Implementation of the basic breeding and mating procedures, does not link to any trait.
More...
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| LCE_Breed_Quanti () |
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virtual | ~LCE_Breed_Quanti () |
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void | setVefromVa (Patch *patch, age_idx AGE) |
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void | setIndPhenotype (Patch *patch, sex_t SEX, age_idx AGE) |
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void | NonWrightFisherPopulation () |
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void | WrightFisherPopulation () |
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virtual bool | setParameters () |
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virtual void | execute () |
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virtual LifeCycleEvent * | clone () |
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virtual void | loadFileServices (FileServices *loader) |
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virtual void | loadStatServices (StatServices *loader) |
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virtual bool | resetParameterFromSource (std::string param, SimComponent *cmpt) |
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virtual age_t | removeAgeClass () |
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virtual age_t | addAgeClass () |
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virtual age_t | requiredAgeClass () |
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| LCE_Breed_base () |
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virtual | ~LCE_Breed_base () |
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virtual Individual * | getFatherPtr (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...
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void | NonWrightFisherPopulation () |
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void | WrightFisherPopulation () |
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Individual * | breed (Individual *mother, Individual *father, unsigned int LocalPatch) |
| Makes a new individual with the right parents. More...
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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 offspring). More...
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Individual * | makeOffspring (Individual *ind) |
| Last step of the breeding process, does inheritance and mutation of the parents' genes. More...
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Individual * | do_breed (Individual *mother, Individual *father, unsigned int LocalPatch) |
| Calls the breeding function unsing its pointer. More...
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bool | checkMatingCondition (Patch *thePatch) |
| Checks if any mating will take place in the patch passed as argument. More...
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bool | checkNoSelfing (Patch *thePatch) |
| Checks whether mating will take place in the current patch when mating is not selfing or cloning. More...
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bool | checkPolygyny (Patch *thePatch) |
| Checks whether mating will take place in the current patch when mating is polygynous. More...
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bool | checkSelfing (Patch *thePatch) |
| Checks whether mating will take place in the current patch when mating is selfing. More...
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bool | checkCloning (Patch *thePatch) |
| Checks whether mating will take place in the current patch when mating is cloning. More...
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bool | setMatingSystem () |
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bool | setFecundity () |
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bool | setSexRatio () |
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double | getMatingProportion () |
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double | getMeanFecundity (unsigned int patch) |
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int | getMatingSystem () |
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bool | doInheritance () |
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double | getPoissonFecundity (double mean) |
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double | getFixedFecundity (double mean) |
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double | getGaussianFecundity (double mean) |
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double | getLogNormalFecundity (double mean) |
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double | getFecundity (unsigned int patch) |
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double | getFecundity (double mean) |
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sex_t | getOffsprgSex () |
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sex_t | getOffsprgSexRandom () |
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sex_t | getOffsprgSexFixed () |
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sex_t | getOffsprgSexSelfing () |
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sex_t | getOffsprgSexCloning () |
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Individual * | RandomMating (Patch *thePatch, Individual *mother, unsigned int motherIndex) |
| Returns a pointer to a male drawn randomly from a patch. More...
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Individual * | fullPolyginy (Patch *thePatch, Individual *mother, unsigned int motherIndex) |
| Returns a pointer to the alpha male of the patch. More...
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Individual * | fullPolyginy_manyMales (Patch *thePatch, Individual *mother, unsigned int motherIndex) |
| Returns a pointer to one of the first _mating_males males of the patch. More...
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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, or the first male otherwise. More...
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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, or one of the _mating_males first males otherwise. More...
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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. More...
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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. More...
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Individual * | fullSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex) |
| Returns the mother pointer. More...
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Individual * | partialSelfing (Patch *thePatch, Individual *mother, unsigned int motherIndex) |
| Returns the mother pointer or a random female if _mating_proportion != 1. More...
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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 model). More...
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| LifeCycleEvent (const char *name, const char *trait_link) |
| Cstor. More...
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virtual | ~LifeCycleEvent () |
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virtual void | init (Metapop *popPtr) |
| Sets the pointer to the current Metapop and the trait link if applicable. More...
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virtual bool | attach_trait (string trait) |
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virtual void | set_paramset (std::string name, bool required, SimComponent *owner) |
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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...
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virtual void | set_event_name (const char *name) |
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virtual string & | get_event_name () |
| Accessor to the LCE's name. More...
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virtual int | get_rank () |
| Accessor to the LCE rank in the life cycle. More...
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virtual void | set_pop_ptr (Metapop *popPtr) |
| Accessors for the population pointer. More...
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virtual Metapop * | get_pop_ptr () |
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| SimComponent () |
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virtual | ~SimComponent () |
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virtual void | loadUpdaters (UpdaterServices *loader) |
| Loads the parameters and component updater onto the updater manager. More...
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virtual void | set_paramset (ParamSet *paramset) |
| Sets the ParamSet member. More...
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virtual void | set_paramsetFromCopy (const ParamSet &PSet) |
| Reset the set of parameters from a another set. More...
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virtual ParamSet * | get_paramset () |
| ParamSet accessor. More...
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virtual void | add_parameter (Param *param) |
| Interface to add a parameter to the set. More...
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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...
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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...
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virtual Param * | get_parameter (std::string name) |
| Param getter. More...
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virtual double | get_parameter_value (std::string name) |
| Param value getter. More...
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virtual string | get_name () |
| Returnd the name of the ParamSet, i.e. More...
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virtual bool | has_parameter (std::string name) |
| Param getter. More...
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Implementation of the basic breeding and mating procedures, does not link to any trait.
Individuals mate according to the mating system chosen. The mated adults are not removed from the population. The offspring containers are filled with the new generation. Note that they are first emptied if still containing offspring individuals when starting the breeding process.
The population's age is set to ALL
. The mating and realized fecundity counters of the reproducing males and females are updated.
- See also
- LCE_Breed_base