbitPOMSummary.txt", ios::app );
     ofile << malenataldisp  << '\t' << femalenataldisp << '\t';
     ofile.close();
 }

void Rabbit_Population_Manager::NatalDispersalRecordOutput ( Rabbit_Base * a_rabbit )

Records the natal dispersal.

If this method is called it records the current location as well as the location of birth to allow natal dispersal calculations.

Definition at line 909 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Base::BeginStep().

 {
     m_NatalDispersalFile << m_TheLandscape->SupplyYear() << '\t' << m_TheLandscape->SupplyDayInYear() << '\t';
     APoint pt = a_rabbit->GetBornLocation();
     m_NatalDispersalFile << pt.m_x << '\t' << pt.m_y << '\t' << a_rabbit->Supply_m_Location_x() << '\t' << a_rabbit->Supply_m_Location_y() << '\t' << a_rabbit->GetRabbitType() << endl;
 }

void Rabbit_Population_Manager::NatalDispersalRecordOutputClose ( )

protected

Closes the reproductive output file.

Definition at line 928 of file Rabbit_Population_Manager.cpp.

Referenced by ~Rabbit_Population_Manager().

 {
     m_NatalDispersalFile.close();
 }

void Rabbit_Population_Manager::NatalDispersalRecordOutputOpen ( )

protected

Opens the reproductive output file.

Definition at line 920 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Population_Manager().

 {
     m_NatalDispersalFile.open("RabbitNatalDispersalRecord.txt", ios::out);
     m_NatalDispersalFile << "Year" << '\t' << "Day" << '\t';
     m_NatalDispersalFile << "Born_X" << '\t' << "Born_Y" << '\t' << "New_X" << '\t' << "New_Y" << '\t' << "Rabbit_Type" << endl;
 }

void Rabbit_Population_Manager::PesticideDeathRecord ( RabbitObjectTypes ob_type )

Records pesticide poisoning incidents.

Definition at line 765 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Base::GeneralOrganoPhosphate(), and Rabbit_Female::st_GiveBirth().

 {
     m_PesticideDeaths[a_ob]++;
 }

void Rabbit_Population_Manager::PesticideDeathRecordOutput ( )

protected

Print pesticide death record to file.

Simply records the number of different types of rabbits that died of direct pesticide poisoning and the date it happened.

Definition at line 849 of file Rabbit_Population_Manager.cpp.

Referenced by DoLast().

 {
     m_PesticideDeathOFile << m_TheLandscape->SupplyYear() << '\t' << m_TheLandscape->SupplyDayInYear() << '\t';
     for (int r = (int)rob_Young; r < (int)rob_foobar; r++)
     {
         m_PesticideDeathOFile << '\t' << m_PesticideDeaths[r];
     }
     m_PesticideDeathOFile << endl;
 }

void Rabbit_Population_Manager::PesticideDeathRecordOutputClose ( )

protected

Closes the pesticide death output file.

Definition at line 879 of file Rabbit_Population_Manager.cpp.

Referenced by ~Rabbit_Population_Manager().

 {
     m_PesticideDeathOFile.close();
 }

void Rabbit_Population_Manager::PesticideDeathRecordOutputOpen ( )

protected

Opens pesticide death output file.

Definition at line 863 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Population_Manager().

 {
     m_PesticideDeathOFile.open("RabbitPesticideDeathRecord.txt", ios::out);
 }

void Rabbit_Population_Manager::PreProcessWarrenLocations ( )

protected

This pre-scans the landscape and determines all potential warren locations on start-up.

Scans the landscape from random,random to width,height, then 0,0 to start location. Moves left to right, then top to bottom. At every location a rabbit warren is possible one is created with no population. Soil type determines the density of burrows possible and alters the requirements for fixed forage. Two options are availabe, 1. calculate the soiltype from the information present in the landscape (if this is present); 2. Read the soil type from a config variable and assume the whole landscape is of this type. see cfg_rabbit_fix_soiltype and cfg_rabbit_use_fixed_soiltype Warrens cannot overlap their fixed areas (they can overlap forage though) and must contain a minimum proportion of fixed forage which varies with soil type.

