Top class of the metapopulation structure, contains the patches. More...

#include <metapop.h>

Inheritance diagram for Metapop:

Collaboration diagram for Metapop:

Public Member Functions
	Metapop ()

virtual	~Metapop ()

bool	init ()
	Inits the population parameters from the ParamSet and builds the pop (adds patches), the prototypes and the life cycle. More...

virtual bool	setParameters ()

bool	setPopulationParameters ()
	Population's size parameters initializing procedure. More...

bool	setSourceParameters ()
	Setter for source population parameters. More...

bool	updatePopulationParameters ()
	Called during simulation to change the population's parameters (temporal argument). More...

void	reset ()
	Called to empty the patches, individuals are move to the garbage collector. More...

void	clear ()
	Called at the end of each simulation, empties the pop and the garbage collector; the Individuals are destroyed. More...

void	setMPImanager (MPImanager *mgr)

void	store_trait (int trait_idx, BinaryStorageBuffer *saver)
	Iterates through the individuals containers to store the trait data to a binary file. More...

void	read_trait (int trait_idx, BinaryStorageBuffer *loader)
	Iterates through the individuals containers to retrieve the trait data from a binary file. More...

void	show_up ()

Population builders
void	resizePatchArray ()
	Resets the patch container to the right number of patches as set by _patchNbr. More...

void	buildPatchArray ()
	Builds the new population from parameter values. More...

void	updatePatchArray ()
	Called during simulation to modify the meta-population size. More...

void	updatePatchState ()
	Update the patch capacities and patch ID (reset to array position). More...

void	setPatchCapacities ()
	Sets the deme capacity matrix from parameter values. More...

void	setPatchCapacities (string param)
	Builds the new population from a single matrix of deme sizes. More...

void	setPatchCapacities (sex_t SEX, string param)
	Builds the new population from a matrix of deme sizes but for one sex only. More...

void	setPatchCapacities (string paramfem, string parammal)
	Builds the new population from matrices of deme sizes. More...

void	loadSourcePopulation ()
	Loads a population from a soure population. More...

void	loadPopFromBinarySource (string &filename)
	Loads the population from a binary data file when setting the first generation of a replicate. More...

void	loadPopFromTraitFile (string &filename)
	Loads a population from a trait's data file (text file). More...

void	setPopulation (unsigned int currentReplicate, unsigned int replicates)
	Sets the population for the first generation of each replicates. More...

void	setPopulationFromSourceInPreserveMode ()

void	setPopulationFromSource ()

void	fillPopulationFromSource (age_idx AGE, sex_t SEX, deque< Individual * > &src_pool)
	Fills the population of the first generation of each replicates with individuals from a population source. More...

void	fillPatchFromSource (sex_t SEX, Patch src, Patch patch, age_t AGE)
	Fills a patch from a source patch loaded from a binary file, used when setting the population in preserve mode. More...

Implementations
virtual void	loadFileServices (FileServices *loader)

virtual void	loadStatServices (StatServices *loader)

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

virtual void	store_data (BinaryStorageBuffer *saver)

virtual bool	retrieve_data (BinaryStorageBuffer *reader)

Getters
Patch *	getPatch (unsigned int i)
	Patch accessor, return the ith+1 patch in the metapop. More...

Patch *	getPatchPtr (unsigned int patch)
	A secure version of the getPatch() method. More...

deque< Patch * > *	getPatchArray ()

unsigned int	getPatchArraySize ()

void	getAllIndividuals (age_idx AGE, deque< Individual * > &fem_pool, deque< Individual * > &mal_pool)

void	setGenerations (unsigned int gen)

unsigned int	getGenerations ()

void	setReplicates (unsigned int repl)

unsigned int	getReplicates ()

unsigned int	getPatchNbr ()

unsigned int	getPatchKFem ()

unsigned int	getPatchKMal ()

unsigned int	getPatchCapacity ()

unsigned int	getPatchCapacity (sex_t SEX, unsigned int patch)

TMatrix *	getPatchCapacities ()

bool	isSourceLoad ()

string	getSourceName ()

string	getSourceFileType ()

unsigned int	getSourceReplDigits ()

void	setPatchNbr (unsigned int val)

void	setPatchSizes (TMatrix &mat)

Population state interface
unsigned int	getCurrentReplicate ()

unsigned int	getCurrentGeneration ()

void	setCurrentReplicate (unsigned int repl)

void	setCurrentGeneration (unsigned int gen)

age_t	getCurrentAge ()

void	setCurrentAge (age_t age)
	Sets the age flag. More...

void	setCurrentAge (LifeCycleEvent *LCE)
	Set the age flag from a LifeCycleEvent object. More...

bool	isAlive ()
	Checks if the population still contains at least one individual in any sex or age class. More...

unsigned int	size ()
	Get the total number of individuals present in the population, all sex and age classes together. More...

unsigned int	size (sex_t SEX, age_t AGE)
	Interface to get the size of a praticular age and sex class(es). More...

unsigned int	size (sex_t SEX, age_idx IDX)
	Interface to get the size of a praticular age class and sex class. More...

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

unsigned int	size (age_idx IDX, unsigned int deme)

unsigned int	size (sex_t SEX, age_idx IDX, unsigned int deme)

unsigned int	size (sex_t SEX, age_t AGE, unsigned int deme)
	Interface to get the size of a praticular age and sex class within a patch. More...

unsigned int	size (age_t AGE)
	Simplified interface to get the size of both sexes of the appropriate age class(es) in the whole population. More...

unsigned int	size (age_t AGE, unsigned int deme)
	Simplified interface to get the size of both sexes of the appropriate age class(es) in one patch. More...

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

void	move (sex_t SEX, age_idx from_age, unsigned int from_deme, age_idx to_age, unsigned int to_deme, unsigned int at)
	Moves an individual from a deme to an other one, both demes sizes are modified. More...

void	flush ()
	Removes all individual pointers and flush them into the recycling pool. More...

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

void	flush (age_idx AGE)
	Removes all individual pointers of both sexes and specified age class and flush them into the recycling pool. More...

void	flush (age_t AGE)
	Removes all individual pointers of both sexes and specified age class(es) and flush them into the recycling pool. More...

Patch *	removePatch (unsigned int i)
	Removes a patch from the patch array and returns it pointer. More...

void	deletePatch (unsigned int i)
	Removes a patch from the patch array and deletes it and its content. More...

void	addPatch (Patch *patch)
	Adds a patch to the population. More...

void	addPatch (unsigned int num)
	Adds num patches to the population. More...

Public Member Functions inherited from StorableComponent
virtual void	store_data (BinaryStorageBuffer *saver)=0
	Interface to store the component data (e.g. gene values) into a binary buffer. More...

virtual bool	retrieve_data (BinaryStorageBuffer *reader)=0
	Interface to retrieve the same data from the binary buffer. More...

virtual	~StorableComponent ()

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_paramset (std::string name, bool required, SimComponent *owner)
	Sets a new ParamSet and name it. 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 IndFactory
	IndFactory ()

virtual	~IndFactory ()

void	recycle (Individual *ind)
	Put an individual in the recycling pool. More...

void	purgeRecyclingPOOL ()
	Empty the recycling pool. More...

void	makePrototype (map< trait_t, TraitPrototype * > TTlist)
	Creates the individuals prototype from the selected trait prototypes. More...

void	clearPrototype ()
	Reset the trait prototypes, mostly done to unregister the genetic maps. More...

Individual *	getPrototypeClone ()
	Return an uninitialized copy of the individual prototype. More...

Individual *	getNewIndividual ()
	Creates a blank individual which has to be "decorated" later. More...

Individual *	makeNewIndividual (Individual mother, Individual father, sex_t sex, unsigned short homepatch)
	Creates an individual with pointers to parents, sex and home ID set but no genetic data. More...

Individual *	makeOffsprg (Individual mother, Individual father, sex_t sex, unsigned short homepatch)
	Completely creates an individual with inheritance and mutations on all traits. More...

Individual *	getIndividualProtoype ()
	Individual prototype accessor. More...

TraitPrototype *	getTraitPrototype (trait_t type)
	Accessor to a TraitPrototype. More...

std::map< trait_t, TraitPrototype * > &	getTraitPrototypes ()
	Accessor to the list of TraitPrototype's. More...

int	getTraitIndex (trait_t type)
	Gives the index of trait with type. More...

Private Attributes
MPImanager *	_mpimgr

MPStatHandler	_statHandler
	The stat handler for the population stats. More...

MPFileHandler *	_writer
	The file handler used to save pedigree info. More...

deque< Patch * >	_vPatch
	The Patch container. More...

age_t	_requiredAge
	The age class flag that is required to fill the population at the beginning of a replicate. More...

unsigned int	_patchNbr
	Number of patches in the population. More...

unsigned int	_patchK
	Patch carrying capacity. More...

unsigned int	_patchKfem
	Sex specific carrying capacities. More...

unsigned int	_patchKmal

TMatrix	_patchSizes
	Matrix of the deme sizes, row 0 for the males, row 1 for the females. More...

unsigned int	_generations
	Number of generations to iterate. More...

unsigned int	_replicates
	Number of replicates to iterate. More...

unsigned int	_currentGeneration
	The current generation in the generation loop, starts at 1. More...

unsigned int	_currentReplicate
	The current replicate in the replicate loop, starts at 1. More...

age_t	_currentAge
	The current age class, might be changed by the LCEs. More...

binary source loader:
BinaryDataLoader	_loader
	A BinaryDataLoader to load a population from a binary data file. More...

Metapop *	_source
	A source population as loaded from a binary data file, used to build a population. More...

bool	_source_preserve
	Flag to specify the loading mode, true means the source pop is the actual population. More...

bool	_source_load
	Flage to specify that the population should be built from the binary loaded source population. More...

unsigned int	_source_replicates
	The number of source files, each file being a different replicate of the source population. More...

unsigned int	_source_replicate_digits
	Number of digits in the replicate counter filename extension. More...

unsigned int	_source_start_at_replicate
	The replicate number to start loading from. More...

unsigned int	_source_generation
	The generation to load from the binary file source file. More...

std::string	_source_name
	The base filename of source population files. More...

std::string	_source_filetype
	The trait type to load from. More...

std::string	_source_required_age
	The age class to fill with the source population. More...

unsigned int	_source_load_periodicity
	The number of replicates to source from a single source replicate. More...

vector< string >	_source_param_override
	List of parameters whose values in the source should override local values in the loading pop. More...

Friends
Metapop *	BinaryDataLoader::extractPop (std::string &, unsigned int, SimBuilder , Metapop )

Additional Inherited Members
Protected Attributes inherited from SimComponent
ParamSet *	_paramSet
	The parameters container. More...

Protected Attributes inherited from IndFactory
std::map< trait_t, TraitPrototype * >	_protoTraits
	Map of the trait prototypes. More...

std::map< trait_t, int >	_TraitsIndex
	Table containing the index of each trait. More...

Individual	_protoIndividual
	The individuals prototype used to create any new individual in a simulation. More...

std::deque< Individual * >	RecyclingPOOL
	Garbage collector for unused Individual's. More...

Detailed Description

Top class of the metapopulation structure, contains the patches.

The basic design for the metapopulation structure is a top-down chain of responsibility where the Metapop class takes care of the patches it contains which are themselves concerned by the management of their individual containers. The Individual class is only concerned by the management of its traits. Thereby, a metapopulation can be viewed as an interleaving of containers where one container class takes care of its directly contained class only, without knowledge of the upward container state.

The Metapop class thus implements methods used to manage and get information from the patches, to manage the parameters necessary to build a population and to get the population state information. It also implements the methods used to load a population from different source files.

