LCE_Disperse_EvolDisp Class Reference

Dispersal event with an evolving dispersal rate given by the "disp" trait. More...

#include <LCEdisperse.h>

Inheritance diagram for LCE_Disperse_EvolDisp:

Collaboration diagram for LCE_Disperse_EvolDisp:

Public Member Functions
	LCE_Disperse_EvolDisp ()
virtual	~LCE_Disperse_EvolDisp ()
Implementations
virtual bool	setParameters ()
virtual void	execute ()
virtual LifeCycleEvent *	clone ()
Public Member Functions inherited from LCE_Disperse_base
	LCE_Disperse_base ()
virtual	~LCE_Disperse_base ()
	Deallocates the disp matrix. More...
bool	setBaseParameters (string prefix)
void	setParamPrefix (string pref)
void	addParameters (string prefix, ParamUpdaterBase *updater)
void	setIndentityDispMatrix (TMatrix *mat)
unsigned int	getMigrationPatchForward (sex_t SEX, unsigned int LocalPatch)
unsigned int	getMigrationPatchBackward (sex_t SEX, unsigned int LocalPatch)
unsigned int	getMigrationIndex (vector< double > &rates)
unsigned int	getMigrationIndexGSLdiscrete (gsl_ran_discrete_t *rates)
void	setPropaguleTargets ()
void	swapPostDisp ()
void	reset_counters ()
void	set_isForward (bool val)
bool	checkForwardDispersalMatrix (TMatrix *mat)
bool	checkBackwardDispersalMatrix (TMatrix *mat)
void	allocateDispMatrix (sex_t sex, unsigned int dim)
bool	updateDispMatrix ()
bool	setDispMatrix ()
bool	setReducedMatricesBySex (sex_t SEX, Param &connectivity, Param &rate)
bool	setReducedDispMatrix ()
	The reduced dispersal matrix contains the indices of the patches to which each patch is connected. More...
bool	setIsland_MigrantPool_Matrix ()
bool	setIsland_PropagulePool_Matrix ()
bool	setSteppingStone1DMatrix ()
bool	setLatticeMatrix ()
	Sets the dispersal matrices for the Lattice dispersal model. More...
bool	setBasicLatticeMatrix (int rows, int cols, double phi_mal, double phi_fem, double disp_mal, double disp_fem)
bool	setLatticeTorrusMatrix (int rows, int cols, double disp_mal, double disp_fem, TMatrix *grid)
bool	setLatticeAbsorbingMatrix ()
bool	setLatticeReflectingMatrix (int rows, int cols, TMatrix *grid)
bool	isForward ()
bool	isByNumber ()
unsigned int	getDispersalModel ()
double	getPropaguleProb ()
unsigned int	getPropaguleTarget (unsigned int home)
vector< double >	getConnectedPatches (sex_t SEX, unsigned int local_patch)
vector< double >	getConnectedRates (sex_t SEX, unsigned int local_patch)
double	getReducedDispersalRate (sex_t SEX, unsigned int row, unsigned int col)
unsigned int	getReducedDispersalPatchID (sex_t SEX, unsigned int row, unsigned int col)
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 Member Functions
unsigned int	Migrate_Island (unsigned int home)
unsigned int	Migrate_Island_Propagule (unsigned int home)
unsigned int	Migrate_SteppingStone1D (unsigned int home)
unsigned int	Migrate_Lattice (unsigned int home)
void	exec_evolmale ()
void	exec_evolfemale ()
void	exec_evol2sex ()
void	evoldisp (sex_t SEX, int trait_link, double cost)
void	fixdisp (sex_t SEX, double rate, double cost)

Private Attributes
double	_fem_cost
double	_mal_cost
double	_fixed_disp_rate
unsigned int(LCE_Disperse_EvolDisp::*	getAimedPatch )(unsigned int)
void(LCE_Disperse_EvolDisp::*	exec )()
int	_fdisp_trait_link
int	_mdisp_trait_link

Additional Inherited Members
Protected Attributes inherited from LCE_Disperse_base
unsigned int	_npatch
	Number of patches in the population. More...
vector< vector< double > >	_reducedDispMat [2]
	Matrix containing the indexes of the patches connected to each patch. More...
vector< vector< double > >	_reducedDispMatProba [2]
	Matrix containing the probability to migrate to/from the connected patches. More...
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

Dispersal event with an evolving dispersal rate given by the "disp" trait.

