LCE_Breed_Selection Class Reference

Composite LCE implementing breeding and viability selection on a given trait type. More...

#include <LCEcomposite.h>

Inheritance diagram for LCE_Breed_Selection:

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Collaboration diagram for LCE_Breed_Selection:

[legend]

List of all members.

Public Member Functions
	LCE_Breed_Selection ()
virtual	~LCE_Breed_Selection ()
Individual *	makeOffspringWithSelection (Individual *ind, unsigned int natalpatch)
	Performs viability selection and breeding at the same time.
Implementations
virtual bool	setParameters ()
	Default interface needed to initialize the component's variables from its input parameters value.
virtual void	execute ()
	Execute the event on the pop.
virtual LifeCycleEvent *	clone ()
	Cloning interface.
virtual void	loadFileServices (FileServices *loader)
	Loads the component's FileHandler onto the FileServices.
virtual void	loadStatServices (StatServices *loader)
	Loads the component's StatHandler onto the StatServices.
virtual age_t	removeAgeClass ()
	Removes the returned age-class flag(s) from the current Metapop age-class flags.
virtual age_t	addAgeClass ()
	Adds the returned age-class flag(s) to the current Metapop age-class flags.
virtual age_t	requiredAgeClass ()
	Specifies what age-classes are required by the LCE to execute.

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Detailed Description

Composite LCE implementing breeding and viability selection on a given trait type.

Inherits from LCE_Breed_base and LCE_Selection_base.

Definition at line 124 of file LCEcomposite.h.

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Constructor & Destructor Documentation

LCE_Breed_Selection::LCE_Breed_Selection

(

)

[inline]

Definition at line 129 of file LCEcomposite.h.

Referenced by clone().

: LifeCycleEvent("breed_selection","") {}

virtual LCE_Breed_Selection::~LCE_Breed_Selection

(

)

[inline, virtual]

Definition at line 130 of file LCEcomposite.h.

{}

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Member Function Documentation

virtual age_t LCE_Breed_Selection::addAgeClass

(

)

[inline, virtual]

Adds the returned age-class flag(s) to the current Metapop age-class flags.

Reimplemented from LCE_Selection_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 149 of file LCEcomposite.h.

{return OFFSPRG;}

virtual LifeCycleEvent* LCE_Breed_Selection::clone

(

)

[inline, virtual]

Cloning interface.

Reimplemented from LCE_Selection_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 145 of file LCEcomposite.h.

{ return new LCE_Breed_Selection(); }

void LCE_Breed_Selection::execute

(

)

[virtual]

Execute the event on the pop.

Reimplemented from LCE_Selection_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 393 of file LCEcomposite.cc.

{
  Patch* current_patch;
  unsigned int nbBaby, ind_count = 0;
  //double mean_fec;
  Individual* FatherPtr;
  Individual* MotherPtr;
  Individual* NewOffsprg;
  
  if(_popPtr->size(OFFSPRG) != 0) {
    warning("offspring containers not empty at time of breeding, flushing.\n");
    _popPtr->flush(OFFSx);
  }
  
#ifdef _DEBUG_
  message("LCE_Breed_Selection::execute, ");
#endif
  
  _scaling_factor = 1;
  _mean_fitness = 0;

  LCE_Selection_base::resetCounters();
  
  for(unsigned int home = 0; home < _popPtr->getPatchNbr(); home++) {
    
    current_patch = _popPtr->getPatch(home);
    
    if( !checkMatingCondition(current_patch) ) continue;
    
    for(unsigned int size = current_patch->size(FEM, ADLTx), indexOfMother = 0;
        indexOfMother < size;
        indexOfMother++) {
      
      MotherPtr = current_patch->get(FEM, ADLTx, indexOfMother);
      
      nbBaby = (unsigned int)MotherPtr->setFecundity( getFecundity() );
      
      ind_count += nbBaby;
      //-----------------------------------------------------------------------
      while(nbBaby != 0) {
        
        FatherPtr = this->getFatherPtr(current_patch, MotherPtr, indexOfMother);
        
