Population_Manager Class Reference

Base class for all population managers. More...

#include <populationmanager.h>

Inheritance diagram for Population_Manager:

Public Member Functions
	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 ()
virtual void	TheNWordOutputProbe ()
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)

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

Protected Attributes
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]

Detailed Description

Base class for all population managers.

The core of the handling of animal populations. All time-step code and most input/output is handled by this class and its descendents. This class effectively implements a state machine to facilitate simulation of animal behaviours and handle potential issues with concurrency. The PopulationManager class is never instantiated but must be used by deriving a descendent class.

Definition at line 401 of file populationmanager.h.

Constructor & Destructor Documentation

Population_Manager::Population_Manager

(

Landscape *

L

)

Constructor for the Population_Manager class

Definition at line 222 of file PopulationManager.cpp.

References cfg_CipeGridSize, cfg_RipleysOutputMonthly_used, Landscape::SupplySimAreaHeight(), CfgInt::value(), and CfgBool::value().

                                                      {
    // Keep a pointer to the landscape this population is in
    m_TheLandscape = L;
    // create 10 empty arrays as default, excess can be removed in descendent classes
    TListOfAnimals alist;
    TheArray.insert( TheArray.end(), 10, alist );
    // Set the simulation bounds
    SimH = m_TheLandscape->SupplySimAreaHeight();
    SimW = m_TheLandscape->SupplySimAreaWidth();
    SimHH = m_TheLandscape->SupplySimAreaHeight()/2;
    SimWH = m_TheLandscape->SupplySimAreaWidth()/2;
    for (int i = 0; i < 10; i++) {
        // Set default BeforeStepActions
        BeforeStepActions[ i ] = 0;
        m_ListNames[ i ] = "Unknown";
        m_LiveArraySize.push_back( 0 );
    }
    // modify this if they need to in descendent classes
    StateNamesLength = 0; // initialise this variable.
    m_catastrophestartyear=-1; // Default is don't do this
#ifdef __LAMBDA_RECORD
    ofstream fout("LambdaGridOuput.txt", ios_base::out);  // open for writing
    fout.close();
    LamdaClear();
#endif
  if ( cfg_RipleysOutputMonthly_used.value() ) {
    OpenTheMonthlyRipleysOutputProbe();
  }
    m_cipegridsize = cfg_CipeGridSize.value();
    m_cgridcountwidth = SimW/m_cipegridsize;
    m_cgridcount = new int[ m_cgridcountwidth * m_cgridcountwidth ];
    m_gridcountsize[0] = 50;
    m_gridcountsize[1] = 100;
    m_gridcountsize[2] = 200;
    m_gridcountsize[3] = 500;
    m_gridcountwidth[0] = SimW/50;
    m_gridcountwidth[1] = SimW/100;
    m_gridcountwidth[2] = SimW/200;
    m_gridcountwidth[3] = SimW/500;
    m_gridcount[0] = new int[ m_gridcountwidth[0] * m_gridcountwidth[0] ];
    m_gridcount[1] = new int[ m_gridcountwidth[1] * m_gridcountwidth[1] ];
    m_gridcount[2] = new int[ m_gridcountwidth[2] * m_gridcountwidth[2] ];
    m_gridcount[3] = new int[ m_gridcountwidth[3] * m_gridcountwidth[3] ];
    // Ensure the GUI pointer is NULL in case we are not in GUI mode
#ifdef __ALMASS_VISUAL
    m_MainForm = NULL;
#endif
    m_SeasonNumber = 0;  // Ensure that we start in season number 0. Season number is incremented at day in year 183
}

Population_Manager::~Population_Manager ( void  )

virtual

Destructor for the Population_Manager class

Definition at line 276 of file PopulationManager.cpp.

References cfg_ReallyBigOutput_used, cfg_RipleysOutput_used, cfg_RipleysOutputMonthly_used, and CfgBool::value().

                                              {
  // clean-up
  for ( unsigned i = 0; i < TheArray.size(); i++ ) {
    // if objects in the list need to be deleted:
    for ( unsigned j = 0; j < (unsigned) GetLiveArraySize(i); j++ ) {
      delete TheArray[ i ] [ j ];
    }
    // empty the array
    TheArray[ i ].clear();
    // --
  }
  if ( cfg_RipleysOutput_used.value() ) {
    CloseTheRipleysOutputProbe();
    fclose( NWordOutputPrb );
  }
 if ( cfg_RipleysOutputMonthly_used.value() ) {
    CloseTheMonthlyRipleysOutputProbe();
  }
  if ( cfg_ReallyBigOutput_used.value() ) {
    CloseTheReallyBigOutputProbe();
  }
  for (int d=0; d<4; d++) delete [] m_gridcount[d];
  delete [] m_cgridcount;
}

Member Function Documentation

bool Population_Manager::BeginningOfMonth

(

)

Is it the first day of the month?

Definition at line 1172 of file PopulationManager.cpp.

References cfg_DayInMonth, and CfgInt::value().

                                          {
  if ( m_TheLandscape->SupplyDayInMonth() == cfg_DayInMonth.value() ) return true;
  return false;
}

virtual void Population_Manager::BreedingPairsOutput ( int  )

inlinevirtual

Definition at line 622 of file populationmanager.h.

                                           {
  }

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

inlinevirtual

Definition at line 630 of file populationmanager.h.

                                                                                        {
  }

virtual void Population_Manager::Catastrophe ( int  )

inlinevirtual

Definition at line 415 of file populationmanager.h.

                                    {
    }

void Population_Manager::Catastrophe ( )

protectedvirtual

This method MUST be overidden in descendent classes if this functionality is does not match with the animals requirements

Definition at line 1179 of file PopulationManager.cpp.

                                     {
    return;
}

bool Population_Manager::CheckXY	(	int	l,
		int	i
	)

Debug method to test for out of bounds coordinates.

Definition at line 1588 of file PopulationManager.cpp.

{
    if (TheArray[l][i]->Supply_m_Location_x() > 10000) return true;
    if (TheArray[l][i]->Supply_m_Location_y() > 10000) return true;
    if (TheArray[l][i]->Supply_m_Location_x() < 0) return true;
    if (TheArray[l][i]->Supply_m_Location_y() < 0) return true;
    return false;
}

void Population_Manager::CloseTheCIPEGridOutputProbe

(

)

close the probe

Definition at line 790 of file PopulationManager.cpp.

                                                     {
  if ( CIPEGridOutputPrb != NULL )
    fclose( CIPEGridOutputPrb );
    fclose( CIPEGridOutputPrbB );
}

void Population_Manager::CloseTheMonthlyRipleysOutputProbe

(

)

close the monthly probes

Definition at line 961 of file PopulationManager.cpp.

                                                           {
  fclose( RipleysOutputPrb1 );
  fclose( RipleysOutputPrb2 );
  fclose( RipleysOutputPrb3 );
  fclose( RipleysOutputPrb4 );
  fclose( RipleysOutputPrb5 );
  fclose( RipleysOutputPrb6 );
  fclose( RipleysOutputPrb7 );
  fclose( RipleysOutputPrb8 );
  fclose( RipleysOutputPrb9 );
  fclose( RipleysOutputPrb10 );
  fclose( RipleysOutputPrb11 );
  fclose( RipleysOutputPrb12 );
}

void Population_Manager::CloseTheReallyBigOutputProbe

(

)

close the probe

Definition at line 980 of file PopulationManager.cpp.

                                                      {
  if ( ReallyBigOutputPrb != 0 )
    fclose( ReallyBigOutputPrb );
  ReallyBigOutputPrb=0;
}

void Population_Manager::CloseTheRipleysOutputProbe

(

)

close the probe

Definition at line 950 of file PopulationManager.cpp.