Population states: given by the number and the position of the individuals (both spatially in demes and temporally in age class containers). The Metapop::_currentAge flag is set according to the age state of the metapopulation. The life cycle events modify that state by moving individuals among individuals containers within the metatpopulation. The Metapop::_currentAge flag can contain the following age class bits as defined in types.h. The OFFSPRNG (=1) age class bit is set whenever the offspring containers are not empty. The ADULTS (=4) age class bit is set whenever the adult containers are not empty. The POSTDISP (=2) age class bit informs about the content of the post-dispersal containers. The ALL (=7) age class is the addition of the previous tags and NONE (=0) is the negation of them. The individual containers are stored in the patches and handled through the Patch class interface. Each age class is represented by two containers, one for the males (index 0) and the other for the females (index 1). These containers are store in a table and are accessed through their age class index as defined by the age_idx enum (see types.h). These indexes are as follows: The OFFSPRNG age class has index OFFSx = 0, the POSTDISP age class has index PDISPx = 1 and the ADULTS age class has index ADLTx = 2.

Constructor & Destructor Documentation

◆ Metapop()

Metapop::Metapop ( )

                 : _mpimgr(0), _statHandler(), _writer(0),_loader(), _source(0),
_source_preserve(0), _source_load(0), _source_replicates(0), _source_replicate_digits(0),
_source_start_at_replicate(1), _source_generation(0), _source_load_periodicity(0),
_patchNbr(0), _patchK(0), _patchKfem(0), _patchKmal(0), _generations(0), _replicates(0),
_currentGeneration(0), _currentReplicate(0), _currentAge(NONE), _requiredAge(0)
{
  set_paramset("population", true, this);
  ParamUpdater<Metapop>* upd = new ParamUpdater<Metapop>( &Metapop::updatePopulationParameters );
  add_parameter("patch_capacity",INT,false,false,0,0, upd);
  add_parameter("patch_nbfem",INT,false,false,0,0, upd);
  add_parameter("patch_nbmal",INT,false,false,0,0, upd);
  add_parameter("patch_number",INT,false,false,0,0, upd);
  
  add_parameter("pop_output", BOOL, false, false, 0, 0);
  add_parameter("pop_output_dir", STR, false, false, 0, 0);
  add_parameter("pop_output_logtime", INT, false, false, 0, 0);
  add_parameter("pop_output_sample_size", INT, false, false, 0, 0);
 
  upd = new ParamUpdater<Metapop>( &Metapop::setSourceParameters );
  add_parameter("source_pop",STR,false,false,0,0, upd);
  add_parameter("source_file_type",STR,false,false,0,0, upd);
  add_parameter("source_preserve",BOOL,false,false,0,0, upd);
  add_parameter("source_replicates",INT,false,false,0,0, upd);
  add_parameter("source_replicate_digit",INT,false,false,0,0, upd);
  add_parameter("source_start_at_replicate",INT,false,false,0,0, upd);
  add_parameter("source_generation",INT,false,false,0,0, upd);
  add_parameter("source_fill_age_class",STR,false,false,0,0, upd);
  add_parameter("source_parameter_override", STR, false, false, 0, 0, upd);
}

References SimComponent::add_parameter(), BOOL, INT, SimComponent::set_paramset(), setSourceParameters(), STR, and updatePopulationParameters().

◆ ~Metapop()

Metapop::~Metapop ( )

virtual

{
#ifdef _DEBUG_
  message("Metapop::~Metapop\n");
#endif
  clear();
}

References clear(), and message().

Member Function Documentation

◆ addPatch() [1/2]

void Metapop::addPatch ( Patch * patch )

inline

Adds a patch to the population.

The patch is added at the end of the array and it is empty.

{
  _vPatch.push_back(patch);
}

References _vPatch.

Referenced by LCE_Resize::buildNewPatchArrayWithBackup(), FileServices::getSampledPop(), and LCE_Resize::removeDesignatedPatch().

Here is the caller graph for this function:

◆ addPatch() [2/2]

void Metapop::addPatch ( unsigned int num )

inline

Adds num patches to the population.

{
  for (unsigned int i = 0; i < num; i++)
    _vPatch.push_back(new Patch());
}

References _vPatch.

◆ buildPatchArray()

void Metapop::buildPatchArray ( )

Builds the new population from parameter values.

Supernumerary patches are deleted. All patches are empty.

{
  resizePatchArray();
  
  //set the population capacities:
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    _vPatch[i]->flush(this);
    _vPatch[i]->init((unsigned int)_patchSizes.get(FEM,i), (unsigned int)_patchSizes.get(MAL,i), i);
  }
}

References _patchNbr, _patchSizes, _vPatch, FEM, TMatrix::get(), MAL, and resizePatchArray().

Referenced by BinaryDataLoader::extractPop(), init(), and setPopulation().

Here is the caller graph for this function:

◆ clear()

void Metapop::clear ( )

Called at the end of each simulation, empties the pop and the garbage collector; the Individuals are destroyed.

{
#ifdef _DEBUG_
  message("Metapop::clear\n");
#endif
  
  for(unsigned int i = 0; i < _vPatch.size(); ++i)
    delete _vPatch[i];
  
  _vPatch.clear();
  
  _patchNbr = 0;
 
  // clean up source metapop only when the source is NOT a binary file
  if(_source && _source_filetype != ".bin") {
    delete _source;
    _source = NULL;
  }
 
}

References _patchNbr, _source, _source_filetype, _vPatch, and message().

Referenced by SimRunner::Replicate_LOOP(), and ~Metapop().

Here is the caller graph for this function:

◆ deletePatch()

void Metapop::deletePatch ( unsigned int i )

inline

Removes a patch from the patch array and deletes it and its content.

The IDs of the remaining patches are updated.

Parameters

i	the index of the patch to remove.

{
  delete _vPatch[i];
  for (unsigned int k = i; k < _vPatch.size() -1; k++) {
    _vPatch[k] = _vPatch[k + 1];
    _vPatch[k]->setID(k);
  }
  _vPatch.pop_back();
}

References _vPatch.

Referenced by LCE_Resize::removeDesignatedPatch().

Here is the caller graph for this function:

◆ fillPatchFromSource()

void Metapop::fillPatchFromSource	(	sex_t	SEX,
		Patch *	src,
		Patch *	patch,
		age_t	AGE
	)

Fills a patch from a source patch loaded from a binary file, used when setting the population in preserve mode.

Parameters

SEX	sex of the individuals to fetch from the source pop
src	the source patch that will be copied.
patch	the local patch to be filled with individuals copied from the source patch.
AGE	age class to copy individuals from the source.

{
  age_idx in_age = (AGE == OFFSPRG? OFFSx : ADLTx);
  age_idx to_age = (_requiredAge | AGE? in_age : ADLTx);//this to be sure we load some
  
  Individual* new_ind;
 
  for(unsigned int j = 0; j < src->size(SEX, in_age); ++j) {
 
    new_ind = getNewIndividual(); //this correctly sets pointers to TProto's, and params
 
    (*new_ind) = (*src->get(SEX, in_age, j)); //this should only copy genes
 
    patch->add(SEX , to_age, new_ind );
  }
}

References _requiredAge, Patch::add(), ADLTx, Patch::get(), IndFactory::getNewIndividual(), OFFSPRG, OFFSx, and Patch::size().

Referenced by setPopulationFromSourceInPreserveMode().

Here is the caller graph for this function:

◆ fillPopulationFromSource()

void Metapop::fillPopulationFromSource	(	age_idx	AGE,
		sex_t	SEX,
		deque< Individual * > &	src_pool
	)

Fills the population of the first generation of each replicates with individuals from a population source.

Parameters

AGE	age of the individuals to fetch from the source pop
SEX	sex of the individuals to fetch from the source pop
src_pool	the container where the source individuals will be placed, they are not removed from the source.

{
  unsigned int Ktot = 0;
  unsigned int ind_pos ;
  Individual* new_ind;
  
  for(unsigned int i = 0; i < _patchNbr; ++i) 
    Ktot += _vPatch[i]->get_K(SEX);
  
  if(src_pool.size() < Ktot)
    warning("Number of %s %s in source metapop (%i) not enough to fill current metapop (%i).\n",
            (SEX ? "female" : "male"), (AGE == OFFSx ? "offspring" : "adults"),
            src_pool.size(), Ktot);
  
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    
    for(unsigned int j = 0, psize = _vPatch[i]->get_K(SEX); j < psize && src_pool.size() != 0; ++j) {
      
      new_ind = getNewIndividual();
      
      ind_pos = RAND::Uniform( src_pool.size() );
      
      _vPatch[i]->add( SEX, AGE, &( (*new_ind) = *(src_pool[ ind_pos ]) ) );
      
      src_pool.erase( src_pool.begin() + ind_pos );  //this is without replacement!!!!
      
    }
  }
  
}

References _patchNbr, _vPatch, IndFactory::getNewIndividual(), OFFSx, RAND::Uniform(), and warning().

Referenced by setPopulationFromSource().

Here is the caller graph for this function:

◆ flush() [1/4]

void Metapop::flush ( )

inline

Removes all individual pointers and flush them into the recycling pool.

Container sizes are reset to null values.

See also: Patch::flush()

{
  for(unsigned int i = 0; i < _patchNbr; i++) _vPatch[i]->flush(this);
}

References _patchNbr, _vPatch, and flush().

Referenced by LCE_Breed::execute(), LCE_Breed_Selection::execute(), LCE_Cross::execute(), LCE_Breed_Quanti::execute(), LCE_Breed_Wolbachia::execute(), flush(), and LCE_Cross::generatePedigree().

Here is the caller graph for this function:

◆ flush() [2/4]

void Metapop::flush ( age_idx AGE )

inline

Removes all individual pointers of both sexes and specified age class and flush them into the recycling pool.

Container sizes are reset to null values.

See also: Patch::flush()

Parameters

AGE	the index of the age class to be flushed

{
  for(unsigned int i = 0; i < _patchNbr; i++) _vPatch[i]->flush(AGE, this);
}

References _patchNbr, _vPatch, and flush().

◆ flush() [3/4]

void Metapop::flush ( age_t AGE )

inline

Removes all individual pointers of both sexes and specified age class(es) and flush them into the recycling pool.

Container sizes are reset to null values.

See also: Patch::flush()

Parameters

AGE	the age class(es) to be flushed

{
  for(unsigned int i = 0; i < _patchNbr; i++) _vPatch[i]->flush(AGE, this);
}

References _patchNbr, _vPatch, and flush().

◆ flush() [4/4]

void Metapop::flush	(	sex_t	SEX,
		age_idx	AGE
	)

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.

See also: Patch::flush()

Parameters

SEX	the sex class of the individual
AGE	the index of the age class to be flushed

{
  for(unsigned int i = 0; i < _patchNbr; i++) _vPatch[i]->flush(SEX, AGE, this);
}

References _patchNbr, _vPatch, and flush().

◆ get()

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

inline

Returns a pointer to the appropriate individual.

Parameters

SEX	sex class container index
AGE	age class container index
at	the index of the individual in its container
deme	the patch where to grab the individual

793{ return getPatchPtr(deme)->get(SEX, AGE, at); }

Metapop::getPatchPtr

Patch * getPatchPtr(unsigned int patch)

A secure version of the getPatch() method.

Definition: metapop.h:260

References Patch::get(), and getPatchPtr().

Referenced by LCE_Cross::create_individual_ancestors(), LCE_NtrlInit::init_allele_freq(), LCE_QuantiInit::init_allele_freq(), LCE_QuantiInit::init_trait_value(), LCE_Init_BDMI::init_value(), move(), read_trait(), store_data(), and store_trait().

Here is the caller graph for this function:

◆ getAllIndividuals()

void Metapop::getAllIndividuals	(	age_idx	AGE,
		deque< Individual * > &	fem_pool,
		deque< Individual * > &	mal_pool
	)

{
  
  for(unsigned int i = 0; i < _vPatch.size(); ++i) {
    
    for(unsigned int j = 0, psize = _vPatch[i]->size(MAL, AGE); j < psize; ++j)
      mal_pool.push_back( _vPatch[i]->get(MAL, AGE, j) );
    
    for(unsigned int j = 0, psize = _vPatch[i]->size(FEM, AGE); j < psize; ++j)
      fem_pool.push_back( _vPatch[i]->get(FEM, AGE, j) );
    
  }
  
}

References _vPatch, FEM, MAL, and size().

