LCE_Breed_Disperse Class Reference

Performs breeding and migration in one, migration rates are backward rates. More...

#include <LCEcomposite.h>

Inheritance diagram for LCE_Breed_Disperse:

Collaboration diagram for LCE_Breed_Disperse:

Public Member Functions
	LCE_Breed_Disperse ()
virtual	~LCE_Breed_Disperse ()
void	do_breed_disperse ()
void	do_breed_disperse_propagule ()
unsigned int	numFemOffspring (Patch *patch)
unsigned int	numFemOffspring_colonizers (Patch *patch)
	The number of females produced in case a max number of colonizers was specified. More...
unsigned int	numMalOffspring_notrandom (Patch *patch)
	The number of males produced is always zero when the mating system is not random mating. More...
unsigned int	numMalOffspring_random (Patch *patch)
unsigned int	numMalOffspring_random_colonizers (Patch *patch)
Growth Functions
unsigned int	instantGrowth (Patch *patch, sex_t SEX)
	The number of offspring produced corresponds to the carrying capacity of the patch. More...
unsigned int	logisticGrowth (Patch *patch, sex_t SEX)
	The number of offspring produced is given by the logistic growth function. More...
unsigned int	stochasticLogisticGrowth (Patch *patch, sex_t SEX)
	The number of offspring produced is drawn from a Poisson with mean equal to the logistic growth predicate. More...
unsigned int	conditionalLogisticGrowth (Patch *patch, sex_t SEX)
	The number of offspring produced depends on the adult density. More...
unsigned int	conditionalStochasticLogisticGrowth (Patch *patch, sex_t SEX)
	The number of offspring produced depends on the adult density, similar to 'conditionalLogisticGrowth' except that this time, the fecundities are drawn from Poisson distributions. More...
unsigned int	fixedFecundityGrowth (Patch *patch, sex_t SEX)
	The number of offspring produced is equal to the carrying capacity multiplied by the mean fecundity of the focal patch. More...
unsigned int	stochasticFecundityGrowth (Patch *patch, sex_t SEX)
	The number of offspring produced is a random number drawn from a Poisson distribution with mean equal to the carrying capacity multiplied by the mean fecundity of the focal patch. More...
Mating Functions
Individual *	mate_random (sex_t SEX, Patch *patch, unsigned int LocalPatch)
Individual *	mate_random_hermaphrodite (sex_t SEX, Patch *patch, unsigned int LocalPatch)
Individual *	mate_selfing (sex_t SEX, Patch *patch, unsigned int LocalPatch)
Individual *	mate_full_selfing (sex_t SEX, Patch *patch, unsigned int LocalPatch)
Individual *	mate_cloning (sex_t SEX, Patch *patch, unsigned int LocalPatch)
Individual *	makeOffspring (Individual *ind)
void	breed_disperse (sex_t SEX, Patch *patch, unsigned int LocalPatch, unsigned int size)
Individual *	get_parent (sex_t SEX, sex_t DispSex, Patch *LocalPatch, unsigned int patchNbr)
Implementations
virtual bool	setParameters ()
virtual void	execute ()
virtual LifeCycleEvent *	clone ()
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 LCE_Breed_base
	LCE_Breed_base ()
virtual	~LCE_Breed_base ()
virtual Individual *	getFatherPtr (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Calls the mating function according to the model chosen using the function pointer, used to get the father from the mother in a patch. More...
void	NonWrightFisherPopulation ()
void	WrightFisherPopulation ()
Individual *	breed (Individual *mother, Individual *father, unsigned int LocalPatch)
	Makes a new individual with the right parents. More...
Individual *	breed_cloning (Individual *mother, Individual *father, unsigned int LocalPatch)
	Makes a new individual by doing a deep copy of the mother (copies the mother's genes into the offspring). More...
Individual *	makeOffspring (Individual *ind)
	Last step of the breeding process, does inheritance and mutation of the parents' genes. More...
Individual *	do_breed (Individual *mother, Individual *father, unsigned int LocalPatch)
	Calls the breeding function unsing its pointer. More...
bool	checkMatingCondition (Patch *thePatch)
	Checks if any mating will take place in the patch passed as argument. More...
bool	checkNoSelfing (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is not selfing or cloning. More...
bool	checkPolygyny (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is polygynous. More...
bool	checkSelfing (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is selfing. More...
bool	checkCloning (Patch *thePatch)
	Checks whether mating will take place in the current patch when mating is cloning. More...
bool	setMatingSystem ()
bool	setFecundity ()
bool	setSexRatio ()
double	getMatingProportion ()
double	getMeanFecundity (unsigned int patch)
int	getMatingSystem ()
bool	doInheritance ()
double	getPoissonFecundity (double mean)
double	getFixedFecundity (double mean)
double	getGaussianFecundity (double mean)
double	getLogNormalFecundity (double mean)
double	getFecundity (unsigned int patch)
double	getFecundity (double mean)
sex_t	getOffsprgSex ()
sex_t	getOffsprgSexRandom ()
sex_t	getOffsprgSexFixed ()
sex_t	getOffsprgSexSelfing ()
sex_t	getOffsprgSexCloning ()
Individual *	RandomMating (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male drawn randomly from a patch. More...
Individual *	fullPolyginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to the alpha male of the patch. More...
Individual *	fullPolyginy_manyMales (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to one of the first _mating_males males of the patch. More...
Individual *	partialPolyginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1, or the first male otherwise. More...
Individual *	partialPolyginy_manyMales (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1, or one of the _mating_males first males otherwise. More...
Individual *	fullMonoginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male with same index as mother (if available) from the focal patch. More...
Individual *	partialMonoginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a pointer to a male with same index as mother (if available) from the focal patch. More...
Individual *	fullSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns the mother pointer. More...
Individual *	partialSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns the mother pointer or a random female if _mating_proportion != 1. More...
Individual *	random_hermaphrodite (Patch *thePatch, Individual *mother, unsigned int motherIndex)
	Returns a random female from the patch, will be the same mother with probability 1/N (Wright-Fisher model). More...
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...
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)
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)

