Second class in the metapopulation design structure, between the Metapop and Individual classes. More...

#include <metapop.h>

Collaboration diagram for Patch:

Public Member Functions
	Patch ()

	~Patch ()

Patch *	init (unsigned int nbfem, unsigned int nbmal, unsigned int id)

void	reset_counters ()

void	reset_containers ()

void	setNewGeneration (age_t AGE, Metapop *pop)
	Fills the patch containers corresponding to the age flags passed, for both sexes. More...

void	setNewGeneration (age_idx AGE, Metapop *pop)
	Fills the patch container corresponding to the age class index passed, for both sexes. More...

void	show_up ()

Setters
void	setID (unsigned int i)

void	set_K (unsigned int k)

void	set_KFem (unsigned int k)

void	set_KMal (unsigned int k)

void	set_isExtinct (bool status)

void	set_age (unsigned int a)

Getters
unsigned int	getID ()

unsigned int	get_K ()

unsigned int	get_K (sex_t SEX)

unsigned int	get_KFem ()

unsigned int	get_KMal ()

bool	get_isExtinct ()

unsigned int	get_age ()

bool	isEmpty ()

unsigned int	getAdultsNumber ()

double	getDensity (age_idx age)

State getter and modifier functions
unsigned int	size (age_t AGE)
	Returns the size of the container of the appropriate age class(es) for both sexes. More...

unsigned int	size (sex_t SEX, age_t AGE)
	Returns the size of the container for the appropriate sex and age classes present in the age flag. More...

unsigned int	size (sex_t SEX, age_idx AGE)
	Returns the size of the container for the appropriate sex and age class. More...

unsigned int	size (age_idx AGE)
	Returns the size of the container for the appropriate age class for both sexes. More...

Individual *	get (sex_t SEX, age_idx AGE, unsigned int at)
	Returns a pointer to the individual sitting at the index passed. More...

void	set (sex_t SEX, age_idx AGE, unsigned int at, Individual *ind)
	Modifies the appropriate container with value of the pointer given. More...

void	add (sex_t SEX, age_idx AGE, Individual *ind)
	Adds an individual to the appropriate container, increments its size, eventually resizing it. More...

void	assign (sex_t SEX, age_idx AGE, size_t n)
	Assigns a new container of given size for the sex and age class passed, sets all values to NULL. More...

void	resize (sex_t SEX, age_idx AGE, size_t new_size)
	Reserves a certain range of values that are assigned to 0 in a given container. More...

Individual *	remove (sex_t SEX, age_idx AGE, unsigned int at)
	Removes the individual sitting at the given index in the appropriate container. More...

void	move (sex_t SEX, age_idx from, age_idx to, unsigned int at)
	Moves an individual from an age class to an other one. More...

void	move (sex_t SEX, age_idx from, age_idx to)
	Copies all elements in the 'from' age-class container to the 'to' age-class container of the same sex. More...

void	swap_new (sex_t SEX, age_idx from, age_idx to)
	Swaps elements between two containers, 'from' age-class container and the 'to' age-class container of the same sex. More...

void	clear (sex_t SEX, age_idx AGE)
	Sets the size of the appropriate container to zero. More...

void	clear ()

void	flush (sex_t SEX, age_idx AGE, Metapop *pop)
	Removes all individual pointers of the appropriate sex and age class and flush them into the recycling pool. More...

void	flush (age_idx AGE, Metapop *pop)

void	flush (age_t AGE, Metapop *pop)
	Removes all individual pointers of the appropriate sex and age class and flush them into the recycling pool. More...

void	flush (Metapop *pop)
	Removes all individual pointers of all sex and age classes and flush them into the recycling pool. More...

void	getCopy (sex_t SEX, age_idx AGE, deque< Individual * > &to)

void	copy2patch (sex_t from_sex, sex_t to_sex, age_idx from_age, age_idx to_age, Patch *to_patch)

void	copy2patch (sex_t SEX, age_idx AGE, Patch *patch)

void	copy2patch (age_idx AGE, Patch *patch)

void	copy2patch (Patch *patch)

Public Attributes
unsigned short	nbEmigrant

unsigned short	nbImigrant

unsigned short	nbPhilopat

short	nbKolonisers

Private Attributes
unsigned int	_ID
	Patch ID is equal to its position in the metapop patch array. More...

unsigned int	_K
	Carrying capacity for males and females. More...

unsigned int	_KFem
	Sex specific carrying capacity. More...

unsigned int	_KMal

bool	_isExtinct
	Extinction flag. More...

unsigned int	_age
	age since last extinction. More...

unsigned int	_nb_age_class
	Number of age classes present. More...

unsigned int	_sizes [2][3]
	Containers size counters, sex X age. More...

unsigned int	_capacities [2][3]
	Total size of the containers, amount of allocated memory. More...

deque< Individual * >	_containers [2][3]
	Individuals containers, sex X age. More...

Detailed Description

Second class in the metapopulation design structure, between the Metapop and Individual classes.

The Patch class is an abstraction of a sub-population or patch concept (also called a deme) in a metapopulation context. It contains the individual containers for the different age classes. Three main age classes are currently implemented, the offspring, post-dispersal and adult classes (see the age_t enum) which are all subdivided into male and female individuals. These containers are accessed using the interface defined here or through the Metapop class interface. The different LCEs will use these interfaces to handle the individuals. They are also responsible to change the age flag of the population (see Metapop).

