LCE_Breed_Wolbachia Class Reference

Breeding LCE when individuals carry the Wolbachia endosymbiotic parasite. More...

#include <ttwolbachia.h>

Inheritance diagram for LCE_Breed_Wolbachia:

Collaboration diagram for LCE_Breed_Wolbachia:

Public Member Functions
	LCE_Breed_Wolbachia ()
virtual	~LCE_Breed_Wolbachia ()
void	wolbachia_model_1 ()
void	wolbachia_model_2 ()
virtual bool	setParameters ()
virtual void	execute ()
virtual LifeCycleEvent *	clone ()
virtual void	loadFileServices (FileServices *loader)
virtual void	loadStatServices (StatServices *loader)
virtual bool	resetParameterFromSource (std::string param, SimComponent *cmpt)
virtual age_t	removeAgeClass ()
virtual age_t	addAgeClass ()
virtual age_t	requiredAgeClass ()
Public Member Functions inherited from LCE_Breed_base
	LCE_Breed_base ()
virtual	~LCE_Breed_base ()
virtual Individual *	getFatherPtr (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Calls the mating function according to the model chosen using the function pointer, used to get the father from the mother in a patch. More...
void	NonWrightFisherPopulation ()
void	WrightFisherPopulation ()
void	doAgingInWFpop ()
Individual *	breed (Individual *mother, Individual *father, unsigned int LocalPatch)
	Makes a new individual with the right parents. More...
Individual *	breed_cloning (Individual *mother, Individual *father, unsigned int LocalPatch)
	Makes a new individual by doing a deep copy of the mother (copies the mother's genes into the offspring). More...
Individual *	makeOffspring (Individual *ind)
	Last step of the breeding process, does inheritance and mutation of the parents' genes. More...
Individual *	makeOffspring (Individual *newind, Individual *mother, Individual *father, unsigned int natalPatch)
	Overloads previous function when a new offspring is created "in-place", that is from existing pointer in a patch. More...
Individual *	do_breed (Individual *mother, Individual *father, unsigned int LocalPatch)
	Calls the breeding function unsing its pointer. More...
bool	checkMatingCondition (Patch *thePatch)
	Checks if any mating will take place in the patch passed as argument. More...
bool	checkNoSelfing (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is not selfing or cloning. More...
bool	checkPolygyny (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is polygynous. More...
bool	checkSelfing (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is selfing. More...
bool	checkCloning (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is cloning. More...
bool	setMatingSystem ()
bool	setFecundity ()
bool	setSexRatio ()
double	getMatingProportion ()
double	getMeanFecundity (unsigned int patch)
int	getMatingSystem ()
bool	doInheritance ()
double	getPoissonFecundity (double mean)
double	getFixedFecundity (double mean)
double	getGaussianFecundity (double mean)
double	getLogNormalFecundity (double mean)
double	getFecundity (unsigned int patch)
double	getFecundity (double mean)
sex_t	getOffsprgSex ()
sex_t	getOffsprgSexRandom ()
sex_t	getOffsprgSexFixed ()
sex_t	getOffsprgSexSelfing ()
sex_t	getOffsprgSexCloning ()
bool	isWrightFisher ()
Individual *	RandomMating (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male drawn randomly from a patch. More...
Individual *	fullPolyginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to the alpha male of the patch. More...
Individual *	fullPolyginy_manyMales (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to one of the first _mating_males males of the patch. More...
Individual *	partialPolyginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1, or the first male otherwise. More...
Individual *	partialPolyginy_manyMales (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1, or one of the _mating_males first males otherwise. More...
Individual *	fullMonoginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male with same index as mother (if available) from the focal patch. More...
Individual *	partialMonoginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male with same index as mother (if available) from the focal patch. More...
Individual *	fullSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns the mother pointer. More...
Individual *	partialSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns the mother pointer or a random female if _mating_proportion != 1. More...
Individual *	random_hermaphrodite (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a random female from the patch, will be the same mother with probability 1/N (Wright-Fisher model). More...
Public Member Functions inherited from LifeCycleEvent
	LifeCycleEvent (const char *name, const char *trait_link)
	Cstor. More...
virtual	~LifeCycleEvent ()
virtual void	init (Metapop *popPtr)
	Sets the pointer to the current Metapop and the trait link if applicable. More...
virtual bool	attach_trait (string trait)
virtual void	set_paramset (std::string name, bool required, SimComponent *owner)
virtual void	set_event_name (std::string &name)
	Set the name of the event (name of the ParamSet) and add the corresponding parameter to the set. More...
virtual void	set_event_name (const char *name)
virtual string &	get_event_name ()
	Accessor to the LCE's name. More...
virtual int	get_rank ()
	Accessor to the LCE rank in the life cycle. More...
virtual void	set_pop_ptr (Metapop *popPtr)
	Accessors for the population pointer. More...
virtual Metapop *	get_pop_ptr ()
Public Member Functions inherited from SimComponent
	SimComponent ()
virtual	~SimComponent ()
virtual void	loadUpdaters (UpdaterServices *loader)
	Loads the parameters and component updater onto the updater manager. More...
virtual void	set_paramset (ParamSet *paramset)
	Sets the ParamSet member. More...
virtual void	set_paramsetFromCopy (const ParamSet &PSet)
	Reset the set of parameters from a another set. More...
virtual ParamSet *	get_paramset ()
	ParamSet accessor. More...
virtual void	add_parameter (Param *param)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd)
	Interface to add a parameter to the set. More...
virtual void	add_parameter (std::string Name, param_t Type, bool isRequired, bool isBounded, double low_bnd, double up_bnd, ParamUpdaterBase *updater)
	Interface to add a parameter and its updater to the set. More...
virtual Param *	get_parameter (std::string name)
	Param getter. More...
virtual double	get_parameter_value (std::string name)
	Param value getter. More...
virtual string	get_name ()
	Returnd the name of the ParamSet, i.e. More...
virtual bool	has_parameter (std::string name)
	Param getter. More...

