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ALMaSS Skylark ODDox
1.1
The skylark model description following ODdox protocol
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Base class for all population managers. More...
#include <PopulationManager.h>
Public Member Functions | |
| Population_Manager (Landscape *L) | |
| virtual | ~Population_Manager (void) |
| void | SetNoProbes (int a_pn) |
| unsigned | GetLiveArraySize (int a_listindex) |
| Gets the number of 'live' objects for a list index in the TheArray. More... | |
| void | IncLiveArraySize (int a_listindex) |
| Increments the number of 'live' objects for a list index in the TheArray. More... | |
| virtual void | Catastrophe (int) |
| unsigned int | FarmAnimalCensus (unsigned int a_farm, unsigned int a_typeofanimal) |
| char * | SpeciesSpecificReporting (int a_species, int a_time) |
| char * | ProbeReport (int a_time) |
| char * | ProbeReportTimed (int a_time) |
| void | ImpactProbeReport (int a_Time) |
| bool | BeginningOfMonth () |
| void | LOG (const char *fname) |
| int | SupplyStepSize () |
| int | SupplySimW () |
| int | SupplySimH () |
| virtual void | Run (int NoTSteps) |
| virtual float | Probe (int ListIndex, probe_data *p_TheProbe) |
| virtual void | ImpactedProbe () |
| int | SupplyListNameLength () |
| TAnimal * | SupplyAnimalPtr (int a_index, int a_animal) |
| Returns the pointer indexed by a_index and a_animal. Note NO RANGE CHECK. More... | |
| unsigned | SupplyListIndexSize () |
| unsigned | SupplyListSize (unsigned listindex) |
| bool | CheckXY (int l, int i) |
| Debug method to test for out of bounds coordinates. More... | |
| const char * | SupplyListName (int i) |
| bool | IsLast (unsigned listindex) |
| int | SupplyState (unsigned listindex, unsigned j) |
| virtual void | SupplyLocXY (unsigned listindex, unsigned j, int &x, int &y) |
| const char * | SupplyStateNames (int i) |
| unsigned | SupplyStateNamesLength () |
| virtual void | DisplayLocations () |
| int | ProbeFileInput (char *p_Filename, int p_ProbeNo) |
| TAnimal * | FindClosest (int x, int y, unsigned Type) |
| bool | OpenTheRipleysOutputProbe (string a_NWordFilename) |
| void | OpenTheAOROutputProbe (string a_AORFilename) |
| bool | OpenTheMonthlyRipleysOutputProbe () |
| bool | OpenTheReallyBigProbe () |
| virtual void | TheAOROutputProbe () |
| virtual void | TheRipleysOutputProbe (FILE *a_prb) |
| virtual void | TheReallyBigOutputProbe () |
| void | CloseTheMonthlyRipleysOutputProbe () |
| virtual void | CloseTheRipleysOutputProbe () |
| virtual void | CloseTheReallyBigOutputProbe () |
| TTypesOfPopulation | GetPopulationType () |
| int | GetSeasonNumber () |
| Get the season number. More... | |
| void | LamdaDeath (int x, int y) |
| void | LamdaBirth (int x, int y) |
| void | LamdaBirth (int x, int y, int z) |
| void | LamdaClear () |
| void | LamdaDumpOutput () |
| virtual int | SupplyPegPosx (int) |
| virtual int | SupplyPegPosy (int) |
| virtual int | SupplyCovPosx (int) |
| virtual int | SupplyCovPosy (int) |
| virtual bool | OpenTheFledgelingProbe () |
| virtual bool | OpenTheBreedingPairsProbe () |
| virtual bool | OpenTheBreedingSuccessProbe () |
| virtual void | BreedingPairsOutput (int) |
| virtual int | TheBreedingFemalesProbe (int) |
| virtual int | TheFledgelingProbe () |
| virtual void | BreedingSuccessProbeOutput (double, int, int, int, int, int, int, int) |
| virtual int | TheBreedingSuccessProbe (int &, int &, int &, int &, int &, int &) |
| virtual void | FledgelingProbeOutput (int, int) |
| virtual void | TheGeneticProbe (unsigned, int, unsigned &) |
| virtual void | GeneticsResultsOutput (FILE *, unsigned) |
Public Attributes | |
| int | IndexArrayX [5][10000] |
| probe_data * | TheProbe [100] |
| int | SimH |
| int | SimW |
| unsigned | SimHH |
| unsigned | SimWH |
| char | m_SimulationName [255] |
| bool | ProbesSet |
| Landscape * | m_TheLandscape |
Protected Member Functions | |
| virtual bool | StepFinished () |
| Overrides the population manager StepFinished - there is no chance that hunters do not finish a step behaviour. More... | |
| virtual void | DoFirst () |
| virtual void | DoBefore () |