The individuals are accessed using their age index value and not the age flag value (e.g., using the Patch::get() method). These indexes are defined in the age_idx enum (see type.h) and differ from the age class flag values. For instance the adults' containers have the index 2 (ADLTx = 2) whereas their age flag is 4 (ADULTS = 4). This might be confusing but it saves a lot of checks at runtime! It also allows to give a flag containing several class bits set instead of a unique index value when needed (see the Patch::size() and Metapop::size() suite of functions).

Constructor & Destructor Documentation

◆ Patch()

Patch::Patch ( )

inline

           : _ID(0), _K(1), _KFem(1), _KMal(1), _isExtinct(0), _age(0), _nb_age_class(3),
       nbEmigrant(0), nbImigrant(0), nbPhilopat(0), nbKolonisers(0)
   { for(unsigned int i = 0; i < _nb_age_class; i++) {
     _sizes[MAL][i] = 0;
     _sizes[FEM][i] = 0;
     _capacities[MAL][i] = 0;
     _capacities[FEM][i] = 0;}
   }

References _capacities, _nb_age_class, _sizes, FEM, and MAL.

◆ ~Patch()

Patch::~Patch ( )

 {
 //#ifdef _DEBUG_
 //  message("Patch::~Patch\n");
 //#endif
   
   for (unsigned int i = 0; i < 2; ++i)
     for(unsigned int j = 0; j < _nb_age_class; ++j)
       for(unsigned int k = 0; k < _sizes[i][j] ; ++k)
         delete _containers[i][j][k];
 }

Member Function Documentation

◆ add()

void Patch::add	(	sex_t	SEX,
		age_idx	AGE,
		Individual *	ind
	)

inline

Adds an individual to the appropriate container, increments its size, eventually resizing it.

Parameters

SEX	the sex class of the individual
AGE	the index of the age class
ind	the pointer to the individual

   {
     if( _sizes[SEX][AGE] + 1 > _capacities[SEX][AGE] ) {
       _containers[SEX][AGE].resize( _capacities[SEX][AGE] + (_K + 1) );
       _capacities[SEX][AGE] += (_K + 1); //the +1 is here to avoid seg faults when K=0
     }
     _containers[SEX][AGE][ _sizes[SEX][AGE]++ ] = ind;
   }

References _capacities, _containers, _K, and _sizes.

Referenced by copy2patch(), LCE_Breed_Selection_Disperse::do_breed(), LCE_Breed_Disperse::do_breed_disperse_in_empty_patch(), LCE_Breed_Disperse::do_breed_disperse_in_patch(), LCE_Breed_Selection::do_breed_selection_FecFitness(), LCE_Breed_Selection::do_breed_selection_OffSurvival(), TTDeletMutBitstrFH::FHread(), TTNeutralGenesFH::FHread(), TTQuantiFH::FHread(), Metapop::fillPatchFromSource(), LCE_Resize::fillPatchNoBackup(), LCE_Resize::fillPatchWithBackup(), LCE_Cross::generatePedigree(), move(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), LCE_Resize::regulateAgeClassWithBackup(), LCE_Cross::sampleAmongPop(), LCE_Cross::sampleWithinPop(), FileServices::subSamplePatch(), LCE_Breed_Wolbachia::wolbachia_model_1(), LCE_Breed_Wolbachia::wolbachia_model_2(), and LCE_Breed_Quanti::WrightFisherPopulation().

◆ assign()

void Patch::assign	(	sex_t	SEX,
		age_idx	AGE,
		size_t	n
	)

inline

Assigns a new container of given size for the sex and age class passed, sets all values to NULL.

   { _containers[SEX][AGE].assign(n,0);
    _sizes[SEX][AGE] = 0;
    _capacities[SEX][AGE] = n;
   }

References _capacities, _containers, and _sizes.

Referenced by TTNOhtaStats::FHwrite(), TTQFreqExtractor::FHwrite(), TTQOhtaStats::FHwrite(), and TTNeutralGenesSH::setHs().

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◆ clear() [1/2]

void Patch::clear ( )

inline

675 { for(int i = 0; i < 3; i++) {_sizes[0][i] = 0;_sizes[1][i] = 0;}}

References _sizes.

Referenced by move().

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◆ clear() [2/2]

void Patch::clear	(	sex_t	SEX,
		age_idx	AGE
	)

inline

Sets the size of the appropriate container to zero.

Note: no memory operation is performed, the capacity of the container is thus not affected. The individual pointers are not flushed to the recycling pool, they will be overwritten by subsequent operations. It is thus a good idea to consider using Patch::flush to be sure no pointers remained in the container.

See also: flush()

Parameters

SEX	the sex class
AGE	the index of the age class

674 { _sizes[SEX][AGE] = 0;}

References _sizes.

Referenced by LCE_Resize::buildNewPatchArrayWithBackup(), FileServices::empty_sampled_pop(), LCE_BreedAssortativeMating::execute(), LCE_Resize::execute(), and LCE_Resize::removeDesignatedPatch().

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◆ copy2patch() [1/4]

void Patch::copy2patch	(	age_idx	AGE,
		Patch *	patch
	)

inline

   {
     copy2patch(FEM, AGE, patch);
     copy2patch(MAL, AGE, patch);
   }

References copy2patch(), FEM, and MAL.

◆ copy2patch() [2/4]

void Patch::copy2patch ( Patch * patch )

inline

   {
     for (unsigned int i = 0; i < _nb_age_class; ++i){
       copy2patch(FEM, static_cast<age_idx> (i), patch);
       copy2patch(MAL, static_cast<age_idx> (i), patch);
     }
   }

References _nb_age_class, copy2patch(), FEM, and MAL.

