LCE_Disperse_ConstDisp Class Reference

Dispersal event with constant dispersal rates. More...

#include <LCEdisperse.h>

Inheritance diagram for LCE_Disperse_ConstDisp:

Collaboration diagram for LCE_Disperse_ConstDisp:

Public Member Functions
	LCE_Disperse_ConstDisp ()
virtual	~LCE_Disperse_ConstDisp ()
bool	setParameters (string prefix)
void	Migrate ()
void	Migrate_propagule ()
void	MigratePatch (sex_t SEX, unsigned int LocalPatch)
void	MigratePatch_AbsorbingBorder (sex_t SEX, unsigned int LocalPatch)
void	MigratePatchByNumber (sex_t SEX, unsigned int LocalPatch)
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 Attributes
void(LCE_Disperse_ConstDisp::*	doMigration )(void)
void(LCE_Disperse_ConstDisp::*	doPatchMigration )(sex_t SEX, unsigned int local_patch)

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 constant dispersal rates.

Sets and uses the dispersal matrices according to the dispersal model chosen. 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)
• 4: Lattice model (stepping stone in 2D)

Constructor & Destructor Documentation

LCE_Disperse_ConstDisp()

LCE_Disperse_ConstDisp::LCE_Disperse_ConstDisp

(

)

: LifeCycleEvent ("disperse",""), doMigration(0), doPatchMigration(0)
{
 
  ParamUpdater< LCE_Disperse_ConstDisp > * updater =
      new ParamUpdater< LCE_Disperse_ConstDisp > (&LCE_Disperse_ConstDisp::setParameters);
 
  LCE_Disperse_base::addParameters("dispersal", updater);
}

References LCE_Disperse_base::addParameters(), and setParameters().

Referenced by clone().

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~LCE_Disperse_ConstDisp()

virtual LCE_Disperse_ConstDisp::~LCE_Disperse_ConstDisp ( )

inlinevirtual

{}

Member Function Documentation

clone()

virtual LifeCycleEvent* LCE_Disperse_ConstDisp::clone ( )

inlinevirtual

Implements LifeCycleEvent.

Reimplemented in LCE_SeedDisp.

{return new LCE_Disperse_ConstDisp();}

References LCE_Disperse_ConstDisp().

execute()

void LCE_Disperse_ConstDisp::execute ( )

virtual

Implements LifeCycleEvent.

{
#ifdef _DEBUG_
  message("LCE_Disperse_ConstDisp::execute (Patch nb: %i offsprg nb: %i adlt nb: %i "
      ,_popPtr->getPatchNbr(), _popPtr->size( OFFSPRG ), _popPtr->size( ADULTS ));
  fflush(stdout);
#endif
  //check whether the number of patches changed during simulation:
  if(_npatch != _popPtr->getPatchNbr()) {
    _npatch = _popPtr->getPatchNbr();
    if(!updateDispMatrix()) fatal("bailing out\n");
  }
 
  reset_counters();
 
  (this->*doMigration)();
 
#ifdef _DEBUG_
  unsigned int c = 0;
  for(unsigned int i = 0; i < _npatch; i++)
    c += _popPtr->getPatch(i)->nbEmigrant;
  message("emigrants nb: %i)\n",c);
#endif
}

References LCE_Disperse_base::_npatch, LifeCycleEvent::_popPtr, ADULTS, doMigration, fatal(), Metapop::getPatch(), Metapop::getPatchNbr(), message(), Patch::nbEmigrant, OFFSPRG, LCE_Disperse_base::reset_counters(), Metapop::size(), and LCE_Disperse_base::updateDispMatrix().

Migrate()

void LCE_Disperse_ConstDisp::Migrate

(

)

{
  Patch *patch;
 
  for(unsigned int i = 0; i < _npatch; i++) {
 
    patch = _popPtr->getPatch(i);
 
    (this->*doPatchMigration)(FEM, i);
 
    (this->*doPatchMigration)(MAL, i);
 
    //set coloniser counter
    if(patch->get_isExtinct())
      patch->nbKolonisers = patch->size(PDISPx);
    else
      patch->nbKolonisers = -1; //value used in stat_demo to check for colonization
 
  }//end for nb_patch
 
  //put back the individuals into the offspring container
  swapPostDisp();
}

References LCE_Disperse_base::_npatch, LifeCycleEvent::_popPtr, doPatchMigration, FEM, Patch::get_isExtinct(), Metapop::getPatch(), MAL, Patch::nbKolonisers, PDISPx, Patch::size(), and LCE_Disperse_base::swapPostDisp().

Referenced by Migrate_propagule(), and setParameters().

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Migrate_propagule()

void LCE_Disperse_ConstDisp::Migrate_propagule

(

)

{
  setIsland_PropagulePool_Matrix();
  Migrate();
}

References Migrate(), and LCE_Disperse_base::setIsland_PropagulePool_Matrix().

Referenced by setParameters().

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MigratePatch()

void LCE_Disperse_ConstDisp::MigratePatch	(	sex_t	SEX,
		unsigned int	LocalPatch
	)

{
  Patch* patch = _popPtr->getPatch(LocalPatch);
  unsigned int AimedPatch;
  unsigned int Limit = _npatch -1;
 
  unsigned int count =1;
  while( patch->size(SEX, OFFSx) != 0 ) {
 
    do{
      AimedPatch = getMigrationPatchForward(SEX, LocalPatch);
    }while ( AimedPatch > Limit );
 
    _popPtr->move(SEX, OFFSx, LocalPatch, PDISPx, AimedPatch, 0);
 
    if(LocalPatch != AimedPatch) {
      patch->nbEmigrant++;
      _popPtr->getPatch(AimedPatch)->nbImigrant++;
    } else
      patch->nbPhilopat++;
 
  }//end while
}

References LCE_Disperse_base::_npatch, LifeCycleEvent::_popPtr, LCE_Disperse_base::getMigrationPatchForward(), Metapop::getPatch(), Metapop::move(), Patch::nbEmigrant, Patch::nbImigrant, Patch::nbPhilopat, OFFSx, PDISPx, and Patch::size().