Protected Attributes
Individual *(LCE_Breed_Disperse::*	_make_offspring )(sex_t SEX, Patch *patch, unsigned int LocalPatch)
unsigned int(LCE_Breed_Disperse::*	_get_numFemOffspring )(Patch *patch)
unsigned int(LCE_Breed_Disperse::*	_get_numMalOffspring )(Patch *patch)
unsigned int(LCE_Breed_Disperse::*	_get_patchFecundity )(Patch *patch, sex_t SEX)
Protected Attributes inherited from LCE_Breed_base
void(LCE_Breed_base::*	PopModelFuncPtr )(void)
TMatrix	_mean_fecundity
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...
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...

Private Attributes
void(LCE_Breed_Disperse::*	_breed_disperse )()
int	_num_colonizers
	Maximum size of a patch after colonisation. More...
sex_t	_dispersing_sex
	Which part of the population is dispersing its gametes. More...
double *	_growthRates
	Patch-specific growth rates. More...

Detailed Description

Performs breeding and migration in one, migration rates are backward rates.

Inherits parameters from LCE_Breed_base and LCE_Disperse_base. Population size is constant, There is no demographic stochasticity with this LCE. The number of colonizers of extinct patches can be set differently from the patch carrying capacities.

Constructor & Destructor Documentation

LCE_Breed_Disperse()

LCE_Breed_Disperse::LCE_Breed_Disperse

(

)

                                       : LifeCycleEvent("breed_disperse",""),_breed_disperse(0),
_num_colonizers(0), _growthRates(0), _dispersing_sex(FEM), _make_offspring(0), _get_numFemOffspring(0),
_get_numMalOffspring(0),_get_patchFecundity(0)
{
  ParamUpdater<LCE_Breed_Disperse>* updater = new ParamUpdater<LCE_Breed_Disperse>(&LCE_Breed_Disperse::setParameters);
  
  LCE_Disperse_base::addParameters("breed_disperse", updater);
  
  add_parameter("breed_disperse_dispersing_sex", STR, false, false, 0, 0, updater);
  add_parameter("breed_disperse_colonizers", INT,false,false,0,0, updater);
  add_parameter("breed_disperse_growth_model", INT, false, true, 1, 7, updater);
  add_parameter("breed_disperse_growth_rate", DBL, false, false, 0, 0, updater);
}

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

Referenced by clone().

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~LCE_Breed_Disperse()

virtual LCE_Breed_Disperse::~LCE_Breed_Disperse ( )

inlinevirtual

{if(_growthRates) delete [] _growthRates;}

References _growthRates.

Member Function Documentation

addAgeClass()

virtual age_t LCE_Breed_Disperse::addAgeClass ( )

inlinevirtual

Reimplemented from LCE_Disperse_base.