◆ copy2patch() [3/4]

void Patch::copy2patch	(	sex_t	from_sex,
		sex_t	to_sex,
		age_idx	from_age,
		age_idx	to_age,
		Patch *	to_patch
	)

inline

   {
     for (unsigned int i = 0; i < _sizes[from_sex][from_age]; ++i)
       to_patch->add(to_sex, to_age, _containers[from_sex][from_age][i] );
   }

References _containers, _sizes, and add().

Referenced by LCE_Resize::buildNewPatchArrayWithBackup(), copy2patch(), and LCE_Resize::removeDesignatedPatch().

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◆ copy2patch() [4/4]

void Patch::copy2patch	(	sex_t	SEX,
		age_idx	AGE,
		Patch *	patch
	)

inline

   {
     for (unsigned int i = 0; i < _sizes[SEX][AGE]; ++i)
       patch->add(SEX, AGE, get(SEX, AGE, i) );
   }

References _sizes, add(), and get().

◆ flush() [1/4]

void Patch::flush	(	age_idx	AGE,
		Metapop *	pop
	)

inline

695 { flush(FEM, AGE, pop); flush(MAL, AGE, pop); }

Patch::flush

void flush(sex_t SEX, age_idx AGE, Metapop *pop)

Removes all individual pointers of the appropriate sex and age class and flush them into the recyclin...

Definition: metapop.h:685

References FEM, flush(), and MAL.

◆ flush() [2/4]

void Patch::flush	(	age_t	AGE,
		Metapop *	pop
	)

inline

Removes all individual pointers of the appropriate sex and age class and flush them into the recycling pool.

Parameters

AGE	an unsigned int containing the flags of the age classes to flush
pop	the pointer to the metapop for access to the recycling pool

See also: flush()

   {
     unsigned int mask = 1;
     
     for(unsigned int i = 0; i < _nb_age_class; i++) {
       if( (mask & AGE) != 0) {
         flush(MAL, age_idx(i), pop);
         flush(FEM, age_idx(i), pop);
       }
       mask <<= 1;
     }
   }

References _nb_age_class, FEM, flush(), and MAL.

◆ flush() [3/4]

void Patch::flush ( Metapop * pop )

inline

Removes all individual pointers of all sex and age classes and flush them into the recycling pool.

   {
     for(unsigned int i = 0; i < _nb_age_class; i++) {
       flush(MAL, age_idx(i), pop);
       flush(FEM, age_idx(i), pop);
     }
   }

References _nb_age_class, FEM, flush(), and MAL.

◆ flush() [4/4]

void Patch::flush	(	sex_t	SEX,
		age_idx	AGE,
		Metapop *	pop
	)

inline

Removes all individual pointers of the appropriate sex and age class and flush them into the recycling pool.

Container sizes are reset to null values. Note: not memory operation is performed, the total amount of memory allocated is left untouched.

Parameters

SEX	the sex class of the individual
AGE	the index of the age class
pop	the pointer to the metapop for access to the recycling pool

   {
     for (unsigned int i = 0; i < _sizes[SEX][AGE]; ++i) {
       pop->recycle(_containers[SEX][AGE][i]);
       _containers[SEX][AGE][i] = 0;
     }
     _sizes[SEX][AGE] = 0;
   }

References _containers, _sizes, and IndFactory::recycle().

Referenced by LCE_Breed_Selection_Disperse::breed_selection_disperse(), LCE_Breed_base::checkCloning(), LCE_Breed_base::checkSelfing(), LCE_Breed_Disperse::do_breed_disperse(), LCE_Breed_Selection::do_breed_selection_WrightFisher_1sex(), LCE_Breed_Selection::do_breed_selection_WrightFisher_2sex(), LCE_Patch_Extinction::do_flush(), LCE_Breed_base::doAgingInWFpop(), LCE_Aging::execute(), flush(), LCE_Disperse_ConstDisp::MigratePatchByNumber(), LCE_Disperse_base::reset_counters(), and LCE_Breed_base::WrightFisherPopulation().

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◆ get()

Individual* Patch::get	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	at
	)

inline

Returns a pointer to the individual sitting at the index passed.

Note: the get operations are unchecked! It's up to the user to check for overflows.

Parameters

SEX	the sex class of the individual
AGE	the index of the age class
at	the index of the individual in the container

533 { return _containers[SEX][AGE][at]; }

References _containers.

