Nemo  2.3.46
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 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...
 
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 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...
 
- 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)
 
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 setDispMatrix ()
 
bool setReducedDispMatrix ()
 The reduced dispersal matrix contains the indices of the patches to which each patch is connected. More...
 
bool updateDispMatrix ()
 
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 side, double phi_mal, double phi_fem, double disp_mal, double disp_fem)
 
bool setLatticeTorrusMatrix (int side, double disp_mal, double disp_fem, TMatrix *grid)
 
bool setLatticeAbsorbingMatrix ()
 
bool setLatticeReflectingMatrix (int side, TMatrix *grid)
 
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)
 
- 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
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
 
- 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< 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 ( )

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

Referenced by clone().

369 : LifeCycleEvent("breed_selection_disperse","")
370 {
371  add_parameter("breed_selection_disperse_fitness_threshold", DBL, false, true, 0, 1,
373 }
Implementation of the ParamUpdaterBase interface.
Definition: param.h:348
LifeCycleEvent(const char *name, const char *trait_link)
Cstor.
Definition: lifecycleevent.h:98
virtual void add_parameter(Param *param)
Interface to add a parameter to the set.
Definition: simcomponent.h:112
Definition: types.h:78
virtual bool setParameters()
Definition: LCEcomposite.cc:377
virtual LCE_Breed_Selection_Disperse::~LCE_Breed_Selection_Disperse ( )
inlinevirtual
269 {}

Member Function Documentation

virtual age_t LCE_Breed_Selection_Disperse::addAgeClass ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

References OFFSPRG.

285 {return OFFSPRG;}
#define OFFSPRG
Offspring age class flag.
Definition: types.h:50
void LCE_Breed_Selection_Disperse::breed_selection_disperse ( int counter)

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, ADLTx, do_breed(), FEM, Patch::flush(), LCE_Selection_base::getMeanPatchFitness(), Metapop::getPatch(), Metapop::getPatchNbr(), MAL, OFFSx, and Patch::size().

Referenced by breed_selection_disperse_propagule(), and setParameters().

444 {
445  Patch* patch;
446  unsigned int nfem, nmal;
447  unsigned int patchNbr = _popPtr->getPatchNbr();
448 
449  for(unsigned int i = 0; i < patchNbr; i++) {
450 
451  patch = _popPtr->getPatch(i);
452 
453  if(patch->size(OFFSx) != 0) patch->flush(OFFSx, _popPtr);
454 
457 
458  nfem = (this->* _get_numFemOffspring)(patch);
459  nmal = (this->* _get_numMalOffspring)(patch);
460 
461  do_breed(FEM, nfem, counter, patch, i);
462  do_breed(MAL, nmal, counter, patch, i);
463 
464  }
465 }
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:634
unsigned int size(age_t AGE)
Returns the size of the container of the appropriate age class(es) for both sexes.
Definition: metapop.h:487
unsigned int(LCE_Breed_Disperse::* _get_numMalOffspring)(Patch *patch)
Definition: LCEcomposite.h:61
Second class in the metapopulation design structure, between the Metapop and Individual classes...
Definition: metapop.h:421
Patch * getPatch(unsigned int i)
Patch accessor, return the ith+1 patch in the metapop.
Definition: metapop.h:251
unsigned int getPatchNbr()
Definition: metapop.h:270
double _mean_fitness
Definition: LCEselection.h:89
Definition: types.h:42
double _base_fitness
Definition: LCEselection.h:88
unsigned int(LCE_Breed_Disperse::* _get_numFemOffspring)(Patch *patch)
Definition: LCEcomposite.h:60
double getMeanPatchFitness(age_idx age, unsigned int p)
Computes the mean fitness in a given patch for a given age class.
Definition: LCEselection.cc:760
Definition: types.h:37
Definition: types.h:42
double _scaling_factor
Definition: LCEselection.h:89
Metapop * _popPtr
The ptr to the current Metapop.
Definition: lifecycleevent.h:81
Definition: types.h:37
void do_breed(sex_t SEX, unsigned int size, int *counter, Patch *patch, unsigned int patchNbr)
Definition: LCEcomposite.cc:477
void LCE_Breed_Selection_Disperse::breed_selection_disperse_propagule ( int counter)

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

Referenced by setParameters().