Reimplemented in LCE_Breed_Selection_Disperse.

{return OFFSPRG;}

References OFFSPRG.

breed_disperse()

void LCE_Breed_Disperse::breed_disperse	(	sex_t	SEX,
		Patch *	patch,
		unsigned int	LocalPatch,
		unsigned int	size
	)

clone()

virtual LifeCycleEvent * LCE_Breed_Disperse::clone ( )

inlinevirtual

Implements LifeCycleEvent.

Reimplemented in LCE_Breed_Selection_Disperse.

{return new LCE_Breed_Disperse();}

References LCE_Breed_Disperse().

conditionalLogisticGrowth()

unsigned int LCE_Breed_Disperse::conditionalLogisticGrowth ( Patch *  patch, sex_t  SEX  )

inline

The number of offspring produced depends on the adult density.

A minimum number of offspring is produced when less than half of the carrying capacity of adults is present. It is logistic otherwise.

  {
    if (patch->size(SEX, ADLTx) < patch->get_K(SEX)/2) {
      return fixedFecundityGrowth(patch, SEX);
    } else {
      return logisticGrowth(patch, SEX);
    }
  }

References ADLTx, fixedFecundityGrowth(), Patch::get_K(), logisticGrowth(), and Patch::size().

Referenced by setParameters().

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conditionalStochasticLogisticGrowth()

unsigned int LCE_Breed_Disperse::conditionalStochasticLogisticGrowth ( Patch *  patch, sex_t  SEX  )

inline

The number of offspring produced depends on the adult density, similar to 'conditionalLogisticGrowth' except that this time, the fecundities are drawn from Poisson distributions.

  {
    if (patch->size(SEX, ADLTx) < patch->get_K(SEX)/2) {
      return stochasticFecundityGrowth(patch, SEX);
    } else {
      return stochasticLogisticGrowth(patch, SEX);
    }
  }

References ADLTx, Patch::get_K(), Patch::size(), stochasticFecundityGrowth(), and stochasticLogisticGrowth().

Referenced by setParameters().

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do_breed_disperse()

void LCE_Breed_Disperse::do_breed_disperse

(

)

{
  Patch* patch;
  unsigned int nfem, nmal;
  
  for(unsigned int i = 0; i < _popPtr->getPatchNbr(); i++) {
    
    patch = _popPtr->getPatch(i);
    
    if(patch->size(OFFSx) != 0) patch->flush(OFFSx, _popPtr);
    
    nfem = (this->* _get_numFemOffspring)(patch);
    nmal = (this->* _get_numMalOffspring)(patch);
    
    for(unsigned int j = 0; j < nfem; j++) 
      patch->add(FEM, OFFSx, 
                 LCE_Breed_base::makeOffspring( (this->*_make_offspring)(FEM, patch, i) )
                 );
    
    //the colonizer counter must be set now, not in get_parent(),
    //otherwise colonizers will be counted twice, once per parent
    if(patch->size(ADULTS) == 0) patch->nbKolonisers += nfem;
 
    for(unsigned int j = 0; j < nmal; j++) 
      patch->add(MAL, OFFSx, 
                 LCE_Breed_base::makeOffspring( (this->*_make_offspring)(MAL, patch, i) )
                 );
 
    if(patch->size(ADULTS) == 0) patch->nbKolonisers += nmal;
  }
}

References _get_numFemOffspring, _get_numMalOffspring, _make_offspring, LifeCycleEvent::_popPtr, Patch::add(), ADULTS, FEM, Patch::flush(), Metapop::getPatch(), Metapop::getPatchNbr(), LCE_Breed_base::makeOffspring(), MAL, OFFSx, and Patch::size().

Referenced by do_breed_disperse_propagule(), and setParameters().

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do_breed_disperse_propagule()

void LCE_Breed_Disperse::do_breed_disperse_propagule

(

)

{
  this->setIsland_PropagulePool_Matrix();
  do_breed_disperse();
}

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

Referenced by setParameters().

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execute()

void LCE_Breed_Disperse::execute ( )

virtual

Implements LifeCycleEvent.

Reimplemented in LCE_Breed_Selection_Disperse.

