Class SIR.IBSPop

Object

IBSPopulation<Discrete, IBSDPopulation>

IBSDPopulation

IBSPop

Enclosing class:

SIR

public class SIR.IBSPop
extends IBSDPopulation

Population for individual based simulations of the SIR module.

Author:

Christoph Hauert

Field Summary

Fields

Modifier and Type	Field	Description
(package private) IBS	ibs	The individual based simulation model for SIR.

Fields inherited from class IBSDPopulation

accuTypeScores, active, groupmodule, init, initCount, optimizeMoran, pairmodule, traitsCount, traitsNext

Fields inherited from class IBSPopulation

adjustScores, competition, compGroup, debugFocal, debugModel, debugModels, debugNModels, debugSame, distrMigrants, engine, fitness, groupScores, hasLookupTable, interaction, interactions, interGroup, isMultispecies, isNeutral, logger, map2fit, maxEffScoreIdx, maxFitness, maxScore, migrationType, minFitness, minScore, module, mutation, nMixedInter, nPopulation, nTraits, opponent, optimizeHomo, pAddwire, playerScoreAveraged, playerScoring, pMigration, pRewire, rng, scores, smallScores, staticmodule, sumFitness, tags, typeFitness, typeScores, vacantIdx

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	IBSPop()	Constructor for SIR population.

Method Summary

Modifier and Type	Method	Description
boolean	checkConvergence()	Check if population has converged.
boolean	updatePlayerAt(int me, int[] refGroup, int rGroupSize)	Perform a single update of the individual with index me using the rGroupSize models in the array refGroup.

Methods inherited from class IBSDPopulation

adjustGameScoresAt, adjustPairGameScoresAt, adjustScoreAt, adjustScoreAt, becomesVacantAt, check, checkConsistentFitness, commitTraitAt, commitTraits, countTraits, debugMarkChange, doAdjustScores, encodeTraits, getFitnessAt, getFitnessHistogramData, getInit, getInitialTraits, getMeanFitness, getMeanTraits, getMonoScore, getPopulationSize, getScoreAt, getStatus, getTraitAt, getTraitData, getTraitNameAt, getTraits, getTraitsCount, haveSameTrait, init, initFrequency, initKaleidoscope, initMono, initMono, initMono, initMutant, initStripes, initTemperature, initUniform, isConsistent, isMonomorphic, isSameTrait, isVacantAt, maybeMutateAt, maybeMutateMoran, mouseHitNode, mutateAt, optimizeMoran2Traits, optimizeMoranNTraits, playGroupGameAt, playPairGameAt, preferredPlayerBest, prepareTraits, reset, resetScoreAt, resetScores, resetTraits, restoreFitness, restoreTraits, setInit, setInitialTraits, setNextTraitAt, setOpponentPop, setScoreAt, setTraitAt, stripGroupVacancies, stripVacancies, swapTraits, updateFromModelAt, updateMixedScores, updatePlayerBestResponse, updatePlayerEcologyAt, updatePlayerMoranBirthDeath, updatePlayerMoranDeathBirth, updatePlayerMoranDeathBirth, updatePlayerMoranImitate, updateScoreAt, updateScores, updateTraitCount, yalpGroupGameAt

Methods inherited from class IBSPopulation

debugScores, debugUpdate, debugUpdatePopulationAt, doBirthDeathMigration, doDeathBirthMigration, doDiffusionMigration, doMigration, doSyncMigration, encodeFitness, encodeGeometry, encodeInteractions, getCompetitionGeometry, getCompGroup, getFitness, getFitnessData, getFitnessNameAt, getFitnessNameAt, getInteractionGeometry, getInteractionsAt, getInterGroup, getMaxScore, getMigrationProb, getMigrationType, getMinScore, getModule, getNMean, getPlayerScoreAveraged, getPlayerScoring, getPopulationUpdate, getScoreNameAt, getScores, getSpeciesUpdateRate, getSyncFraction, getTagAt, getTagData, getTagNameAt, getTags, getTotalFitness, migrateMoran, mouseHitNode, mutate, nextBinomial, pickFitFocalIndividual, pickFitFocalIndividual, pickFitNeighborAt, pickFitNeighborAt, pickFocalIndividual, pickFocalIndividual, pickFocalSite, pickFocalSite, pickNeighborSiteAt, playGameAt, playGameSyncAt, processScore, random01, random0n, randomGaussian, removeScoreAt, removeScoreAt, restoreGeometry, restoreInteractions, setAddwire, setConsistencyCheck, setMaxEffScoreIdx, setMigrationProb, setMigrationType, setPlayerScoreAveraged, setPlayerScoring, setPopulationUpdate, setRewire, setSyncFraction, setTagAt, step, swapScoresAt, updateEffScoreRange, updateFitnessAt, updateMinMaxScores, updatePlayerAsync, updatePlayerAsyncAt, updatePlayerAt, updatePlayerBest, updatePlayerBestHalf, updatePlayerEcology, updatePlayerMoranBirthDeathAt, updatePlayerMoranDeathBirthAt, updatePlayerMoranImitateAt, updatePlayerSwap, updateProportionalAbs, updateReplicatorHalf, updateReplicatorPlus, updateScoreAt, updateScoreAt, updateThermal

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

ibs

IBS ibs

The individual based simulation model for SIR. Convenience variable to avoid casts when retrieving the elapsed time with getRealtime().

Constructor Details

IBSPop

protected IBSPop()

Constructor for SIR population.

Method Details

updatePlayerAt

public boolean updatePlayerAt(int me,
 int[] refGroup,
 int rGroupSize)

Description copied from class: IBSPopulation

Perform a single update of the individual with index me using the rGroupSize models in the array refGroup. Returns true if the individual changed its trait to signal that the focal individual's score will need to be reset.

Overrides:

updatePlayerAt in class IBSPopulation<Discrete, IBSDPopulation>

Parameters:

me - the index of the focal individual

refGroup - the group of reference individuals

rGroupSize - the number of reference individuals

Returns:

true if trait of reference adopted

See Also:

• IBSPopulation.resetScoreAt(int)

checkConvergence

public boolean checkConvergence()

Description copied from class: IBSPopulation

Check if population has converged. By default true if population is monomorphic and no (zero) mutations. However, different implementations may have different criteria for convergence.

Note: This tends to be less restrictive than reaching an absorbing state. Typically convergence is used as a criterion to abort simulations.

Overrides:

checkConvergence in class IBSDPopulation

Returns:

true if converged.