Class IBSPop

Object

IBSPopulation<Discrete, IBSDPopulation>

IBSDPopulation

IBSPop

class IBSPop
extends IBSDPopulation

Individual based simulation implementation of the Lotka-Volterra model.

Field Summary

Fields inherited from class IBSDPopulation

accuTypeScores, active, groupmodule, init, initCount, maxRate, 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(EvoLudo engine, Discrete module)	Create a new custom implementation for IBS simulations.

Method Summary

Modifier and Type	Method	Description
boolean	setInitialTraits(double[] init)	Set the initial trait frequencies in the population.
protected void	updateMaxRate()	Computes the maximum ecological event rate for this species given the current set of rates.

Methods inherited from class IBSDPopulation

adjustGameScoresAt, adjustPairGameScoresAt, adjustScoreAt, adjustScoreAt, becomesVacantAt, check, checkConsistentFitness, checkConvergence, commitTraitAt, commitTraits, countTraits, debugMarkChange, doAdjustScores, encodeTraits, getFitnessAt, getFitnessHistogramData, getInit, getInitialTraits, getMeanFitness, getMeanTraits, getMonoScore, getPopulationSize, getScoreAt, getSpeciesUpdateRate, 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, setNextTraitAt, setOpponentPop, setScoreAt, setTraitAt, stripGroupVacancies, stripVacancies, swapTraits, updateFromModelAt, updateMinMaxScores, 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, 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, updatePlayerAsync, updatePlayerAsyncAt, updatePlayerAt, 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

Constructor Details

IBSPop

protected IBSPop(EvoLudo engine,
 Discrete module)

Create a new custom implementation for IBS simulations.

Parameters:

engine - the pacemaker for running the model

module - the reference to the module implementing the model

Method Details

updateMaxRate

protected void updateMaxRate()

Description copied from class: IBSDPopulation

Computes the maximum ecological event rate for this species given the current set of rates. Needed both for rejection sampling of events and to weight species selection in multi-species simulations.

Overrides:

updateMaxRate in class IBSDPopulation

setInitialTraits

public boolean setInitialTraits(double[] init)

Description copied from class: IBSDPopulation

Set the initial trait frequencies in the population. Switches the initialization type to IBSD.Init.Type.FREQUENCY.

Overrides:

setInitialTraits in class IBSDPopulation

Parameters:

init - the initial traits

Returns:

true if the initialization was successful