{
#ifdef _DEBUG_
  message("LCE_Breed_Disperse::execute (Patch nb: %i offsprg nb: %i adlt nb: %i "
          ,_popPtr->getPatchNbr(), _popPtr->size( OFFSPRG ), _popPtr->size( ADULTS ));
#endif
  
  if(_npatch != _popPtr->getPatchNbr()) {
    _npatch = _popPtr->getPatchNbr();
    if(!updateDispMatrix()) fatal("bailing out\n");
  }
  
  LCE_Disperse_base::reset_counters();
  
  (this->*_breed_disperse)();
  
#ifdef _DEBUG_
  unsigned int a = 0, b = 0, c = 0;
  for(unsigned int i = 0; i < _popPtr->getPatchNbr(); i++){
    a += _popPtr->getPatch(i)->nbEmigrant;
    b += _popPtr->getPatch(i)->nbImigrant;
    c += _popPtr->getPatch(i)->nbPhilopat;
  }
  message("immigrate: %f, emigrants: %i, imigrants: %i)\n",(double)b/(b+c), a, b);
#endif
}

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

fixedFecundityGrowth()

unsigned int LCE_Breed_Disperse::fixedFecundityGrowth ( Patch *  patch, sex_t  SEX  )

inline

The number of offspring produced is equal to the carrying capacity multiplied by the mean fecundity of the focal patch.

  {
    return patch->get_K(SEX)*LCE_Breed_base::getMeanFecundity(patch->getID());
  }

References Patch::get_K(), Patch::getID(), and LCE_Breed_base::getMeanFecundity().

Referenced by conditionalLogisticGrowth(), and setParameters().

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get_parent()

Individual * LCE_Breed_Disperse::get_parent	(	sex_t	SEX,
		sex_t	DispSex,
		Patch *	LocalPatch,
		unsigned int	patchNbr
	)

{
  unsigned int SourcePatch = 0;
  Patch* src_patch;
    
  //this algorithm does not check for the availability of migrants in connected patches
  //it may thus hang if all connected patches are empty
  //one work around is to impose a maximum number of trials before it abandons the search
 
  do {
    
    SourcePatch = LCE_Disperse_base::getMigrationPatchBackward(DispSex, LocalPatch);
    src_patch = _popPtr->getPatchPtr(SourcePatch);
    
    
  } while (src_patch->size( SEX, ADLTx ) == 0);
  //redraw if source patch is empty; we don't use DispSex because it may be different from the SEX we want (e.g. DispSex = mal for pollen dispersal with hermaphrodites where SEX = fem)
    
  //set migrant counters for the stats
  if(LocalPatch != SourcePatch) {
    src_patch->nbEmigrant++;
    
    if( local_patch->size(ADLTx) != 0 ) // only count immigrants, not colonizers
      local_patch->nbImigrant++;
    
  } else
    src_patch->nbPhilopat++;
  
  //return a pointer to an individual randomly chosen from the source patch:
  return src_patch->get(SEX, ADLTx, RAND::Uniform( src_patch->size( SEX, ADLTx ) ) );
}

References LifeCycleEvent::_popPtr, ADLTx, Patch::get(), LCE_Disperse_base::getMigrationPatchBackward(), Metapop::getPatchPtr(), Patch::nbEmigrant, Patch::nbImigrant, Patch::nbPhilopat, Patch::size(), and RAND::Uniform().

Referenced by mate_cloning(), mate_full_selfing(), mate_random(), mate_random_hermaphrodite(), and mate_selfing().

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instantGrowth()

unsigned int LCE_Breed_Disperse::instantGrowth ( Patch *  patch, sex_t  SEX  )

inline

The number of offspring produced corresponds to the carrying capacity of the patch.

  {
    return patch->get_K(SEX);
  }

References Patch::get_K().

Referenced by setParameters().

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loadFileServices()

virtual void LCE_Breed_Disperse::loadFileServices ( FileServices *  loader )

inlinevirtual

Reimplemented from LCE_Disperse_base.

Reimplemented in LCE_Breed_Selection_Disperse.

{}

loadStatServices()

virtual void LCE_Breed_Disperse::loadStatServices ( StatServices *  loader )

inlinevirtual

Reimplemented from LCE_Disperse_base.

Reimplemented in LCE_Breed_Selection_Disperse.

{}

logisticGrowth()

unsigned int LCE_Breed_Disperse::logisticGrowth ( Patch *  patch, sex_t  SEX  )

inline

The number of offspring produced is given by the logistic growth function.

  {
    double K = (double)patch->get_K(SEX);
    double r = _growthRates[ patch->getID() ];
    double N = (double)patch->size(ADLTx);
    if( K <= N )
      return K;
    else
      return (unsigned int)ceil(N + r*N*((K-N)/K));
  }

References _growthRates, ADLTx, Patch::get_K(), Patch::getID(), and Patch::size().

