LCE_Cross Class Reference

A class to perform crosses within patches, implements the NC1 mating design. More...

#include <LCEmisc.h>

Inheritance diagram for LCE_Cross:

Collaboration diagram for LCE_Cross:

Public Member Functions
	LCE_Cross ()
virtual	~LCE_Cross ()
void	sampleAmongPop (Patch *patch, deque< Individual * > &males, unsigned int nsire)
void	sampleWithinPop (Patch *patch, deque< Individual * > &males, deque< Individual * > &females, unsigned int nsire)
void	generatePedigree ()
bool	create_individual_ancestors (Individual *ind)
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 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 Attributes
unsigned int	_nSire
unsigned int	_nDam
unsigned int	_nOffspring
unsigned int	_atGeneration
bool	_doAmongPop
bool	_doWithinPop
bool	_doReplace
FHPedigreeReader *	_reader
string	_pedigree_file
map< unsigned long, Individual * >	_pedigree_pop

Additional Inherited Members
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

A class to perform crosses within patches, implements the NC1 mating design.

Constructor & Destructor Documentation

LCE_Cross()

LCE_Cross::LCE_Cross

(

)

                     : LifeCycleEvent("cross",""), _nSire(0), _nDam(0), _nOffspring(0), 
_atGeneration(0), _doAmongPop(0), _doWithinPop(0), _doReplace(0), _reader(0)
{
  ParamUpdater< LCE_Cross > * updater = new ParamUpdater< LCE_Cross > (&LCE_Cross::setParameters);
  add_parameter("cross_num_sire", INT, 0, 0, 0, 0, updater);
  add_parameter("cross_num_dam", INT, 0, 0, 0, 0, updater);
  add_parameter("cross_num_offspring", INT, 0, 0, 0, 0, updater);
  add_parameter("cross_at_generation", INT, 1, 0, 0, 0, updater);
  add_parameter("cross_do_among_pop", BOOL, 0, 0, 0, 0, updater);
  add_parameter("cross_do_within_pop", BOOL, 0, 0, 0, 0, updater);
  add_parameter("cross_with_replacement", BOOL, 0, 0, 0, 0, updater);
 
  add_parameter("cross_with_pedigree_file", STR, 0, 0, 0, 0, updater);
 
}

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

Referenced by clone().

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~LCE_Cross()

virtual LCE_Cross::~LCE_Cross ( )

inlinevirtual

{ }

Member Function Documentation

addAgeClass()

virtual age_t LCE_Cross::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return OFFSPRG;}

References OFFSPRG.

clone()

virtual LifeCycleEvent * LCE_Cross::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_Cross();}

References LCE_Cross().

create_individual_ancestors()

bool LCE_Cross::create_individual_ancestors

(

Individual *

ind

)

{
  Individual *mother = ind->getMother();
  Individual *father = ind->getFather();
  unsigned long sire = ind->getFatherID();
  unsigned long dam = ind->getMotherID();
 
  //the individual is set when the mum and dad ptrs are set, exit
  if(mother && father) return true;
 
  //check parents' ID for sampling in the whole pop; choose individuals in first patch
  if(dam == 0) {
 
    if(_popPtr->size(FEM, ADLTx, 0) != 0) {
 
      mother = _popPtr->get(FEM, ADLTx, RAND::Uniform( _popPtr->size(FEM, ADLTx, 0) ), 0);
 
    } else {
      mother = _popPtr->makeNewIndividual(0, 0, FEM, 0);
      mother->create_first_gen();
    }
 
    ind->setMother(mother);
    ind->setMotherID(mother->getID());
 
  } else if( !mother ) {
 
    if( create_individual_ancestors( _pedigree_pop[ dam ] ) ) {
      ind->setMother(_pedigree_pop[ dam ]);
    }
  }
 
  //father
  if(sire == 0) {
 
    if(_popPtr->size(MAL, ADLTx, 0) != 0 ) {
 
      father = _popPtr->get(MAL, ADLTx, RAND::Uniform( _popPtr->size(MAL, ADLTx, 0) ), 0);
 
    } else {
      father = _popPtr->makeNewIndividual(0, 0, MAL, 0);
      father->create_first_gen();
    }
 
    ind->setFather(father);
    ind->setFatherID(father->getID());
 