The dispersal models implemented so far are:

• 1: Island Model with migrant pool
• 2: Island Model with propagule pool
• 3: Stepping stone model in 1 dimension (ring population)

Constructor & Destructor Documentation

LCE_Disperse_EvolDisp()

LCE_Disperse_EvolDisp::LCE_Disperse_EvolDisp

(

)

: LifeCycleEvent("disperse_evoldisp",""), _fem_cost(-1.0), _mal_cost(-1.0), _fixed_disp_rate(0),
  getAimedPatch(0), exec(0), _fdisp_trait_link(0), _mdisp_trait_link(0)
{
  ParamUpdater<LCE_Disperse_EvolDisp> * updater =
      new ParamUpdater<LCE_Disperse_EvolDisp> (&LCE_Disperse_EvolDisp::setParameters);
 
  LCE_Disperse_base::addParameters("dispersal", updater);
 
  add_parameter("dispersal_cost",DBL,false,true,0,1, updater);
  add_parameter("dispersal_cost_fem",DBL,false,true,0,1, updater);
  add_parameter("dispersal_cost_mal",DBL,false,true,0,1, updater);
  add_parameter("dispersal_fixed_trait",STR,false,false,0,0, updater);
  add_parameter("dispersal_fixed_rate",DBL,false,true,0,1, updater);
}

References SimComponent::add_parameter(), LCE_Disperse_base::addParameters(), DBL, setParameters(), and STR.

Referenced by clone().

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~LCE_Disperse_EvolDisp()

virtual LCE_Disperse_EvolDisp::~LCE_Disperse_EvolDisp ( )

inlinevirtual

{}

Member Function Documentation

clone()

virtual LifeCycleEvent* LCE_Disperse_EvolDisp::clone ( )

inlinevirtual

Implements LifeCycleEvent.

{return new LCE_Disperse_EvolDisp();}

References LCE_Disperse_EvolDisp().

evoldisp()

void LCE_Disperse_EvolDisp::evoldisp ( sex_t  SEX, int  trait_link, double  cost  )

private

{
 
  Patch *current_patch;
  unsigned int AimedPatch;
  unsigned int sink_patch = _npatch; // this is the sink patch in case of absorbing border model
 
  for(unsigned int i = 0; i < _npatch; i++) {
 
    current_patch = _popPtr->getPatch(i);
 
    while( current_patch->size(SEX, OFFSx) != 0 ) {
 
      if(RAND::Uniform() < *(double*)current_patch->get(SEX, OFFSx, 0)->getTraitValue(trait_link)) {
        //this one disperses
        AimedPatch = (this->*getAimedPatch)(i);
 
        current_patch->nbEmigrant++;
 
        if(RAND::Uniform() < cost || AimedPatch == sink_patch) {
          //also check if sink patch number has been returned
 
          _popPtr->recycle( current_patch->get(SEX, OFFSx, 0) );
 
          current_patch->remove(SEX, OFFSx, 0);
 
        } else {
          //survives
          _popPtr->move(SEX, OFFSx, i, PDISPx, AimedPatch, 0);
 
          _popPtr->getPatch(AimedPatch)->nbImigrant++;
 
        }
      } else {
        //no dispersal
        current_patch->move(SEX,OFFSx,PDISPx,0);
        current_patch->nbPhilopat++;
      }
 
    }//end while
  }//end for
}

References LCE_Disperse_base::_npatch, LifeCycleEvent::_popPtr, Patch::get(), getAimedPatch, Metapop::getPatch(), Individual::getTraitValue(), Patch::move(), Metapop::move(), Patch::nbEmigrant, Patch::nbImigrant, Patch::nbPhilopat, OFFSx, PDISPx, IndFactory::recycle(), Patch::remove(), Patch::size(), and RAND::Uniform().

Referenced by exec_evol2sex(), exec_evolfemale(), and exec_evolmale().

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exec_evol2sex()

void LCE_Disperse_EvolDisp::exec_evol2sex ( )

private

{
  evoldisp(FEM, _fdisp_trait_link, _fem_cost);
  evoldisp(MAL, _mdisp_trait_link, _mal_cost);
}

References _fdisp_trait_link, _fem_cost, _mal_cost, _mdisp_trait_link, evoldisp(), FEM, and MAL.

