Nemo  2.3.56
Simulate forward-in-time genetic evolution in a spatially explicit, individual-based stochastic simulator
LCE_Breed_Selection_Disperse Class Reference

Composite LCE performing breeding, migration and viability selection all in one. More...

#include <LCEcomposite.h>

+ Inheritance diagram for LCE_Breed_Selection_Disperse:
+ Collaboration diagram for LCE_Breed_Selection_Disperse:

Public Member Functions

 LCE_Breed_Selection_Disperse ()
 
virtual ~LCE_Breed_Selection_Disperse ()
 
void breed_selection_disperse (int *counter)
 
void breed_selection_disperse_propagule (int *counter)
 
void do_breed (sex_t SEX, unsigned int size, int *counter, Patch *patch, unsigned int patchNbr)
 
Implementations
virtual bool setParameters ()
 
virtual void execute ()
 
virtual LifeCycleEventclone ()
 
virtual void loadFileServices (FileServices *loader)
 
virtual void loadStatServices (StatServices *loader)
 
virtual bool resetParameterFromSource (std::string param, SimComponent *cmpt)
 
virtual age_t removeAgeClass ()
 
virtual age_t addAgeClass ()
 
virtual age_t requiredAgeClass ()
 
- Public Member Functions inherited from LCE_Breed_Disperse
 LCE_Breed_Disperse ()
 
virtual ~LCE_Breed_Disperse ()
 
void do_breed_disperse ()
 
void do_breed_disperse_propagule ()
 
unsigned int numFemOffspring (Patch *patch)
 
unsigned int numFemOffspring_colonizers (Patch *patch)
 The number of females produced in case a max number of colonizers was specified. More...
 
unsigned int numMalOffspring_notrandom (Patch *patch)
 The number of males produced is always zero when the mating system is not random mating. More...
 
unsigned int numMalOffspring_random (Patch *patch)
 
unsigned int numMalOffspring_random_colonizers (Patch *patch)
 
unsigned int instantGrowth (Patch *patch, sex_t SEX)
 The number of offspring produced corresponds to the carrying capacity of the patch. More...
 
unsigned int logisticGrowth (Patch *patch, sex_t SEX)
 The number of offspring produced is given by the logistic growth function. More...
 
unsigned int stochasticLogisticGrowth (Patch *patch, sex_t SEX)
 The number of offspring produced is drawn from a Poisson with mean equal to the logistic growth predicate. More...
 
unsigned int conditionalLogisticGrowth (Patch *patch, sex_t SEX)
 The number of offspring produced depends on the adult density. More...
 
unsigned int conditionalStochasticLogisticGrowth (Patch *patch, sex_t SEX)
 The number of offspring produced depends on the adult density, similar to 'conditionalLogisticGrowth' except that this time, the fecundities are drawn from Poisson distributions. More...
 
unsigned int fixedFecundityGrowth (Patch *patch, sex_t SEX)
 The number of offspring produced is equal to the carrying capacity multiplied by the mean fecundity of the focal patch. More...
 
unsigned int stochasticFecundityGrowth (Patch *patch, sex_t SEX)
 The number of offspring produced is a random number drawn from a Poisson distribution with mean equal to the carrying capacity multiplied by the mean fecundity of the focal patch. More...
 
Individualmate_random (sex_t SEX, Patch *patch, unsigned int LocalPatch)
 
Individualmate_random_hermaphrodite (sex_t SEX, Patch *patch, unsigned int LocalPatch)
 
Individualmate_selfing (sex_t SEX, Patch *patch, unsigned int LocalPatch)
 
Individualmate_full_selfing (sex_t SEX, Patch *patch, unsigned int LocalPatch)
 
Individualmate_cloning (sex_t SEX, Patch *patch, unsigned int LocalPatch)
 
IndividualmakeOffspring (Individual *ind)
 
void breed_disperse (sex_t SEX, Patch *patch, unsigned int LocalPatch, unsigned int size)
 
Individualget_parent (sex_t SEX, sex_t DispSex, Patch *LocalPatch, unsigned int patchNbr)
 
- Public Member Functions inherited from LCE_Breed_base
 LCE_Breed_base ()
 
virtual ~LCE_Breed_base ()
 
virtual IndividualgetFatherPtr (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Calls the mating function according to the model chosen using the function pointer, used to get the father from the mother in a patch. More...
 
void NonWrightFisherPopulation ()
 
void WrightFisherPopulation ()
 
Individualbreed (Individual *mother, Individual *father, unsigned int LocalPatch)
 Makes a new individual with the right parents. More...
 