If the warren position is possible then we need to assess the element contents. This should be above a minimum % fixed forage.

If forage percentages is OK then we can make a warren here, so an empty warren location is created. Note that the Rabbit_Warren constructor takes care of ensuring the warren is intiated to being 'virgin'.

Definition at line 376 of file Rabbit_Population_Manager.cpp.

References AssessPctForage(), cfg_rabbit_fix_soiltype, cfg_rabbit_use_fixed_soiltype, CreateObjects(), struct_Rabbit::m_L, struct_Rabbit::m_NPM, struct_Rabbit::m_soil, Population_Manager::m_TheLandscape, m_warrenfixedsize, struct_Rabbit::m_x, struct_Rabbit::m_y, rob_Warren, Population_Manager::SimH, Population_Manager::SimW, Landscape::SupplySoilTypeR(), Population_Manager::TheArray, CfgInt::value(), CfgBool::value(), and WarrenLegalPos().

Referenced by Rabbit_Population_Manager().

 {
     cout << "Preprocessing Warren Locations" << endl;
     int x = 0;
     int y = 0;
     int soil = 0;
     for (int j=y; j<SimH-m_warrenfixedsize; j++)
     {
         for (int i=x; i<SimW-m_warrenfixedsize; i++)
         {
             if ( WarrenLegalPos(i,j) )
             {
                 if (cfg_rabbit_use_fixed_soiltype.value()) soil = cfg_rabbit_fix_soiltype.value();
                 else
                 {
                     soil = m_TheLandscape->SupplySoilTypeR(i, j);
                 }
                 double pct = AssessPctForage(i,j);
                 if ((soil) != 3)  // Soil type 3 is unsuitable therefore skipped
                 {
                     // Soil type 1 is sandy, 0 is chalk or otherwise hard soil
                     if (pct >= 1.0)
                     {
                         struct_Rabbit sR;
                         sR.m_NPM = this;
                         sR.m_L = m_TheLandscape;
                         sR.m_x = i;
                         sR.m_y = j;
                         sR.m_soil = soil;
                         CreateObjects(rob_Warren, NULL, &sR, 1);
                         --i += m_warrenfixedsize;
                         if (static_cast<unsigned>(TheArray.size()) % 1000 == 0) cout << TheArray.size() << '\t';
                     }
                 }
             }
         }
     }
 }

void Rabbit_Population_Manager::ReproOutputRecordOutput ( Rabbit_Female * a_female )

Print reproductive record to file.

Records the age and reproductive output of the rabbit and the date it died

Definition at line 885 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Female::st_Dying().

 {
     m_ReproOutputFile << m_TheLandscape->SupplyYear() << '\t' << m_TheLandscape->SupplyDayInYear() << '\t';
     m_ReproOutputFile << '\t' << a_female->GetAge() << '\t' << a_female->GetTotalOffspring() << '\t' << a_female->GetTotalLitters() << endl;
 }

void Rabbit_Population_Manager::ReproOutputRecordOutputClose ( )

protected

Closes the reproductive output file.

Definition at line 903 of file Rabbit_Population_Manager.cpp.

Referenced by ~Rabbit_Population_Manager().

 {
     m_ReproOutputFile.close();
 }

void Rabbit_Population_Manager::ReproOutputRecordOutputOpen ( )

protected

Opens the reproductive output file.

Definition at line 895 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Population_Manager().

 {
     m_ReproOutputFile.open( "RabbitLifetimeReproRecord.txt", ios::out );
     m_ReproOutputFile << "Year" << '\t' << "Day" << '\t';
     m_ReproOutputFile << '\t' << "Age" << '\t' << "Offpring" << '\t' << "Litters" << endl;
 }

void Rabbit_Population_Manager::SaveWarrenLocations ( void )

protected

Save warren locations.

Save the warren locations to "RabbitWarrenLocations.txt" so that these can be loaded again without having to go through the pre-process warren network step each time a landscape is used.

