LCE_QuantiInit Class Reference

Set patch-specifiec initial genotypes values. More...

#include <LCEquanti.h>

Inheritance diagram for LCE_QuantiInit:

Collaboration diagram for LCE_QuantiInit:

Public Member Functions
	LCE_QuantiInit ()
virtual	~LCE_QuantiInit ()
virtual void	execute ()
void	init_trait_value (sex_t SEX, age_idx AGE, unsigned int size, unsigned int deme, double *values)
void	init_allele_freq (sex_t SEX, age_idx AGE, unsigned int size, unsigned int deme, double *values, const TMatrix &all_val)
virtual LifeCycleEvent *	clone ()
virtual bool	setParameters ()
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
TMatrix	_init_values
TMatrix	_init_freq
bool	_doByTraitValue
bool	_doByAlleleFreq
unsigned int	_nTraits
unsigned int	_nLoci
TProtoQuanti *	_QuantiProto

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

Set patch-specifiec initial genotypes values.

Constructor & Destructor Documentation

LCE_QuantiInit()

LCE_QuantiInit::LCE_QuantiInit

(

)

                                 : LifeCycleEvent("quanti_init","quant"), _doByTraitValue(0),
  _doByAlleleFreq(0), _nTraits(0), _nLoci(0), _QuantiProto(0)
 {
   add_parameter("quanti_init_trait_values",MAT,0,0,0,0);
   add_parameter("quanti_init_freq",MAT,0,0,0,0);
 }

References SimComponent::add_parameter(), and MAT.

Referenced by clone().

~LCE_QuantiInit()

virtual LCE_QuantiInit::~LCE_QuantiInit ( )

inlinevirtual

{ }

Member Function Documentation

addAgeClass()

virtual age_t LCE_QuantiInit::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

clone()

virtual LifeCycleEvent* LCE_QuantiInit::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_QuantiInit();}

References LCE_QuantiInit().

execute()

void LCE_QuantiInit::execute ( )

virtual

Implements LifeCycleEvent.

{
  if(!(_popPtr->getCurrentGeneration() == 1)) return;
 
  unsigned int patchNbr = _popPtr->getPatchNbr();
 
  if (_doByTraitValue) {
    
    double values[_nTraits];
    
    for (unsigned int i = 0; i < patchNbr ; i++) { 
      
      _init_values.getRowView(i, _nTraits, &values[0]);
      
      _QuantiProto->set_init_values(&values[0], _nTraits); // the individuals use the proto to set the init values
 
      init_trait_value(FEM, OFFSx, _popPtr->size(FEM, OFFSPRG, i), i, &values[0]);
      init_trait_value(MAL, OFFSx, _popPtr->size(MAL, OFFSPRG, i), i, &values[0]);
      init_trait_value(FEM, ADLTx, _popPtr->size(FEM, ADULTS, i), i, &values[0]);
      init_trait_value(MAL, ADLTx, _popPtr->size(MAL, ADULTS, i), i, &values[0]);
    }
  }
  
  if (_doByAlleleFreq) {
 
#ifdef _DEBUG_
    message("--- Initializing trait QUANT by frequency ---\n");
#endif
 
    double ifreq[_nLoci];
 
    const TMatrix allele_val = dynamic_cast<TProtoQuanti*> ( _popPtr->getTraitPrototype("quant") )->get_diallele_values();
 
    for (unsigned int i = 0; i < patchNbr ; i++) { 
 
      _init_freq.getRowView(i, _nLoci, &ifreq[0]);
 
      init_allele_freq(FEM, OFFSx, _popPtr->size(FEM, OFFSPRG, i), i, &ifreq[0], allele_val);
      init_allele_freq(MAL, OFFSx, _popPtr->size(MAL, OFFSPRG, i), i, &ifreq[0], allele_val);
      init_allele_freq(FEM, ADLTx, _popPtr->size(FEM, ADULTS, i), i, &ifreq[0], allele_val);
      init_allele_freq(MAL, ADLTx, _popPtr->size(MAL, ADULTS, i), i, &ifreq[0], allele_val);
    }
  }
 