Individualbreed_cloning (Individual *mother, Individual *father, unsigned int LocalPatch)
 Makes a new individual by doing a deep copy of the mother (copies the mother's genes into the offspring). More...
 
IndividualmakeOffspring (Individual *ind)
 Last step of the breeding process, does inheritance and mutation of the parents' genes. More...
 
Individualdo_breed (Individual *mother, Individual *father, unsigned int LocalPatch)
 Calls the breeding function unsing its pointer. More...
 
bool checkMatingCondition (Patch *thePatch)
 Checks if any mating will take place in the patch passed as argument. More...
 
bool checkNoSelfing (Patch *thePatch)
 Checks whether mating will take place in the current patch when mating is not selfing or cloning. More...
 
bool checkPolygyny (Patch *thePatch)
 Checks whether mating will take place in the current patch when mating is polygynous. More...
 
bool checkSelfing (Patch *thePatch)
 Checks whether mating will take place in the current patch when mating is selfing. More...
 
bool checkCloning (Patch *thePatch)
 Checks whether mating will take place in the current patch when mating is cloning. More...
 
bool setMatingSystem ()
 
bool setFecundity ()
 
bool setSexRatio ()
 
double getMatingProportion ()
 
double getMeanFecundity (unsigned int patch)
 
int getMatingSystem ()
 
bool doInheritance ()
 
double getPoissonFecundity (double mean)
 
double getFixedFecundity (double mean)
 
double getGaussianFecundity (double mean)
 
double getLogNormalFecundity (double mean)
 
double getFecundity (unsigned int patch)
 
double getFecundity (double mean)
 
sex_t getOffsprgSex ()
 
sex_t getOffsprgSexRandom ()
 
sex_t getOffsprgSexFixed ()
 
sex_t getOffsprgSexSelfing ()
 
sex_t getOffsprgSexCloning ()
 
IndividualRandomMating (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a pointer to a male drawn randomly from a patch. More...
 
IndividualfullPolyginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a pointer to the alpha male of the patch. More...
 
IndividualfullPolyginy_manyMales (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a pointer to one of the first _mating_males males of the patch. More...
 
IndividualpartialPolyginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1, or the first male otherwise. More...
 
IndividualpartialPolyginy_manyMales (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1, or one of the _mating_males first males otherwise. More...
 
IndividualfullMonoginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a pointer to a male with same index as mother (if available) from the focal patch. More...
 
IndividualpartialMonoginy (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a pointer to a male with same index as mother (if available) from the focal patch. More...
 
IndividualfullSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns the mother pointer. More...
 
IndividualpartialSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns the mother pointer or a random female if _mating_proportion != 1. More...
 
Individualrandom_hermaphrodite (Patch *thePatch, Individual *mother, unsigned int motherIndex)
 Returns a random female from the patch, will be the same mother with probability 1/N (Wright-Fisher model). More...
 
- Public Member Functions inherited from LifeCycleEvent
 LifeCycleEvent (const char *name, const char *trait_link)
 Cstor. More...
 
virtual ~LifeCycleEvent ()
 
virtual void init (Metapop *popPtr)
 Sets the pointer to the current Metapop and the trait link if applicable. More...
 
virtual bool attach_trait (string trait)
 
virtual void set_paramset (std::string name, bool required, SimComponent *owner)
 
virtual void set_event_name (std::string &name)
 Set the name of the event (name of the ParamSet) and add the corresponding parameter to the set. More...
 
virtual void set_event_name (const char *name)
 
virtual string & get_event_name ()
 Accessor to the LCE's name. More...
 
virtual int get_rank ()
 Accessor to the LCE rank in the life cycle. More...
 
virtual void set_pop_ptr (Metapop *popPtr)
 Accessors for the population pointer. More...
 