Referenced by LCE_Selection_base::addPhenotypicSD(), copy2patch(), TTBDMI_SH::countAllele_diplo(), TTBDMI_SH::countAllele_haplo(), MPFileHandler::createAndPrintSample(), LCE_Breed_Selection::do_breed_selection_FecFitness(), LCE_Breed_Selection::do_breed_selection_OffSurvival(), LCE_Breed_Selection::do_breed_selection_WrightFisher_1sex(), LCE_Breed_Selection::do_breed_selection_WrightFisher_2sex(), LCE_Selection_base::doViabilitySelection(), LCE_Disperse_EvolDisp::evoldisp(), LCE_BreedAssortativeMating::execute(), TTDeletMutBitstrFH::FHwrite(), TTNOhtaStats::FHwrite(), TTQFreqExtractor::FHwrite(), TTQOhtaStats::FHwrite(), Metapop::fillPatchFromSource(), LCE_Resize::fillPatchWithBackup(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Breed_base::fullMonoginy(), LCE_Breed_base::fullPolyginy(), LCE_Breed_base::fullPolyginy_manyMales(), Metapop::get(), LCE_Breed_Disperse::get_parent(), TTNeutralGenesSH::getDxyPerPatch(), LCE_Selection_base::getMaxPatchFitness(), MPStatHandler::getMeanAssignedFecundity(), TTDispersalSH::getMeanDispRate(), TTDispersalSH::getMeanDispRateInPatch(), TTDeletMutBitstrSH::getMeanFecWithPatchMate(), TTWolbachiaSH::getMeanFemaleInfection_perPatch(), TTDispersalSH::getMeanFemDispRate(), LCE_Selection_base::getMeanFitness(), TTDispersalSH::getMeanMalDispRate(), TTWolbachiaSH::getMeanMaleInfection_perPatch(), MPStatHandler::getMeanMatings(), TTWolbachiaSH::getMeanOffsprgFemaleInfection_perPatch(), TTWolbachiaSH::getMeanOffsprgInfection(), TTWolbachiaSH::getMeanOffsprgMaleInfection_perPatch(), LCE_Selection_base::getMeanPatchFitness(), TTDispersalSH::getOffsprgMeanDispRate(), TTDeletMutBitstrSH::getPatchLoad(), TTQuantiSH::getSNPalleleFreqInPatch(), TTQuantiSH::getVaNoDominance(), TTQuantiSH::getVaWithDominance(), LCE_Breed_Wolbachia::hasInfectedFemale(), LCE_Breed_Wolbachia::inoculate_wolbachia(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), LCE_Breed_base::partialMonoginy(), LCE_Breed_base::partialSelfing(), GenotyperFH::prepare_data_table(), TTQuantiFH::print(), LCE_SelectionFH::print(), GenotyperFH::print_genotypes(), GenotyperFH::print_PLINK(), TTQuantiFH::print_PLINK_FAM(), TTNeutralGenesFH::print_PLINK_PED(), TTQuantiFH::print_PLINK_PED(), GenotyperFH::print_snp_genotypes(), GenotyperFH::print_snp_id(), MPFileHandler::printNoSample(), LCE_Breed_base::random_hermaphrodite(), LCE_Breed_base::RandomMating(), LCE_Resize::regulateAgeClassNoBackup(), LCE_Resize::regulateAgeClassWithBackup(), LCE_Cross::sampleAmongPop(), TTNeutralGenesSH::setAdults_Theta(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setCoaMatrix(), LCE_SelectionSH::setDataTable(), TTDeletMutBitstrSH::setDeletStats(), TTNeutralGenesSH::setFstat_bitstring(), TTNeutralGenesSH::setFstatWeirCockerham_bitstring(), TTNeutralGenesSH::setHeteroTable(), TTNeutralGenesSH::setHo(), TTNeutralGenesSH::setHo2(), LCE_PhenotypeExpression::setIndLiability(), LCE_PhenotypeExpression::setIndLiability_evolving(), LCE_PhenotypeExpression::setIndLiability_evolving_sigmoid(), LCE_PhenotypeExpression::setIndLiability_sigmoid(), LCE_PhenotypeExpression::setIndPhenotype(), LCE_QuantiModifier::setIndPhenotype(), LCE_Breed_Quanti::setIndPhenotype(), LCE_PhenotypeExpression::setIndPhenotype_labile(), TTWolbachiaSH::setInfectionStats(), MPStatHandler::setKinship(), TTDeletMutBitstrSH::setMeanViability(), MPStatHandler::setPedegreeCount(), MPStatHandler::setReproductiveStats(), LCE_Breed_Selection::setReproScaledFitness_gsl(), LCE_Breed_Selection::setReproScaledFitness_sum(), LCE_Selection_base::setScalingFactorForLinearSelection(), TTNeutralGenesSH::setSibStats(), TTDeletMutBitstrSH::setViability(), store_quanti_trait_values(), FileServices::subSamplePatch(), LCE_Breed_Wolbachia::wolbachia_model_1(), LCE_Breed_Wolbachia::wolbachia_model_2(), LCE_Breed_base::WrightFisherPopulation(), LCE_Breed_Quanti::WrightFisherPopulation(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), and TTNeutralGenesFH::write_patch_TAB().

◆ get_age()

unsigned int Patch::get_age ( )

inline

485 {return _age;}

References _age.

Referenced by LCE_Aging::execute(), and MPStatHandler::getPatchAge().

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◆ get_isExtinct()

bool Patch::get_isExtinct ( )

inline

484 {return _isExtinct;}

References _isExtinct.

Referenced by LCE_Disperse_EvolDisp::execute(), LCE_Patch_Extinction::execute(), MPStatHandler::getMeanImigrantPerPatch(), MPStatHandler::getMeanResidantPerPatch(), LCE_Breed_Wolbachia::inoculate_wolbachia(), and LCE_Disperse_ConstDisp::Migrate().

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◆ get_K() [1/2]

unsigned int Patch::get_K ( )

inline

480 {return _K;}

References _K.

Referenced by LCE_Breed_Disperse::conditionalLogisticGrowth(), LCE_Breed_Disperse::conditionalStochasticLogisticGrowth(), LCE_Breed_Selection::do_breed_selection_WrightFisher_1sex(), LCE_Breed_Selection::do_breed_selection_WrightFisher_2sex(), LCE_Patch_Extinction::execute(), LCE_Breed_Disperse::exponentialGrowth(), MPStatHandler::getMeanKolonisersProportion(), FileServices::getSampledPop(), LCE_Breed_Disperse::instantGrowth(), LCE_Breed_Disperse::logisticGrowth(), LCE_Regulation::regulatePatch(), LCE_Breed_base::WrightFisherPopulation(), and LCE_Breed_Quanti::WrightFisherPopulation().