  } else if(!father) {
 
    if( create_individual_ancestors( _pedigree_pop[ sire ] ) )
      ind->setFather( _pedigree_pop[ sire ] );
 
  }
 
  mother = ind->getMother();
  father = ind->getFather();
 
  if(mother && father) {
    ind->create(true, true); //create with inheritance and mutation
  }
 
  return( mother && father ); //return false when parents are not created
}

References _pedigree_pop, LifeCycleEvent::_popPtr, ADLTx, Individual::create(), Individual::create_first_gen(), create_individual_ancestors(), FEM, Metapop::get(), Individual::getFather(), Individual::getFatherID(), Individual::getID(), Individual::getMother(), Individual::getMotherID(), IndFactory::makeNewIndividual(), MAL, Individual::setFather(), Individual::setFatherID(), Individual::setMother(), Individual::setMotherID(), Metapop::size(), and RAND::Uniform().

Referenced by create_individual_ancestors(), and generatePedigree().

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execute()

void LCE_Cross::execute ( )

virtual

Implements LifeCycleEvent.

{
  Patch* patch;
  unsigned int nsire;
  deque<Individual*> males, females;
 
  if(_popPtr->getCurrentGeneration() != _atGeneration) return;
  
#ifdef _DEBUG_
  message("LCE_Cross::execute\n");
#endif
  
  if(get_parameter("cross_with_pedigree_file")->isSet())
 
    generatePedigree();
 
  else {
  
    if(_popPtr->size(OFFSPRG) != 0) {
      warning("Offspring are still present at time of crossing, flushing\n");
      _popPtr->flush(OFFSPRG);
    }
 
    for(unsigned int i = 0; i < _popPtr->getPatchNbr(); i ++) {
 
      patch = _popPtr->getPatch(i);
 
      if(patch->size(MAL, ADLTx) == 0) continue;
 
      if(_nSire > patch->size(MAL, ADLTx)) {
        warning("LCE_Cross:: num_sire greater than actual number of males in patch %i (size = %i), reseting.\n", i+1, patch->size(MAL, ADLTx));
        nsire = patch->size(MAL, ADLTx);
      } else
        nsire = _nSire;
 
      males.clear();
      patch->getCopy(MAL, ADLTx, males);
 
      if(_doAmongPop) sampleAmongPop(patch, males, nsire);
 
      males.clear();
      females.clear();
 
      if(patch->size(FEM, ADLTx) == 0) continue;
 
 
      if(_doWithinPop) {
        patch->getCopy(MAL, ADLTx, males);
        patch->getCopy(FEM, ADLTx, females);
        sampleWithinPop(patch, males, females, nsire);
      }
    }
  }
}

References _atGeneration, _doAmongPop, _doWithinPop, _nSire, LifeCycleEvent::_popPtr, ADLTx, FEM, Metapop::flush(), generatePedigree(), SimComponent::get_parameter(), Patch::getCopy(), Metapop::getCurrentGeneration(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, message(), OFFSPRG, sampleAmongPop(), sampleWithinPop(), Metapop::size(), Patch::size(), and warning().

generatePedigree()

void LCE_Cross::generatePedigree

(

)

{
  Individual* ind;;
 
#ifndef USE_MPI
  //read the pedigree file only once per simulation (but only for non-MPI jobs):
  if(_popPtr->getCurrentReplicate() == 1)
#endif
    _reader->FHread(_pedigree_file);
 
 
  vector< unsigned long * > pedigree = _reader->getPedigree();
 
  _pedigree_pop.clear();
 
  //read in the individual ID of each record and create individuals
  for(unsigned int i = 0; i < pedigree.size(); ++i) {
 
    if(_pedigree_pop.find(pedigree[i][0]) != _pedigree_pop.end())
      warning("found duplicated ID %i in pedigree, replacing it with latest record"
          , pedigree[i][0]);
    else
      _pedigree_pop[ pedigree[i][0] ] = _popPtr->getPrototypeClone();
 
    ind = _pedigree_pop[ pedigree[i][0] ];
 
    ind->init(); //need to allocate traits' memory; warning: sets parents' ID to 0!!!
    ind->setID( pedigree[i][0] );
    ind->setFatherID( pedigree[i][1] );
    ind->setMotherID( pedigree[i][2] );
 