Referenced by conditionalLogisticGrowth(), setParameters(), and stochasticLogisticGrowth().

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makeOffspring()

Individual * LCE_Breed_Disperse::makeOffspring

(

Individual *

ind

)

mate_cloning()

Individual * LCE_Breed_Disperse::mate_cloning	(	sex_t	SEX,
		Patch *	patch,
		unsigned int	LocalPatch
	)

{
  Individual *mom = get_parent(FEM, FEM, patch, LocalPatch);
  return LCE_Breed_base::breed_cloning(mom, mom, LocalPatch);
}

References LCE_Breed_base::breed_cloning(), FEM, and get_parent().

Referenced by setParameters().

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mate_full_selfing()

Individual * LCE_Breed_Disperse::mate_full_selfing	(	sex_t	SEX,
		Patch *	patch,
		unsigned int	LocalPatch
	)

{
  Individual *mom = get_parent(FEM, FEM, patch, LocalPatch);
  
  return _popPtr->makeNewIndividual(mom, mom, FEM, LocalPatch);
}

References LifeCycleEvent::_popPtr, FEM, get_parent(), and IndFactory::makeNewIndividual().

Referenced by setParameters().

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mate_random()

Individual * LCE_Breed_Disperse::mate_random	(	sex_t	SEX,
		Patch *	patch,
		unsigned int	LocalPatch
	)

{
  return _popPtr->makeNewIndividual(get_parent(FEM, FEM, patch, LocalPatch), 
                                    get_parent(MAL, MAL, patch, LocalPatch),
                                    SEX, LocalPatch);
}

References LifeCycleEvent::_popPtr, FEM, get_parent(), IndFactory::makeNewIndividual(), and MAL.

Referenced by setParameters().

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mate_random_hermaphrodite()

Individual * LCE_Breed_Disperse::mate_random_hermaphrodite	(	sex_t	SEX,
		Patch *	patch,
		unsigned int	LocalPatch
	)

{
  return _popPtr->makeNewIndividual(get_parent(FEM, FEM, patch, LocalPatch), 
                                    get_parent(FEM, _dispersing_sex, patch, LocalPatch),
                                    FEM, LocalPatch);
}

References _dispersing_sex, LifeCycleEvent::_popPtr, FEM, get_parent(), and IndFactory::makeNewIndividual().

Referenced by setParameters().

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mate_selfing()

Individual * LCE_Breed_Disperse::mate_selfing	(	sex_t	SEX,
		Patch *	patch,
		unsigned int	LocalPatch
	)

{
  Individual *mom, *dad;
  //  cout << "--- choosing mum in patch "<<LocalPatch<<" ("<<patch->size(FEM, ADLTx)<<")\n";
  mom = get_parent(FEM, FEM, patch, LocalPatch);
  
  //  cout << "--- choosing dad \n";
  
  if( RAND::Uniform() > this->getMatingProportion() ) {
    //random mating
    do{
      dad = get_parent(FEM, _dispersing_sex, patch, LocalPatch);
    }while(dad == mom && _popPtr->getPatchNbr() != 1 && patch->size(FEM,ADLTx) != 1);
  } else
    dad = mom;
  
  //  cout << "--- make offspring by crossing "<<mom->getID()<<" with "<<dad->getID()<<endl;
  
  
  return _popPtr->makeNewIndividual(mom, dad, FEM, LocalPatch);
}

References _dispersing_sex, LifeCycleEvent::_popPtr, ADLTx, FEM, get_parent(), LCE_Breed_base::getMatingProportion(), Metapop::getPatchNbr(), IndFactory::makeNewIndividual(), Patch::size(), and RAND::Uniform().

Referenced by setParameters().

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numFemOffspring()

unsigned int LCE_Breed_Disperse::numFemOffspring ( Patch *  patch )

inline

  {
    if (patch->size(FEM, ADLTx) == 0 && _dispersing_sex != FEM)//to avoid choosing a local female when there is none
      return 0;
    else
      return (this->*_get_patchFecundity)(patch, FEM);
  }

References _dispersing_sex, _get_patchFecundity, ADLTx, FEM, and Patch::size().

Referenced by setParameters().