virtual Metapopget_pop_ptr ()
 
- Public Member Functions inherited from SimComponent
 SimComponent ()
 
virtual ~SimComponent ()
 
virtual void loadUpdaters (UpdaterServices *loader)
 Loads the parameters and component updater onto the updater manager. More...
 
virtual void set_paramset (ParamSet *paramset)
 Sets the ParamSet member. More...
 
virtual void set_paramsetFromCopy (const ParamSet &PSet)
 Reset the set of parameters from a another set. More...
 
virtual ParamSetget_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 Paramget_parameter (std::string name)
 Param getter. More...
 
virtual double get_parameter_value (std::string name)
 Param value getter. More...
 
virtual string get_name ()
 Returnd the name of the ParamSet, i.e. More...
 
virtual bool has_parameter (std::string name)
 Param getter. More...
 
- Public Member Functions inherited from LCE_Disperse_base
 LCE_Disperse_base ()
 
virtual ~LCE_Disperse_base ()
 Deallocates the disp matrix. More...
 
bool setBaseParameters (string prefix)
 
void setParamPrefix (string pref)
 
void addParameters (string prefix, ParamUpdaterBase *updater)
 
void setIndentityDispMatrix (TMatrix *mat)
 
unsigned int getMigrationPatchForward (sex_t SEX, unsigned int LocalPatch)
 
unsigned int getMigrationPatchBackward (sex_t SEX, unsigned int LocalPatch)
 
void setPropaguleTargets ()
 
void swapPostDisp ()
 
void reset_counters ()
 
void set_isForward (bool val)
 
bool checkForwardDispersalMatrix (TMatrix *mat)
 
bool checkBackwardDispersalMatrix (TMatrix *mat)
 
void allocateDispMatrix (sex_t sex, unsigned int dim)
 
bool updateDispMatrix ()
 
bool setDispMatrix ()
 
bool setReducedMatricesBySex (sex_t SEX, Param &connectivity, Param &rate)
 
bool setReducedDispMatrix ()
 The reduced dispersal matrix contains the indices of the patches to which each patch is connected. More...
 
bool setIsland_MigrantPool_Matrix ()
 
bool setIsland_PropagulePool_Matrix ()
 
bool setSteppingStone1DMatrix ()
 
bool setLatticeMatrix ()
 Sets the dispersal matrices for the Lattice dispersal model. More...
 
bool setBasicLatticeMatrix (int rows, int cols, double phi_mal, double phi_fem, double disp_mal, double disp_fem)
 
bool setLatticeTorrusMatrix (int rows, int cols, double disp_mal, double disp_fem, TMatrix *grid)
 
bool setLatticeAbsorbingMatrix ()
 
bool setLatticeReflectingMatrix (int rows, int cols, TMatrix *grid)
 
bool isForward ()
 
bool isByNumber ()
 
unsigned int getDispersalModel ()
 
double getPropaguleProb ()
 
unsigned int getPropaguleTarget (unsigned int home)
 
- Public Member Functions inherited from LCE_Breed_Selection
 LCE_Breed_Selection ()
 
virtual ~LCE_Breed_Selection ()
 
bool setNonSelectedTraitTable ()
 Builds the vector of traits not under selection. More...
 
IndividualmakeOffspringWithSelection (Individual *ind, unsigned int natalpatch)
 Performs viability selection and breeding at the same time. More...
 
void do_breed_selection_FecFitness (Patch *patch, unsigned int patchID, unsigned int *cntr)
 
void do_breed_selection_OffSurvival (Patch *patch, unsigned int patchID, unsigned int *cntr)
 
void do_breed_selection_WrightFisher_2sex (Patch *patch, unsigned int patchID, unsigned int *cntr)
 
void do_breed_selection_WrightFisher_1sex (Patch *patch, unsigned int patchID, unsigned int *cntr)
 
void setReproScaledFitness_sum (sex_t SEX, valarray< double > &survival, unsigned int numReproFem, Patch *patch)
 