Referenced by setParameters().

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exec_evolfemale()

void LCE_Disperse_EvolDisp::exec_evolfemale ( )

private

{
  evoldisp(FEM, _fdisp_trait_link, _fem_cost);
  fixdisp(MAL, _fixed_disp_rate, _mal_cost);
}

References _fdisp_trait_link, _fem_cost, _fixed_disp_rate, _mal_cost, evoldisp(), FEM, fixdisp(), and MAL.

Referenced by setParameters().

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exec_evolmale()

void LCE_Disperse_EvolDisp::exec_evolmale ( )

private

{
  evoldisp(MAL, _mdisp_trait_link, _mal_cost);
  fixdisp(FEM, _fixed_disp_rate, _fem_cost);
}

References _fem_cost, _fixed_disp_rate, _mal_cost, _mdisp_trait_link, evoldisp(), FEM, fixdisp(), and MAL.

Referenced by setParameters().

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execute()

void LCE_Disperse_EvolDisp::execute ( )

virtual

Implements LifeCycleEvent.

{
#ifdef _DEBUG_
  message("LCE_Disperse_EvolDisp::execute (Patch nb: %i offsprg nbr: %i)\n"
      ,_popPtr->getPatchNbr(),_popPtr->size( OFFSPRG ));
#endif
  if( getDispersalModel() == 2 ) setPropaguleTargets();
 
 
  reset_counters();
 
  (this->*exec)();
 
  Patch *current_patch;
 
  _npatch = _popPtr->getPatchNbr();
 
  for(unsigned int i = 0; i < _npatch; i++) {
 
    current_patch = _popPtr->getPatch(i);
 
    //set coloniser counter
    if(current_patch->get_isExtinct())
      current_patch->nbKolonisers = current_patch->size(PDISPx);
    else
      current_patch->nbKolonisers = -1;
 
  }//end_for
 
  swapPostDisp();
 
}

References LCE_Disperse_base::_npatch, LifeCycleEvent::_popPtr, exec, Patch::get_isExtinct(), LCE_Disperse_base::getDispersalModel(), Metapop::getPatch(), Metapop::getPatchNbr(), message(), Patch::nbKolonisers, OFFSPRG, PDISPx, LCE_Disperse_base::reset_counters(), LCE_Disperse_base::setPropaguleTargets(), Metapop::size(), Patch::size(), and LCE_Disperse_base::swapPostDisp().

fixdisp()

void LCE_Disperse_EvolDisp::fixdisp ( sex_t  SEX, double  rate, double  cost  )

private

{
 
  Patch *current_patch;
  unsigned int AimedPatch;
 
  for(unsigned int i = 0; i < _npatch; i++) {
 
    current_patch = _popPtr->getPatch(i);
 
    while( current_patch->size(SEX, OFFSx) != 0 ) {
 
      if(RAND::Uniform() < rate) {
        //this one disperses
        AimedPatch = (this->*getAimedPatch)(i);
 
        current_patch->nbEmigrant++;
 
        if(RAND::Uniform() > cost) {
          //survives
          _popPtr->move(SEX, OFFSx, i, PDISPx, AimedPatch, 0);
 
          _popPtr->getPatch(AimedPatch)->nbImigrant++;
        } else {
 
          _popPtr->recycle( current_patch->get(SEX, OFFSx, 0) );
 
          current_patch->remove(SEX, OFFSx, 0);
        }
      } else {
        //no dispersal
        current_patch->move(SEX,OFFSx,PDISPx,0);
        current_patch->nbPhilopat++;
      }
 
    }//end while
  }//end for
}

References LCE_Disperse_base::_npatch, LifeCycleEvent::_popPtr, Patch::get(), getAimedPatch, Metapop::getPatch(), Patch::move(), Metapop::move(), Patch::nbEmigrant, Patch::nbImigrant, Patch::nbPhilopat, OFFSx, PDISPx, IndFactory::recycle(), Patch::remove(), Patch::size(), and RAND::Uniform().

Referenced by exec_evolfemale(), and exec_evolmale().

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Migrate_Island()

unsigned int LCE_Disperse_EvolDisp::Migrate_Island ( unsigned int  home )

private

{
  unsigned int AimedPatch;
  //assign a Patch of arrival at random
  do{
    AimedPatch = RAND::Uniform(_npatch);
  }while(AimedPatch == home);
 
  return AimedPatch;
}

References LCE_Disperse_base::_npatch, and RAND::Uniform().

