MPStatHandler Class Reference

A StatHandler for the Metapop SimComponent. More...

#include <MPStatHandler.h>

Inheritance diagram for MPStatHandler:

Collaboration diagram for MPStatHandler:

Public Member Functions
	MPStatHandler ()
virtual	~MPStatHandler ()
virtual bool	setStatRecorders (std::string &token)
void	setStatsForDemography (age_t AGE)
void	setStatsForPop ()
void	setStatsForPopPerPatch ()
void	setStatsForMigrants ()
void	setStatsForMigrantsPerPatch ()
void	addIndNumPerPatch (sex_t SEX, age_t AGE)
void	addPatchAge ()
Migration
double	getMeanEmigrantPerPatch ()
double	getMeanImigrantPerPatch ()
double	getMeanMigrantRatio ()
double	getMeanResidantPerPatch ()
double	getMeanKolonisersProportion ()
double	getMeanKolonisersPerPatch ()
double	getEmigrantInPatch (unsigned int i)
double	getResidantInPatch (unsigned int i)
double	getImigrateInPatch (unsigned int i)
double	getKolonisersInPatch (unsigned int i)
Patch extinction
void	setObsrvdExtinctionRate ()
double	getObsrvdExtinctionRate ()
double	get_isAlive ()
double	getPatchAge (unsigned int i)
double	getMeanPatchAge ()
Demography
double	getAdultSexRatio ()
double	getOffsprgSexRatio ()
double	getPatchSize (unsigned int age, unsigned int patch)
double	getPopulationSize (unsigned int age)
double	getMeanPatchSize (unsigned int age)
double	getMeanPatchSizePerSex (unsigned int sex, unsigned int age)
double	getMeanPatchDensity (age_t AGE)
double	getMeanPatchDensityVariance (age_t AGE)
double	getFemNumber (unsigned int i)
double	getMalNumber (unsigned int i)
double	getOffFemNumber (unsigned int i)
double	getOffMalNumber (unsigned int i)
double	getMeanAssignedFecundity (unsigned int sex)
double	getMeanMatings (unsigned int sex)
double	setReproductiveStats (unsigned int sex)
double	getReproductiveVar ()
Kinship
void	setKinship ()
void	setKinClassCounter (Individual *I1, Individual *I2)
double	getSibProportion (unsigned int i)
Pedegree
void	setPedegreeCount ()
double	getPedProportion (unsigned int i)
Public Member Functions inherited from StatHandler< MPStatHandler >
	StatHandler ()
virtual	~StatHandler ()
virtual void	clear ()
	Empties the _recorders list, they are destroyed in StatHandlerBase::reset(). More...
virtual StatRecorder< MPStatHandler > *	add (std::string Title, std::string Name, age_t AGE, unsigned int ARG1, unsigned int ARG2, double(SH::*getStatNoArg)(void), double(SH::*getStatOneArg)(unsigned int), double(SH::*getStatTwoArg)(unsigned int, unsigned int), void(SH::*setStat)(void))
	Adds a StatRecorder to the list, it is also added to the StatHandlerBase::_stats list. More...
Public Member Functions inherited from StatHandlerBase
	StatHandlerBase ()
virtual	~StatHandlerBase ()
virtual void	reset ()
	Empties the _stats list and calls clear() (defined in the derived class). More...
Metapop *	get_pop_ptr ()
void	set_service (StatServices *srv)
StatServices *	get_service ()
unsigned int	getOccurrence ()
unsigned int	getNumOccurrences ()
unsigned int	getCurrentOccurrence ()
unsigned int	getNbRecorders ()
std::list< StatRecBase * > &	getStats ()
virtual void	add (StatRecBase *rec)
virtual void	init ()
virtual void	update ()
	This function is left empty as the StatServices calls StatRecorder::setVal directly. More...
Public Member Functions inherited from Handler
virtual void	init ()=0
	Inits state. More...
virtual void	update ()=0
	Updates the handler state. More...
virtual	~Handler ()

Private Attributes
double	meanEmigrant
double	meanImigrant
double	meanResidant
double	meanKolonisers
double	meanDeadDisp
double	ObservedExtinctionRate
double	_sib_prop [5]
double	_ped_prop [5]
double	_var_reprod_success

Additional Inherited Members
Protected Types inherited from StatHandler< MPStatHandler >
typedef std::list< StatRecorder< MPStatHandler > * >::iterator	REC_IT
Protected Attributes inherited from StatHandler< MPStatHandler >
std::list< StatRecorder< MPStatHandler > * >	_recorders
	The list of stat recorders. More...
Protected Attributes inherited from StatHandlerBase
Metapop *	_pop
	Link to the current population, set through the link to the StatService. More...

Detailed Description

A StatHandler for the Metapop SimComponent.