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numFemOffspring_colonizers()

unsigned int LCE_Breed_Disperse::numFemOffspring_colonizers ( Patch *  patch )

inline

The number of females produced in case a max number of colonizers was specified.

  {
    if(patch->get_isExtinct()) {
      //check if only one sex sends gametes around, capturing the case of pollen dispersal
      if(_dispersing_sex != FEM)
        return 0;
      else
        return _num_colonizers; 
    } else
      return (this->*_get_patchFecundity)(patch, FEM);
  }

References _dispersing_sex, _get_patchFecundity, _num_colonizers, FEM, and Patch::get_isExtinct().

Referenced by setParameters().

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numMalOffspring_notrandom()

unsigned int LCE_Breed_Disperse::numMalOffspring_notrandom ( Patch *  patch )

inline

The number of males produced is always zero when the mating system is not random mating.

  {
    return 0;
  }

Referenced by setParameters().

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numMalOffspring_random()

unsigned int LCE_Breed_Disperse::numMalOffspring_random ( Patch *  patch )

inline

  { //return 0 if only males gametes migrate and there is no females in the patch
    //to avoid choosing a local female when there is none
    //(we assume it doesn't make sense to have only female gametes migrating)
    if (patch->size(FEM, ADLTx) == 0 && _dispersing_sex != FEM)
      return 0;
    else
      return (this->*_get_patchFecundity)(patch, MAL);
  }

References _dispersing_sex, _get_patchFecundity, ADLTx, FEM, MAL, and Patch::size().

Referenced by setParameters().

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numMalOffspring_random_colonizers()

unsigned int LCE_Breed_Disperse::numMalOffspring_random_colonizers ( Patch *  patch )

inline

  {
    if(patch->get_isExtinct()) {
      //check if only one sex sends gametes around, capturing the case of pollen dispersal
      if(_dispersing_sex != FEM)
        return 0;
      else
        return _num_colonizers; 
    } else
      return (this->*_get_patchFecundity)(patch, MAL);
  }

References _dispersing_sex, _get_patchFecundity, _num_colonizers, FEM, Patch::get_isExtinct(), and MAL.

Referenced by setParameters().

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removeAgeClass()

virtual age_t LCE_Breed_Disperse::removeAgeClass ( )

inlinevirtual

Reimplemented from LCE_Disperse_base.

Reimplemented in LCE_Breed_Selection_Disperse.

{return NONE;}

References NONE.

requiredAgeClass()

virtual age_t LCE_Breed_Disperse::requiredAgeClass ( )

inlinevirtual

Reimplemented from LCE_Disperse_base.

Reimplemented in LCE_Breed_Selection_Disperse.

{return ADULTS;}

References ADULTS.

resetParameterFromSource()

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

inlinevirtual

Reimplemented from LCE_Disperse_base.

Reimplemented in LCE_Breed_Selection_Disperse.

{return false;}

setParameters()

bool LCE_Breed_Disperse::setParameters ( )

virtual

Reimplemented from LCE_Breed_base.

Reimplemented in LCE_Breed_Selection_Disperse.

{
  if(!LCE_Breed_base::setParameters()) return false;
  
  LCE_Disperse_base::set_isForward(false);
  
  if(!LCE_Disperse_base::setBaseParameters("breed_disperse")) return false;
  
  _num_colonizers = (int)get_parameter_value("breed_disperse_colonizers");
  
  //some default settings, reset below depending on mating system
  _get_numFemOffspring = (_num_colonizers == -1 ?
                          &LCE_Breed_Disperse::numFemOffspring : 
                          &LCE_Breed_Disperse::numFemOffspring_colonizers);
  _get_numMalOffspring = &LCE_Breed_Disperse::numMalOffspring_notrandom;
  
  if(get_parameter("breed_disperse_dispersing_sex")->isSet()) {
    
    if (get_parameter("breed_disperse_dispersing_sex")->getArg() == "female") {
      _dispersing_sex = FEM;
    } else if (get_parameter("breed_disperse_dispersing_sex")->getArg() == "male") {
      _dispersing_sex = MAL;
    } else {
      error("the \"breed_disperse_dispersing_sex\" parameter only takes \"female\" or \"male\" as argument\n");
    }
    
  } else { //default
    _dispersing_sex = FEM;
  }
  
  //check mating system:  
  unsigned int model = this->getMatingSystem();
  
  if(model == 2 || model == 3) {
  
    return error("Polygyny and Monogamy are not implemented within the breed_disperse LCE.\n");
 