Referenced by setParameters().

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Migrate_Island_Propagule()

unsigned int LCE_Disperse_EvolDisp::Migrate_Island_Propagule ( unsigned int  home )

private

{
  unsigned int AimedPatch, PropaguleTarget = getPropaguleTarget(home);
 
  if(!(RAND::Uniform() > getPropaguleProb()) )
    AimedPatch = PropaguleTarget;
  else
    do{
      AimedPatch = RAND::Uniform(_npatch);
    }while(AimedPatch == home || AimedPatch == PropaguleTarget);
 
  return AimedPatch;
}

References LCE_Disperse_base::_npatch, LCE_Disperse_base::getPropaguleProb(), LCE_Disperse_base::getPropaguleTarget(), and RAND::Uniform().

Referenced by setParameters().

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Migrate_Lattice()

unsigned int LCE_Disperse_EvolDisp::Migrate_Lattice ( unsigned int  home )

private

{
  //take one of the two, no difference b/n males and females
  return( _reducedDispMat[0][home][ RAND::Uniform( _reducedDispMat[0][home].size() ) ] );
}

References LCE_Disperse_base::_reducedDispMat, and RAND::Uniform().

Referenced by setParameters().

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Migrate_SteppingStone1D()

unsigned int LCE_Disperse_EvolDisp::Migrate_SteppingStone1D ( unsigned int  home )

private

{
  int neighbours[2] = {(int)(home - 1),(int)(home + 1)};
  //if we are at one of the bound of the Patch array, we may migrate to the other bound:
  if(neighbours[0] < 0) neighbours[0] = _npatch -1;
  else if(neighbours[1] == (int)_npatch) neighbours[1] = 0;
 
  return(RAND::RandBool() ? neighbours[0] : neighbours[1]);
}

References LCE_Disperse_base::_npatch, and RAND::RandBool().

Referenced by setParameters().

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setParameters()

bool LCE_Disperse_EvolDisp::setParameters ( )

virtual

Implements SimComponent.

{
  //we do not call the LCE_Disperse_base::setParameters here because we don't use
  //dispersal matrices in input
  _npatch = _popPtr->getPatchNbr();
 
  _prefix = "dispersal";
 
  _disp_model = (int)_paramSet->getValue("dispersal_model");
 
  _disp_propagule_prob = _paramSet->getValue("dispersal_propagule_prob");
 
  if(_disp_model == -1 && !_paramSet->isSet("dispersal_connectivity_matrix")) {
    return error("disperse_evoldisp: a dispersal model or a patch connectivity matrix must be specified!\n");
  }
 
  if(_disp_model == 2 && _disp_propagule_prob == -1) {
    return error("dispersal propagule probability is missing!\n");
  }
 
  _fdisp_trait_link = _popPtr->getTraitIndex("fdisp");
  _mdisp_trait_link = _popPtr->getTraitIndex("mdisp");
 
  // connectivity matrix is specified in input --------------------------------------------
  if(_paramSet->isSet(_prefix + "_connectivity_matrix")) {
 
    _disp_model=0;
 
    get_parameter(_prefix + "_connectivity_matrix")->getVariableMatrix(&_reducedDispMat[0]);
 
    //need to copy matrices for the other sex (a single matrix is given in input)
 
    _reducedDispMat[FEM].clear();
 
    for (unsigned int i = 0; i < _reducedDispMat[0].size(); ++i) {
 
      _reducedDispMat[FEM].push_back(vector<double>());
 
      for (unsigned int j = 0; j < _reducedDispMat[0][i].size(); ++j) {
        //        _reducedDispMat[0][i][j]--; //remove 1 to make sure that the indexes start with 0, not 1!!!!
        _reducedDispMat[FEM][i].push_back( _reducedDispMat[0][i][j] );
      }
    }
  }
 
  if(_paramSet->isSet("dispersal_cost")) {
 
    _fem_cost = _mal_cost = _paramSet->getValue("dispersal_cost");
 
  } else if(_paramSet->isSet("dispersal_cost_fem") && _paramSet->isSet("dispersal_cost_mal")) {
 