Referenced by setPopulationFromSource().

Here is the caller graph for this function:

◆ getCurrentAge()

age_t Metapop::getCurrentAge ( )

inline

297{return _currentAge;}

References _currentAge.

Referenced by LCE_Resize::execute(), LCE_Resize::fillPop(), FileServices::getSampledPop(), loadSourcePopulation(), StatServices::recordStats(), setPopulationFromSourceInPreserveMode(), TTNeutralGenesFH::write_PLINK(), TTQuantiFH::write_PLINK(), TTQuantiFH::write_TABLE(), and TTNeutralGenesFH::write_varcompWC().

Here is the caller graph for this function:

◆ getCurrentGeneration()

unsigned int Metapop::getCurrentGeneration ( )

inline

◆ getCurrentReplicate()

unsigned int Metapop::getCurrentReplicate ( )

inline

293{return _currentReplicate;}

References _currentReplicate.

Referenced by LCE_Breed_Wolbachia::execute(), BinaryDataSaver::finish(), LCE_Cross::generatePedigree(), FileServices::getReplicateCounter(), FileServices::getSampledPop(), TTNeutralGenesSH::setAlleleTables(), LCE_SelectionSH::setDataTable(), TTQuantiSH::setStats(), and FileHandler::update().

Here is the caller graph for this function:

◆ getGenerations()

unsigned int Metapop::getGenerations ( )

inline

273{return _generations;}

References _generations.

Referenced by TTQFreqExtractor::FHwrite(), FileServices::getGenerationCounter(), BinaryDataSaver::ifExist(), FileHandler::ifExist(), FileHandler::init(), and BinaryDataSaver::setParameters().

Here is the caller graph for this function:

◆ getPatch()

Patch * Metapop::getPatch ( unsigned int i )

inline

Patch accessor, return the ith+1 patch in the metapop.

257{return (i > _vPatch.size() -1 ? 0 : _vPatch[i]);}

References _vPatch.

Referenced by LCE_Selection_base::addPhenotypicSD(), LCE_Breed_Selection_Disperse::breed_selection_disperse(), LCE_Breed_Disperse::do_breed_disperse(), LCE_Disperse_EvolDisp::evoldisp(), LCE_Breed_Disperse::execute(), LCE_Breed_Selection::execute(), LCE_Breed_Selection_Disperse::execute(), LCE_Disperse_ConstDisp::execute(), LCE_Disperse_EvolDisp::execute(), LCE_Regulation::execute(), LCE_Aging::execute(), LCE_Patch_Extinction::execute(), LCE_Cross::execute(), LCE_QuantiModifier::execute(), LCE_Selection_base::execute(), TTDeletMutBitstrFH::FHread(), TTNeutralGenesFH::FHread(), TTQuantiFH::FHread(), LCE_SelectionFH::FHwrite(), MPFileHandler::FHwrite(), TTBDMI_FH::FHwrite(), TTDeletMutBitstrFH::FHwrite(), TTQFreqExtractor::FHwrite(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Cross::generatePedigree(), MPStatHandler::getEmigrantInPatch(), MPStatHandler::getImigrateInPatch(), MPStatHandler::getKolonisersInPatch(), TTDeletMutBitstrSH::getLoad(), LCE_Selection_base::getMaxPatchFitness(), MPStatHandler::getMeanAssignedFecundity(), TTDispersalSH::getMeanDispRate(), MPStatHandler::getMeanEmigrantPerPatch(), TTDeletMutBitstrSH::getMeanFecWithPatchMate(), TTWolbachiaSH::getMeanFemaleInfection_perPatch(), TTDispersalSH::getMeanFemDispRate(), LCE_Selection_base::getMeanFitness(), MPStatHandler::getMeanImigrantPerPatch(), MPStatHandler::getMeanKolonisersPerPatch(), MPStatHandler::getMeanKolonisersProportion(), TTDispersalSH::getMeanMalDispRate(), TTWolbachiaSH::getMeanMaleInfection_perPatch(), MPStatHandler::getMeanMatings(), TTWolbachiaSH::getMeanOffsprgFemaleInfection_perPatch(), TTWolbachiaSH::getMeanOffsprgInfection(), TTWolbachiaSH::getMeanOffsprgMaleInfection_perPatch(), MPStatHandler::getMeanPatchAge(), MPStatHandler::getMeanPatchDensity(), MPStatHandler::getMeanPatchDensityVariance(), LCE_Selection_base::getMeanPatchFitness(), MPStatHandler::getMeanResidantPerPatch(), TTDispersalSH::getOffsprgMeanDispRate(), MPStatHandler::getPatchAge(), TTDeletMutBitstrSH::getPatchLoad(), MPStatHandler::getResidantInPatch(), FileServices::getSampledPop(), LCE_Breed_Wolbachia::hasInfectedFemale(), LCE_Breed_Wolbachia::inoculate_wolbachia(), LCE_Disperse_ConstDisp::Migrate(), LCE_Disperse_ConstDisp::MigratePatch(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), LCE_Disperse_ConstDisp::MigratePatchByNumber(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), TTQuantiFH::print(), LCE_Disperse_base::reset_counters(), LCE_Selection_base::set_std_rate_of_change(), TTNeutralGenesSH::setAdults_Theta(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setCoaMatrix(), LCE_SelectionSH::setDataTable(), TTQuantiSH::setDataTables(), TTDeletMutBitstrSH::setDeletStats(), TTDeletMutBitstrSH::setFst(), TTNeutralGenesSH::setHeteroTable(), TTNeutralGenesSH::setHeterozygosity(), TTNeutralGenesSH::setHo(), TTNeutralGenesSH::setHo2(), TTNeutralGenesSH::setHs(), TTNeutralGenesSH::setHs2(), TTWolbachiaSH::setInfectionStats(), MPStatHandler::setKinship(), TTDeletMutBitstrSH::setMeanViability(), MPStatHandler::setObsrvdExtinctionRate(), MPStatHandler::setPedegreeCount(), MPStatHandler::setReproductiveStats(), TTNeutralGenesSH::setSibStats(), TTBDMI_SH::setStats(), TTDeletMutBitstrSH::setViability(), size(), LCE_Disperse_base::swapPostDisp(), LCE_Breed_Wolbachia::wolbachia_model_1(), LCE_Breed_Wolbachia::wolbachia_model_2(), LCE_Breed_base::WrightFisherPopulation(), LCE_Breed_Quanti::WrightFisherPopulation(), TTNeutralGenesFH::write_FSTAT(), TTNeutralGenesFH::write_GENEPOP(), TTNeutralGenesFH::write_PLINK(), TTQuantiFH::write_PLINK(), TTNeutralGenesFH::write_PLINK_BED(), and TTNeutralGenesFH::write_TAB().

◆ getPatchArray()

deque< Patch * > * Metapop::getPatchArray ( )

inline

269{return &_vPatch;}

References _vPatch.

◆ getPatchArraySize()

unsigned int Metapop::getPatchArraySize ( )

inline

270{return _vPatch.size();}

References _vPatch.

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

Here is the caller graph for this function:

◆ getPatchCapacities()

TMatrix * Metapop::getPatchCapacities ( )

inline

281{return &_patchSizes;}

References _patchSizes.

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

Here is the caller graph for this function:

◆ getPatchCapacity() [1/2]

unsigned int Metapop::getPatchCapacity ( )

inline

279{return _patchK;}

References _patchK.

◆ getPatchCapacity() [2/2]

unsigned int Metapop::getPatchCapacity	(	sex_t	SEX,
		unsigned int	patch
	)

inline

280{return (unsigned int)_patchSizes.get(SEX, patch);}

References _patchSizes, and TMatrix::get().

◆ getPatchKFem()

unsigned int Metapop::getPatchKFem ( )

inline

277{return _patchKfem;}

References _patchKfem.

Referenced by LCE_Resize::execute().

Here is the caller graph for this function:

◆ getPatchKMal()

unsigned int Metapop::getPatchKMal ( )

inline

278{return _patchKmal;}

References _patchKmal.

Referenced by LCE_Resize::execute().

Here is the caller graph for this function:

◆ getPatchNbr()

unsigned int Metapop::getPatchNbr ( )

inline

276{return _patchNbr;}

References _patchNbr.

◆ getPatchPtr()

Patch * Metapop::getPatchPtr ( unsigned int patch )

inline

A secure version of the getPatch() method.

                                                         {
    if(!(patch < _vPatch.size())) 
      fatal("Metapop::getPatchPtr()::_vPatch overflow (id=%i nb=%i)\n", patch, _vPatch.size());
    
    if (_vPatch[patch] == NULL) fatal("Metapop::getPatchPtr()::NULL ptr\n");
    
    return _vPatch[patch];
  }

References _vPatch, and fatal().

Referenced by LCE_Resize::buildNewPatchArrayWithBackup(), LCE_Resize::fillPatchNoBackup(), LCE_Resize::fillPatchWithBackup(), get(), LCE_Breed_Disperse::get_parent(), TTNeutralGenesSH::getDxyPerPatch(), TTDispersalSH::getMeanDispRateInPatch(), LCE_SelectionSH::getMeanPatchFitness(), LCE_SelectionSH::getVarPatchFitness(), LCE_Resize::regulate(), LCE_Resize::removeDesignatedPatch(), removePatch(), LCE_Cross::sampleAmongPop(), setPopulationFromSourceInPreserveMode(), and LCE_Resize::updatePatchCapacities().

Here is the caller graph for this function:

◆ getReplicates()

unsigned int Metapop::getReplicates ( )

inline

275{return _replicates;}

References _replicates.

Referenced by FileServices::getFirstReplicateFileName(), FileServices::getReplicateCounter(), BinaryDataSaver::ifExist(), FileHandler::ifExist(), and FileHandler::init().

Here is the caller graph for this function:

◆ getSourceFileType()

string Metapop::getSourceFileType ( )

inline

284{return _source_filetype;}

References _source_filetype.

Referenced by SimRunner::run().

Here is the caller graph for this function:

◆ getSourceName()

string Metapop::getSourceName ( )

inline

283{return _source_name;}

Metapop::_source_name

std::string _source_name

The base filename of source population files.

Definition: metapop.h:116

References _source_name.

Referenced by SimRunner::run().

Here is the caller graph for this function:

◆ getSourceReplDigits()

unsigned int Metapop::getSourceReplDigits ( )

inline

285{return _source_replicate_digits;}

References _source_replicate_digits.

◆ init()

bool Metapop::init ( )

Inits the population parameters from the ParamSet and builds the pop (adds patches), the prototypes and the life cycle.

Called at the start of each simulation, resets the individual garbage collector.

{
  if( !(_paramSet->isSet()) ) {
    return error("parameters in \"population\" are not properly set!\n");
  }
  
  if(!setParameters()) return false;
  
  buildPatchArray();
  
  //empty and clean the RecyclingPOOL, safer...
  purgeRecyclingPOOL();
  
  return true;
}

References SimComponent::_paramSet, buildPatchArray(), error(), ParamSet::isSet(), IndFactory::purgeRecyclingPOOL(), and setParameters().

Referenced by SimRunner::init_components().

Here is the caller graph for this function:

◆ isAlive()

bool Metapop::isAlive ( )

inline

Checks if the population still contains at least one individual in any sex or age class.

307{return size() != 0;}

References size().

Referenced by SimRunner::Cycle(), MPFileHandler::FHwrite(), TTBDMI_FH::FHwrite(), TTNeutralGenesFH::FHwrite(), TTQuantiFH::FHwrite(), and SimRunner::Replicate_LOOP().

Here is the caller graph for this function:

◆ isSourceLoad()

bool Metapop::isSourceLoad ( )

inline

282{return _source_load;}

References _source_load.

Referenced by SimRunner::run().