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◆ get_K() [2/2]

unsigned int Patch::get_K ( sex_t SEX )

inline

481 {return (SEX ? _KFem : _KMal);}

References _KFem, and _KMal.

◆ get_KFem()

unsigned int Patch::get_KFem ( )

inline

482 {return _KFem;}

References _KFem.

Referenced by LCE_Aging::execute(), LCE_Resize::fillPatchNoBackup(), LCE_Resize::fillPatchWithBackup(), FileServices::getSampledPop(), LCE_Resize::regulateAgeClassNoBackup(), and LCE_Resize::regulateAgeClassWithBackup().

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◆ get_KMal()

unsigned int Patch::get_KMal ( )

inline

483 {return _KMal;}

References _KMal.

Referenced by LCE_Aging::execute(), LCE_Resize::fillPatchNoBackup(), LCE_Resize::fillPatchWithBackup(), FileServices::getSampledPop(), LCE_Resize::regulateAgeClassNoBackup(), and LCE_Resize::regulateAgeClassWithBackup().

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◆ getAdultsNumber()

unsigned int Patch::getAdultsNumber ( )

inline

487 {return size(ADLTx);}

Patch::size

unsigned int size(age_t AGE)

Returns the size of the container of the appropriate age class(es) for both sexes.

Definition: metapop.h:496

ADLTx

@ ADLTx

Definition: types.h:40

References ADLTx, and size().

◆ getCopy()

void Patch::getCopy	(	sex_t	SEX,
		age_idx	AGE,
		deque< Individual * > &	to
	)

inline

   {
     for (unsigned int i = 0; i < _sizes[SEX][AGE]; ++i) {
       to.push_back(_containers[SEX][AGE][i]);
     }
   }

References _containers, and _sizes.

Referenced by LCE_BreedAssortativeMating::execute(), and LCE_Cross::execute().

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◆ getDensity()

double Patch::getDensity ( age_idx age )

inline

488 {return (double)size(age)/_K;}

References _K, and size().

◆ getID()

unsigned int Patch::getID ( )

inline

479 {return _ID;}

References _ID.

Referenced by TTBDMI_SH::countAllele_diplo(), TTBDMI_SH::countAllele_haplo(), MPFileHandler::createAndPrintSample(), LCE_Patch_Extinction::do_remove(), LCE_Breed_Disperse::exponentialGrowth(), TTDeletMutBitstrFH::FHwrite(), LCE_Resize::fillPatchNoBackup(), LCE_Breed_Disperse::fixedFecundityGrowth(), LCE_Patch_Extinction::get_harvest_size(), TTQuantiSH::getVaWithDominance(), LCE_Breed_Disperse::logisticGrowth(), LCE_Breed_Disperse::numFemOffspring_colonizers(), LCE_Breed_Disperse::numMalOffspring_random_colonizers(), TTQuantiFH::print(), GenotyperFH::print_genotypes(), GenotyperFH::print_snp_genotypes(), GenotyperFH::print_snp_id(), MPFileHandler::printNoSample(), LCE_Resize::removeDesignatedPatch(), LCE_Cross::sampleAmongPop(), LCE_Cross::sampleWithinPop(), LCE_PhenotypeExpression::setIndPhenotype(), LCE_PhenotypeExpression::setIndPhenotype_labile(), LCE_Breed_Selection::setReproScaledFitness_gsl(), LCE_Breed_Selection::setReproScaledFitness_sum(), LCE_Breed_Disperse::stochasticFecundityGrowth(), TTBDMI_FH::write_diplo(), TTBDMI_FH::write_haplo(), TTNeutralGenesFH::write_patch_FSTAT(), TTNeutralGenesFH::write_patch_GENEPOP(), and TTNeutralGenesFH::write_patch_TAB().

◆ init()

Patch * Patch::init	(	unsigned int	nbfem,
		unsigned int	nbmal,
		unsigned int	id
	)

 {
   _ID = id;
   _KFem = nbfem;
   _KMal = nbmal;
   _K = _KFem + _KMal;
   _isExtinct = false;
   _age = 0;
   
   reset_counters();
  
   reset_containers();
   
   return this;
 }

Referenced by LCE_Resize::execute().

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◆ isEmpty()

bool Patch::isEmpty ( )

inline

486 {return (size(ALL) == 0);}

ALL

#define ALL

All ages age class flag.

Definition: types.h:54

References ALL, and size().

Referenced by LCE_Breed_base::doAgingInWFpop(), LCE_Breed_Disperse::numFemOffspring_colonizers(), and LCE_Breed_Disperse::numMalOffspring_random_colonizers().

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◆ move() [1/2]

void Patch::move	(	sex_t	SEX,
		age_idx	from,
		age_idx	to
	)

inline

Copies all elements in the 'from' age-class container to the 'to' age-class container of the same sex.

The previous elements of the 'to' container are overwritten, it is thus worth considering using flush() before moving to avoid memory leaks! After the call to move(), the size of the 'from' container is set to 0.