References cfg_RipleysOutputMonthly_used, and CfgBool::value().

                                                    {
  if ( cfg_RipleysOutputMonthly_used.value() )
    fclose( RipleysOutputPrb );
  RipleysOutputPrb=NULL;
}

void Population_Manager::DisplayLocations ( )

virtual

Used to update the graphics when control is not returned to the ALMaSS_GUI between timesteps.

Definition at line 571 of file PopulationManager.cpp.

{
#ifdef __ALMASS_VISUAL
    m_MainForm->UpdateGraphics();
#endif
}

void Population_Manager::DoAfter ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Rabbit_Population_Manager.

Definition at line 524 of file PopulationManager.cpp.

                                 {
  //TODO: Add your source code here
}

void Population_Manager::DoAlmostLast ( )

protectedvirtual

Can be used in descendent classes

Definition at line 533 of file PopulationManager.cpp.

                                      {
  //TODO: Add your source code here
}

void Population_Manager::DoBefore ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Rabbit_Population_Manager.

Definition at line 340 of file PopulationManager.cpp.

                                  {
}

void Population_Manager::DoFirst ( )

protectedvirtual

Can be used in descendent classes

Reimplemented in Rabbit_Population_Manager.

Definition at line 332 of file PopulationManager.cpp.

                                 {
}

void Population_Manager::DoLast ( )

protectedvirtual

Collects some data to describe the number of animals in each state at the end of the day

Reimplemented in Rabbit_Population_Manager.

Definition at line 541 of file PopulationManager.cpp.

                                {

/*
#ifdef __UNIX__
  for ( unsigned i = 0; i < 100; i++ ) {
    StateList.n[ i ] = 0;
  }
#else
  // Zero results
  for ( unsigned listindex = 0; listindex < m_ListNameLength; listindex++ ) {
    for ( unsigned i = 0; i < 100; i++ ) {
      Counts[ listindex ] [ i ] = 0;
    }
  }
#endif
  // How many animals in each state?
  for ( unsigned listindex = 0; listindex < TheArray.size(); listindex++ ) {
    unsigned size = (unsigned) TheArray[ listindex ].size();
    for ( unsigned j = 0; j < size; j++ ) {
#ifdef __UNIX__
      StateList.n[ TheArray[ listindex ] [ j ]->WhatState() ] ++;
#else
      Counts[ listindex ] [ TheArray[ listindex ] [ j ]->WhatState() ] ++;
#endif
    }
  }
*/
}

void Population_Manager::EmptyTheArray ( )

protected

Removes all objects from the TheArray by deleting them and clearing TheArray.

Sort TheArray w.r.t. the m_Location_x attribute

Definition at line 1032 of file PopulationManager.cpp.

{
    for ( unsigned i = 0; i < TheArray.size(); i++ )
    {
        // if objects in the list need to be deleted:
        for (unsigned j = 0; j < (unsigned) TheArray[i].size(); j++)
        {
            delete TheArray[ i ] [ j ];
        }
        // empty the array
        TheArray[ i ].clear();
    }
}

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

Definition at line 1331 of file PopulationManager.cpp.

{
    unsigned int No = 0;
    unsigned sz = (unsigned)GetLiveArraySize( a_typeofanimal );
    for ( unsigned j = 0; j < sz; j++ ) 
    {
        if (a_farm == TheArray[ a_typeofanimal ] [ j ]->SupplyFarmOwnerRef()) No++;
    }
    return No;
}

TAnimal * Population_Manager::FindClosest	(	int	x,
		int	y,
		unsigned	Type
	)

Finds the closest individual to an x,y point

Definition at line 1007 of file PopulationManager.cpp.

References TAnimal::Supply_m_Location_x().

                                                                       {
  int distance = 100000000;
  TAnimal * TA = NULL;
  int dx, dy, d;
  for (unsigned j = 0; j < (unsigned)GetLiveArraySize( Type ); j++) {
    dx = TheArray[ Type ] [ j ]->Supply_m_Location_x();
    dy = TheArray[ Type ] [ j ]->Supply_m_Location_y();
    dx = ( dx - x );
    dx *= dx;
    dy = ( dy - y );

    dy *= dy;
    d = dx + dy;
    if ( d < distance ) {
      distance = d;
      TA = TheArray[ Type ] [ j ];
    }
  }
  return TA;
}

virtual void Population_Manager::FledgelingProbeOutput ( int  , int    )

inlinevirtual

Definition at line 635 of file populationmanager.h.

                                                 {
  }

virtual void Population_Manager::GeneticsResultsOutput ( FILE *  , unsigned    )

inlinevirtual

Definition at line 639 of file populationmanager.h.

                                                           {
  }

unsigned Population_Manager::GetLiveArraySize ( int  a_listindex )

inline

Gets the number of 'live' objects for a list index in the TheArray.

Definition at line 408 of file populationmanager.h.

Referenced by Rabbit_Warren::CalcDisease().

                                               {
        return m_LiveArraySize[a_listindex];
    }

TTypesOfPopulation Population_Manager::GetPopulationType ( )

inline

Definition at line 549 of file populationmanager.h.

{ return m_population_type; }

int Population_Manager::GetSeasonNumber ( )

inline

Get the season number.

Definition at line 551 of file populationmanager.h.

{return m_SeasonNumber;}

void Population_Manager::ImpactedProbe ( )

virtual

Special pesticide related probe. Overidden in descendent classes

Definition at line 683 of file PopulationManager.cpp.

                                        {

}

void Population_Manager::ImpactProbeReport

(

int

a_Time

)

Special probe

Definition at line 1391 of file PopulationManager.cpp.

                                                       {

  for ( int ProbeNo = 0; ProbeNo < 1; ProbeNo++ ) {
    // See if we need to record/update this one
    // if time/months/years ==0 or every time
    if ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 3 )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 2 ) && ( BeginningOfMonth() ) )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 1 ) && ( a_Time % 365 == 0 ) ) ) {
             ImpactedProbe();
    }
  }
}

void Population_Manager::IncLiveArraySize ( int  a_listindex )

inline

Increments the number of 'live' objects for a list index in the TheArray.

Definition at line 412 of file populationmanager.h.

                                           {
        m_LiveArraySize[a_listindex]++;
    }

bool Population_Manager::IsLast ( unsigned  listindex )

inline

Definition at line 452 of file populationmanager.h.

                                    {
    if ( TheArray[ listindex ].size() > 1 ) return false; else
      return true;
  }

void Population_Manager::LamdaBirth ( int  x, int  y  )

inline

Definition at line 584 of file populationmanager.h.

                                     {
               lamdagrid[0][x / __lgridsize][y / __lgridsize ]++;
       }

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

inline

Definition at line 587 of file populationmanager.h.

                                            {
               lamdagrid[0][x / __lgridsize][y / __lgridsize ]+=z;
       }

void Population_Manager::LamdaClear ( )

inline

Definition at line 590 of file populationmanager.h.

                         {
               for (int i=0; i<257; i++ ) {
                       for (int j=0; j<257; j++) {
                               lamdagrid[0][i][j]=0;
                               lamdagrid[1][i][j]=0;
                       }
               }
       }

void Population_Manager::LamdaDeath ( int  x, int  y  )

inline

Definition at line 580 of file populationmanager.h.

                                     {
               // inlined for speed
               lamdagrid[1][x / __lgridsize][y / __lgridsize ]++;
       }

void Population_Manager::LamdaDumpOutput

(

)

Special probe

Definition at line 668 of file PopulationManager.cpp.