Definition at line 585 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Population_Manager().

 {
     ofstream ofile(cfg_warrenlocationsfile.value());
     if ( !ofile.is_open() ) 
     {
         g_msg->Warn("Rabbit_Population_Manager::SaveWarrenLocations() Cannot open file: ", cfg_warrenlocationsfile.value());
       exit( 1 );
     }
     int sz = (int) TheArray[rob_Warren].size();
     ofile << sz << endl;
     for (int i=0; i< sz; i++) 
     {
         Rabbit_Warren* awarren = dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][i]);
         ofile << awarren->Supply_m_Location_x() - m_warrenfixedsizediv2 << '\t' << awarren->Supply_m_Location_y() - m_warrenfixedsizediv2 << '\t' << awarren->GetSoilType() << endl;
     }
     ofile.close();
 }

unsigned Rabbit_Population_Manager::SupplyAllBigRabbits ( )

inline

Returns the total number of rabbits.

Definition at line 110 of file Rabbit_Population_Manager.h.

References rob_foobar, and rob_Male.

Referenced by Rabbit_Warren::CalcDisease().

                                   {
        unsigned sum = 0;
        for (unsigned r = rob_Male; r < rob_foobar; r++) sum += (unsigned) TheArray[r].size();
        return sum;
    }

void Rabbit_Population_Manager::TheNWordOutputProbe ( )

protectedvirtual

Calculates the AOR data for output for the Rabbit

Output file facility added in November 2009

Reimplemented from Population_Manager.

Definition at line 1160 of file Rabbit_Population_Manager.cpp.

                                                     {
     Rabbit_Female* FS;
     unsigned int totalF = (unsigned int)TheArray[ rob_Female ].size();
     int x, y;
     int totalcells[ 4 ];
     for (int grid = 0; grid<4; grid++) {
         totalcells[ grid ] = m_gridcountwidth[ grid ] * m_gridcountwidth[ grid ];
         for (int i = 0; i<totalcells[ grid ]; i++) m_gridcount[ grid ][ i ] = 0;
         for (unsigned j = 0; j<totalF; j++)      //adult females
         {
             FS = dynamic_cast<Rabbit_Female*>(TheArray[ rob_Female ][ j ]);
             x = FS->Supply_m_Location_x();
             y = FS->Supply_m_Location_y();
             int gx = x / m_gridcountsize[ grid ]; // 50, 100, 200, 400
             int gy = y / m_gridcountsize[ grid ];
             m_gridcount[ grid ][ gx + gy*m_gridcountwidth[ grid ] ]++;
         }
     }
     NWordOutput();
 }

bool Rabbit_Population_Manager::WarrenLegalPos	(	int &	a_x,
		int	a_y
	)

protected

Tests the warrens list to see if this position is legal.

Parameters

[in]	a_x	The x-coordinate to assess
[in]	a_y	The x-coordinate to assess

Returns: Whether the location is a legal one for a warren

Loops through all warrens and asks whether they are closer than m_warrenfixedsize, if so returns false. Must loop through all warrens to return true.

Todo:: Use a temporary binary map to achieve this without the loop - speed optimisation if we have time.

Definition at line 429 of file Rabbit_Population_Manager.cpp.

References ClassifyHabitat(), Population_Manager::m_TheLandscape, m_warrenfixedsize, m_warrenfixedsizediv2, rob_Warren, Landscape::SupplyElementType(), Population_Manager::TheArray, and torh_Forage.

Referenced by PreProcessWarrenLocations().

 {
     if (ClassifyHabitat(m_TheLandscape->SupplyElementType(a_x+m_warrenfixedsizediv2,a_y+m_warrenfixedsizediv2)) != torh_Forage) return false;
     // If it is not in a warren already then we are legal here. 
     int sz = (int) TheArray[rob_Warren].size();
     for (int i=0; i< sz; i++) 
     {
         APoint pt = dynamic_cast<Rabbit_Warren*>(TheArray[rob_Warren][i])->SupplyPoint();   
         if ((abs(pt.m_x-a_x) < m_warrenfixedsize) && (abs(pt.m_y-a_y) < m_warrenfixedsize))
         {
             a_x += m_warrenfixedsize;
             return false;
         }
     }
     return true;
 }

void Rabbit_Population_Manager::WarrenOccupancyRecordOutput ( )

protected

Print warren occupancy record to file.