Constructor & Destructor Documentation

MPStatHandler()

MPStatHandler::MPStatHandler ( )

inline

{ }

~MPStatHandler()

virtual MPStatHandler::~MPStatHandler ( )

inlinevirtual

{}

Member Function Documentation

addIndNumPerPatch()

void MPStatHandler::addIndNumPerPatch	(	sex_t	SEX,
		age_t	AGE
	)

{
  double (MPStatHandler::* setter) (unsigned int) = 0;
  
  if (SEX) {
    
    if (AGE == ADULTS) {
      setter = &MPStatHandler::getFemNumber;
    } else if (AGE == OFFSPRG) {
      setter =  &MPStatHandler::getOffFemNumber;
    }
  
  } else {
    
    if (AGE == ADULTS) {
      setter = &MPStatHandler::getMalNumber;
    } else if (AGE == OFFSPRG) {
      setter =  &MPStatHandler::getOffMalNumber;
    }
    
  }
  
  string suffix = (AGE == ADULTS ? "adlt.":"off.");
  string name = (SEX == FEM ? suffix + "fem." : suffix + "mal.");
  string patch = "p1";
    
  add("", name + patch, AGE, 0, 0, 0, setter, 0, 0);
  for(unsigned int i = 1; i < _pop->getPatchNbr(); i++) {
    patch = "p" + tstring::int2str(i+1);
    add("", name + patch, AGE, i, 0, 0, setter, 0, 0);
  }
}

References StatHandlerBase::_pop, StatHandler< MPStatHandler >::add(), ADULTS, FEM, getFemNumber(), getMalNumber(), getOffFemNumber(), getOffMalNumber(), Metapop::getPatchNbr(), tstring::int2str(), and OFFSPRG.

Referenced by setStatRecorders(), and setStatsForPopPerPatch().

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addPatchAge()

void MPStatHandler::addPatchAge

(

)

{
  
  std::ostringstream name, sub_name;
  
  add("Patch 1 age","age.patch1",ALL,0,0,0,&MPStatHandler::getPatchAge,0,0);
  for(unsigned int i = 1; i < _pop->getPatchNbr(); i++) {
    name<<"Patch "<<i+1<<" age";
    sub_name<<"age.patch"<<i+1;
    add(name.str(),sub_name.str(),ALL,i,0,0,&MPStatHandler::getPatchAge,0,0);
    name.str("");
    sub_name.str("");
  }
  
  add("Mean patch age","patch.avg.age",ALL,0,0,&MPStatHandler::getMeanPatchAge,0,0,0);
  add("Extinction rate","extrate",ALL,0,0,&MPStatHandler::getObsrvdExtinctionRate,0,0,
      &MPStatHandler::setObsrvdExtinctionRate);
}

References StatHandlerBase::_pop, StatHandler< MPStatHandler >::add(), ALL, getMeanPatchAge(), getObsrvdExtinctionRate(), getPatchAge(), Metapop::getPatchNbr(), and setObsrvdExtinctionRate().

Referenced by setStatsForPopPerPatch().

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get_isAlive()

double MPStatHandler::get_isAlive

(

)

getAdultSexRatio()

double MPStatHandler::getAdultSexRatio

(

)

{return (_pop->size(MAL, ADULTS) != 0 ? (double)_pop->size(FEM, ADULTS)/_pop->size(MAL, ADULTS) : 0);}

References StatHandlerBase::_pop, ADULTS, FEM, MAL, and Metapop::size().

Referenced by setStatRecorders(), and setStatsForPop().

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getEmigrantInPatch()

double MPStatHandler::getEmigrantInPatch

(

unsigned int

i

)

{
  Patch* patch = _pop->getPatch(i);
  return (patch != 0 ? patch->nbEmigrant : 0);
}

References StatHandlerBase::_pop, Metapop::getPatch(), and Patch::nbEmigrant.

Referenced by setStatsForMigrantsPerPatch().

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getFemNumber()

double MPStatHandler::getFemNumber

(

unsigned int

i

)

{return _pop->size(FEM, ADULTS, i);}

References StatHandlerBase::_pop, ADULTS, FEM, and Metapop::size().

Referenced by addIndNumPerPatch().

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getImigrateInPatch()

double MPStatHandler::getImigrateInPatch

(

unsigned int

i

)

{
  Patch* patch = _pop->getPatch(i);
  return (patch != 0 ? (double)patch->nbImigrant/(double)(patch->nbImigrant + patch->nbPhilopat)
          : nanf("NULL"));
}

References StatHandlerBase::_pop, Metapop::getPatch(), Patch::nbImigrant, and Patch::nbPhilopat.

Referenced by setStatsForMigrantsPerPatch().

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getKolonisersInPatch()

double MPStatHandler::getKolonisersInPatch

(

unsigned int

i

)

{
  Patch* patch = _pop->getPatch(i);
  int colon = (patch != 0 ? patch->nbKolonisers : 0);
  return (colon != -1 ? colon : nanf("NULL"));
}

References StatHandlerBase::_pop, Metapop::getPatch(), and Patch::nbKolonisers.

Referenced by setStatsForMigrantsPerPatch().

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getMalNumber()

double MPStatHandler::getMalNumber

(

unsigned int

i

)

{return _pop->size(MAL, ADULTS, i);}

References StatHandlerBase::_pop, ADULTS, MAL, and Metapop::size().

Referenced by addIndNumPerPatch().