                                         {
   ofstream fout("LambdaGridOuput.txt", ios_base::app);  // open for writing
   for (int i=0; i<257; i++ ) {
       for (int j=0; j<257; j++) {
           fout << lamdagrid[0][i][j] << "\t" << lamdagrid[1][i][j] << endl;
       }
   }
   //fout << "NEXT" << endl;
   fout.close();
}

void Population_Manager::LOG

(

const char *

fname

)

Debug function used to log whatever is needed - this is just a place to write whatever is needed at the time - so contents vary

Definition at line 306 of file PopulationManager.cpp.

References AnimalPosition::m_x, and AnimalPosition::m_y.

                                                {
  FILE * PFile = fopen(fname, "w" );
  if (PFile) {
      m_TheLandscape->Warn("PopulationManager::LOG - Could not open file ",fname);
      exit(0);
  }
  AnimalPosition AP;
  for ( unsigned listindex = 0; listindex < TheArray.size(); listindex++ ) {
#ifndef __BCB__
    fprintf( PFile, "%s :\n", m_ListNames[ listindex ] );
#else
    fprintf( PFile, "%s :\n", m_ListNames[ listindex ].c_str() );
#endif
    for ( unsigned j = 0; j < (unsigned) m_LiveArraySize[listindex]; j++ ) {
      AP = TheArray[ listindex ] [ j ]->SupplyPosition();
      fprintf( PFile, "%i %i %i\n", j, AP.m_x, AP.m_y );
    }
  }
  fclose( PFile );
}

void Population_Manager::NWordOutput ( )

protected

The output section for the NWord probe.
.

A common output stub for the NWord output probe. Specialist counting for each species occurs as part of the CIPE grid probe, then this method deals with the final output.

Definition at line 804 of file PopulationManager.cpp.

                                     {
    int Counted[4];
    int totalcells[4];
    int OccupiedCells[4];
    for (int cellwidth=0; cellwidth<4; cellwidth++) {
        Counted[cellwidth] = 0;
        totalcells[cellwidth] = m_gridcountwidth[cellwidth] * m_gridcountwidth[cellwidth];
        OccupiedCells[cellwidth] = 0;
        for (int i=0; i<m_gridcountwidth[cellwidth]; i++) {
          for (int j=0; j<m_gridcountwidth[cellwidth]; j++) {
            int res=m_gridcount[cellwidth][i+j*m_gridcountwidth[cellwidth]];
            Counted[cellwidth] += res;
            if (res>0) OccupiedCells[cellwidth]++;
          }
        }
    }
    fprintf(NWordOutputPrb,"%d\t%d\t%d\t", m_TheLandscape->SupplyYearNumber() ,(int)m_TheLandscape->SupplyDayInYear(), Counted[0] );
    for (int c=0; c<4; c++) {
        fprintf(NWordOutputPrb,"%d\t%d\t", totalcells[c], OccupiedCells[c]);
    }
    fprintf(NWordOutputPrb,"\n");
    fflush(NWordOutputPrb);
}

virtual bool Population_Manager::OpenTheBreedingPairsProbe ( )

inlinevirtual

Definition at line 616 of file populationmanager.h.

                                           {
    return false;
  }

virtual bool Population_Manager::OpenTheBreedingSuccessProbe ( )

inlinevirtual

Definition at line 619 of file populationmanager.h.

                                             {
    return false;
  }

bool Population_Manager::OpenTheCIPEGridOutputProbe

(

)

open the probe

Definition at line 769 of file PopulationManager.cpp.

References cfg_CIPEGridOutput_filename, cfg_CIPEGridOutput_filenameB, g_msg, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

                                                    {
  CIPEGridOutputPrb = fopen(cfg_CIPEGridOutput_filename.value(), "w" );
  if ( !CIPEGridOutputPrb ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheCIPEGridOutputProbe(): ""Unable to open probe file",
         cfg_CIPEGridOutput_filename.value() );
    exit( 1 );
  }
  CIPEGridOutputPrbB = fopen(cfg_CIPEGridOutput_filenameB.value(), "w" );
  if ( !CIPEGridOutputPrbB ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheCIPEGridOutputProbe(): ""Unable to open probe file",
         cfg_CIPEGridOutput_filenameB.value() );
    exit( 1 );
  }
  return true;
}

virtual bool Population_Manager::OpenTheFledgelingProbe ( )

inlinevirtual

Definition at line 613 of file populationmanager.h.

                                        {
    return false;
  }

bool Population_Manager::OpenTheMonthlyRipleysOutputProbe

(

)

open 12 ripley output probles, one for each month

Definition at line 854 of file PopulationManager.cpp.

References cfg_RipleysOutput_filename, g_msg, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

                                                          {
  RipleysOutputPrb1 = fopen("RipleyOutput_Jan.txt", "w" );
  if ( !RipleysOutputPrb1 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb2 = fopen("RipleyOutput_Feb.txt", "w" );
  if ( !RipleysOutputPrb2 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb3 = fopen("RipleyOutput_Mar.txt", "w" );
  if ( !RipleysOutputPrb3 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb4 = fopen("RipleyOutput_Apr.txt", "w" );
  if ( !RipleysOutputPrb4 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb5 = fopen("RipleyOutput_May.txt", "w" );
  if ( !RipleysOutputPrb5 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb6 = fopen("RipleyOutput_Jun.txt", "w" );
  if ( !RipleysOutputPrb6 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb7 = fopen("RipleyOutput_Jul.txt", "w" );
  if ( !RipleysOutputPrb7 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb8 = fopen("RipleyOutput_Aug.txt", "w" );
  if ( !RipleysOutputPrb8 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb9 = fopen("RipleyOutput_Sep.txt", "w" );
  if ( !RipleysOutputPrb9 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb10 = fopen("RipleyOutput_Oct.txt", "w" );
  if ( !RipleysOutputPrb10 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb11 = fopen("RipleyOutput_Nov.txt", "w" );
  if ( !RipleysOutputPrb11 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  RipleysOutputPrb12 = fopen("RipleyOutput_Dec.txt", "w" );
  if ( !RipleysOutputPrb12 ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  return true;
}

bool Population_Manager::OpenTheReallyBigProbe

(

)

open the probe

Definition at line 935 of file PopulationManager.cpp.

References cfg_ReallyBigOutput_filename, g_msg, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

                                               {
  ReallyBigOutputPrb = fopen(cfg_ReallyBigOutput_filename.value(), "w" );
  if ( !ReallyBigOutputPrb ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_ReallyBigOutput_filename.value() );
    exit( 1 );
  }
  return true;
}

bool Population_Manager::OpenTheRipleysOutputProbe

(

)

open the probe

Definition at line 834 of file PopulationManager.cpp.

References cfg_RipleysOutput_filename, g_msg, CfgStr::value(), MapErrorMsg::Warn(), and WARN_FILE.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager().

                                                   {
  RipleysOutputPrb = fopen(cfg_RipleysOutput_filename.value(), "w" );
  if ( !RipleysOutputPrb ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheRipleysOutputProbe(): ""Unable to open probe file",
         cfg_RipleysOutput_filename.value() );
    exit( 1 );
  }
  NWordOutputPrb = fopen("NWordOutputPrb.txt", "w" );
  if ( !NWordOutputPrb ) {
    g_msg->Warn( WARN_FILE, "Population_Manager::OpenTheCIPEGridOutputProbe(): ""Unable to open NWord probe file", "" );
    exit( 1 );
  }
  fprintf(NWordOutputPrb,"%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t\n","Year","Day","Total no.","Cells50","Occupied50","Cells100","Occupied100","Cells200","Occupied200","Cells400","Occupied400");
  return true;
}

unsigned Population_Manager::PartitionLiveDead ( unsigned  Type )

protected

Sort TheArray w.r.t. the current state attribute in reverse order

Definition at line 1085 of file PopulationManager.cpp.

