TTWolbachiaSH Class Reference

StatHandler of the Wolbachia trait. More...

#include <ttwolbachia.h>

Inheritance diagram for TTWolbachiaSH:

Collaboration diagram for TTWolbachiaSH:

Public Member Functions
	TTWolbachiaSH (TProtoWolbachia *TT)
virtual	~TTWolbachiaSH ()
virtual bool	setStatRecorders (string &token)
void	setInfectionStats ()
double	getMeanInfection (unsigned int sex)
double	getMeanOffsprgInfection (unsigned int sex)
double	getMeanFemaleInfection_perPatch (unsigned int patch)
double	getMeanMaleInfection_perPatch (unsigned int patch)
double	getMeanOffsprgFemaleInfection_perPatch (unsigned int patch)
double	getMeanOffsprgMaleInfection_perPatch (unsigned int patch)
double	getIcompatibleMatingFreq ()
double	getDemicInfectionVar ()
double	getDemicExtinctionRate ()
Public Member Functions inherited from TraitStatHandler< TProtoWolbachia, TTWolbachiaSH >
	TraitStatHandler (TProtoWolbachia *trait_proto)
virtual	~TraitStatHandler ()
Public Member Functions inherited from StatHandler< SH >
	StatHandler ()
virtual	~StatHandler ()
virtual void	clear ()
	Empties the _recorders list, they are destroyed in StatHandlerBase::reset(). More...
virtual StatRecorder< SH > *	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
TProtoWolbachia *	_trait
int	_TTidx
double	_Fmean
double	_Mmean
double	_var
double	_extrate

Additional Inherited Members
Protected Types inherited from StatHandler< SH >
typedef std::list< StatRecorder< SH > * >::iterator	REC_IT
Protected Attributes inherited from TraitStatHandler< TProtoWolbachia, TTWolbachiaSH >
TProtoWolbachia *	_SHLinkedTrait
	Pointer to a TraitProtoype object. More...
int	_SHLinkedTraitIndex
	Index of the trait in the Individual::Traits table. More...
Protected Attributes inherited from StatHandler< SH >
std::list< StatRecorder< SH > * >	_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

StatHandler of the Wolbachia trait.

Constructor & Destructor Documentation

TTWolbachiaSH()

TTWolbachiaSH::TTWolbachiaSH ( TProtoWolbachia *  TT )

inline

  : TraitStatHandler<TProtoWolbachia, TTWolbachiaSH> (TT),
  _trait(TT), _TTidx(TT->get_index()), _Fmean(0), _Mmean(0), _var(0), _extrate(0) {}

~TTWolbachiaSH()

virtual TTWolbachiaSH::~TTWolbachiaSH ( )

inlinevirtual

{ }

Member Function Documentation

getDemicExtinctionRate()

double TTWolbachiaSH::getDemicExtinctionRate ( )

inline

{return _extrate;}

References _extrate.

Referenced by setStatRecorders().

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getDemicInfectionVar()

double TTWolbachiaSH::getDemicInfectionVar ( )

inline

{return _var;}

References _var.

Referenced by setStatRecorders().

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getIcompatibleMatingFreq()

double TTWolbachiaSH::getIcompatibleMatingFreq

(

)

{
//  double sum = 0;
//  Patch* crnt_patch;
//  
//  for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
//      crnt_patch = _pop->getPatch(i);
//      for(unsigned int j = 0; j < crnt_patch->size(FEM, ADLTx);++j)
//        sum += crnt_patch->get(FEM, ADLTx, j)->getFecundity();
//  }
//  return (double)Patch::DeadOffsprgs/sum;
  return nanf("NULL");
}

getMeanFemaleInfection_perPatch()

double TTWolbachiaSH::getMeanFemaleInfection_perPatch

(

unsigned int

patch

)

{
  double indNbr = 0, mean = 0;
  Patch* crnt_patch = _pop->getPatch(i);
  
  indNbr = crnt_patch->size(FEM, ADLTx);
  for(unsigned int j = 0; j < indNbr; ++j)
    mean += (double)*(bool*)crnt_patch->get(FEM, ADLTx, j)->getTraitValue(_TTidx);
  
  return (indNbr != 0 ? mean/indNbr : nanf("NULL"));
}

References StatHandlerBase::_pop, _TTidx, ADLTx, FEM, Patch::get(), Metapop::getPatch(), Individual::getTraitValue(), and Patch::size().

Referenced by setStatRecorders().

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getMeanInfection()

double TTWolbachiaSH::getMeanInfection ( unsigned int  sex )

inline

{return ((bool)sex ? _Fmean : _Mmean);}

References _Fmean, and _Mmean.

Referenced by setStatRecorders().