| virtual void | DoAfter () |
| virtual void | DoAlmostLast () |
| virtual void | DoLast () |
| void | EmptyTheArray () |
| Removes all objects from the TheArray by deleting them and clearing TheArray. More... | |
| void | SortX (unsigned Type) |
| void | SortXIndex (unsigned Type) |
| void | SortY (unsigned Type) |
| void | SortState (unsigned Type) |
| void | SortStateR (unsigned Type) |
| unsigned | PartitionLiveDead (unsigned Type) |
| void | Shuffle_or_Sort (unsigned Type) |
| void | Shuffle (unsigned Type) |
| virtual void | Catastrophe () |
Protected Attributes | |
| vector< unsigned > | m_LiveArraySize |
| int | m_NoProbes |
| AOR_Probe * | m_AOR_Probe |
| FILE * | m_GeneticsFile |
| FILE * | m_AlleleFreqsFile |
| FILE * | m_EasyPopRes |
| const char * | StateNames [100] |
| int | m_catastrophestartyear |
| int | m_StepSize |
| vector< TListOfAnimals > | TheArray |
| unsigned | StateNamesLength |
| const char * | m_ListNames [32] |
| unsigned | m_ListNameLength |
| FILE * | TestFile |
| FILE * | TestFile2 |
| unsigned | BeforeStepActions [12] |
| int | m_SeasonNumber |
| Holds the season number. Used when running goose and hunter sims. More... | |
| TTypesOfPopulation | m_population_type |
| ofstream * | AOROutputPrb |
| FILE * | RipleysOutputPrb |
| FILE * | RipleysOutputPrb1 |
| FILE * | RipleysOutputPrb2 |
| FILE * | RipleysOutputPrb3 |
| FILE * | RipleysOutputPrb4 |
| FILE * | RipleysOutputPrb5 |
| FILE * | RipleysOutputPrb6 |
| FILE * | RipleysOutputPrb7 |
| FILE * | RipleysOutputPrb8 |
| FILE * | RipleysOutputPrb9 |
| FILE * | RipleysOutputPrb10 |
| FILE * | RipleysOutputPrb11 |
| FILE * | RipleysOutputPrb12 |
| FILE * | ReallyBigOutputPrb |
| long int | lamdagrid [2][257][257] |
Base class for all population managers.
The core of the handling of animal populations. All time-step code and most input/output is handled by this class and its descendents. This class effectively implements a state machine to facilitate simulation of animal behaviours and handle potential issues with concurrency. The PopulationManager class is never instantiated but must be used by deriving a descendent class.
| Population_Manager::Population_Manager | ( | Landscape * | L | ) |
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| bool Population_Manager::BeginningOfMonth | ( | ) |
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
| bool Population_Manager::CheckXY | ( | int | l, |
| int | i | ||
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Debug method to test for out of bounds coordinates.
| void Population_Manager::CloseTheMonthlyRipleysOutputProbe | ( | ) |
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Reimplemented in Skylark_Population_Manager.
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Removes all objects from the TheArray by deleting them and clearing TheArray.
| unsigned int Population_Manager::FarmAnimalCensus | ( | unsigned int | a_farm, |
| unsigned int | a_typeofanimal | ||
| ) |
| TAnimal* Population_Manager::FindClosest | ( | int | x, |
| int | y, | ||
| unsigned | Type | ||
| ) |
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Reimplemented in Skylark_Population_Manager.
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Gets the number of 'live' objects for a list index in the TheArray.
References m_LiveArraySize.
Referenced by Skylark_Population_Manager::BreedingPairsOutput(), Skylark_Population_Manager::Catastrophe(), Skylark_Population_Manager::CreateObjects(), Skylark_Population_Manager::ProbePOM(), Skylark_Population_Manager::ReHouse(), Skylark_Population_Manager::TheBreedingFemalesProbe(), Skylark_Population_Manager::TheBreedingSuccessProbe(), Skylark_Population_Manager::TheFledgelingProbe(), and Skylark_Population_Manager::TheRipleysOutputProbe().
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References m_population_type.
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| void Population_Manager::ImpactProbeReport | ( | int | a_Time | ) |
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Increments the number of 'live' objects for a list index in the TheArray.
References m_LiveArraySize.