                                                            {
    auto it = partition(TheArray[Type].begin(), TheArray[Type].begin() + m_LiveArraySize[Type], CompareStateAlive());
    // it now points at the first dead element
    // the number of live ones before it is it-TheArray[Type].begin(). This is the new vector size for live animals.
    return unsigned(it - TheArray[Type].begin());
}

float Population_Manager::Probe ( int  ListIndex, probe_data *  p_TheProbe  )

virtual

Default data probe. Rarely used in actuality but always available

Definition at line 691 of file PopulationManager.cpp.

References AnimalPosition::m_EleType, probe_data::m_NoAreas, probe_data::m_NoEleTypes, probe_data::m_NoFarms, probe_data::m_NoVegTypes, probe_data::m_Rect, probe_data::m_RefEle, probe_data::m_RefFarms, probe_data::m_RefVeg, AnimalPosition::m_VegType, AnimalPosition::m_x, rectangle::m_x1, rectangle::m_x2, AnimalPosition::m_y, rectangle::m_y1, and rectangle::m_y2.

                                                                        {
    // Counts through the list and goes through each area to see if the animal
    // is standing there and if the farm, veg or element conditions are met
    AnimalPosition Sp;
    float NumberSk = 0;
    // Four possibilites
    // either NoVegTypes or NoElementTypes or NoFarmTypes is >0 or all==0
    if ( p_TheProbe->m_NoFarms != 0 ) {
        for (unsigned j = 0; j < (unsigned)GetLiveArraySize( ListIndex ); j++) {
            Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();
            unsigned Farm = TheArray[ ListIndex ] [ j ]->SupplyFarmOwnerRef();
            for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
                if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
                        && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) )
                for ( unsigned k = 0; k < p_TheProbe->m_NoFarms; k++ ) {
                    if ( p_TheProbe->m_RefFarms[ k ] == Farm )
                    NumberSk++; // it is in the square so increment number
                }

            }
    }
    } else if ( p_TheProbe->m_NoEleTypes != 0 ) {
        for (unsigned j = 0; j < (unsigned)GetLiveArraySize( ListIndex ); j++) {
      Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();
      for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
        if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
             && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) )
               for ( unsigned k = 0; k < p_TheProbe->m_NoEleTypes; k++ ) {
                 if ( p_TheProbe->m_RefEle[ k ] == Sp.m_EleType )
                   NumberSk++; // it is in the square so increment number
               }
      }
    }
    } else {
    if ( p_TheProbe->m_NoVegTypes != 0 ) {
        for (unsigned j = 0; j < (unsigned)GetLiveArraySize( ListIndex ); j++) {
        Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();

        for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
          if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
               && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) ) {
                 for ( unsigned k = 0; k < p_TheProbe->m_NoVegTypes; k++ ) {
                   if ( p_TheProbe->m_RefVeg[ k ] == Sp.m_VegType )
                     NumberSk++; // it is in the square so increment number
                 }
          }
        }
      }
    } else // both must be zero
    {
        unsigned sz = (unsigned)GetLiveArraySize( ListIndex );
        // It is worth checking whether we have a total dump of all individuals
        // if so don't bother with asking each where it is
        if (p_TheProbe->m_NoAreas==1) {
            if ((p_TheProbe->m_Rect[0].m_x1==0) && (p_TheProbe->m_Rect[0].m_y1==0) && (p_TheProbe->m_Rect[0].m_x2==(unsigned)SimW) &&
                (p_TheProbe->m_Rect[0].m_y2==(unsigned)SimH)) {
                    return (float) sz;
            }
        }
        // Asking for a subset - need to test them all
        for ( unsigned j = 0; j < sz; j++ ) {
            Sp = TheArray[ ListIndex ] [ j ]->SupplyPosition();
            for ( unsigned i = 0; i < p_TheProbe->m_NoAreas; i++ ) {
                if ( ( Sp.m_x >= p_TheProbe->m_Rect[ i ].m_x1 ) && ( Sp.m_y >= p_TheProbe->m_Rect[ i ].m_y1 )
                       && ( Sp.m_x <= p_TheProbe->m_Rect[ i ].m_x2 ) && ( Sp.m_y <= p_TheProbe->m_Rect[ i ].m_y2 ) )
                        NumberSk++; // it is in the square so increment number
            }
        }
    }
    }
    return NumberSk;
}

int Population_Manager::ProbeFileInput	(	char *	p_Filename,
		int	p_ProbeNo
	)

Default probe file input

Definition at line 585 of file PopulationManager.cpp.

                                                                         {
  FILE * PFile;
  int data = 0;
  int data2 = 0;
  char S[ 255 ];
  PFile = fopen(p_Filename, "r" );
  if ( !PFile ) {
    m_TheLandscape->Warn( "Population Manager - cannot open Probe File ", p_Filename );
    exit( 0 );
  }
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d\n", & data ); // Reporting interval
  TheProbe[ p_ProbeNo ]->m_ReportInterval = data;
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d\n", & data ); // Write to file
  if ( data == 0 ) TheProbe[ p_ProbeNo ]->m_FileRecord = false; else
    TheProbe[ p_ProbeNo ]->m_FileRecord = true;
  fgets( S, 255, PFile ); // dummy line
  for ( int i = 0; i < 10; i++ ) {
    fscanf( PFile, "%d", & data );
    if ( data > 0 ) TheProbe[ p_ProbeNo ]->m_TargetTypes[ i ] = true; else
      TheProbe[ p_ProbeNo ]->m_TargetTypes[ i ] = false;
  }

  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d", & data );
  TheProbe[ p_ProbeNo ]->m_NoAreas = data;
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d", & data2 ); // No References areas
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  fscanf( PFile, "%d", & data ); // Type reference for probe
  if ( data == 1 ) TheProbe[ p_ProbeNo ]->m_NoEleTypes = data2; else
    TheProbe[ p_ProbeNo ]->m_NoEleTypes = 0;
  if ( data == 2 ) TheProbe[ p_ProbeNo ]->m_NoVegTypes = data2; else
    TheProbe[ p_ProbeNo ]->m_NoVegTypes = 0;
  if ( data == 3 ) TheProbe[ p_ProbeNo ]->m_NoFarms = data2; else
    TheProbe[ p_ProbeNo ]->m_NoFarms = 0;
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  // Now read in the areas data
  for ( int i = 0; i < 10; i++ ) {
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_x1 = data;
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_y1 = data;
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_x2 = data;
    fscanf( PFile, "%d", & data );
    TheProbe[ p_ProbeNo ]->m_Rect[ i ].m_y2 = data;
  }
  fgets( S, 255, PFile ); // dummy line
  fgets( S, 255, PFile ); // dummy line
  if ( TheProbe[ p_ProbeNo ]->m_NoVegTypes > 0 ) {
    for ( int i = 0; i < 25; i++ ) {
      fscanf( PFile, "%d", & data );
      if ( data != 999 )
        TheProbe[ p_ProbeNo ]->m_RefVeg[ i ] = m_TheLandscape->TranslateVegTypes( data );
    }
  } else if ( TheProbe[ p_ProbeNo ]->m_NoFarms > 0 ) {
    for ( int i = 0; i < 25; i++ ) {
      fscanf( PFile, "%d", & data );
      if ( data != 999 )
        TheProbe[ p_ProbeNo ]->m_RefFarms[ i ] = data;
    }
  } else {
    for ( int i = 0; i < 25; i++ ) {
      fscanf( PFile, "%d", & data );
      if ( data != 999 ) TheProbe[ p_ProbeNo ]->m_RefEle[ i ] = m_TheLandscape->TranslateEleTypes( data );
    }
  }
  fclose( PFile );
  return data2; // number of data references
}

char * Population_Manager::ProbeReport

(

int

a_time

)

Definition at line 1343 of file PopulationManager.cpp.

