323 }
while(fem == motherIndex && thePatch->
size(
FEM,
ADLTx) != 1);
A class to manage the files associated with each components of the simulation.
Definition: fileservices.h:52
This class contains traits along with other individual information (sex, pedigree,...
Definition: individual.h:49
Base class for the breeding (and mating) life cycle events.
Definition: LCEbreed.h:44
bool checkPolygyny(Patch *thePatch)
Checks whether mating will take place in the current patch when mating is polygynous.
Definition: LCEbreed.h:182
sex_t getOffsprgSex()
Definition: LCEbreed.h:108
Individual * partialMonoginy(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a pointer to a male with same index as mother (if available) from the focal patch.
Definition: LCEbreed.h:294
void NonWrightFisherPopulation()
Definition: LCEbreed.cc:454
unsigned int _alpha_male
Definition: LCEbreed.h:49
void WrightFisherPopulation()
Definition: LCEbreed.cc:502
Individual *(LCE_Breed_base::* MatingFuncPtr)(Patch *, Individual *, unsigned int)
Definition: LCEbreed.h:53
Individual * do_breed(Individual *mother, Individual *father, unsigned int LocalPatch)
Calls the breeding function unsing its pointer.
Definition: LCEbreed.h:156
Individual * random_hermaphrodite(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a random female from the patch, will be the same mother with probability 1/N (Wright-Fisher m...
Definition: LCEbreed.h:334
virtual ~LCE_Breed_base()
Definition: LCEbreed.h:68
double getFixedFecundity(double mean)
Definition: LCEbreed.h:99
sex_t getOffsprgSexSelfing()
Definition: LCEbreed.h:111
Individual * partialPolyginy(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1,...
Definition: LCEbreed.h:252
Individual * breed(Individual *mother, Individual *father, unsigned int LocalPatch)
Makes a new individual with the right parents.
Definition: LCEbreed.cc:419
Individual * partialSelfing(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns the mother pointer or a random female if _mating_proportion != 1.
Definition: LCEbreed.h:317
Individual * partialPolyginy_manyMales(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a pointer to a male from a patch chosen at random if _mating_proportion != 1,...
Definition: LCEbreed.h:266
int getMatingSystem()
Definition: LCEbreed.h:96
virtual Individual * getFatherPtr(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Calls the mating function according to the model chosen using the function pointer,...
Definition: LCEbreed.h:76
double getFecundity(double mean)
Definition: LCEbreed.h:107
bool _do_inherit
Definition: LCEbreed.h:51
double getGaussianFecundity(double mean)
Definition: LCEbreed.h:100
Individual * fullPolyginy_manyMales(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a pointer to one of the first _mating_males males of the patch.
Definition: LCEbreed.h:239
Individual * fullMonoginy(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a pointer to a male with same index as mother (if available) from the focal patch.
Definition: LCEbreed.h:280
Individual * makeOffspring(Individual *ind)
Last step of the breeding process, does inheritance and mutation of the parents' genes.
Definition: LCEbreed.cc:407
double _sd_fecundity
Definition: LCEbreed.h:50
sex_t(LCE_Breed_base::* GetOffsprgSex)()
Definition: LCEbreed.h:57
double(LCE_Breed_base::* FecundityFuncPtr)(double mean)
Definition: LCEbreed.h:55
Individual * fullPolyginy(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a pointer to the alpha male of the patch.
Definition: LCEbreed.h:231
double getMatingProportion()
Definition: LCEbreed.h:94
void(LCE_Breed_base::* PopModelFuncPtr)(void)
Definition: LCEbreed.h:61
double getLogNormalFecundity(double mean)
Definition: LCEbreed.h:103
Individual * breed_cloning(Individual *mother, Individual *father, unsigned int LocalPatch)
Makes a new individual by doing a deep copy of the mother (copies the mother's genes into the offspri...
Definition: LCEbreed.cc:426
double _mating_proportion
Definition: LCEbreed.h:50
bool setMatingSystem()
Definition: LCEbreed.cc:82
bool checkCloning(Patch *thePatch)
Checks whether mating will take place in the current patch when mating is cloning.
Definition: LCEbreed.h:207
bool checkNoSelfing(Patch *thePatch)
Checks whether mating will take place in the current patch when mating is not selfing or cloning.