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getMeanMaleInfection_perPatch()

double TTWolbachiaSH::getMeanMaleInfection_perPatch

(

unsigned int

patch

)

{
  double indNbr = 0, mean = 0;
  Patch* crnt_patch = _pop->getPatch(i);
  
  indNbr = crnt_patch->size(MAL, ADLTx);
  for(unsigned int j = 0; j < indNbr; ++j)
    mean += (double)*(bool*)crnt_patch->get(MAL, ADLTx, j)->getTraitValue(_TTidx);
  
  return (indNbr != 0 ? mean/indNbr : nanf("NULL"));
}

References StatHandlerBase::_pop, _TTidx, ADLTx, Patch::get(), Metapop::getPatch(), Individual::getTraitValue(), MAL, and Patch::size().

getMeanOffsprgFemaleInfection_perPatch()

double TTWolbachiaSH::getMeanOffsprgFemaleInfection_perPatch

(

unsigned int

patch

)

{
  double indNbr = 0, mean = 0;
  Patch* crnt_patch = _pop->getPatch(i);
  
  indNbr = crnt_patch->size(FEM, OFFSx);
  
  for(unsigned int j = 0; j < indNbr; ++j)
      mean += (double)*(bool*)crnt_patch->get(FEM, OFFSx, j)->getTraitValue(_TTidx);
 
  return (indNbr != 0 ? mean/indNbr : nanf("NULL"));
}

References StatHandlerBase::_pop, _TTidx, FEM, Patch::get(), Metapop::getPatch(), Individual::getTraitValue(), OFFSx, and Patch::size().

getMeanOffsprgInfection()

double TTWolbachiaSH::getMeanOffsprgInfection

(

unsigned int

sex

)

{
  unsigned int i,j;
  double indNbr = 0, mean = 0;
  Patch* crnt_patch;
  
  
  if(sex) {//females:
    for(i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      for(j = 0; j < crnt_patch->size(FEM, OFFSx); ++j)
        mean += (double)*(bool*)crnt_patch->get(FEM, OFFSx, j)->getTraitValue(_TTidx);
        }
    indNbr = _pop->size(FEM, OFFSPRG);
  } else { //males
    for(i = 0; i < _pop->getPatchNbr(); ++i) {
          crnt_patch = _pop->getPatch(i);
      for(j = 0; j < crnt_patch->size(MAL, OFFSx); ++j)
        mean += (double)*(bool*)crnt_patch->get(MAL, OFFSx, j)->getTraitValue(_TTidx);
        }
    indNbr = _pop->size(MAL, OFFSPRG);
  }
  
  return (indNbr != 0 ? mean/indNbr : nanf("NULL"));  
}

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

Referenced by setStatRecorders().

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getMeanOffsprgMaleInfection_perPatch()

double TTWolbachiaSH::getMeanOffsprgMaleInfection_perPatch

(

unsigned int

patch

)

{
  double indNbr = 0, mean = 0;
  Patch* crnt_patch = _pop->getPatch(i);
  
  indNbr = crnt_patch->size(MAL, OFFSx);
  
  for(unsigned int j = 0; j < indNbr; ++j)
    mean += (double)*(bool*)crnt_patch->get(MAL, OFFSx, j)->getTraitValue(_TTidx);
 
  return (indNbr != 0 ? mean/indNbr : nanf("NULL"));
}

References StatHandlerBase::_pop, _TTidx, Patch::get(), Metapop::getPatch(), Individual::getTraitValue(), MAL, OFFSx, and Patch::size().

setInfectionStats()

void TTWolbachiaSH::setInfectionStats

(

)

{
  double Fsize = 0, Msize = 0, val, local_inf;
  double *all;
  Patch* crnt_patch;
    
  Fsize = _pop->size(FEM, ADULTS);
  Msize = _pop->size(MAL, ADULTS);
 
  if( Fsize != 0 )
    all = new double [ _pop->getPatchNbr() ];
  else {
    _Fmean = nanf("NULL");
    _Mmean = nanf("NULL");
    _extrate = nanf("NULL");
    _var = nanf("NULL");
    return;
  }
    
  _Fmean = _Mmean = 0;
  _extrate = 0;
 
  //females:
  for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
    crnt_patch = _pop->getPatch(i);
    local_inf = 0;
    all[i] = 0;
    unsigned int fsize = crnt_patch->size(FEM, ADLTx);
    for(unsigned int j = 0; j < fsize; ++j) {
      val = (double)*(bool*)(crnt_patch->get(FEM, ADLTx, j)->getTraitValue(_TTidx));
      local_inf += val;
    }
    
    if(local_inf != 0) {
      all[i] = local_inf / fsize;
      _Fmean += all[i];
    } else  _extrate++;
      
  }
  
  _Fmean = (Fsize != 0 ? _Fmean / (_pop->getPatchNbr() - _extrate) : nanf("NULL"));
  
  _extrate /= _pop->getPatchNbr();
 
  _var = 0;
  double local_mean = 0;
  
  for (unsigned int i = 0; i < _pop->getPatchNbr(); i++)
    local_mean += all[i];
  
  local_mean /= _pop->getPatchNbr();
  
  //hacked from the GSL:
  for (unsigned int i = 0; i < _pop->getPatchNbr(); i++) {
    const long double delta = (all[i] - local_mean);
    _var += (delta * delta - _var) / (i + 1);
  }
 
 //males
  for(unsigned int i = 0; i < _pop->getPatchNbr(); ++i) {
    crnt_patch = _pop->getPatch(i);
    for(unsigned int j = 0, msize = crnt_patch->size(MAL, ADLTx); j < msize; ++j)
      _Mmean += (double)*(bool*)(crnt_patch->get(MAL, ADLTx, j)->getTraitValue(_TTidx));
  }
  
  _Mmean = (Msize != 0 ? _Mmean / Msize : nanf("NULL"));
  
  delete [] all;
}

References _extrate, _Fmean, _Mmean, StatHandlerBase::_pop, _TTidx, _var, ADLTx, ADULTS, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTraitValue(), MAL, Metapop::size(), and Patch::size().