Parameters

SEX	the sex class of the individual
from	the original age class of the individual
to	the destination age class of the individual

   {
     if( _sizes[SEX][from] > _capacities[SEX][to] ) {
       _containers[SEX][to].resize( _sizes[SEX][from] );
       _capacities[SEX][to] = _sizes[SEX][from];
     }
     
     for(unsigned int i = 0; i < _sizes[SEX][from]; ++i)
       _containers[SEX][to][i] = _containers[SEX][from][i];
 //    _containers[SEX][to].assign(_containers[SEX][from].begin(), _containers[SEX][from].end());
     
     _sizes[SEX][to] = _sizes[SEX][from];
     clear(SEX, from);
   }

References _capacities, _containers, _sizes, and clear().

◆ move() [2/2]

void Patch::move	(	sex_t	SEX,
		age_idx	from,
		age_idx	to,
		unsigned int	at
	)

inline

Moves an individual from an age class to an other one.

Note: both containers are transformed by this operation. The 'from' container size is reduced by one while the 'to' container size is increased by one.

Parameters

SEX	the sex class of the individual
from	the original age class of the individual
to	the destination age class of the individual
at	the index of the individual in the container

   {
     add( SEX, to, _containers[SEX][from][at] );
     remove( SEX, from, at );
   }

References _containers, add(), and remove().

Referenced by LCE_Breed_Selection::do_breed_selection_WrightFisher_1sex(), LCE_Breed_Selection::do_breed_selection_WrightFisher_2sex(), LCE_Breed_base::doAgingInWFpop(), LCE_Disperse_EvolDisp::evoldisp(), LCE_Aging::execute(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Disperse_base::swapPostDisp(), and LCE_Breed_base::WrightFisherPopulation().

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◆ remove()

Individual* Patch::remove	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	at
	)

inline

Removes the individual sitting at the given index in the appropriate container.

Parameters

SEX	the sex class of the individual
AGE	the index of the age class
at	the index of the individual in the container

Returns: pointer to the individual that has been removed

   {
     if(_sizes[SEX][AGE] == 0) {
       error("Patch::remove:: container already empty!!");
       return NULL;
     }
     unsigned int last = _sizes[SEX][AGE] - 1;
     Individual* ind = _containers[SEX][AGE][at];
     _containers[SEX][AGE][at] = _containers[SEX][AGE][ last ];
     _containers[SEX][AGE][ last ] = 0;
     _sizes[SEX][AGE]--;
     return ind;
   }

References _containers, _sizes, and error().

Referenced by LCE_Patch_Extinction::do_remove(), LCE_Selection_base::doViabilitySelection(), LCE_Disperse_EvolDisp::evoldisp(), LCE_Resize::fillPatchWithBackup(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), move(), LCE_Resize::regulateAgeClassNoBackup(), LCE_Resize::regulateAgeClassWithBackup(), and LCE_Regulation::regulatePatch().

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◆ reset_containers()

void Patch::reset_containers ( )

 {  
   for(unsigned int i=0; i < _nb_age_class; i++) {
     _containers[MAL][i].assign( _KMal, 0 );
     _containers[FEM][i].assign( _KFem, 0 );
     _sizes[MAL][i] = 0;
     _sizes[FEM][i] = 0;
     _capacities[MAL][i] = _KMal;
     _capacities[FEM][i] = _KFem;
   }
 }

References FEM, and MAL.

◆ reset_counters()

void Patch::reset_counters ( )

 {
   nbEmigrant = 0;
   nbImigrant = 0;
   nbPhilopat = 0;
   nbKolonisers = 0;
 }

Referenced by LCE_Disperse_base::reset_counters().

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◆ resize()

void Patch::resize	(	sex_t	SEX,
		age_idx	AGE,
		size_t	new_size
	)

inline

Reserves a certain range of values that are assigned to 0 in a given container.

Container's size is set to the new size, thus add() will not fill from [0] but from [size]. the new_size first elements of the container ARE NOT reset to NULL. It is best to use set() to then fill the patch from [0] -> [new_size-1]

Parameters

SEX	the sex class of the individual
AGE	the index of the age class
new_size	the new size of the container

   {
     if( new_size > _capacities[SEX][AGE] ) {
       _containers[SEX][AGE].resize( new_size );
       _capacities[SEX][AGE] = new_size;
     }
     _sizes[SEX][AGE] = new_size;
   }

References _capacities, _containers, and _sizes.

Referenced by LCE_Breed_Selection::do_breed_selection_WrightFisher_1sex(), LCE_Breed_Selection::do_breed_selection_WrightFisher_2sex(), and LCE_Breed_base::WrightFisherPopulation().

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◆ set()

void Patch::set	(	sex_t	SEX,
		age_idx	AGE,
		unsigned int	at,
		Individual *	ind
	)

inline

Modifies the appropriate container with value of the pointer given.

Parameters

SEX	the sex class of the individual
AGE	the index of the age class
at	the index of the individual in the container
ind	the pointer to the individual

542 { _containers[SEX][AGE][at] = ind; }

References _containers.

Referenced by LCE_Breed_Selection::do_breed_selection_WrightFisher_1sex(), LCE_Breed_Selection::do_breed_selection_WrightFisher_2sex(), and LCE_Breed_base::WrightFisherPopulation().

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◆ set_age()

void Patch::set_age ( unsigned int a )

inline

475 {_age = a;}

References _age.

Referenced by LCE_Patch_Extinction::do_flush(), and LCE_Aging::execute().

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◆ set_isExtinct()

void Patch::set_isExtinct ( bool status )

inline

474 {_isExtinct = status;}

References _isExtinct.

Referenced by LCE_Patch_Extinction::do_flush(), LCE_Breed_base::doAgingInWFpop(), and LCE_Aging::execute().

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◆ set_K()

void Patch::set_K ( unsigned int k )

inline

471 {_K = k;}

References _K.