    _fem_cost = _paramSet->getValue("dispersal_cost_fem");
 
    _mal_cost = _paramSet->getValue("dispersal_cost_mal");
 
  } else {
    return error("dispersal cost params are not set !\n");
  }
 
  if(_paramSet->isSet("dispersal_fixed_trait")) {
 
    if(_paramSet->getArg("dispersal_fixed_trait").compare("female") == 0) {
 
      exec = &LCE_Disperse_EvolDisp::exec_evolmale;
 
    } else if(_paramSet->getArg("dispersal_fixed_trait").compare("male") == 0) {
 
      exec = &LCE_Disperse_EvolDisp::exec_evolfemale;
 
    } else {
      error("wrong argument value for \"dispersal_fixed_trait\"\n");
      return false;
    }
 
    _fixed_disp_rate = _paramSet->getValue("dispersal_fixed_rate");
 
  } else
    exec = &LCE_Disperse_EvolDisp::exec_evol2sex;
 
  switch ( getDispersalModel() ) {
  case 0:
  case 1:
    getAimedPatch = &LCE_Disperse_EvolDisp::Migrate_Island;
    break;
  case 2:
    getAimedPatch = &LCE_Disperse_EvolDisp::Migrate_Island_Propagule;
    break;
  case 3:
    getAimedPatch = &LCE_Disperse_EvolDisp::Migrate_SteppingStone1D;
    break;
  case 4:
  {
    if(!LCE_Disperse_base::setLatticeMatrix()) return false;
    if(!LCE_Disperse_base::setReducedDispMatrix()) return false;
    getAimedPatch = &LCE_Disperse_EvolDisp::Migrate_Lattice;
    break;
  }
  default: {
    error("\nDispersal model %i not yet implemented with evolving dispersal!\n",
        getDispersalModel());
    return false;
  }
  }
  return true;
}

References LCE_Disperse_base::_disp_model, LCE_Disperse_base::_disp_propagule_prob, _fdisp_trait_link, _fem_cost, _fixed_disp_rate, _mal_cost, _mdisp_trait_link, LCE_Disperse_base::_npatch, SimComponent::_paramSet, LifeCycleEvent::_popPtr, LCE_Disperse_base::_prefix, LCE_Disperse_base::_reducedDispMat, error(), exec, exec_evol2sex(), exec_evolfemale(), exec_evolmale(), FEM, SimComponent::get_parameter(), getAimedPatch, ParamSet::getArg(), LCE_Disperse_base::getDispersalModel(), Metapop::getPatchNbr(), IndFactory::getTraitIndex(), ParamSet::getValue(), Param::getVariableMatrix(), ParamSet::isSet(), Migrate_Island(), Migrate_Island_Propagule(), Migrate_Lattice(), Migrate_SteppingStone1D(), LCE_Disperse_base::setLatticeMatrix(), and LCE_Disperse_base::setReducedDispMatrix().

Referenced by LCE_Disperse_EvolDisp().

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Member Data Documentation

_fdisp_trait_link

int LCE_Disperse_EvolDisp::_fdisp_trait_link

private

Referenced by exec_evol2sex(), exec_evolfemale(), and setParameters().

_fem_cost

double LCE_Disperse_EvolDisp::_fem_cost

private

Referenced by exec_evol2sex(), exec_evolfemale(), exec_evolmale(), and setParameters().

_fixed_disp_rate

double LCE_Disperse_EvolDisp::_fixed_disp_rate

private

Referenced by exec_evolfemale(), exec_evolmale(), and setParameters().

_mal_cost

double LCE_Disperse_EvolDisp::_mal_cost

private

Referenced by exec_evol2sex(), exec_evolfemale(), exec_evolmale(), and setParameters().

_mdisp_trait_link

int LCE_Disperse_EvolDisp::_mdisp_trait_link

private

Referenced by exec_evol2sex(), exec_evolmale(), and setParameters().

exec

void(LCE_Disperse_EvolDisp::* LCE_Disperse_EvolDisp::exec) ()

private

Referenced by execute(), and setParameters().

getAimedPatch

unsigned int(LCE_Disperse_EvolDisp::* LCE_Disperse_EvolDisp::getAimedPatch) (unsigned int)

private

Referenced by evoldisp(), fixdisp(), and setParameters().

---

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

• LCEdisperse.h
• LCEdisperse.cc