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getMeanAssignedFecundity()

double MPStatHandler::getMeanAssignedFecundity

(

unsigned int

sex

)

{
  double mean = 0, sum = 0;
  unsigned int nbpatch = 0;
  Patch* crnt_patch;
 
  if((bool)sex) {
    for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      if(crnt_patch->size(FEM, ADLTx) != 0) {
        nbpatch++;
        sum = 0;
        for(unsigned int j = 0; j < crnt_patch->size(FEM, ADLTx);++j)
          sum += crnt_patch->get(FEM, ADLTx, j)->getFecundity();
        mean += sum/crnt_patch->size(FEM, ADLTx);
      }
    }
  } else {
    for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      if(crnt_patch->size(MAL, ADLTx) != 0) {
        nbpatch++;
        sum = 0;
        for(unsigned int j = 0; j < crnt_patch->size(MAL, ADLTx);++j)
          sum += crnt_patch->get(MAL, ADLTx, j)->getFecundity();
        mean += sum/crnt_patch->size(MAL, ADLTx);
      }
    }
  }
  return (nbpatch != 0 ? mean/nbpatch : nanf("NULL"));
}

References StatHandlerBase::_pop, ADLTx, FEM, Patch::get(), Individual::getFecundity(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, and Patch::size().

getMeanEmigrantPerPatch()

double MPStatHandler::getMeanEmigrantPerPatch

(

)

{
  unsigned int meanM = 0;
 
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++)
    meanM += _pop->getPatch(i)->nbEmigrant;
  meanEmigrant = (double)meanM/_pop->getPatchNbr();
  return meanEmigrant;
}

References StatHandlerBase::_pop, Metapop::getPatch(), Metapop::getPatchNbr(), meanEmigrant, and Patch::nbEmigrant.

Referenced by setStatsForMigrants().

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getMeanImigrantPerPatch()

double MPStatHandler::getMeanImigrantPerPatch

(

)

{
  double meanM = 0,nbpatch = 0;
  Patch* current_patch;
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++) {
    current_patch = _pop->getPatch(i);
    if(!current_patch->get_isExtinct()){
      meanM += current_patch->nbImigrant;
      nbpatch++;
    }
  }
  meanImigrant = (nbpatch != 0 ? meanM/nbpatch : nanf("NULL"));
  return meanImigrant;
}

References StatHandlerBase::_pop, Patch::get_isExtinct(), Metapop::getPatch(), Metapop::getPatchNbr(), meanImigrant, and Patch::nbImigrant.

Referenced by setStatsForMigrants().

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getMeanKolonisersPerPatch()

double MPStatHandler::getMeanKolonisersPerPatch

(

)

{
  double mean = 0,nbpatch = 0;
  Patch* current_patch;
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++){
    current_patch = _pop->getPatch(i);
    if(current_patch->nbKolonisers >= 0) {
      mean += current_patch->nbKolonisers;
      nbpatch++;
    }
  }
  meanKolonisers = (nbpatch != 0 ? mean/nbpatch : nanf("NULL"));
  return meanKolonisers;
}

References StatHandlerBase::_pop, Metapop::getPatch(), Metapop::getPatchNbr(), meanKolonisers, and Patch::nbKolonisers.

Referenced by setStatsForMigrants().

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getMeanKolonisersProportion()

double MPStatHandler::getMeanKolonisersProportion

(

)

{
  double nbpatch = 0, mean = 0;
  Patch* current_patch;
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++){
    current_patch = _pop->getPatch(i);
    if(current_patch->nbKolonisers >= 0) {
      mean += fmin((double)current_patch->nbKolonisers / current_patch->get_K(), 1.0);
      nbpatch++;
    }
  }
 
  return  (nbpatch != 0 ? mean/nbpatch : nanf("NULL"));
}

References StatHandlerBase::_pop, Patch::get_K(), Metapop::getPatch(), Metapop::getPatchNbr(), and Patch::nbKolonisers.

Referenced by setStatsForMigrants().

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getMeanMatings()

double MPStatHandler::getMeanMatings

(

unsigned int

sex

)

{
  double mean = 0, sum = 0;
  unsigned int nbpatch = 0;
  Patch* crnt_patch;
 
  if((bool)sex) {
    for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      if(crnt_patch->size(FEM, ADLTx) != 0) {
        nbpatch++;
        sum = 0;
        for(unsigned int j = 0; j < crnt_patch->size(FEM, ADLTx);++j)
          sum += crnt_patch->get(FEM, ADLTx, j)->getTotMatings();
        mean += sum/crnt_patch->size(FEM, ADLTx);
      }
    }
  } else {
    for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      if(crnt_patch->size(MAL, ADLTx) != 0) {
        nbpatch++;
        sum = 0;
        for(unsigned int j = 0; j < crnt_patch->size(MAL, ADLTx);++j)
          sum += crnt_patch->get(MAL, ADLTx, j)->getTotMatings();
        mean += sum/crnt_patch->size(MAL, ADLTx);
      }
    }
  }
  return (nbpatch != 0 ? mean/nbpatch : nanf("NULL"));
}

References StatHandlerBase::_pop, ADLTx, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTotMatings(), MAL, and Patch::size().

Referenced by setStatRecorders().

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getMeanMigrantRatio()

double MPStatHandler::getMeanMigrantRatio

(

)

{
  return ((meanImigrant+meanResidant) != 0 ? meanImigrant/(meanImigrant+meanResidant) : 0);
}

References meanImigrant, and meanResidant.

Referenced by setStatsForMigrants().

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getMeanPatchAge()

double MPStatHandler::getMeanPatchAge

(

)

{
  int mean = 0;
  for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i)
    mean += _pop->getPatch(i)->get_age();
  return mean/_pop->getPatchNbr();
}

References StatHandlerBase::_pop, Patch::get_age(), Metapop::getPatch(), and Metapop::getPatchNbr().

Referenced by addPatchAge().