Here is the caller graph for this function:

◆ loadFileServices()

void Metapop::loadFileServices ( FileServices * loader )

virtual

Implements SimComponent.

{
 
  if(get_parameter("pop_output")->isSet()){
 
    if(!get_parameter("pop_output_logtime")->isSet())
      fatal("parameter \"pop_output_logtime\" is missing when pop_output is set\n");
 
 
          if(_writer == 0) _writer = new MPFileHandler();
 
          int size = 0;
 
          if(get_parameter("pop_output_sample_size")->isSet())
                  size = get_parameter_value("pop_output_sample_size");
 
          _writer->setOption(size);
 
          Param* param = get_parameter("pop_output_logtime");
 
          if(param->isMatrix()) {
 
                TMatrix temp;
                param->getMatrix(&temp);
                _writer->set_multi(true, true, 1, &temp, get_parameter("pop_output_dir")->getArg());
 
          } else   //  rpl_per, gen_per, rpl_occ, gen_occ, rank (0), path, self-ref
                _writer->set(true, true, 1, (param->isSet() ? (int)param->getValue() : 0),
                                         0, get_parameter("pop_output_dir")->getArg());
 
          loader->attach(_writer);
 
  } else if(_writer) {
          delete _writer;
          _writer = NULL;
  }
}

References _writer, FileServices::attach(), fatal(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), Param::getMatrix(), Param::getValue(), Param::isMatrix(), Param::isSet(), FileHandler::set(), FileHandler::set_multi(), MPFileHandler::setOption(), and size().

◆ loadPopFromBinarySource()

void Metapop::loadPopFromBinarySource ( string & filename )

Loads the population from a binary data file when setting the first generation of a replicate.

{
  Individual  *new_ind, *src_tmp;
  
  // EXTRACT DATA FROM SOURCE -------------------------------------------------------------
 
  // here the data is put in the _source Metapop, it is not yet copied to fill the current pop
 
  if(!(_source = _loader.extractPop(filename,_source_generation,SIMenv::MainSim, this)))
    fatal("Metapop::loadPopFromBinarySource:could not extract pop from binary file \"%s\"\n",filename.c_str());
  
#ifdef _DEBUG_
  message("+++Metapop::loadPopFromBinarySource::data read from %s\n",filename.c_str());
#endif
 
  // PERFORM CHECKS -----------------------------------------------------------------------
 
  //check trait parameters; we want to have equal genetic architecture for the traits
  new_ind = getNewIndividual();
  src_tmp = _source->getNewIndividual();
  
  if( (*new_ind) != (*src_tmp) ) {  //the operator= for each trait is called within operator= of Individual
    fatal("loading population from source file failed: trait genetic architecture differs.\n");
  }
  
  delete new_ind;
  delete src_tmp;
  
 
  // PARAMETER OVERRIDE FROM SOURCE -------------------------------------------------------
 
  // check if we need to override some local parameter values with the values from the source
  if(get_parameter("source_parameter_override")->isSet() )
  {
    string param;
    bool checked = false;
    SimComponent *cmpt = NULL, *localcmpt = NULL;
 
    for( unsigned int p; p < _source_param_override.size(); ++p )
    {
      param = _source_param_override[p];
 
      // check among the traits:
      cmpt = _loader.getSim()->get_current_traitWithParameter(param);
 
      if( cmpt ) {
 
        // find the local corresponding trait to reset its parameter
        localcmpt = SIMenv::MainSim->get_current_trait(dynamic_cast<TraitPrototype*> (cmpt)->get_type());
 
        if( localcmpt ) {
          // we found it, reset;
          checked = localcmpt->resetParameterFromSource(param, cmpt);
        }
 
      }
 
      //check among the LCEs
      if( !checked ){
        cmpt = _loader.getSim()->get_current_eventWithParameter(param);
 
        if( cmpt ) {
 
          // find the local corresponding trait to reset its parameter
          localcmpt = SIMenv::MainSim->get_current_event(dynamic_cast<LifeCycleEvent*> (cmpt)->get_event_name());
 
          if( localcmpt ) {
            // we found it, reset;
            checked = localcmpt->resetParameterFromSource(param, cmpt);
          }
 
        }
      }
 
      if( !checked ){
        if( _loader.getPop()->has_parameter(param) ) {
 
          cmpt = _loader.getPop();
 
          checked = resetParameterFromSource(param, cmpt);
        }
      }
 
      string message = "while loading population from binary source: resetting parameter value\
 from the source value failed for parameter";
 
      if(!checked) //resetting failed
        fatal("%s \"%s\" (a specific routine may need to be implemented, contact the developers)\n",
              message.c_str(), param.c_str());
 
      if(!localcmpt) //we didn't find a corresponding local component, abort;
        fatal("%s \"%s\", no corresponding local component could be found.\n",
              message.c_str(), param.c_str());
 
      if(!cmpt) //no source component has this parameter
        fatal("%s \"%s\", no component holding this parameter exists in the source.\n",
              message.c_str(), param.c_str());
 
 
      // need to log the new parameter value into the simulation .log file
      // because the log file is written before the replicate loop starts
      SIMenv::MainSim->_FileServices.log("## " + param + " set from binary source value at replicate "
                                         + tstring::int2str(_currentReplicate));
      SIMenv::MainSim->_FileServices.log("# " + param + " " + cmpt->get_parameter(param)->getArg());
 
      cmpt = localcmpt = NULL;
      checked = false;
 
    }
  }
 
}

References _currentReplicate, SimRunner::_FileServices, _loader, _source, _source_generation, _source_param_override, BinaryDataLoader::extractPop(), fatal(), SimBuilder::get_current_event(), SimBuilder::get_current_eventWithParameter(), SimBuilder::get_current_trait(), SimBuilder::get_current_traitWithParameter(), SimComponent::get_parameter(), Param::getArg(), IndFactory::getNewIndividual(), BinaryDataLoader::getPop(), BinaryDataLoader::getSim(), SimComponent::has_parameter(), tstring::int2str(), FileServices::log(), SIMenv::MainSim, message(), resetParameterFromSource(), and SimComponent::resetParameterFromSource().

Referenced by loadSourcePopulation().

Here is the caller graph for this function:

◆ loadPopFromTraitFile()

void Metapop::loadPopFromTraitFile ( string & filename )

Loads a population from a trait's data file (text file).

{
  if(_source != NULL) _source = NULL;
//
//  _source = new Metapop();
//  _source->setMPImanager( _mpimgr );
//
//  //the population's parameters from current params
//  _source->set_paramsetFromCopy((*this->get_paramset()));
//
//  //we need this to be able to create new individuals in the source:
//  _source->init( );
//  _source->makePrototype(this->getTraitPrototypes());
  
  //now read data from genotype file:
  FileServices *FS = SIMenv::MainSim->get_FileServices();
  
  FileHandler* file = FS->getReader(_source_filetype);
  
  if(!file)
    fatal("no file reader exists with source file extension \"%s\".\n",_source_filetype.c_str());
  
  //attach the source pop to the reader
  file->set_pop_ptr(this);
 
//  cout << "\n --- pop size BEFORE loading inds from genotype file: "<<size()<<endl;
 
  //read the genotypes from files into the source metapop object
  file->FHread(filename);
  
 
//  cout << "\n --- pop size AFTER loading inds from genotype file: "<<size()<<endl;
 
  if(size() == 0)
      fatal("source population in file \"%s\" is empty.\n",filename.c_str());
 
 
  if(size( ADULTS ) != 0)
    _currentAge |= ADULTS;
 
  if(size( OFFSPRG ) != 0)
    _currentAge |= OFFSPRG;
 
//  if(_source->size() == 0)
//    fatal("source population in file \"%s\" is empty.\n",filename.c_str());
}

References _currentAge, _source, _source_filetype, ADULTS, fatal(), FileHandler::FHread(), SimRunner::get_FileServices(), FileServices::getReader(), SIMenv::MainSim, OFFSPRG, FileHandler::set_pop_ptr(), and size().

Referenced by loadSourcePopulation().

Here is the caller graph for this function:

◆ loadSourcePopulation()

void Metapop::loadSourcePopulation ( )

Loads a population from a soure population.

{  
  std::string filename;
  
  if(_source_replicates != 0) {
    //find the replicate string of the source file
    ostringstream rpl;
    rpl.fill('0');
    rpl.width(_source_replicate_digits);
    
    if(_source_replicates >= _replicates)
      rpl << _currentReplicate + _source_start_at_replicate - 1;
    else if (_source_replicates != 1)
      //less replicates in source, reload the same repl every `source_replicates'
      rpl << ((_currentReplicate-1) / _source_load_periodicity) + 1;
    else
      rpl << 1; //a bit dumb but just in case...
    
    filename = _source_name + "_" + rpl.str() + _source_filetype;
    
  } else {
    
    filename = _source_name;
    
  }
  
  if(_source_filetype == ".bin") {
 
    // loading pop from a binary file
 
    loadPopFromBinarySource(filename);
 
    if(_source->size() == 0)  fatal("source population is empty!\n");
    else {
      if(_source->size(OFFSPRG) != 0)
        _source->setCurrentAge( (_source->getCurrentAge() | OFFSPRG) );
 
      if(_source->size(ADULTS)  != 0)
        _source->setCurrentAge( (_source->getCurrentAge() | ADULTS)  );
    }
 
  } else
    // loading pop from a trait's genotype text file
    loadPopFromTraitFile(filename);
 
#ifdef _DEBUG_
  if(_source)
    message("+++source pop loaded: offspring: %i f, %i m; adults: %i f, %i m\n", _source->size(FEM,OFFSPRG),
          _source->size(MAL,OFFSPRG), _source->size(FEM,ADULTS), _source->size(MAL,ADULTS));
#endif
}

References _currentReplicate, _replicates, _source, _source_filetype, _source_load_periodicity, _source_name, _source_replicate_digits, _source_replicates, _source_start_at_replicate, ADULTS, fatal(), FEM, getCurrentAge(), loadPopFromBinarySource(), loadPopFromTraitFile(), MAL, message(), OFFSPRG, setCurrentAge(), and size().

Referenced by setPopulation().

Here is the caller graph for this function:

◆ loadStatServices()

virtual void Metapop::loadStatServices ( StatServices * loader )

inlinevirtual

Implements SimComponent.

236{loader->attach(&_statHandler);}

StatServices::attach

virtual void attach(Handler *H)

attach the StatHandler to the current list (_statHandlers) of the StatServices

Definition: statservices.cc:177

References _statHandler, and StatServices::attach().

◆ move()

void Metapop::move	(	sex_t	SEX,
		age_idx	from_age,
		unsigned int	from_deme,
		age_idx	to_age,
		unsigned int	to_deme,
		unsigned int	at
	)

inline

Moves an individual from a deme to an other one, both demes sizes are modified.

Parameters

SEX	sex class container index
from_age	age class container index in the deme of origin
from_deme	index of the deme of origin
to_age	age class container index in the destination deme
to_deme	index of the destination deme
at	index of the focal individual in the 'from' deme

{//cout << "  add "<<get(SEX, from_age, at, from_deme)->getID()<<" to "<<to_deme<<endl;
  _vPatch[to_deme]->add( SEX, to_age, get(SEX, from_age, at, from_deme));
  //cout << "  remove "<<get(SEX, from_age, at, from_deme)->getID()<<" from "<<from_deme<<endl;
  _vPatch[from_deme]->remove(SEX, from_age, at);
  //cout << "  sizes: "<<from_deme<<": "<<_vPatch[from_deme]->size(SEX, from_age)<<", "
  //     << to_deme << ": " <<_vPatch[to_deme]->size( SEX, to_age)<<endl;
}

References _vPatch, and get().

Referenced by LCE_Disperse_EvolDisp::evoldisp(), LCE_Disperse_EvolDisp::fixdisp(), LCE_Disperse_ConstDisp::MigratePatch(), LCE_Disperse_ConstDisp::MigratePatch_AbsorbingBorder(), and LCE_Disperse_ConstDisp::MigratePatchByNumber().

