LCE_QuantiModifier Class Reference

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

#include <LCEquanti.h>

Inheritance diagram for LCE_QuantiModifier:

Collaboration diagram for LCE_QuantiModifier:

Public Member Functions
	LCE_QuantiModifier ()
virtual	~LCE_QuantiModifier ()
virtual void	execute ()
void	setVefromVa (Patch *patch, age_idx AGE)
void	setIndPhenotype (Patch *patch, sex_t SEX, age_idx AGE)
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
TProtoQuanti *	_QuantiProto
vector< double >	_h2
TMatrix	_occurrences
unsigned int	_next_occurrence
bool	_is_permanent
age_t	_age_flag
vector< double >(TTQuantiSH::*	_get_VA_func_ptr )(Patch *, const age_idx)

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_QuantiModifier()

LCE_QuantiModifier::LCE_QuantiModifier

(

)

                                         : LifeCycleEvent("quanti_modifier","quant"),
    _QuantiProto(0),
    _next_occurrence(0),
    _is_permanent(0),
    _age_flag(0),
    _get_VA_func_ptr(0)
 {
  ParamUpdater<LCE_QuantiModifier> *updater = new ParamUpdater<LCE_QuantiModifier>(&LCE_QuantiModifier::setParameters);
 
  add_parameter("quanti_modifier_at_generation", INT, true, false, 0, 0, NULL);
  add_parameter("quanti_modifier_at_age", STR, true, false, 0, 0, updater);
  add_parameter("quanti_modifier_is_permanent", BOOL, false, false, 0, 0, updater);
 
//  add_parameter("quanti_modifier_target", STR, false, false, 0, 0, updater);  // what to affect
//  add_parameter("quanti_modifier_values", MAT, false, false, 0, 0, updater); // how to affect target
 
 }

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

Referenced by clone().

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~LCE_QuantiModifier()

virtual LCE_QuantiModifier::~LCE_QuantiModifier ( )

inlinevirtual

{ }

Member Function Documentation

addAgeClass()

virtual age_t LCE_QuantiModifier::addAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

clone()

virtual LifeCycleEvent* LCE_QuantiModifier::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_QuantiModifier();}

References LCE_QuantiModifier().

execute()

void LCE_QuantiModifier::execute ( )

virtual

Implements LifeCycleEvent.

{
  unsigned int gen = _popPtr->getCurrentGeneration();
 
  if(!(
       gen == _occurrences.get(0, _next_occurrence) ||
      (gen >= _occurrences.get(0, _next_occurrence) && _is_permanent)
     ))
    return;
 
  // update the next occurrence:
  if(!_is_permanent && _next_occurrence < _occurrences.ncols()-1)
    _next_occurrence++;
 
 
  // for now only implementing the heritability setting
  _h2 = _QuantiProto->get_heritability(); //may have been reset during a run
 
  // we have to make sure that the phenotype will be calculated with Ve
  // this is not guaranteed if Ve was not given in input
  _QuantiProto->set_trait_value_func_ptr(true);
 
  Patch *patch;
 
  // compute Va in each patch to set Ve to match the h2 required
  for(unsigned int i = 0; i < _popPtr->getPatchNbr(); ++i)
  {
 
    patch = _popPtr->getPatch(i);
 
    if(_age_flag & OFFSPRG) {
      setVefromVa(patch, OFFSx);
      setIndPhenotype(patch, FEM, OFFSx);
      setIndPhenotype(patch, MAL, OFFSx);
    }
 
    if(_age_flag & ADULTS) {
      setVefromVa(patch, ADLTx);
      setIndPhenotype(patch, FEM, ADLTx);
      setIndPhenotype(patch, MAL, ADLTx);
    }
  }
 
}

References _age_flag, _h2, _is_permanent, _next_occurrence, _occurrences, LifeCycleEvent::_popPtr, _QuantiProto, ADLTx, ADULTS, FEM, TMatrix::get(), TProtoQuanti::get_heritability(), Metapop::getCurrentGeneration(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, TMatrix::ncols(), OFFSPRG, OFFSx, TProtoQuanti::set_trait_value_func_ptr(), setIndPhenotype(), and setVefromVa().

loadFileServices()

virtual void LCE_QuantiModifier::loadFileServices ( FileServices *  loader )

inlinevirtual

Implements SimComponent.

{}

loadStatServices()

virtual void LCE_QuantiModifier::loadStatServices ( StatServices *  loader )

inlinevirtual

Implements SimComponent.

{}

removeAgeClass()

virtual age_t LCE_QuantiModifier::removeAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

requiredAgeClass()

virtual age_t LCE_QuantiModifier::requiredAgeClass ( )

inlinevirtual

Implements LifeCycleEvent.