Produces a record of mean warren occupancy, number of burrows, disease level, and a a measure of variation in occupancy (CV of occupancy).
For convenience some global stats on population numbers are also produced here.

Definition at line 771 of file Rabbit_Population_Manager.cpp.

Referenced by DoLast().

                                                             {
     ofstream warrenrecord( "WarrenOccupancyRecord.txt", ios::app );
     double occupancy = 0;
     double var_occupancy = 0;
     double sumsqr = 0.0;
     double totalrabbits = 0;
     double burrows = 0;
     double disease = 0;
     int warrensoccupied = 0;
     int kits = 0;
     int juvs = 0;
     int ads = 0;
     int breedingfemales = 0;
     double breedingfemalesAv = 0;
     int oneyroldfemales = 0;
     int nonbreedingfemales = 0;
     int litters = 0;
     double lrc = 0;
     double n = (double)TheArray[ rob_Warren ].size();
     for (unsigned i = 0; i < TheArray[ rob_Warren ].size(); i++) {
         Rabbit_Warren* warren = dynamic_cast<Rabbit_Warren*>(TheArray[ rob_Warren ][ i ]);
         double occ = warren->GetCarryingCapacityRatio();
         occupancy += occ;
         sumsqr += occ * occ;
         totalrabbits += warren->GetPopulationSize();
         if (warren->GetPopulationSize()>0) warrensoccupied++;
         burrows += warren->GetCarryingCapacity();
         disease += warren->GetDiseaseConstant();
         kits += warren->GetRabbitProductionRecord( rob_Young );
         juvs += warren->GetRabbitProductionRecord( rob_Juvenile );
         ads += warren->GetRabbitProductionRecord( rob_Male );
         ads += warren->GetRabbitProductionRecord( rob_Female );
         warren->UpdateThisYearsBreeders();
         breedingfemales += warren->GetThisYearsBreeders();
         breedingfemalesAv += warren->GetThisYearsBreedersAv();
         oneyroldfemales += warren->GetThisYears1yrOldFemales();
         nonbreedingfemales += warren->GetThisYearsNonBreeders();
         litters += warren->GetLittersThisYear();
         lrc += warren->GetLitterReabsortionConst();
         warren->ResetAllRabbitProductionRecord();
     }
     double littersperfemale = 0;
     double CV_occ = 0;
     if ((occupancy > 0) && (ads > 0)) {
         var_occupancy = (sumsqr - (occupancy*occupancy) / n) / (n - 1);
         if (var_occupancy < 0) var_occupancy = 0.0; // Rounding errors cause this
         occupancy /= n;
         burrows /= n;
         disease /= n;
         totalrabbits /= n;
         kits /= (int)n;
         juvs /= (int)n;
         ads /= (int)n;
         CV_occ = sqrt( var_occupancy ) / occupancy;
         if (breedingfemales > 0) littersperfemale = litters / double( breedingfemales );
     }
     else {
         var_occupancy = 0;
         occupancy = 0;
         burrows = 0;
         disease = 0;
         totalrabbits = 0;
         kits = 0;
         juvs = 0;
         ads = 0;
         CV_occ = 0;
     }
     lrc /= n;
     warrenrecord << m_TheLandscape->SupplyYearNumber() << '\t' << m_TheLandscape->SupplyDayInYear() << '\t' << (int)n << '\t' << warrensoccupied << '\t' << burrows << '\t' << totalrabbits << '\t' << disease << '\t' << occupancy << '\t' << CV_occ << '\t' << kits << '\t' << juvs << '\t' << ads;
     for (int r = (int)rob_Young; r < rob_Warren; r++) warrenrecord << '\t' << TheArray[ r ].size();
     warrenrecord << '\t' << breedingfemales << '\t' << breedingfemalesAv << '\t' << oneyroldfemales << '\t' << nonbreedingfemales << '\t' << littersperfemale << '\t' << lrc << '\t' << litters << endl;
 }

void Rabbit_Population_Manager::WarrenOccupancyRecordOutputClose ( )

protected

Closes the warren occupancy output file.