}

References _doByAlleleFreq, _doByTraitValue, _init_freq, _init_values, _nLoci, _nTraits, LifeCycleEvent::_popPtr, _QuantiProto, ADLTx, ADULTS, FEM, Metapop::getCurrentGeneration(), Metapop::getPatchNbr(), TMatrix::getRowView(), IndFactory::getTraitPrototype(), init_allele_freq(), init_trait_value(), MAL, message(), OFFSPRG, OFFSx, TProtoQuanti::set_init_values(), and Metapop::size().

init_allele_freq()

void LCE_QuantiInit::init_allele_freq	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	size,
		unsigned int	deme,
		double *	values,
		const TMatrix &	all_val
	)

{ 
  if(!size) return;
  
  Individual* ind;
  TTQuanti_diallelic* trait;
 
 
  if(size == 1) {  // just one individual in a patch
 
    unsigned int allele;
 
    for(unsigned a = 0; a < 2; a++) {
      for(unsigned l = 0; l < _nLoci; ++l) {
 
        if(RAND::Uniform() < ifreq[l])
          allele = 0;
        else
          allele = 1;
 
        ind = _popPtr->get(SEX, age, 0, deme);
        trait = dynamic_cast<TTQuanti_diallelic*> ( ind->getTrait(_LCELinkedTraitIndex) );
        trait->set_allele_bit(l, a, bool(allele));
      }
    }
 
  } else {
 
    unsigned int num_A, num_a;
 
    for(unsigned a = 0; a < 2; a++) {
      for(unsigned l = 0; l < _nLoci; ++l) {
 
        num_A = (unsigned int)(size * ifreq[l]);
 
        num_a = size - num_A;
 
        int ind_A[num_A];
        int ind_a[num_a];
 
        RAND::SampleSeqWithReciprocal(0, size, 1, num_A, &ind_A[0], num_a, &ind_a[0]); //sample individuals within deme, without replacement
 
        for (unsigned int i = 0; i < num_A ; i++) {
          ind = _popPtr->get(SEX, age, ind_A[i], deme);
          trait = dynamic_cast<TTQuanti_diallelic*> ( ind->getTrait(_LCELinkedTraitIndex) );
          trait->set_allele_bit(l, a, 0);
        }
 
        for (unsigned int i = 0; i < num_a ; i++) {
          ind = _popPtr->get(SEX, age, ind_a[i], deme);
          trait = dynamic_cast<TTQuanti_diallelic*> ( ind->getTrait(_LCELinkedTraitIndex) );
          trait->set_allele_bit(l, a, 1);
        }
      }
    }
  }
  
  for (unsigned int i = 0; i < size; ++i) {
    _popPtr->get(SEX, age, i, deme)->setTraitValue(_LCELinkedTraitIndex);
  }
  
}

References LifeCycleEvent::_LCELinkedTraitIndex, _nLoci, LifeCycleEvent::_popPtr, Metapop::get(), Individual::getTrait(), RAND::SampleSeqWithReciprocal(), TTQuanti_diallelic::set_allele_bit(), Individual::setTraitValue(), and RAND::Uniform().

Referenced by execute().

init_trait_value()

void LCE_QuantiInit::init_trait_value	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	size,
		unsigned int	deme,
		double *	values
	)

{ 
  TTrait* trait;
 
  for (unsigned int i = 0; i < size ; i++) {
    trait = _popPtr->get(SEX, age, i, deme)->getTrait(_LCELinkedTraitIndex);
    trait->init_sequence(); // this function reads the init values from the trait prototype
    trait->set_value();
  }
 
}

References LifeCycleEvent::_LCELinkedTraitIndex, LifeCycleEvent::_popPtr, Metapop::get(), Individual::getTrait(), TTrait::init_sequence(), and TTrait::set_value().

