#include <RodenticidePredators.h>

Public Member Functions
virtual	~RodenticidePredators_Population_Manager ()

	RodenticidePredators_Population_Manager (Landscape *L)

void	Tick ()
	Updates the rodenticide exposure for all predator territories. More...

void	PreCachePoly (int a_poly)

vector< RP_Territory > *	SupplyTerritories ()

int	HowManyTerritoriesHere (int a_x, int a_y)

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	TheAOROutputProbe ()

virtual void	TheRipleysOutputProbe (FILE *a_prb)

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)

Protected Member Functions
double	EvaluatePoly (int a_poly)
	Get the habitat quality based on polygon type. More...

void	ReadHabitatValues (int a_type)
	Read in specific predator type habitat scores. More...

void	CreatHabitatQualGrid (void)
	Evaluate the landscape and create the habitat quality grid. More...

void	CreateTerritories ()
	Populates the landscape with predatory territories. More...

void	PredatorTerritoryOutput (bool a_initial)
	Output functions for predator territories. More...

void	PredatorTerritoryInput ()
	Output functions for predator territories. More...

bool	IsGridPositionValid (int &x, int &y, int range)
	Tests whether a square has any occupied cells. More...

double	EvaluateHabitat (int a_x, int a_y, int a_range)
	Gets the total habitat score for a square UL x,y diameter of range. More...

void	NewTerritory (int a_x, int a_y, int a_range, double a_qual)
	Create a new territory and claim the grid. 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	DoFirst ()

virtual void	DoBefore ()

virtual void	DoAfter ()

virtual void	DoAlmostLast ()

virtual void	DoLast ()

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 ()

Protected Attributes
int	m_sim_w

int	m_sim_h

int	m_sim_w_div_10

int	m_sim_h_div_10

int	m_hash_size

double *	m_qual_cache

double *	m_qual_grid

bool *	m_occupancy_grid

double	m_habquals [tole_Foobar]

int	m_predator_minHR

int	m_predator_maxHR

double	m_predator_targetQual

vector< RP_Territory >	m_Territories

int	m_NoTerritories

double	m_summeddays
	Keeps track of the number of days we have rodenticide exposure summation for. More...

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]

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

Constructor & Destructor Documentation

◆ ~RodenticidePredators_Population_Manager()

RodenticidePredators_Population_Manager::~RodenticidePredators_Population_Manager ( )

virtual

When the manager is destroyed call the output functions for predator territories

 {
     PredatorTerritoryOutput(false);
     delete m_qual_cache;
     delete m_qual_grid;
     delete m_occupancy_grid;
 }

References m_occupancy_grid, m_qual_cache, m_qual_grid, and PredatorTerritoryOutput().

◆ RodenticidePredators_Population_Manager()

RodenticidePredators_Population_Manager::RodenticidePredators_Population_Manager ( Landscape * L )

On construction the first thing to do is to read the quality scores in from the correct predator input file. This depends on a config variable being correctly set: cfg_RodenticidePredatoryType

Create the habitat quality grid ready for predatory habitat assessment

Now populate the landscape with predatory territories

                                                                                                 : Population_Manager(a_L)
 {
     m_predator_minHR = cfg_RodenticidePredatoryMinTerr.value() / 10; // Need divind by 10 for the grid (it is in 10 x 10m grids)
     m_predator_maxHR = cfg_RodenticidePredatoryMaxTerr.value() / 10;
     m_predator_targetQual = cfg_RodenticidePredatoryTargetQual.value();
     m_summeddays = 0.0;
     ReadHabitatValues(cfg_RodenticidePredatoryType.value());
     CreatHabitatQualGrid();
     if (cfg_rodenticide_read_predators.value()) PredatorTerritoryInput(); 
     else 
     {
         CreateTerritories(); 
         PredatorTerritoryOutput(true);
     }
  
 }

References cfg_rodenticide_read_predators(), cfg_RodenticidePredatoryMaxTerr(), cfg_RodenticidePredatoryMinTerr(), cfg_RodenticidePredatoryTargetQual(), cfg_RodenticidePredatoryType(), CreateTerritories(), CreatHabitatQualGrid(), m_predator_maxHR, m_predator_minHR, m_predator_targetQual, m_summeddays, PredatorTerritoryInput(), PredatorTerritoryOutput(), and ReadHabitatValues().

Member Function Documentation

◆ CreateTerritories()

void RodenticidePredators_Population_Manager::CreateTerritories ( )

protected

Populates the landscape with predatory territories.

Starts with a minimum territory size territory and then increases the size until either a occupied square is found or max size is reached, or the quality level has been met.