Referenced by setStatRecorders().

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setStatRecorders()

bool TTWolbachiaSH::setStatRecorders ( string &  token )

virtual

Implements StatHandlerBase.

{
//  cout << "TTWolbachiaSH::setStatRecorders("<<token<<")\n";
 
  if(token == "wolbachia") {
    
          add("Wolbachia female infection (offsprng)","off.fwoinf",OFFSPRG,1,0,0,&TTWolbachiaSH::getMeanOffsprgInfection,0,0);
          add("Wolbachia male infection   (offsprng)","off.mwoinf",OFFSPRG,0,0,0,&TTWolbachiaSH::getMeanOffsprgInfection,0,0);
    //    add("Wolbachia incompatible mating freq   ","off.incmating",OFFSPRG,0,&TTWolbachiaSH::getIcompatibleMatingFreq,0,0,0);
          add("Wolbachia female infection (adults)  ","adlt.fwoinf",ADULTS,1,0,0,&TTWolbachiaSH::getMeanInfection,0,&TTWolbachiaSH::setInfectionStats);
          add("Wolbachia male infection   (adults)  ","adlt.mwoinf",ADULTS,0,0,0,&TTWolbachiaSH::getMeanInfection,0,0);
    add("Wolbachia demic infection variance   ","wolb.infvar",ADULTS,0,0,&TTWolbachiaSH::getDemicInfectionVar,0,0,0);
    add("Wolbachia demic extinction rate      ","wolb.extrate",ADULTS,0,0,&TTWolbachiaSH::getDemicExtinctionRate,0,0,0);
    
  } else if(token == "wolbachia_perpatch") {
    
    ostringstream name, sub_name;
    
    //  for(unsigned int i = 0; i < _pop->getPatchNbr(); i++) {
    //    _name<<"Wolbachia fem infctn: patch "<<i+1;
    //    sub_name<<"off.p"<<i+1<<"fwoinf";
    //    add(_name.str(),sub_name.str(),OFFSPRG,i,0,0,&TTWolbachiaSH::getMeanOffsprgFemaleInfection_perPatch,0);
    //    _name.str("");
    //    _name<<"Wolbachia mal infctn: patch "<<i+1;
    //    sub_name.str("");
    //    sub_name<<"off.p"<<i+1<<"mwoinf";
    //    add(_name.str(),sub_name.str(),OFFSPRG,i,0,0,&TTWolbachiaSH::getMeanOffsprgMaleInfection_perPatch,0);
    //    sub_name.str("");
    //    _name.str("");
    //  }
    
    for(unsigned int i = 0; i < _pop->getPatchNbr(); i++) {
      name<<"Patch "<<i+1;
      sub_name<<"adlt.p"<<i+1<<"fwoinf";
      add(name.str(),sub_name.str(),ADULTS,i,0,0,&TTWolbachiaSH::getMeanFemaleInfection_perPatch,0,0);
      //          sub_name.str("");
      //          sub_name<<"adlt.p"<<i+1<<"mwoinf";
      //          add(_name.str(),sub_name.str(),ADULTS,i,0,0,&TTWolbachiaSH::getMeanMaleInfection_perPatch,0);
      sub_name.str("");
      name.str("");
    }
    
  }else
    return false;
  
  return true;
}

References StatHandlerBase::_pop, StatHandler< SH >::add(), ADULTS, getDemicExtinctionRate(), getDemicInfectionVar(), getMeanFemaleInfection_perPatch(), getMeanInfection(), getMeanOffsprgInfection(), Metapop::getPatchNbr(), OFFSPRG, and setInfectionStats().

Member Data Documentation

_extrate

double TTWolbachiaSH::_extrate

private

Referenced by getDemicExtinctionRate(), and setInfectionStats().

_Fmean

double TTWolbachiaSH::_Fmean

private

Referenced by getMeanInfection(), and setInfectionStats().

_Mmean

double TTWolbachiaSH::_Mmean

private

Referenced by getMeanInfection(), and setInfectionStats().

_trait

TProtoWolbachia* TTWolbachiaSH::_trait

private

_TTidx

int TTWolbachiaSH::_TTidx

private

Referenced by getMeanFemaleInfection_perPatch(), getMeanMaleInfection_perPatch(), getMeanOffsprgFemaleInfection_perPatch(), getMeanOffsprgInfection(), getMeanOffsprgMaleInfection_perPatch(), and setInfectionStats().

_var

double TTWolbachiaSH::_var

private

Referenced by getDemicInfectionVar(), and setInfectionStats().

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

• ttwolbachia.h
• stats_wolbachia.cc
• ttwolbachia.cc