References g_str.

                                                {

  int No;
  char str[100]; // 100 out to be enough!!
  strcpy(g_str,"");
  for ( int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++ ) {
    No = 0;
    // See if we need to record/update this one
    // if time/months/years ==0 or every time
    if ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 3 )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 2 ) && ( BeginningOfMonth() ) )
         || ( ( TheProbe[ ProbeNo ]->m_ReportInterval == 1 ) && ( Time % 365 == 0 ) ) ) {
           // Goes through each area and sends a value to OutputForm
           unsigned Index = SupplyListIndexSize();
           for ( unsigned listindex = 0; listindex < Index; listindex++ ) {
             if ( TheProbe[ ProbeNo ]->m_TargetTypes[ listindex ] )
               No += (int) Probe( listindex, TheProbe[ ProbeNo ] );
           }
           TheProbe[ ProbeNo ]->FileOutput( No, Time, ProbeNo );
            sprintf(str," %d ", No );
            strcat(g_str,str);
    }
  }
  return g_str;
}

char * Population_Manager::ProbeReportTimed

(

int

a_time

)

Definition at line 1370 of file PopulationManager.cpp.

References g_str.

                                                    {
    int No;
    char str[100]; // 100 ought to be enough!!
    strcpy(g_str,"");
    for ( int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++ ) {
    No = 0;
    unsigned Index = SupplyListIndexSize();
    for ( unsigned listindex = 0; listindex < Index; listindex++ ) {
        if ( TheProbe[ ProbeNo ]->m_TargetTypes[ listindex ] ) No += (int) Probe( listindex, TheProbe[ ProbeNo ] );
    }
    TheProbe[ ProbeNo ]->FileOutput( No, Time, ProbeNo );
    sprintf(str," %d ", No );
    strcat(g_str,str);
  }
  return g_str;
}

void Population_Manager::Run ( int  NoTSteps )

virtual

This is the main scheduling method for the population manager.
Note the structure of Shuffle_or_Sort(), DoFirst(), BeginStep, DoBefore(), Step looping until all are finished, DoAfter(), DoAlmostLast(), EndStep, DoLast().

Can do multiple time-steps here inside one landscape time-step (a day). This is used in the roe deer model to provide 10 minute behavioural time-steps.

It is necessary to remove any dead animals before the timestep starts. It is possible that animals are killed after their population manager Run method has been executed. This is the case with geese and hunters. Checking death first prevents this becomming a problem.

Definition at line 349 of file PopulationManager.cpp.

References cfg_CatastropheEventStartYear, cfg_CIPEGridOutput_day, cfg_CIPEGridOutput_Interval, cfg_CIPEGridOutput_used, cfg_ReallyBigOutput_day1, cfg_ReallyBigOutput_day2, cfg_ReallyBigOutput_day3, cfg_ReallyBigOutput_day4, cfg_ReallyBigOutput_interval, cfg_ReallyBigOutput_used, cfg_ReallyBigOutputFirstYear, cfg_RipleysOutput_day, cfg_RipleysOutput_interval, cfg_RipleysOutput_used, cfg_RipleysOutputFirstYear, cfg_RipleysOutputMonthly_used, CfgInt::value(), and CfgBool::value().

                                           {
  for ( int TSteps = 0; TSteps < NoTSteps; TSteps++ )
  {
      unsigned size2;
      unsigned size1 =  (unsigned) TheArray.size();
      for ( unsigned listindex = 0; listindex < size1; listindex++ )
      {
          // Must check each object in the list for m_CurrentStateNo==-1
          m_LiveArraySize[listindex] = PartitionLiveDead(listindex);
      }
#ifdef __ALMASS_VISUAL
      if (m_MainForm!=NULL)
      {
          int n = 0;
          for ( unsigned listindex = 0; listindex < size1; listindex++ ) n += (int) m_LiveArraySize[ listindex ];
          //if (n>0) DisplayLocations();
      }
#endif
      // begin step actions ...
      // set all stepdone to false.... is this really necessary??
      for ( unsigned listindex = 0; listindex < size1; listindex++ )
      {
          size2 = (unsigned) GetLiveArraySize(listindex);
          for ( unsigned j = 0; j < size2; j++ )
          {
              TheArray[ listindex ] [ j ]->SetStepDone( false );
          }
      }

      for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
          // Call the Shuffle/Sort procedures
          Shuffle_or_Sort( listindex );
      }
      // Need to check if Ripleys Statistic needs to be saved
      if ( cfg_RipleysOutput_used.value() ) {
          int Year = m_TheLandscape->SupplyYearNumber();
          if (Year>=cfg_RipleysOutputFirstYear.value()) {
              if ( Year % cfg_RipleysOutput_interval.value() == 0 ) {
                  int day = m_TheLandscape->SupplyDayInYear();
                  if ( cfg_RipleysOutput_day.value() == day ) {
                      // Do the Ripley Probe
                      TheRipleysOutputProbe( RipleysOutputPrb );
                      TheNWordOutputProbe(); // These two go hand in hand.
                  }
              }
          }
      }
    // Need to check if Monthly Ripleys Statistic needs to be saved
    if ( cfg_RipleysOutputMonthly_used.value() ) {
        if (m_TheLandscape->SupplyDayInMonth()==1) {
            int Year = m_TheLandscape->SupplyYearNumber();
            if (Year>=cfg_RipleysOutputFirstYear.value()) {
                if ( Year % cfg_RipleysOutput_interval.value() == 0 ) {
                    int month = m_TheLandscape->SupplyMonth();
                    // Do the Ripley Probe
                    switch (month) {
                        case 1: TheRipleysOutputProbe( RipleysOutputPrb1 );
                            break;
                        case 2: TheRipleysOutputProbe( RipleysOutputPrb2 );
                            break;
                        case 3: TheRipleysOutputProbe( RipleysOutputPrb3 );
                            break;
                        case 4: TheRipleysOutputProbe( RipleysOutputPrb4 );
                            break;
                        case 5: TheRipleysOutputProbe( RipleysOutputPrb5 );
                            break;
                        case 6: TheRipleysOutputProbe( RipleysOutputPrb6 );
                            break;
                        case 7: TheRipleysOutputProbe( RipleysOutputPrb7 );
                            break;
                        case 8: TheRipleysOutputProbe( RipleysOutputPrb8 );
                            break;
                        case 9: TheRipleysOutputProbe( RipleysOutputPrb9 );
                            break;
                        case 10: TheRipleysOutputProbe( RipleysOutputPrb10 );
                            break;
                        case 11: TheRipleysOutputProbe( RipleysOutputPrb11 );
                            break;
                        case 12: TheRipleysOutputProbe( RipleysOutputPrb12 );
                            break;
                    }
                }
            }
        }
    }
    // Need to check if Really Big Probe needs to be saved
    if ( cfg_ReallyBigOutput_used.value() ) {
      int Year = m_TheLandscape->SupplyYearNumber();
      if (Year>=cfg_ReallyBigOutputFirstYear.value()) {
          if ( Year % cfg_ReallyBigOutput_interval.value() == 0 ) {
            int day = m_TheLandscape->SupplyDayInYear();
            if (( cfg_ReallyBigOutput_day1.value() == day )|| ( cfg_ReallyBigOutput_day2.value() == day )|| ( cfg_ReallyBigOutput_day3.value() == day )|| ( cfg_ReallyBigOutput_day4.value() == day )||( cfg_ReallyBigOutput_day1.value() == -1 ))
            {
              // Do the Ripley Probe
              TheReallyBigOutputProbe();
            }
          }
        }
    }
    // Need to check if CIPEGrid Statistic needs to be saved
    if ( cfg_CIPEGridOutput_used.value() ) {
      int Year = m_TheLandscape->SupplyYearNumber();
      if ( Year % cfg_CIPEGridOutput_Interval.value() == 0 ) {
        int day = m_TheLandscape->SupplyDayInYear();
        if ( cfg_CIPEGridOutput_day.value() == day ) {
          // Do the Ripley Probe
          TheCIPEGridOutputProbe();
        }
      }
    }
    int yr=m_TheLandscape->SupplyYearNumber();
    if ( yr > cfg_CatastropheEventStartYear.value() ) {
        if (m_catastrophestartyear==-1) m_catastrophestartyear=yr;
        Catastrophe(); // This method must be overidden in descendent classes
    }
    DoFirst();
    // call the begin-step-method of all objects
    for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
        size2 = (unsigned)GetLiveArraySize( listindex );
        for (unsigned j = 0; j < size2; j++)
        TheArray[ listindex ] [ j ]->BeginStep();
    }
    DoBefore();
    // call the step-method of all objects
    do {
      for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
          size2 = (unsigned)GetLiveArraySize( listindex );
          for (unsigned j = 0; j < size2; j++) {
          TheArray[ listindex ] [ j ]->Step();
        }
      } // for listindex
    } while ( !StepFinished() );
    DoAfter();
    // call the end-step-method of all objects
    for ( unsigned listindex = 0; listindex < size1; listindex++ ) {
        size2 = (unsigned)GetLiveArraySize( listindex );
        for (unsigned j = 0; j < size2; j++) {
        TheArray[ listindex ] [ j ]->EndStep();
      }
    }
    // ----------------
    // end of this step actions
    // For each animal list
    DoAlmostLast();