Referenced by execute().

loadFileServices()

virtual void LCE_QuantiInit::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{}

loadStatServices()

virtual void LCE_QuantiInit::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_QuantiInit::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_QuantiInit::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

setParameters()

bool LCE_QuantiInit::setParameters ( )

virtual

Implements SimComponent.

{
  TMatrix pat_mat;
 
  // setting default values
  unsigned int patchNbr = _popPtr->getPatchNbr();
  _QuantiProto = dynamic_cast<TProtoQuanti*> ( _popPtr->getTraitPrototype("quant") );
  
  _nTraits = _QuantiProto -> get_num_traits();
  _nLoci   = _QuantiProto->get_num_locus();
 
  _doByAlleleFreq = false;
  _doByTraitValue = false;
  
  // checking user's options
  if(_paramSet->isSet("quanti_init_trait_values")) {
  
    if(!get_parameter("quanti_init_trait_values")->isMatrix()) {
      fatal("\"quanti_init_trait_values\" accepts only a matrix as argument.\n");
    }
 
    _paramSet->getMatrix("quanti_init_trait_values", &pat_mat);
  
    _doByTraitValue = setSpatialMatrix("quanti_init_trait_values", "num of quanti traits", &pat_mat, &_init_values, _nTraits, patchNbr);
  
  }
  
  if(_paramSet->isSet("quanti_init_freq")) {
    
    if (_QuantiProto->get_allele_model() > 2) {
      error("quanti_init::allelic model of quanti trait incompatible with initialization by allele frequency.\n");
      error("quanti_init::allelic model must be di-allelic instead of continuous.\n");
      return false;
    }
    _paramSet->getMatrix("quanti_init_freq", &pat_mat);
        
    _doByAlleleFreq = setSpatialMatrix("quanti_init_freq", "num of quanti trait loci", &pat_mat, &_init_freq, _nLoci, patchNbr);
    
  }
  
  if (_doByTraitValue && _doByAlleleFreq) {
    warning("quanti_init::trying to initialize quanti traits both by trait values and allele frequencies.");
    warning("quanti_init::forcing initialization by allele frequencies.\n");
    _doByTraitValue = false;
  }
  
  if (!_doByAlleleFreq && !_doByTraitValue) {
    error("quanti_init::either \"quanti_init_trait_values\" or \"quanti_init_freq\" are missing.\n");
  }
  
  return (_doByTraitValue || _doByAlleleFreq);
}

References _doByAlleleFreq, _doByTraitValue, _init_freq, _init_values, _nLoci, _nTraits, SimComponent::_paramSet, LifeCycleEvent::_popPtr, _QuantiProto, error(), fatal(), TProtoQuanti::get_allele_model(), TProtoQuanti::get_num_locus(), SimComponent::get_parameter(), ParamSet::getMatrix(), Metapop::getPatchNbr(), IndFactory::getTraitPrototype(), ParamSet::isSet(), setSpatialMatrix(), and warning().

Member Data Documentation

_doByAlleleFreq

bool LCE_QuantiInit::_doByAlleleFreq

private

Referenced by execute(), and setParameters().

_doByTraitValue

bool LCE_QuantiInit::_doByTraitValue

private

Referenced by execute(), and setParameters().

_init_freq

TMatrix LCE_QuantiInit::_init_freq

private

Referenced by execute(), and setParameters().

_init_values

TMatrix LCE_QuantiInit::_init_values

private

Referenced by execute(), and setParameters().

_nLoci

unsigned int LCE_QuantiInit::_nLoci

private

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

_nTraits

unsigned int LCE_QuantiInit::_nTraits

private

Referenced by execute(), and setParameters().

_QuantiProto

TProtoQuanti* LCE_QuantiInit::_QuantiProto

private

Referenced by execute(), and setParameters().

---

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

• LCEquanti.h
• LCEquanti.cc