470 {
472  breed_selection_disperse(counter);
473 }
bool setIsland_PropagulePool_Matrix()
Definition: LCEdisperse.cc:469
void breed_selection_disperse(int *counter)
Definition: LCEcomposite.cc:443
virtual LifeCycleEvent* LCE_Breed_Selection_Disperse::clone ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

References LCE_Breed_Selection_Disperse().

281 {return new LCE_Breed_Selection_Disperse();}
LCE_Breed_Selection_Disperse()
Definition: LCEcomposite.cc:368
void LCE_Breed_Selection_Disperse::do_breed ( sex_t  SEX,
unsigned int  size,
int counter,
Patch patch,
unsigned int  patchNbr 
)

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

Referenced by breed_selection_disperse().

479 {
480  // int viab_count;
481  Individual *new_ind;
482  for(unsigned int j = 0; j < size; j++) {
483  // viab_count = (*counter);
484  do{
485  new_ind = makeOffspringWithSelection( (this->*_make_offspring)(SEX, patch, cpatch), cpatch);
486  (*counter)++;
487  // if((*counter) - viab_count > _max_try) {
488  // warning("it took more than 500 trials to get a fit offspring.");
489  // }
490  } while (new_ind == NULL);
491 
492  patch->add(SEX, OFFSx, new_ind);
493  }
494 }
Individual * makeOffspringWithSelection(Individual *ind, unsigned int natalpatch)
Performs viability selection and breeding at the same time.
Definition: LCEcomposite.cc:690
Individual *(LCE_Breed_Disperse::* _make_offspring)(sex_t SEX, Patch *patch, unsigned int LocalPatch)
Definition: LCEcomposite.h:59
Definition: types.h:42
This class contains traits along with other individual information (sex, pedigree, etc. ).
Definition: individual.h:49
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:540
void LCE_Breed_Selection_Disperse::execute ( )
virtual

Reimplemented from LCE_Breed_Disperse.

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().

407 {
408  int ind_count = 0;
409 
410 #ifdef _DEBUG_
411  message("LCE_Breed_Selection_Disperse::execute (mean fitness(adlt): %f, fit scale: %f, offsprg nb: %i, adlt nb: %i, "
413  fflush(stdout);
414 #endif
415 
416  // _scaling_factor = (_mean_fitness >= _base_fitness ? 1 : _base_fitness/_mean_fitness);
417 
418  if(_npatch != _popPtr->getPatchNbr()) {
420  if(!updateDispMatrix()) fatal("bailing out\n");
421  }
422 
425 
426  (this->*_breed_selection_disperse)(&ind_count);
427 
428  LCE_Selection_base::setMeans(ind_count);
429 
430 #ifdef _DEBUG_
431  unsigned int a = 0, b = 0, c = 0;
432  for(unsigned int i = 0; i < _popPtr->getPatchNbr(); i++){
433  a += _popPtr->getPatch(i)->nbEmigrant;
434  b += _popPtr->getPatch(i)->nbImigrant;
435  c += _popPtr->getPatch(i)->nbPhilopat;
436  }
437  message("immigrate: %f, emigrants: %i, imigrants: %i, mean fitness(offsprg): %f)\n",(double)b/(b+c), a, b, _mean_fitness);
438 #endif
439 }
void message(const char *message,...)
Definition: output.cc:40
#define ADULTS
Adults age class flag (breeders).
Definition: types.h:54
void setMeans(unsigned int tot_ind)
Computes the average fitness of each pedigree class.
Definition: LCEselection.h:164
void reset_counters()
Definition: LCEdisperse.cc:290
void fatal(const char *str,...)
Definition: output.cc:90
bool updateDispMatrix()
Definition: LCEdisperse.cc:265
Patch * getPatch(unsigned int i)
Patch accessor, return the ith+1 patch in the metapop.
Definition: metapop.h:251
unsigned short nbImigrant
Definition: metapop.h:444
unsigned int _npatch
Definition: LCEdisperse.h:60
unsigned int getPatchNbr()
Definition: metapop.h:270
double _mean_fitness
Definition: LCEselection.h:89
Definition: types.h:42
void resetCounters()
Resets the fitness counters.
Definition: LCEselection.h:153
#define OFFSPRG
Offspring age class flag.
Definition: types.h:50
unsigned int size()
Get the total number of individuals present in the population, all sex and age classes together...
Definition: metapop.h:302
double _scaling_factor
Definition: LCEselection.h:89
void(LCE_Breed_Selection_Disperse::* _breed_selection_disperse)(int *counter)
Definition: LCEcomposite.h:263
Metapop * _popPtr
The ptr to the current Metapop.
Definition: lifecycleevent.h:81
unsigned short nbPhilopat
Definition: metapop.h:444
double getMeanFitness(age_idx age)
Computes the mean fitness of the whole population for a given age class.
Definition: LCEselection.cc:742
unsigned short nbEmigrant
Definition: metapop.h:444
virtual void LCE_Breed_Selection_Disperse::loadFileServices ( FileServices loader)
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