- Public Member Functions inherited from LCE_Selection_base
 LCE_Selection_base ()
 
virtual ~LCE_Selection_base ()
 
bool setSelectionMatrix ()
 
bool setLocalOptima ()
 
bool set_sel_model ()
 
bool set_fit_model ()
 
bool set_local_optima ()
 
bool set_param_rate_of_change ()
 
void set_std_rate_of_change ()
 
void addPhenotypicSD (unsigned int deme, double *stDev)
 
void changeLocalOptima ()
 
void resetCounters ()
 Resets the fitness counters. More...
 
void setMeans (unsigned int tot_ind)
 Computes the average fitness of each pedigree class. More...
 
double getMeanFitness (age_idx age)
 Computes the mean fitness of the whole population for a given age class. More...
 
double getMeanPatchFitness (age_idx age, unsigned int p)
 Computes the mean fitness in a given patch for a given age class. More...
 
double getMaxFitness (age_idx age)
 Computes the maximum fitness value of the whole population for a given age class. More...
 
double getMaxPatchFitness (age_idx age, unsigned int p)
 Computes the maximum fitness value in a given patch for a given age class. More...
 
double setMeanFitness (age_idx age)
 Sets the _mean_fitness variable to the value of the mean population fitness. More...
 
double getFitness (Individual *ind, unsigned int patch)
 Calls the fitness function according to the fitness model. More...
 
double getFitnessFixedEffect (Individual *offsprg, unsigned int patch, unsigned int trait)
 Returns the fitness of an individual in the fixed selection model. More...
 
double getFitnessDirect (Individual *offsprg, unsigned int patch, unsigned int trait)
 Returns the fitness of an individual following the direct selection model. More...
 
double getFitnessUnivariateQuadratic (Individual *ind, unsigned int patch, unsigned int trait)
 Quadratic fitness surface, approximates the Gaussian model for weak selection and/or small deviation from the optimum. More...
 
double getFitnessMultivariateGaussian (Individual *offsprg, unsigned int patch, unsigned int trait)
 Returns the fitness of an individual following the Gaussian selection model with one trait under selection. More...
 
double getFitnessUnivariateGaussian (Individual *offsprg, unsigned int patch, unsigned int trait)
 Returns the fitness of an individual following the Gaussian selection model with several traits under selection. More...
 
double getFitnessMultivariateGaussian_VE (Individual *offsprg, unsigned int patch, unsigned int trait)
 Returns the fitness of an individual following the Gaussian selection model with one trait under selection and environmental variance. More...
 
double getFitnessUnivariateGaussian_VE (Individual *offsprg, unsigned int patch, unsigned int trait)
 Returns the fitness of an individual following the Gaussian selection model with several traits under selection and environmental variance. More...
 
double getFitnessAbsolute (Individual *ind, unsigned int patch)
 Returns the raw fitness of the individual, without adjustment (absolute fitness). More...
 
double getFitnessRelative (Individual *ind, unsigned int patch)
 Returns the relative fitness of the individual, adjusted by a scaling factor. More...
 
void setScalingFactorLocal (age_idx age, unsigned int p)
 Sets the fitness scaling factor equal to the inverse of the mean local patch fitness. More...
 
void setScalingFactorGlobal (age_idx age, unsigned int p)
 Sets the fitness scaling factor equal to the inverse of the mean population fitness. More...
 
void setScalingFactorMaxLocal (age_idx age, unsigned int p)
 Sets the fitness scaling factor equal to the inverse of the maximum local patch fitness value. More...
 
void setScalingFactorMaxGlobal (age_idx age, unsigned int p)
 Sets the fitness scaling factor equal to the inverse of the maximum population fitness value. More...
 
void setScalingFactorAbsolute (age_idx age, unsigned int p)
 Resets the fitness scaling factor equal to one. More...
 
void doViabilitySelection (sex_t SEX, age_idx AGE, Patch *patch, unsigned int p)
 Selectively removes individuals in the population depending on their fitness. More...
 