 {
     m_NoTerritories = 0;
     int x0 = m_predator_maxHR / 2; // Our starting point x
     int x = (int) (x0+g_rand_uni()*(m_sim_w_div_10 - x0));
     int y = x0;  // Our starting point y
     int x1 = m_sim_w_div_10 - x0;   // End point x
     int y1 = m_sim_h_div_10 - x0;   // End point y
     //bool toggle = false;
     double qual;
     int range; 
     int tries = m_sim_w_div_10 * m_sim_h_div_10; // the number of grid points in the grid
     while ( tries-- > 0)
     {
         //if (toggle) if (y>=starty) break;
         range = m_predator_minHR; 
         bool found = false;
         while ( ( range <= m_predator_maxHR ) && ( !found ))
         {
             if ( !IsGridPositionValid( x, y, range ) ) 
             {
                 if ( ++x >= x1 ) 
                 {
                     x = 0; //random( 3 );
                     if ( ++y >= y1 ) 
                     {
                         tries = 0; // Gone all the way round so stop
                         range = m_predator_maxHR +1;
                         //toggle = true;
                     }
                 }
                 continue;
             }
             // Location was OK, ie. not occupied.
             // Try the smallest possible territory located right at our starting
             // position.
             qual = EvaluateHabitat( x, y, range );
             // Is it suitable?
             if ( qual >= m_predator_targetQual ) 
             {
                 // If so create it and claim the area on the grid
                 // Is OK so create a territory
                 NewTerritory( x, y, range, 0.0 );
                 found = true;
             }
             else range++;
         }
         // Take a step and try again
         if (++x >= x1) 
         {
             x = x0;
             if (++y >= y1)
             {
                 tries = 0; // Gone all the way round so stop
                 range = m_predator_maxHR + 1;
                 //toggle = true;
             }
         }
     }
 }

References EvaluateHabitat(), g_rand_uni, IsGridPositionValid(), m_NoTerritories, m_predator_maxHR, m_predator_minHR, m_predator_targetQual, m_sim_h_div_10, m_sim_w_div_10, and NewTerritory().

Referenced by RodenticidePredators_Population_Manager().

◆ CreatHabitatQualGrid()

void RodenticidePredators_Population_Manager::CreatHabitatQualGrid ( void )

protected

Evaluate the landscape and create the habitat quality grid.

Need to do the basic read and quality assessment for the landscape, before creating and allocating the predatory territories. The first step is to get the map dimensions saved to local attributes.

Following that all the polygons in the landscape are pre-cached for their quality score - this is important for speed because it only needs to be done once per polygon.

Finally go through the whole landscape in 10x10m blocks and fill in the quality grid scoresas a the mean of 100m2 i.e. 10 x 10 m squares

 {
     m_sim_w = m_TheLandscape->SupplySimAreaWidth();
     m_sim_h = m_TheLandscape->SupplySimAreaHeight();
     m_sim_w_div_10 = m_sim_w / 10;
     m_sim_h_div_10 = m_sim_h / 10;
     m_hash_size = m_TheLandscape->SupplyLargestPolyNumUsed() + 1;
     m_qual_cache = new double[m_hash_size];
     m_TheLandscape->RodenticidePredatorsEvaluation( this );
     /*
     * Next the memory required for operations is reserved for the quality grid and occupancy grid that we need for the territory finding operations. 
     * The occupancy grid also needs all elements set to false.
     */
     int totalgrids = m_sim_w_div_10 * m_sim_h_div_10;
     m_qual_grid = new double[ totalgrids ];
     m_occupancy_grid = new bool [ totalgrids ];
     for (int i=0; i<totalgrids; i++)
     {
         m_occupancy_grid[ i ] = false;
     }
     for (int x=0; x< m_sim_w_div_10; x++)
     {
         for (int y = 0; y < m_sim_h_div_10; y++)
         {
             int cx = x*10;
             int cy = y*10;
             double qual = 0.0;
             for (int xx = cx; xx < cx+10; xx++)
             {
                 for (int yy = cy; yy < cy+10; yy++)
                 {
                     int poly = m_TheLandscape->SupplyPolyRef(xx,yy);
                     qual += m_qual_cache[poly];
                 }
             }
             m_qual_grid[x + (y * m_sim_w_div_10)] = qual/=100.0;
         }
     }
 }

References m_hash_size, m_occupancy_grid, m_qual_cache, m_qual_grid, m_sim_h, m_sim_h_div_10, m_sim_w, m_sim_w_div_10, Population_Manager::m_TheLandscape, Landscape::RodenticidePredatorsEvaluation(), Landscape::SupplyLargestPolyNumUsed(), Landscape::SupplyPolyRef(), Landscape::SupplySimAreaHeight(), and Landscape::SupplySimAreaWidth().

Referenced by RodenticidePredators_Population_Manager().