DoLast();
  } // End of time step loop
}

void Population_Manager::SetNoProbes ( int  a_pn )

inline

Definition at line 406 of file populationmanager.h.

{ m_NoProbes=a_pn; }

void Population_Manager::Shuffle ( unsigned  Type )

protected

Run once through the list swapping randomly chosen elements

Definition at line 1125 of file PopulationManager.cpp.

                                                {
    unsigned s = (unsigned)GetLiveArraySize( Type );
  for ( unsigned i = 0; i < s; i++ ) {
    TAnimal * temp;
    unsigned a = random( s );
    unsigned b = random( s );
    temp = TheArray[ Type ] [ a ];
    TheArray[ Type ] [ a ] = TheArray[ Type ] [ b ];
    TheArray[ Type ] [ b ] = temp;
  }
}

void Population_Manager::Shuffle_or_Sort ( unsigned  Type )

protected

This method is used to determine whether the array of animals should be shuffled or sorted.
To do nothing ensure that the BeforeStepActions[] is set appropriately // 0 = Shuffle, 1 = SortX, 2 = SortY, 3 = sortXIndex, 4 = do nothing

Definition at line 1143 of file PopulationManager.cpp.

References g_rand_uni.

                                                        {
  switch ( BeforeStepActions[ Type ] ) {
    case 0:
      Shuffle( Type );
      break;
    case 1:
      SortX( Type );
      break;
    case 2:
      SortY( Type );
      break;
    case 3:
      SortXIndex( Type );
      break;
    case 4: // Do nothing
      break;
    case 5: 
      if (g_rand_uni() < double (1/500)) Shuffle( Type );
      break;
    default:
      m_TheLandscape->Warn( "Population_Manager::Shuffle_or_Sort- BeforeStepAction Unknown", NULL );
      exit( 1 );
  }
}

void Population_Manager::SortState ( unsigned  Type )

protected

Sort TheArray w.r.t. the current state attribute

Definition at line 1069 of file PopulationManager.cpp.

                                                  {
  sort( TheArray[ Type ].begin(), TheArray[ Type ].end(), CompareState() );
}

void Population_Manager::SortStateR ( unsigned  Type )

protected

Sort TheArray w.r.t. the current state attribute in reverse order

Definition at line 1078 of file PopulationManager.cpp.

                                                 {
    sort(TheArray[Type].begin(), TheArray[Type].begin()+m_LiveArraySize[Type], CompareStateR());
}

void Population_Manager::SortX ( unsigned  Type )

protected

Sort TheArray w.r.t. the m_Location_x attribute

Definition at line 1049 of file PopulationManager.cpp.

                                              {
    vector<TAnimal*>::iterator nth = TheArray[Type].begin() + m_LiveArraySize[Type];
    sort( TheArray[ Type ].begin(), nth, CompareX() );
}

void Population_Manager::SortXIndex ( unsigned  Type )

protected

Sort TheArray w.r.t. the m_Location_x attribute, and make an indexing array

Definition at line 1097 of file PopulationManager.cpp.

                                                   {
    vector<TAnimal*>::iterator nth = TheArray[Type].begin() + m_LiveArraySize[Type];
    sort(TheArray[Type].begin(), nth, CompareX());
  unsigned s = (unsigned)GetLiveArraySize( Type );
  // Now make the index array to X;
  int counter = 0;
  int x;
  // for each individual
  for ( unsigned i = 0; i < s; i++ ) {
    // Get Next co-ordiated
    x = TheArray[ Type ] [ i ]->Supply_m_Location_x();
    // fill gaps up to x
    while ( counter < x ) IndexArrayX[ Type ] [ counter++ ] = -1;
    if ( x == counter ) {
      IndexArrayX[ Type ] [ counter++ ] = i;
    }
  }
  // Fill up the rest of the array with -1;
  for ( int c = counter; c < 10000; c++ ) {
    IndexArrayX[ Type ] [ c ] = -1;
  }
}

void Population_Manager::SortY ( unsigned  Type )

protected

Sort TheArray w.r.t. the m_Location_y attribute

Definition at line 1059 of file PopulationManager.cpp.

                                              {
    vector<TAnimal*>::iterator nth = TheArray[Type].begin() + m_LiveArraySize[Type];
    sort(TheArray[Type].begin(), nth, CompareY());
}

char * Population_Manager::SpeciesSpecificReporting	(	int	a_species,
		int	a_time
	)

This method handles species specific outputs. This is one place to do it. More commonly this is done in descendent classes

Definition at line 1191 of file PopulationManager.cpp.

References g_str.