Private Attributes

void(LCE_Breed_Selection_Disperse::* _breed_selection_disperse )(int *counter)
 

Additional Inherited Members

- Protected Attributes inherited from LCE_Breed_Disperse
Individual *(LCE_Breed_Disperse::* _make_offspring )(sex_t SEX, Patch *patch, unsigned int LocalPatch)
 
unsigned int(LCE_Breed_Disperse::* _get_numFemOffspring )(Patch *patch)
 
unsigned int(LCE_Breed_Disperse::* _get_numMalOffspring )(Patch *patch)
 
unsigned int(LCE_Breed_Disperse::* _get_patchFecundity )(Patch *patch, sex_t SEX)
 
- Protected Attributes inherited from LCE_Breed_base
void(LCE_Breed_base::* PopModelFuncPtr )(void)
 
TMatrix _mean_fecundity
 
- Protected Attributes inherited from LifeCycleEvent
std::string _event_name
 The param name to be read in the init file. More...
 
Metapop_popPtr
 The ptr to the current Metapop. More...
 
std::string _LCELinkedTraitType
 The name of the linked trait. More...
 
int _LCELinkedTraitIndex
 The index in the individual's trait table of the linked trait. More...
 
- Protected Attributes inherited from SimComponent
ParamSet_paramSet
 The parameters container. More...
 
- Protected Attributes inherited from LCE_Disperse_base
unsigned int _npatch
 Number of patches in the population. More...
 
vector< vector< double > > _reducedDispMat [2]
 Matrix containing the indexes of the patches connected to each patch. More...
 
vector< vector< double > > _reducedDispMatProba [2]
 Matrix containing the probability to migrate to/from the connected patches. More...
 
- Protected Attributes inherited from LCE_Selection_base
double _letheq
 
double _base_fitness
 
double _mean_fitness
 
double _max_fitness
 
double _scaling_factor
 
bool _is_local
 
bool _is_absolute
 
double _fitness [5]
 Fitness counters, one for each pedigree class. More...
 
double _survival [5]
 
double _ind_cntr [5]
 
vector< string > _Traits
 The list of trait types under selection. More...
 
vector< unsigned int_TraitIndices
 The indices of the traits under selection. More...
 
vector< string > _SelectionModels
 The selection models associated with each trait under selection. More...
 
LCE_SelectionSH_stater
 
LCE_SelectionFH_writer
 
int _selectTraitDimension
 Number of quantitative traits under selection. More...
 
vector< double > _selection_variance
 Patch-specific selection variance. More...
 
double _eVariance
 Evironmental variance. More...
 
vector< double(LCE_Selection_base::*)(Individual *, unsigned int, unsigned int) > _getRawFitness
 A vector containing pointers to fitness function related to each trait under selection. More...
 
double(LCE_Selection_base::* _getFitness )(Individual *, unsigned int)
 Pointer to the function returning the individual fitness. More...
 
void(LCE_Selection_base::* _setScalingFactor )(age_idx, unsigned int)
 Pointer to the function used to set the fitness scaling factor when fitness is relative. More...
 
void(LCE_Selection_base::* _setNewLocalOptima )(void)
 Pointer to the function used to change the local phenotypic optima or its rate of change. More...
 

Detailed Description

Composite LCE performing breeding, migration and viability selection all in one.

Migration rates are backward rates and population sizes are constant. Inherits from LCE_Breed_Disperse and LCE_Breed_Selection (and thus from LCE_Breed_base, LCE_Selection_base, and LCE_Disperse_base as well). Fitness is always absolute here.

Constructor & Destructor Documentation

◆ LCE_Breed_Selection_Disperse()

LCE_Breed_Selection_Disperse::LCE_Breed_Selection_Disperse ( )
383: LifeCycleEvent("breed_selection_disperse",""), _breed_selection_disperse(0)
384{
385 add_parameter("breed_selection_disperse_fitness_threshold", DBL, false, true, 0, 1,
387}
virtual bool setParameters()
Definition: LCEcomposite.cc:391
void(LCE_Breed_Selection_Disperse::* _breed_selection_disperse)(int *counter)
Definition: LCEcomposite.h:271
Base class of the Life Cycle Events, declares the LCE interface.
Definition: lifecycleevent.h:73
Implementation of the ParamUpdaterBase interface.
Definition: param.h:363
virtual void add_parameter(Param *param)
Interface to add a parameter to the set.
Definition: simcomponent.h:112
@ DBL
Definition: types.h:78

References SimComponent::add_parameter(), DBL, and setParameters().