Referenced by Skylark_Population_Manager::CreateObjects().
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| void Population_Manager::LamdaDumpOutput | ( | ) |
| void Population_Manager::LOG | ( | const char * | fname | ) |
| void Population_Manager::OpenTheAOROutputProbe | ( | string | a_AORFilename | ) |
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
| bool Population_Manager::OpenTheMonthlyRipleysOutputProbe | ( | ) |
| bool Population_Manager::OpenTheReallyBigProbe | ( | ) |
Referenced by Skylark_Population_Manager::Init().
| bool Population_Manager::OpenTheRipleysOutputProbe | ( | string | a_NWordFilename | ) |
Referenced by Skylark_Population_Manager::Init().
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| int Population_Manager::ProbeFileInput | ( | char * | p_Filename, |
| int | p_ProbeNo | ||
| ) |
| char* Population_Manager::ProbeReport | ( | int | a_time | ) |
| char* Population_Manager::ProbeReportTimed | ( | int | a_time | ) |
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References m_NoProbes.
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| char* Population_Manager::SpeciesSpecificReporting | ( | int | a_species, |
| int | a_time | ||
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Overrides the population manager StepFinished - there is no chance that hunters do not finish a step behaviour.
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References TheArray.
Referenced by Skylark_Population_Manager::ProbeReportPOM().
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References m_ListNames.
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References m_ListNameLength.
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References SimH.
Referenced by Skylark_Female::st_Floating(), Skylark_Male::st_Floating(), and Skylark_Female::st_Laying().
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References SimW.
Referenced by Skylark_Female::st_Floating(), Skylark_Male::st_Floating(), and Skylark_Female::st_Laying().
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IntArray100 * SupplyStateList() { return & StateList; }
References TheArray.
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References StateNames.
Referenced by Skylark_Female::Step(), and Skylark_Male::Step().
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References StateNamesLength.
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References m_StepSize.
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
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Reimplemented in Skylark_Population_Manager.
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Referenced by Skylark_Population_Manager::Init().
| int Population_Manager::IndexArrayX[5][10000] |
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Referenced by LamdaBirth(), LamdaClear(), and LamdaDeath().
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Referenced by Skylark_Population_Manager::TheAOROutputProbe().
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Referenced by Skylark_Population_Manager::Catastrophe().
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Referenced by Skylark_Population_Manager::Init(), and SupplyListNameLength().
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Referenced by Skylark_Population_Manager::Init(), and SupplyListName().
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Referenced by GetLiveArraySize(), and IncLiveArraySize().
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Referenced by Skylark_Population_Manager::ProbeReportPOM(), and SetNoProbes().
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Referenced by GetPopulationType(), and Skylark_Population_Manager::Init().
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Holds the season number. Used when running goose and hunter sims.
Referenced by GetSeasonNumber().
| char Population_Manager::m_SimulationName[255] |
Referenced by Skylark_Population_Manager::Init().
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Referenced by SupplyStepSize().
| Landscape* Population_Manager::m_TheLandscape |
| bool Population_Manager::ProbesSet |
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Referenced by Skylark_Population_Manager::Init().
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| int Population_Manager::SimH |
Referenced by Skylark_Male::EstablishingATerritory(), Skylark_Female::EstablishTerritory(), and SupplySimH().
| unsigned Population_Manager::SimHH |
| int Population_Manager::SimW |
Referenced by Skylark_Male::EstablishingATerritory(), Skylark_Female::EstablishTerritory(), and SupplySimW().
| unsigned Population_Manager::SimWH |
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Referenced by Skylark_Population_Manager::Init(), and SupplyStateNames().
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Referenced by SupplyStateNamesLength().
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Referenced by Skylark_Population_Manager::BreedingPairsOutput(), Skylark_Population_Manager::Catastrophe(), Skylark_Population_Manager::CreateObjects(), IsLast(), Skylark_Population_Manager::ProbePOM(), Skylark_Population_Manager::ReHouse(), Skylark_Population_Manager::Skylark_Population_Manager(), SupplyAnimalPtr(), SupplyListIndexSize(), SupplyListSize(), SupplyLocXY(), SupplyState(), Skylark_Population_Manager::TheBreedingFemalesProbe(), Skylark_Population_Manager::TheBreedingSuccessProbe(), Skylark_Population_Manager::TheFledgelingProbe(), and Skylark_Population_Manager::TheRipleysOutputProbe().
| probe_data* Population_Manager::TheProbe[100] |
Referenced by Skylark_Population_Manager::ProbeReportPOM().