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getMeanPatchDensity()

double MPStatHandler::getMeanPatchDensity

(

age_t

AGE

)

{
  double mean = 0;
  unsigned int nb_patch = 0;
  age_idx age = (AGE == ADULTS ? ADLTx : OFFSx);
  
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++) {
    nb_patch += (_pop->size(AGE, i) != 0);
    mean += _pop->getPatch(i)->getDensity(age);
  }
 
  return (nb_patch != 0 ? mean/nb_patch : nanf("NULL"));
}

References StatHandlerBase::_pop, ADLTx, ADULTS, Patch::getDensity(), Metapop::getPatch(), Metapop::getPatchNbr(), OFFSx, and Metapop::size().

Referenced by setStatsForDemography().

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getMeanPatchDensityVariance()

double MPStatHandler::getMeanPatchDensityVariance

(

age_t

AGE

)

{
  unsigned int i,nb_patch;
  vector<double> stat;
  double var = 0, mean = 0, val;
  age_idx age = (AGE == ADULTS ? ADLTx : OFFSx);
  
  for(i = 0; i < _pop->getPatchNbr(); i++) {
    if(_pop->size(AGE,i) != 0){
      val = _pop->getPatch(i)->getDensity(age);
      stat.push_back(val);
      mean += val;
    }
  }
  nb_patch = stat.size();
  mean = (nb_patch != 0 ? mean/nb_patch : 0);
 
  for(i = 0; i < nb_patch; i++)
    var += pow((stat[i]-mean),2);
 
  return (nb_patch != 0 ? var/nb_patch : nanf("NULL"));
}

References StatHandlerBase::_pop, ADLTx, ADULTS, Patch::getDensity(), Metapop::getPatch(), Metapop::getPatchNbr(), OFFSx, and Metapop::size().

Referenced by setStatsForDemography().

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getMeanPatchSize()

double MPStatHandler::getMeanPatchSize

(

unsigned int

age

)

{
  double mean = 0;
  unsigned int nb_patch = 0;
  
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++) {
    nb_patch += (_pop->size(age_t(age),i) != 0);
    mean += _pop->size(age_t(age),i);
  }
  
  return (nb_patch != 0 ? mean/nb_patch : nanf("NULL"));
}

References StatHandlerBase::_pop, Metapop::getPatchNbr(), and Metapop::size().

getMeanPatchSizePerSex()

double MPStatHandler::getMeanPatchSizePerSex	(	unsigned int	sex,
		unsigned int	age
	)

{
  double mean = 0;
  unsigned int nb_patch = 0;
  
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++) {
    nb_patch += (_pop->size(sex_t(sex),age_t(age),i) != 0);
    mean += _pop->size(sex_t(sex),age_t(age),i);
  }
  
  return (nb_patch != 0 ? mean/nb_patch : nanf("NULL"));  
}

References StatHandlerBase::_pop, Metapop::getPatchNbr(), and Metapop::size().

Referenced by setStatsForDemography().

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getMeanResidantPerPatch()

double MPStatHandler::getMeanResidantPerPatch

(

)

{
  double meanR = 0,nbpatch = 0;
  Patch* current_patch;
  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++){
    current_patch = _pop->getPatch(i);
    if(!current_patch->get_isExtinct()){
      meanR += current_patch->nbPhilopat;
      nbpatch++;
    }
  }
  meanResidant = (nbpatch != 0 ? meanR/nbpatch : nanf("NULL"));
  return meanResidant;
}

References StatHandlerBase::_pop, Patch::get_isExtinct(), Metapop::getPatch(), Metapop::getPatchNbr(), meanResidant, and Patch::nbPhilopat.

Referenced by setStatsForMigrants().

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getObsrvdExtinctionRate()

double MPStatHandler::getObsrvdExtinctionRate ( )

inline

{return ObservedExtinctionRate;}

References ObservedExtinctionRate.

Referenced by addPatchAge(), setStatRecorders(), and setStatsForPop().

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getOffFemNumber()

double MPStatHandler::getOffFemNumber

(

unsigned int

i

)

{return _pop->size(FEM, OFFSPRG,i);}

References StatHandlerBase::_pop, FEM, OFFSPRG, and Metapop::size().

Referenced by addIndNumPerPatch().

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getOffMalNumber()

double MPStatHandler::getOffMalNumber

(

unsigned int

i

)

{return _pop->size(MAL, OFFSPRG,i);}

References StatHandlerBase::_pop, MAL, OFFSPRG, and Metapop::size().

Referenced by addIndNumPerPatch().

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getOffsprgSexRatio()

double MPStatHandler::getOffsprgSexRatio

(

)

{return (_pop->size(MAL, OFFSPRG)!= 0 ? (double)_pop->size(FEM, OFFSPRG)/_pop->size(MAL, OFFSPRG) : 0);}

References StatHandlerBase::_pop, FEM, MAL, OFFSPRG, and Metapop::size().

Referenced by setStatRecorders(), and setStatsForPop().

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getPatchAge()

double MPStatHandler::getPatchAge

(

unsigned int

i

)

{
  Patch* patch = _pop->getPatch(i);
  return (patch != 0 ? patch->get_age() : 0);
}

References StatHandlerBase::_pop, Patch::get_age(), and Metapop::getPatch().

Referenced by addPatchAge().

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getPatchSize()

double MPStatHandler::getPatchSize	(	unsigned int	age,
		unsigned int	patch
	)

{return _pop->size(age_t(age), patch);}

References StatHandlerBase::_pop, and Metapop::size().

getPedProportion()

double MPStatHandler::getPedProportion ( unsigned int  i )

inline

{return _ped_prop[i];}

References _ped_prop.