Definition: LCEbreed.h:173
bool setFecundity()
Definition: LCEbreed.cc:319
sex_t getOffsprgSexRandom()
Definition: LCEbreed.h:109
Individual *(LCE_Breed_base::* DoBreedFuncPtr)(Individual *mother, Individual *father, unsigned int LocalPatch)
Definition: LCEbreed.h:54
bool doInheritance()
Definition: LCEbreed.h:97
bool checkMatingCondition(Patch *thePatch)
Checks if any mating will take place in the patch passed as argument.
Definition: LCEbreed.h:165
Individual * RandomMating(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns a pointer to a male drawn randomly from a patch.
Definition: LCEbreed.h:222
bool(LCE_Breed_base::* CheckMatingConditionFuncPtr)(Patch *thePatch)
Definition: LCEbreed.h:56
double getPoissonFecundity(double mean)
Definition: LCEbreed.h:98
sex_t getOffsprgSexFixed()
Definition: LCEbreed.cc:397
unsigned int _mating_males
Definition: LCEbreed.h:48
LCE_Breed_base()
Definition: LCEbreed.cc:44
sex_t getOffsprgSexCloning()
Definition: LCEbreed.h:112
Individual * fullSelfing(Patch *thePatch, Individual *mother, unsigned int motherIndex)
Returns the mother pointer.
Definition: LCEbreed.h:307
TMatrix _mean_fecundity
Definition: LCEbreed.h:62
bool checkSelfing(Patch *thePatch)
Checks whether mating will take place in the current patch when mating is selfing.
Definition: LCEbreed.h:197
int _mating_system
Definition: LCEbreed.h:47
bool setSexRatio()
Definition: LCEbreed.cc:279
double getMeanFecundity(unsigned int patch)
Definition: LCEbreed.h:95
double getFecundity(unsigned int patch)
Definition: LCEbreed.h:106
virtual bool setParameters()
Definition: LCEbreed.cc:75
Implementation of the basic breeding and mating procedures, does not link to any trait.
Definition: LCEbreed.h:355
virtual age_t requiredAgeClass()
Definition: LCEbreed.h:375
virtual bool setParameters()
Definition: LCEbreed.cc:554
virtual void loadFileServices(FileServices *loader)
Definition: LCEbreed.h:370
virtual bool resetParameterFromSource(std::string param, SimComponent *cmpt)
Definition: LCEbreed.h:372
virtual void execute()
Definition: LCEbreed.cc:561
virtual void loadStatServices(StatServices *loader)
Definition: LCEbreed.h:371
virtual ~LCE_Breed()
Definition: LCEbreed.h:361
virtual LifeCycleEvent * clone()
Definition: LCEbreed.h:368
virtual age_t addAgeClass()
Definition: LCEbreed.h:374
LCE_Breed()
Definition: LCEbreed.h:359
virtual age_t removeAgeClass()
Definition: LCEbreed.h:373
Base class of the Life Cycle Events, declares the LCE interface.
Definition: lifecycleevent.h:73
Metapop * _popPtr
The ptr to the current Metapop.
Definition: lifecycleevent.h:81
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
Individual * get(sex_t SEX, age_idx AGE, unsigned int at)
Returns a pointer to the individual sitting at the index passed.
Definition: metapop.h:532
static double Poisson(double mean)
From the Numerical Recieps.
Definition: Uniform.h:220
static double Gaussian(double sigma)
Definition: Uniform.h:262
static double Uniform()
Generates a random number from [0.0, 1.0[ uniformly distributed.
Definition: Uniform.h:125
static bool RandBool()
Returns a random boolean.
Definition: Uniform.h:163
static double LogNormal(double zeta, double sigma)
Definition: Uniform.h:358
Interface to all basic components of a simulation (traits, life cycle events, pop,...
Definition: simcomponent.h:45
The Service class used to manage the StatHandler objects.
Definition: statservices.h:50
A class to handle matrix in params, coerces matrix into a vector of same total size.
Definition: tmatrix.h:49
double get(unsigned int i, unsigned int j)
Accessor to element at row i and column j.
Definition: tmatrix.h:147
sex_t
Sex types, males are always 0 and females 1!!
Definition: types.h:36
@ FEM
Definition: types.h:37
@ MAL
Definition: types.h:37
unsigned int age_t
Age class flags.
Definition: types.h:46
#define ADULTS
Adults age class flag (breeders).
Definition: types.h:54
#define OFFSPRG
Offspring age class flag.
Definition: types.h:50
@ ADLTx
Definition: types.h:42