  }
 
  //create the genetics
  map< unsigned long, Individual*>::const_iterator REC = _pedigree_pop.begin();
 
  while(REC != _pedigree_pop.end()) {
 
    //recursively create ancestors of an individual, and the individual by inheritance
    // adding mutations as well
    if(!create_individual_ancestors( REC->second ))
      error("while creating individuals on a pedigree (ID=%i)\n",REC->first);
 
    REC++;
  }
 
  //deal with pedigreed population
  //for now, empty all patches and dump the ped pop in the first patch (offspring fems)
  _popPtr->flush();
  _popPtr->setCurrentAge(OFFSPRG);
 
  Patch* patch = _popPtr->getPatch(0);
 
  REC = _pedigree_pop.begin();
  while(REC != _pedigree_pop.end()) {
 
    patch->add(FEM, OFFSx, REC->second);
 
    REC++;
  }
 
}

References _pedigree_file, _pedigree_pop, LifeCycleEvent::_popPtr, _reader, Patch::add(), create_individual_ancestors(), error(), FEM, FHPedigreeReader::FHread(), Metapop::flush(), Metapop::getCurrentReplicate(), Metapop::getPatch(), FHPedigreeReader::getPedigree(), IndFactory::getPrototypeClone(), Individual::init(), OFFSPRG, OFFSx, Metapop::setCurrentAge(), Individual::setFatherID(), Individual::setID(), Individual::setMotherID(), and warning().

Referenced by execute().

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loadFileServices()

void LCE_Cross::loadFileServices ( FileServices *  loader )

virtual

Implements SimComponent.

{
        if( ! get_parameter("cross_with_pedigree_file")->isSet() ) return;
 
        if(_reader) delete _reader;
        _reader = new FHPedigreeReader(this);
        //set to read mode:
        _reader->set_isInputHandler(true);
        //attach to file manager:
        loader->attach_reader(_reader);
 
        _pedigree_file = get_parameter("cross_with_pedigree_file")->getArg();
 
        _reader->set(true, false, 1, _atGeneration, 0, "", this);
 
}

References _atGeneration, _pedigree_file, _reader, FileServices::attach_reader(), SimComponent::get_parameter(), Param::getArg(), EventFileHandler< LCE >::set(), and FileHandler::set_isInputHandler().

loadStatServices()

virtual void LCE_Cross::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_Cross::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_Cross::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return ADULTS;}

References ADULTS.

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

sampleAmongPop()

void LCE_Cross::sampleAmongPop	(	Patch *	patch,
		deque< Individual * > &	males,
		unsigned int	nsire
	)

{
  unsigned int at, deme, npatch = _popPtr->getPatchNbr();
  Individual *sire, *dam;
  Patch* aimedPatch;
  
  for(unsigned int s = 0; s < nsire; ++s) {
    
    //sampling parents
    at = (unsigned int)RAND::Uniform( males.size() );
    
    sire = males[at];
    
    if( !_doReplace ) males.erase(males.begin() + at);
    
    for(unsigned int d = 0; d < _nDam; ++d) {
      //sample a deme
      do {
        deme = (unsigned int)RAND::Uniform(npatch);
      } while(deme == patch->getID() || patch->size(FEM, ADLTx) == 0);
      
      aimedPatch = _popPtr->getPatchPtr(deme);
      //sample a female
      dam = aimedPatch->get( FEM, ADLTx, (unsigned int)RAND::Uniform( aimedPatch->size(FEM, ADULTS) ) );
      
      if(dam == NULL) {d--; continue;}
      
      //mate and breed; ignore sex, put all offs in females' container
      for(unsigned int k = 0; k < _nOffspring; ++k) {
        
        patch->add(FEM, OFFSx, _popPtr->makeOffsprg(dam, sire, FEM, patch->getID()) );
        
      }
    }
  }
}

References _doReplace, _nDam, _nOffspring, LifeCycleEvent::_popPtr, Patch::add(), ADLTx, ADULTS, FEM, Patch::get(), Patch::getID(), Metapop::getPatchNbr(), Metapop::getPatchPtr(), IndFactory::makeOffsprg(), OFFSx, Patch::size(), and RAND::Uniform().

Referenced by execute().