Referenced by setStatRecorders().

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getPopulationSize()

double MPStatHandler::getPopulationSize

(

unsigned int

age

)

{return _pop->size(age_t(age));}

References StatHandlerBase::_pop, and Metapop::size().

Referenced by setStatsForDemography().

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getReproductiveVar()

double MPStatHandler::getReproductiveVar ( )

inline

{return _var_reprod_success;}

References _var_reprod_success.

Referenced by setStatRecorders().

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getResidantInPatch()

double MPStatHandler::getResidantInPatch

(

unsigned int

i

)

{
  Patch* patch = _pop->getPatch(i);
  return (patch != 0 ? patch->nbPhilopat : 0);
}

References StatHandlerBase::_pop, Metapop::getPatch(), and Patch::nbPhilopat.

Referenced by setStatsForMigrantsPerPatch().

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getSibProportion()

double MPStatHandler::getSibProportion ( unsigned int  i )

inline

{return _sib_prop[i];}

References _sib_prop.

Referenced by setStatRecorders().

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setKinClassCounter()

void MPStatHandler::setKinClassCounter	(	Individual *	I1,
		Individual *	I2
	)

{
  //non sibs
  if((I1->getMotherID() != I2->getMotherID()) && (I1->getFatherID() != I2->getFatherID()))
    _sib_prop[0]++;
  
  //maternal half sibs
  else if((I1->getMotherID() == I2->getMotherID()) && (I1->getFatherID() != I2->getFatherID()))
    _sib_prop[1]++;
  
  //paternal half sibs
  else if((I1->getMotherID() != I2->getMotherID()) && (I1->getFatherID() == I2->getFatherID()))
    _sib_prop[2]++;
  
  //full sibs
  else if((I1->getMotherID() == I2->getMotherID()) && (I1->getFatherID() == I2->getFatherID()))
    _sib_prop[3]++;
}  

References _sib_prop, Individual::getFatherID(), and Individual::getMotherID().

Referenced by setKinship().

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setKinship()

void MPStatHandler::setKinship

(

)

{
  unsigned int i,j,k;
  unsigned int patchNbr = this->_pop->getPatchNbr(), Msize=0, Fsize=0;
  Patch* current_patch;
  Individual *I1,*I2;
  
  //counters initialization
  for(i = 0; i < 5; ++i) _sib_prop[i] = 0.0;
  
  for( i = 0; i < patchNbr; ++i) {
    
    current_patch = _pop->getPatch(i);
    
    //male-male
        if ( (Msize = current_patch->size(MAL, OFFSx)) != 0) {
      
          for(j = 0; j < Msize -1; ++j) {
        
        I1 = current_patch->get(MAL, OFFSx, j);
        
                for(k = j+1; k < Msize; ++k) {
          
          I2 = current_patch->get(MAL, OFFSx, k);
          
          setKinClassCounter(I1, I2);
          
                } //end for k < size
        
        //selfed offspring counter:
        if(I1->getIsSelfed()) _sib_prop[4]++;
                
          } //end for j < size-1    
      
      //don't forget the last one!
      if(current_patch->get(MAL, OFFSx, Msize -1)->getIsSelfed()) _sib_prop[4]++;
      
        }//endif
    
    //female-female
        if ( (Fsize = current_patch->size(FEM, OFFSx)) != 0) {
      
          for(j = 0; j < Fsize -1; ++j) {
        
        I1 = current_patch->get(FEM, OFFSx, j);
        
                for(k = j+1; k < Fsize; ++k) {
          
          I2 = current_patch->get(FEM, OFFSx, k);
          
          setKinClassCounter(I1, I2);
          
                } //end for k < size  
        
          //selfed offspring counter:
        if(I1->getIsSelfed()) _sib_prop[4]++;
        
          } //end for j < size-1
      
      //don't forget the last one!
      if(current_patch->get(FEM, OFFSx, Fsize -1)->getIsSelfed()) _sib_prop[4]++;
 
        }//endif
    
    //male-female
    for(j = 0; j < Msize; ++j) {
      
      I1 = current_patch->get(MAL, OFFSx, j);
      
      for(k = 0; k < Fsize; ++k) {
        
        I2 = current_patch->get(FEM, OFFSx, k);
        
        setKinClassCounter(I1, I2);        
      } //end for k
    } //end for j
 
  } //end for i < patchNbr
  
  //total number of pairwise comparisons:
  double tot = _sib_prop[0] + _sib_prop[1] + _sib_prop[2] + _sib_prop[3];
  
  for(i = 0 ; i < 4; ++i) _sib_prop[i] /= tot;
 
  _sib_prop[4] /= _pop->size(OFFSPRG);
}

References StatHandlerBase::_pop, _sib_prop, FEM, Patch::get(), Individual::getIsSelfed(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, OFFSPRG, OFFSx, setKinClassCounter(), Metapop::size(), and Patch::size().

Referenced by setStatRecorders().

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setObsrvdExtinctionRate()

void MPStatHandler::setObsrvdExtinctionRate

(

)

{
  ObservedExtinctionRate = 0;
  
  for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i)
        ObservedExtinctionRate += _pop->getPatch(i)->isEmpty();
  
  ObservedExtinctionRate /= _pop->getPatchNbr();
}

References StatHandlerBase::_pop, Metapop::getPatch(), Metapop::getPatchNbr(), Patch::isEmpty(), and ObservedExtinctionRate.