Referenced by FileServices::getSampledPop().

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◆ set_KFem()

void Patch::set_KFem ( unsigned int k )

inline

472 {_KFem = k;}

References _KFem.

Referenced by FileServices::getSampledPop(), and LCE_Resize::updatePatchCapacities().

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◆ set_KMal()

void Patch::set_KMal ( unsigned int k )

inline

473 {_KMal = k;}

References _KMal.

Referenced by FileServices::getSampledPop(), and LCE_Resize::updatePatchCapacities().

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◆ setID()

void Patch::setID ( unsigned int i )

inline

470 {_ID = i;}

References _ID.

Referenced by FileServices::getSampledPop().

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◆ setNewGeneration() [1/2]

void Patch::setNewGeneration	(	age_idx	AGE,
		Metapop *	pop
	)

Fills the patch container corresponding to the age class index passed, for both sexes.

 {  
   Individual *new_ind;
  
   //--------------------------------------------------------------------
   //if too much females in the Patch, flush them into the RecyclingPOOL
   if(size(FEM, AGE) > 0) flush(FEM, AGE, pop);
   
   for(unsigned int i = 0; i < _KFem; i++) {
     new_ind = pop->makeNewIndividual(0,0,FEM,_ID);
     new_ind->create_first_gen();
     add(FEM, AGE, new_ind);
   }
   
   //--------------------------------------------------------------------
   //males: same as for the females....
   if(size(MAL, AGE) > 0) flush(MAL, AGE, pop);
   
   for(unsigned int i = 0; i < _KMal; i++) {
     new_ind = pop->makeNewIndividual(0,0,MAL,_ID);
     new_ind->create_first_gen();
     add(MAL, AGE, new_ind);
   }
   
 }

References Individual::create_first_gen(), FEM, IndFactory::makeNewIndividual(), and MAL.

◆ setNewGeneration() [2/2]

void Patch::setNewGeneration	(	age_t	AGE,
		Metapop *	pop
	)

Fills the patch containers corresponding to the age flags passed, for both sexes.

 {
   unsigned int mask = 1;
  
   for(unsigned int i = 0; i < _nb_age_class; i++) {
     if( (mask & AGE) != 0) setNewGeneration(static_cast<age_idx>(i), pop);
     mask<<=1;
   }
 }

◆ show_up()

void Patch::show_up ( )

 {
   message("Patch %i:\n  age: %i; K: %i, K_fem: %i; K_mal: %i\n",_ID, _age, _K, _KFem, _KMal);
   for(unsigned int j = 0; j < _nb_age_class; ++j)
     message("   age class %i: females: %i; males: %i\n", j, _sizes[FEM][j], _sizes[MAL][j]);
 }

References FEM, MAL, and message().

◆ size() [1/4]

unsigned int Patch::size ( age_idx AGE )

inline

Returns the size of the container for the appropriate age class for both sexes.

Parameters

AGE	the index of the age class

524 { return _sizes[0][AGE] + _sizes[1][AGE]; }

References _sizes.

◆ size() [2/4]

unsigned int Patch::size ( age_t AGE )

inline

Returns the size of the container of the appropriate age class(es) for both sexes.

Parameters

AGE	the flag value of the age class

497 { return size(MAL,AGE) + size(FEM,AGE); }

References FEM, and MAL.

◆ size() [3/4]

unsigned int Patch::size	(	sex_t	SEX,
		age_idx	AGE
	)

inline

Returns the size of the container for the appropriate sex and age class.

Parameters

SEX	the sex class
AGE	the index of the age class

518 { return _sizes[SEX][AGE]; }

References _sizes.

◆ size() [4/4]

unsigned int Patch::size	(	sex_t	SEX,
		age_t	AGE
	)

inline

Returns the size of the container for the appropriate sex and age classes present in the age flag.

Parameters

SEX	the sex class
AGE	the flag value of the age class

   { 
     unsigned int mask = 1, s = 0;
     for(unsigned int i = 0; i < _nb_age_class; i++) {
       if( (mask & AGE) != 0) s +=  _sizes[SEX][i];
       mask <<= 1;
     }
     return s;
   }

References _nb_age_class, and _sizes.

◆ swap_new()

void Patch::swap_new	(	sex_t	SEX,
		age_idx	from,
		age_idx	to
	)

inline

Swaps elements between two containers, 'from' age-class container and the 'to' age-class container of the same sex.

No elements are overwritten.

Parameters

SEX	the sex class of the individual
from	the original age class of the individual
to	the destination age class of the individual

   {
     deque<Individual*> temp(_containers[SEX][to].begin(), _containers[SEX][to].end());
     unsigned int to_size = _sizes[SEX][to];
  
     if( _sizes[SEX][from] > _capacities[SEX][to] ) {
       _containers[SEX][to].resize( _sizes[SEX][from] );
       _capacities[SEX][to] = _sizes[SEX][from];
     }
     
     // copy content of 'from' into 'to', but restrict to the 'size' of 'from' to not copy over the actual number of individuals
     _containers[SEX][to].assign(_containers[SEX][from].begin(), _containers[SEX][from].begin() + _sizes[SEX][from]);
     _sizes[SEX][to] = _containers[SEX][to].size(); // this should be equal to _sizes[SEX][from]
  
     if( _sizes[SEX][to] > _capacities[SEX][from] ) {
       _capacities[SEX][from] = _sizes[SEX][to];
     }
  
     _containers[SEX][from].assign(temp.begin(), temp.begin()+to_size);
     _sizes[SEX][from] = _containers[SEX][from].size();
   }

References _capacities, _containers, and _sizes.