Here is the caller graph for this function:

◆ read_trait()

void Metapop::read_trait	(	int	trait_idx,
		BinaryStorageBuffer *	loader
	)

Iterates through the individuals containers to retrieve the trait data from a binary file.

{ 
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    
    //first offspring:
    for(unsigned int j = 0; j < _vPatch[i]->size(FEM, OFFSx); ++j){
      _vPatch[i]->get(FEM, OFFSx, j)->getTrait(trait_idx)->retrieve_data(loader);       
    }
    
    for(unsigned int j = 0; j < _vPatch[i]->size(MAL, OFFSx); ++j){
      _vPatch[i]->get(MAL, OFFSx, j)->getTrait(trait_idx)->retrieve_data(loader);       
    }
    
    //then adults:
    for(unsigned int j = 0; j < _vPatch[i]->size(FEM, ADLTx); ++j)
      _vPatch[i]->get(FEM, ADLTx, j)->getTrait(trait_idx)->retrieve_data(loader);
    
    for(unsigned int j = 0; j < _vPatch[i]->size(MAL, ADLTx); ++j)
      _vPatch[i]->get(MAL, ADLTx, j)->getTrait(trait_idx)->retrieve_data(loader);
  }
}

References _patchNbr, _vPatch, ADLTx, FEM, get(), Individual::getTrait(), MAL, OFFSx, and StorableComponent::retrieve_data().

Referenced by retrieve_data().

Here is the caller graph for this function:

◆ removePatch()

Patch * Metapop::removePatch ( unsigned int i )

inline

Removes a patch from the patch array and returns it pointer.

The patch and its content are NOT deleted. The IDs of the remaining patches are NOT updated.

Parameters

i	the index of the patch to remove.

{
  Patch* patch = getPatchPtr(i);
  _vPatch.erase(_vPatch.begin() + i);
  return patch;
}

References _vPatch, and getPatchPtr().

Referenced by LCE_Resize::buildNewPatchArrayWithBackup(), FileServices::getSampledPop(), and LCE_Resize::removeDesignatedPatch().

Here is the caller graph for this function:

◆ reset()

void Metapop::reset ( )

Called to empty the patches, individuals are move to the garbage collector.

Resets each Patch, all individuals are moved to the POOL.

{
  unsigned int i;
  
  for(i = 0; i < _patchNbr; ++i) {
    _vPatch[i]->flush(this);
    _vPatch[i]->reset_counters();
  }
}

References _patchNbr, and _vPatch.

Referenced by LCE_Breed_Wolbachia::execute().

Here is the caller graph for this function:

◆ resetParameterFromSource()

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

inlinevirtual

Implements SimComponent.

238{return false;}

Referenced by loadPopFromBinarySource().

Here is the caller graph for this function:

◆ resizePatchArray()

void Metapop::resizePatchArray ( )

Resets the patch container to the right number of patches as set by _patchNbr.

Called at the beginning of each new simulation. Extra patches are destroyed and new ones are added if missing.

{
  //reset the right number of patches for the new simulation
  if(_vPatch.size() > _patchNbr) {
    while(_vPatch.size() > _patchNbr) {
      delete _vPatch[0];
      _vPatch.pop_front();
    }
  } else while(_vPatch.size() < _patchNbr) _vPatch.push_back(new Patch());
}

References _patchNbr, and _vPatch.

Referenced by buildPatchArray(), and updatePatchArray().

Here is the caller graph for this function:

◆ retrieve_data()

bool Metapop::retrieve_data ( BinaryStorageBuffer * reader )

virtual

Implements StorableComponent.

{
#ifdef _DEBUG_ 
  message("Metapop::retrieve_data, %iB of data read so far\n",loader->getBytesOut()); 
#endif
  unsigned int *sizes[3], dummy_int;
  unsigned char separator[2];
  
  sizes[0] = new unsigned int [_patchNbr]; 
  sizes[1] = new unsigned int [_patchNbr]; 
  sizes[2] = new unsigned int [_patchNbr];
  
  loader->read(&separator, 2 * sizeof(unsigned char));
  
  if(separator[0] != '@' || separator[1] != 'P')
    return error("Binary file appears corrupted:\n\
 >>>> Metapop::retrieve_data::wrong population seprarator\n");
  
  // read patch number
  loader->read(&dummy_int, sizeof(unsigned int));
  
  if(dummy_int != _patchNbr)
    return error("Population in binary file differs from simulation settings:\n\
 >>>> Metapop::retrieve_data:number of Patch differ from parameter value\n");
 
  //get the Patch sizes
  //offspring
  loader->read(sizes[0], _patchNbr * sizeof(unsigned int));
  //females adults
  loader->read(sizes[1], _patchNbr * sizeof(unsigned int));
  //males adults
  loader->read(sizes[2], _patchNbr * sizeof(unsigned int));
  
  Individual* ind;
  unsigned int bytes_cnt = loader->getBytesOut();
  //retrieve all individual informations: IDs, matings, etc.
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    //first, offspring:
    for(unsigned int j = 0; j < sizes[0][i]; ++j) {
      ind = this->getNewIndividual();
      ind->retrieve_data(loader);
      _vPatch[i]->add(ind->getSex(), OFFSx, ind);       
    }
    //then adult females:
    for(unsigned int j = 0; j < sizes[1][i]; ++j) {
      ind = this->getNewIndividual();
      ind->retrieve_data(loader);
      _vPatch[i]->add(FEM, ADLTx, ind);
    }
    //and adult males:
    for(unsigned int j = 0; j < sizes[2][i]; ++j) {
      ind = this->getNewIndividual();
      ind->retrieve_data(loader);
      _vPatch[i]->add(MAL, ADLTx, ind);
    }
    
  }
  
#ifdef _DEBUG_ 
  message("Metapop::retrieve_data::retrieved %ikB of ind data (%i individuals)\n",
          (loader->getBytesOut()-bytes_cnt)/1024, size()); 
#endif
  //retrieve traits sequences
  map<trait_t, TraitPrototype *>::iterator tt = _protoTraits.begin();
  
  char trait_name[6] = {'\0','\0','\0','\0','\0','\0'};
  
  unsigned int trait_cntr = 0;
  
  loader->read(&separator, 2 * sizeof(unsigned char));
  
  if(separator[0] != '@' || separator[1] != 'T') {
    error("Binary file appears corrupted:\n >>>> Metapop::retrieve_data::wrong trait seprarator\n");
    return false;
  }
  
  bytes_cnt = loader->getBytesOut();
  
  do {
    //get the trait type:
    loader->read(&trait_name[0], TRAIT_T_MAX);
    
    string dummy_trait(trait_name);
    
    //get the prototype:
    tt = _protoTraits.find(dummy_trait);
    
    if( tt == _protoTraits.end() )
      return error("Trait(s) in binary file differ from simulation settings:\n\
 >>>> Metapop::retrieve_data::trait in file not present in prototype\n");
 
    //then ask the prototype to retrieve its data:
    tt->second->retrieve_data(loader);
    
#ifdef _DEBUG_ 
    message("%iB of trait data read so far (trait %s)\n",loader->getBytesOut()-bytes_cnt,tt->first.c_str()); 
#endif
    
    //get the traits data:
    read_trait(tt->second->get_index(), loader);
    
    trait_cntr++;
    
    //get the next separator, should be present if right number of bytes have been read
    loader->read(&separator, 2 * sizeof(unsigned char));
    
    
  } while (separator[0] == '@' && separator[1] == 'T') ;
  
#ifdef _DEBUG_ 
  message("Metapop::retrieve_data::retrieved %ikB of trait data\n",(loader->getBytesOut()-bytes_cnt)/1024); 
#endif
  
  if(trait_cntr != _protoTraits.size())
    return error("Trait(s) in binary file differ from simulation settings:\n\
 >>>> Metapop::retrieve_data::some traits are missing from binary file\n");
 
  if(separator[0] != '@') 
    return error("Binary file appears corrupted:\n\
 >>>> Metapop::retrieve_data::separator not found at end of pop record!\n");
  
  for(unsigned int i = 0; i < 3; i++)
    delete [] sizes[i];
  
  return true;
}

References _patchNbr, IndFactory::_protoTraits, _vPatch, ADLTx, error(), FEM, BinaryStorageBuffer::getBytesOut(), IndFactory::getNewIndividual(), Individual::getSex(), MAL, message(), OFFSx, BinaryStorageBuffer::read(), read_trait(), Individual::retrieve_data(), size(), and TRAIT_T_MAX.

Referenced by BinaryDataLoader::extractPop().

Here is the caller graph for this function:

◆ setCurrentAge() [1/2]

void Metapop::setCurrentAge ( age_t age )

inline

Sets the age flag.

Parameters

age	the current age.

301{_currentAge = age;}

References _currentAge.

Referenced by LCE_Cross::generatePedigree(), FileServices::getSampledPop(), loadSourcePopulation(), and SimRunner::step().

Here is the caller graph for this function:

◆ setCurrentAge() [2/2]

void Metapop::setCurrentAge ( LifeCycleEvent * LCE )

Set the age flag from a LifeCycleEvent object.

Parameters

LCE	the LifeCycleEvent object.

{
  _currentAge ^= LCE->removeAgeClass();
  _currentAge |= LCE->addAgeClass();
}

References _currentAge, LifeCycleEvent::addAgeClass(), and LifeCycleEvent::removeAgeClass().

◆ setCurrentGeneration()

void Metapop::setCurrentGeneration ( unsigned int gen )

inline

296{_currentGeneration = gen;}

References _currentGeneration.

Referenced by SimRunner::Cycle(), SimRunner::Replicate_LOOP(), SimRunner::setCurrentGeneration(), and SimRunner::setForFirstGeneration().

Here is the caller graph for this function:

◆ setCurrentReplicate()

void Metapop::setCurrentReplicate ( unsigned int repl )

inline

295{_currentReplicate = repl;}

References _currentReplicate.

Referenced by SimRunner::Replicate_LOOP(), and SimRunner::setCurrentReplicate().

Here is the caller graph for this function:

◆ setGenerations()

void Metapop::setGenerations ( unsigned int gen )

inline

272{_generations = gen;}

References _generations.

Referenced by SimRunner::init_components(), and SimRunner::setGenerations().

Here is the caller graph for this function:

◆ setMPImanager()

void Metapop::setMPImanager ( MPImanager * mgr )

inline

174{_mpimgr = mgr;}

References _mpimgr.

Referenced by BinaryDataLoader::extractPop().

Here is the caller graph for this function:

◆ setParameters()

bool Metapop::setParameters ( )

virtual

Implements SimComponent.

{
  if(!setPopulationParameters()) return false;
  if(!setSourceParameters()) return false;
  return true;
}

References setPopulationParameters(), and setSourceParameters().

Referenced by BinaryDataLoader::extractPop(), and init().

Here is the caller graph for this function:

◆ setPatchCapacities() [1/4]

void Metapop::setPatchCapacities ( )

Sets the deme capacity matrix from parameter values.

{
  _patchSizes.reset(2, _patchNbr);
  
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    _patchSizes.set(FEM, i, _patchKfem);
    _patchSizes.set(MAL, i, _patchKmal);
  }
}

References _patchKfem, _patchKmal, _patchNbr, _patchSizes, FEM, MAL, TMatrix::reset(), and TMatrix::set().

Referenced by setPopulationParameters().

Here is the caller graph for this function:

◆ setPatchCapacities() [2/4]

void Metapop::setPatchCapacities	(	sex_t	SEX,
		string	param
	)

Builds the new population from a matrix of deme sizes but for one sex only.

Sizes for the other sex class(es) must be given separately.

Parameters

SEX	the sex class of the given deme sizes.
param	the name of the parameter to take the matrix argument from.