Referenced by addPatchAge(), setStatRecorders(), and setStatsForPop().

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setPedegreeCount()

void MPStatHandler::setPedegreeCount

(

)

{
  
  unsigned int i,j;
  unsigned int patchNbr = _pop->getPatchNbr();
  Patch* patch;
  
  //counters initialization
  for(i = 0; i < 5; ++i) _ped_prop[i] = 0.0;
  
  for(i = 0; i < patchNbr; ++i) {
    
    patch = _pop->getPatch(i);
    
    //males
    for(j = 0; j < patch->size(MAL, OFFSx); ++j) {
      
      _ped_prop[ patch->get(MAL, OFFSx, j)->getPedigreeClass() ]++;
      
    }  
    
    //females
    for(j = 0; j < patch->size(FEM, OFFSx); ++j) {
      
      _ped_prop[ patch->get(FEM, OFFSx, j)->getPedigreeClass() ]++;
      
    }
    
    
  } //end for i < patchNbr
  
  //total:
  double tot = _ped_prop[0] + _ped_prop[1] + _ped_prop[2] + _ped_prop[3] + _ped_prop[4];
  
  for(i = 0 ; i < 5; ++i) _ped_prop[i] /= tot;
  
}

References _ped_prop, StatHandlerBase::_pop, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getPedigreeClass(), MAL, OFFSx, and Patch::size().

Referenced by setStatRecorders().

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setReproductiveStats()

double MPStatHandler::setReproductiveStats

(

unsigned int

sex

)

{
  double var = 0, mean = 0;
  unsigned int tot_size = _pop->size( (sex_t)sex, ADULTS ), v = 0;
  double *stat;
  Patch *crnt_patch;
 
  if(tot_size == 0) {
    _var_reprod_success = nanf("NULL");
    return nanf("NULL");
  }
  
  stat = new double [tot_size];
  
  //females
  if((bool)sex) {
    
    for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      for(unsigned int j = 0, size = crnt_patch->size(FEM, ADLTx);
          j < size;
          ++j)
      {
        stat[v] = crnt_patch->get(FEM, ADLTx, j)->getTotRealizedFecundity();
        mean += stat[v];
        v++;
      }
    }
    
    mean /= tot_size;
    
    for(unsigned int i = 0; i < tot_size; ++i)
      var += pow( (stat[i] - mean), 2);
   
    var /= tot_size;
  //males
  } else {
    
    for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      for(unsigned int j = 0, size = crnt_patch->size(MAL, ADLTx);
          j < size;
          ++j)
      {
        stat[v] = crnt_patch->get(MAL, ADLTx, j)->getTotRealizedFecundity();
        mean += stat[v];
        v++;
      }
    }
    
    mean /= tot_size;
    
    for(unsigned int i = 0; i < tot_size; ++i)
      var += pow( (stat[i] - mean), 2);
    
    var /= tot_size;
    
  }
  
  _var_reprod_success = var;
  
  delete [] stat;
  
  return mean;
}

References StatHandlerBase::_pop, _var_reprod_success, ADLTx, ADULTS, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTotRealizedFecundity(), MAL, Metapop::size(), and Patch::size().

Referenced by setStatRecorders().

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setStatRecorders()

bool MPStatHandler::setStatRecorders ( std::string &  token )

virtual

Implements StatHandlerBase.

{
#ifdef _DEBUG_
  message("-MPStatHandler::setStatRecorders ");
#endif
  
  if(token.compare("extrate") == 0) {
    
    add("Extinction rate","extrate",ALL,0,0,&MPStatHandler::getObsrvdExtinctionRate,0,0,
        &MPStatHandler::setObsrvdExtinctionRate);
                
  } else if(token.compare("pop") == 0) {
    
    setStatsForPop();
    
  } else if(token.compare("pop.patch") == 0) {
    
    setStatsForPopPerPatch();
    
  } else if(token.compare("off.fem.patch") == 0) {
 
    addIndNumPerPatch(FEM, OFFSPRG);
    
  } else if(token.compare("off.mal.patch") == 0) {
  
    addIndNumPerPatch(MAL, OFFSPRG);
 
  } else if(token.compare("adlt.fem.patch") == 0) {
  
    addIndNumPerPatch(FEM, ADULTS);
 
  } else if(token.compare("adlt.mal.patch") == 0) {
 
    addIndNumPerPatch(MAL, ADULTS);
 
  } else if(token.compare("adlt.sexratio") == 0) {
    
    add("Adults sex ratio","adlt.sexratio",ADULTS,0,0,&MPStatHandler::getAdultSexRatio,0,0,0);
    
  } else if(token.compare("off.sexratio") == 0) {
    
    add("Offspring Sex Ratio","off.sexratio",OFFSPRG,0,0,&MPStatHandler::getOffsprgSexRatio,0,0,0);
    
  } else if(token.compare("migrants") == 0) {
    
    setStatsForMigrants();
    
  } else if(token.compare("migrants.patch") == 0) {
    
    setStatsForMigrantsPerPatch();
    
  } else if(token.compare("demography") == 0) {
    
    setStatsForDemography(OFFSPRG);
    setStatsForDemography(ADULTS);
    
  } else if(token.compare("off.demography") == 0) {
    
    setStatsForDemography(OFFSPRG);
 
  } else if(token.compare("adlt.demography") == 0) {
 
    setStatsForDemography(ADULTS);
    