Member Data Documentation

◆ _age

unsigned int Patch::_age

private

age since last extinction.

Referenced by get_age(), and set_age().

◆ _capacities

unsigned int Patch::_capacities[2][3]

private

Total size of the containers, amount of allocated memory.

Referenced by add(), assign(), move(), Patch(), resize(), and swap_new().

◆ _containers

deque<Individual*> Patch::_containers[2][3]

private

Individuals containers, sex X age.

Referenced by add(), assign(), copy2patch(), flush(), get(), getCopy(), move(), remove(), resize(), set(), and swap_new().

◆ _ID

unsigned int Patch::_ID

private

Patch ID is equal to its position in the metapop patch array.

Referenced by getID(), and setID().

◆ _isExtinct

bool Patch::_isExtinct

private

Extinction flag.

Referenced by get_isExtinct(), and set_isExtinct().

◆ _K

unsigned int Patch::_K

private

Carrying capacity for males and females.

Referenced by add(), get_K(), getDensity(), and set_K().

◆ _KFem

unsigned int Patch::_KFem

private

Sex specific carrying capacity.

Referenced by get_K(), get_KFem(), and set_KFem().

◆ _KMal

unsigned int Patch::_KMal

private

Referenced by get_K(), get_KMal(), and set_KMal().

◆ _nb_age_class

unsigned int Patch::_nb_age_class

private

Number of age classes present.

Referenced by copy2patch(), flush(), Patch(), and size().

◆ _sizes

unsigned int Patch::_sizes[2][3]

private

Containers size counters, sex X age.

Referenced by add(), assign(), clear(), copy2patch(), flush(), getCopy(), move(), Patch(), remove(), resize(), size(), and swap_new().

◆ nbEmigrant

unsigned short Patch::nbEmigrant

Referenced by LCE_Disperse_EvolDisp::evoldisp(), LCE_Breed_Disperse::execute(), LCE_Breed_Selection_Disperse::execute(), LCE_Disperse_ConstDisp::execute(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Breed_Disperse::get_parent(), MPStatHandler::getEmigrantInPatch(), LCE_Disperse_ConstDisp::MigratePatch(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), and LCE_Disperse_ConstDisp::MigratePatchByNumber().

◆ nbImigrant

unsigned short Patch::nbImigrant

Referenced by LCE_Disperse_EvolDisp::evoldisp(), LCE_Breed_Disperse::execute(), LCE_Breed_Selection_Disperse::execute(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Breed_Disperse::get_parent(), MPStatHandler::getImigrateInPatch(), MPStatHandler::getMeanImigrantPerPatch(), LCE_Disperse_ConstDisp::MigratePatch(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), and LCE_Disperse_ConstDisp::MigratePatchByNumber().

◆ nbKolonisers

short Patch::nbKolonisers

Referenced by LCE_Breed_Selection_Disperse::do_breed(), LCE_Breed_Disperse::do_breed_disperse_in_empty_patch(), LCE_Disperse_EvolDisp::execute(), MPStatHandler::getKolonisersInPatch(), MPStatHandler::getMeanKolonisersPerPatch(), MPStatHandler::getMeanKolonisersProportion(), and LCE_Disperse_ConstDisp::Migrate().

◆ nbPhilopat

unsigned short Patch::nbPhilopat

Referenced by LCE_Disperse_EvolDisp::evoldisp(), LCE_Breed_Disperse::execute(), LCE_Breed_Selection_Disperse::execute(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Breed_Disperse::get_parent(), MPStatHandler::getImigrateInPatch(), MPStatHandler::getMeanResidantPerPatch(), MPStatHandler::getResidantInPatch(), LCE_Disperse_ConstDisp::MigratePatch(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), and LCE_Disperse_ConstDisp::MigratePatchByNumber().

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

Public Member Functions

Public Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Patch()

◆ ~Patch()

Member Function Documentation

◆ add()

◆ assign()

◆ clear() [1/2]

◆ clear() [2/2]

◆ copy2patch() [1/4]

◆ copy2patch() [2/4]

◆ copy2patch() [3/4]

◆ copy2patch() [4/4]

◆ flush() [1/4]

◆ flush() [2/4]

◆ flush() [3/4]

◆ flush() [4/4]

◆ get()

◆ get_age()

◆ get_isExtinct()

◆ get_K() [1/2]

◆ get_K() [2/2]

◆ get_KFem()

◆ get_KMal()

◆ getAdultsNumber()

◆ getCopy()

◆ getDensity()

◆ getID()

◆ init()

◆ isEmpty()

◆ move() [1/2]

◆ move() [2/2]

◆ remove()

◆ reset_containers()

◆ reset_counters()

◆ resize()

◆ set()

◆ set_age()

◆ set_isExtinct()

◆ set_K()

◆ set_KFem()

◆ set_KMal()

◆ setID()

◆ setNewGeneration() [1/2]

◆ setNewGeneration() [2/2]

◆ show_up()

◆ size() [1/4]

◆ size() [2/4]

◆ size() [3/4]

◆ size() [4/4]

◆ swap_new()

Member Data Documentation

◆ _age

◆ _capacities

◆ _containers

◆ _ID

◆ _isExtinct

◆ _K

◆ _KFem

◆ _KMal

◆ _nb_age_class

◆ _sizes

◆ nbEmigrant

◆ nbImigrant

◆ nbKolonisers

◆ nbPhilopat