{
  double* size_array;
  unsigned int size_, Knum;
  TMatrix popK;
  
  _paramSet->getMatrix(param, &popK);
  
  Knum = popK.length();
  
  if(_patchNbr == 0 || _patchNbr < Knum)  _patchNbr = Knum;
  
  _patchSizes.reset(2, _patchNbr);
  
  size_array = popK.get();
  
  if(SEX == FEM)
    size_ = _patchKmal;
  else
    size_ = _patchKfem;
  
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    _patchSizes.set(SEX, i, (unsigned int)size_array[i % Knum]);
    _patchSizes.set(!SEX, i, size_);
  }
}

References SimComponent::_paramSet, _patchKfem, _patchKmal, _patchNbr, _patchSizes, FEM, TMatrix::get(), ParamSet::getMatrix(), TMatrix::length(), TMatrix::reset(), and TMatrix::set().

◆ setPatchCapacities() [3/4]

void Metapop::setPatchCapacities ( string param )

Builds the new population from a single matrix of deme sizes.

The sex-specific patch capacities will be half of the numbers given in the matrix.

Parameters

param the name of the parameter to take the matrix argument from.

{
  double* size_array;
  unsigned int Knum;
  TMatrix popK;
  
  _paramSet->getMatrix(param, &popK);
  
  Knum = popK.length();
  
  if(_patchNbr == 0 || _patchNbr < Knum)  _patchNbr = Knum;
  
  _patchSizes.reset(2, _patchNbr);
  
  size_array = popK.get();
  
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    _patchSizes.set(FEM, i, (unsigned int)size_array[i % Knum]/2);
    _patchSizes.set(MAL, i, (unsigned int)size_array[i % Knum]/2);
  }
}

References SimComponent::_paramSet, _patchNbr, _patchSizes, FEM, TMatrix::get(), ParamSet::getMatrix(), TMatrix::length(), MAL, TMatrix::reset(), and TMatrix::set().

◆ setPatchCapacities() [4/4]

void Metapop::setPatchCapacities	(	string	paramfem,
		string	parammal
	)

Builds the new population from matrices of deme sizes.

Parameters

paramfem	the name of the parameter to take the matrix argument from.
parammal	the name of the parameter to take the matrix argument from.

{
  double *size_fem, *size_mal;
  unsigned int KFnum, KMnum;
  TMatrix popKfem, popKmal;
  
  _paramSet->getMatrix(paramfem,&popKfem);
  _paramSet->getMatrix(parammal,&popKmal);
  
  KFnum = popKfem.length();
  KMnum = popKmal.length();
  
  if(_patchNbr == 0 && KFnum != KMnum){
    warning("not same number of elements in females and males capacity matrices!\n");
    warning("setting the number of populations from size of longest capacity array (= %i).\n",max(KFnum, KMnum));
  }
  if(_patchNbr < max(KFnum, KMnum)) _patchNbr = max(KFnum, KMnum);
  
  _patchSizes.reset(2, _patchNbr);
  
  size_fem = popKfem.get();
  size_mal = popKmal.get();
  
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    _patchSizes.set(FEM, i, (unsigned int)size_fem[i % KFnum]);
    _patchSizes.set(MAL, i, (unsigned int)size_mal[i % KMnum]);
  }   
}

References SimComponent::_paramSet, _patchNbr, _patchSizes, FEM, TMatrix::get(), ParamSet::getMatrix(), TMatrix::length(), MAL, TMatrix::reset(), TMatrix::set(), and warning().

◆ setPatchNbr()

void Metapop::setPatchNbr ( unsigned int val )

inline

287{_patchNbr = val;}

References _patchNbr.

Referenced by FileServices::getSampledPop().

Here is the caller graph for this function:

◆ setPatchSizes()

void Metapop::setPatchSizes ( TMatrix & mat )

inline

288{_patchSizes.copy(mat);}

TMatrix::copy

void copy(const TMatrix &mat)

Copy a matrix.

Definition: tmatrix.h:77

References _patchSizes, and TMatrix::copy().

Referenced by FileServices::getSampledPop().

Here is the caller graph for this function:

◆ setPopulation()

void Metapop::setPopulation	(	unsigned int	currentReplicate,
		unsigned int	replicates
	)

Sets the population for the first generation of each replicates.

{
#ifdef _DEBUG_
  message("\n+++Metapop::setPopulation: ");
  fflush(stdout);
#endif
  
  _currentReplicate = currentReplicate;
  
 
  //reset the population parameters, they may have changed during the life cycle
  setPopulationParameters();
 
 
  //reset the patch array, flush the patches and reset the patch capacities.
  buildPatchArray();
  
  _currentAge = NONE;
  
  //find the age class required to start the life cycle with:
  if(_requiredAge == NONE) 
    _requiredAge = SIMenv::MainSim->getFirstRequiredAgeInLifeCycle();
  
 
#ifdef _DEBUG_
  message("required age is: %i ", _requiredAge);
  fflush(stdout);
#endif
 
  //load first generation from a source population
  if(_source_load) {
    
    //delete ind in recycler, needed when dealing with large source pop and lots of replicates:
    
    purgeRecyclingPOOL();
    
    _source_load_periodicity = (unsigned int)ceil((double)replicates/_source_replicates);
    
    // check whether we need to read in a new binary file
    if(currentReplicate == 1 ||
       _source_replicates >= replicates || //load from a different source every replicate
       !(_source_replicates != 0 && (currentReplicate - 1) % _source_load_periodicity) ) {
         //change source every _source_replicates-nth replicates
      
      // load the population from the input file
      // a new metapop object will be created to hold the individuals
      // from the source
      // _loader.extractPop() will be called
      // some current parameters may be reset to match parameter values in the source pop
      
      loadSourcePopulation();
    }
    
    if(_source_filetype == ".bin") {
      // once the data is loaded in the _source Metapop, we can use it to fill in the current Metapop:
      // this only applies to binary file loading, trait file loading is done directly
      if(_source_preserve) {
 
        //load in preserve mode
        // i.e. make a copy of the saved pop
        // the population structure in the source is preserved
        // patches are loaded sequentially using the same patch index as in the source
        // the number of individuals loaded per patch will match that of the source
 
        setPopulationFromSourceInPreserveMode();
 
      } else {
 
        // the individuals are put in a big bag, destroying the existing structure
        // individuals will be randomly drawn from this bag with replacement
 
        setPopulationFromSource();
 
      }
 
    }
    
  } else {
    
    //not source_load, use regular set routine
    
    for(unsigned int i = 0; i < _patchNbr; ++i)
      _vPatch[i]->setNewGeneration( _requiredAge, this );
    
    _currentAge = _requiredAge;
    
  }
  
#ifdef _DEBUG_
  message("+++loaded age is: %i \n", _currentAge);
#endif
  
  if(_currentAge == NONE && size() == 0)
    warning("Metapop::setPopulation: generation 0 is empty!!\n");
}

References _currentAge, _currentReplicate, _patchNbr, _requiredAge, _source_filetype, _source_load, _source_load_periodicity, _source_preserve, _source_replicates, _vPatch, buildPatchArray(), SimBuilder::getFirstRequiredAgeInLifeCycle(), loadSourcePopulation(), SIMenv::MainSim, message(), NONE, IndFactory::purgeRecyclingPOOL(), setPopulationFromSource(), setPopulationFromSourceInPreserveMode(), setPopulationParameters(), size(), and warning().

Referenced by SimRunner::setForFirstGeneration().

Here is the caller graph for this function:

◆ setPopulationFromSource()

void Metapop::setPopulationFromSource ( )

{
  //load in non-preserve mode, i.e. use saved pop as a source of new individuals
  //individuals are drawn without replacement, sex and age are preserved.
  deque< Individual* > src_fem_pool;
  deque< Individual* > src_mal_pool;
  
  if( _requiredAge & OFFSPRG ) {
    
    if(_source->size(OFFSPRG) != 0)
      _source->getAllIndividuals(OFFSx, src_fem_pool, src_mal_pool);
    else {
      warning("source population does not contain offspring individuals, using adults instead.\n"); 
      //total size of source has been checked before
      _source->getAllIndividuals(ADLTx, src_fem_pool, src_mal_pool);
    }
    
    fillPopulationFromSource(OFFSx, FEM, src_fem_pool);
    fillPopulationFromSource(OFFSx, MAL, src_mal_pool);
    src_fem_pool.clear();
    src_mal_pool.clear();
    
    _currentAge |= OFFSPRG;
  }
  
  if( _requiredAge & ADULTS ) {
    
    if(_source->size(ADULTS) != 0)
      _source->getAllIndividuals(ADLTx, src_fem_pool, src_mal_pool);
    else {
      warning("source population does not contain adult individuals, using offspring instead.\n"); 
      //total size of source has been checked before
      _source->getAllIndividuals(OFFSx, src_fem_pool, src_mal_pool);
    }
    
    fillPopulationFromSource(ADLTx, FEM, src_fem_pool);
    fillPopulationFromSource(ADLTx, MAL, src_mal_pool);
    src_fem_pool.clear();
    src_mal_pool.clear();
    
    _currentAge |= ADULTS;
  }
  
} 

References _currentAge, _requiredAge, _source, ADLTx, ADULTS, FEM, fillPopulationFromSource(), getAllIndividuals(), MAL, OFFSPRG, OFFSx, size(), and warning().

Referenced by setPopulation().

Here is the caller graph for this function:

◆ setPopulationFromSourceInPreserveMode()

void Metapop::setPopulationFromSourceInPreserveMode ( )

{
  Patch* src_patch;
  age_t source_age;
  
  // set the number of patches to load relative to the number present in the source
  unsigned int num_patch = (unsigned int)min((double)_vPatch.size(), (double)_source->getPatchNbr());
   
  if(_requiredAge != NONE && _source->size(_requiredAge) == 0 && _source->size() != 0) {
    
    source_age = _source->getCurrentAge();
    
    warning("required age %i not present in source, using age class %i instead (preserve mode).\n"
            ,_requiredAge,source_age);
    
    for(unsigned int i = 0; i < num_patch; ++i) {
 
      src_patch = _source->getPatchPtr(i);
 
      fillPatchFromSource(FEM, src_patch, _vPatch[i], source_age);
      fillPatchFromSource(MAL, src_patch, _vPatch[i], source_age);
    }
    
  } else {
    
    if (_requiredAge == NONE) _requiredAge = ALL;
    
    for(unsigned int i = 0; i < num_patch; ++i) {
 
      src_patch = _source->getPatchPtr(i);
 
      if(_requiredAge & OFFSPRG) {
        fillPatchFromSource(FEM, src_patch, _vPatch[i], OFFSPRG);
        fillPatchFromSource(MAL, src_patch, _vPatch[i], OFFSPRG);
      }
 
      if(_requiredAge & ADULTS) {
        fillPatchFromSource(FEM, src_patch, _vPatch[i], ADULTS);
        fillPatchFromSource(MAL, src_patch, _vPatch[i], ADULTS);
      }
    }
  }
  
  if(size( ADULTS ) != 0)
    _currentAge |= ADULTS;
  
  if(size( OFFSPRG ) != 0)
    _currentAge |= OFFSPRG;
  
#ifdef _DEBUG_
  message("+++pop set from source: offspring: %i f, %i m; adults: %i f, %i m\n", size(FEM,OFFSPRG),
      size(MAL,OFFSPRG), size(FEM,ADULTS), size(MAL,ADULTS));
#endif
} 

References _currentAge, _requiredAge, _source, _vPatch, ADULTS, ALL, FEM, fillPatchFromSource(), getCurrentAge(), getPatchNbr(), getPatchPtr(), MAL, message(), NONE, OFFSPRG, size(), and warning().

Referenced by setPopulation().

Here is the caller graph for this function:

◆ setPopulationParameters()

bool Metapop::setPopulationParameters ( )

Population's size parameters initializing procedure.