  } else if(token.compare("fecundity") == 0) {
    
    add("Females assigned fecundity","adlt.femfec",ADULTS,1,0,0,&MPStatHandler::getMeanMatings,0,0);
    add("Females realized fecundity","adlt.femrealfec",ADULTS,1,0,0,&MPStatHandler::setReproductiveStats,0,0);
    add("Females reproductive var  ","adlt.femvarfec",ADULTS,0,0,&MPStatHandler::getReproductiveVar,0,0,0);
    add("Males realized fecundity  ","adlt.malrealfec",ADULTS,0,0,0,&MPStatHandler::setReproductiveStats,0,0);   
    add("Males reproductive var    ","adlt.malvarfec",ADULTS,0,0,&MPStatHandler::getReproductiveVar,0,0,0); 
    
  } else if(token.compare("kinship") == 0) {
    
    add("Proportion of full-sib offspring","off.fsib",OFFSPRG,3,0,0,&MPStatHandler::getSibProportion,0,&MPStatHandler::setKinship);
    add("Proportion of paternal half-sib ","off.phsib",OFFSPRG,2,0,0,&MPStatHandler::getSibProportion,0,0);
    add("Proportion of maternal half-sib ","off.mhsib",OFFSPRG,1,0,0, &MPStatHandler::getSibProportion,0,0);
    add("Proportion of non-sib offspring ","off.nsib",OFFSPRG,0,0,0,&MPStatHandler::getSibProportion,0,0);
    add("Proportion of selfed offspring  ","off.self",OFFSPRG,4,0,0,&MPStatHandler::getSibProportion,0,0);
    
  } else if(token == "pedigree") {
    
    add("Proportion of other deme mated","ped.outb",OFFSPRG,0,0,0,&MPStatHandler::getPedProportion,0,&MPStatHandler::setPedegreeCount);
    add("Proportion of same deme mated ","ped.outw",OFFSPRG,1,0,0,&MPStatHandler::getPedProportion,0,0);
    add("Proportion of half-sib mated ","ped.hsib",OFFSPRG,2,0,0, &MPStatHandler::getPedProportion,0,0);
    add("Proportion of full-sib mated ","ped.fsib",OFFSPRG,3,0,0,&MPStatHandler::getPedProportion,0,0);
    add("Proportion of selfed mated ","ped.self",OFFSPRG,4,0,0,&MPStatHandler::getPedProportion,0,0);    
    
  } else
    return false;
  
  return true;
}

References StatHandler< MPStatHandler >::add(), addIndNumPerPatch(), ADULTS, ALL, FEM, getAdultSexRatio(), getMeanMatings(), getObsrvdExtinctionRate(), getOffsprgSexRatio(), getPedProportion(), getReproductiveVar(), getSibProportion(), MAL, message(), OFFSPRG, setKinship(), setObsrvdExtinctionRate(), setPedegreeCount(), setReproductiveStats(), setStatsForDemography(), setStatsForMigrants(), setStatsForMigrantsPerPatch(), setStatsForPop(), and setStatsForPopPerPatch().

setStatsForDemography()

void MPStatHandler::setStatsForDemography

(

age_t

AGE

)

{
  string suffix = (AGE == ADULTS ? "adlt.":"off.");
  string name = (AGE == ADULTS ? "Adults ":"Offspring ");
  
  add(name + "number", suffix + "nbr", AGE, AGE, 0, 0, &MPStatHandler::getPopulationSize,0,0);
  add(name + "fem nbr", suffix + "nbfem", AGE, FEM, AGE, 0, 0, &MPStatHandler::getMeanPatchSizePerSex,0);
  add(name + "mal nbr", suffix + "nbmal", AGE, MAL, AGE, 0, 0, &MPStatHandler::getMeanPatchSizePerSex,0);
  add(name + "density", suffix + "density", AGE, AGE, 0, 0, &MPStatHandler::getMeanPatchDensity,0,0);
  add(name + "density var", suffix + "dvar", AGE, AGE, 0, 0, &MPStatHandler::getMeanPatchDensityVariance,0,0);
  
}

References StatHandler< MPStatHandler >::add(), ADULTS, FEM, getMeanPatchDensity(), getMeanPatchDensityVariance(), getMeanPatchSizePerSex(), getPopulationSize(), and MAL.

Referenced by setStatRecorders(), and setStatsForPop().

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setStatsForMigrants()

void MPStatHandler::setStatsForMigrants

(

)

{
  add("Emigrant nbr","emigrants",ALL,0,0,&MPStatHandler::getMeanEmigrantPerPatch,0,0,0);
  add("Imigrant nbr","imigrants",ALL,0,0,&MPStatHandler::getMeanImigrantPerPatch,0,0,0);
  add("Residant nbr","residents",ALL,0,0,&MPStatHandler::getMeanResidantPerPatch,0,0,0);
  add("Imigration rate","imigrate",ALL,0,0,&MPStatHandler::getMeanMigrantRatio,0,0,0);
  add("Coloniser nbr","colonisers",ALL,0,0,&MPStatHandler::getMeanKolonisersPerPatch,0,0,0);
  add("Colonisation rate","colonrate",ALL,0,0,&MPStatHandler::getMeanKolonisersProportion,0,0,0);
}

References StatHandler< MPStatHandler >::add(), ALL, getMeanEmigrantPerPatch(), getMeanImigrantPerPatch(), getMeanKolonisersPerPatch(), getMeanKolonisersProportion(), getMeanMigrantRatio(), and getMeanResidantPerPatch().