  } else if(model == 1) { //promiscuity/random mating
    
    _make_offspring = &LCE_Breed_Disperse::mate_random;
    
    _get_numMalOffspring = (_num_colonizers == -1 ?
                            &LCE_Breed_Disperse::numMalOffspring_random : 
                            &LCE_Breed_Disperse::numMalOffspring_random_colonizers);
    
  } else if(model == 4) { //selfing
    
    if(this->getMatingProportion() != 1)
      _make_offspring = &LCE_Breed_Disperse::mate_selfing;
    else
      _make_offspring = &LCE_Breed_Disperse::mate_full_selfing;
  
  } else if(model == 5) { //cloning
  
    _make_offspring = &LCE_Breed_Disperse::mate_cloning;
  
  } else if(model == 6) { //random mating among hermaphrodites (selfing = 1/N)
   
    _make_offspring = &LCE_Breed_Disperse::mate_random_hermaphrodite;
 
  }
  
  //check dispersal model:
  model = this->getDispersalModel();
  
  if(model == 2) //propagule-pool island model
    _breed_disperse = &LCE_Breed_Disperse::do_breed_disperse_propagule;
  else
    _breed_disperse = &LCE_Breed_Disperse::do_breed_disperse;
  
  //growth model
  if(_paramSet->isSet("breed_disperse_growth_model"))
    model = get_parameter_value("breed_disperse_growth_model");
  else 
    model = 1;
  
  switch (model) {
    case 1:
      _get_patchFecundity = &LCE_Breed_Disperse::instantGrowth;
      break;
    case 2:
      _get_patchFecundity = &LCE_Breed_Disperse::logisticGrowth;
      break;
    case 3:
      _get_patchFecundity = &LCE_Breed_Disperse::stochasticLogisticGrowth;
      break;
    case 4:
      _get_patchFecundity = &LCE_Breed_Disperse::conditionalLogisticGrowth;
      break;
    case 5:
      _get_patchFecundity = &LCE_Breed_Disperse::conditionalStochasticLogisticGrowth;
      break;
    case 6:
      _get_patchFecundity = &LCE_Breed_Disperse::fixedFecundityGrowth;
      break;
    case 7:
      _get_patchFecundity = &LCE_Breed_Disperse::stochasticFecundityGrowth;
      break;
    default:
      _get_patchFecundity = &LCE_Breed_Disperse::instantGrowth;
      break;
  }
  //mean fecundity
  if(_mean_fecundity.get(0,0) == -1) //wasn't set
    if(model > 3 && model < 8) //4 - 7: conditional logistic growth, fecundity growth
      return error("parameter \"mean_fecundity\" is needed with growth models 4 to 7 in LCE breed_disperse\n");
 
  //growth rate
  if (model > 1 && model < 6) {
    
    if(!_paramSet->isSet("breed_disperse_growth_rate")) {
    
      return error("parameter \"breed_disperse_growth_rate\" needs to be set\n");
 
    }
    
    if(_growthRates) delete [] _growthRates;
    _growthRates = new double [ _popPtr->getPatchNbr() ];
    
    if(_paramSet->isMatrix("breed_disperse_growth_rate")) {
      
      TMatrix tmp;
      
      _paramSet->getMatrix("breed_disperse_growth_rate", &tmp);
      
      if(tmp.getNbCols() != _popPtr->getPatchNbr()){
        return error("matrix argument to \"breed_disperse_growth_rate\" has wrong number of elements,\
              must equal the number of patches.\n");
      }
      
      for (unsigned int i = 0; i < _popPtr->getPatchNbr(); i++) {
        _growthRates[i] = tmp.get(0, i);
      }
      
      
    } else { //not a matrix
      
      _growthRates[0] = get_parameter_value("breed_disperse_growth_rate");
      
      for (unsigned int i = 1; i < _popPtr->getPatchNbr(); i++) {
        _growthRates[i] = _growthRates[0];
      }
    }
    