{
 
  //population structure:
  if(_paramSet->isSet("patch_number")) 
    _patchNbr = (unsigned int)_paramSet->getValue("patch_number");
  else _patchNbr = 0;
  
  if(_paramSet->isSet("patch_capacity")) {
    
    if( _paramSet->isMatrix("patch_capacity") ) {
      
      setPatchCapacities("patch_capacity");
      
    } else if( !(_paramSet->isSet("patch_number")) ) {
      
      return error("param \"patch_number\" is missing!\n");;
      
    } else {
      _patchK = (unsigned int)_paramSet->getValue("patch_capacity");
      _patchKfem = _patchKmal = _patchK/2;
      setPatchCapacities();
    }
    
  } else if(_paramSet->isSet("patch_nbfem") && _paramSet->isSet("patch_nbmal")) {
    
    if( !(_paramSet->isMatrix("patch_nbfem")) && !(_paramSet->isMatrix("patch_nbmal")) ) {
      
      if( !(_paramSet->isSet("patch_number")) ) {
        
        return error("param \"patch_number\" is missing!\n");;
        
      } else {
        _patchKfem = (unsigned int)_paramSet->getValue("patch_nbfem");
        _patchKmal = (unsigned int)_paramSet->getValue("patch_nbmal");
        _patchK = _patchKfem + _patchKmal;
        setPatchCapacities();
      }
      
    } else {
      
      if( !(_paramSet->isMatrix("patch_nbfem")) && _paramSet->isMatrix("patch_nbmal") ) {
        _patchKfem = (unsigned int)_paramSet->getValue("patch_nbfem");
        setPatchCapacities(MAL,"patch_nbmal");
      } else if( _paramSet->isMatrix("patch_nbfem") && !(_paramSet->isMatrix("patch_nbmal")) ) {
        _patchKmal = (unsigned int)_paramSet->getValue("patch_nbmal");
        setPatchCapacities(FEM,"patch_nbfem");
      } else
        setPatchCapacities("patch_nbfem","patch_nbmal");
    }
    
  } else {
    return error("population parameters are not properly set!\n");;
  }
 
  return true;
}

References SimComponent::_paramSet, _patchK, _patchKfem, _patchKmal, _patchNbr, error(), FEM, ParamSet::getValue(), ParamSet::isMatrix(), ParamSet::isSet(), MAL, and setPatchCapacities().

Referenced by LCE_Resize::execute(), setParameters(), setPopulation(), and updatePopulationParameters().

Here is the caller graph for this function:

◆ setReplicates()

void Metapop::setReplicates ( unsigned int repl )

inline

274{_replicates = repl;}

References _replicates.

Referenced by SimRunner::init_components(), and SimRunner::setReplicates().

Here is the caller graph for this function:

◆ setSourceParameters()

bool Metapop::setSourceParameters ( )

Setter for source population parameters.

{
  if(_paramSet->isSet("source_pop")) {
 
    _source_load = true;
    _source_name = _paramSet->getArg("source_pop");
    _source_preserve = _paramSet->isSet("source_preserve");
    _source_replicates = _paramSet->isSet("source_replicates") ? 
                         (unsigned int)_paramSet->getValue("source_replicates") : 0;
    
    _source_replicate_digits = _paramSet->isSet("source_replicate_digit") ? 
                            (unsigned int)_paramSet->getValue("source_replicate_digit") : 1;
    
    _source_start_at_replicate = _paramSet->isSet("source_start_at_replicate") ? 
                         (unsigned int)_paramSet->getValue("source_start_at_replicate") : 1;
    
    _source_generation = _paramSet->isSet("source_generation") ? 
                        (unsigned int)_paramSet->getValue("source_generation") : 0;
    
    if(_paramSet->isSet("source_file_type"))
      _source_filetype = _paramSet->getArg("source_file_type");
    else
      _source_filetype = ".bin";
    
    _source_required_age = _paramSet->getArg("source_fill_age_class");
    
    if(_source_required_age.length() == 0) _requiredAge = NONE;
    else if(_source_required_age == "OFFSPRG" || _source_required_age == "offspring" ||
            _source_required_age == "0"){
      _requiredAge = OFFSPRG;
    } else if(_source_required_age=="ADULTS" || _source_required_age=="adults" ||
              _source_required_age=="1") {
      _requiredAge = ADULTS;
    } else if(_source_required_age=="ALL" || _source_required_age=="all") {
          _requiredAge = ALL;
    } else
      _requiredAge = NONE; //for now...
    
    
    // source parameter override:
    // a set of parameters that need to be set from the values stored in the source
    // e.g. the fitness effects of the deleterious mutations
    _source_param_override.clear();
 
    if( _paramSet->isSet("source_parameter_override")) {
 
      if( get_parameter("source_parameter_override")->hasMultipleArgs() )
      {
        _source_param_override = get_parameter("source_parameter_override")->getMultiArgs();
      }
      else
      {
        _source_param_override.push_back(get_parameter("source_parameter_override")->getArg());
      }
    }
 
 
  } else {
    _source = NULL;
    _source_preserve = false;
    _source_load = false;
    _source_replicates = 0;
    _source_generation = 0;
    _source_name = "";
    _source_filetype = ".bin";
    _source_param_override.clear();
  }
  return true;
}

References SimComponent::_paramSet, _requiredAge, _source, _source_filetype, _source_generation, _source_load, _source_name, _source_param_override, _source_preserve, _source_replicate_digits, _source_replicates, _source_required_age, _source_start_at_replicate, ADULTS, ALL, SimComponent::get_parameter(), ParamSet::getArg(), Param::getMultiArgs(), ParamSet::getValue(), Param::hasMultipleArgs(), ParamSet::isSet(), NONE, and OFFSPRG.

Referenced by Metapop(), and setParameters().

Here is the caller graph for this function:

◆ show_up()

void Metapop::show_up ( )

{
  message("Metapop:\n");
  message("nbre. of patches: %i(%i)\n", _vPatch.size(),_patchNbr);
  message("population size : %i\n", size());
  message("K = %i, K_fem = %i, K_mal = %i\n",_patchK, _patchKfem, _patchKmal);
  message("patch capacities: \n");
  _patchSizes.show_up();
  message("Patches:\n");
  for(unsigned int i = 0; i < _vPatch.size(); i++)
    _vPatch[i]->show_up();
}

References _patchK, _patchKfem, _patchKmal, _patchNbr, _patchSizes, _vPatch, message(), show_up(), TMatrix::show_up(), and size().

Referenced by FileServices::getSampledPop(), and show_up().

Here is the caller graph for this function:

◆ size() [1/9]

unsigned int Metapop::size ( )

inline

Get the total number of individuals present in the population, all sex and age classes together.

310{return size(ALL);}

References ALL, and size().

◆ size() [2/9]

unsigned int Metapop::size ( age_idx IDX )

inline

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

Parameters

IDX	the index of the age class

{ 
  return size(FEM, IDX) + size(MAL, IDX); 
}

References FEM, MAL, and size().

◆ size() [3/9]

unsigned int Metapop::size	(	age_idx	IDX,
		unsigned int	deme
	)

inline

{ 
  return size(FEM, IDX, deme) + size(MAL, IDX, deme); 
}

References FEM, MAL, and size().

◆ size() [4/9]

unsigned int Metapop::size ( age_t AGE )

inline

Simplified interface to get the size of both sexes of the appropriate age class(es) in the whole population.

Parameters

AGE	age class flags

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

References FEM, MAL, and size().

◆ size() [5/9]

unsigned int Metapop::size	(	age_t	AGE,
		unsigned int	deme
	)

inline

Simplified interface to get the size of both sexes of the appropriate age class(es) in one patch.

Parameters

AGE	age class flags
deme	the focal deme

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

References FEM, MAL, and size().

◆ size() [6/9]

unsigned int Metapop::size	(	sex_t	SEX,
		age_idx	IDX
	)

inline

Interface to get the size of a praticular age class and sex class.

Parameters

SEX	sex class
IDX	index of age class

{
  unsigned int s = 0;
  for(unsigned int i = 0; i < _patchNbr; i++)
    s += _vPatch[i]->size(SEX, IDX);
  return s;
}

References _patchNbr, _vPatch, and size().

◆ size() [7/9]

unsigned int Metapop::size	(	sex_t	SEX,
		age_idx	IDX,
		unsigned int	deme
	)

inline

{
  return _vPatch[deme]->size(SEX, IDX);
}

References _vPatch.

◆ size() [8/9]

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

inline

Interface to get the size of a praticular age and sex class(es).

Parameters

AGE	age class flags
SEX	sex class

{
  unsigned int s = 0;
  for(unsigned int i = 0; i < _vPatch.size(); i++)
    s += _vPatch[i]->size(SEX, AGE);
  return s;
}

References _vPatch, and size().

◆ size() [9/9]

unsigned int Metapop::size	(	sex_t	SEX,
		age_t	AGE,
		unsigned int	deme
	)

inline

Interface to get the size of a praticular age and sex class within a patch.

Parameters

AGE	age class flags
SEX	sex class
deme	the focal patch

{
  Patch* patch = getPatch(deme);
  return (patch!=0? patch->size(SEX, AGE) : 0);
}  

References getPatch(), and Patch::size().

◆ store_data()

void Metapop::store_data ( BinaryStorageBuffer * saver )

virtual

Implements StorableComponent.

{
  unsigned int *sizes[3];
  unsigned char separator[2] = {'@','P'};
  
  sizes[0] = new unsigned int [_patchNbr]; 
  sizes[1] = new unsigned int [_patchNbr]; 
  sizes[2] = new unsigned int [_patchNbr];
  
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    sizes[0][i] = size(OFFSPRG,i);
    sizes[1][i] = size(FEM,ADULTS,i);
    sizes[2][i] = size(MAL,ADULTS,i);
  }
  //store the data, begin with pop separator and number of patches:
  saver->store(&separator, 2 * sizeof(unsigned char));
  
  saver->store(&_patchNbr, sizeof(unsigned int));
  //store the Patch sizes
  //offspring
  saver->store(sizes[0], _patchNbr * sizeof(unsigned int));
  //females adults
  saver->store(sizes[1], _patchNbr * sizeof(unsigned int));
  //males adults
  saver->store(sizes[2], _patchNbr * sizeof(unsigned int));
  
  int byte_count = saver->getTotByteRecorded();
  //record all individual informations: IDs, matings, etc.
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    //first offspring:
    for(unsigned int j = 0; j < _vPatch[i]->size(FEM,OFFSx); ++j)
      _vPatch[i]->get(FEM, OFFSx, j)->store_data(saver);        
    
    for(unsigned int j = 0; j < _vPatch[i]->size(MAL,OFFSx); ++j)
      _vPatch[i]->get(MAL, OFFSx, j)->store_data(saver);        
    
    //then adults:
    for(unsigned int j = 0; j < _vPatch[i]->size(FEM, ADLTx); ++j)
      _vPatch[i]->get(FEM, ADLTx, j)->store_data(saver);
    
    for(unsigned int j = 0; j < _vPatch[i]->size(MAL, ADLTx); ++j)
      _vPatch[i]->get(MAL, ADLTx, j)->store_data(saver);
  }
  
#ifdef _DEBUG_
  message("Metapop::store_data :stored %ikB of individual data (%i individuals)\n",
          (saver->getTotByteRecorded()-byte_count)/1024, size());
#endif
  
  //records the trait sequences:
  map<trait_t, TraitPrototype *> traits = this->getTraitPrototypes();
  map<trait_t, TraitPrototype *>::iterator tt = traits.begin();
  //  trait_t type;
  separator[1] = 'T'; //trait separator = '@T'
  
  byte_count = saver->getTotByteRecorded();
  
  while(tt != traits.end()) {
    saver->store(&separator, 2 * sizeof(unsigned char));
    //store the trait type:
    saver->store((void*)tt->first.c_str(), TRAIT_T_MAX); 
    
    //then ask the prototype to store its data:
    tt->second->store_data(saver);
    //store the traits data:
    store_trait(tt->second->get_index(), saver);
    
    tt++;
  }
#ifdef _DEBUG_
  message("Metapop::store_data :stored %ikB of traits data\n",
          (saver->getTotByteRecorded()-byte_count)/1024);
#endif
  
  for(unsigned int i = 0; i < 3; i++)
    delete [] sizes[i];
}

References _patchNbr, _vPatch, ADLTx, ADULTS, FEM, get(), BinaryStorageBuffer::getTotByteRecorded(), IndFactory::getTraitPrototypes(), MAL, message(), OFFSPRG, OFFSx, size(), BinaryStorageBuffer::store(), Individual::store_data(), store_trait(), and TRAIT_T_MAX.