Referenced by setParameters().

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MigratePatch_AbsorbingBorder()

void LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder	(	sex_t	SEX,
		unsigned int	LocalPatch
	)

{
  Patch* patch = _popPtr->getPatch(LocalPatch);
  unsigned int AimedPatch;
 
  while( patch->size(SEX, OFFSx) != 0 ) {
 
    do{
      AimedPatch = getMigrationPatchForward(SEX, LocalPatch);
    }while ( AimedPatch > _npatch );
 
    if(AimedPatch == _npatch) {
      _popPtr->recycle( patch->get(SEX, OFFSx, 0) );
      patch->remove(SEX, OFFSx, 0);
    } else
      _popPtr->move(SEX, OFFSx, LocalPatch, PDISPx, AimedPatch, 0);
 
    if(LocalPatch != AimedPatch) {
      patch->nbEmigrant++;
      if(AimedPatch < _npatch)
        _popPtr->getPatch(AimedPatch)->nbImigrant++;
    } else
      patch->nbPhilopat++;
 
  }//end while
}

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

Referenced by setParameters().

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MigratePatchByNumber()

void LCE_Disperse_ConstDisp::MigratePatchByNumber	(	sex_t	SEX,
		unsigned int	LocalPatch
	)

{
  Patch* patch = _popPtr->getPatch(LocalPatch);
  unsigned int AimedPatch, at;
//  unsigned int Limit = _npatch -1;
 
  // cycle through the connected patches
  for(unsigned int i = 0; i < _reducedDispMat[SEX][LocalPatch].size(); ++i) {
 
    AimedPatch = _reducedDispMat[SEX][LocalPatch][i];
 
    // move as many individual as we can until either the specified number is reached or the patch is empty
    for(unsigned int m = _reducedDispMatProba[SEX][LocalPatch][i]; m > 0 && patch->size(SEX, OFFSx) > 0; --m) {
 
      // take an individual at random:
      at = RAND::Uniform(patch->size(SEX, OFFSx));
 
      _popPtr->move(SEX, OFFSx, LocalPatch, PDISPx, AimedPatch, at);
 
      if(LocalPatch != AimedPatch) {
 
        patch->nbEmigrant++;
 
        _popPtr->getPatch(AimedPatch)->nbImigrant++;
 
      } else
 
        patch->nbPhilopat++;
    }//end for num migrants
 
  }//end for num connected patches
 
  // there might be individuals still in the patch, we flush them to avoid memory leaks
  patch->flush(SEX, OFFSx, _popPtr);
 
}

References LifeCycleEvent::_popPtr, LCE_Disperse_base::_reducedDispMat, LCE_Disperse_base::_reducedDispMatProba, Patch::flush(), Metapop::getPatch(), Metapop::move(), Patch::nbEmigrant, Patch::nbImigrant, Patch::nbPhilopat, OFFSx, PDISPx, Patch::size(), and RAND::Uniform().

Referenced by setParameters().

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setParameters() [1/2]

virtual bool LCE_Disperse_ConstDisp::setParameters ( )

inlinevirtual

Implements SimComponent.

Reimplemented in LCE_SeedDisp.

{return setParameters("dispersal");}

References setParameters().

Referenced by LCE_Disperse_ConstDisp(), setParameters(), and LCE_SeedDisp::setParameters().

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setParameters() [2/2]

bool LCE_Disperse_ConstDisp::setParameters

(

string

prefix

)

{
 
  if(!LCE_Disperse_base::setBaseParameters(prefix)) return false;
 
  switch ( getDispersalModel() ) {
  case 0: //dispersal matrix given in input
  case 1:
  case 3:
  case 4:
    doMigration = &LCE_Disperse_ConstDisp::Migrate;
    break;
  case 2:
    doMigration = &LCE_Disperse_ConstDisp::Migrate_propagule;
    break;
  default:
    return error("\nDispersal model '%i' not yet implemented\n",getDispersalModel());
  }
 
  switch ((int)get_parameter_value(prefix + "_border_model")) {
  case -1:
  case 1:
  case 2:
    doPatchMigration = &LCE_Disperse_ConstDisp::MigratePatch;
    break;
  case 3:
    doPatchMigration = &LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder;
    break;
  default:
    return error("\nDispersal border model '%i' not yet implemented\n",
        (int)get_parameter_value(prefix + "_border_model"));
  }
 
  if(isByNumber())
    doPatchMigration = &LCE_Disperse_ConstDisp::MigratePatchByNumber;
 
  return true;
}

References doMigration, doPatchMigration, error(), SimComponent::get_parameter_value(), LCE_Disperse_base::getDispersalModel(), LCE_Disperse_base::isByNumber(), Migrate(), Migrate_propagule(), MigratePatch(), MigratePatch_AbsorbingBorder(), MigratePatchByNumber(), and LCE_Disperse_base::setBaseParameters().

Member Data Documentation

doMigration

void(LCE_Disperse_ConstDisp::* LCE_Disperse_ConstDisp::doMigration) (void)

private

Referenced by execute(), and setParameters().

doPatchMigration

void(LCE_Disperse_ConstDisp::* LCE_Disperse_ConstDisp::doPatchMigration) (sex_t SEX, unsigned int local_patch)

private

Referenced by Migrate(), and setParameters().

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

• LCEdisperse.h
• LCEdisperse.cc