282 {}
void LCE_Breed_Selection_Disperse::loadStatServices ( StatServices loader)
virtual

Reimplemented from LCE_Breed_Disperse.

References LCE_Selection_base::loadStatServices().

400 {
402 }
virtual void loadStatServices(StatServices *loader)
Definition: LCEselection.cc:106
virtual age_t LCE_Breed_Selection_Disperse::removeAgeClass ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

References NONE.

284 {return NONE;}
#define NONE
No age flag.
Definition: types.h:48
virtual age_t LCE_Breed_Selection_Disperse::requiredAgeClass ( )
inlinevirtual

Reimplemented from LCE_Breed_Disperse.

References ADULTS.

286 {return ADULTS;}
#define ADULTS
Adults age class flag (breeders).
Definition: types.h:54
bool LCE_Breed_Selection_Disperse::setParameters ( )
virtual

Reimplemented from LCE_Breed_Disperse.

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().

378 {
379  if(!LCE_Breed_Disperse::setParameters()) return false;
380  if(!LCE_Selection_base::setParameters()) return false;
382 
383  if(get_parameter("breed_selection_disperse_fitness_threshold")->isSet())
384  _base_fitness = get_parameter_value("breed_selection_disperse_fitness_threshold");
385  else
386  _base_fitness = 0.05;
387 
388  unsigned int model = this->getDispersalModel();
389  if(model == 2)
391  else
393 
394  return true;
395 }
unsigned int getDispersalModel()
Definition: LCEdisperse.h:98
void breed_selection_disperse_propagule(int *counter)
Definition: LCEcomposite.cc:469
virtual double get_parameter_value(std::string name)
Param value getter.
Definition: simcomponent.h:143
virtual bool setParameters()
Definition: LCEselection.cc:150
double _base_fitness
Definition: LCEselection.h:88
bool setNonSelectedTraitTable()
Builds the vector of traits not under selection.
Definition: LCEcomposite.cc:531
virtual bool setParameters()
Definition: LCEcomposite.cc:55
virtual Param * get_parameter(std::string name)
Param getter.
Definition: simcomponent.h:139
void(LCE_Breed_Selection_Disperse::* _breed_selection_disperse)(int *counter)
Definition: LCEcomposite.h:263
void breed_selection_disperse(int *counter)
Definition: LCEcomposite.cc:443

Member Data Documentation

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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