Referenced by BinaryDataSaver::storeData().

Here is the caller graph for this function:

◆ store_trait()

void Metapop::store_trait	(	int	trait_idx,
		BinaryStorageBuffer *	saver
	)

Iterates through the individuals containers to store the trait data to a binary file.

{  
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    //first offspring:
    for(unsigned int j = 0; j < _vPatch[i]->size(FEM, OFFSx); ++j) {
      _vPatch[i]->get(FEM, OFFSx, j)->getTrait(trait_idx)->store_data(saver);   
    }
    
    for(unsigned int j = 0; j < _vPatch[i]->size(MAL, OFFSx); ++j) {
      _vPatch[i]->get(MAL, OFFSx, j)->getTrait(trait_idx)->store_data(saver);   
    }
    //then adults:
    for(unsigned int j = 0; j < _vPatch[i]->size(FEM, ADLTx); ++j)
      _vPatch[i]->get(FEM, ADLTx, j)->getTrait(trait_idx)->store_data(saver);
    
    for(unsigned int j = 0; j < _vPatch[i]->size(MAL, ADLTx); ++j)
      _vPatch[i]->get(MAL, ADLTx, j)->getTrait(trait_idx)->store_data(saver);
  }
}

References _patchNbr, _vPatch, ADLTx, FEM, get(), Individual::getTrait(), MAL, OFFSx, and StorableComponent::store_data().

Referenced by store_data().

Here is the caller graph for this function:

◆ updatePatchArray()

void Metapop::updatePatchArray ( )

Called during simulation to modify the meta-population size.

Patch number and capacities are updated, new patches are empty, existing patches containers are untouched.

{
  //remove or add patches as needed:
  resizePatchArray();
  //reset the patch capacities and patch ID:
  updatePatchState();
}

References resizePatchArray(), and updatePatchState().

Referenced by LCE_Resize::buildNewPatchArrayNoBackup(), and updatePopulationParameters().

Here is the caller graph for this function:

◆ updatePatchState()

void Metapop::updatePatchState ( )

Update the patch capacities and patch ID (reset to array position).

{
  //reset the patch capacities and patch ID:
  for(unsigned int i = 0; i < _patchNbr; ++i) {
    _vPatch[i]->setID(i);
    _vPatch[i]->set_K((unsigned int)_patchSizes.get(FEM,i) + (unsigned int)_patchSizes.get(MAL,i));
    _vPatch[i]->set_KFem((unsigned int)_patchSizes.get(FEM,i));
    _vPatch[i]->set_KMal((unsigned int)_patchSizes.get(MAL,i));
  }
}

References _patchNbr, _patchSizes, _vPatch, FEM, TMatrix::get(), and MAL.

Referenced by LCE_Resize::buildNewPatchArrayWithBackup(), and updatePatchArray().

Here is the caller graph for this function:

◆ updatePopulationParameters()

bool Metapop::updatePopulationParameters ( )

Called during simulation to change the population's parameters (temporal argument).

{
  if(!setPopulationParameters()) return false;
  updatePatchArray();
  //if we added patches, they will be empty
  //fusion of existing pop is not possible here, 
  //the individuals are flushed when deleting the patches
  return true;
}

References setPopulationParameters(), and updatePatchArray().

Referenced by Metapop().

Here is the caller graph for this function:

Friends And Related Function Documentation

◆ BinaryDataLoader::extractPop

Metapop * BinaryDataLoader::extractPop	(	std::string &	,
		unsigned int	,
		SimBuilder *	,
		Metapop *
	)

friend

Member Data Documentation

◆ _currentAge

age_t Metapop::_currentAge

private

The current age class, might be changed by the LCEs.

Referenced by getCurrentAge(), loadPopFromTraitFile(), setCurrentAge(), setPopulation(), setPopulationFromSource(), and setPopulationFromSourceInPreserveMode().

◆ _currentGeneration

unsigned int Metapop::_currentGeneration

private

The current generation in the generation loop, starts at 1.

Referenced by getCurrentGeneration(), and setCurrentGeneration().

◆ _currentReplicate

unsigned int Metapop::_currentReplicate

private

The current replicate in the replicate loop, starts at 1.

Referenced by getCurrentReplicate(), loadPopFromBinarySource(), loadSourcePopulation(), setCurrentReplicate(), and setPopulation().

◆ _generations

unsigned int Metapop::_generations

private

Number of generations to iterate.

Referenced by getGenerations(), and setGenerations().

◆ _loader

BinaryDataLoader Metapop::_loader

private

A BinaryDataLoader to load a population from a binary data file.

Referenced by loadPopFromBinarySource().

◆ _mpimgr

MPImanager* Metapop::_mpimgr

private

Referenced by BinaryDataLoader::extractPop(), and setMPImanager().

◆ _patchK

unsigned int Metapop::_patchK

private

Patch carrying capacity.

Referenced by getPatchCapacity(), setPopulationParameters(), and show_up().

◆ _patchKfem

unsigned int Metapop::_patchKfem

private

Sex specific carrying capacities.

Referenced by getPatchKFem(), setPatchCapacities(), setPopulationParameters(), and show_up().

◆ _patchKmal

unsigned int Metapop::_patchKmal

private

Referenced by getPatchKMal(), setPatchCapacities(), setPopulationParameters(), and show_up().

◆ _patchNbr

unsigned int Metapop::_patchNbr

private

Number of patches in the population.

Referenced by buildPatchArray(), clear(), fillPopulationFromSource(), flush(), getPatchNbr(), read_trait(), reset(), resizePatchArray(), retrieve_data(), setPatchCapacities(), setPatchNbr(), setPopulation(), setPopulationParameters(), show_up(), size(), store_data(), store_trait(), and updatePatchState().

◆ _patchSizes

TMatrix Metapop::_patchSizes

private

Matrix of the deme sizes, row 0 for the males, row 1 for the females.

Referenced by buildPatchArray(), getPatchCapacities(), getPatchCapacity(), setPatchCapacities(), setPatchSizes(), show_up(), and updatePatchState().

◆ _replicates

unsigned int Metapop::_replicates

private

Number of replicates to iterate.

Referenced by getReplicates(), loadSourcePopulation(), and setReplicates().

◆ _requiredAge

age_t Metapop::_requiredAge

private

The age class flag that is required to fill the population at the beginning of a replicate.

Referenced by fillPatchFromSource(), setPopulation(), setPopulationFromSource(), setPopulationFromSourceInPreserveMode(), and setSourceParameters().

◆ _source

Metapop* Metapop::_source

private

A source population as loaded from a binary data file, used to build a population.

Referenced by clear(), loadPopFromBinarySource(), loadPopFromTraitFile(), loadSourcePopulation(), setPopulationFromSource(), setPopulationFromSourceInPreserveMode(), and setSourceParameters().

◆ _source_filetype

std::string Metapop::_source_filetype

private

The trait type to load from.

Referenced by clear(), getSourceFileType(), loadPopFromTraitFile(), loadSourcePopulation(), setPopulation(), and setSourceParameters().

◆ _source_generation

unsigned int Metapop::_source_generation

private

The generation to load from the binary file source file.

Referenced by loadPopFromBinarySource(), and setSourceParameters().

◆ _source_load

bool Metapop::_source_load

private

Flage to specify that the population should be built from the binary loaded source population.

Referenced by isSourceLoad(), setPopulation(), and setSourceParameters().

◆ _source_load_periodicity

unsigned int Metapop::_source_load_periodicity

private

The number of replicates to source from a single source replicate.

Referenced by loadSourcePopulation(), and setPopulation().

◆ _source_name

std::string Metapop::_source_name

private

The base filename of source population files.

Referenced by getSourceName(), loadSourcePopulation(), and setSourceParameters().

◆ _source_param_override

vector< string > Metapop::_source_param_override

private

List of parameters whose values in the source should override local values in the loading pop.

Referenced by loadPopFromBinarySource(), and setSourceParameters().

◆ _source_preserve

bool Metapop::_source_preserve

private

Flag to specify the loading mode, true means the source pop is the actual population.

Referenced by setPopulation(), and setSourceParameters().

◆ _source_replicate_digits

unsigned int Metapop::_source_replicate_digits

private

Number of digits in the replicate counter filename extension.

Referenced by getSourceReplDigits(), loadSourcePopulation(), and setSourceParameters().

◆ _source_replicates

unsigned int Metapop::_source_replicates

private

The number of source files, each file being a different replicate of the source population.

Used to automatically build the source filename.

Referenced by loadSourcePopulation(), setPopulation(), and setSourceParameters().

◆ _source_required_age

std::string Metapop::_source_required_age

private

The age class to fill with the source population.

Referenced by setSourceParameters().

◆ _source_start_at_replicate

unsigned int Metapop::_source_start_at_replicate

private

The replicate number to start loading from.

Referenced by loadSourcePopulation(), and setSourceParameters().

◆ _statHandler

MPStatHandler Metapop::_statHandler

private

The stat handler for the population stats.

Referenced by loadStatServices().

◆ _vPatch

deque< Patch* > Metapop::_vPatch

private

◆ _writer

MPFileHandler* Metapop::_writer

private

The file handler used to save pedigree info.

Referenced by loadFileServices().

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

Public Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Metapop()

◆ ~Metapop()

Member Function Documentation

◆ addPatch() [1/2]

◆ addPatch() [2/2]

◆ buildPatchArray()

◆ clear()

◆ deletePatch()

◆ fillPatchFromSource()

◆ fillPopulationFromSource()

◆ flush() [1/4]

◆ flush() [2/4]

◆ flush() [3/4]

◆ flush() [4/4]

◆ get()

◆ getAllIndividuals()

◆ getCurrentAge()

◆ getCurrentGeneration()

◆ getCurrentReplicate()

◆ getGenerations()

◆ getPatch()

◆ getPatchArray()

◆ getPatchArraySize()

◆ getPatchCapacities()

◆ getPatchCapacity() [1/2]

◆ getPatchCapacity() [2/2]

◆ getPatchKFem()

◆ getPatchKMal()

◆ getPatchNbr()

◆ getPatchPtr()

◆ getReplicates()

◆ getSourceFileType()

◆ getSourceName()

◆ getSourceReplDigits()

◆ init()

◆ isAlive()

◆ isSourceLoad()

◆ loadFileServices()

◆ loadPopFromBinarySource()

◆ loadPopFromTraitFile()

◆ loadSourcePopulation()

◆ loadStatServices()

◆ move()

◆ read_trait()

◆ removePatch()

◆ reset()

◆ resetParameterFromSource()

◆ resizePatchArray()

◆ retrieve_data()

◆ setCurrentAge() [1/2]

◆ setCurrentAge() [2/2]

◆ setCurrentGeneration()

◆ setCurrentReplicate()

◆ setGenerations()

◆ setMPImanager()

◆ setParameters()

◆ setPatchCapacities() [1/4]

◆ setPatchCapacities() [2/4]

◆ setPatchCapacities() [3/4]

◆ setPatchCapacities() [4/4]

◆ setPatchNbr()

◆ setPatchSizes()

◆ setPopulation()

◆ setPopulationFromSource()

◆ setPopulationFromSourceInPreserveMode()

◆ setPopulationParameters()

◆ setReplicates()

◆ setSourceParameters()

◆ show_up()

◆ size() [1/9]

◆ size() [2/9]

◆ size() [3/9]

◆ size() [4/9]

◆ size() [5/9]