{return 0;}

resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

{return false;}

setIndPhenotype()

void LCE_QuantiModifier::setIndPhenotype	(	Patch *	patch,
		sex_t	SEX,
		age_idx	AGE
	)

{
  for(unsigned int i = 0; i < patch->size(SEX, AGE); ++i)
  {
    patch->get(SEX, AGE, i)->setTraitValue(_LCELinkedTraitIndex);
  }
}

References LifeCycleEvent::_LCELinkedTraitIndex, Patch::get(), Individual::setTraitValue(), and Patch::size().

Referenced by execute().

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setParameters()

bool LCE_QuantiModifier::setParameters ( )

virtual

Implements SimComponent.

{
  _QuantiProto = dynamic_cast<TProtoQuanti*> ( _popPtr->getTraitPrototype("quant") );
 
  if(!get_parameter("quanti_modifier_at_generation")->isMatrix()) {
 
    _occurrences.reset(1, 1, get_parameter_value("quanti_modifier_at_generation"));
 
  } else {
 
    get_parameter("quanti_modifier_at_generation")->getMatrix(&_occurrences);
 
    if(_occurrences.nrows()>1)
      return error("LCE quanti_modifier:: multiple generations must be provided in a 1D array, with a single row\n");
 
  }
 
  _next_occurrence = 0; //this is the index in the array
 
  string flag =  get_parameter("quanti_modifier_at_age")->getArg();
 
  std::for_each(flag.begin(), flag.end(), [](char& c){c = ::tolower(c);});
 
  if (flag == "adults" || flag == "adult" || flag == "4") {
 
    _age_flag = ADULTS;
 
  } else if (flag == "offsprings" || flag == "offspring" || flag == "1" ) {
 
    _age_flag = OFFSPRG;
 
  } else if (flag == "all" || flag == "7") {
 
    _age_flag = ALL;
 
  } else {
 
    fatal("LCE quanti_modifier:: targeted age class must be specified as \"adults\", \"offspring\", or \"all\" (%s)\n", flag.c_str());
  }
 
  if(get_parameter("quanti_modifier_is_permanent")->isSet())
    _is_permanent = true;
  else
    _is_permanent = false;
 
  //check for allele model
  if(_QuantiProto->get_dominance_model() == 0)
    _get_VA_func_ptr = &TTQuantiSH::getVaNoDominance;
  else
    _get_VA_func_ptr = &TTQuantiSH::getVaWithDominance;
 
  return true;
}

References _age_flag, _get_VA_func_ptr, _is_permanent, _next_occurrence, _occurrences, LifeCycleEvent::_popPtr, _QuantiProto, ADULTS, ALL, error(), fatal(), TProtoQuanti::get_dominance_model(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getArg(), Param::getMatrix(), IndFactory::getTraitPrototype(), TTQuantiSH::getVaNoDominance(), TTQuantiSH::getVaWithDominance(), Param::isMatrix(), TMatrix::nrows(), OFFSPRG, and TMatrix::reset().

Referenced by LCE_QuantiModifier().

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setVefromVa()

void LCE_QuantiModifier::setVefromVa	(	Patch *	patch,
		age_idx	AGE
	)

{
  vector<double> Va;
 
  Va = (_QuantiProto->get_stater()->*_get_VA_func_ptr)(patch, AGE);  // compute Va, and Vg
 
//  cout << "LCE_QuantiModifier::setVefromVa("<<AGE<<"):: Va/Ve = ";
 
 
  // set Ve to match h2 given computed value of Va
  // Vg has been set during the process, its value is accessible via the stater's interface
  for(unsigned int j = 0; j < _QuantiProto->get_num_traits(); ++j) {
 
//    cout << Va[j] <<"/"<< Va[j]/_h2[j] - _QuantiProto->get_stater()->getVg(j) <<" ";
 
    _QuantiProto->set_eVarianceSD( j, sqrt( Va[j]/_h2[j] - _QuantiProto->get_stater()->getVg(j) ) );
  }
 
//  cout<<endl;
}

References _get_VA_func_ptr, _h2, _QuantiProto, TProtoQuanti::get_num_traits(), TProtoQuanti::get_stater(), TTQuantiSH::getVg(), and TProtoQuanti::set_eVarianceSD().

Referenced by execute().

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Member Data Documentation

_age_flag

age_t LCE_QuantiModifier::_age_flag

private

Referenced by execute(), and setParameters().

_get_VA_func_ptr

vector<double>(TTQuantiSH::* LCE_QuantiModifier::_get_VA_func_ptr) (Patch *, const age_idx)

private

Referenced by setParameters(), and setVefromVa().

_h2

vector<double> LCE_QuantiModifier::_h2

private

Referenced by execute(), and setVefromVa().

_is_permanent

bool LCE_QuantiModifier::_is_permanent

private

Referenced by execute(), and setParameters().

_next_occurrence

unsigned int LCE_QuantiModifier::_next_occurrence

private

Referenced by execute(), and setParameters().

_occurrences

TMatrix LCE_QuantiModifier::_occurrences

private

Referenced by execute(), and setParameters().

_QuantiProto

TProtoQuanti* LCE_QuantiModifier::_QuantiProto

private

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

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

• LCEquanti.h
• LCEquanti.cc