    
  }
  
  return true;
}

References _breed_disperse, _dispersing_sex, _get_numFemOffspring, _get_numMalOffspring, _get_patchFecundity, _growthRates, _make_offspring, LCE_Breed_base::_mean_fecundity, _num_colonizers, SimComponent::_paramSet, LifeCycleEvent::_popPtr, conditionalLogisticGrowth(), conditionalStochasticLogisticGrowth(), do_breed_disperse(), do_breed_disperse_propagule(), error(), FEM, fixedFecundityGrowth(), TMatrix::get(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getArg(), LCE_Disperse_base::getDispersalModel(), LCE_Breed_base::getMatingProportion(), LCE_Breed_base::getMatingSystem(), ParamSet::getMatrix(), TMatrix::getNbCols(), Metapop::getPatchNbr(), instantGrowth(), ParamSet::isMatrix(), Param::isSet(), ParamSet::isSet(), logisticGrowth(), MAL, mate_cloning(), mate_full_selfing(), mate_random(), mate_random_hermaphrodite(), mate_selfing(), numFemOffspring(), numFemOffspring_colonizers(), numMalOffspring_notrandom(), numMalOffspring_random(), numMalOffspring_random_colonizers(), LCE_Disperse_base::set_isForward(), LCE_Disperse_base::setBaseParameters(), LCE_Breed_base::setParameters(), stochasticFecundityGrowth(), and stochasticLogisticGrowth().

Referenced by LCE_Breed_Disperse(), and LCE_Breed_Selection_Disperse::setParameters().

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stochasticFecundityGrowth()

unsigned int LCE_Breed_Disperse::stochasticFecundityGrowth ( Patch *  patch, sex_t  SEX  )

inline

The number of offspring produced is a random number drawn from a Poisson distribution with mean equal to the carrying capacity multiplied by the mean fecundity of the focal patch.

  {
    return RAND::Uniform(patch->get_K(SEX)*LCE_Breed_base::getMeanFecundity(patch->getID()));
  }

References Patch::get_K(), Patch::getID(), LCE_Breed_base::getMeanFecundity(), and RAND::Uniform().

Referenced by conditionalStochasticLogisticGrowth(), and setParameters().

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stochasticLogisticGrowth()

unsigned int LCE_Breed_Disperse::stochasticLogisticGrowth ( Patch *  patch, sex_t  SEX  )

inline

The number of offspring produced is drawn from a Poisson with mean equal to the logistic growth predicate.

  {
    return (unsigned int)RAND::Poisson((double)logisticGrowth(patch, SEX));
  }

References logisticGrowth(), and RAND::Poisson().

Referenced by conditionalStochasticLogisticGrowth(), and setParameters().

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Member Data Documentation

_breed_disperse

void(LCE_Breed_Disperse::* LCE_Breed_Disperse::_breed_disperse) ()

private

Referenced by execute(), and setParameters().

_dispersing_sex

sex_t LCE_Breed_Disperse::_dispersing_sex

private

Which part of the population is dispersing its gametes.

Referenced by mate_random_hermaphrodite(), mate_selfing(), numFemOffspring(), numFemOffspring_colonizers(), numMalOffspring_random(), numMalOffspring_random_colonizers(), and setParameters().

_get_numFemOffspring

unsigned int(LCE_Breed_Disperse::* LCE_Breed_Disperse::_get_numFemOffspring) (Patch *patch)

protected

Referenced by LCE_Breed_Selection_Disperse::breed_selection_disperse(), do_breed_disperse(), and setParameters().

_get_numMalOffspring

unsigned int(LCE_Breed_Disperse::* LCE_Breed_Disperse::_get_numMalOffspring) (Patch *patch)

protected

Referenced by LCE_Breed_Selection_Disperse::breed_selection_disperse(), do_breed_disperse(), and setParameters().

_get_patchFecundity

unsigned int(LCE_Breed_Disperse::* LCE_Breed_Disperse::_get_patchFecundity) (Patch *patch, sex_t SEX)

protected

Referenced by numFemOffspring(), numFemOffspring_colonizers(), numMalOffspring_random(), numMalOffspring_random_colonizers(), and setParameters().

_growthRates

double* LCE_Breed_Disperse::_growthRates

private

Patch-specific growth rates.

Referenced by logisticGrowth(), setParameters(), and ~LCE_Breed_Disperse().

_make_offspring

Individual *(LCE_Breed_Disperse::* LCE_Breed_Disperse::_make_offspring) (sex_t SEX, Patch *patch, unsigned int LocalPatch)

protected

Referenced by LCE_Breed_Selection_Disperse::do_breed(), do_breed_disperse(), and setParameters().

_num_colonizers

int LCE_Breed_Disperse::_num_colonizers

private

Maximum size of a patch after colonisation.

Referenced by numFemOffspring_colonizers(), numMalOffspring_random_colonizers(), and setParameters().

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

• LCEcomposite.h
• LCEcomposite.cc