Private Member Functions
void	inoculate_wolbachia ()
double	hasInfectedFemale ()

Private Attributes
double	_incomp_cost
double	_fec_cost
double	_infected_fec
TMatrix *	_inoculum_size
unsigned int	_inoculum_time
unsigned int	_model
void(LCE_Breed_Wolbachia::*	_breed_func_ptr )()
TTWolbachiaFH *	_writer

Additional Inherited Members
Protected Attributes inherited from LCE_Breed_base
TMatrix	_mean_fecundity
Individual *(LCE_Breed_base::*	MatingFuncPtr )(Patch *, Individual *, unsigned int)
Individual *(LCE_Breed_base::*	DoBreedFuncPtr )(Individual *mother, Individual *father, unsigned int LocalPatch)
double(LCE_Breed_base::*	FecundityFuncPtr )(double mean)
bool(LCE_Breed_base::*	CheckMatingConditionFuncPtr )(Patch *thePatch)
sex_t(LCE_Breed_base::*	GetOffsprgSex )()
void(LCE_Breed_base::*	PopModelFuncPtr )(void)
Protected Attributes inherited from LifeCycleEvent
std::string	_event_name
	The param name to be read in the init file. More...
Metapop *	_popPtr
	The ptr to the current Metapop. More...
std::string	_LCELinkedTraitType
	The name of the linked trait. More...
int	_LCELinkedTraitIndex
	The index in the individual's trait table of the linked trait. More...
Protected Attributes inherited from SimComponent
ParamSet *	_paramSet
	The parameters container. More...

Detailed Description

Breeding LCE when individuals carry the Wolbachia endosymbiotic parasite.

See the user manual for an explanation of the parameters defined here.

Constructor & Destructor Documentation

LCE_Breed_Wolbachia()

LCE_Breed_Wolbachia::LCE_Breed_Wolbachia

(

)

                                          : LifeCycleEvent("breed_wolbachia",WOLB),
_incomp_cost(0), _fec_cost(0), _infected_fec(0), _inoculum_size(0), _inoculum_time(0), 
_writer(0)
{
  ParamUpdater< LCE_Breed_Wolbachia > * updater =
  new ParamUpdater< LCE_Breed_Wolbachia > (&LCE_Breed_Wolbachia::setParameters);
  add_parameter("wolbachia_fecundity_cost",DBL,true,true,-1,1, updater);
  add_parameter("wolbachia_incompatibility_cost",DBL,true,true,-1,1, updater);
  add_parameter("wolbachia_inoculum_size",MAT,true,false,0,0, updater);
  add_parameter("wolbachia_inoculum_time",INT,true,false,0,0, updater);
  add_parameter("wolbachia_model",INT,false,true,1,2, updater);
  add_parameter("wolbachia_output_dir", STR, false, false, 0, 0);
}

References SimComponent::add_parameter(), DBL, INT, MAT, setParameters(), and STR.

Referenced by clone().

Here is the caller graph for this function:

~LCE_Breed_Wolbachia()

LCE_Breed_Wolbachia::~LCE_Breed_Wolbachia ( )

virtual

{
  if(_writer) delete _writer; 
}

References _writer.