                                                                            {
  strcpy(g_str,"");
// Vole Model
  if ( a_species == 1 ) {
/*
// The next lines are obselete code from genetic simulations
float MeanNoAlleles;
    float MeanHO;
    float MeanHE;
    unsigned size;

    if ( m_time % ( 365 * 24 * 60 ) == 0 ) // End of year
    {

      // empty the GenStruc data
      for ( int ProbeNo = 0; ProbeNo < ( int )m_NoProbes; ProbeNo++ ) {
        fprintf( m_GeneticsFile, "%d ", m_time );
        int TotalSize = 0;
        m_AManager->AlFreq->Flush();
        for ( unsigned listindex = 0; listindex <= 1; listindex++ ) {
          size = 0;
          m_AManager->TheGeneticProbe( listindex, ProbeNo, size );
          TotalSize += size;
        }
        if ( TotalSize > 0 ) {
          m_AManager->AlFreq->CalcAF();
          m_AManager->AlFreq->CalcNoAlleles();
          m_AManager->AlFreq->CalcHE();
          m_AManager->AlFreq->CalcHO( TotalSize );
        }
        // Get the means
        // For N alleles
        int NA = 0;
        float NHO = 0;
        float NHE = 0;
        for ( int l = 0; l < 16; l++ ) {
          NA += m_AManager->AlFreq->SupplyNoAlleles( l );
        }
        MeanNoAlleles = ( float )NA / 16.0;
        for ( int l = 0; l < 16; l++ ) {
          NHO += m_AManager->AlFreq->SupplyHO( l );
        }
        MeanHO = NHO / 16.0;
        for ( int l = 0; l < 16; l++ ) {
          NHE += m_AManager->AlFreq->SupplyHE( l );
        }
        MeanHE = NHE / 16.0;

        // Do some output
        // Output is to two files, the genetics file and the AllelerequencyFile
        fprintf( m_GeneticsFile, "%2.2f ", MeanNoAlleles );
        fprintf( m_GeneticsFile, "%1.3f ", MeanHO );
        fprintf( m_GeneticsFile, "%1.3f ", MeanHE );
        for ( int l = 0; l < 16; l++ ) {
          fprintf( m_GeneticsFile, "%04i ", m_AManager->AlFreq->SupplyNoAlleles( l ) );
        }
        for ( int l = 0; l < 16; l++ ) {
          fprintf( m_GeneticsFile, "%1.3f ", m_AManager->AlFreq->SupplyHO( l ) );
        }
        for ( int l = 0; l < 16; l++ ) {
          fprintf( m_GeneticsFile, "%1.3f ", m_AManager->AlFreq->SupplyHE( l ) );
        }
        fprintf( m_GeneticsFile, "\n" );
        fprintf( m_AlleleFreqsFile, "%d ", m_time );
        for ( int l = 0; l < 16; l++ ) {
          for ( int al = 0; al < 4; al++ ) {
            fprintf( m_AlleleFreqsFile, "%1.3f ", m_AManager->AlFreq->SupplyAF( l, al ) );
          }
        }
        fprintf( m_AlleleFreqsFile, "\n" );
      }
      // make sure progress reaches the disk
      fflush( m_GeneticsFile );
      fflush( m_AlleleFreqsFile );
    }

    if ( cfg_UseEasyPop.value()) {
      int targettime=a_time % ( 365 * 100 );
      if ( (  targettime == 59 ) ||(targettime == 181)||(targettime ==304)||(targettime ==59+365)||(targettime ==181+365)||(targettime ==304+365)) {
          for ( unsigned listindex = 0; listindex <= 1; listindex++ ) {
            GeneticsResultsOutput( m_EasyPopRes, listindex);
        }
        fflush( m_EasyPopRes );
      }
    }
*/
    /* Three times a year reporting
    if ( m_time % 365 == 60 ) ProbeReportNow( m_time );
    if ( m_time % 365 == 152 ) ProbeReportNow( m_time );
    if ( m_time % 365 == 273 ) ProbeReportNow( m_time ); */
    ProbeReport( a_time );
#ifdef __SpecificPesticideEffectsVinclozolinLike__
    ImpactProbeReport( a_time );
#endif
#ifdef __WithinOrchardPesticideSim__
    ImpactProbeReport( a_time );
#endif

  }
  // Skylark Model
  else if ( a_species == 0 ) {
    int No;
    int a_day = a_time % 365;
    if ( a_time % 365 == 364 )
    {
      //Write the Breeding Attempts Probe
      int BreedingFemales, YoungOfTheYear, TotalPop, TotalFemales, TotalMales, BreedingAttempts;
      int No = TheBreedingSuccessProbe( BreedingFemales, YoungOfTheYear, TotalPop, TotalFemales, TotalMales, BreedingAttempts );
      float bs = 0;
      if ( BreedingFemales > 0 ) {
        bs = No / ( float )BreedingFemales; //bs = successful breeding attempt per attempting to breed female
      }
      BreedingSuccessProbeOutput( bs, BreedingFemales, YoungOfTheYear, TotalPop,
           TotalFemales, TotalMales, a_time, BreedingAttempts );
    }
    if ( a_day == 152 ) {
      // Need to fill in the landscape from 1st June, it will change before
      // the count of fledgelings is needed
      m_TheLandscape->FillVegAreaData();
    }
    if ( a_day == 197 ) {
      for ( int ProbeNo = 0; ProbeNo < m_NoProbes; ProbeNo++ ) {
        No = TheFledgelingProbe();
        // Do some output
        FledgelingProbeOutput( No, a_time );
      }
    }
#ifdef __SKPOM
    // This is clunky but for purposes of validation we want probes throughout the year
    // First get the breeding pairs data.
    BreedingPairsOutput(a_day);
#else
    ProbeReport( a_time );
#endif
  }
  else return ProbeReport( a_time );
  return g_str;
}

bool Population_Manager::StepFinished ( void  )

protectedvirtual

Overrides the population manager StepFinished - there is no chance that hunters do not finish a step behaviour.

Returns true if and only if all objects have finished the current step

Definition at line 509 of file PopulationManager.cpp.

                                            {
  for ( unsigned listindex = 0; listindex < TheArray.size(); listindex++ ) {
      for (unsigned j = 0; j < (unsigned)GetLiveArraySize( listindex ); j++) {
      if ( TheArray[ listindex ] [ j ]->GetStepDone() == false ) {
        return false;
      }
    }
  }
  return true;
}

virtual int Population_Manager::SupplyCovPosx ( int  )

inlinevirtual

Definition at line 607 of file populationmanager.h.

                                   {
    return 0;
  }

virtual int Population_Manager::SupplyCovPosy ( int  )

inlinevirtual

Definition at line 610 of file populationmanager.h.

                                   {
    return 0;
  }

unsigned Population_Manager::SupplyListIndexSize ( )

inline

Definition at line 439 of file populationmanager.h.

                                 {
    return (unsigned)TheArray.size();
  }

const char* Population_Manager::SupplyListName ( int  i )

inline

Definition at line 449 of file populationmanager.h.

                                      {
    return m_ListNames[ i ];
  }

int Population_Manager::SupplyListNameLength ( )

inline

Definition at line 436 of file populationmanager.h.

                             {
    return m_ListNameLength;
  }

unsigned Population_Manager::SupplyListSize ( unsigned  listindex )

inline

Definition at line 442 of file populationmanager.h.

                                                {
    return (unsigned) TheArray[ listindex ].size();
  }

virtual void Population_Manager::SupplyLocXY ( unsigned  listindex, unsigned  j, int &  x, int &  y  )

inlinevirtual

Definition at line 464 of file populationmanager.h.

                                                                               {
    x = TheArray[ listindex ] [ j ]->Supply_m_Location_x();
    y = TheArray[ listindex ] [ j ]->Supply_m_Location_y();
  }

virtual int Population_Manager::SupplyPegPosx ( int  )

inlinevirtual

Definition at line 601 of file populationmanager.h.

                                   {
    return 0;
  }

virtual int Population_Manager::SupplyPegPosy ( int  )

inlinevirtual

Definition at line 604 of file populationmanager.h.

                                   {
    return 0;
  }

int Population_Manager::SupplySimH ( )

inline

Definition at line 430 of file populationmanager.h.

                   {
    return SimH;
  }

int Population_Manager::SupplySimW ( )

inline

Definition at line 427 of file populationmanager.h.