Referenced by clone().

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◆ ~LCE_Breed_Selection_Disperse()

virtual LCE_Breed_Selection_Disperse::~LCE_Breed_Selection_Disperse ( )
inlinevirtual
277{}

Member Function Documentation

◆ addAgeClass()

virtual age_t LCE_Breed_Selection_Disperse::addAgeClass ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

294{return OFFSPRG;}
#define OFFSPRG
Offspring age class flag.
Definition: types.h:50

References OFFSPRG.

◆ breed_selection_disperse()

void LCE_Breed_Selection_Disperse::breed_selection_disperse ( int counter)
458{
459 Patch* patch;
460 unsigned int nfem, nmal;
461 unsigned int patchNbr = _popPtr->getPatchNbr();
462
463 for(unsigned int i = 0; i < patchNbr; i++) {
464
465 patch = _popPtr->getPatch(i);
466
467 if(patch->size(OFFSx) != 0) patch->flush(OFFSx, _popPtr);
468
470//-----------------------------------------------------------------------------
471 if(_mean_fitness == 0) {
472 warning("The mean adult fitness in patch %i is zero!", i+1);
473 warning("The breed_selection_disperse LCE will stall with zero\n\
474 fitness among reproducers. Please check the parameter values\n\
475 of your trait(s) under selection: e.g. check the initial trait\n\
476 values or initial allele frequencies, and selection params.\n");
477 abort();
478 }
479//-----------------------------------------------------------------------------
480
482
483 // determine how many male and female offspring we need to produce
484 nfem = (this->* _get_numFemOffspring)(patch);
485 nmal = (this->* _get_numMalOffspring)(patch);
486
487 // perform breeding
488 do_breed(FEM, nfem, counter, patch, i);
489 do_breed(MAL, nmal, counter, patch, i);
490
491 }
492}
unsigned int(LCE_Breed_Disperse::* _get_numMalOffspring)(Patch *patch)
Definition: LCEcomposite.h:61
unsigned int(LCE_Breed_Disperse::* _get_numFemOffspring)(Patch *patch)
Definition: LCEcomposite.h:60
void do_breed(sex_t SEX, unsigned int size, int *counter, Patch *patch, unsigned int patchNbr)
Definition: LCEcomposite.cc:504
double _base_fitness
Definition: LCEselection.h:88
double _scaling_factor
Definition: LCEselection.h:89
double getMeanPatchFitness(age_idx age, unsigned int p)
Computes the mean fitness in a given patch for a given age class.
Definition: LCEselection.cc:809
double _mean_fitness
Definition: LCEselection.h:89
Metapop * _popPtr
The ptr to the current Metapop.
Definition: lifecycleevent.h:81
unsigned int getPatchNbr()
Definition: metapop.h:276
Patch * getPatch(unsigned int i)
Patch accessor, return the ith+1 patch in the metapop.
Definition: metapop.h:257
Second class in the metapopulation design structure, between the Metapop and Individual classes.
Definition: metapop.h:430
unsigned int size(age_t AGE)
Returns the size of the container of the appropriate age class(es) for both sexes.
Definition: metapop.h:496
void flush(sex_t SEX, age_idx AGE, Metapop *pop)
Removes all individual pointers of the appropriate sex and age class and flush them into the recyclin...
Definition: metapop.h:643
void abort()
Definition: output.cc:115
void warning(const char *str,...)
Definition: output.cc:58
@ FEM
Definition: types.h:37
@ MAL
Definition: types.h:37
@ OFFSx
Definition: types.h:42
@ ADLTx
Definition: types.h:42

References LCE_Selection_base::_base_fitness, LCE_Breed_Disperse::_get_numFemOffspring, LCE_Breed_Disperse::_get_numMalOffspring, LCE_Selection_base::_mean_fitness, LifeCycleEvent::_popPtr, LCE_Selection_base::_scaling_factor, abort(), ADLTx, do_breed(), FEM, Patch::flush(), LCE_Selection_base::getMeanPatchFitness(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, OFFSx, Patch::size(), and warning().

Referenced by breed_selection_disperse_propagule(), and setParameters().