Definition at line 934 of file Rabbit_Population_Manager.cpp.

Referenced by ~Rabbit_Population_Manager().

 {
     m_WarrenOccupancyFile.close();
 }

void Rabbit_Population_Manager::WarrenOccupancyRecordOutputOpen ( )

protected

Opens the warren occupancy output file.

Definition at line 869 of file Rabbit_Population_Manager.cpp.

Referenced by Rabbit_Population_Manager().

 {
     m_WarrenOccupancyFile.open("WarrenOccupancyRecord.txt", ios::out);
     m_WarrenOccupancyFile << "Year" << '\t' << "Day" << '\t' << "No. Warrens" << '\t' << "No.Occ.Warrens" << '\t' << "Mean Burrows" << '\t' << "Mean Rabbits" << '\t' << "Mean Disease" 
         << '\t' << "Mean Occupancy" << '\t' << "CV Occupancy" << '\t' << "Mean Kits" << '\t' << "Mean Juvs" << '\t' << "Mean Ads" << '\t' << "TotalYoung" << '\t' << "TotalJuvs" 
         << '\t' << "TotalMales" << '\t' << "TotalFemales" << '\t' << "BreedingFemales" << '\t' << "BreedingDensityAv" << '\t' << "1yr old females" << '\t' << "NonBreedingFems.>1yr" 
         << '\t' << "Littersperfemale" << '\t' << "lrc" << '\t' << "litters" << endl;
 }

void Rabbit_Population_Manager::WarrenOutputAnalysis ( )

protected

Does analysis on the warren output file and saves the results to RabbitPOMSummary.txt.

Definition at line 940 of file Rabbit_Population_Manager.cpp.

Referenced by ~Rabbit_Population_Manager().

                                                      {
     double Year, Day, NoWarrens, NoOccWarrens, MeanBurrows, MeanRabbits, MeanDisease, MeanOccupancy, CVOccupancy, MeanKits, MeanJuvs, MeanAds, TotalYoung, TotalJuvs, TotalMales,
         TotalFemales, BreedingFemales, yroldfemales, NonBreedingFems;
     vector<double>  totalfemales;
     vector<double>  totalbrfemalesdensity;
     vector<double>  nonbreedingdensity;
     vector<double>  yrolddensity;
     vector<double>  breedingdensity;
     vector<double>  yearlingpct;
     vector<double>  kitsperfemale;
 
     double meantotalbrpop;
     double maxbreedingpop = -1;
     double minbreedingpop = 100000;
     double maxyroldspct = -1;
     double minyroldspct = 100000;
     double correlation;
     double correlation_b;
     double littersperfemale;
     double lrc;
     double BreedingDensityAv;
     double litters;
 