Member Function Documentation

addAgeClass()

virtual age_t LCE_Breed_Wolbachia::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return OFFSPRG;}

References OFFSPRG.

clone()

virtual LifeCycleEvent* LCE_Breed_Wolbachia::clone ( )

inlinevirtual

Implements LifeCycleEvent.

  { return new LCE_Breed_Wolbachia(); }

References LCE_Breed_Wolbachia().

execute()

void LCE_Breed_Wolbachia::execute ( )

virtual

Implements LifeCycleEvent.

{
  
#ifdef _DEBUG_
  message("LCE_Breed_Wolbachia::execute\n");
#endif
  double infection_status;
  
  if( _popPtr->getCurrentGeneration() == _inoculum_time) {
           inoculate_wolbachia();}
  
  if( _popPtr->getCurrentGeneration() > _inoculum_time) {
    
    infection_status = hasInfectedFemale();
    
    if( infection_status == 0 || infection_status == 1) {
      _writer->record(_popPtr->getCurrentReplicate(), _popPtr->getCurrentGeneration(), infection_status);
      _popPtr->reset();
      return;
    }}
  
  
  if(_popPtr->size(OFFSPRG) != 0) {
    warning("offspring containers not empty at time of breeding, flushing.\n");
    _popPtr->flush(OFFSx);
  }
  
  (this->*_breed_func_ptr)();
  
  if (_popPtr->getCurrentGeneration() == SIMenv::getGenerations() ) {
    _writer->record(_popPtr->getCurrentReplicate(), _popPtr->getCurrentGeneration(), hasInfectedFemale());
  }
  
}

References _breed_func_ptr, _inoculum_time, LifeCycleEvent::_popPtr, _writer, Metapop::flush(), Metapop::getCurrentGeneration(), Metapop::getCurrentReplicate(), SIMenv::getGenerations(), hasInfectedFemale(), inoculate_wolbachia(), message(), OFFSPRG, OFFSx, TTWolbachiaFH::record(), Metapop::reset(), Metapop::size(), and warning().

hasInfectedFemale()

double LCE_Breed_Wolbachia::hasInfectedFemale ( )

private

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

References LifeCycleEvent::_LCELinkedTraitIndex, LifeCycleEvent::_popPtr, ADLTx, FEM, Patch::get(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getTraitValue(), and Patch::size().

Referenced by execute().

Here is the caller graph for this function:

inoculate_wolbachia()

void LCE_Breed_Wolbachia::inoculate_wolbachia ( )

private

{
  Patch* current_patch;
  bool T = 1;
  
  for (unsigned int i = 0; i < _popPtr->getPatchNbr(); i++) {
    
    current_patch = _popPtr->getPatch(i);
    
    if(current_patch->get_isExtinct()) continue;
    
      for (unsigned int j = 0;
                  j < _inoculum_size->get(i, 0) && j < current_patch->size(FEM, ADLTx); j++) {
        current_patch->get(FEM, ADLTx, j)->setTrait(_LCELinkedTraitIndex, &T);
      }
 
    for (unsigned int j = 0;
                j < _inoculum_size->get(i, 1) && j < current_patch->size(MAL, ADLTx); j++) {
        current_patch->get(MAL, ADLTx, j)->setTrait(_LCELinkedTraitIndex, &T);
    }
  }
//  if(!ok) fatal("could not inoculate wolbachia, check the inoculum size!\n");
}

References _inoculum_size, LifeCycleEvent::_LCELinkedTraitIndex, LifeCycleEvent::_popPtr, ADLTx, FEM, Patch::get(), TMatrix::get(), Patch::get_isExtinct(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, and Individual::setTrait().

Referenced by execute().

Here is the caller graph for this function:

loadFileServices()

void LCE_Breed_Wolbachia::loadFileServices ( FileServices *  loader )

virtual

Implements SimComponent.

{
  if(_writer != NULL) delete _writer;
  
  _writer = new TTWolbachiaFH(this);
  
  _writer->set(false, false, SIMenv::getReplicates(), SIMenv::getGenerations(), 0,
               get_parameter("wolbachia_output_dir")->getArg(), this);
  
  loader->attach(_writer);
}

References _writer, FileServices::attach(), SimComponent::get_parameter(), SIMenv::getGenerations(), SIMenv::getReplicates(), and EventFileHandler< LCE >::set().

loadStatServices()

virtual void LCE_Breed_Wolbachia::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_Breed_Wolbachia::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_Breed_Wolbachia::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return ADULTS;}

References ADULTS.

resetParameterFromSource()

virtual bool LCE_Breed_Wolbachia::resetParameterFromSource ( std::string  param, SimComponent *  cmpt  )

inlinevirtual

Implements SimComponent.