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◆ breed_selection_disperse_propagule()

void LCE_Breed_Selection_Disperse::breed_selection_disperse_propagule ( int counter)
497{
500}
void breed_selection_disperse(int *counter)
Definition: LCEcomposite.cc:457
bool setIsland_PropagulePool_Matrix()
Definition: LCEdisperse.cc:567

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

Referenced by setParameters().

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◆ clone()

virtual LifeCycleEvent * LCE_Breed_Selection_Disperse::clone ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

289{return new LCE_Breed_Selection_Disperse();}
LCE_Breed_Selection_Disperse()
Definition: LCEcomposite.cc:382

References LCE_Breed_Selection_Disperse().

◆ do_breed()

void LCE_Breed_Selection_Disperse::do_breed ( sex_t  SEX,
unsigned int  size,
int counter,
Patch patch,
unsigned int  patchNbr 
)
506{
507// int viab_count;
508 Individual *new_ind;
509 for(unsigned int j = 0; j < size; j++) {
510// viab_count = (*counter);
511 do{
512 new_ind = makeOffspringWithSelection( (this->*_make_offspring)(SEX, patch, cpatch), cpatch);
513 (*counter)++;
514// if((*counter) - viab_count > 500) {
515// warning("it took more than %i trials to get a fit offspring.",(*counter) - viab_count);
516// }
517 } while (new_ind == NULL);
518
519 patch->add(SEX, OFFSx, new_ind);
520 }
521}
This class contains traits along with other individual information (sex, pedigree,...
Definition: individual.h:49
Individual *(LCE_Breed_Disperse::* _make_offspring)(sex_t SEX, Patch *patch, unsigned int LocalPatch)
Definition: LCEcomposite.h:59
Individual * makeOffspringWithSelection(Individual *ind, unsigned int natalpatch)
Performs viability selection and breeding at the same time.
Definition: LCEcomposite.cc:880
void add(sex_t SEX, age_idx AGE, Individual *ind)
Adds an individual to the appropriate container, increments its size, eventually resizing it.
Definition: metapop.h:549

References LCE_Breed_Disperse::_make_offspring, Patch::add(), LCE_Breed_Selection::makeOffspringWithSelection(), and OFFSx.

Referenced by breed_selection_disperse().

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◆ execute()

void LCE_Breed_Selection_Disperse::execute ( )
virtual

Reimplemented from LCE_Breed_Disperse.

421{
422 int ind_count = 0;
423
424#ifdef _DEBUG_
425 message("LCE_Breed_Selection_Disperse::execute (mean fitness(adlt): %f, fit scale: %f, offsprg nb: %i, adlt nb: %i, "
427 fflush(stdout);
428#endif
429
430 // _scaling_factor = (_mean_fitness >= _base_fitness ? 1 : _base_fitness/_mean_fitness);
431
432 if(_npatch != _popPtr->getPatchNbr()) {
434 if(!updateDispMatrix()) fatal("LCE_Breed_Selection_Disperse::execute: bailing out\n");
435 }
436
439
440 (this->*_breed_selection_disperse)(&ind_count);
441
443
444#ifdef _DEBUG_
445 unsigned int a = 0, b = 0, c = 0;
446 for(unsigned int i = 0; i < _popPtr->getPatchNbr(); i++){
447 a += _popPtr->getPatch(i)->nbEmigrant;
448 b += _popPtr->getPatch(i)->nbImigrant;
449 c += _popPtr->getPatch(i)->nbPhilopat;
450 }
451 message("immigrate: %f, emigrants: %i, imigrants: %i, mean fitness(offsprg): %f)\n",(double)b/(b+c), a, b, _mean_fitness);
452#endif
453}
void reset_counters()
Definition: LCEdisperse.cc:387
bool updateDispMatrix()
Definition: LCEdisperse.cc:362
unsigned int _npatch
Number of patches in the population.
Definition: LCEdisperse.h:60
double getMeanFitness(age_idx age)
Computes the mean fitness of the whole population for a given age class.
Definition: LCEselection.cc:791
void setMeans(unsigned int tot_ind)
Computes the average fitness of each pedigree class.
Definition: LCEselection.cc:983
void resetCounters()
Resets the fitness counters.
Definition: LCEselection.cc:972
unsigned int size()
Get the total number of individuals present in the population, all sex and age classes together.
Definition: metapop.h:310
unsigned short nbEmigrant
Definition: metapop.h:452
unsigned short nbPhilopat
Definition: metapop.h:452
unsigned short nbImigrant
Definition: metapop.h:452
void fatal(const char *str,...)
Definition: output.cc:96
void message(const char *message,...)
Definition: output.cc:40
#define ADULTS
Adults age class flag (breeders).
Definition: types.h:54