Referenced by setStatRecorders().

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setStatsForMigrantsPerPatch()

void MPStatHandler::setStatsForMigrantsPerPatch

(

)

{  std::ostringstream name, sub_name;
  
  add("Emigrants patch 1","emigr.p1", ALL,0,0,0,&MPStatHandler::getEmigrantInPatch,0,0);
  for(unsigned int i = 1; i < _pop->getPatchNbr(); i++) {
    name<<"Emigrants patch "<<i+1;
    sub_name<<"emigr.p"<<i+1;
    add(name.str(),sub_name.str(),ALL,i,0,0,&MPStatHandler::getEmigrantInPatch,0,0);
    name.str("");
    sub_name.str("");
  }
  
  add("Residants patch 1","resid.p1", ALL,0,0,0,&MPStatHandler::getResidantInPatch,0,0);
  for(unsigned int i = 1; i < _pop->getPatchNbr(); i++) {
    name<<"Residants patch "<<i+1;
    sub_name<<"resid.p"<<i+1;
    add(name.str(),sub_name.str(),ALL,i,0,0,&MPStatHandler::getResidantInPatch,0,0);
    name.str("");
    sub_name.str("");
  }
  
  add("Imig. rate patch 1","imrate.p1", ALL,0,0,0,&MPStatHandler::getImigrateInPatch,0,0);
  for(unsigned int i = 1; i < _pop->getPatchNbr(); i++) {
    name<<"Imig. rate patch "<<i+1;
    sub_name<<"imrate.p"<<i+1;
    add(name.str(),sub_name.str(),ALL,i,0,0,&MPStatHandler::getImigrateInPatch,0,0);
    name.str("");
    sub_name.str("");
  }
  
  add("Colons patch 1","colo.p1", ALL,0,0,0,&MPStatHandler::getKolonisersInPatch,0,0);
  for(unsigned int i = 1; i < _pop->getPatchNbr(); i++) {
    name<<"Colons patch "<<i+1;
    sub_name<<"colo.p"<<i+1;
    add(name.str(),sub_name.str(),ALL,i,0,0,&MPStatHandler::getKolonisersInPatch,0,0);
    name.str("");
    sub_name.str("");
  }
}

References StatHandlerBase::_pop, StatHandler< MPStatHandler >::add(), ALL, getEmigrantInPatch(), getImigrateInPatch(), getKolonisersInPatch(), Metapop::getPatchNbr(), and getResidantInPatch().

Referenced by setStatRecorders().

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setStatsForPop()

void MPStatHandler::setStatsForPop

(

)

{
  setStatsForDemography(OFFSPRG);
  add("Offspring Sex Ratio","off.sexratio",OFFSPRG,0,0,&MPStatHandler::getOffsprgSexRatio,0,0,0);
 
  setStatsForDemography(ADULTS);
  add("Adults sex ratio","adlt.sexratio",ADULTS,0,0,&MPStatHandler::getAdultSexRatio,0,0,0);
  
  add("Extinction rate","extrate",ALL,0,0,&MPStatHandler::getObsrvdExtinctionRate,0,0,
      &MPStatHandler::setObsrvdExtinctionRate);
}

References StatHandler< MPStatHandler >::add(), ADULTS, ALL, getAdultSexRatio(), getObsrvdExtinctionRate(), getOffsprgSexRatio(), OFFSPRG, setObsrvdExtinctionRate(), and setStatsForDemography().

Referenced by setStatRecorders().

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setStatsForPopPerPatch()

void MPStatHandler::setStatsForPopPerPatch

(

)

{
  addIndNumPerPatch(FEM, OFFSPRG);
  addIndNumPerPatch(MAL, OFFSPRG);
  addIndNumPerPatch(FEM, ADULTS);
  addIndNumPerPatch(MAL, ADULTS);
  addPatchAge();
}

References addIndNumPerPatch(), addPatchAge(), ADULTS, FEM, MAL, and OFFSPRG.

Referenced by setStatRecorders().

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Member Data Documentation

_ped_prop

double MPStatHandler::_ped_prop[5]

private

Referenced by getPedProportion(), and setPedegreeCount().

_sib_prop

double MPStatHandler::_sib_prop[5]

private

Referenced by getSibProportion(), setKinClassCounter(), and setKinship().

_var_reprod_success

double MPStatHandler::_var_reprod_success

private

Referenced by getReproductiveVar(), and setReproductiveStats().

meanDeadDisp

double MPStatHandler::meanDeadDisp

private

meanEmigrant

double MPStatHandler::meanEmigrant

private

Referenced by getMeanEmigrantPerPatch().

meanImigrant

double MPStatHandler::meanImigrant

private

Referenced by getMeanImigrantPerPatch(), and getMeanMigrantRatio().

meanKolonisers

double MPStatHandler::meanKolonisers

private

Referenced by getMeanKolonisersPerPatch().

meanResidant

double MPStatHandler::meanResidant

private

Referenced by getMeanMigrantRatio(), and getMeanResidantPerPatch().

ObservedExtinctionRate

double MPStatHandler::ObservedExtinctionRate

private

Referenced by getObsrvdExtinctionRate(), and setObsrvdExtinctionRate().

---

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

• MPStatHandler.h
• MPStatHandler.cc
• stats_demo.cc