{return false;}

setParameters()

bool LCE_Breed_Wolbachia::setParameters ( )

virtual

Reimplemented from LCE_Breed_base.

{
  if(!LCE_Breed_base::setParameters( )) return false;
  
  _fec_cost = this->get_parameter_value("wolbachia_fecundity_cost");
  _infected_fec = this->getMeanFecundity(0) * (1 - _fec_cost);
  _incomp_cost = this->get_parameter_value("wolbachia_incompatibility_cost");
  _inoculum_time = (unsigned int)this->get_parameter_value("wolbachia_inoculum_time");
  
  TMatrix tmp;
 
  get_parameter("wolbachia_inoculum_size")->getMatrix(&tmp);
 
  if( !_inoculum_size ) _inoculum_size = new TMatrix();
 
  if(tmp.ncols() == 2 && tmp.nrows() == _popPtr->getPatchNbr())
          _inoculum_size->copy(tmp);
  else
          setSpatialMatrix("wolbachia_inoculum_size", "2", &tmp, _inoculum_size, 2, _popPtr->getPatchNbr());
 
  if (get_parameter("wolbachia_model")->isSet()) {
    _model = (unsigned int)get_parameter_value("wolbachia_model");
  } else
    _model = 1;
  
  
  switch(_model) {
    case 1: 
      _breed_func_ptr = &LCE_Breed_Wolbachia::wolbachia_model_1;
      break;
    case 2:
      _breed_func_ptr = &LCE_Breed_Wolbachia::wolbachia_model_2;
      break;
    default:  _breed_func_ptr = &LCE_Breed_Wolbachia::wolbachia_model_1;
  }
  
  
  return true;
}

References _breed_func_ptr, _fec_cost, _incomp_cost, _infected_fec, _inoculum_size, _inoculum_time, _model, LifeCycleEvent::_popPtr, TMatrix::copy(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getMatrix(), LCE_Breed_base::getMeanFecundity(), Metapop::getPatchNbr(), TMatrix::ncols(), TMatrix::nrows(), LCE_Breed_base::setParameters(), setSpatialMatrix(), wolbachia_model_1(), and wolbachia_model_2().

Referenced by LCE_Breed_Wolbachia().

Here is the caller graph for this function:

wolbachia_model_1()

void LCE_Breed_Wolbachia::wolbachia_model_1

(

)

{
  Patch* current_patch;
  unsigned int indexOfMother, nbBaby;
  Individual* FatherPtr;
  Individual* MotherPtr;
  Individual* NewOffsprg;
  
  for(unsigned int i = 0; i < _popPtr->getPatchNbr(); i++) {
    
    current_patch = _popPtr->getPatch(i);
    
    if(current_patch->size(FEM, ADLTx) == 0 || current_patch->size(MAL, ADLTx) == 0) continue;
    
    for(indexOfMother = 0; indexOfMother < current_patch->size(FEM, ADLTx); indexOfMother++) {
      
      MotherPtr = current_patch->get(FEM, ADLTx, indexOfMother);
      
      if(*(bool*)MotherPtr->getTraitValue(_LCELinkedTraitIndex))
        nbBaby = (unsigned int)MotherPtr->setFecundity( getFecundity( _infected_fec ) );
      else
        nbBaby = (unsigned int)MotherPtr->setFecundity( getFecundity(i) );
      //-----------------------------------------------------------------------
      while(nbBaby != 0) {
        
        FatherPtr = getFatherPtr(current_patch, MotherPtr, indexOfMother);
        
        NewOffsprg = _popPtr->makeOffsprg(MotherPtr,FatherPtr,(sex_t)RAND::RandBool(),i);
        
        if(!(*(bool*)NewOffsprg->getTraitValue(_LCELinkedTraitIndex)) &&
           *(bool*)FatherPtr->getTraitValue(_LCELinkedTraitIndex)) {
          if(RAND::Uniform() < _incomp_cost) {
            _popPtr->recycle(NewOffsprg);
          } else
            current_patch->add( NewOffsprg->getSex(), OFFSx, NewOffsprg );
        } else
          current_patch->add( NewOffsprg->getSex(), OFFSx, NewOffsprg );
        
        nbBaby--;
      }//_END_WHILE nbBaby
    }//end_for indexOfMother
  }//end_for patch
}

References _incomp_cost, _infected_fec, LifeCycleEvent::_LCELinkedTraitIndex, LifeCycleEvent::_popPtr, Patch::add(), ADLTx, FEM, Patch::get(), LCE_Breed_base::getFatherPtr(), LCE_Breed_base::getFecundity(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getSex(), Individual::getTraitValue(), IndFactory::makeOffsprg(), MAL, OFFSx, RAND::RandBool(), IndFactory::recycle(), Individual::setFecundity(), Patch::size(), and RAND::Uniform().