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sampleWithinPop()

void LCE_Cross::sampleWithinPop	(	Patch *	patch,
		deque< Individual * > &	males,
		deque< Individual * > &	females,
		unsigned int	nsire
	)

{  
  unsigned int ndam, at;
  Individual *sire, *dam;
  
  if(!_doReplace && nsire * _nDam > patch->size(FEM,ADLTx)) {
    ndam = patch->size(FEM,ADLTx)/nsire;
    warning("LCE_Cross:: total num of dam greater than available females in patch %i, reseting num_dam to %i.\n",patch->getID()+1, ndam);
  } else
    ndam = _nDam;
  
  if(nsire == 0 || ndam == 0) return;
  
  for(unsigned int s = 0; s < nsire; ++s) {
    
    //sampling parents
    at = (unsigned int)RAND::Uniform( males.size() );
    
    sire = males[at];
    
    if( !_doReplace ) males.erase(males.begin() + at);
    
    for(unsigned int d = 0; d < ndam; ++d) {
      
      at = (unsigned int)RAND::Uniform( females.size() );
      
      dam = females[at];
      
      if( !_doReplace ) females.erase(females.begin() + at);
      
      //now mate and breed; ignore sex, put all offs in females' container
      for(unsigned int k = 0; k < _nOffspring; ++k) {
        
        patch->add(FEM, OFFSx, _popPtr->makeOffsprg(dam, sire, FEM, patch->getID()) );
        
      }
    }
  }
}

References _doReplace, _nDam, _nOffspring, LifeCycleEvent::_popPtr, Patch::add(), ADLTx, FEM, Patch::getID(), IndFactory::makeOffsprg(), OFFSx, Patch::size(), RAND::Uniform(), and warning().

Referenced by execute().

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setParameters()

bool LCE_Cross::setParameters ( )

virtual

Implements SimComponent.

{
  _nSire = (unsigned int)get_parameter_value("cross_num_sire");
  _nDam = (unsigned int)get_parameter_value("cross_num_dam");
  _nOffspring = (unsigned int)get_parameter_value("cross_num_offspring");
  _atGeneration = (unsigned int)get_parameter_value("cross_at_generation");
  
  if(get_parameter("cross_do_among_pop")->isSet())
    _doAmongPop = (unsigned int)get_parameter_value("cross_do_among_pop");
  else
    _doAmongPop = 0;
  
  if(get_parameter("cross_do_within_pop")->isSet()) {
    string arg = get_parameter("cross_do_within_pop")->getArg();
    if (tstring::str2int(arg) == 1) {
      _doWithinPop = 1;
    } else if (tstring::str2int(arg) == 0) {
      _doWithinPop = 0;
    } else {
      _doWithinPop = 1;
    }
  } else
    _doWithinPop = true; //by default
  
  if(get_parameter("cross_with_replacement")->isSet())
    _doReplace = (unsigned int)get_parameter_value("cross_with_replacement");
  else 
    _doReplace = 0;
  
  return true;
}

References _atGeneration, _doAmongPop, _doReplace, _doWithinPop, _nDam, _nOffspring, _nSire, SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getArg(), Param::isSet(), and tstring::str2int().

Referenced by LCE_Cross().

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Member Data Documentation

_atGeneration

unsigned int LCE_Cross::_atGeneration

private

Referenced by execute(), loadFileServices(), and setParameters().

_doAmongPop

bool LCE_Cross::_doAmongPop

private

Referenced by execute(), and setParameters().

_doReplace

bool LCE_Cross::_doReplace

private

Referenced by sampleAmongPop(), sampleWithinPop(), and setParameters().

_doWithinPop

bool LCE_Cross::_doWithinPop

private

Referenced by execute(), and setParameters().

_nDam

unsigned int LCE_Cross::_nDam

private

Referenced by sampleAmongPop(), sampleWithinPop(), and setParameters().

_nOffspring

unsigned int LCE_Cross::_nOffspring

private

Referenced by sampleAmongPop(), sampleWithinPop(), and setParameters().

_nSire

unsigned int LCE_Cross::_nSire

private

Referenced by execute(), and setParameters().

_pedigree_file

string LCE_Cross::_pedigree_file

private

Referenced by generatePedigree(), and loadFileServices().

_pedigree_pop

map<unsigned long, Individual* > LCE_Cross::_pedigree_pop

private

Referenced by create_individual_ancestors(), and generatePedigree().

_reader

FHPedigreeReader* LCE_Cross::_reader

private

Referenced by generatePedigree(), and loadFileServices().

---

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

• LCEmisc.h
• LCEmisc.cc