◆ EvaluateHabitat()

double RodenticidePredators_Population_Manager::EvaluateHabitat	(	int	a_x,
		int	a_y,
		int	a_range
	)

protected

Gets the total habitat score for a square UL x,y diameter of range.

Looks through the area summing all scores.

 {
     double l_qual = 0.0;
     int r2 = a_range / 2;
     int l_min_x = a_x - r2;
     int l_min_y = a_y - r2;
     int l_max_x = a_x + r2;
     int l_max_y = a_y + r2;
     for (int x = l_min_x; x < l_max_x; x++)
     {
         for ( int y = l_min_y; y < l_max_y; y++ ) 
         {
             l_qual += m_qual_grid[ x + y * m_sim_w_div_10 ];
         }
     }
     return l_qual;
 }

References m_qual_grid, and m_sim_w_div_10.

Referenced by CreateTerritories().

◆ EvaluatePoly()

double RodenticidePredators_Population_Manager::EvaluatePoly ( int a_poly )

protected

Get the habitat quality based on polygon type.

Returns the specific score for this polygon based on the polygon type and the score stored in m_habquals

 {
     TTypesOfLandscapeElement l_type = m_TheLandscape->SupplyElementType( a_poly );
     return m_habquals[(int) l_type];
 }

References m_habquals, Population_Manager::m_TheLandscape, and Landscape::SupplyElementType().

Referenced by PreCachePoly().

◆ HowManyTerritoriesHere()

int RodenticidePredators_Population_Manager::HowManyTerritoriesHere	(	int	a_x,
		int	a_y
	)

 {
     int sum = 0;
     int sz = (int)m_Territories.size();
     for (int t = 0; t< sz; t++)
     {
         int r = m_Territories[t].m_range;
         int x = m_Territories[t].m_x - (r / 2);
         int y = m_Territories[t].m_y - (r / 2);
         if ((a_x >= x) && (a_x<x + r) && (a_y >= y) && (a_y <= y + r)) sum++;
     }
     return sum;
 }

References m_Territories.

◆ IsGridPositionValid()

bool RodenticidePredators_Population_Manager::IsGridPositionValid	(	int &	x,
		int &	y,
		int	range
	)

protected

Tests whether a square has any occupied cells.

Returns: false if any occupied grid cell is found If we are too near the edge then do not evaluate,

otherwise test each potential location to see if they are occupied - if so return false

 {
     int r2 = a_range / 2;
     int l_min_x = a_x - r2;
     int l_min_y = a_y - r2;
     int l_max_x = a_x + r2;
     int l_max_y = a_y + r2;
     for (int i = l_min_x; i < l_max_x; i++)
     {
         for (int j = l_min_y; j < l_max_y; j++)
         {
             if ( m_occupancy_grid[ i + j * m_sim_w_div_10 ]  ) 
             {
                 return false;
             }
         }
     }
     // No occupied squares found so return true
     return true;
 }

References m_occupancy_grid, and m_sim_w_div_10.

Referenced by CreateTerritories().

◆ NewTerritory()

void RodenticidePredators_Population_Manager::NewTerritory	(	int	a_x,
		int	a_y,
		int	a_range,
		double	a_qual
	)

protected

Create a new territory and claim the grid.

 {
     RP_Territory rpt;
     rpt.m_exposure = a_exposure;
     rpt.m_range = (int) floor(0.5+(a_range * 10 * cfg_RodenticidePredatoryTerrOverlap.value()));
     rpt.m_x = a_x * 10;
     rpt.m_y = a_y * 10;
     m_Territories.push_back(rpt);
     // Claim the territory in the grid
     int r2 = a_range / 2;
     int l_min_x = a_x - r2;
     int l_min_y = a_y - r2;
     int l_max_x = a_x + r2;
     int l_max_y = a_y + r2;
     
     for (int i = l_min_x; i < l_max_x; i++)
     {
         for (int j = l_min_y; j < l_max_y; j++)
         {
             m_occupancy_grid[ i + j * m_sim_w_div_10 ] = true;
         }
     }
 }

References cfg_RodenticidePredatoryTerrOverlap(), RP_Territory::m_exposure, m_occupancy_grid, RP_Territory::m_range, m_sim_w_div_10, m_Territories, RP_Territory::m_x, and RP_Territory::m_y.

Referenced by CreateTerritories().

◆ PreCachePoly()

void RodenticidePredators_Population_Manager::PreCachePoly ( int a_poly )

inline

     {
         m_qual_cache[a_poly] = EvaluatePoly(a_poly);
     }

References EvaluatePoly(), and m_qual_cache.

Referenced by Landscape::RodenticidePredatorsEvaluation().

◆ PredatorTerritoryInput()

void RodenticidePredators_Population_Manager::PredatorTerritoryInput ( )

protected

Output functions for predator territories.