        NewOffsprg = makeOffspringWithSelection( LCE_Breed_base::do_breed(MotherPtr, FatherPtr, home), home );
        
        if(NewOffsprg != NULL)
          current_patch->add(NewOffsprg->getSex(), OFFSx, NewOffsprg);
        
        nbBaby--;
        
      }//_END__WHILE;
    }//end_for
  }//end_for
  
  LCE_Selection_base::setMeans(ind_count);
  
#ifdef _DEBUG_
  message("(offsprg nb: %i adults nb: %i, mean fitness: %f)\n",_popPtr->size(OFFSPRG),
          _popPtr->size(ADULTS), _mean_fitness);
#endif
  
}

virtual void LCE_Breed_Selection::loadFileServices

(

FileServices *

loader

)

[inline, virtual]

Loads the component's FileHandler onto the FileServices.

Parameters:

loader

the file service

Reimplemented from LCE_Selection_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 146 of file LCEcomposite.h.

{}

void LCE_Breed_Selection::loadStatServices

(

StatServices *

loader

)

[virtual]

Loads the component's StatHandler onto the StatServices.

Parameters:

loader

the stat service

Reimplemented from LCE_Selection_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 386 of file LCEcomposite.cc.

{
  LCE_Selection_base::loadStatServices(loader);
}

Individual * LCE_Breed_Selection::makeOffspringWithSelection	(	Individual *	ind,
		unsigned int	natalpatch
	)

Performs viability selection and breeding at the same time.

The selected trait is first inherited (with recombination and mutations) and survival checked before the remaining traits are inherited. This helps save some computing time. The function returns a null pointer in case of selective death.

Parameters:

	ind	the newborn, its new traits have not been computed yet
	natalpatch	the index of the natal patch of the offfspring where selectin takes palce

Definition at line 458 of file LCEcomposite.cc.

Referenced by LCE_Breed_Selection_Disperse::do_breed(), and execute().

{
  
  if(_LCELinkedTraitIndex != -1)
    ind->createTrait(_LCELinkedTraitIndex, LCE_Breed_base::doInheritance(), true);
  
  register double fitness = getFitness(ind, natalpatch);
  register unsigned int cat = ind->getPedigreeClass();
  
  _fitness[cat] += fitness;
  _ind_cntr[cat]++;
  
  if(RAND::Uniform() > fitness * _scaling_factor ) {
    //this one dies
        _popPtr->recycle(ind);
    
    ind->getMother()->addMating(cat);
    if(cat!=4) ind->getFather()->addMating(cat);
    
    return NULL;
    
  } else {
    
    //update counters
    _survival[cat]++;
    
    ind->getMother()->DidHaveABaby(cat);
    if(cat!=4) ind->getFather()->DidHaveABaby(cat);
  }
  
  //compute inheritance and mutation of the other traits:
  for(int i = 0; i < (int)_nb_trait; i++)
        if(i != _LCELinkedTraitIndex)
          ind->createTrait(i, LCE_Breed_base::doInheritance(), true);
  
  return ind;
}

virtual age_t LCE_Breed_Selection::removeAgeClass

(

)

[inline, virtual]

Removes the returned age-class flag(s) from the current Metapop age-class flags.

Reimplemented from LCE_Selection_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 148 of file LCEcomposite.h.

{return NONE;}

virtual age_t LCE_Breed_Selection::requiredAgeClass

(

)

[inline, virtual]

Specifies what age-classes are required by the LCE to execute.

Reimplemented from LCE_Selection_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 150 of file LCEcomposite.h.

{return ADULTS;}

bool LCE_Breed_Selection::setParameters

(

)

[virtual]

Default interface needed to initialize the component's variables from its input parameters value.

Formerly called 'init'.

Reimplemented from LCE_Breed_base.

Reimplemented in LCE_Breed_Selection_Disperse.

Definition at line 372 of file LCEcomposite.cc.

{
  if( !LCE_Breed_base::setParameters( ) ||  !LCE_Selection_base::setParameters( ) )
    return false;
  
  if(getMeanFecundity() <= 0) {
    error("\"mean_fecundity\" is not set!\n");
    return false;
  }
  return true;
}

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

• LCEcomposite.h
• LCEcomposite.cc