 
     ifstream WarrenOccupancyFile( "WarrenOccupancyRecord.txt", ios::in );
     // Read the header line
     char st[ 2000 ];
     WarrenOccupancyFile.getline( st, 2000 );
     while (!WarrenOccupancyFile.eof()) {
         WarrenOccupancyFile >> Year >> Day >> NoWarrens >> NoOccWarrens >> MeanBurrows >> MeanRabbits >> MeanDisease
             >> MeanOccupancy >> CVOccupancy >> MeanKits >> MeanJuvs >> MeanAds >> TotalYoung >> TotalJuvs
             >> TotalMales >> TotalFemales >> BreedingFemales >> BreedingDensityAv >> yroldfemales >> NonBreedingFems >> littersperfemale >> lrc >> litters;
         // Here we create the actual data that we need
         // We want:
         // - correlation between total breeding pop and 1yr olds
         // - mean of total breeding pop
         // - mean of 1yr olds
         // - range max-min of total breeding pop
         // - range max-min of 1yr olds
         if ((yroldfemales + BreedingFemales + NonBreedingFems) > 0) {
             yearlingpct.push_back( yroldfemales / (yroldfemales + BreedingFemales + NonBreedingFems) );
             totalbrfemalesdensity.push_back( (yroldfemales + BreedingFemales + NonBreedingFems) / 2.0 );
             totalfemales.push_back( (BreedingFemales + NonBreedingFems) / 2.0 );
             breedingdensity.push_back( BreedingFemales / 2.0 );
             nonbreedingdensity.push_back( NonBreedingFems / 2.0 );
             yrolddensity.push_back( yroldfemales / 2.0 );
             kitsperfemale.push_back( littersperfemale );
         }
         else {
             // All dead so save the results
             ofstream ofile( "RabbitPOMSummary.txt", ios::app );
             ofile << 0
                 << '\t' << 0
                 << '\t' << 0
                 << '\t' << 0
                 << '\t' << 0
                 << '\t' << 0
                 << '\t' << 0 << endl;
             ofile.close();
             return;
         }
     }
     WarrenOccupancyFile.close();
     // Now we have all the useful data we can create the stats for this analysis
     // 
     // Get the ranges skipping the first 10 years
     int sz = static_cast<int>(yearlingpct.size());
     double sumx = 0;
     double sumx2 = 0;
     double sumy = 0;
     double sumy2 = 0;
     double sumxy = 0;
     double sumx_b = 0;
     double sumx2_b = 0;
     double sumy_b = 0;
     double sumy2_b = 0;
     double sumxy_b = 0;
     double n = sz - 1 - 10;
     // Do the correlation for yearlingpct and total female density
     for (int i = 10; i < sz - 1; i++) {
         if (totalbrfemalesdensity[ i ]>maxbreedingpop)maxbreedingpop = totalbrfemalesdensity[ i ];
         if (totalbrfemalesdensity[ i ] < minbreedingpop)minbreedingpop = totalbrfemalesdensity[ i ];
         if (yearlingpct[ i ] > maxyroldspct) maxyroldspct = yearlingpct[ i ];
         if (yearlingpct[ i ] < minyroldspct) minyroldspct = yearlingpct[ i ];
         sumx += totalbrfemalesdensity[ i ];
         sumx2 += totalbrfemalesdensity[ i ] * totalbrfemalesdensity[ i ];
         sumy += yearlingpct[ i ];
         sumy2 += yearlingpct[ i ] * yearlingpct[ i ];
         sumxy += totalbrfemalesdensity[ i ] * yearlingpct[ i ];
     }
     meantotalbrpop = sumx / n;
     double intermediate = (n*sumxy) - (sumx*sumy);
     correlation = intermediate / sqrt( ((n*sumx2) - (sumx*sumx))*((n*sumy2) - (sumy*sumy)) );
     //
     n = n - 1;
     for (int i = 10; i < sz - 2; i++) {
         // Here we need the numbers from the year before
         sumx_b += totalfemales[ i ];
         sumx2_b += totalfemales[ i ] * totalfemales[ i ];
         sumy_b += kitsperfemale[ i+1 ];
         sumy2_b += kitsperfemale[ i+1 ] * kitsperfemale[ i+1 ];
         sumxy_b += totalfemales[ i ] * kitsperfemale[ i+1 ];
     }
     intermediate = (n*sumxy_b) - (sumx_b*sumy_b);
     correlation_b = intermediate / sqrt( ((n*sumx2_b) - (sumx_b*sumx_b))*((n*sumy2_b) - (sumy_b*sumy_b)) );
     // Now save the results
     ofstream ofile( "RabbitPOMSummary.txt", ios::app );
     ofile << meantotalbrpop
           << '\t' << maxbreedingpop
           << '\t' << minbreedingpop
           << '\t' << maxyroldspct
           << '\t' << minyroldspct
           << '\t' << correlation
           << '\t' << correlation_b << endl;
     ofile.close();
 }