Opens a standard output tab-delimited text file and reads all predatory territory information in the format:
Number of entries
Entry 1 x, Entry 1 y, Entry 1 size, Entry 1 exposure
Entry 2 x, Entry 2 y, Entry 2 size, Entry 2 exposure
Entry 3 x etc....

 {
     ifstream ifile("PredatorTerritoryOutputInfo.txt",ios::in);
     int sz;
     ifile >> sz;
     double skip;
     int x,y,range;
     m_Territories.resize(0);
     for (int i=0; i< sz; i++)
     {
         ifile >> x >> y  >> range >> skip;
         RP_Territory rpt;
         rpt.m_exposure = 0.0;
         rpt.m_range = range;
         rpt.m_x = x;
         rpt.m_y = y;
         m_Territories.push_back(rpt);
     }
     ifile.close();
 }

References RP_Territory::m_exposure, RP_Territory::m_range, m_Territories, RP_Territory::m_x, and RP_Territory::m_y.

Referenced by RodenticidePredators_Population_Manager().

◆ PredatorTerritoryOutput()

void RodenticidePredators_Population_Manager::PredatorTerritoryOutput ( bool a_initial )

protected

Output functions for predator territories.

Opens a standard output tab-delimited text file and dumps all predatory territory information in the format:
Number of entries
Entry 1 x, Entry 1 y, Entry 1 size, Entry 1 exposure
Entry 2 x, Entry 2 y, Entry 2 size, Entry 2 exposure
Entry 3 x etc....

 {
     ofstream ofile("PredatorTerritoryOutputInfo.txt",ios::out);
     int sz =  (int) m_Territories.size();
     ofile << sz << endl;
     double asum=0.0;
     for (int i=0; i< sz; i++) asum+=m_Territories[i].m_exposure;
     if ((asum==0.0) || (m_summeddays<1)) a_initial = true;
     for (int i=0; i< sz; i++)
     {
         ofile << m_Territories[i].m_x << '\t';
         ofile << m_Territories[i].m_y << '\t';
         ofile << m_Territories[i].m_range << '\t';
         if (a_initial) ofile << 0.0 << endl; else ofile << m_Territories[i].m_exposure/m_summeddays << endl;
     }
     ofile.close();
 }

References m_summeddays, and m_Territories.

Referenced by RodenticidePredators_Population_Manager(), and ~RodenticidePredators_Population_Manager().

◆ ReadHabitatValues()

void RodenticidePredators_Population_Manager::ReadHabitatValues ( int a_type )

protected

Read in specific predator type habitat scores.

This method picks the input file based on the parameter a_type and reads in the scores for each habitat for that predator type. These are stored in m_habquals for later use in habitat evaluation.

 {
     fstream ifile;
     switch (a_type)
     {
     case 0:
         ifile.open("RodenticidePredator0_HabitatScores.txt",ios::in);
         break;
     default:
         ifile.open("RodenticidePredatorNone_HabitatScores.txt",ios::in);
     }
     if (!ifile)
     {
             m_TheLandscape->Warn("RodenticidePredators_Population_Manager::ReadHabitatValues","Could Not Open Predator Habitat Scores File");
             exit(0);
     }
     int n_values;
     ifile >> n_values;
     if (n_values != tole_Foobar)
     {
             m_TheLandscape->Warn("RodenticidePredators_Population_Manager::ReadHabitatValues"," - wrong number of habitat scores in RodenticidePredator_HabitatScores.txt");
             exit(0);
     }
     for (int i = 0; i< tole_Foobar; i++) ifile >> m_habquals[i];
     ifile.close();
 }

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

Referenced by RodenticidePredators_Population_Manager().

◆ SupplyTerritories()

vector<RP_Territory>* RodenticidePredators_Population_Manager::SupplyTerritories ( )

inline

64 { return &m_Territories; }

References m_Territories.

◆ Tick()

void RodenticidePredators_Population_Manager::Tick ( void )

Updates the rodenticide exposure for all predator territories.

Runs through all the territories and sums up the rodenticide exposure and accumulates this in each territory

 {
     int sz =  (int) m_Territories.size();
     for (int t=0; t< sz; t++)
     {
         int x = m_Territories[t].m_x;
         int y = m_Territories[t].m_y;
         int r = m_Territories[t].m_range;
         int xr = x+r;
         int yr = y+r;
         if (xr >= m_sim_w ) xr = m_sim_w-1;
         if (yr >= m_sim_h ) yr = m_sim_h-1;
         for (int i=x; i<xr; i++)
             for (int j=y; j< yr; j++)
             {
                 m_Territories[t].m_exposure += m_TheLandscape->SupplyRodenticide(i,j);
             }
     }
     m_summeddays++;
 }