                   {
    return SimW;
  }

int Population_Manager::SupplyState ( unsigned  listindex, unsigned  j  )

inline

IntArray100 * SupplyStateList() { return & StateList; }

Definition at line 461 of file populationmanager.h.

                                                    {
    return TheArray[ listindex ] [ j ]->WhatState();
  }

const char* Population_Manager::SupplyStateNames ( int  i )

inline

Definition at line 468 of file populationmanager.h.

                                        {
    return StateNames[ i ];
  }

unsigned Population_Manager::SupplyStateNamesLength ( )

inline

Definition at line 471 of file populationmanager.h.

                                    {
    return StateNamesLength;
  }

int Population_Manager::SupplyStepSize ( )

inline

Definition at line 424 of file populationmanager.h.

                       {
    return m_StepSize;
  }

virtual int Population_Manager::TheBreedingFemalesProbe ( int  )

inlinevirtual

Definition at line 624 of file populationmanager.h.

                                             {
    return 0;
  }

virtual int Population_Manager::TheBreedingSuccessProbe ( int &  , int &  , int &  , int &  , int &  , int &    )

inlinevirtual

Definition at line 632 of file populationmanager.h.

                                                                                       {
         return 0;
  }

void Population_Manager::TheCIPEGridOutputProbe ( )

virtual

This method MUST be overridden in descendent classes, if you want it to work

Definition at line 799 of file PopulationManager.cpp.

                                                {
}

virtual int Population_Manager::TheFledgelingProbe ( )

inlinevirtual

Definition at line 627 of file populationmanager.h.

                                   {
    return 0;
  }

virtual void Population_Manager::TheGeneticProbe ( unsigned  , int  , unsigned &    )

inlinevirtual

Definition at line 637 of file populationmanager.h.

                                                               {
  }

virtual void Population_Manager::TheNWordOutputProbe ( )

inlinevirtual

Reimplemented in Rabbit_Population_Manager.

Definition at line 542 of file populationmanager.h.

{};

void Population_Manager::TheReallyBigOutputProbe ( )

virtual

This method must be overridden in descendent classes

Definition at line 989 of file PopulationManager.cpp.

                                                 {
}

void Population_Manager::TheRipleysOutputProbe ( FILE *  a_prb )

virtual

This method must be overridden in descendent classes

Definition at line 994 of file PopulationManager.cpp.

                                                       {
}

Member Data Documentation

unsigned Population_Manager::BeforeStepActions[10]

protected

Definition at line 511 of file populationmanager.h.

FILE* Population_Manager::CIPEGridOutputPrb

protected

Definition at line 567 of file populationmanager.h.

FILE* Population_Manager::CIPEGridOutputPrbB

protected

Definition at line 568 of file populationmanager.h.

int Population_Manager::IndexArrayX[5][10000]

Definition at line 480 of file populationmanager.h.

long int Population_Manager::lamdagrid[2][257][257]

protected

Definition at line 578 of file populationmanager.h.

FILE* Population_Manager::m_AlleleFreqsFile

protected

Definition at line 498 of file populationmanager.h.

int Population_Manager::m_catastrophestartyear

protected

Definition at line 502 of file populationmanager.h.

int* Population_Manager::m_cgridcount

protected

Definition at line 571 of file populationmanager.h.

int Population_Manager::m_cgridcountwidth

protected

Definition at line 573 of file populationmanager.h.

int Population_Manager::m_cipegridsize

protected

Definition at line 575 of file populationmanager.h.

FILE* Population_Manager::m_EasyPopRes

protected

Definition at line 499 of file populationmanager.h.

FILE* Population_Manager::m_GeneticsFile

protected

Definition at line 497 of file populationmanager.h.

int* Population_Manager::m_gridcount[4]

protected

Definition at line 572 of file populationmanager.h.

int Population_Manager::m_gridcountsize[4]

protected

Definition at line 576 of file populationmanager.h.

int Population_Manager::m_gridcountwidth[4]

protected

Definition at line 574 of file populationmanager.h.

unsigned Population_Manager::m_ListNameLength

protected

Definition at line 508 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager().

const char* Population_Manager::m_ListNames[10]

protected

Definition at line 507 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager().

vector<unsigned> Population_Manager::m_LiveArraySize

protected

Definition at line 495 of file populationmanager.h.

int Population_Manager::m_NoProbes

protected

Definition at line 496 of file populationmanager.h.

TTypesOfPopulation Population_Manager::m_population_type

protected

Definition at line 553 of file populationmanager.h.

int Population_Manager::m_SeasonNumber

protected

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

Definition at line 513 of file populationmanager.h.

char Population_Manager::m_SimulationName[255]

Definition at line 484 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::Rabbit_Population_Manager().

int Population_Manager::m_StepSize

protected

Definition at line 503 of file populationmanager.h.

Landscape* Population_Manager::m_TheLandscape

Definition at line 486 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::AssignStaticVariables(), Rabbit_Population_Manager::ClassifyHabitat(), Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::DoLast(), Rabbit_Population_Manager::PreProcessWarrenLocations(), Rabbit_Population_Manager::Rabbit_Population_Manager(), and Rabbit_Population_Manager::WarrenLegalPos().

FILE* Population_Manager::NWordOutputPrb

protected

Definition at line 570 of file populationmanager.h.

bool Population_Manager::ProbesSet

Definition at line 485 of file populationmanager.h.

FILE* Population_Manager::ReallyBigOutputPrb

protected

Definition at line 569 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb

protected

Definition at line 554 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb1

protected

Definition at line 555 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb10

protected

Definition at line 564 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb11

protected

Definition at line 565 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb12

protected

Definition at line 566 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb2

protected

Definition at line 556 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb3

protected

Definition at line 557 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb4

protected

Definition at line 558 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb5

protected

Definition at line 559 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb6

protected

Definition at line 560 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb7

protected

Definition at line 561 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb8

protected

Definition at line 562 of file populationmanager.h.

FILE* Population_Manager::RipleysOutputPrb9

protected

Definition at line 563 of file populationmanager.h.

int Population_Manager::SimH

Definition at line 482 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::PreProcessWarrenLocations(), and Rabbit_Population_Manager::Rabbit_Population_Manager().

unsigned Population_Manager::SimHH

Definition at line 483 of file populationmanager.h.

int Population_Manager::SimW

Definition at line 482 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::PreProcessWarrenLocations(), and Rabbit_Population_Manager::Rabbit_Population_Manager().

unsigned Population_Manager::SimWH

Definition at line 483 of file populationmanager.h.

const char* Population_Manager::StateNames[100]

protected

Definition at line 501 of file populationmanager.h.

unsigned Population_Manager::StateNamesLength

protected

Definition at line 505 of file populationmanager.h.

FILE* Population_Manager::TestFile

protected

Definition at line 509 of file populationmanager.h.

FILE* Population_Manager::TestFile2

protected

Definition at line 510 of file populationmanager.h.

vector< TListOfAnimals > Population_Manager::TheArray

protected

Definition at line 504 of file populationmanager.h.

Referenced by Rabbit_Population_Manager::CreateObjects(), Rabbit_Population_Manager::DoFirst(), Rabbit_Population_Manager::PreProcessWarrenLocations(), Rabbit_Population_Manager::WarrenLegalPos(), and Rabbit_Population_Manager::~Rabbit_Population_Manager().

probe_data* Population_Manager::TheProbe[100]

Definition at line 481 of file populationmanager.h.

---

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

• D:/CJT/Repos/ALMaSS_all/BatchALMaSS/populationmanager.h
• D:/CJT/Repos/ALMaSS_all/BatchALMaSS/PopulationManager.cpp