Referenced by setParameters().

Here is the caller graph for this function:

wolbachia_model_2()

void LCE_Breed_Wolbachia::wolbachia_model_2

(

)

{
  Patch* current_patch;
  unsigned int indexOfMother, nbBaby;
  double fec;
  Individual* FatherPtr;
  Individual* MotherPtr;
  Individual* NewOffsprg;
  
  for(unsigned int i = 0; i < _popPtr->getPatchNbr(); i++) {
    
    current_patch = _popPtr->getPatch(i);
    
    if(current_patch->size(FEM, ADLTx) == 0 || current_patch->size(MAL, ADLTx) == 0) continue;
    
    for(indexOfMother = 0; indexOfMother < current_patch->size(FEM, ADLTx); indexOfMother++) {
      
      MotherPtr = current_patch->get(FEM, ADLTx, indexOfMother);
      
      FatherPtr = getFatherPtr(current_patch, MotherPtr, indexOfMother);
      
      if(*(bool*)MotherPtr->getTraitValue(_LCELinkedTraitIndex)) {
        if(*(bool*)FatherPtr->getTraitValue(_LCELinkedTraitIndex))
          fec = _infected_fec * (1 - _incomp_cost);
        else
          fec = _infected_fec;
      } else if (*(bool*)FatherPtr->getTraitValue(_LCELinkedTraitIndex)) {
        fec = getMeanFecundity(i) * (1 - _incomp_cost);
      } else {
        fec = getMeanFecundity(i);
      }
      
      nbBaby = (unsigned int)MotherPtr->setFecundity( getFecundity( fec ) );
      
      //-----------------------------------------------------------------------
      for(;nbBaby != 0;nbBaby--) {
        
        NewOffsprg = _popPtr->makeOffsprg(MotherPtr,FatherPtr,(sex_t)RAND::RandBool(),i);
        
        current_patch->add( NewOffsprg->getSex(), OFFSx, NewOffsprg );
        
      }//end_for nbBaby
    }//end_for indexOfMother
  }//end_for patch
}

References _incomp_cost, _infected_fec, LifeCycleEvent::_LCELinkedTraitIndex, LifeCycleEvent::_popPtr, Patch::add(), ADLTx, FEM, Patch::get(), LCE_Breed_base::getFatherPtr(), LCE_Breed_base::getFecundity(), LCE_Breed_base::getMeanFecundity(), Metapop::getPatch(), Metapop::getPatchNbr(), Individual::getSex(), Individual::getTraitValue(), IndFactory::makeOffsprg(), MAL, OFFSx, RAND::RandBool(), Individual::setFecundity(), and Patch::size().

Referenced by setParameters().

Here is the caller graph for this function:

Member Data Documentation

_breed_func_ptr

void(LCE_Breed_Wolbachia::* LCE_Breed_Wolbachia::_breed_func_ptr) ()

private

Referenced by execute(), and setParameters().

_fec_cost

double LCE_Breed_Wolbachia::_fec_cost

private

Referenced by setParameters().

_incomp_cost

double LCE_Breed_Wolbachia::_incomp_cost

private

Referenced by setParameters(), wolbachia_model_1(), and wolbachia_model_2().

_infected_fec

double LCE_Breed_Wolbachia::_infected_fec

private

Referenced by setParameters(), wolbachia_model_1(), and wolbachia_model_2().

_inoculum_size

TMatrix* LCE_Breed_Wolbachia::_inoculum_size

private

Referenced by inoculate_wolbachia(), and setParameters().

_inoculum_time

unsigned int LCE_Breed_Wolbachia::_inoculum_time

private

Referenced by execute(), and setParameters().

_model

unsigned int LCE_Breed_Wolbachia::_model

private

Referenced by setParameters().

_writer

TTWolbachiaFH* LCE_Breed_Wolbachia::_writer

private

Referenced by execute(), loadFileServices(), and ~LCE_Breed_Wolbachia().

---

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

• ttwolbachia.h
• ttwolbachia.cc