References _breed_selection_disperse, LCE_Selection_base::_mean_fitness, LCE_Disperse_base::_npatch, LifeCycleEvent::_popPtr, LCE_Selection_base::_scaling_factor, ADLTx, ADULTS, fatal(), LCE_Selection_base::getMeanFitness(), Metapop::getPatch(), Metapop::getPatchNbr(), message(), Patch::nbEmigrant, Patch::nbImigrant, Patch::nbPhilopat, OFFSPRG, LCE_Disperse_base::reset_counters(), LCE_Selection_base::resetCounters(), LCE_Selection_base::setMeans(), Metapop::size(), and LCE_Disperse_base::updateDispMatrix().

◆ loadFileServices()

virtual void LCE_Breed_Selection_Disperse::loadFileServices ( FileServices loader)
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

290{}

◆ loadStatServices()

void LCE_Breed_Selection_Disperse::loadStatServices ( StatServices loader)
virtual

Reimplemented from LCE_Breed_Disperse.

414{
416}
virtual void loadStatServices(StatServices *loader)
Definition: LCEselection.cc:108

References LCE_Selection_base::loadStatServices().

◆ removeAgeClass()

virtual age_t LCE_Breed_Selection_Disperse::removeAgeClass ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

293{return NONE;}
#define NONE
No age flag.
Definition: types.h:48

References NONE.

◆ requiredAgeClass()

virtual age_t LCE_Breed_Selection_Disperse::requiredAgeClass ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

295{return ADULTS;}

References ADULTS.

◆ resetParameterFromSource()

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

Reimplemented from LCE_Breed_Disperse.

292{return false;}

◆ setParameters()

bool LCE_Breed_Selection_Disperse::setParameters ( )
virtual

Reimplemented from LCE_Breed_Disperse.

392{
393 if(!LCE_Breed_Disperse::setParameters()) return false;
394 if(!LCE_Selection_base::setParameters()) return false;
396
397 if(get_parameter("breed_selection_disperse_fitness_threshold")->isSet())
398 _base_fitness = get_parameter_value("breed_selection_disperse_fitness_threshold");
399 else
400 _base_fitness = 0.05;
401
402 unsigned int model = this->getDispersalModel();
403 if(model == 2)
405 else
407
408 return true;
409}
virtual bool setParameters()
Definition: LCEcomposite.cc:60
void breed_selection_disperse_propagule(int *counter)
Definition: LCEcomposite.cc:496
bool setNonSelectedTraitTable()
Builds the vector of traits not under selection.
Definition: LCEcomposite.cc:580
unsigned int getDispersalModel()
Definition: LCEdisperse.h:107
virtual bool setParameters()
Definition: LCEselection.cc:152
virtual double get_parameter_value(std::string name)
Param value getter.
Definition: simcomponent.h:143
virtual Param * get_parameter(std::string name)
Param getter.
Definition: simcomponent.h:139

References LCE_Selection_base::_base_fitness, _breed_selection_disperse, breed_selection_disperse(), breed_selection_disperse_propagule(), SimComponent::get_parameter(), SimComponent::get_parameter_value(), LCE_Disperse_base::getDispersalModel(), LCE_Breed_Selection::setNonSelectedTraitTable(), LCE_Breed_Disperse::setParameters(), and LCE_Selection_base::setParameters().

Referenced by LCE_Breed_Selection_Disperse().

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Member Data Documentation

◆ _breed_selection_disperse

void(LCE_Breed_Selection_Disperse::* LCE_Breed_Selection_Disperse::_breed_selection_disperse) (int *counter)
private

Referenced by execute(), and setParameters().


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

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