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().

◆ ~LCE_Disperse_EvolDisp()

virtual LCE_Disperse_EvolDisp::~LCE_Disperse_EvolDisp ( )

inlinevirtual

220 {}

Member Function Documentation

◆ clone()

virtual LifeCycleEvent* LCE_Disperse_EvolDisp::clone ( )

inlinevirtual

Implements LifeCycleEvent.

226 {return new LCE_Disperse_EvolDisp();}

LCE_Disperse_EvolDisp::LCE_Disperse_EvolDisp

LCE_Disperse_EvolDisp()

Definition: LCEdisperse.cc:1570

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().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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().

◆ 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;
 }